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Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea.

Makarova KS, Koonin EV - Biol. Direct (2010)

Bottom Line: Several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling.Here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the FtsZ-tubulin superfamily.One of these families is limited in its spread to Proteobacteria whereas the other is represented in diverse bacteria and archaea, and might be the key component of a novel, multicomponent membrane remodeling system that also includes a Von Willebrand A domain-containing protein, a distinct GTPase and membrane transport proteins of the OmpA family.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, NLM, National Institutes of Health Bethesda, Maryland 20894, USA.

ABSTRACT
Several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. Here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the FtsZ-tubulin superfamily. One of these families is limited in its spread to Proteobacteria whereas the other is represented in diverse bacteria and archaea, and might be the key component of a novel, multicomponent membrane remodeling system that also includes a Von Willebrand A domain-containing protein, a distinct GTPase and membrane transport proteins of the OmpA family.

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Phylogentic analysis of the FtsZ-tubulin superfamily and representative operonic architectures of FtsZl1 family genes. Color code: eukaryotes - blue; bacteria - green; archaea - orange. The RELL bootstrap values (%) are indicated for selected major branches. A. Phylogeny of the FtsZ-tubulin superfamily. The tree was reconstructed from 118 phylogenetically informative positions. B. Phylogeny of FtsZl1 family. The tree was reconstructed from 103 phylogenetically informative positions. C. Genomic context of the FtsZl1 family genes. Homologous genes are shown by arrows of the same color; genes are shown not to scale. Color code for the gene context: green arrows, VWA-domain-containing proteins; red, FtsZ-like 1 family proteins; brown, OmpA-like proteins; pale blue, serine/threonine protein kinases; yellow, GTPase; empty arrows (A1-A2; B1-B9) represent families that are associated with the FtsZ-like 1 genes in many genomes (see Additional File 6); gray arrows, genes associated with the FtsZ-like 1 family genes in one or a few related genomes.
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Figure 2: Phylogentic analysis of the FtsZ-tubulin superfamily and representative operonic architectures of FtsZl1 family genes. Color code: eukaryotes - blue; bacteria - green; archaea - orange. The RELL bootstrap values (%) are indicated for selected major branches. A. Phylogeny of the FtsZ-tubulin superfamily. The tree was reconstructed from 118 phylogenetically informative positions. B. Phylogeny of FtsZl1 family. The tree was reconstructed from 103 phylogenetically informative positions. C. Genomic context of the FtsZl1 family genes. Homologous genes are shown by arrows of the same color; genes are shown not to scale. Color code for the gene context: green arrows, VWA-domain-containing proteins; red, FtsZ-like 1 family proteins; brown, OmpA-like proteins; pale blue, serine/threonine protein kinases; yellow, GTPase; empty arrows (A1-A2; B1-B9) represent families that are associated with the FtsZ-like 1 genes in many genomes (see Additional File 6); gray arrows, genes associated with the FtsZ-like 1 family genes in one or a few related genomes.

Mentions: To characterize the relationships between the new Ftzl1 and FtsZl2 families and the rest of the FtsZ-tubulin proteins, we employed the alignable blocks of the FtsZ-tubulin nucleotide-binding domain to construct a tree for a representative set of sequences from all families, with a special emphasis on FtsZl1 and FtsZl2 (103 sequences in total, including 41 from the FtsZl1 family and 10 from the FtsZl2 family) (Figure 2A). Generally, the tree topology reproduces all previously established major branches and relationships between them [8,9]. These include the monophyletic bacterial FtsZ and eukaryotic α,β,γ tubulin branches, 3 major archaeal clades, and distinct branches for the RepX and TubZ families, suggesting that the alignment of the nucleotide-binding domains contains sufficient information for phylogenetic inference.


Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea.

Makarova KS, Koonin EV - Biol. Direct (2010)

Phylogentic analysis of the FtsZ-tubulin superfamily and representative operonic architectures of FtsZl1 family genes. Color code: eukaryotes - blue; bacteria - green; archaea - orange. The RELL bootstrap values (%) are indicated for selected major branches. A. Phylogeny of the FtsZ-tubulin superfamily. The tree was reconstructed from 118 phylogenetically informative positions. B. Phylogeny of FtsZl1 family. The tree was reconstructed from 103 phylogenetically informative positions. C. Genomic context of the FtsZl1 family genes. Homologous genes are shown by arrows of the same color; genes are shown not to scale. Color code for the gene context: green arrows, VWA-domain-containing proteins; red, FtsZ-like 1 family proteins; brown, OmpA-like proteins; pale blue, serine/threonine protein kinases; yellow, GTPase; empty arrows (A1-A2; B1-B9) represent families that are associated with the FtsZ-like 1 genes in many genomes (see Additional File 6); gray arrows, genes associated with the FtsZ-like 1 family genes in one or a few related genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2875224&req=5

Figure 2: Phylogentic analysis of the FtsZ-tubulin superfamily and representative operonic architectures of FtsZl1 family genes. Color code: eukaryotes - blue; bacteria - green; archaea - orange. The RELL bootstrap values (%) are indicated for selected major branches. A. Phylogeny of the FtsZ-tubulin superfamily. The tree was reconstructed from 118 phylogenetically informative positions. B. Phylogeny of FtsZl1 family. The tree was reconstructed from 103 phylogenetically informative positions. C. Genomic context of the FtsZl1 family genes. Homologous genes are shown by arrows of the same color; genes are shown not to scale. Color code for the gene context: green arrows, VWA-domain-containing proteins; red, FtsZ-like 1 family proteins; brown, OmpA-like proteins; pale blue, serine/threonine protein kinases; yellow, GTPase; empty arrows (A1-A2; B1-B9) represent families that are associated with the FtsZ-like 1 genes in many genomes (see Additional File 6); gray arrows, genes associated with the FtsZ-like 1 family genes in one or a few related genomes.
Mentions: To characterize the relationships between the new Ftzl1 and FtsZl2 families and the rest of the FtsZ-tubulin proteins, we employed the alignable blocks of the FtsZ-tubulin nucleotide-binding domain to construct a tree for a representative set of sequences from all families, with a special emphasis on FtsZl1 and FtsZl2 (103 sequences in total, including 41 from the FtsZl1 family and 10 from the FtsZl2 family) (Figure 2A). Generally, the tree topology reproduces all previously established major branches and relationships between them [8,9]. These include the monophyletic bacterial FtsZ and eukaryotic α,β,γ tubulin branches, 3 major archaeal clades, and distinct branches for the RepX and TubZ families, suggesting that the alignment of the nucleotide-binding domains contains sufficient information for phylogenetic inference.

Bottom Line: Several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling.Here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the FtsZ-tubulin superfamily.One of these families is limited in its spread to Proteobacteria whereas the other is represented in diverse bacteria and archaea, and might be the key component of a novel, multicomponent membrane remodeling system that also includes a Von Willebrand A domain-containing protein, a distinct GTPase and membrane transport proteins of the OmpA family.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, NLM, National Institutes of Health Bethesda, Maryland 20894, USA.

ABSTRACT
Several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. Here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the FtsZ-tubulin superfamily. One of these families is limited in its spread to Proteobacteria whereas the other is represented in diverse bacteria and archaea, and might be the key component of a novel, multicomponent membrane remodeling system that also includes a Von Willebrand A domain-containing protein, a distinct GTPase and membrane transport proteins of the OmpA family.

Show MeSH
Related in: MedlinePlus