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

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.

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:

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:

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. [...]


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.

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

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