Hologs that appeared to encode proteins with similar functions, namely secretedHologs that appeared to encode

Hologs that appeared to encode proteins with similar functions, namely secreted
Hologs that appeared to encode proteins with similar functions, namely secreted and membrane proteins that were identified by signal peptide and transmembrane helix prediction. The difference in the Kn/Ks ratios for paralogous versus orthologous genes was approximately the same for the predicted secreted and membrane proteins as it was for the complete analyzed gene sets (Table 4), indicating that the acceleration of evolution probably is an inherent feature of duplicated genes.DiscussionThe present analysis confirms the earlier observations that paralogs evolve under purifying selection [21], which typically acts with similar strength on both duplicated copies of genes [9,22]. Additionally, however, we found that paralogs evolve significantly faster than unduplicated genes with a similar level of divergence, which is compatible with the notion that gene duplications are a source of new protein functions. The inconsistency of empirical evidence with Ohno’s model prompts questions on the validity of some of the assumptions underlying this model. One major assumption, which was inherited by the subfunctionalization model, is that one gene copy is sufficient to perform the respective function, so that a gene duplication is redundant and has no effect on fitness [1,10]. This notion has been widely accepted, and often becomes one of the central postulates of models of duplicated gene evolution [3,7,26,27]. Should this be the case, however, a duplication event would only very rarely achieve fixation [28,29]; moreover, in the event that a duplication is slightly deleterious, it would be effectively prevented from achieving fixation [30]. Although the notion of duplication producing redundant genes is central to current theories of duplicated gene evolution, the short-term benefits of gene duplications are well known. This is MK-5172 web illustrated by the numerous observations of adaptive gene amplifications in response to antibiotics [3133], anticancer drug treatments and exposure to various toxins [34-39] or heavy metals [40-44], nutrient limitations [32,33,45-50], pesticide treatments [51-53], extreme temperatures [54,55] and symbiotic and parasitic interactions [56,57]. Combining this information with the observations that recently duplicated genes evolve under purifying selection ([21] and our present work), it seems reasonable to hypothesize that a majority of duplicated genes that achieve fixation in a population increase fitness when present in two or more copies in a genome and thus are subject to purifying selection from the moment of duplication.Recently duplicated paralogs appear to be a nonrandom group enriched in genes coding for proteins involved in different aspects of the organisms’ interaction with the environment (see Additional data files). In particular, a PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/25962748 substantial fraction of these paralogs encode (predicted) membrane or secreted proteins. The prevalent functions of duplicated genes varied among different organisms. In bacteria, the majority of these genes encoded different types of surface molecules, which, PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27797473 in pathogens, are involved in interaction with substrate cells. In yeast, there was an emphasis on membrane transporters as well as on genes involved in stress response (for example, heat shock). In multicellular eukaryotes, receptors (for example, olfactory receptors) and (predicted) secreted signaling molecules were predominant. Proteins with a predicted signal peptide were more prevalent in Arabidopsis thaliana (35 of all.