Reductive Evolution

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Reductive Evolution

Postby stcordova » Mon Mar 19, 2018 12:31 am

http://www.pnas.org/content/108/29/11954.full

The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P < 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically disordered regions as well. Reductively evolved linker sequence lengths in growth rate maximized cells should be proportional to proteome diversity. By using total in-frame coding capacity of a genome [i.e., coding sequence (CDS)] as a reliable measure of proteome diversity, we find linker lengths of prokaryotes clearly evolve in proportion to CDS values, whereas those of eukaryotes are more randomly larger than expected. Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not.
....
The lengths of proteins are subject to systematic variation that relates to the cellular context in which they function. So, randomly chosen proteins from Archaea and Bacteria tend to be only two thirds as long as those chosen from Eukarya (1–3). Likewise, mean values for 300,000 protein sequences arranged in 18,000 orthologous families average 508, 309, and 311 aa for Eukarya, Bacteria, and Archaea, respectively (4).

These characteristic differences in protein lengths are thought to reflect the degree to which reductive pressure is expressed in the three superkingdoms (4). The length or mass of proteins is a potentially important characteristic because, for growth rate-optimized cells, there is always an advantage for proteins to be as small as possible to increase their mass-normalized kinetic efficiencies (4–6). Shorter proteins that retain maximum rates of function are expected to support faster growth rates of cells than longer proteins that have the same kinetic characteristics. However, the intensity of this reductive pressure will decrease as its cellular mass fraction decreases (4). As the complexity of the cellular proteomes of eukaryotes is, in general, much greater than that of prokaryotes (7, 8), an average individual eukaryotic protein will be present at a much lower mass fraction than its orthologues in Archaea and Bacteria. For this reason alone, we expect the selective pressure constraining a representative protein sequence length to be weaker in eukaryotes, which may account for the observation that the standard deviations (SDs) for orthologous protein lengths are twice the magnitude in eukaryotes compared with those for Archaea and Bacteria (4).

stcordova
 
Posts: 444
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Re: Reductive Evolution

Postby stcordova » Mon Mar 19, 2018 12:34 am

Lenski's Black Queen

http://mbio.asm.org/content/3/2/e00036-12.full


Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and “Candidatus Pelagibacter,” and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We present the Black Queen Hypothesis (BQH), a novel theory of reductive evolution that explains how selection leads to such dependencies; its name refers to the queen of spades in the game Hearts, where the usual strategy is to avoid taking this card. Gene loss can provide a selective advantage by conserving an organism’s limiting resources, provided the gene’s function is dispensable. Many vital genetic functions are leaky, thereby unavoidably producing public goods that are available to the entire community. Such leaky functions are thus dispensable for individuals, provided they are not lost entirely from the community. The BQH predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost. Evolution in accordance with the BQH thus generates “beneficiaries” of reduced genomic content that are dependent on leaky “helpers,” and it may explain the observed nonuniversality of prototrophy, stress resistance, and other cellular functions in the microbial world.



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Opinion/Hypothesis

There is a tendency in evolutionary discourse to describe life’s history as a progression towards increasing complexity. However, there is no reason to expect that complexity will be selectively advantageous at all times and for all species. Indeed, Gould (1) argued that the appearance of progress in the fossil record is a mere artifact: because there is a minimum complexity necessary to sustain life but no apparent upper limit to complexity, even undirected change may produce more complex species by a “drunkard’s walk” mechanism while preserving relatively simple bacteria as the dominant mode of life. In fact, nature offers numerous examples of “reductive evolution,” where simple organisms derive from more complex ancestors. This phenomenon is typified by macro- and microscopic parasites and symbionts, particularly those that reside inside their hosts (e.g., see reference 2). Such organisms tend to lose the capacity to synthesize metabolites provided by their hosts. For example, tapeworms lack digestive tracts, absorbing all their required nutrients transdermally from their host’s gut (3). Similarly, many host-associated bacteria (e.g., Lactobacillus spp.) are no longer able to synthesize certain essential metabolites, such as amino acids (4, 5).

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