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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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Phylogenetic analysis of Omp85 proteins. The BamA, TamA, and TamL sequences of organisms as given in supplementary table S6, Supplementary Material online, were used in a phylogenetic tree calculation. The branches indicate taxonomic lineage with the same color scheme as shown in the legend for figure 2C, the icons represent the number of POTRA domains and the nature of the protein (red, BamA; orange, TamA; pink, TamL). The ring indicates if the proteins are encoded in an operon with TamB; where gray indicates no operon, and blue indicates an operon with TamB. The tree was calculated using RAxML as described in the Materials and Methods. An unrooted display of this tree including bootstrap support values is given in supplementary figure S9A, Supplementary Material online.
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evv097-F7: Phylogenetic analysis of Omp85 proteins. The BamA, TamA, and TamL sequences of organisms as given in supplementary table S6, Supplementary Material online, were used in a phylogenetic tree calculation. The branches indicate taxonomic lineage with the same color scheme as shown in the legend for figure 2C, the icons represent the number of POTRA domains and the nature of the protein (red, BamA; orange, TamA; pink, TamL). The ring indicates if the proteins are encoded in an operon with TamB; where gray indicates no operon, and blue indicates an operon with TamB. The tree was calculated using RAxML as described in the Materials and Methods. An unrooted display of this tree including bootstrap support values is given in supplementary figure S9A, Supplementary Material online.

Mentions: Phylogenetic analysis of TamB revealed no clear correlation of the TamB proteins with respect to their presence in an operon with an Omp85 protein besides the monophyletic origin of the sequences associated with TamA or TamL (fig. 6 and supplementary fig. S8, Supplementary Material online). The chlamydial TamA–TamB operon seems to be derived through horizontal gene transfer (HGT) from the Alphaproteobacteria; this is also supported in the analysis of the Omp85 proteins (fig. 7 and supplementary fig. S9, Supplementary Material online). Although the Proteobacteria TamB forms a large monophyletic cluster (with the Chlamydiae; fig. 6 and supplementary fig. S8, Supplementary Material online), several Deltaproteobacteria and Epsilonproteobacteria cluster with the early-branching Phyla (such as Fusobacteria and Bacteroidetes); this likely HGT event is also reflected in the Omp85 sequences (Heinz and Lithgow 2014; fig. 7 and supplementary fig. S9, Supplementary Material online). The Acidobacteria and Aquificae both encode a second copy of BamA, which branches off monophyletic with TamA, indicating this to be the putative origin of the TAM (figs. 7 and 8 and supplementary fig. S9, Supplementary Material online). A consistent clustering of the early-branching Phyla including Spirochaetes, Deinococcus-Thermus, Firmicutes, and Cyanobacteria was also observed for TamB.Fig. 6.—


Evolution of the Translocation and Assembly Module (TAM).

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

Phylogenetic analysis of Omp85 proteins. The BamA, TamA, and TamL sequences of organisms as given in supplementary table S6, Supplementary Material online, were used in a phylogenetic tree calculation. The branches indicate taxonomic lineage with the same color scheme as shown in the legend for figure 2C, the icons represent the number of POTRA domains and the nature of the protein (red, BamA; orange, TamA; pink, TamL). The ring indicates if the proteins are encoded in an operon with TamB; where gray indicates no operon, and blue indicates an operon with TamB. The tree was calculated using RAxML as described in the Materials and Methods. An unrooted display of this tree including bootstrap support values is given in supplementary figure S9A, Supplementary Material online.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv097-F7: Phylogenetic analysis of Omp85 proteins. The BamA, TamA, and TamL sequences of organisms as given in supplementary table S6, Supplementary Material online, were used in a phylogenetic tree calculation. The branches indicate taxonomic lineage with the same color scheme as shown in the legend for figure 2C, the icons represent the number of POTRA domains and the nature of the protein (red, BamA; orange, TamA; pink, TamL). The ring indicates if the proteins are encoded in an operon with TamB; where gray indicates no operon, and blue indicates an operon with TamB. The tree was calculated using RAxML as described in the Materials and Methods. An unrooted display of this tree including bootstrap support values is given in supplementary figure S9A, Supplementary Material online.
Mentions: Phylogenetic analysis of TamB revealed no clear correlation of the TamB proteins with respect to their presence in an operon with an Omp85 protein besides the monophyletic origin of the sequences associated with TamA or TamL (fig. 6 and supplementary fig. S8, Supplementary Material online). The chlamydial TamA–TamB operon seems to be derived through horizontal gene transfer (HGT) from the Alphaproteobacteria; this is also supported in the analysis of the Omp85 proteins (fig. 7 and supplementary fig. S9, Supplementary Material online). Although the Proteobacteria TamB forms a large monophyletic cluster (with the Chlamydiae; fig. 6 and supplementary fig. S8, Supplementary Material online), several Deltaproteobacteria and Epsilonproteobacteria cluster with the early-branching Phyla (such as Fusobacteria and Bacteroidetes); this likely HGT event is also reflected in the Omp85 sequences (Heinz and Lithgow 2014; fig. 7 and supplementary fig. S9, Supplementary Material online). The Acidobacteria and Aquificae both encode a second copy of BamA, which branches off monophyletic with TamA, indicating this to be the putative origin of the TAM (figs. 7 and 8 and supplementary fig. S9, Supplementary Material online). A consistent clustering of the early-branching Phyla including Spirochaetes, Deinococcus-Thermus, Firmicutes, and Cyanobacteria was also observed for TamB.Fig. 6.—

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