Limits...
Evolution of the Translocation and Assembly Module (TAM).

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

Bottom Line: Bacterial outer membrane proteins require the beta-barrel assembly machinery (BAM) for their correct folding and function.An additional feature of the BAM is the translocation and assembly module (TAM), comprised TamA (an Omp85 family protein) and TamB.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.

View Article: PubMed Central - PubMed

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

Show MeSH

Related in: MedlinePlus

The evolution of the TAM operon. The left panel shows transcriptional units of tamB homologs as given in the BioCyc database collection (Caspi et al. 2014), the right panel highlights the presence or absence of an Omp85 protein in a putative operon with the respective TamB sequence. The orange dashed arrow indicates the likely HGT from the Alphaproteobacteria to a subgroup of Chlamydiae, as also seen in figure 6 and supplementary figure S9, Supplementary Material online; the orange/magenta dashed arrow indicates an HGT event of TamA from the ancestor of the Beta- and Gammaproteobacteria to the ancestor of the Bacteroidetes/Chlorobi, which acquired the lipid anchor and became TamL. Stars at the guidance tree reflect these two HGT events. For several genes, a gene encoding an Omp85 protein is present in the vicinity, but not in the same transcriptional unit. In the absence of experimental verification, these were interpreted as putative operons and are indicated by a dashed line separating the operons (left panel) and by round brackets surrounding the Omp85 protein icon (right panel). Protein icons enclosed by square brackets indicate the Omp85 protein most likely to interact with the respective TamB, but encoded elsewhere on the genome. The taxonomic guidance tree was derived as described for figure 3.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4494059&req=5

evv097-F8: The evolution of the TAM operon. The left panel shows transcriptional units of tamB homologs as given in the BioCyc database collection (Caspi et al. 2014), the right panel highlights the presence or absence of an Omp85 protein in a putative operon with the respective TamB sequence. The orange dashed arrow indicates the likely HGT from the Alphaproteobacteria to a subgroup of Chlamydiae, as also seen in figure 6 and supplementary figure S9, Supplementary Material online; the orange/magenta dashed arrow indicates an HGT event of TamA from the ancestor of the Beta- and Gammaproteobacteria to the ancestor of the Bacteroidetes/Chlorobi, which acquired the lipid anchor and became TamL. Stars at the guidance tree reflect these two HGT events. For several genes, a gene encoding an Omp85 protein is present in the vicinity, but not in the same transcriptional unit. In the absence of experimental verification, these were interpreted as putative operons and are indicated by a dashed line separating the operons (left panel) and by round brackets surrounding the Omp85 protein icon (right panel). Protein icons enclosed by square brackets indicate the Omp85 protein most likely to interact with the respective TamB, but encoded elsewhere on the genome. The taxonomic guidance tree was derived as described for figure 3.

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)

The evolution of the TAM operon. The left panel shows transcriptional units of tamB homologs as given in the BioCyc database collection (Caspi et al. 2014), the right panel highlights the presence or absence of an Omp85 protein in a putative operon with the respective TamB sequence. The orange dashed arrow indicates the likely HGT from the Alphaproteobacteria to a subgroup of Chlamydiae, as also seen in figure 6 and supplementary figure S9, Supplementary Material online; the orange/magenta dashed arrow indicates an HGT event of TamA from the ancestor of the Beta- and Gammaproteobacteria to the ancestor of the Bacteroidetes/Chlorobi, which acquired the lipid anchor and became TamL. Stars at the guidance tree reflect these two HGT events. For several genes, a gene encoding an Omp85 protein is present in the vicinity, but not in the same transcriptional unit. In the absence of experimental verification, these were interpreted as putative operons and are indicated by a dashed line separating the operons (left panel) and by round brackets surrounding the Omp85 protein icon (right panel). Protein icons enclosed by square brackets indicate the Omp85 protein most likely to interact with the respective TamB, but encoded elsewhere on the genome. The taxonomic guidance tree was derived as described for figure 3.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv097-F8: The evolution of the TAM operon. The left panel shows transcriptional units of tamB homologs as given in the BioCyc database collection (Caspi et al. 2014), the right panel highlights the presence or absence of an Omp85 protein in a putative operon with the respective TamB sequence. The orange dashed arrow indicates the likely HGT from the Alphaproteobacteria to a subgroup of Chlamydiae, as also seen in figure 6 and supplementary figure S9, Supplementary Material online; the orange/magenta dashed arrow indicates an HGT event of TamA from the ancestor of the Beta- and Gammaproteobacteria to the ancestor of the Bacteroidetes/Chlorobi, which acquired the lipid anchor and became TamL. Stars at the guidance tree reflect these two HGT events. For several genes, a gene encoding an Omp85 protein is present in the vicinity, but not in the same transcriptional unit. In the absence of experimental verification, these were interpreted as putative operons and are indicated by a dashed line separating the operons (left panel) and by round brackets surrounding the Omp85 protein icon (right panel). Protein icons enclosed by square brackets indicate the Omp85 protein most likely to interact with the respective TamB, but encoded elsewhere on the genome. The taxonomic guidance tree was derived as described for figure 3.
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: Bacterial outer membrane proteins require the beta-barrel assembly machinery (BAM) for their correct folding and function.An additional feature of the BAM is the translocation and assembly module (TAM), comprised TamA (an Omp85 family protein) and TamB.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.

View Article: PubMed Central - PubMed

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

Show MeSH
Related in: MedlinePlus