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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: 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


Full text  (may need subscription)

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:

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:

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.


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