Abstract
Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification.
Highlights
Protein function is not set in stone—it can undergo both gradual and drastic changes due to a variety of evolutionary events, including mutations, insertions, deletions, and duplications
Computational prediction of signal peptides is an indispensable step in bacterial genome annotation, but their evolutionary dynamics has not been comprehensively studied
We investigated the gain and loss patterns of signal peptides between orthologous proteins from Enterobacterales and found that 1.9% of clusters of orthologous groups (COGs) contain proteins both with and without signal peptides
Summary
Protein function is not set in stone—it can undergo both gradual and drastic changes due to a variety of evolutionary events, including mutations, insertions, deletions, and duplications. The evolutionary dynamics of enzymatic and binding activities has been extensively studied, functional shifts associated with the evolution of cellular targeting signals have received much less attention, and most of the work done so far focused on the sequence diversity of eukaryotic signal peptides, mitochondrial targeting signals, and chloroplast transit peptides (Williams et al 2000; Doyle et al 2013; Fukasawa et al 2014).
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