Abstract
Lineage-specific expansion (LSE) of protein families is a widespread phenomenon in many eukaryotic genomes, but is generally more limited in bacterial genomes. Here, we report the presence of 434 genes encoding solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family, within the 8.2 Mb genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860, a gene family over-representation of unprecedented abundance in prokaryotes. Representing over 6 % of the total number of coding sequences, the SBP genes are distributed across the whole genome but are found rarely in low-GC islands, where the gene density for this family is much lower. This observation, and the much higher sequence identity between the 434 Rhodoplanes TTT SBPs compared with the average identity between homologues from different species, is indicative of a key role for LSE in the expansion. The TTT SBP genes were found in the vicinity of genes encoding membrane components of transport systems from different families, as well as regulatory proteins such as histidine-kinases and transcription factors, indicating a broad range of functions around the sensing, response and transport of organic compounds. A smaller expansion of TTT SBPs is known in some species of the β-proteobacteria Bordetella and we observed similar expansions in other β-proteobacterial lineages, including members of the genus Comamonas and the industrial biotechnology organism Cupriavidus necator, indicating that strong environmental selection can drive SBP duplication and specialisation from multiple evolutionary starting points.
Highlights
Gene family expansions result from events of gene duplication and horizontal gene transfer (HGT), and are major drivers for metabolic versatility and adaptation in prokaryotes and eukaryotes [1,2,3]
HGT seems to have played an important role in the expansion of this gene family, the largest over-representations are a consequence of gene duplication leading to lineage-specific expansions (LSE), which results in the occurrence of ‘orphan’ HPKs, that subsequently diverge through rearrangements in their Nterminal signalling domain to sense different environmental conditions [9]
The over-representation of a gene family of unprecedented magnitude in a prokaryotic genome is described, with 434 genes belonging to the tripartite tricarboxylate transporter solute-binding proteins family in the a-proteobacterium Rhodoplanes sp
Summary
Gene family expansions result from events of gene duplication and horizontal gene transfer (HGT), and are major drivers for metabolic versatility and adaptation in prokaryotes and eukaryotes [1,2,3]. A final example of a large gene over-representation in bacterial genomes, relates to solute-binding proteins (SBPs) of the tripartite tricarboxylate transporters (TTT) family [13].
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