The origins of polypeptide domains

Abstract

SummaryThree decades ago Gilbert posited that novel proteins arise by re-shuffling genomic sequences encoding polypeptide domains. Today, with numerous genomes and countless genes sequenced, it is well established that recombination of sequences encoding polypeptide domains plays a major role in protein evolution. There is, however, less evidence to suggest how the novel polypeptide domains, themselves, arise. Recent comparisons of genomes from closely related species have revealed numerous species-specific exons, supporting models of domain origin based on "exonization" of intron sequences. Also, a mechanism for the origin of novel polypeptide domains has been proposed based on analyses of insertion-based polymorphisms between orthologous genes across broad phylogenetic spectra and between allelic variants of genes within species. This review discusses these processes and how each might participate in the evolutionary emergence of novel polypeptide domains.

Cyclic Peptides Arising by Evolutionary Parallelism via Asparaginyl-Endopeptidase–Mediated Biosynthesis

“…Novel proteins arise typically by two processes: divergence of gene duplicates and recombination events that alter DNA sequences for existing proteins (Schmidt and Davies, 2007). One recombination-mediated evolutionary event is the internal expansion of genes to create a string of repeated protein domains.…”

“…One recombination-mediated evolutionary event is the internal expansion of genes to create a string of repeated protein domains. Although 10 to 20% of eukaryotic proteins contain domain repeats, their genesis is not well understood (Marcotte et al, 1999;Björklund et al, 2006;Schmidt and Davies, 2007). Nevertheless, several features seem to be shared by repetitive protein domains.…”

Novel and Expanded Roles for MAPK Signaling inArabidopsisStomatal Cell Fate Revealed by Cell Type–Specific Manipulations

“…In plants, MAPK networks regulate a similar array of processes, but genomic sequence data have revealed that, in comparison to other eukaryotes, plant genomes encode enlarged gene families of MAPK kinase kinases (MAPKKKs), MAPK kinases (MAPKKs), and MAPKs (Ichimura et al, 2002;Hamel et al, 2006). Furthermore, large-scale gene expression studies indicate that many of these genes are broadly expressed throughout the plant (Schmid et al, 2005;Schmidt, 2007). These extended gene families may have evolved to allow plants, which are sessile, to sense and respond to a continuous flux of environmental conditions.…”

The Evolutionary History of CBF Transcription Factors: Gene Duplication of CCAAT – Binding Factors NF-Y in Plants

“…This leads to the creation of new genes and new gene functions (Hurley et al, 2005;Woollard, 2005;Schmidt and Davies, 2007), two important factors in the origin of genomic and organismal complexity (Gu et al, 2002;Taylor and Raes, 2004;Sterck et al, 2007). The plasticity of a genome or species in adapting to environmental changes would be severely limited without gene duplication, because no more than two variants (alleles) exist at any locus within a diploid individual.…”