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Evolution of the Translocation and Assembly Module (TAM).

Heinz E, Selkrig J, Belousoff MJ, Lithgow T - Genome Biol Evol (2015)

Bottom Line: We report that TamA and a closely related protein TamL are confined almost exclusively to Proteobacteria and Bacteroidetes/Chlorobi respectively, whereas TamB is widely distributed across the majority of Gram-negative bacterial lineages.Several sequence characteristics were discovered to define the TamB protein family: A signal-anchor linkage to the inner membrane, beta-helical structure, conserved domain architecture and a C-terminal region that mimics outer membrane protein beta-strands.Taken together, the structural and phylogenetic analyses suggest that the TAM likely evolved from an original combination of BamA and TamB, with a later gene duplication event of BamA, giving rise to an additional Omp85 sequence that evolved to be TamA in Proteobacteria and TamL in Bacteroidetes/Chlorobi.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Monash University, Melbourne, Victoria, Australia.

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Conserved secondary structure features of TamB. Selected TamB sequences from the organisms indicated are shown as diagrams, and secondary structure prediction results are indicated, the right panel shows the percentages of helices, sheets or coils as predicted by psipred for the respective TamB sequence. The taxonomic guidance tree is adapted from (Errington 2013). The location of the Acidobacteria was modified to more closely resemble the phylogenetic pattern observed in the canonical BamA sequences; the Aquificae were placed at the root of the Proteobacteria although their true position is uncertain due to extensive HGT in this group of organisms (Eveleigh et al. 2013).
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evv097-F3: Conserved secondary structure features of TamB. Selected TamB sequences from the organisms indicated are shown as diagrams, and secondary structure prediction results are indicated, the right panel shows the percentages of helices, sheets or coils as predicted by psipred for the respective TamB sequence. The taxonomic guidance tree is adapted from (Errington 2013). The location of the Acidobacteria was modified to more closely resemble the phylogenetic pattern observed in the canonical BamA sequences; the Aquificae were placed at the root of the Proteobacteria although their true position is uncertain due to extensive HGT in this group of organisms (Eveleigh et al. 2013).

Mentions: The protein sequences defined as TamB show a relatively consistent length profile, with only few exceptions of very long length (supplementary fig. S3, Supplementary Material online). A characteristic feature of these sequences is a C-terminally located DUF490 domain (fig. 3 and supplementary fig. S4, Supplementary Material online). Those sequences classified as TamB, but with no Pfam-defined domains recognized with the given cutoff (fig. 3), have predicted secondary structure features that suggest a conserved structure (fig. 3). In E. coli, the DUF490 domain corresponds to a 37-kDa region within TamB (residues 914–1,259), and the number of residues in the DUF490 domains in other TamB sequences is relatively conserved. In contrast, AsmA proteins show more diversity regarding sequence length (supplementary fig. S3, Supplementary Material online), and the AsmA domain covers either the entire protein or only the N-terminal region (supplementary fig. S4, Supplementary Material online).Fig. 3.—


Evolution of the Translocation and Assembly Module (TAM).

Heinz E, Selkrig J, Belousoff MJ, Lithgow T - Genome Biol Evol (2015)

Conserved secondary structure features of TamB. Selected TamB sequences from the organisms indicated are shown as diagrams, and secondary structure prediction results are indicated, the right panel shows the percentages of helices, sheets or coils as predicted by psipred for the respective TamB sequence. The taxonomic guidance tree is adapted from (Errington 2013). The location of the Acidobacteria was modified to more closely resemble the phylogenetic pattern observed in the canonical BamA sequences; the Aquificae were placed at the root of the Proteobacteria although their true position is uncertain due to extensive HGT in this group of organisms (Eveleigh et al. 2013).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494059&req=5

evv097-F3: Conserved secondary structure features of TamB. Selected TamB sequences from the organisms indicated are shown as diagrams, and secondary structure prediction results are indicated, the right panel shows the percentages of helices, sheets or coils as predicted by psipred for the respective TamB sequence. The taxonomic guidance tree is adapted from (Errington 2013). The location of the Acidobacteria was modified to more closely resemble the phylogenetic pattern observed in the canonical BamA sequences; the Aquificae were placed at the root of the Proteobacteria although their true position is uncertain due to extensive HGT in this group of organisms (Eveleigh et al. 2013).
Mentions: The protein sequences defined as TamB show a relatively consistent length profile, with only few exceptions of very long length (supplementary fig. S3, Supplementary Material online). A characteristic feature of these sequences is a C-terminally located DUF490 domain (fig. 3 and supplementary fig. S4, Supplementary Material online). Those sequences classified as TamB, but with no Pfam-defined domains recognized with the given cutoff (fig. 3), have predicted secondary structure features that suggest a conserved structure (fig. 3). In E. coli, the DUF490 domain corresponds to a 37-kDa region within TamB (residues 914–1,259), and the number of residues in the DUF490 domains in other TamB sequences is relatively conserved. In contrast, AsmA proteins show more diversity regarding sequence length (supplementary fig. S3, Supplementary Material online), and the AsmA domain covers either the entire protein or only the N-terminal region (supplementary fig. S4, Supplementary Material online).Fig. 3.—

Bottom Line: We report that TamA and a closely related protein TamL are confined almost exclusively to Proteobacteria and Bacteroidetes/Chlorobi respectively, whereas TamB is widely distributed across the majority of Gram-negative bacterial lineages.Several sequence characteristics were discovered to define the TamB protein family: A signal-anchor linkage to the inner membrane, beta-helical structure, conserved domain architecture and a C-terminal region that mimics outer membrane protein beta-strands.Taken together, the structural and phylogenetic analyses suggest that the TAM likely evolved from an original combination of BamA and TamB, with a later gene duplication event of BamA, giving rise to an additional Omp85 sequence that evolved to be TamA in Proteobacteria and TamL in Bacteroidetes/Chlorobi.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Monash University, Melbourne, Victoria, Australia.

Show MeSH