RSS 2.0 Feed

» Welcome Guest Log In :: Register

Pages: (2) < [1] 2 >   
  Topic: The Origin of "Information" via natural causes, Refuting a key ID claim (refs, webpages)< Next Oldest | Next Newest >  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 30 2002,00:02   

Hi,

While reading this interview with Phil Johnson, leader of the ID movement:

Berkeley’s Radical
An Interview with Phillip E. Johnson


...I was struck by this section:

Quote

You have said there is no natural explanation for the rise of genetic information. How important is that question in the debate?

PJ: The Wedge of Truth is all about those issues. The scientific key is, "No natural processes create genetic information." As soon as we get that out, there’s only one way the debate can go because Darwinists aren’t going to come up with a mechanism. They’ll start out talking about the peppered moth, and when that self-destructs, then they’ll say, "Oh, self-organizing systems, or the fourth law of thermodynamics," and other nonsense, which is just covering up ignorance.

Genetic information is the issue, but it isn’t the final issue. After you make that breakthrough, then you see other ways in which the theory is questionable. Darwinists will say, "Oh, well, maybe the mechanism has some problems, but the "fact of evolution"—common ancestry—is not in question. We distinguish the fact of evolution from the mechanism of evolution."

But that’s a bogus distinction because the "fact"—common ancestry—incorporates the mechanism. It’s just a matter of "now you see it, now you don’t." They are saying the mechanism by which a father and mother give birth to children is the same mechanism by which our "bacterial ancestors" gave birth to human beings. They say it’s all a process of natural reproduction and naturally occurring variation in the offspring.

Biologists affiliated with the Intelligent Design movement nail down the distinction by showing that DNA mutations do not create evolution in any significant sense. Instead, they make birth defects, so the whole thing is false from the get-go. There is no way you can establish that a bacterium is the parent of a complex animal. There is no mechanism to make the change, no historical or fossil evidence that such a change ever occurred, and there’s no way to duplicate the process in a lab.

Once you get that in the debate, then we will be poised for a metaphysical and intellectual reversal that is every bit as profound as the one with Copernicus. People will say, "My gosh, we’ve been completely misled by this fundamental truth of the creation story of our culture. We can no longer understand the world that way."

How do you change the way people regard the authority of science? Get them to think of it as a much more limited thing. Science is very reliable when scientists stick to the kinds of things that can be tested by refutable experiments, but much of what they tell us is outside that. When they have to fake the mechanisms, it becomes a very dubious philosophy. That raises the question of why so many very brilliant people were misled for so long and did such a good job of rationalizing these things.

When the mechanism of Darwinism becomes discredited, it’s like a train that’s been turned around. You can say, "Well, that’s interesting, but the train is still in the same place. The world, Yale, Berkeley, are still there. The New York Times is still telling us what to think. So why isn’t everything different?" Well, it is different, but you can’t see it yet. The train is turned in the opposite direction. It’s going to start out very slowly, but it’s moving on the logical tracks towards something very different, and when we get there, our great-great-grand-children will see how different things are.


Note that the "scientific key" to the whole ID argument (according to Johnson) is this: "No natural processes create genetic information."  

This strikes me as easily and trivially refutable by numerous examples.  Anything that starts with genetic information amount X, and ends up with genetic information amount X+Y, should qualify.  The classic case would be X=information in a genome before a gene duplicates & diverges under selection, and X+Y being the information in the genome after this has occurred.

Another less-often considered example should be (IMO) when a mutation (let's say "beneficial to at least part of the population" to avoid the obvious objection) arises in a *population*.  Here,

X=information in the genomes of a population
Y=information in the beneficial mutation

I realize that "information" has no single definition in biology, one could also argue that "new information" would arise through novel combinations of alleles, etc.  For the purposes of this thread, I suggest the following working definition:

Genetic information=functional DNA that encodes useful/beneficial proteins or regulatory sequences

...as this is what the IDers mean by "genetic information" (except of course when they are challenged on the topic, wherein they promptly begin the obfuscation and goal-post moving, rather like eternally elusive creationist definition of "kind").

So, let's use this thread to accumulate examples of natural processes increasing "genetic information" in the above-described sense.  Other things that might be relevant, e.g. studies of the increase of Shannon information in selective algorithms, could also be posted, just note the form of information as relevant.

nic

PS: I'll start off with one of my favorite examples:

Sdic, sperm dynein intermediate chain, a new gene which evolved over the past few million years by the duplication, fusion, and modification of two genes that are now on each side of Sdic on the chromosome.

Here is a brief introduction from Ian Musgrave:

Quote

My second favorite example is the Sdic gene, where the annexin and dynenin intermediate chain genes were duplicated in tandem, then the intervening sequences deleted to form a single new gene, (the Sperm specific dynenin intermediate chain gene Sdic). The good thing about this example is that a previously non-coding part of the sequence became the protein coding sequence, and the protein coding sequence has a non-coding role.


Capy P. (1998 Dec 10). Evolutionary biology. A plastic genome [news; comment] Nature, 396, 522-3.

Nurminsky DI, Nurminskaya MV, De Aguiar D, and Hartl DL. (1998 Dec 10). Selective sweep of a newly evolved sperm-specific gene in Drosophila [see comments] Nature, 396, 572-5.



Here is the Nurminsky et al. 1998 article:

Quote

pubmed link

Nature 1998 Dec 10;396(6711):572-5

Selective sweep of a newly evolved sperm-specific gene in Drosophila.

Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL.

Harvard University, Department of Organismic & Evolutionary Biology, Cambridge, Massachusetts 02138, USA.

The pattern of genetic variation across the genome of Drosophila melanogaster is consistent with the occurrence of frequent 'selective sweeps', in which new favourable mutations become incorporated into the species so quickly that linked alleles can 'hitchhike' and also become fixed. Because of the hitchhiking of linked genes, it is generally difficult to identify the target of any putative selective sweep. Here, however, we identify a new gene in D. melanogaster that codes for a sperm-specific axonemal dynein subunit. The gene has a new testes-specific promoter derived from a protein-coding region in a gene encoding the cell-adhesion protein annexin X (AnnX), and it contains a new protein-coding exon derived from an intron in a gene encoding a cytoplasmic dynein intermediate chain (Cdic). The new transcription unit, designated Sdic (for sperm-specific dynein intermediate chain), has been duplicated about tenfold in a tandem array. Consistent with the selective sweep of this gene, the level of genetic polymorphism near Sdic is unusually low. The discovery of this gene supports other results that point to the rapid molecular evolution of male reproductive functions.



Since then, this article has been published:

Quote

Pubmed link

Nurminsky D, Aguiar DD, Bustamante CD, Hartl DL.
Chromosomal effects of rapid gene evolution in Drosophila melanogaster.
Science. 2001 Jan 5;291(5501):128-30.

Rapid adaptive fixation of a new favorable mutation is expected to affect neighboring genes along the chromosome. Evolutionary theory predicts that the chromosomal region would show a reduced level of genetic variation and an excess of rare alleles. We have confirmed these predictions in a region of the X chromosome of Drosophila melanogaster that contains a newly evolved gene for a component of the sperm axoneme. In D. simulans, where the novel gene does not exist, the pattern of genetic variation is consistent with selection against recurrent deleterious mutations. These findings imply that the pattern of genetic variation along a chromosome may be useful for inferring its evolutionary history and for revealing regions in which recent adaptive fixations have taken place.



This article is a good review of the general topic of the evolution of new genes:

Quote

pubmed link

Curr Opin Genet Dev 2001 Dec;11(6):673-80

Evolution of novel genes.

Long M.

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago Illinois 60637, USA. mlong@midway.uchicago.edu

Much progress in understanding the evolution of new genes has been accomplished in the past few years. Molecular mechanisms such as illegitimate recombination and LINE element mediated 3' transduction underlying exon shuffling, a major process for generating new genes, are better understood. The identification of young genes in invertebrates and vertebrates has revealed a significant role of adaptive evolution acting on initially rudimentary gene structures created as if by evolutionary tinkers. New genes in humans and our primate relatives add a new component to the understanding of genetic divergence between humans and non-humans.


Have fun,
nic

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: May 30 2002,16:43   

Here's another well studied one:

The jingwei gene in Drosophila.

(quick side note:  you find most of these suckers in well studied organisms like Drosophila whose genome has been sequenced.  The particular significance of this is that we can trace the ancestry of the gene in question by looking at closely related species Drosophila, whose common ancestry is not even doubted by YECs.  Their only recourse here would be to claim that the gene had always existed and that every other species of Drosophila had lost the gene independently.  This would a) be extremely unparsimonious, given that it requires multiple parallelisms with no known non-random mechanism and b) force us to ignore all of the other evidence of recent origin.)  

Onto jingwei:

In a 1993 issue of Science, Manyuan Long, and CH Langley published their findings of a novel Drosophila gene, located on chromosome 3, that is found in sister species D. teissieri and D. yakuba and thus presumably first appeared in the common ancestor of both.  They dubbed this new gene jingwei (jwg).  The evidence that they uncovered, especially the lack of introns, suggested that the gene was derived from a retrotransposed mRNA from an alcohol dehydrogenase (adh) gene on chromosome 2.  Further results suggested that jwg is not a pseudogene as was first thought, but is rather a functional novel gene, though its exact function is still not clear.  The gene not only has specific RNA expression patterns, but has also undergone extensive evolution without suffering from any frameshift or nonsense mutations that are the hallmark of pseudogenes; the evidence strongly suggests that jwg has been under positve Darwinian selection.  Not only that, but Long and Langely’s results suggest that selection is playing a role throughout the origin of new genes, rather than being initially relaxed as was previously thought.
 
Perhaps the most interesting aspect of jwg is that its gene product is a chimera, meaning that it has function portions that are derived from different ancestral genes (aka gene fusion).  The C-terminal portion of jwg was almost certainly derived from the ancestral adh gene via retrotransposition, but that left the origin of the N-terminal exons still unexplained.  Did they come from non-coding upstream regions of DNA, or were they derived from parts of non-related functional genes?  Further study by Long et al. (1999) demonstrated that the N-terminal regions were the result of duplications of exons from a gene named yellow-emperor (ymp).  A follow-up study by Wang et al. (2000) showed that ymp is also a functional gene whose first three exons are the donor for the recruited portion of jwg.









Quote
Fig. 2.—Origin of the three novel proteins, YMP-1, YMP-2, and JGW, as a consequence of exon recombination. E1–E12 represent exons 1–12 of ymp (for the origin of YMP-1 and YMP-2); E1–E3, making up JGW, are the first three exons of ynd (Long and Langley 1993 ), a duplicate copy of ymp. The hatched boxes are the regions encoding protein sequences, with different patterns showing different peptide sequences. The open boxes represent untranslated regions (UTRs) of mRNAs (the open boxes on the left represent 5' UTRs; those on the right represent 3' UTRs)
{from Wang et al, 2000}

That's not the world's best image, but it gets across the general idea of how these new genes evolve.  Notice also that this graphically demonstrates the evolution of the yellow emperor genes as well.  As for jingwei, the basic idea is as follows, and I'd like to get it (and all other such examples) into a fancy colored graphic when possible (if anyone knows of a good program for this, let me know.)

Ald ---> retrotransposition ---> Jingwei Ct portion

YMP --> duplication of first three exons ---> exon shuffling ---> fusion of Jingwei Nt and Ct portions.


Refs:

Long M, Langley CH, Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila.  Science 1993 Apr 2;260(5104):91-5
PubMed

Long M, Wang W, Zhang J., Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila.  Gene 1999 Sep 30;238(1):135-41
full text pdf

Luque T, Marfany G, Gonzalez-Duarte R., Characterization and molecular analysis of Adh retrosequences in species of the Drosophila obscura group.  Mol Biol Evol 1997 Dec;14(12):1316-25
PubMed

Wang W, Zhang J, Alvarez C, Llopart A, Long M., The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster.  Mol Biol Evol 2000 Sep;17(9):1294-301
full text

Edited by theyeti on May 30 2002,16:58

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: May 31 2002,00:21   

Here's the most recent one that I know of off hand:

PNAS, Vol. 99, Issue 7, 4448-4453, April 2, 2002

Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster

Quote
Non-protein-coding RNA genes play an important role in various biological processes. How new RNA genes originated and whether this process is controlled by similar evolutionary mechanisms for the origin of protein-coding genes remains unclear. A young chimeric RNA gene that we term sphinx (spx) provides the first insight into the early stage of evolution of RNA genes. spx originated as an insertion of a retroposed sequence of the ATP synthase chain F gene at the cytological region 60DB since the divergence of Drosophila melanogaster from its sibling species 2-3 million years ago. This retrosequence, which is located at 102F on the fourth chromosome, recruited a nearby exon and intron, thereby evolving a chimeric gene structure. This molecular process suggests that the mechanism of exon shuffling, which can generate protein-coding genes, also plays a role in the origin of RNA genes. The subsequent evolutionary process of spx has been associated with a high nucleotide substitution rate, possibly driven by a continuous positive Darwinian selection for a novel function, as is shown in its sex- and development-specific alternative splicing. To test whether spx has adapted to different environments, we investigated its population genetic structure in the unique "Evolution Canyon" in Israel, revealing a similar haplotype structure in spx, and thus similar evolutionary forces operating on spx between environments.


This is an RNA gene, and the role that RNAs play in terms of regulation is only now starting to be fully realized.  RNA genes can probably evolve by retrotransposition easier than protein coding genes can, since the characteristic 5' truncation is less likely to have a major effect, and there is no worry about frameshifts.  In the case of small RNAs, there should be no 5' truncation.  (Retrogenes and processed pseudogenes are caused when a reverse transcriptase creates a cDNA from a mature mRNA (or other RNA).  The reverse transcrpitase starts at the poly A tail and works its way 3'.  However, if the mRNA is of decent size, it usually falls off before finishing, resulting in a cDNA that is truncated at the 5' end.  This truncation, along with a degenerate poly A tail and flanking repeats, are smoking gun evidence of a retrogene or processed pseudogene.  There's just no denying it, Johnson.)  Furthermore, many small RNAs can act as anti-sense oligos, binding complemetary mRNA or DNA for regulation.  These are easy to evolve, because they can be derived straight from the complemetary strand of the gene they regulate.

There is a furhter significance to this example in the fact that sphinx was derived from retrotransposition of an ATP synthase gene.  But sphinx is not a protein coding gene as ATP synthase is, so the functionality of the sequence is not derived from the already adapted sequence of ATP synthase.  Rather, this is more like a random sequence becoming functional, and is thus similar to the example of URF13 that Dembski sweats over in NFL (idea: let's apply Dembski's uniform probability to sphinx like he did with URF13 and see if it beats his universal probability bound.  Better yet, let's multiply the probabilities of both).

On top of all of this, we have a (potential) transposition event too.  So the origin of the gene goes something like this:

Quote
Although the role of retroposition is well defined in the origin of this gene, it should be pointed out that this is an unusual retroposition process. An independent DNA transposon, S element, moved together in the process with the ATP synthase chain F gene. A consequence of this process leaves a partial S fragment attached to the ATP synthase element-derived region in spx. There are several hypothetical scenarios for the origin of this complex structure. The first hypothesis is that the retroposed sequence of ATP synthase gene might have been inserted first into the S element located in the current position of the chromosome. Then the chimeric gene structure evolved by using the sequence of degenerated S element as the recipient site for splicing of the newly created intron between the recruited exon and ATP synthase chain F derived exon. The second hypothesis is that the retrosequence might have landed first in the S element, located in another portion of the genome, before the S element carrying the retrosequence jumped into the current position and degenerated in the S element structure. The third hypothesis is that the portion of the S element, which was located upstream of spx, might have been cotranscribed with the ATP synthase chain F gene and retroposed. The observation that the short repeats flank both S element fragment and the ATP synthase derived portion of spx is consistent with the third hypothesis.


theyeti

Edited by theyeti on May 31 2002,00:22

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 31 2002,01:31   

Another classic case is the evolution of antifreeze genes from proteases in arctic & subarctic fish, which has happened independently at least a couple of times:

I believe this article is freely available online from PNAS:

Proc. Natl. Acad. Sci. USA
Vol. 94, pp. 3485-3487, April 1997

Origin of antifreeze protein genes: A cool tale in molecular evolution
John M. Logsdon Jr. and W. Ford Doolittle

http://www.pnas.org/cgi/content/full/94/8/3485

Quote

Where do new genes come from? Duplication, divergence, and exon shuffling are the expected answers, so it is especially exciting when new genes are cobbled together from DNA of no related function (or no function at all). In this issue, Chen et al. (1) describe an antifreeze glycoprotein (AFGP) gene in an Antarctic fish that has arisen (in part) from noncoding DNA. Further, they show that a very similar AFGP from an Arctic fish is the product of some completely unrelated molecular processes (2). Together, these papers shed light on a number of key issues in molecular evolution.

In the late 1960s Arthur DeVries showed that freezing resistance in Antarctic fish was due to blood serum glycoproteins that lowered their freezing temperature below that of the subzero sea surrounding them (3, 4). The ensuing years have witnessed a great deal of work on AFPs (antifreeze proteins; not all are glycoproteins) in a number of phylogenetically diverse fish species, much of it by DeVries and his colleagues (5-7), revealing a number of types differing in their structure and amino-acid composition. These proteins, despite their diversity, function in similar ways to deter ice crystal growth (7, 8). But where did they come from, and how did they arise?

Birth of a Gene

In the first of the two papers, Chen et al. (1) demonstrate that an AFGP gene from the Antarctic notothenioid Dissostichus mawsoni derives from a gene encoding a pancreatic trypsinogen. The relationship of these two genes is not simply one of duplication and divergence (9), co-option/recruitment (10), or exon shuffling (11), processes that have been appreciated by molecular evolutionists for some time now. Instead, the novel portion of the AFGP gene (encoding the ice-binding function) derives from the recruitment and iteration of a small region spanning the boundary between the first intron and second exon of the trypsinogen gene (Fig. 1). This newborn segment was expanded and then iteratively duplicated (perhaps by replication slippage or unequal crossing-over) to produce 41 tandemly repeated segments. Nonetheless, the contemporary AFGP gene retains, as its birthmark, sequences at both ends which are nearly identical to trypsinogen. Retention of the 5 end of the trypsinogen gene may be significant, since this region encodes a signal peptide used for secretion from the pancreas into the digestive tract. Chen et al. (1) hypothesize that an early version of the notothenioid AFGP gene may have had its first function preventing freezing in the intestinal fluid, with this function later expanded into the circulatory system by way of its expression in the liver.


Here is Figure 1:



Quote

Figure 1. Comparison of gene structures and their sequence similarities. The regions shown represent genomic regions encompassed by sequenced cDNAs, and are not to scale. Exons are shown as large boxes; introns are shown as thinner boxes; inferred initiation and termination codons are indicated. Untranslated regions are hatched, and regions encoding putative signal peptides are stippled. Regions in different genes that are the same color share sequence similarity, but only regions of the same color shade are homologous; dotted lines delineate regions of clear homology between Dissostichus trypsinogen and AFGP genes. The open region of the trypsinogen gene is absent in AFGP. The segment below the double-headed arrow represents expansion of a sequence element present in the Dissostichus trypsinogen gene that appears to have given rise to the canonical AFGP repeat; its subsequent tandem iteration is shown by thin dashed lines. AFGP repeats are numbered and discontinuities are indicated for presentation. Regions between the AFGP repeats (spacers; indicated as either yellow or black) are the presumed sites of posttranslational cleavage. A discontinuity in the intron Dissostichus AFGP gene is shown to represent an internal segment not present in the homologous trypsinogen gene intron.


(source)

Thanks, nic

Edited by niiicholas on May 31 2002,01:32

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 31 2002,01:44   

Interesting...scrolling down to the bottom of the PNAS article, there is a link to a Science article that cited it.  Guess what?  Plants have evolved antifreeze proteins as well:

A Carrot Leucine-Rich-Repeat Protein That Inhibits Ice Recrystallization

Dawn Worrall, Luisa Elias, David Ashford, Maggie Smallwood, * Chris Sidebottom, Peter Lillford, Julia Telford, Chris Holt, Dianna Bowles

http://www.sciencemag.org/cgi/content/full/282/5386/115

Quote

It appears that proteins have been coopted to antifreeze activity from other functions quite recently in evolution (20). In plants, pathogenesis-related proteins such as the (1-3)endoglucanase and chitinase of winter rye (5) and the PGIP-related carrot protein have been recruited. The cell wall is modified in response to both low temperature and pathogen attack (21). Because ice crystallizes in the apoplast, proteins involved in such cell wall modification are well suited for cooption into antifreeze activity if their protein structures permit.

PGIPs belong to a large family of proteins known as the leucine-rich-repeat (LRR) proteins (22). LRR proteins contain 10 to 30 repeated units of a ~24-amino acid peptide containing regularly spaced leucine residues. The carrot AFP consensus sequence is similar to the motif found in other LRR proteins (Fig. 3B). One LRR protein exhibits an unusual nonglobular protein structure with a solvent-exposed parallel  sheet (23), and this structure has been compared with the related parallel  sheet found in pectin-degrading enzymes such as pectate lyase (22). In this context, it may be relevant that fish AFPIII contains a  sheet on its presumptive ice-binding face (24) and that the AFPII ice-binding face may also contain a  sheet structure (25).

The co-option of an LRR protein into antifreeze function in carrot suggests an additional common structural feature of AFPs. Of the seven AFPs known (1, 2), four contain repeated sequences. Thus, a repetitive structure may correlate with antifreeze activity.

The carrot AFP can be stably produced in tobacco plants grown under normal greenhouse conditions. The RI properties of this protein may be useful for improving food storage and protecting crop plants against cold temperatures.


Thanks, nic

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Oct. 01 2002,14:02   

Here's a different one:

http://www.pnas.org/cgi/content/abstract/152445399v1

Quote

Published online before print September 17, 2002
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.152445399
Evolution of moth sex pheromones via ancestral genes

Wendell L. Roelofs *, Weitian Liu *, Guixia Hao *, Hongmei Jiao *, Alejandro P. Rooney , and Charles E. Linn Jr. *
*Department of Entomology, Cornell University, Geneva, NY 14456; and Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762

Contributed by Wendell L. Roelofs, July 28, 2002

Mate finding in most moth species involves long-distance signaling via female-emitted sex pheromones. There is a great diversity of pheromone structures used throughout the Lepidoptera, even among closely related species. The conundrum is how signal divergence has occurred. With strong normalizing selection pressure on blend composition and response preferences, it is improbable that shifts to pheromones of diverse structures occur through adaptive changes in small steps. Here, we present data supporting the hypothesis that a major shift in the pheromone of an Ostrinia species occurred by activation of a nonfunctional desaturase gene transcript present in the pheromone gland. We also demonstrate the existence of rare males that respond to the new pheromone blend. Their presence would allow for asymmetric tracking of male response to the new blend and, thus, evolution of an Ostrinia species with structurally different sex pheromone components.


Edited by niiicholas on Oct. 01 2002,14:03

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Dec. 01 2002,20:38   

Might as well add these as I'm discussing them over at EvC:
http://www.evcforum.net/ubb/Forum10/HTML/000029.html


On the evolution of PCP degradation:

Quote

Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach.

Trends Biochem Sci 2000 Jun;25(6):261-5

Copley SD.

Dept of Chemistry and Biochemistry and Cooperative Institute for Research in Environmental Studies, University of Colorado at Boulder, Boulder, CO 80309, USA. copley@cires.colorado.edu

The pathway for degradation of the xenobiotic pesticide pentachlorophenol in Sphingomonas chlorophenolica probably evolved in the past few decades by the recruitment of enzymes from two other catabolic pathways. The first and third enzymes in the pathway, pentachlorophenol hydroxylase and 2,6-dichlorohydroquinone dioxygenase, may have originated from enzymes in a pathway for degradation of a naturally occurring chlorinated phenol. The second enzyme, a reductive dehalogenase, may have evolved from a maleylacetoacetate isomerase normally involved in degradation of tyrosine. This apparently recently assembled pathway does not function very well: pentachlorophenol hydroxylase is quite slow, and tetrachlorohydroquinone dehalogenase is subject to severe substrate inhibition.


[On the key step of the origin of PcpC, the central step in the origin of PCP degradation]

Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol.

Biochemistry 2000 May 9;39(18):5303-11

Anandarajah K, Kiefer PM Jr, Donohoe BS, Copley SD.

Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA.

Tetrachlorohydroquinone dehalogenase catalyzes the replacement of chlorine atoms on tetrachlorohydroquinone and trichlorohydroquinone with hydrogen atoms during the biodegradation of pentachlorophenol by Sphingomonas chlorophenolica. The sequence of the active site region of tetrachlorohydroquinone dehalogenase is very similar to those of the corresponding regions of maleylacetoacetate isomerases, enzymes that catalyze the glutathione-dependent isomerization of a cis double bond in maleylacetoacetate to the trans configuration during the catabolism of phenylalanine and tyrosine. Furthermore, tetrachlorohydroquinone dehalogenase catalyzes the isomerization of maleylacetone (an analogue of maleylacetoacetate) at a rate nearly comparable to that of a bona fide bacterial maleylacetoacetate isomerase. Since maleylacetoacetate isomerase is involved in a common and presumably ancient pathway for catabolism of tyrosine, while tetrachlorohydroquinone dehalogenase catalyzes a more specialized reaction, it is likely that tetrachlorohydroquinone dehalogenase arose from a maleylacetoacetate isomerase. The substrates and overall transformations involved in the dehalogenation and isomerization reactions are strikingly different. This enzyme provides a remarkable example of Nature's ability to recruit an enzyme with a useful structural scaffold and elaborate upon its basic catalytic capabilities to generate a catalyst for a newly needed reaction.

[atrazine degradation, a similar case]
Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different.

J Bacteriol 2001 Apr;183(8):2405-10

Seffernick JL, de Souza ML, Sadowsky MJ, Wackett LP.

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, USA.

The gene encoding melamine deaminase (TriA) from Pseudomonas sp. strain NRRL B-12227 was identified, cloned into Escherichia coli, sequenced, and expressed for in vitro study of enzyme activity. Melamine deaminase displaced two of the three amino groups from melamine, producing ammeline and ammelide as sequential products. The first deamination reaction occurred more than 10 times faster than the second. Ammelide did not inhibit the first or second deamination reaction, suggesting that the lower rate of ammeline hydrolysis was due to differential substrate turnover rather than product inhibition. Remarkably, melamine deaminase is 98% identical to the enzyme atrazine chlorohydrolase (AtzA) from Pseudomonas sp. strain ADP. Each enzyme consists of 475 amino acids and differs by only 9 amino acids. AtzA was shown to exclusively catalyze dehalogenation of halo-substituted triazine ring compounds and had no activity with melamine and ammeline. Similarly, melamine deaminase had no detectable activity with the halo-triazine substrates. Melamine deaminase was active in deamination of a substrate that was structurally identical to atrazine, except for the substitution of an amino group for the chlorine atom. Moreover, melamine deaminase and AtzA are found in bacteria that grow on melamine and atrazine compounds, respectively. These data strongly suggest that the 9 amino acid differences between melamine deaminase and AtzA represent a short evolutionary pathway connecting enzymes catalyzing physiologically relevant deamination and dehalogenation reactions, respectively.


Edited by niiicholas on Dec. 01 2002,20:39

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Dec. 08 2002,22:26   

A new study finds dozens of retrogenes in Drosophila.

Retroposed New Genes Out of the X in Drosophila

Esther Betrán, Kevin Thornton, and Manyuan Long

Genome Res 2002 Dec;12(12):1854-9

PubMed

Full text  (may need subscription)

Abstract:
Quote
New genes that originated by various molecular mechanisms are an essential component in understanding the evolution of genetic systems. We investigated the pattern of origin of the genes created by retroposition in Drosophila. We surveyed the whole Drosophila melanogaster genome for such new retrogenes and experimentally analyzed their functionality and evolutionary process. These retrogenes, functional as revealed by the analysis of expression, substitution, and population genetics, show a surprisingly asymmetric pattern in their origin. There is a significant excess of retrogenes that originate from the X chromosome and retropose to autosomes; new genes retroposed from autosomes are scarce. Further, we found that most of these X-derived autosomal retrogenes had evolved a testis expression pattern. These observations may be explained by natural selection favoring those new retrogenes that moved to autosomes and avoided the spermatogenesis X inactivation, and suggest the important role of genome position for the origin of new genes.


I'm going to include this little quote from the opening paragraph because it's useful IMO as a summary of sources of new gene evolution, and with references to the earliest papers about them:

Quote
New genes that originated by various molecular mechanisms are an essential component in understanding the evolution of genetic systems (Long 2001). These mechanisms include the classic mechanism of duplication (Ohno 1970), exon shuffling (Gilbert 1978), retroposition (Brosius 1991), and gene fusion through deletions or recruitment of new regions (Nurminsky et al. 1998), or a combination of these mechanisms (Long and Langley 1993; Begun 1997; Nurminsky et al. 1998).


Here are a few other important passages:

Quote
There is increasing evidence, fortunately, that retroposition, which generates new genes in new genomic positions via reverse transcription of mRNA from a parental gene, is important for the origin of new gene functions (Brosius 1999). In mammalian systems, a classic example is the human retrogene Pgk-2 with male specific function (McCarrey and Thomas 1987). Pgk-2 is autosomal (chromosome 19) whereas the parental copy Pgk-1 is X-linked. Pgk-2 evolved late spermatogenesis-specific expression. [theyeti:  I think I posted Pgk-2 before the crash.  I will do it again shortly] This new expression pattern is related to the fact that late spermatogenesis cells are the only ones that do not express Pgk-1 because of male germline X inactivation (McCarrey 1994). Subsequent analyses of retroposed genes in mammalian genomes suggested that retroposition had efficiently sown the seeds of evolution in genomes (Brosius 1991).
...
We have identified, from the annotated genes in the D. melanogaster genome, all pairs of homologs (70% amino acid identity or more) that are located on different chromosomes with hallmarks of retroposition (Table 1). Twenty-four young paralogous pairs fulfilled these criteria: 23 pairs in which the new copy lost the introns (CG12628, one of the 23, is additionally flanked by short repeats), and one pair with no introns in either copy but with the new copy retaining a degenerated poly-A tract (CG 12324/Rp515A). Interestingly, CG12628, which seems to be the youngest of the described retrogenes, is the only one that retains the direct repeats, a hallmark of the recent insertion event. Some other retrogenes also retained a degenerated poly-A tract: CG12628, CG10174, and CG13732. The parental genes have diverse functions, consistent with results from the human genome (Gonçalves et al. 2000).
...
Four possible explanations could account for the observed pattern: (1) nonrandom generation of retrogenes by a disproportionate number of X-linked genes that express in the germline cells; (2) negative selection against insertions in the X chromosome; (3) different recombination rates (or possibly deletion rates) between the autosomes and the X chromosome; and (4) positive Darwinian selection favoring retrogenes generated from the X chromosome to the autosomes.
...
The fourth hypothesis, positive selection, seems more parsimonious to interpret the excess of retroposition from X to autosomes. X inactivation during early spermatogenesis could produce a selective advantage for the retroposed genes with novel functions that escape X linkage and become expressed in testis, as previously suggested (Lifschytz and Lindsley 1972; McCarrey 1994). X inactivation early in spermatogenesis is well documented in Drosophila, mouse, and human (Lifschytz and Lindsley 1972; Richler et al. 1992). Thus, a mutant with a newly retroposed gene on autosomes will have some advantage over an X-linked form, because the mutant can carry out a new function putatively required in male germline cells after the X chromosome becomes inactivated. This hypothesis assumes that retroposition occurs from genes on all chromosomes with the same probability but natural selection favors the ones that avoid X-linkage by moving to an autosome and developing expression in testis.


theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Dec. 10 2002,21:00   

This one appears to be somewhat speculative (and I don't have the full text) but it's highly relevant nonetheless.

Mol Neurobiol 2002 Oct-Dec;26(2-3):235-50

Structure of the sodium channel gene SCN11A: evidence for intron-to-exon conversion model and implications for gene evolution.

Dib-Hajj SD, Tyrrell L, Waxman SG.

Quote
Exon/intron boundaries in the regions encoding the trans-membrane segments of voltage-gated Na channel genes are conserved, supporting their proposed evolution from a single domain channel, while the exons encoding the cytoplasmic loops are less conserved with their evolutionary heritage being less defined. SCN11A encodes the tetrodotoxin-resistant (TTX-R) sodium channel Nav1.9a/NaN, which is preferentially expressed in nociceptive primary sensory neurons of dorsal root ganglia (DRG) and trigeminal ganglia. SCN11A is localized to human chromosome 3 (3p21-24) close to the other TTX-R sodium channel genes SCN5A and SCN10A. An alternative transcript, Nav1.9b, has been detected in rat DRG and trigeminal ganglion. Nav1.9b is predicted to produce a truncated protein due to a frame-shift, which is introduced by the new sequence of exon 23c (E23c). In human and mouse SCN11A, divergent splicing signals prevent utilization of E23c. Unlike exons 5A/N in genes encoding TTX-sensitive sodium channels, which appear to have resulted from exon duplication, E23c might have evolved from the conversion of an intronic sequence. Although a functional role for Nav1.9b has yet to be established, intron-to-exon conversion may represent a mechanism for ion channels to acquire novel features.


Given that intronic sequences, with the exception of some 5' and 3' conserved bases, are sequence non-specific, this would be the equivalent of a more or less random sequence being converted into a biological function.

theyeti

edited to add this diddy:

Evolution of voltage-gated Na(+) channels.

Edited by theyeti on Dec. 10 2002,21:08

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Dec. 10 2002,23:26   

Birth of two chimeric genes in the Hominidae lineage.


Courseaux A, Nahon JL.

Science 2001 Feb 16;291(5507):1293-7

PubMed, Full text (May require subscription)

Quote
How genes with newly characterized functions originate remains a fundamental question. PMCHL1 and PMCHL2, two chimeric genes derived from the melanin-concentrating hormone (MCH) gene, offer an opportunity to examine such an issue in the human lineage. Detailed structural, expression, and phylogenetic analysis showed that the PMCHL1 gene was created near 25 million years ago (Ma) by a complex mechanism of exon shuffling through retrotransposition of an antisense MCH messenger RNA coupled to de novo creation of splice sites. PMCHL2 arose 5 to 10 Ma by an event of duplication involving a large chromosomal region encompassing the PMCHL1 locus. The RNA expression patterns of those chimeric genes suggest that they have been submitted to strong regulatory constraints during primate evolution.


Here is the proposed model for the evolution of these genes (B):

(Larger Image)
Quote
(B) Proposed model for the emergence of MCH-derived sequence onto chromosome 5p. (a) An AROM mRNA initiating in the CS3-5 region and ending at poly A (b) polyadenylation site was retrotransposed onto the equivalent of chromosome 5p at the time of Catarrhini divergence 25 to 30 Ma. (b) After this first event or concurrent to it, an Alu sequence was inserted in intron A and a fragment corresponding to the 3' end of the retrotransposed mRNA (part of exon II-intron A-Alu) was broken and transposed to the downstream insertion site. This led to the PMCHL gene versions observed in Cercopithecoidea and Hominoidea.


theyeti

Edited by theyeti on Dec. 10 2002,23:33

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Dec. 12 2002,22:52   

Here is a good example of novel gene evolution due to duplication.

Nat Genet 2002 Apr;30(4):411-5

Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey.

Zhang J, Zhang YP, Rosenberg HF.

Quote

Abstract:

One of the two ribonuclease genes in a leaf-eating monkey has adapted to a role in the digestion of bacterial RNA. Following duplication of the ancestral ribonuclease gene, adaptation occurred through a series of changes in the amino acid sequence of the protein it encodes. This example is a good illustration of how specialization of protein function after gene duplication can be as source of novel protein functions.


Quote

A subfamily of Old World monkeys, colobines are unique primates that use leaves rather than fruits and insects as their primary food source; these leaves are then fermented by symbiotic bacteria in the foregut13. Similar to ruminants, colobines recover nutrients by breaking and digesting the bacteria with various enzymes, including pancreatic ribonuclease (RNASE1), which is secreted from the pancreas and transported into the small intestine to degrade RNA.
[...]
...we detected one RNASE1 gene in each of the 15 non-colobine primates examined, including 5 hominoids, 5 Old World monkeys, 4 New World monkeys and 1 prosimian. We determined the DNA sequences of these RNASE1 genes; the deduced protein sequences are shown in Fig. 1a. The phylogenetic tree of the RNASE1 sequences (Fig. 2a) is consistent with the known species relationships16 at all nodes, with greater than 55% bootstrap support, suggesting that the RNASE1 genes are orthologous. By contrast, two RNASE1 genes were found in the Asian colobine, douc langur (Pygathrix nemaeus). Phylogenetic analysis (Fig. 2a) suggests that these two genes were generated by recent duplication postdating the separation of colobines from other Old World monkeys (cercopithecines). The branch lengths of the gene tree indicate that the nucleotide sequence of one daughter gene (RNASE1) has not changed since duplication, whereas that of the other gene (RNASE1B) has accumulated many substitutions.
[...]
Taken together, these analyses suggest that the synonymous and noncoding sites at the RNASE1B locus are not subject to selective constraints and that the accelerated evolution of the coding sequence of RNASE1B is due to positive Darwinian selection.
[...]
Earlier studies showed that, for most mammalian genes, the rate of radical substitution is lower than that of conservative substitution, owing to stronger purifying selection on radical substitution22. In RNASE1B, however, the opposite is found. The number of radical substitutions per site since duplication (0.067) is significantly greater than that (0.012) of conservative substitutions per site (P<0.02; Fisher's exact test). There are nine amino-acid substitutions in the mature peptide of RNASE1B, and seven of them involve charge changes. Unexpectedly, all seven charge-altering substitutions increase the negative charge of the protein.
[...]
The charge-altering substitutions reduced the net charge of RNASE1B from 8.8 to 0.8 (at pH 7) and the isoelectric point from 9.1 to 7.3 (Fig. 1a). Because RNA is negatively charged, the net charge of RNase influences its interaction with the substrate and its catalytic performance23. We therefore hypothesized that the charge-altering substitutions may have changed the optimal pH of RNASE1B in catalyzing the digestion of RNA.
[...]
We determined that the optimal pH for human RNASE1 is 7.4, a value that is within the pH range (7.4–8.0) measured in the small intestine of humans24, 25. The same optimal pH was observed for RNASE1 of rhesus monkey and douc langur (Fig. 4a). Probably because of foregut fermentation and related changes in digestive physiology, the pH in the small intestine of colobine monkeys shifts to 6–7 (ref. 13). Notably, the optimal pH for douc langur RNASE1B was found to be 6.3 (Fig. 4a). At pH 6.3, RNASE1B is about six times as active as RNASE1 in digesting RNA, and the difference in their activities is statistically significant (P<0.001, t-test). These results suggest that the rapid amino acid substitutions in RNASE1B were driven by selection for enhanced RNase activity at the relatively low pH environment of the colobine small intestine.


Long story short:  Monkey shifts diet from fruits and insects to leaves.  This causes foregut fermentation which lowers pH in the digestive tract.  A ribonuclease gene duplicates, and one of the duplicates evolves through positive selection for optimal activity at the lower pH.    

Another paper concerning this (shorter for those who don't want to plow through the one above) is here:

Hughes AL.  Adaptive evolution after gene duplication., Trends Genet 2002 Sep;18(9):433-4.

theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Dec. 12 2002,23:28   

Ah, another example of ribonuclease duplication.

Proc Natl Acad Sci U S A 1998 Mar 31;95(7):3708-13

Positive Darwinian selection after gene duplication in primate ribonuclease genes.

Zhang J, Rosenberg HF, Nei M.

Full Text

Quote

Abstract:

Evolutionary mechanisms of origins of new gene function have been a subject of long-standing debate. Here we report a convincing case in which positive Darwinian selection operated at the molecular level during the evolution of novel function by gene duplication. The genes for eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) in primates belong to the ribonuclease gene family, and the ECP gene, whose product has an anti-pathogen function not displayed by EDN, was generated by duplication of the EDN gene about 31 million years ago. Using inferred nucleotide sequences of ancestral organisms, we showed that the rate of nonsynonymous nucleotide substitution was significantly higher than that of synonymous substitution for the ECP gene. This strongly suggests that positive Darwinian selection operated in the early stage of evolution of the ECP gene. It was also found that the number of arginine residues increased substantially in a short period of evolutionary time after gene duplication, and these amino acid changes probably produced the novel anti-pathogen function of ECP.




theyeti

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Dec. 13 2002,01:13   

And in the "duplicated genes aren't necessarily selectively neutral, dammit" category:

(bold added)
Quote

Genome Biol 2002;3(2):RESEARCH0008
 
Selection in the evolution of gene duplications.

free online at pubmed central


Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV.

National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA. fkondras@ncbi.nlm.nih.gov

BACKGROUND: Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolution of a new function. RESULTS: In search of systematic evidence of accelerated evolution after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic genomes to compare the mode and strength of selection acting on recently duplicated genes (paralogs) and on similarly diverged, unduplicated orthologous genes in different species. We find that the ratio of nonsynonymous to synonymous substitutions (Kn/Ks) in most paralogous pairs is <<1 and that paralogs typically evolve at similar rates, without significant asymmetry, indicating that both paralogs produced by a duplication are subject to purifying selection. This selection is, however, substantially weaker than the purifying selection affecting unduplicated orthologs that have diverged to the same extent as the analyzed paralogs. Most of the recently duplicated genes appear to be involved in various forms of environmental response; in particular, many of them encode membrane and secreted proteins. CONCLUSIONS: The results of this analysis indicate that recently duplicated paralogs evolve faster than orthologs with the same level of divergence and similar functions, but apparently do not experience a phase of neutral evolution. We hypothesize that gene duplications that persist in an evolving lineage are beneficial from the time of their origin, due primarily to a protein dosage effect in response to variable environmental conditions; duplications are likely to give rise to new functions at a later phase of their evolution once a higher level of divergence is reached.


[...]

Discussion:

[...]
Thus, the observation that purifying selection appears to act on all recent duplicates and examination of the functions of recently duplicated genes do not support the notion that gene duplication results in true functional redundancy and duplications may achieve fixation despite being redundant [26]. The alternative hypothesis - that gene duplications are fixed in a population by positive selection in all organisms - is supported by a combination of evidence of adaptive duplications from many types of living organisms: prokaryotes [31,33,45,46,48,50,55,56], protists [35,58,59], plants [39,44], fungi [43,49], invertebrates [40,41,51,52,53], non-mammalian vertebrates [54], as well as mammalian somatic tissues [34,36,37,38]. Combining these observations with the suggestion that gene duplication may be a general mechanism of adaptation to various conditions of environmental stress [32,33,46,48,49,50,52,53,55,60], we suggest that, in both prokaryotes and eukaryotes, most paralogs that are fixed in a population have a direct effect on fitness from the moment of duplication, and aid in the adaptation to various environmental conditions, primarily through a protein dosage effect.

That the short-term benefit of a gene duplication is a direct effect on protein dosage also stems from a variety of experimental observations in a number of organisms, prokaryotic and eukaryotic. Gene duplication may be a temporary mechanism to increase protein or RNA dosage, as in the case of rRNA genes in amphibian oocytes and ciliate macronuclei, the chorion genes in some dipterans, actin genes in chicken as well as drug transporters in somatic tissues (see [34,37] for reviews). Protein dosage effects have also been demonstrated in a number of other studies of inheritable adaptive gene duplications [32,34,35,43,44,46,49,51,53,61]. Furthermore, there is evidence from the analysis of the yeast genome that duplicated genes tend to be from those sets of functions that are more highly expressed [62], supporting a general role for selection on protein dosage in duplicated genes.
[...]
[...]
The present observation that duplicated genes experience a substantial relaxation of selection compared to unduplicated genes is compatible with the traditional view that gene duplications make a major contribution to the evolution of new gene functions. Additionally, the repertoire of protein functions among recent duplicates suggests that many gene duplications contribute to adaptation of the organism to various forms of environmental stress. The results of the present analysis of recent duplications suggest a two-stage evolutionary model of gene duplication: in the first stage, immediately after duplication and during the early phase of their evolution, paralogs are retained and are subject to purifying selection because of the short-term advantage of protein dosage regulation; at a later stage in their evolution, gene duplications are likely to provide a long-term advantage by enabling the creation of new functions.


What would be interesting to know would be the relative roles of regulation mutations vs. gene duplications in effecting adaptation (via amount of proteins produced) to changing conditions as discussed above.  One would think that regulatory changes would be the more "elegant" or "efficient" way to adapt, but apparently evolution doesn't know or care, at least sometimes...

(it may be that regulatory changes have a "limit" that could only be exceeded by duplicating the gene...but now I'm at the limits of my knowledge...)

nic

(PS: The assumption that duplicating a gene doubles the level of a particular protein may not be a good one, particularly if the expression of the gene is regulated by some kind of feedback mechanism...just something to keep in mind)

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Dec. 13 2002,11:27   

Curr Opin Genet Dev 2002 Dec;12(6):711-8

Conflict begets complexity: the evolution of centromeres.

Malik HS, Henikoff S.

Quote

Abstract:

Centromeres mediate the faithful segregation of eukaryotic chromosomes. Yet they display a remarkable range in size and complexity across eukaryotes, from approximately 125 bp in budding yeast to megabases of repetitive satellites in human chromosomes. Mapping the fine-scale structure of complex centromeres has proven to be daunting, but recent studies have provided a first glimpse into this unexplored bastion of our genomes and the evolutionary pressures that shape it. Evolutionary studies of proteins that bind centromeric DNA suggest genetic conflict as the underlying basis of centromere complexity, drawing interesting parallels with the myriad selfish elements that employ centromeric activity for their own survival.


Quote
...
Despite these difficulties, recent studies have begun to provide `evolutionary snapshots' of the centromere. They suggest that different sequence variants jockey for evolutionary dominance, even as homogeneous arrays of satellite repeats are destroyed by the insertion of a variety of mobile elements. Parallel studies of centromere-binding proteins also suggest that competition may drive the sequence complexity at centromeres, and may be responsible for rapidly changing karyotypes throughout evolution.
...

Female meiotic success as a major evolutionary force

Another means to turn the tables on `centromere-drive' would be to alter the meiotic tetrad at female meiosis, in effect switching the preferred position in the tetrad to an unpreferred position. One case where centromeres exploit female meiosis is evident in the relative ability of Robertsonian fusions –– when acrocentrics (chromosomes in which the centromere is towards one end) fuse at their centromeres to form a metacentric (chromosomes in which the centromere is in the middle) –– to survive female meiosis relative to its two acrocentric ancestors. In humans and chicken, Robertsonian fusions do better than acrocentrics in female meiosis, whereas the reverse is true in mice [37 and 38]; there is no difference in male meiotic transmission. A survey of karyotype evolution in mammals reveals that genomes have a high proportion of all acrocentric (e.g. mouse) or all metacentric (e.g. human) karyotypes with a distinct paucity of `mixed' karyotypes. This suggests that the switch in female meiotic `preference' has occurred frequently in mammalian evolution and can quickly reshape karyotypes once it happens ( Fig. 4). No other selective force would be expected to make such a rapid impact on karyotype evolution [38].
...

Conclusions

In yeast that have symmetric meioses, centromere competition is not expected to occur at all; removal of this genetic conflict may have allowed the optimal co-evolution of centromeric histones and centromeres, along with the gradual simplification of the centromeric sequences themselves. Under this model, S. cerevisiae centromeres, which are believed to consist of one nucleosome each, represent the ultimate stage of centromere optimization, whereas other genomes, including our own, constantly struggle with the consequences of unfair advantages in female meiosis.

Update

In humans, the bias in favor of transmitting Robertsonian fusions in female meiosis has been documented [37 and 38], but Daniel et al. [48 and 49] also reiterate another dramatic effect of Robertsonians –– reduced male fertility. Among families with Robertsonian arrangements coming to prenatal diagnosis, there are 2.4 fold fewer male parent carriers compared to female parents. This is despite the fact that in their progeny there is an ~1:1 ratio of male:female transmission of Robertsonian rearrangements. This points to a significant decline in fertility in male carriers of Robertsonian fusions, compared to female carriers. This duality (i.e. increased chromosomal transmission in female meiosis offset by lowered male fertility) provides strong support for the centromere-drive model.



theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Dec. 13 2002,12:12   

Curr Issues Mol Biol 2002 Jul;4(3):65-76

Transposable elements and the evolution of eukaryotic complexity.

Bowen NJ, Jordan IK.

Quote
Eukaryotic transposable elements are ubiquitous and widespread mobile genetic entities. These elements often make up a substantial fraction of the host genomes in which they reside. For example, approximately 1/2 of the human genome was recently shown to consist of transposable element sequences. There is a growing body of evidence that demonstrates that transposable elements have been major players in genome evolution. A sample of this evidence is reviewed here with an emphasis on the role that transposable elements may have played in driving the evolution of eukaryotic complexity. A number of specific scenarios are presented that implicate transposable elements in the evolution of the complex molecular and cellular machinery that are characteristic of the eukaryotic domain of life.


Will want to get the full text and see some of these "specifc scenarios" for the evolution of "complex molecular and cellular machinery"...  

Let me know if you can get your hands on it Nic (or anyone).

theyeti

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Dec. 18 2002,15:40   

Atrazine degradation pathways appear to have arisen recently:

This lab studies 'em:
http://www.cbs.umn.edu/bpti/mice/faculty/wacket1.htm


...Some of their papers are free online:

DeSouza, M. L., J. Seffernick, B. Martinez, and M. J. Sadowsky, L. P. Wackett (1998) Atrazine catabolism genes atzABC are widespread and highly conserved J. Bacteriol. 180(1):1951-1954.
http://jb.asm.org/cgi/content/full/180/7/1951

De Souza, M. L., L. P. Wackett, and M. J. Sadowsky (1998) The atzABC genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl. Envir. Microbiol. 64(6): 2323-2326.
http://aem.asm.org/cgi/content/full/64/6/2323


M.L. deSouza, D. Newcombe, S. Alvey, Crowley, D.E., A. Hay, M.J. Sadowsky, and L.P. Wackett (1998) Molecular basis of a bacterial consortium: Interspecies catabolism of atrazine. Appl. Environ. Microbiol. 64(1):178-184.
http://aem.asm.org/cgi/content/full/64/1/178

In the latter paper, it looks as if three different enzymes found in different bacteria were first combine in multispecies consortia that could metabolize atrazine, and that eventually the 3 genes were combined on a plasmid which then spread around the world in an evolutionary eyeblink.  If this is basically what happened it is yet another method of producing IC (as well as new information).

Quote

Atrazine is the most widely used s-triazine herbicide; it is utilized globally to control broadleaf weeds. Atrazine has been deployed only over the last 40 years and was previously considered to be nonmetabolizable by the majority of soil bacteria. During the first 35 years of its use, bacterial atrazine catabolism was proposed to occur largely via N-dealkylation reactions, resulting in the accumulation of aminotriazine compounds in both soils and laboratory media (3-5, 11, 20, 21). More recently, pure cultures of bacteria that catabolize atrazine to CO2 have been described (8, 26, 27, 30, 37).

The nearly simultaneous reports of atrazine-mineralizing pure cultures by five research groups (8, 26, 27, 30, 37) after years of unsuccessful efforts suggested a recent evolutionary origin and distribution of atrazine degradation genes. Consistent with this, all of the recently identified atrazine-degrading bacteria, isolated from around the world, have been shown to contain similar genes that encode enzymes which catabolize atrazine to cyanuric acid (16) (see Fig. 1). Cyanuric acid can be used by many soil bacteria as the sole nitrogen source (10-12, 19, 23). The enzymes for atrazine catabolism to cyanuric acid are encoded by the atzABC genes, which are found on a self-transmissible plasmid in Pseudomonas sp. strain ADP, the best characterized atrazine-metabolizing bacterium studied at the molecular level (7, 16, 17, 26, 32). Moreover, multiple insertion sequence-like elements have been identified in DNA flanking the atz genes. These studies are beginning to yield insights into atrazine gene evolution and dispersion.

These data also provide the tools for investigating bacterial atrazine genes in situ or in microbial consortia cultured in the laboratory on atrazine. For example, an atrazine-catabolizing consortium was reported in 1994 (3), but that predated the identification of catabolic genes and pure cultures which metabolize atrazine to carbon dioxide. More recently, a stable aerobic consortium was obtained from an agricultural soil and characterized with respect to its ability to catabolize atrazine (1, 2).

The present study was conducted to determine whether the genes and metabolism of the consortium (1, 2) resembled those found in recently described atrazine-metabolizing pure cultures. Our results show that different consortium members separately contained the atzA, -B, and -C genes. Coupled with biochemical studies, this revealed the interspecies metabolic interactions relevant to atrazine catabolism by the consortium. Our findings begin to provide a framework for understanding how catabolic pathways may evolve and the different conditions under which pure-culture or consortial metabolism may be selected for during the global recycling of organic matter.

[...]

The present study extends previous work by demonstrating the individual metabolic and genetic contributions of consortium members that use a proposed recently evolved catabolic pathway (16). Atrazine and related s-triazine herbicides have been in commercial use for approximately 40 years. The wide use of s-triazine herbicides has led to their detection as contaminants in groundwater (6, 28, 29) and to point source soil contamination problems where these herbicides have been spilled. Previously, many isolates and mixed cultures that partially degrade atrazine have been found (3, 10); more recently, several bacterial pure cultures which can completely mineralize atrazine and other s-triazines have been isolated (8, 26, 27, 30, 37). In 1995, Mandelbaum et al. (26) isolated a single atrazine-mineralizing bacterium from a mixture of bacteria originally reported to be a consortium (24, 25), which suggested that the isolate arose from gene transfer which occurred in the mixed culture. The possibility of this has been heightened by our observation that the atzABC genes are located on a 96-kb plasmid, with at least two genes having flanking regions with high homologies to known insertion sequence elements (16). Thus, the present study may offer a window to the evolution of a catabolic pathway by beginning to reveal how genes move from a consortium to individual strains and how mixed cultures containing metabolically cooperating genes may be stably maintained.

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Jan. 15 2003,02:53   

Bump as this thread is being cited on ISCID:

http://www.iscid.org/ubbcgi....279&p=2

In the "origin of new information in the evolution of humans" category:

Quote

Genetics 2002 Dec;162(4):1825-35
 
Accelerated Protein Evolution and Origins of Human-Specific Features. Foxp2 as an example.

Zhang J, Webb DM, Podlaha O.

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109.

Genes responsible for human-specific phenotypes may have been under altered selective pressures in human evolution and thus exhibit changes in substitution rate and pattern at the protein sequence level. Using comparative analysis of human, chimpanzee, and mouse protein sequences, we identified two genes (PRM2 and FOXP2) with significantly enhanced evolutionary rates in the hominid lineage. PRM2 is a histone-like protein essential to spermatogenesis and was previously reported to be a likely target of sexual selection in humans and chimpanzees. FOXP2 is a transcription factor involved in speech and language development. Human FOXP2 experienced a >60-fold increase in substitution rate and incorporated two fixed amino acid changes in a broadly defined transcription suppression domain. A survey of a diverse group of placental mammals reveals the uniqueness of the human FOXP2 sequence and a population genetic analysis indicates possible adaptive selection behind the accelerated evolution. Taken together, our results suggest an important role that FOXP2 may have played in the origin of human speech and demonstrate a strategy for identifying candidate genes underlying the emergences of human-specific features.



Another one for good measure:

Quote

Science 2001 Feb 16;291(5507):1293-7
 
Birth of two chimeric genes in the Hominidae lineage.

Courseaux A, Nahon JL.

Institut de Pharmacologie Moleculaire et Cellulaire, UMR CNRS 6097, 660 route des Lucioles Sophia Antipolis 06560 Valbonne, France.

How genes with newly characterized functions originate remains a fundamental question. PMCHL1 and PMCHL2, two chimeric genes derived from the melanin-concentrating hormone (MCH) gene, offer an opportunity to examine such an issue in the human lineage. Detailed structural, expression, and phylogenetic analysis showed that the PMCHL1 gene was created near 25 million years ago (Ma) by a complex mechanism of exon shuffling through retrotransposition of an antisense MCH messenger RNA coupled to de novo creation of splice sites. PMCHL2 arose 5 to 10 Ma by an event of duplication involving a large chromosomal region encompassing the PMCHL1 locus. The RNA expression patterns of those chimeric genes suggest that they have been submitted to strong regulatory constraints during primate evolution.


[added in edit: oh wait, this was discussed in detail by theyeti back on p. 1


Some points that I think IDists in particular tend to neglect:

1) These are not rare cases, rather discoveries like those referenced here happen every day. The origin of novel genes with divergent functions via natural processes is a ubiquitous and continuing occurrence.

2) I think it is useful to point out how the reconstructed origins of these various genes are *not* due to some single-step process -- rather, we have alternating rounds of duplication, mutation (and *way more* than just point mutation, e.g. exon shuffling) and selection.  IDists will often say something like "gene duplication does not create new information because you just have a copy of the gene".  But no biologist invokes gene duplication alone.  Why don't IDists ever address the case of a gene duplication where one of the copies is mutated and selected, resulting in (1) the original gene and (2) a modified copy with different function.  How can the progression of one gene-->two genes with distinct useful functions *not* be an increase in genetic "information" in any biologically relevant sense?

3) If the process described in step 2 is accepted, repeat in a few billion organisms for a few billion years.  Does this not go at least a fair distance in explaining the information content of genomes?

4) If the leader of the ID movement, Phil Johnson, is horribly, blatantly wrong about simple biological facts, why has he not been criticized by other IDists?  Are they perhaps similarly mislead?

Nick

Edited by niiicholas on Feb. 17 2003,19:27

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Feb. 05 2003,15:35   

Reading a back issue of Science during lunch today, I read an interesting letter about the creation of functional protein modules via selfish DNA.  Here's the original paper to which the letter refers:

Science 2000 Oct 13;290(5490):347-50

Selfish DNA in protein-coding genes of Rickettsia.

Ogata H, Audic S, Barbe V, Artiguenave F, Fournier PE, Raoult D, Claverie JM.


abstract:
Quote
Rickettsia conorii, the aetiological agent of Mediterranean spotted fever, is an intracellular bacterium transmitted by ticks. Preliminary analyses of the nearly complete genome sequence of R. conorii have revealed 44 occurrences of a previously undescribed palindromic repeat (150 base pairs long) throughout the genome. Unexpectedly, this repeat was found inserted in-frame within 19 different R. conorii open reading frames likely to encode functional proteins. We found the same repeat in proteins of other Rickettsia species. The finding of a mobile element inserted in many unrelated genes suggests the potential role of selfish DNA in the creation of new protein sequences.
 

Here is the PubMed link to the letter by Donard S. Dwyer that was written in response:

Selfish DNA and the origin of genes.

Here are some excerpts from that letter:

Quote
The authors suggest that the amino acid segments in the DNA conform to a general motif -- an alpha helix flanked by turns or loops.  Finally, Ogata et al. propose that these Rickettsia palindromic elements (RPEs) represent an example of selfish DNA (DNA that has no apparent cellular function) participating directly in the creation of new protein sequences.
...
[skip a bunch of stuff where Dwyer says that his previous work corroborates that of Ogata et al.]
...

I also found that the duplication unit was encoded by a short inverted repeat segment of DNA that resembled transposable genetic elements (see the figure).  I termed these segments "trexons," for transposable exons.  The RPE's described by Ogata et al. appear to be very similar to trexons.  I proposed that the trexons arose from the initial building blocks of RNA and suggested that these segments represented "selfish DNA" acting at the level of the exon rather than the intron.
[...]


The reference for Dwyer's earlier work is   J Theor Biol 1998 Sep 7;194(1):11-27.

Ogata et al. reply to Dwyer's letter:

Quote
Structural and functional modularity of proteins is well established.  Occurrences of homologous domains in otherwise different proteins suggest the recurrent use orf modular units in evolution.  The combinatorial advantage of modular units to design diverse proteins is obvious, but the precise relation between evolutionarily successful modules and mobile sequence units is not yet clear.  The "trexon" hypothesis proposed by Dwyer and the palindromic element (RPE) that we discovered in several Rickettsia species provide an interesting alternative to the "exon shuffling theory," in which the mobile element precisely coincides with the limitsof existing coding exons, thus restricting the evolutionary game to some sort of "card shuffling."  The finding of the RPE's suggests a greater flexibility in the evolution of genes.

First, the insertions of RPEs realize a flow of genetic material across the boundary between noncoding and protein-coding sequences. [...]


theyeti

edited to add this recent paper by Ogata which addresses the same issue:

Trends Biochem Sci 2003 Feb;28(2):75-80.

The insertion of palindromic repeats in the evolution of proteins.

Claverie JM, Ogata H.

Quote
The current theory of protein evolution is that all contemporary proteins are derived from an ancestral subset. However, each new sequenced genome exhibits many genes with no detectable homologues in other species, leading to the paradoxical picture of a universal ancestor with more genes than any of its progeny. Standard explanations indicate that fast evolving genes might disappear into the 'twilight zone' of sequence similarity. Regardless of the size of the original ancestral subset, its origin and the potential mechanisms of its subsequent enlargement are rarely addressed. Sequencing of Rickettsia conorii genome recently led to the discovery of three families of repeat-mobile elements frequently inserted into the middle of protein coding genes. Although not yet identified in other species of bacteria, this discovery has provided the first clear evidence for the de novo creation of long protein segments (up to 50 amino acid residues) by repeat insertion. Based on previous results and theories on the coding potential of palindromic elements, we speculate that their insertion and mobility might have played a significant role in the early stages of protein evolution.


Edited by theyeti on Feb. 19 2003,10:40

  
VoxRat



Posts: 8
Joined: Dec. 2002

(Permalink) Posted: Feb. 06 2003,15:31   

Here's one of my favorite examples:

Nature 2000 Feb 17;403(6771):785-9

Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis.

Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, Keith JC Jr, McCoy JM.

Quote

Many mammalian viruses have acquired genes from their hosts during their evolution. The rationale for these acquisitions is usually quite clear: the captured genes are subverted to provide a selective advantage to the virus. Here we describe the opposite situation, where a viral gene has been sequestered to serve an important function in the physiology of a mammalian host. This gene, encoding a protein that we have called syncytin, is the envelope gene of a recently identified human endogenous defective retrovirus, HERV-W. We find that the major sites of syncytin expression are placental syncytiotrophoblasts, multinucleated cells that originate from fetal trophoblasts. We show that expression of recombinant syncytin in a wide variety of cell types induces the formation of giant syncytia, and that fusion of a human trophoblastic cell line expressing endogenous syncytin can be inhibited by an anti-syncytin antiserum. Our data indicate that syncytin may mediate placental cytotrophoblast fusion in vivo, and thus may be important in human placental morphogenesis

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Feb. 18 2003,16:37   

This is way cool:

J Mol Evol 2003 Feb;56(2):162-8

Can an arbitrary sequence evolve towards acquiring a biological function?

Hayashi Y, Sakata H, Makino Y, Urabe I, Yomo T.

Quote
To explore the possibility that an arbitrary sequence can evolve towards acquiring functional role when fused with other pre-existing protein modules, we replaced the D2 domain of the fd-tet phage genome with the soluble random polypeptide RP3-42. The replacement yielded an fd-RP defective phage that is six-order magnitude lower infectivity than the wild-type fd-tet phage. The evolvability of RP3-42 was investigated through iterative mutation and selection. Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed. The experimental evolution attested that, from an initial single random sequence, there will be selectable variation in a property of interest and that the property in question was able to improve over several generations. fd-7, the clone with highest infectivity at the end of the experimental evolution, showed a 240-fold increase in infectivity as compared to its origin, fd-RP. Analysis by phage ELISA using anti-M13 antibody and anti-T7 antibody revealed that about 37-fold increase in the infectivity of fd-7 was attributed to the changes in the molecular property of the single polypeptide that replaced the D2 domain of the g3p protein. This study therefore exemplifies the process of a random polypeptide generating a functional role in rejuvenating the infectivity of a defective bacteriophage when fused to some preexisting protein modules, indicating that an arbitrary sequence can evolve toward acquiring a functional role. Overall, this study could herald the conception of new perspective regarding primordial polypeptides in the field of molecular evolution.


theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Feb. 18 2003,16:46   

And also from the lab of Dr. Yomo:

Protein Eng 2002 Jul;15(7):619-26.

Evolvability of random polypeptides through functional selection within a small library.

Yamauchi A, Nakashima T, Tokuriki N, Hosokawa M, Nogami H, Arioka S, Urabe I, Yomo T.

Quote
A directed evolution with phage-displayed random polypeptides of about 140 amino acid residues was followed until the sixth generation under a selection based on affinity to a transition state analog for an esterase reaction. The experimental design deliberately limits the observation to only 10 clones per generation. The first generation consists of three soluble random polypeptides and seven arbitrarily chosen clones from a previously constructed library. The clone showing the highest affinity in a generation was selected and subjected to random mutagenesis to generate variants for the next generation. Even within only 10 arbitrarily chosen polypeptides in each of the generations, there are enough variants in accord to capacity of binding affinity. In addition, the binding capacity of the selected polypeptides showed a gradual continuous increase over the generation. Furthermore, the purified selected random polypeptides exhibited a gradual but significant increase in esterase activity. The ease of the functional development within a small sequence variety implies that enzyme evolution is prompted even within a small population of random polypeptides.


Those wily Japanese.  Such willing partners in the Grand Evolutionist Conspiracy.  ;)

theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Feb. 18 2003,16:56   

Plant Physiol 2003 Feb;131(2):610-20.

Recently Duplicated Maize R2R3 Myb Genes Provide Evidence for Distinct Mechanisms of Evolutionary Divergence after Duplication.

Dias AP, Braun EL, McMullen MD, Grotewold E.

Quote
R2R3 Myb genes are widely distributed in the higher plants and comprise one of the largest known families of regulatory proteins. Here, we provide an evolutionary framework that helps explain the origin of the plant-specific R2R3 Myb genes from widely distributed R1R2R3 Myb genes, through a series of well-established steps. To understand the routes of sequence divergence that followed Myb gene duplication, we supplemented the information available on recently duplicated maize (Zea mays) R2R3 Myb genes (C1/Pl1 and P1/P2) by cloning and characterizing ZmMyb-IF35 and ZmMyb-IF25. These two genes correspond to the recently expanded P-to-A group of maize R2R3 Myb genes. Although the origins of C1/Pl1 and ZmMyb-IF35/ZmMyb-IF25 are associated with the segmental allotetraploid origin of the maize genome, other gene duplication events also shaped the P-to-A clade. Our analyses indicate that some recently duplicated Myb gene pairs display substantial differences in the numbers of synonymous substitutions that have accumulated in the conserved MYB domain and the divergent C-terminal regions. Thus, differences in the accumulation of substitutions during evolution can explain in part the rapid divergence of C-terminal regions for these proteins in some cases. Contrary to previous studies, we show that the divergent C termini of these R2R3 MYB proteins are subject to purifying selection. Our results provide an in-depth analysis of the sequence divergence for some recently duplicated R2R3 Myb genes, yielding important information on general patterns of evolution for this large family of plant regulatory genes.


theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Mar. 16 2003,12:57   

Proc Natl Acad Sci U S A 2003 Mar 4;100(5):2507-11

The Tre2 (USP6) oncogene is a hominoid-specific gene.

Paulding CA, Ruvolo M, Haber DA.


Quote
Gene duplication and domain accretion are thought to be the major mechanisms for the emergence of novel genes during evolution. Such events are thought to have occurred at early stages in the vertebrate lineage, but genomic sequencing has recently revealed extensive amplification events during the evolution of higher primates. We report here that the Tre2 (USP6) oncogene is derived from the chimeric fusion of two genes, USP32 (NY-REN-60), and TBC1D3. USP32 is an ancient, highly conserved gene, whereas TBC1D3 is derived from a recent segmental duplication, which is absent in most other mammals and shows rapid amplification and dispersal through the primate lineage. Remarkably, the chimeric gene Tre2 exists only in the hominoid lineage of primates. This hominoid-specific oncogene arose as recently as 21-33 million years ago, after proliferation of the TBC1D3 segmental duplication in the primate lineage. In contrast to the broad expression pattern of USP32 and TBC1D3, expression of Tre2 is testis-specific, a pattern proposed for novel genes implicated in the emergence of reproductive barriers. The sudden emergence of chimeric proteins, such as that encoded by Tre2, may have contributed to hominoid speciation.


Thumbs up to "MyKell" on IIDB for pointing this one out.

theyeti

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: April 04 2003,21:26   

Good little one that Ian Musgrave posted at t.o. in rebuttal to a creo reiterating Behe's argument regarding Ken Miller's citation of Barry Hall's work on lactose metabolism:

Quote

G'Day All
Address altered to avoid spam, delete RemoveInsert

On Thu, 3 Apr 2003 17:59:50 +0000 (UTC),
seanpitnospam@naturalselection.0catch.com (Sean Pitman M.D.) wrote:

>Evolving Rube Goldberg Machines
>http://naturalselection.0catch.com/Files/Rube%20Goldberg.html

[enormous snip]
>But what if the E. coli had
>not been so fortunate as to have this spare tire gene?  What would
>have happened then?  Hall wondered about this himself.  He then
>deleted the spare tire gene as well as the lacZ genes.  Would there be
>lactase evolution now?

See Matsumura I, Ellington AD. In vitro evolution of
beta-glucuronidase into a beta-galactosidase proceeds through
non-specific intermediates. J Mol Biol. 2001 Jan 12;305(2):331-9)
where they have evolved a beta glactosidase from an enzyme other than
the "spare tyre". I believe I have directed you to this paper before.

link to thread



Da paper:

Quote

Matsumura I, Ellington AD. In vitro evolution of
beta-glucuronidase into a beta-galactosidase proceeds through
non-specific intermediates.
J Mol Biol. 2001 Jan 12;305(2):331-9

The Escherichia coli beta-glucuronidase (GUS) was evolved in vitro to catalyze the hydrolysis of a beta-galactoside substrate 500 times more efficiently (k(cat)/K(m)) than the wild-type, with a 52 million-fold inversion in specificity. The amino acid substitutions that recurred among 32 clones isolated in three rounds of DNA shuffling and screening were mapped to the active site. The functional consequences of these mutations were investigated by introducing them individually or in combination into otherwise wild-type gusA genes. The kinetic behavior of the purified mutant proteins in reactions with a series of substrate analogues show that four mutations account for the changes in substrate specificity, and that they are synergistic. An evolutionary intermediate, unlike the wild-type and evolved forms, exhibits broadened specificity for substrates dissimilar to either glucuronides or galactosides. These results are consistent with the "patchwork" hypothesis, which postulates that modern enzymes diverged from ancestors with broad specificity.


Edited by niiicholas on April 04 2003,21:27

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: April 10 2003,13:07   

This is interesting.

Genomics 2003 Apr;81(4):391-9

BAGE genes generated by juxtacentromeric reshuffling in the hominidae lineage are under selective pressure.

Ruault M, Ventura M, Galtier N, Brun ME, Archidiacono N, Roizes G G, De Sario A.

Quote
In this paper, we show that the BAGE (B melanoma antigen) gene family was generated by chromosome rearrangements that occurred during the evolution of hominoids. An 84-kb DNA fragment derived from the phylogenetic 7q36 region was duplicated in the juxtacentromeric region of either chromosome 13 or chromosome 21. The duplicated region contained a fragment of the MLL3 gene, which, after juxtacentromeric reshuffling, generated the ancestral BAGE gene. Then, this ancestral gene gave rise to several independent genes through successive rounds of inter- and intrachromosome duplications. Comparison of synonymous and nonsynonymous mutations in putative coding regions shows that BAGE genes, but not the BAGE gene fragments, are under selective pressure. Our data strongly suggest that BAGE proteins have a function and that juxtacentromeric regions, whose plasticity is now largely proved, are not a simple junkyard of gene fragments, but may be the birth site of novel genes.


theyeti

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 20 2003,14:13   

From t.o.:

http://tinyurl.com/c8h0

Code Sample

>> Just a couple of thoughts: another problem with Hall's selection
>> experiments on bacteria is that he's relying on existing genes to pick
>> up the function of a deleted gene. But they aren't entirely free to
>> evolve, even neutrally. Each of those proteins has a function which it
>> must maintain. A mutation that helps to replace the lost function must
>> also preserve the protein's current function, so there is the
>> possibility of selection rejecting mutations because, even if they help
>> regain the lost function, they may degrade the protein's current
>> function enough to make net selection negative. I don't know how
>> important that factor would be in practice, but it's something to
>> consider. A lot of evolution can get around this problem by beginning
>> with a gene duplication, allowing different copies to experience
>> selection in different directions.
>
>Yes, this is quite a problem indeed.  Gene duplication is supposed to
>get around this problem by creating sequences that can undergo neutral
>drift while maintaining previous functional sequences.  However,
>Hall's E. coli didn't do this either.  They simply didn't evolve the
>lactase function by any means, not even by gene duplication.  Neither
>have many other types of bacteria despite huge numbers of observed
>generations (over a million).

See Matsumura I, Ellington AD. In vitro evolution of
beta-glucuronidase into a beta-galactosidase proceeds through
non-specific intermediates. J Mol Biol. 2001 Jan 12;305(2):331-9)
where they have evolved a beta galactosidase that acts on lactose from
an enzyme other than the "spare tyre". I believe I have directed you
to this paper before.


  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: June 17 2003,14:41   

Retrotransposable, non-coding Alu elements being turned into protein coding exons.  Pretty cool.  

Science. 2003 May 23;300(5623):1288-91.

The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons.

Lev-Maor G, Sorek R, Shomron N, Ast G.

Quote
Alu repetitive elements can be inserted into mature messenger RNAs via a splicing-mediated process termed exonization. To understand the molecular basis and the regulation of the process of turning intronic Alus into new exons, we compiled and analyzed a data set of human exonized Alus. We revealed a mechanism that governs 3' splice-site selection in these exons during alternative splicing. On the basis of these findings, we identified mutations that activated the exonization of a silent intronic Alu.


About 5% of alternatively spliced internal exons lead with an Alu sequence, which makes this a fairly common method of creating new "information".  

Here's a excerpt from the commentary that appears in the issue:

Quote
It appears that in addition to the distance between two AG dinucleotides, a nucleotide immediatesly upstream of proximal AG is also important.  Hence, a proximal GAG sequence serves as a signal weak enough to create an alternatively spliced Alu exon.  Any mutation of a proximal GAG in the first position results in a constitutive Alu exon.  This is an important observation, because most of the more than 1 million Alu elements in the human genome contain such a potential 3' splice site.  Of these, 238,000 are located within introns of protein-coding genes, and each one can become an exon.  Unfortunately, most mutations will lead to abnormal proteins and are likely to result in disease.  Yet a a small number may create an evolutionary novelty, and nature's "alternative splicing approach" guarantees that such a novelty may be tested while the original protein stays intact.

Another way to exploit an evolutionary novelty without disturbing the function of the original protein is gene duplication (see the figure.)  Gene duplication is one of the major ways in which organisms can generate new genes.  After a gene duplicates, one copy maintains its original function while the other is free to evolve and can be used for "nature's experiments."  Usually, this is accomplished through point mutations and the whole process is very slow.  However, recycling some modules that already exist in a genome (for example, in transposons) can speed up the natural mutagenesis process tremendously.  Several years ago, Iwashita and colleagues discovered a bovine gene containing a piece of a transposable element (called a TE-cassette) in the middle of its open reading-frame.  This cassette contributes a whole new domain to the bovine BCNT protein, namely an endonuclease domain native to the ruminant retrotransposable element-1 (RTE-1).

[Skip stuff about how BCNT is the result of a gene duplication.]

The reports by Lev-Maor et al. and Iwashita and collegues describe different ways in which genes can be rapidly rearranged and acquire evolutionary novelty through the use of so-called junk DNA. These discoveries wouldn't be so exciting if they didn't show how genomes achieve this wihtout disturbing an original protein.  To quote an old Polish proverb: "A wolf is sated and a lamb survived."


The Iwashita paper is still in press, to be published in Molecular Biology and Evolution.  Will be posted here when it's available on PubMed.  :D  

theyeti

Edited by theyeti on June 17 2003,14:45

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: July 24 2003,19:28   

Quote (niiicholas @ May 30 2002,00:02)
PS: I'll start off with one of my favorite examples:

Sdic, sperm dynein intermediate chain, a new gene which evolved over the past few million years by the duplication, fusion, and modification of two genes that are now on each side of Sdic on the chromosome.

Here is a brief introduction from Ian Musgrave:

A new paper is out about Sdic, giving more detail about its origins and some insight about the evolution of novel genes in general:

Genetica. 2003 Jul;118(2-3):233-44.

Origin and evolution of a new gene expressed in the Drosophila sperm axoneme.

Ranz JM, Ponce AR, Hartl DL, Nurminsky D.

Quote
Sdic is a new gene that evolved recently in the lineage of Drosophila melanogaster. It was formed from a duplication and fusion of the gene AnnX, which encodes annexin X, and Cdic, which encodes the intermediate polypeptide chain of the cytoplasmic dynein. The fusion joins AnnX exon 4 with Cdic intron 3, which brings together three putative promoter elements for testes-specific expression of Sdic: the distal conserved element (DCE) and testes-specific element (TSE) are derived from AnnX, and the proximal conserved element (PCE) from Cdic intron 3. Sdic transcription initiates within the PCE, and translation is initiated within the sequence derived from Cdic intron 3, continuing through a 10 base pair insertion that creates a new splice donor site that enables the new coding sequence derived from intron 3 to be joined with the coding sequence of Cdic exon 4. A novel protein is created lacking 100 residues at the amino end that contain sequence motifs essential for the function of cytoplasmic dynein intermediate chains. Instead, the amino end is a hydrophobic region of 16 residues that resembles the amino end of axonemal dynein intermediate chains from other organisms. The downstream portion of Sdic features large deletions eliminating Cdic exons v2 and v3, as well as multiple frameshift deletions or insertions. The new protein becomes incorporated into the tail of the mature sperm and may function as an axonemal dynein intermediate chain. The new Sdic gene is present in about 10 tandem repeats between the wildtype Cdic and AnnX genes located near the base of the X chromosome. The implications of these findings are discussed relative to the origin of new gene functions and the process of speciation.


theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: July 27 2003,15:34   

In the same issue of Genetica as the above article, there are two more articles relevant here:

Genetica. 2003 Jul;118(2-3):171-82.

Origin of new genes: evidence from experimental and computational analyses.

Long M, Deutsch M, Wang W, Betran E, Brunet FG, Zhang J.
Department of Ecology and Evolution, The University of Chicago,

Quote

Exon shuffling is an essential molecular mechanism for the formation of new genes. Many cases of exon shuffling have been reported in vertebrate genes. These discoveries revealed the importance of exon shuffling in the origin of new genes. However, only a few cases of exon shuffling were reported from plants and invertebrates, which gave rise to the assertion that the intron-mediated recombination mechanism originated very recently. We focused on the origin of new genes by exon shuffling and retroposition. We will first summarize our experimental work, which revealed four new genes in Drosophila, plants, and humans. These genes are 10(6) to 10(8) million years old. The recency of these genes allows us to directly examine the origin and evolution of genes in detail. These observations show firstly the importance of exon shuffling and retroposition in the rapid creation of new gene structures. They also show that the resultant chimerical structures appearing as mosaic proteins or as retroposed coding structures with novel regulatory systems, often confer novel functions. Furthermore, these newly created genes appear to have been governed by positive Darwinian selection throughout their history, with rapid changes of amino acid sequence and gene structure in very short periods of evolution. We further analyzed the distribution of intron phases in three non-vertebrate species, Drosophila melanogaster, Caenorhabditis elegans, and Arabidosis thaliana, as inferred from their genome sequences. As in the case of vertebrate genes, we found that intron phases in these species are unevenly distributed with an excess of phase zero introns and a significant excess of symmetric exons. Both findings are consistent with the requirements for the molecular process of exon shuffling. Thus, these non-vertebrate genomes may have also been strongly impacted by exon shuffling in general.


And..

Genetica. 2003 Jul;118(2-3):193-208.

Birth of 'human-specific' genes during primate evolution.
Nahon JL.


Quote
Humans and other Anthropoids share very similar chromosome structure and genomic sequence as seen in the 98.5% homology at the DNA level between us and Great Apes. However, anatomical and behavioral traits distinguish Homo sapiens from his closest relatives. I review here several recent studies that address the issue by using different approaches: large-scale sequence comparison (first release) between human and chimpanzee, characterization of recent segmental duplications in the human genome and analysis of exemplary gene families. As a major breakthrough in the field, the heretical concept of 'human-specific' genes has recently received some supporting data. In addition, specific chromosomal regions have been mapped that display all the features of 'gene nurseries' and could have played a major role in gene innovation and speciation during primate evolution. A model is proposed that integrates all known molecular mechanisms that can create new genes in the human lineage.


That would be a good issue to get ahold of.

theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Aug. 01 2003,18:14   

Nucleic Acids Res. 2003 Aug 1;31(15):4401-9.

Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations.

Vandenbussche M, Theissen G, Van de Peer Y, Gerats T.

Quote
Frameshift mutations generally result in loss-of-function changes since they drastically alter the protein sequence downstream of the frameshift site, besides creating premature stop codons. Here we present data suggesting that frameshift mutations in the C-terminal domain of specific ancestral MADS-box genes may have contributed to the structural and functional divergence of the MADS-box gene family. We have identified putative frameshift mutations in the conserved C-terminal motifs of the B-function DEF/AP3 subfamily, the A-function SQUA/AP1 subfamily and the E-function AGL2 subfamily, which are all involved in the specification of organ identity during flower development. The newly evolved C-terminal motifs are highly conserved, suggesting a de novo generation of functionality. Interestingly, since the new C-terminal motifs in the A- and B-function subfamilies are only found in higher eudicotyledonous flowering plants, the emergence of these two C-terminal changes coincides with the origin of a highly standardized floral structure. We speculate that the frameshift mutations described here are examples of co-evolution of the different components of a single transcription factor complex. 3' terminal frameshift mutations might provide an important but so far unrecognized mechanism to generate novel functional C-terminal motifs instrumental to the functional diversification of transcription factor families.


From the discussion:

Quote
Based on these observations and the results presented here, we propose a model for the functional diversification of duplicated members of transcription factor families (Fig. 5). After duplication of an ancestral gene X, one of the copies (Y) may accumulate mutations in the C-terminus, while retaining features such as DNA binding, essential for its function as a transcription factor, in the upstream coding regions. Apart from in frame insertions/deletions and single nucleotide substitutions, mutations in the coding sequence at the 3' end will also induce frameshifts, as such masking the ancestral origin of the motif at the protein level. While most frameshift mutations will be deleterious for the existing function, in specific cases they may yield novel functional C-terminal motifs. The three cases we have described are perfect examples of such a neo-functionalization process. This widens the emerging view that plant transcription factors evolve mainly by changes in cis-regulatory elements that affect their expression pattern (37,38), and that after gene duplication, mainly degeneration and selection of complementary functioning, i.e. sub-functionalization occurs (39,40). At first sight, it may seem extraordinary that in all three cases, frameshift mutations of highly conserved motifs yielded novel highly conserved motifs. However, this specific situation is the only type of motif generation that can still be recognized after millions of years of independent evolution of both copies. If the new motif had been recruited from a sequence in a non-conserved (Y3 and Y4, Fig. 5) or less conserved region of the C-terminus (e.g. Y2), it would be impossible to trace back the ancestral motif. Equally important, either the new or the ancestral motif must contain amino acid residues that are not too highly degenerate in order to be able to recognize the related motif after frameshifting. Thus, the only cases of frameshift mutations that we still can recognize are those in highly conserved motifs that yield novel highly conserved motifs. Finally, novel motifs may be acquired in an additive way downstream of existing motifs as an extra feature, with retention of the ancestral motif that in such a case becomes internal (e.g. Y3); or with subsequent loss of the ancestral motif (all other cases).


'Da model:


Quote
Figure 5. Model for the generation of novel C-terminal motifs within the MADS-box gene family. After duplication of an ancestral gene X, the Y copy accumulates mutations in the C-terminal domain, while retaining the essential MIK domain. Insertions or deletions will cause a frameshift in the coding sequence. Rarely, these frameshift mutations may yield novel functional motifs that consequently will be conserved. In cases where the novel motif is recruited from poorly conserved regions (e.g. Y 2–4) in the ancestral sequence, the sequence relation with the ancestral gene X will become unclear after a period of independent evolution. In the Y copy, new motifs may be added downstream of the ancestral motif as an extra feature, with retention of the ancestral motif which in this case becomes internal (e.g. Y3); or with subsequent loss of the ancestral motif (all other cases).


...other good stuff in the paper too long to reproduce here.

theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Aug. 26 2003,18:18   

Evidence of more retrogenes in the human genome.    

Nucleic Acids Res. 2003 Aug 1;31(15):4385-90.

The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination.

Buzdin A, Gogvadze E, Kovalskaya E, Volchkov P, Ustyugova S, Illarionova A, Fushan A, Vinogradova T, Sverdlov E.

Quote
L1 retrotransposons play an important role in mammalian genome shaping. In particular, they can transduce their 3'-flanking regions to new genomic loci or produce pseudogenes or retrotranscripts through reverse transcription of different kinds of cellular RNAs. Recently, we found in the human genome an unusual family of chimeric retrotranscripts composed of full-sized copies of U6 small nuclear RNAs fused at their 3' termini with 5'-truncated, 3'-poly(A)-tailed L1s. The chimeras were flanked by 11-21 bp long direct repeats, and contained near their 5' ends T2A4 hexanucleotide motifs, preferably recognized by L1 nicking endonuclease. These features suggest that the chimeras were formed using the L1 integration machinery. Here we report the identification of 81 chimeras consisting of fused DNA copies of different RNAs, including mRNAs of known human genes. Based on their structural features, the chimeras were subdivided into nine distinct families. 5' Parts of the chimeras usually originated from different nuclear RNAs, whereas their 3' parts represented cytoplasmic RNAs: mRNAs, including L1 mRNA and Alu RNA. Some of these chimeric retrotranscripts are expressed in a variety of human tissues. These findings suggest that RNA-RNA recombination during L1 reverse transcription followed by the integration of the recombinants into the host genome is a general event in genome evolution.


To remind everyone, retrogenes are created as follows:

1.  mRNA from existing gene --> reverse transcription into cDNA.

This is carried out by an endogenous reverse transcriptase, which may come from endogenous retroviruses, Alu elements, etc.

2.  cDNA is integrated into genome.

This is also carried out by endogenous integration proteins.  Again, these can also come from endogenous retroviruses, etc.

The result is a gene duplicate that usually has the following attributes:

A.  No introns.
B.  Trucated at the 5' end.
C.  The remnants of a poly-A tail at the 3' end.
D.  Flanking repeats.

These attributes make identifying retrogenes relatively easy, and they provide extremely strong evidence that these genes did indeed arise through retrotransposition.  Given that they contain a truncation, and are integrated without regulatory sequences, the most common fate for a retroelement of this kind is to be non-functional.  However, examples of functional retrogenes exist.  

The chimeras observed in the present study are formed when an RNA-RNA hybrid, consisting of two unrelated RNA transcripts, is acted upon by a reverse transcriptase.  Here is the proposed mechanism:

Quote
Figure 4. A probable mechanism for the chimeras’ formation. (Step 1) An L1 pre-integration complex binds L1, Alu or the host mRNA in the cytoplasm. (Step 2) The ribonucleoprotein formed is transferred to the nucleus. (Step 3) Reverse transcription of the bound mRNA primed by a genomic DNA single-stranded break within the TTTTAA sequence. (Step 4) Another (nuclear) RNA binds to the L1 reverse transcription/integration complex. (Step 5) Switch of templates for the reverse transcription. (Step 6) The DNA reparation mediated formation of a new chimeric retrogene insertion flanked by short direct repeats and carrying a poly(A) sequence at the 3' terminus.


The authors found that at least 6 of the chimeric retrogenes that they found (out of 81) are being expressed in human tissues, indicating that they likely have a function.  Whether or not the rest have a function isn't known, but the authors only directly tested (via RT-PCR analysis) 6 of the sequences and found that 4 were unexpressed.  So these identified retroelements probably contain a mixture of functional and non-functional sequences.

Moreover, the presence of these chimeric retrogenes also provides evidence for common descent, since they have integrated at various times during primate evolution, and yet they follow the standard phylogeny:

Quote
Figure 3. Results of the 12 chimeric retrogenes insertional polymorphism study. The chimeras’ integration times were estimated according to the presence/ absence of the inserts in genomic DNAs of different primate species.


One of the retrogenes is polymorphic within the human population, indicating that it arose since the last common ancestor of all humans.

This is very strong evidence for common descent, along the lines of shared errors in pseudogenes.  

theyeti

Edited by theyeti on Aug. 26 2003,18:19

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Sep. 01 2003,15:36   

Quote (theyeti @ June 17 2003,14:41)
The Iwashita paper is still in press, to be published in Molecular Biology and Evolution.  Will be posted here when it's available on PubMed.  :D  

Well, it's available:

Mol Biol Evol. 2003 Sep;20(9):1556-63.

A Transposable Element-Mediated Gene Divergence that Directly Produces a Novel Type Bovine Bcnt Protein Including the Endonuclease Domain of RTE-1.

Iwashita S, Osada N, Itoh T, Sezaki M, Oshima K, Hashimoto E, Kitagawa-Arita Y, Takahashi I, Masui T, Hashimoto K, Makalowski W.

Quote
Ruminant Bcnt protein with a molecular mass of 97 kDa (designated p97Bcnt) includes a region derived from the endonuclease domain of a retrotransposable element RTE-1. Human and mouse Bcnt proteins lack the corresponding region but have a highly conserved 82-amino acid region at the C-terminus that is not present in p97Bcnt. By screening a bovine BAC library, we found two more bcnt-related genes: human-type bcnt (h-type bcnt) and its processed pseudogene. Whereas the pseudogene is localized on chromosome 26, both bcntp97 and the h-type bcnt genes are found on bovine chromosome 18, a synteny region of human chromosome 16 on which human BCNT is localized. Complete nucleotide sequencing of the BAC clone reveals that the bcntp97 and h-type bcnt genes are located just 6 kb apart in a tandem manner. The two h-type bcnt and bcntp97genes are active at both the transcriptional level and the protein level. H-type bovine Bcnt is more like human BCNT than p97Bcnt, when compared at their N-terminal regions. However, phylogenetic analysis using the N-terminal region of the bcnt gene family revealed that the duplication of bovine genes occurred within the bovine lineage with significantly accelerated substitution in bcntp97. This acceleration was not ascribed definitely to positive selection. After duplication, one of the bovine bcnt genes recruited the endonuclease domain of an intronic RTE-1 repeat accompanied by the accelerated substitution at the 5'-ORF, resulting in creation of a novel type of Bcnt protein in bovine.


theyeti

edit:  Here's an earlier paper on this protein:

Gene. 2001 May 2;268(1-2):59-66.

Gene organization of bovine BCNT that contains a portion corresponding to an endonuclease domain derived from an RTE-1 (Bov-B LINE), non-LTR retrotransposable element: duplication of an intramolecular repeat unit downstream of the truncated RTE-1.

Edited by theyeti on Sep. 01 2003,15:39

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Sep. 04 2003,14:10   

I don't think this one's been posted yet.  

Gene. 2002 May 1;289(1-2):1-6.

SCAN domain-containing 2 gene (SCAND2) is a novel nuclear protein derived from the zinc finger family by exon shuffling.

Dupuy D, Duperat VG, Arveiler B.

Quote
The SCAN domain is a recently recognized protein domain that characterizes a subfamily of the Kruppel-like zinc finger proteins. We have previously described a novel SCAN domain-containing 2 gene (SCAND2) that does not belong to the zinc finger family. We report structural and sequence analyzes of all known members of the SCAN family and use these data to illustrate a model of gene family evolution. Most of the SCAN containing genes share common gene organization features that support the proposed origin for SCAND2 by disruption of an ancestral SCAN-zinc finger gene by a retroposition event and subsequent exon shuffling.


Here's their model:

[oops, can't post it]

Quote
Fig. 2. Proposed model for SCAND2 gene origin. (A) Insertion of a C1orf12 cDNA in the first intron of a SCAN-containing ancestor gene located in 15q25 allowed a shadow exon from C1orf12 to be spliced downstream of a SCAN encoding exon, thus producing a new protein product. White boxes: exons from C1orf12; Hatched boxes: exons from the ancestral SCAN gene; dotted box: shadow exon from C1orf12. (B) Alignment between C1orf12 and SCAND2 cDNAs. The inserted retroposon contains a consensus acceptor splice site located upstream of the C1orf12 original translation start site. Asterisks indicate differences between the nucleotide sequences.


theyeti

  
Wesley R. Elsberry



Posts: 4506
Joined: May 2002

(Permalink) Posted: Jan. 21 2004,07:45   

A commonly overlooked reference

Kimura, Motoo. 1961. Natural selection as the process of accumulating genetic information in adaptive evolution. Genetical Research 2:127-140.

Quote
The purposes of the present paper are threefold. First, a method will be proposed by which the rate of accumulation of genetic information in the process of adaptive evolution may be measured. Secondly, for the first time, an approximate estimate of the actual amount of genetic information in higher animals will be derived which might have been accumulated since the beginning of the Cambrian epoch (500 million years), and thirdly, there is a discussion of problems involved in the storage and transformation of the genetic information thus acquired. There is a vast field of fundamental importance which awaits the fruitful activities of statisticians and other applied mathematicians collaborating with biologists.


I don't recall ever seeing a discussion of Kimura's paper in any antievolution argument on information.

Wesley

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Jan. 28 2004,11:36   

Mol Biol Evol. 2004 Jan 22

Leptin Receptor Isoform 219.1: An Example of Protein Evolution by LINE-1 Mediated Human Specific Retrotransposition of a Coding SVA Element.

Damert A, Lower J, Lower R.

Quote

Phylogenetically new insertions of repetitive sequences may contribute to genome evolution by altering the function of pre-existing proteins. One example is the SVA sequence which forms the C-terminal coding exon of the human leptin receptor isoform 219.1. Here, we report that the SVA insertion into the LEPR locus has occurred after divergence of humans and chimpanzees. The SVA element was inserted into a Hal-1/LINE element present in all monkeys and apes tested. Structural features point towards an integration event that was mediated by the L1 protein machinery acting in trans. Thus our findings add evidence to the hypothesis that retrotransposition events are a driving force in genomic evolution and that the presence or absence of specific retroelements are one distinguishing feature that separates humans from chimpanzees.


theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Feb. 14 2004,17:21   

Here's a good one.  A recently aquired endogenous retrovirus has had its Env gene coopted to serve a function in placental physiology.  The Env gene normally codes for envelope proteins in retroviruses.

Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1731-6.

The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology.

Mallet F, Bouton O, Prudhomme S, Cheynet V, Oriol G, Bonnaud B, Lucotte G, Duret L, Mandrand B.

Quote
The definitive demonstration of a role for a recently acquired gene is a difficult task, requiring exhaustive genetic investigations and functional analysis. The situation is indeed much more complicated when facing multicopy gene families, because most or portions of the gene are conserved among the hundred copies of the family. This is the case for the ERVWE1 locus of the human endogenous retrovirus W family (HERV-W), which encodes an envelope glycoprotein (syncytin) likely involved in trophoblast differentiation. Here we describe, in 155 individuals, the positional conservation of this locus and the preservation of the envelope ORF. Sequencing of the critical elements of the ERVWE1 provirus showed a striking conservation among the 48 alleles of 24 individuals, including the LTR elements involved in the transcriptional machinery, the splice sites involved in the maturation of subgenomic Env mRNA, and the Env ORF. The functionality and tissue specificity of the 5' LTR were demonstrated, as well as the fusogenic activity of the envelope polymorphic variants. Such functions were also shown to be preserved in the orthologous loci isolated from chimpanzee, gorilla, orangutan, and gibbon. This functional preservation among humans and during evolution strongly argued for the involvement of this recently acquired retroviral envelope glycoprotein in hominoid placental physiology.


theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Feb. 14 2004,17:38   

Nat Genet. 2004 Feb 1 Epub 2004 Feb 01.

Evolutionary innovation of the excretory system in Caenorhabditis elegans.

Wang X, Chamberlin HM.

Quote
The evolution of complexity relies on changes that result in new gene functions. Here we show that the unique morphological and functional features of the excretory duct cell in C. elegans result from the gain of expression of a single gene. Our results show that innovation can be achieved by altered expression of a transcription factor without coevolution of all target genes.


theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Mar. 11 2004,17:31   

Cockroaches making milk.  How adorable.

Evol Dev. 2004 Mar-Apr;6(2):67-77.

Evolution of a novel function: nutritive milk in the viviparous cockroach, Diploptera punctata.

Williford A, Stay B, Bhattacharya D.

Quote
Cockroach species show different degrees of maternal contribution to the developing offspring. In this study, we identify a multigene family that encodes water-soluble proteins that are a major component of nutritive "Milk" in the cockroach, Diploptera punctata. This gene family is associated with the evolution of a new trait, viviparity, in which the offspring receive nutrition during the gestation period. Twenty-five distinct Milk complementary DNAs were cloned and partially characterized. These complementary DNAs encode 22 distinct Milk peptides, each of length 171 amino acids, including a 16-amino acid signal peptide sequence. Southern blot analysis confirms the presence of multiple copies of Milk genes in D. punctata. Northern analysis indicates tissue- and stage-specific Milk gene expression. Examination of the deduced amino acid sequences identifies the presence of structurally conserved regions diagnostic of the lipocalin protein family. The shared exon/intron structure of one of the Milk loci with lipocalin genes further supports a close evolutionary relationship between these sequences.


theyeti

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Mar. 22 2004,03:13   

Don't think this has been posted before:

Quote

Dean, Anthony (1998).  The Molecular Anatomy of an Ancient Adaptive Event.  American Scientist, 86(1), p. 26.

Not long ago after the first living organisms appeared on earth about 3.5 billion years ago, they started undergoing mutations and adaptations. One of the very earliest of these created two enzymes, each with distinct but related functions, where only one previously existed. Using a combination of the modern techniques of structural biochemistry and protein engineering, combined with molecular phylogeny, the author recreates the story of this very ancient event.


The article is about the origin of two ancient proteins from a common ancestor (enzymes that handle NAD or NADH) and is quite detailed but also written for the nonexpert.  I believe Ken Miller has used the technical paper it was based on as an example.  It is now freely online at American Scientist.


Adding this also to the EvoWiki page on the evolution of new information.

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: May 26 2004,10:04   

This is a good review article about the origin of alternative splicing, and provides evidence of non-coding intronic sequences being transcribed as part of the protein.  In other words, more or less random non-coding DNA being adapted to be part of a functional protein.

Trends Genet. 2003 Mar;19(3):115-9.

Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences.

Kondrashov FA, Koonin EV.

Abstract:

Quote
Alternative splicing is thought to be a major source of functional diversity in animal proteins. We analyzed the evolutionary conservation of proteins encoded by alternatively spliced genes and predicted the ancestral state for 73 cases of alternative splicing (25 insertions and 48 deletions). The amino acid sequences of most of the inserts in proteins produced by alternative splicing are as conserved as the surrounding sequences. Thus, alternative splicing often creates novel isoforms by the insertion of new, functional protein sequences that probably originated from noncoding sequences of introns.


Some relevant text:

Quote
From the evolutionary standpoint, inserted alternative sequences could be expected to be short if they evolved from noncoding sequences because in-frame stop codons are likely to occur in long noncoding sequences. None of the inserted alternative sequences showed significant similarity to any protein sequences except for their counterparts in orthologs from other species. Furthermore, inserted alternative sequences never included more than one exon (Fig. 2). These observations are compatible with the origin of inserts in LDAS [length difference alternative splicing] from noncoding sequences, most likely from a part of the intron separating the adjacent constitutive exons. On four occasions, this was supported by more direct observations whereby the inserted alternative sequence comprised either an entire intron or a portion of intron joining the adjacent exon.

....

Thus, in addition to straightforward exon skipping, a major route for origin of LDAS is insertion of new exons, which encode new, functionally important protein sequences, thus creating functionally distinct isoforms of the respective proteins. Such new exons might in some cases have evolved by tandem duplication of adjacent exons, but more often, they appear to have evolved de novo from noncoding intron sequences. Most of these intron sequences apparently have been recruited to become new coding sequences relatively recently; for example, only in mammals (supplementary material at http://archive.bmn.com/supp/tig/march_Kondrashov_supply.pdf). These observations suggest that evolution of new coding sequences from noncoding ones is an active, ongoing process in eukaryotes. It seems probable that we uncovered only the tip of the proverbial iceberg.  Indeed, we detected insertion of new exons that probably originate from intron sequences only for LDAS and only for those cases where yeast and/or prokaryotic orthologs were readily detectable. The actual contribution of intron sequences to the emergence of new protein sequences in eukaryotes is probably substantially greater.


theyeti

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Sep. 21 2004,17:25   

Nat Genet. 2004 Sep 19

Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux.

Burki F, Kaessmann H.

Quote
The enzyme glutamate dehydrogenase (GDH) is important for recycling the chief excitatory neurotransmitter, glutamate, during neurotransmission. Human GDH exists in housekeeping and brain-specific isotypes encoded by the genes GLUD1 and GLUD2, respectively. Here we show that GLUD2 originated by retroposition from GLUD1 in the hominoid ancestor less than 23 million years ago. The amino acid changes responsible for the unique brain-specific properties of the enzyme derived from GLUD2 occurred during a period of positive selection after the duplication event.

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Jan. 26 2005,13:06   

Curr Biol. 2005 Jan 26;15(2):87-93.

Origin and neofunctionalization of a Drosophila paternal effect gene essential for zygote viability.

Loppin B, Lepetit D, Dorus S, Couble P, Karr TL.

Quote
Background: Although evolutionary novelty by gene duplication is well established, the origin and maintenance of essential genes that provide entirely new functions (neofunctionalization) is still largely unknown. Drosophila is a good model for the search of genes that are young enough to allow deciphering the molecular details of their evolutionary history. Recent years have seen increased interest in genes specifically required for male fertility because they often evolve rapidly. A special class of genes affecting male fertility, the paternal effect genes, have also become a focus of study to geneticists and reproductive biologists interested in fertilization and sperm-egg interactions. Results: Using molecular genetics and the annotated Drosophila melanogaster genome, we identified CG14251 as the Drosophila paternal effect gene, ms(3)K81 (K81). This assignment was subsequently confirmed by P-element rescue of K81. A search for orthologous K81 sequences revealed that the distribution of K81 is surprisingly restricted to the 9 species comprising the melanogaster subgroup. Phylogenetic analyses indicate that K81 arose through duplication, most likely retroposition, of a ubiquitously expressed gene before the radiation of the melanogaster subgroup, followed by a period of rapid divergence and acquisition of a critical male germline-specific function. Interestingly, K81 has adopted the expression profile of a flanking gene suggesting that transcriptional coregulation may have been important in the neofunctionalization of K81. Conclusion: We present a detailed case history of the origin and evolution of a new essential gene and, in so doing, provide the first molecular identification of a Drosophila paternal effect gene, ms(3)K81 (K81).

  
  42 replies since May 30 2002,00:02 < Next Oldest | Next Newest >  

Pages: (2) < [1] 2 >   


Track this topic Email this topic Print this topic

[ Read the Board Rules ] | [Useful Links] | [Evolving Designs]