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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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Multiple alignment of conserved blocks of all previously described and the two new protein families of the FtsZ-tubulin superfamily. The sequences are denoted by their GI numbers and species names. The positions of the first and the last residues of the aligned region in the corresponding protein are indicated for each sequence. Key elements of secondary structure based on known FtsZ tertiary structures are shown on two lines above the alignment [6,12,44]. The evolutionarily conserved functional motifs of the FtsZ and tubulin families are shown underneath the alignment for the corresponding groups [8,9]. The alignment columns are colored on the basis of the respective position conservation throughout the superfamily: yellow background indicates hydrophobic residues (ACFILMVWY), red letters indicate polar residues (DEHKNQR), blue letters indicate hydroxyl-containing residues (TS), and green background indicates small residues (ACGNPSTV). Species abbreviations: Methu - Methanospirillum hungatei JF-1; Magma - Magnetospirillum magneticum AMB-1; Deira - Deinococcus radiodurans R1; Plepa - Plesiocystis pacifica SIR-1; Bacca - Bacteroides caccae ATCC 43185; Bacbr - Brevibacillus brevis NBRC 100599; Clokl - Clostridium kluyveri DSM 555; Polna - Polaromonas naphthalenivorans; Glovi - Gloeobacter violaceus PCC 7421; Micch - Microcoleus chthonoplastes; Nosto - Nostoc sp. PCC 7120; Metin - Methylacidiphilum infernorum V4; Theel - Thermosynechococcus elongatus BP-1; Chlag - Chloroflexus aggregans DSM 9485; Metac - Methanosarcina acetivorans C2A; Pyrab - Pyrococcus abyssi GE5; Halut - Halorhabdus utahensis DSM 12940; Rhoba - Rhodopirellula baltica; Blama - Blastopirellula marina DSM 3645; Chrvi - Chromobacterium violaceum; Marin - Marinomonas sp.; Psefl - Pseudomonas fluorescens; BaccH - Bacillus cereus H3081-97; Bacce - Bacillus cereus 03BB102; Metja - Methanocaldococcus jannaschii; Korcr - Korarchaeum cryptofilum OPF8; Naneq - Nanoarchaeum equitans Kin4-M; Myctu - Mycobacterium tuberculosis H37Rv; Aquae - Aquifex aeolicus VF5; Thema - Thermotoga maritima MSB8; Escco - Escherichia coli K-12; Theth - Thermus thermophilus HB8; Sacce - Saccharomyces cerevisiae.
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Figure 1: Multiple alignment of conserved blocks of all previously described and the two new protein families of the FtsZ-tubulin superfamily. The sequences are denoted by their GI numbers and species names. The positions of the first and the last residues of the aligned region in the corresponding protein are indicated for each sequence. Key elements of secondary structure based on known FtsZ tertiary structures are shown on two lines above the alignment [6,12,44]. The evolutionarily conserved functional motifs of the FtsZ and tubulin families are shown underneath the alignment for the corresponding groups [8,9]. The alignment columns are colored on the basis of the respective position conservation throughout the superfamily: yellow background indicates hydrophobic residues (ACFILMVWY), red letters indicate polar residues (DEHKNQR), blue letters indicate hydroxyl-containing residues (TS), and green background indicates small residues (ACGNPSTV). Species abbreviations: Methu - Methanospirillum hungatei JF-1; Magma - Magnetospirillum magneticum AMB-1; Deira - Deinococcus radiodurans R1; Plepa - Plesiocystis pacifica SIR-1; Bacca - Bacteroides caccae ATCC 43185; Bacbr - Brevibacillus brevis NBRC 100599; Clokl - Clostridium kluyveri DSM 555; Polna - Polaromonas naphthalenivorans; Glovi - Gloeobacter violaceus PCC 7421; Micch - Microcoleus chthonoplastes; Nosto - Nostoc sp. PCC 7120; Metin - Methylacidiphilum infernorum V4; Theel - Thermosynechococcus elongatus BP-1; Chlag - Chloroflexus aggregans DSM 9485; Metac - Methanosarcina acetivorans C2A; Pyrab - Pyrococcus abyssi GE5; Halut - Halorhabdus utahensis DSM 12940; Rhoba - Rhodopirellula baltica; Blama - Blastopirellula marina DSM 3645; Chrvi - Chromobacterium violaceum; Marin - Marinomonas sp.; Psefl - Pseudomonas fluorescens; BaccH - Bacillus cereus H3081-97; Bacce - Bacillus cereus 03BB102; Metja - Methanocaldococcus jannaschii; Korcr - Korarchaeum cryptofilum OPF8; Naneq - Nanoarchaeum equitans Kin4-M; Myctu - Mycobacterium tuberculosis H37Rv; Aquae - Aquifex aeolicus VF5; Thema - Thermotoga maritima MSB8; Escco - Escherichia coli K-12; Theth - Thermus thermophilus HB8; Sacce - Saccharomyces cerevisiae.

Mentions: To compare the two new families of FtsZ-like proteins with the previously described families, we examined in detail the multiple alignment of a representative set of sequences from FtsZ-tubulin families (Figure 1). Both new families possess several family-specific inserts in the region between the highly conserved structural elements located in loops T1 and T4 (see also the complete alignment in Additional file 2). The FtsZl2 family contains all conserved motifs of the nucleotide-binding domain including functionally important loops T1, T4, T6 and T7, and the connector helix H7, whereas in the FtsZl1 family, counterparts to the T6-H7 structural elements could not be confidently identified. In this case, the most distal structural element that could be reliably aligned is the H5 helix (Figure 1). Furthermore, the secondary structure prediction for the FtsZl1 family was not fully compatible with the known structure of the S6-T7 region of the nucleotide-binding and connector domains (Additional File 2). Along the same lines, we did not detect any similarity between the C-terminal domain of the FtsZl1 family and C-terminal domains of previously characterized FtsZ-tubulin superfamily proteins. These structural elements have been shown to contribute to the formation of FtsZ filaments [6]. Accordingly, the FtsZl1 proteins might form filaments via a novel mechanism or, less likely, might not form filaments at all. In general, the FtsZl2 and especially FtsZl1 families seem to include the most structurally diverged proteins in the entire FtsZ-tubulin superfamily and therefore are of particular interest for further structural and functional analysis.


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)

Multiple alignment of conserved blocks of all previously described and the two new protein families of the FtsZ-tubulin superfamily. The sequences are denoted by their GI numbers and species names. The positions of the first and the last residues of the aligned region in the corresponding protein are indicated for each sequence. Key elements of secondary structure based on known FtsZ tertiary structures are shown on two lines above the alignment [6,12,44]. The evolutionarily conserved functional motifs of the FtsZ and tubulin families are shown underneath the alignment for the corresponding groups [8,9]. The alignment columns are colored on the basis of the respective position conservation throughout the superfamily: yellow background indicates hydrophobic residues (ACFILMVWY), red letters indicate polar residues (DEHKNQR), blue letters indicate hydroxyl-containing residues (TS), and green background indicates small residues (ACGNPSTV). Species abbreviations: Methu - Methanospirillum hungatei JF-1; Magma - Magnetospirillum magneticum AMB-1; Deira - Deinococcus radiodurans R1; Plepa - Plesiocystis pacifica SIR-1; Bacca - Bacteroides caccae ATCC 43185; Bacbr - Brevibacillus brevis NBRC 100599; Clokl - Clostridium kluyveri DSM 555; Polna - Polaromonas naphthalenivorans; Glovi - Gloeobacter violaceus PCC 7421; Micch - Microcoleus chthonoplastes; Nosto - Nostoc sp. PCC 7120; Metin - Methylacidiphilum infernorum V4; Theel - Thermosynechococcus elongatus BP-1; Chlag - Chloroflexus aggregans DSM 9485; Metac - Methanosarcina acetivorans C2A; Pyrab - Pyrococcus abyssi GE5; Halut - Halorhabdus utahensis DSM 12940; Rhoba - Rhodopirellula baltica; Blama - Blastopirellula marina DSM 3645; Chrvi - Chromobacterium violaceum; Marin - Marinomonas sp.; Psefl - Pseudomonas fluorescens; BaccH - Bacillus cereus H3081-97; Bacce - Bacillus cereus 03BB102; Metja - Methanocaldococcus jannaschii; Korcr - Korarchaeum cryptofilum OPF8; Naneq - Nanoarchaeum equitans Kin4-M; Myctu - Mycobacterium tuberculosis H37Rv; Aquae - Aquifex aeolicus VF5; Thema - Thermotoga maritima MSB8; Escco - Escherichia coli K-12; Theth - Thermus thermophilus HB8; Sacce - Saccharomyces cerevisiae.
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Figure 1: Multiple alignment of conserved blocks of all previously described and the two new protein families of the FtsZ-tubulin superfamily. The sequences are denoted by their GI numbers and species names. The positions of the first and the last residues of the aligned region in the corresponding protein are indicated for each sequence. Key elements of secondary structure based on known FtsZ tertiary structures are shown on two lines above the alignment [6,12,44]. The evolutionarily conserved functional motifs of the FtsZ and tubulin families are shown underneath the alignment for the corresponding groups [8,9]. The alignment columns are colored on the basis of the respective position conservation throughout the superfamily: yellow background indicates hydrophobic residues (ACFILMVWY), red letters indicate polar residues (DEHKNQR), blue letters indicate hydroxyl-containing residues (TS), and green background indicates small residues (ACGNPSTV). Species abbreviations: Methu - Methanospirillum hungatei JF-1; Magma - Magnetospirillum magneticum AMB-1; Deira - Deinococcus radiodurans R1; Plepa - Plesiocystis pacifica SIR-1; Bacca - Bacteroides caccae ATCC 43185; Bacbr - Brevibacillus brevis NBRC 100599; Clokl - Clostridium kluyveri DSM 555; Polna - Polaromonas naphthalenivorans; Glovi - Gloeobacter violaceus PCC 7421; Micch - Microcoleus chthonoplastes; Nosto - Nostoc sp. PCC 7120; Metin - Methylacidiphilum infernorum V4; Theel - Thermosynechococcus elongatus BP-1; Chlag - Chloroflexus aggregans DSM 9485; Metac - Methanosarcina acetivorans C2A; Pyrab - Pyrococcus abyssi GE5; Halut - Halorhabdus utahensis DSM 12940; Rhoba - Rhodopirellula baltica; Blama - Blastopirellula marina DSM 3645; Chrvi - Chromobacterium violaceum; Marin - Marinomonas sp.; Psefl - Pseudomonas fluorescens; BaccH - Bacillus cereus H3081-97; Bacce - Bacillus cereus 03BB102; Metja - Methanocaldococcus jannaschii; Korcr - Korarchaeum cryptofilum OPF8; Naneq - Nanoarchaeum equitans Kin4-M; Myctu - Mycobacterium tuberculosis H37Rv; Aquae - Aquifex aeolicus VF5; Thema - Thermotoga maritima MSB8; Escco - Escherichia coli K-12; Theth - Thermus thermophilus HB8; Sacce - Saccharomyces cerevisiae.
Mentions: To compare the two new families of FtsZ-like proteins with the previously described families, we examined in detail the multiple alignment of a representative set of sequences from FtsZ-tubulin families (Figure 1). Both new families possess several family-specific inserts in the region between the highly conserved structural elements located in loops T1 and T4 (see also the complete alignment in Additional file 2). The FtsZl2 family contains all conserved motifs of the nucleotide-binding domain including functionally important loops T1, T4, T6 and T7, and the connector helix H7, whereas in the FtsZl1 family, counterparts to the T6-H7 structural elements could not be confidently identified. In this case, the most distal structural element that could be reliably aligned is the H5 helix (Figure 1). Furthermore, the secondary structure prediction for the FtsZl1 family was not fully compatible with the known structure of the S6-T7 region of the nucleotide-binding and connector domains (Additional File 2). Along the same lines, we did not detect any similarity between the C-terminal domain of the FtsZl1 family and C-terminal domains of previously characterized FtsZ-tubulin superfamily proteins. These structural elements have been shown to contribute to the formation of FtsZ filaments [6]. Accordingly, the FtsZl1 proteins might form filaments via a novel mechanism or, less likely, might not form filaments at all. In general, the FtsZl2 and especially FtsZl1 families seem to include the most structurally diverged proteins in the entire FtsZ-tubulin superfamily and therefore are of particular interest for further structural and functional analysis.

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