We have identified all homologues in the current databases of the ubiquitous protein constituents of the general secretory (Sec) pathway. These prokaryotic/eukaryotic proteins include (1) SecY/Sec61alpha, (2) SecE/Sec61gamma, (3) SecG/Sec61beta, (4) Ffh/SRP54 and (5) FtsY/SRP receptor subunit-alpha. Phylogenetic and sequence analyses lead to major conclusions concerning (1) the ubiquity of these proteins in living organisms, (2) the topological uniformity of some but not other Sec constituents, (3) the orthologous nature of almost all of them, (4) a total lack of paralogues in almost all organisms for which complete genome sequences are available, (5) the occurrence of two or even three paralogues in a few bacteria, plants, and yeast, depending on the Sec constituent, and (6) a tremendous degree of sequence divergence in bacteria compared with that in archaea or eukaryotes. The phylogenetic analyses lead to the conclusion that with a few possible exceptions, the five families of Sec constituents analyzed generally underwent sequence divergence in parallel but at different characteristic rates. The results provide evolutionary insights as well as guides for future functional studies. Because every organism with a fully sequenced genome exhibits at least one orthologue of each of these Sec proteins, we conclude that all living organisms have relied on the Sec system as their primary protein secretory/membrane insertion system. Because most prokaryotes and many eukaryotes encode within their genomes only one of each constituent, we also conclude that strong evolutionary pressure has minimized gene duplication events leading to the establishment of Sec paralogues. Finally, the sequence diversity of bacterial proteins as compared with their archaeal and eukaryotic counterparts is in agreement with the suggestion that bacteria were the evolutionary predecessors of archaea and eukaryotes.

OverviewType IV secretory pathway (IVSP) systems are multicomponent, transenvelope complexes in Gram-negative bacteria that translocate proteins and nucleoprotein complexes from donor cells to recipient cells in processes related to bacterial conjugation. At least ten protein constituents have been shown to mediate protein or nucleoprotein translocation, but the phylogenetic relationships of these proteins have not previously been defined. We have identified all recognizable homologues of the agrobacterial VirB2-11 proteins, retrieved their sequences from the databases, and characterized these homologues with respect to size, topology and organismal source. The homologous sequences were aligned in preparation for derivation of mean hydropathy, similarity and amphipathicity plots as well as phylogenetic trees. The results allowed us to make structural and functional predictions and show that although these systems have been repeatedly exchanged between Gramnegative bacteria, the constituents of these complex systems have not undergone appreciable shuffling during evolutionary divergence. This last observation further suggests that macromolecular transfer occurs by a concerted mechanism. Some homologues of IVSP constituents are likely to provide functions in some organisms that are unrelated to IVSP-mediated secretion. For example, homologues of VirB8, 9, 10 and 11 found in Helicobacter pylori, Campylobacter jejuni and Rickettsia prowazekii, as well as species of Wolbachia, may serve virulence-related functions not requiring a complete type IV secretion system. Both of the two IVSPassociated ATPases (VirB4 and VirB11 homologues) are found in prokaryotic organisms that lack the other constituents of the system, and VirB11 homologues are also found in archaea. It is proposed that IVSP systems evolved late as mosaic secretory systems that at least in part derived their constituents from other pre-existing sources, initially for conjugation with other prokaryotes and later to facilitate virulence relationships with eukaryotes.