Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging

Abstract

Recently, it has been shown that a predicted P-loop ATPase (the HerA or MlaA protein), which is highly conserved in archaea and also present in many bacteria but absent in eukaryotes, has a bidirectional helicase activity and forms hexameric rings similar to those described for the TrwB ATPase. In this study, the FtsK-HerA superfamily of P-loop ATPases, in which the HerA clade comprises one of the major branches, is analyzed in detail. We show that, in addition to the FtsK and HerA clades, this superfamily includes several families of characterized or predicted ATPases which are predominantly involved in extrusion of DNA and peptides through membrane pores. The DNA-packaging ATPases of various bacteriophages and eukaryotic double-stranded DNA viruses also belong to the FtsK-HerA superfamily. The FtsK protein is the essential bacterial ATPase that is responsible for the correct segregation of daughter chromosomes during cell division. The structural and evolutionary relationship between HerA and FtsK and the nearly perfect complementarity of their phyletic distributions suggest that HerA similarly mediates DNA pumping into the progeny cells during archaeal cell division. It appears likely that the HerA and FtsK families diverged concomitantly with the archaeal-bacterial division and that the last universal common ancestor of modern life forms had an ancestral DNA-pumping ATPase that gave rise to these families. Furthermore, the relationship of these cellular proteins with the packaging ATPases of diverse DNA viruses suggests that a common DNA pumping mechanism might be operational in both cellular and viral genome segregation. The herA gene forms a highly conserved operon with the gene for the NurA nuclease and, in many archaea, also with the orthologs of eukaryotic double-strand break repair proteins MRE11 and Rad50. HerA is predicted to function in a complex with these proteins in DNA pumping and repair of double-stranded breaks introduced during this process and, possibly, also during DNA replication. Extensive comparative analysis of the 'genomic context' combined with in-depth sequence analysis led to the prediction of numerous previously unnoticed nucleases of the NurA superfamily, including a specific version that is likely to be the endonuclease component of a novel restriction-modification system. This analysis also led to the identification of previously uncharacterized nucleases, such as a novel predicted nuclease of the Sir2-type Rossmann fold, and phosphatases of the HAD superfamily that are likely to function as partners of the FtsK-HerA superfamily ATPases.

Figure 1

Topology diagram of the ASCE ATPases showing the putative higher order relationships of the FtsK–HerA superfamily. Strands are shown as arrows with the arrowhead at the C-terminus, helices are shown as cylinders. Strands and helices conserved across the ASCE group are numbered, and colored yellow and blue, respectively. The C-terminal β-hairpin synapomorphic to the RecA–ABC clade and the helix-strand unit synapomorphic to the RecA clade are colored pink. This hairpin is secondarily lost in most helicases. STAND is a large clade of NTPases that include the previously described AP-ATPases and NACHT NTPases, as well as several uncharacterized ATPase lineages predicted to participate in signal transduction (D. D. Leipe, Eugene V. Koonin and L. Aravind, unpublished data). Non-conserved secondary structural elements are colored white. Abbreviations: WA, Walker A; WB, Walker B and Sen1, sensor-1. The dotted connecting lines in the topology diagrams represent regions of the protein where insertions are observed. Broken lines in the cladogram reflect an uncertainty in relationship of the members within the clade supported by the broken line.

Figure 2

Multiple alignment of the FtsK–HerA superfamily. Proteins are denoted by their gene names, species abbreviations and gi numbers, separated by underscores. Amino acid residues are colored according to their side-chain properties and conservation in the multiple alignment. The coloring reflects 80% consensus and is shown underneath the alignment. The secondary structure shown above the alignment, is derived from the crystal structure of TrwB and secondary structure prediction programs. E and H represent a strand and helix, respectively. The consensus abbreviations and coloring scheme are as follows: h, hydrophobic residues (ACFILMVWY) shaded yellow; s, small residues (AGSVCDN) and u, tiny residues (GAS) colored green; o, alcohol group containing residues (ST) colored blue; p, polar residues (STEDKRNQHC) −, acidic residues (DE) and +, basic residues (HRK) colored purple. The conserved histidine in the Walker A strand, the arginine finger and the glutamine in sensor-1 are shaded red. Secondary structure elements that are conserved across the ASCE fold are numbered as integers. Species abbreviations are as follows: Aae, A.aeolicus; AMEPV, Amsacta moorei entomopoxvirus; Ape, Aeropyrum pernix; Asni, Aspergillus nidulans; Atu, Agrobacterium tumefaciens; Bce, Bacillus cereus; Bjap, Bradyrhizobium japonicum; Bme, Brucella melitensis; Bs, B.subtilis; Bsph, Bacillus sphaericus; Bthu, B.thuringiensis; CIV, Chilo iridescent virus; Cbrig, Caenorhabditis briggsae; Chte, C.tepidum; Cje, Campylobacter jejuni; Clth, C.thermocellum; Deha, Desulfitobacterium hafniense; ESV, Ectocarpus siliculosus virus; Ec, E.coli; Ec, Plasmid R100; Fnu, Fusobacterium nucleatum; fs2, V.cholerae filamentous bacteriophage fs-2; Hehe, H.hepaticus; Hp, Helicobacter pylori; Lepn, Legionella pneumophila; M13, Enterobacteria phage M13; Mac, Methanosarcina acetivorans; Mgi, Magnaporthe grisea; Mj, Methanococcus jannaschii; Mtu, Mycobacterium tuberculosis; NaNbHV, non-A, non-B hepatitis-associated virus; Neu, Nitrosomonas europaea; Nm, Neisseria meningitidis; Npu, Nostoc punctiforme; PBCV, Paramecium bursaria Chlorella virus 1; PM2, Alteromonas phage PM2; PR4, Bacteriophage PR4; Pae, Pseudomonas aeruginosa; Pf1, Pseudomonas phage Pf1; Pf3, Pseudomonas phage Pf3; Rheq, Rhodococcus equi; Rme, Ralstonia metallidurans; Rp, Rickettsia prowazekii; Rsol, Ralstonia solanacearum; Rsph, Rhodobacter sphaeroides; Scoe, Streptomyces coelicolor; Sep, Staphylococcus epidermidis; Sau, Staphylococcus aureus; Sme, Sinorhizobium meliloti; StiV, Sulfolobus turreted icosahedral virus; Sso, Sulfolobus solfataricus; St, Salmonella typhi, Sty, Salmonella typhimurium; Syn, Synechocystis sp.; Tel, Thermosynechococcus elongatus; Teth, Tetrahymena thermophila; Tma, Thermotoga maritima; Tp, Treponema pallidum; VacV, Vaccinia virus; Vc, V.cholerae; Vpar, Vibrio parahaemolyticus; VsKK, Bacteriophage VSKK; Vvul, Vibrio vulnificus; Wol, Wolbachia sp.; Xfas, Xylella fastidiosa and Yp, Yersinia pestis.

Figure 2

Multiple alignment of the FtsK–HerA superfamily. Proteins are denoted by their gene names, species abbreviations and gi numbers, separated by underscores. Amino acid residues are colored according to their side-chain properties and conservation in the multiple alignment. The coloring reflects 80% consensus and is shown underneath the alignment. The secondary structure shown above the alignment, is derived from the crystal structure of TrwB and secondary structure prediction programs. E and H represent a strand and helix, respectively. The consensus abbreviations and coloring scheme are as follows: h, hydrophobic residues (ACFILMVWY) shaded yellow; s, small residues (AGSVCDN) and u, tiny residues (GAS) colored green; o, alcohol group containing residues (ST) colored blue; p, polar residues (STEDKRNQHC) −, acidic residues (DE) and +, basic residues (HRK) colored purple. The conserved histidine in the Walker A strand, the arginine finger and the glutamine in sensor-1 are shaded red. Secondary structure elements that are conserved across the ASCE fold are numbered as integers. Species abbreviations are as follows: Aae, A.aeolicus; AMEPV, Amsacta moorei entomopoxvirus; Ape, Aeropyrum pernix; Asni, Aspergillus nidulans; Atu, Agrobacterium tumefaciens; Bce, Bacillus cereus; Bjap, Bradyrhizobium japonicum; Bme, Brucella melitensis; Bs, B.subtilis; Bsph, Bacillus sphaericus; Bthu, B.thuringiensis; CIV, Chilo iridescent virus; Cbrig, Caenorhabditis briggsae; Chte, C.tepidum; Cje, Campylobacter jejuni; Clth, C.thermocellum; Deha, Desulfitobacterium hafniense; ESV, Ectocarpus siliculosus virus; Ec, E.coli; Ec, Plasmid R100; Fnu, Fusobacterium nucleatum; fs2, V.cholerae filamentous bacteriophage fs-2; Hehe, H.hepaticus; Hp, Helicobacter pylori; Lepn, Legionella pneumophila; M13, Enterobacteria phage M13; Mac, Methanosarcina acetivorans; Mgi, Magnaporthe grisea; Mj, Methanococcus jannaschii; Mtu, Mycobacterium tuberculosis; NaNbHV, non-A, non-B hepatitis-associated virus; Neu, Nitrosomonas europaea; Nm, Neisseria meningitidis; Npu, Nostoc punctiforme; PBCV, Paramecium bursaria Chlorella virus 1; PM2, Alteromonas phage PM2; PR4, Bacteriophage PR4; Pae, Pseudomonas aeruginosa; Pf1, Pseudomonas phage Pf1; Pf3, Pseudomonas phage Pf3; Rheq, Rhodococcus equi; Rme, Ralstonia metallidurans; Rp, Rickettsia prowazekii; Rsol, Ralstonia solanacearum; Rsph, Rhodobacter sphaeroides; Scoe, Streptomyces coelicolor; Sep, Staphylococcus epidermidis; Sau, Staphylococcus aureus; Sme, Sinorhizobium meliloti; StiV, Sulfolobus turreted icosahedral virus; Sso, Sulfolobus solfataricus; St, Salmonella typhi, Sty, Salmonella typhimurium; Syn, Synechocystis sp.; Tel, Thermosynechococcus elongatus; Teth, Tetrahymena thermophila; Tma, Thermotoga maritima; Tp, Treponema pallidum; VacV, Vaccinia virus; Vc, V.cholerae; Vpar, Vibrio parahaemolyticus; VsKK, Bacteriophage VSKK; Vvul, Vibrio vulnificus; Wol, Wolbachia sp.; Xfas, Xylella fastidiosa and Yp, Yersinia pestis.

Figure 3

Multiple alignment of the HAS-barrel domain. The coloring reflects 80% consensus. The coloring scheme, consensus abbreviations and secondary structure representations are as in Figure 2. Additionally, big residues (LIYERFQKMW) are shaded gray. Species abbreviations are as follows: Af, Archaeoglobus fulgidus; Ape, A.pernix; Aae, A.aeolicus; Atu, A.tumefaciens; Bacs, Bacillus species; Bota, Bos Taurus; Caro, Cafeteria roenbergensis; Cau, C.aurantiacus; Cth, C. thermocellum; Cwat, Crocosphaera watsonii; Dr, D.radiodurans; Ec, E.coli; Efae, Enterococcus faecalis; Fac, Ferroplasma acidarmanus; Fnu, F.nucleatum; Glvi, Gloeobacter violaceus; Hp, H.pylori; Mj, M.jannaschii; Mlo, Mesorhizobium loti; Mth, Methanothermobacter thermautotrophicus; Npun, N.punctiforme; Ph, Pyrococcus horikoshii; Pyae, Pyrobaculum aerophilum; Rno, Rattus norvegicus; Sac, S.acidocaldarius; Sc, Saccharomyces cerevisiae; Smel, S.meliloti; Spol, Spinacia oleracea; Sso, S.solfataricus; Syn, Synechocystis sp.; Tery, Trichodesmium erythraeum; Thel, T.elongatus; Thth, Thermus thermophilus; Tma, T.maritima and Tvo, Thermoplasma volcanium.

Figure 4

Major lineages of the FtsK–HerA superfamily. The horizontal lines show temporal epochs corresponding to two major transitions in evolution, namely, the LUCA and the divergence between the archaeo-eukaryotic lineage and the bacterial lineage. Solid lines indicate the maximum depth in time to which a particular lineage can be traced. The broken lines indicate uncertainty with respect to the exact point of origin of a lineage. Bacterial lineages are colored in red, archaeal in blue and viral in green. Black lines indicate lineages with representatives from more than one of the three major superkingdoms, bacteria, archaea or eukaryotes. In such mixed lineages the phyletic distribution is shown in brackets with A denoting archaea; B, bacteria; FF, filamentous fungi; Nem, Nematodes; Pl, plants; Teth, T.thermophila and > lateral transfer.

Figure 5

Domain architectures, conserved gene neighborhoods and contextual network graph for the FtsK–HerA superfamily. (A) Domain architectures of proteins containing a FtsK–HerA like ATPase. SSO0283-N, CT1915-N and VirB4-N are conserved N-terminal regions found in the SSO0283, CT1915 and VirB4 families respectively. Transmembrane regions are labeled TM. (B) Genes that have a conserved neighborhood are shown as boxed arrows. A representative gene, the species in which it is present and its gi number are shown below the boxes. The phyletic distribution of a particular gene context is shown in brackets. Species abbreviations are as in Figure 2. The dotted lines bounded by brackets indicate that the genes bounding the bracket are in the general neighborhood and do not show a close operonic association. Genes that are poorly characterized are repesented as white boxed arrows. (C) Contextual network graph for the FtsK–HerA family. Each vertex represents a domain and the edges represent a contextual association. Domain combinations are shown as black arrows, with the arrow pointing from the N-terminus to the C-terminus of the multi-domain protein. Circular arrows indicate multiple copies of the same domain. Operonic and neighborhood associations are shown as red arrows with an O at the tail and the direction of the arrows point from the 5′–3′ direction of the coding sequence. Lines with O at both ends indicate that the genes bounding the line are in not operonic but in close vicinity of each other. The blue arrows with the boxed tails represent experimentally observed functional associations. The green arrow with the feathered tail indicates an insertion of a Zn-ribbon with the arrow head pointing to the location of the insertion in NurA. Additional species abbreviations not in Figure 2. Aful, A.fulgidus; Ana, Anabaena sp.; Cab, Clostridium acetobutylicum; Cau, C.aurantiacus; Cwat, C.watsonii; Glvi, G.violaceus; Mth, M.thermautotrophicus; Pfu, P.furiosus; Suac, S.acidocaldarius; Tac, Thermoplasma acidophilum and Tery, T.erythraeum.

Figure 6

Multiple alignment of the NurA superfamily. The coloring reflects 80% consensus and the coloring scheme, consensus abbreviations and secondary structure representations are as in Figures 2 and 3. Species abbreviations are as follows. Aae, A.aeolicus; Aful, A.fulgidus; Ana, Anabaena sp.; Ape, A.pernix; Bha, B.halodurans; Cau, C.aurantiacus; Ctep, C.tepidum; Dr, D.radiodurans; Feac, F.acidarmanus; Glvi, G.violaceus; Halsp, Halobacterium sp.; Hehe, H.hepaticus; Mac, M.acetivorans; Mba, Methanosarcina c; Mebu, Methanococcoides burtonii; Mj, M.jannaschii; Mkan, Methanopyrus kandleri; Mma, M.mazei; Mth, M.thermautotrophicus; Naeq, Nanoarchaeum equitans; Npun, N.punctiforme; Pab, Pyrococcus abyssi; Pfu, P.furiosus; Pho, P.horikoshii; Pyae, P.aerophilum; Sac, S.acidocaldarius; Sso, S.solfataricus; Stok, Sulfolobus tokodaii; Syn, Synechocystis sp.; Tac, T.acidophilum; Tery, T.erythraeum; Thel, T.elongatus; Tma, T.maritima; Tvo, T.volcanium and Unk, Uncultured crenarchaeote.

Figure 6

Multiple alignment of the NurA superfamily. The coloring reflects 80% consensus and the coloring scheme, consensus abbreviations and secondary structure representations are as in Figures 2 and 3. Species abbreviations are as follows. Aae, A.aeolicus; Aful, A.fulgidus; Ana, Anabaena sp.; Ape, A.pernix; Bha, B.halodurans; Cau, C.aurantiacus; Ctep, C.tepidum; Dr, D.radiodurans; Feac, F.acidarmanus; Glvi, G.violaceus; Halsp, Halobacterium sp.; Hehe, H.hepaticus; Mac, M.acetivorans; Mba, Methanosarcina c; Mebu, Methanococcoides burtonii; Mj, M.jannaschii; Mkan, Methanopyrus kandleri; Mma, M.mazei; Mth, M.thermautotrophicus; Naeq, Nanoarchaeum equitans; Npun, N.punctiforme; Pab, Pyrococcus abyssi; Pfu, P.furiosus; Pho, P.horikoshii; Pyae, P.aerophilum; Sac, S.acidocaldarius; Sso, S.solfataricus; Stok, Sulfolobus tokodaii; Syn, Synechocystis sp.; Tac, T.acidophilum; Tery, T.erythraeum; Thel, T.elongatus; Tma, T.maritima; Tvo, T.volcanium and Unk, Uncultured crenarchaeote.

Figure 7

Multiple alignment of the predicted Sir2-like nuclease. The coloring reflects 80% consensus and the consensus abbreviations, coloring scheme and secondary structure designations are as in Figures 2 and 3. The histidine and aspartate residue conserved in the predicted nucleases are shaded red. Secondary structure elements are numbered according to their position in the core Rossmann fold. Helix 0.1 and 0.2 reflect helices that are synapomorphic to the Sir2-clade. Species abbreviations are as follows: Aae, A.aeolicus; Acpl, Actinobacillus pleuropneumoniae; Aful, A.fulgidus; Ape, A.pernix; Ban, Bacillus anthracis; Bce, B.cereus; bk5-t, Lactococcus phage bk5-t; Bobr, Bordetella bronchiseptica; Brja, B.japonicum; Brsu, Brucella suis; Chvi, Chromobacterium violaceum; Clpe, Clostridium perfringens; Ec, E.coli; Efae, E.faecalis; Hs, Homo sapiens; Lajo, Lactobacillus johnsonii; Lepin, Leptospira c; Mesp, Mesorhizobium sp.; Neu, N.europaea; Pab, P.abyssi; Pepe, Pediococcus pentosaceus; Pfl, Pseudomonas fluorescens; Phlu, Photorhabdus luminescens; Porgi, Porphyromonas gingivalis; Pput, Pseudomonas putida; Rhpa, Rhodopseudomonas palustris; Saga, Streptococcus agalactiae; Sc, S.cerevisiae; Seen, Serratia entomophila; Smel, S.meliloti; Sso, Sulfolobus solfataricus; Tden, Treponema denticola; Thth, T.thermophilus; Tma, T.maritima; Vipa, V.parahaemolyticus; Vivul, V.vulnificus; Xax, Xanthomonas axonopodis and Xca, Xanthomonas campesteris.

Figure 7

Multiple alignment of the predicted Sir2-like nuclease. The coloring reflects 80% consensus and the consensus abbreviations, coloring scheme and secondary structure designations are as in Figures 2 and 3. The histidine and aspartate residue conserved in the predicted nucleases are shaded red. Secondary structure elements are numbered according to their position in the core Rossmann fold. Helix 0.1 and 0.2 reflect helices that are synapomorphic to the Sir2-clade. Species abbreviations are as follows: Aae, A.aeolicus; Acpl, Actinobacillus pleuropneumoniae; Aful, A.fulgidus; Ape, A.pernix; Ban, Bacillus anthracis; Bce, B.cereus; bk5-t, Lactococcus phage bk5-t; Bobr, Bordetella bronchiseptica; Brja, B.japonicum; Brsu, Brucella suis; Chvi, Chromobacterium violaceum; Clpe, Clostridium perfringens; Ec, E.coli; Efae, E.faecalis; Hs, Homo sapiens; Lajo, Lactobacillus johnsonii; Lepin, Leptospira c; Mesp, Mesorhizobium sp.; Neu, N.europaea; Pab, P.abyssi; Pepe, Pediococcus pentosaceus; Pfl, Pseudomonas fluorescens; Phlu, Photorhabdus luminescens; Porgi, Porphyromonas gingivalis; Pput, Pseudomonas putida; Rhpa, Rhodopseudomonas palustris; Saga, Streptococcus agalactiae; Sc, S.cerevisiae; Seen, Serratia entomophila; Smel, S.meliloti; Sso, Sulfolobus solfataricus; Tden, Treponema denticola; Thth, T.thermophilus; Tma, T.maritima; Vipa, V.parahaemolyticus; Vivul, V.vulnificus; Xax, Xanthomonas axonopodis and Xca, Xanthomonas campesteris.

Figure 7

Multiple alignment of the predicted Sir2-like nuclease. The coloring reflects 80% consensus and the consensus abbreviations, coloring scheme and secondary structure designations are as in Figures 2 and 3. The histidine and aspartate residue conserved in the predicted nucleases are shaded red. Secondary structure elements are numbered according to their position in the core Rossmann fold. Helix 0.1 and 0.2 reflect helices that are synapomorphic to the Sir2-clade. Species abbreviations are as follows: Aae, A.aeolicus; Acpl, Actinobacillus pleuropneumoniae; Aful, A.fulgidus; Ape, A.pernix; Ban, Bacillus anthracis; Bce, B.cereus; bk5-t, Lactococcus phage bk5-t; Bobr, Bordetella bronchiseptica; Brja, B.japonicum; Brsu, Brucella suis; Chvi, Chromobacterium violaceum; Clpe, Clostridium perfringens; Ec, E.coli; Efae, E.faecalis; Hs, Homo sapiens; Lajo, Lactobacillus johnsonii; Lepin, Leptospira c; Mesp, Mesorhizobium sp.; Neu, N.europaea; Pab, P.abyssi; Pepe, Pediococcus pentosaceus; Pfl, Pseudomonas fluorescens; Phlu, Photorhabdus luminescens; Porgi, Porphyromonas gingivalis; Pput, Pseudomonas putida; Rhpa, Rhodopseudomonas palustris; Saga, Streptococcus agalactiae; Sc, S.cerevisiae; Seen, Serratia entomophila; Smel, S.meliloti; Sso, Sulfolobus solfataricus; Tden, Treponema denticola; Thth, T.thermophilus; Tma, T.maritima; Vipa, V.parahaemolyticus; Vivul, V.vulnificus; Xax, Xanthomonas axonopodis and Xca, Xanthomonas campesteris.