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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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The sequence diversity of TamB. TamB sequences mostly cluster according to their taxonomic group as indicated by colors; (A) represents full-length TamB sequences, the displayed sequences of TamB and related proteins were reduced to identity 0.9, the edges represent all-against-all BLAST e values with a cutoff of 1e-5, and the network visualization shows a force-directed network without weight. (B) represents only the 50 most amino-terminal sequences of the same sequences as in (A); the edges represent an e value cutoff of 1e-1 and the visualization is force-directed without weight. Several exceptions indicated in (B) are discussed in the text.
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evv097-F5: The sequence diversity of TamB. TamB sequences mostly cluster according to their taxonomic group as indicated by colors; (A) represents full-length TamB sequences, the displayed sequences of TamB and related proteins were reduced to identity 0.9, the edges represent all-against-all BLAST e values with a cutoff of 1e-5, and the network visualization shows a force-directed network without weight. (B) represents only the 50 most amino-terminal sequences of the same sequences as in (A); the edges represent an e value cutoff of 1e-1 and the visualization is force-directed without weight. Several exceptions indicated in (B) are discussed in the text.

Mentions: A surprising result was the finding of such a broad distribution of TamB sequences, given the restriction of TamA proteins predominantly to the Proteobacteria (Heinz and Lithgow 2014). To interrogate the extent of codistribution of TamB and TamA, we generated a heatmap of all complete proteomes with a color gradient indicating the percentage of encoded respective combinations of proteins, irrespective of whether they are coencoded in an operon (fig. 4). This shows that TamB can be found in all bacterial Phyla with an outer membrane, with a few exceptions like the early-branching Phyla Thermotogae and Thermodesulfobacteria. It should be noted that the representation of TamB within any given Phylum is not complete, emphasizing that TamB does not have an essential function (fig. 4 and 5A).Fig. 4.—


Evolution of the Translocation and Assembly Module (TAM).

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

The sequence diversity of TamB. TamB sequences mostly cluster according to their taxonomic group as indicated by colors; (A) represents full-length TamB sequences, the displayed sequences of TamB and related proteins were reduced to identity 0.9, the edges represent all-against-all BLAST e values with a cutoff of 1e-5, and the network visualization shows a force-directed network without weight. (B) represents only the 50 most amino-terminal sequences of the same sequences as in (A); the edges represent an e value cutoff of 1e-1 and the visualization is force-directed without weight. Several exceptions indicated in (B) are discussed in the text.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4494059&req=5

evv097-F5: The sequence diversity of TamB. TamB sequences mostly cluster according to their taxonomic group as indicated by colors; (A) represents full-length TamB sequences, the displayed sequences of TamB and related proteins were reduced to identity 0.9, the edges represent all-against-all BLAST e values with a cutoff of 1e-5, and the network visualization shows a force-directed network without weight. (B) represents only the 50 most amino-terminal sequences of the same sequences as in (A); the edges represent an e value cutoff of 1e-1 and the visualization is force-directed without weight. Several exceptions indicated in (B) are discussed in the text.
Mentions: A surprising result was the finding of such a broad distribution of TamB sequences, given the restriction of TamA proteins predominantly to the Proteobacteria (Heinz and Lithgow 2014). To interrogate the extent of codistribution of TamB and TamA, we generated a heatmap of all complete proteomes with a color gradient indicating the percentage of encoded respective combinations of proteins, irrespective of whether they are coencoded in an operon (fig. 4). This shows that TamB can be found in all bacterial Phyla with an outer membrane, with a few exceptions like the early-branching Phyla Thermotogae and Thermodesulfobacteria. It should be noted that the representation of TamB within any given Phylum is not complete, emphasizing that TamB does not have an essential function (fig. 4 and 5A).Fig. 4.—

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