Species of the phylum Aquificae are of great interest due to their strict extreme thermophilic growth characteristics. Presently, there is no known molecular characteristic which is unique to this group of bacteria. This work describes six conserved inserts and deletions (indels or signature sequences) in four widely distributed proteins that are distinctive features of species from the phylum Aquificae. These include three signatures consisting of a 2 aa insert, a 5–6 aa insert and a 6 aa deletion in DNA polymerase I (PolA), a 6–7 aa insert in glucose-inhibited protein A (GidA), a 52 aa insert in the RNA polymerase β′-subunit (RpoC) and a 4 aa insert in elongation factor Tu (EF-Tu). Fragments of these genes were amplified in most cases from Hydrogenobacter hydrogenophilus, Hydrogenothermus marinus and Thermocrinis ruber and combined with available sequence data from ‘Aquifex aeolicus’ and Sulfurihydrogenibium azorense. The presence of the PolA, GidA and RpoC indels in all of the species sequenced provides evidence that they are probably distinctive characteristics of the entire phylum. The indel in EF-Tu, which is shared by Aquifex species and Hydrogenobacter but not Hydrogenothermus and Sulfurihydrogenibium, may provide a molecular marker for the family Aquificaceae. We have also identified a 51 aa insert in SecA preprotein translocase that is commonly shared by various species of the Aquificae as well as two Thermotoga species (Thermotoga maritima and Thermotoga neapolitana) which may be due to lateral gene transfer between these groups. In phylogenetic trees based on a concatenated dataset of fragments from eight different proteins as well as 16S rRNA, the observed branching pattern of these species was very similar and it was consistent with the relationships inferred from various indels. The identified indels provide a novel means for distinguishing species of the Aquificae from all other bacteria in molecular terms and may prove useful for functional studies aimed at understanding the unique biochemical and physiological characteristics of the Aquificae.
Aguiar, P., Beveridge, T. J. & Reysenbach, A. L.(2004).Sulfurihydrogenibium azorense sp. nov., a thermophilic hydrogen-oxidizing microaerophile from terrestrial hot springs in the Azores. Int J Syst Evol Microbiol54, 33–39.[CrossRef][Google Scholar]
Aravind, L., Tatusov, R. L., Wolf, Y. I., Walker, D. R. & Koonin, E. V.(1998). Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet14, 442–444.[CrossRef][Google Scholar]
Bocchetta, M., Gribaldo, S., Sanangelantoni, A. & Cammarano, P.(2000). Phylogenetic depth of the bacterial genera Aquifex and Thermotoga inferred from analysis of ribosomal protein, elongation factor, and RNA polymerase subunit sequences. J Mol Evol50, 366–380.
[Google Scholar]
Burggraf, S., Olsen, G. J., Stetter, K. O. & Woese, C. R.(1992). A phylogenetic analysis of Aquifex pyrophilus. Syst Appl Microbiol15, 353–356.
[Google Scholar]
Cavalier-Smith, T.(2002). The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol52, 7–76.
[Google Scholar]
Coenye, T. & Vandamme, P.(2004). A genomic perspective on the relationship between the Aquificales and the epsilon-Proteobacteria. Syst Appl Microbiol27, 313–322.[CrossRef][Google Scholar]
Coenye, T., Gevers, D., Van de Peer, Y., Vandamme, P. & Swings, J.(2005). Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev29, 147–167.
[Google Scholar]
Deckert, G., Warren, P. V., Gaasterland, T. & 12 other authors(1998). The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature392, 353–358.[CrossRef][Google Scholar]
Eder, W. & Huber, R.(2002). New isolates and physiological properties of the Aquificales and description of Thermocrinis albus sp. nov. Extremophiles6, 309–318.[CrossRef][Google Scholar]
Götz, D., Banta, A., Beveridge, T. J., Rushdi, A. I., Simoneit, B. R. & Reysenbach, A. L.(2002).Persephonella marina gen. nov., sp. nov. and Persephonella guaymasensis sp. nov., two novel, thermophilic, hydrogen-oxidizing microaerophiles from deep-sea hydrothermal vents. Int J Syst Evol Microbiol52, 1349–1359.[CrossRef][Google Scholar]
Griffiths, E. & Gupta, R. S.(2002). Protein signatures distinctive of chlamydial species: horizontal transfer of cell wall biosynthesis genes glmU from archaea to chlamydiae, and murA between chlamydiae and Streptomyces. Microbiology148, 2541–2549.
[Google Scholar]
Griffiths, E. & Gupta, R. S.(2004a). Distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the Deinococcus-Thermus phylum. J Bacteriol186, 3097–3107.[CrossRef][Google Scholar]
Griffiths, E. & Gupta, R. S.(2004b). Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales. Int Microbiol7, 41–52.
[Google Scholar]
Gupta, R. S.(1998). Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev62, 1435–1491.
[Google Scholar]
Gupta, R. S.(2000). The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev24, 367–402.[CrossRef][Google Scholar]
Gupta, R. S.(2004). The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi and Bacteroidetes. Crit Rev Microbiol30, 123–143.[CrossRef][Google Scholar]
Gupta, R. S.(2005). Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for alpha proteobacterial evolution. Crit Rev Microbiol31, 101–135.[CrossRef][Google Scholar]
Gupta, R. S. & Griffiths, E.(2002). Critical issues in bacterial phylogeny. Theor Popul Biol61, 423–434.[CrossRef][Google Scholar]
Gupta, R. S., Pereira, M., Chandrasekera, C. & Johari, V.(2003). Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues. Int J Syst Evol Microbiol53, 1833–1842.[CrossRef][Google Scholar]
Hashimoto, T. & Hasegawa, M.(1996). Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1alpha/Tu and 2/G. Adv Biophys32, 73–120.[CrossRef][Google Scholar]
Huber, R. & Eder, W.(2002).Aquificales. In The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community. Release 3.8. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer & E. Stackebrandt. New York: Springer. http://link.springer-ny.com/link/service/books/10125/
Huber, H. & Stetter, K. O.(1998). Hyperthermophiles and their possible potential in biotechnology. J Biotechnol64, 39–52.[CrossRef][Google Scholar]
Huber, R., Eder, W., Heldwein, S., Wanner, G., Huber, H., Rachel, R. & Stetter, K. O.(1998).Thermocrinis ruber gen. nov., sp. nov., a pink-filament-forming hyperthermophilic bacterium isolated from Yellowstone national park. Appl Environ Microbiol64, 3576–3583.
[Google Scholar]
Iyer, L. M., Koonin, E. V. & Aravind, L.(2004). Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene335, 73–88.[CrossRef][Google Scholar]
Jahnke, L. L., Eder, W., Huber, R., Hope, J. M., Hinrichs, K. U., Hayes, J. M., Des Marais, D. J., Cady, S. L. & Summons, R. E.(2001). Signature lipids and stable carbon isotope analyses of Octopus Spring hyperthermophilic communities compared with those of Aquificales representatives. Appl Environ Microbiol67, 5179–5189.[CrossRef][Google Scholar]
Kawasumi, T., Igarshi, Y., Kodama, T. & Minoda, Y.(1984).Hydrogenobacter thermophilus gen. nov., sp. nov., an extremely thermophilic, aerobic, hydrogen-oxidizing bacterium. Int J Syst Bacteriol34, 5–10.[CrossRef][Google Scholar]
Klenk, H. P., Meier, T. D., Durovic, P., Schwass, V., Lottspeich, F., Dennis, P. P. & Zillig, W.(1999). RNA polymerase of Aquifex pyrophilus: implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria. J Mol Evol48, 528–541.[CrossRef][Google Scholar]
L'Haridon, S., Cilia, V., Messner, P., Raguenes, G., Gambacorta, A., Sleytr, U. B., Prieur, D. & Jeanthon, C.(1998).Desulfurobacterium thermolithotrophum gen. nov., sp. nov., a novel autotrophic, sulphur-reducing bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Bacteriol48, 701–711.[CrossRef][Google Scholar]
Ludwig, W. & Klenk, H.-P.(2001). Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 49–65. Edited by D. R. Boone & R. W. Castenholz. Berlin: Springer.
Mikulik, K., Qiao, C. L., Petrik, T., Puscheva, M. A. & Zavarzin, G. A.(1988). Elongation factor Tu of the extreme thermophilic hydrogen oxidizing bacterium Calderobacterium hydrogenophilum. Biochem Biophys Res Commun155, 384–391.[CrossRef][Google Scholar]
Minnick, D. T., Bebenek, K., Osheroff, W. P., Turner, R. M., Jr, Astatke, M., Liu, L., Kunkel, T. A. & Joyce, C. M.(1999). Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment). J Biol Chem274, 3067–3075.[CrossRef][Google Scholar]
Nakagawa, S., Takai, K., Horikoshi, K. & Sako, Y.(2003).Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol53, 863–869.[CrossRef][Google Scholar]
Nakagawa, S., Nakamura, S., Inagaki, F., Takai, K., Shirai, N. & Sako, Y.(2004).Hydrogenivirga caldilitoris gen. nov., sp. nov., a novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium from a coastal hydrothermal field. Int J Syst Evol Microbiol54, 2079–2084.[CrossRef][Google Scholar]
Nelson, K. E., Clayton, R. A., Gill, S. R. & 26 other authors(1999). Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature399, 323–329.[CrossRef][Google Scholar]
Nesbo, C. L., L'Haridon, S., Stetter, K. O. & Doolittle, W. F.(2001). Phylogenetic analyses of two "Archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria. Mol Biol Evol18, 362–375.[CrossRef][Google Scholar]
Olsen, G. J. & Woese, C. R.(1997). Archaeal genomics: an overview. Cell89, 991–994.[CrossRef][Google Scholar]
Osborne, A. R., Clemons, W. M., Jr & Rapoport, T. A.(2004). A large conformational change of the translocation ATPase SecA. Proc Natl Acad Sci U S A101, 10937–10942.[CrossRef][Google Scholar]
Reysenbach, A.-L.(2001). Phylum BI. Aquificae phy. nov. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 359–367. Edited by D. R. Boone & R. W. Castenholz. Berlin: Springer.
Rokas, A. & Holland, P. W.(2000). Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol15, 454–459.[CrossRef][Google Scholar]
Savic, D. J., Jankovic, M. & Kostic, T.(1990). Cellular role of DNA polymerase I. J Basic Microbiol30, 769–784.[CrossRef][Google Scholar]
Sha, J., Kozlova, E. V., Fadl, A. A., Olano, J. P., Houston, C. W., Peterson, J. W. & Chopra, A. K.(2004). Molecular characterization of a glucose-inhibited division gene, gidA, that regulates cytotoxic enterotoxin of Aeromonas hydrophila. Infect Immun72, 1084–1095.[CrossRef][Google Scholar]
Shatalkin, A. I.(2004). Highest level of division in classification of organisms. 3. Monodermata and Didermata. Zh Obshch Biol65, 195–210 (in Russian).
[Google Scholar]
Stöhr, R., Waberski, A., Volker, H., Tindall, B. J. & Thomm, M.(2001).Hydrogenothermus marinus gen. nov., sp. nov., a novel thermophilic hydrogen-oxidizing bacterium, recognition of Calderobacterium hydrogenophilum as a member of the genus Hydrogenobacter and proposal of the reclassification of Hydrogenobacter acidophilus as Hydrogenobaculum acidophilum gen. nov., comb. nov., in the phylum ‘Hydrogenobacter/Aquifex’. Int J Syst Evol Microbiol51, 1853–1862.[CrossRef][Google Scholar]
Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K.(2003).Sulfurihydrogenibium subterraneum gen. nov., sp. nov., from a subsurface hot aquifer. Int J Syst Evol Microbiol53, 823–827.[CrossRef][Google Scholar]
Van de Peer, Y. & De Wachter, R.(1994).treecon for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci10, 569–570.
[Google Scholar]
van den Burg, B.(2003). Extremophiles as a source for novel enzymes. Curr Opin Microbiol6, 213–218.[CrossRef][Google Scholar]
Vogeley, L., Palm, G. J., Mesters, J. R. & Hilgenfeld, R.(2001). Conformational change of elongation factor Tu (EF-Tu) induced by antibiotic binding. Crystal structure of the complex between EF-Tu.GDP and aurodox. J Biol Chem276, 17149–17155.[CrossRef][Google Scholar]
White, D. J., Merod, R., Thomasson, B. & Hartzell, P. L.(2001). GidA is an FAD-binding protein involved in development of Myxococcus xanthus. Mol Microbiol42, 503–517.[CrossRef][Google Scholar]