Signature Protein of the PVC Superphylum

Applied and Environmental Microbiology

Volumn 80, Issue 2, 2014, Pages 440-445

  Lagkouvardos, Ilias ^a   Jehl, Marc André ^b   Rattei, Thomas ^a   Horna, Matthias ^a  

^a UNIVERSITY OF VIENNA   (Austria)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ACTIVITIES; ECOLOGICAL FEATURES; EVOLUTIONARY HISTORY; GEL-RETARDATION ASSAY; GENOME SEQUENCES; HOUSEKEEPING FUNCTIONS; PHYLOGENETIC ANALYSIS; PHYSICOCHEMICAL CHARACTERISTICS;

ESCHERICHIA COLI;

PROTEINS;

BIOASSAY; BIOMARKER; CHEMICAL BINDING; COLIFORM BACTERIUM; COMPARATIVE STUDY; GENE EXPRESSION; GENOME; PHYLOGENETICS; PROTEIN;

BACTERIAL PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; CHLAMYDIA; EVOLUTION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANCTOMYCETALES; VERRUCOMICROBIA;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BIOLOGICAL EVOLUTION; CHLAMYDIA; CONSERVED SEQUENCE; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANCTOMYCETALES; VERRUCOMICROBIA;

EID: 84892462366     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02655-13     Document Type: Article

References (50)

1. Wagner M, Horn M. 2006. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr. Opin. Biotechnol. 17:241-249. http://dx.doi.org/10.1016/j.copbio.2006.05.005.
2. Pilhofer M, Rappl K, Eckl C, Bauer AP, Ludwig W, Schleifer KH, Petroni G. 2008. Characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes and phylogenetic comparison with rRNA genes. J. Bacteriol. 190:3192-3202. http://dx.doi.org/10.1128/JB.01797-07.
3. Griffiths E, Gupta RS. 2007. Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae. Microbiology 153:2648-2654. http: //dx.doi.org/10.1099/mic.0.2007/009118-0.
4. Kamneva OK, Knight SJ, Liberles DA, Ward NL. 2012. Analysis of genome content evolution in PVC bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. Genome Biol. Evol. 4:1375-1390. http://dx.doi.org/10.1093/gbe/evs113.
5. Gupta RS, Bhandari V, Naushad HS. 2012. Molecular signatures for the PVC clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of bacteria provide insights into their evolutionary relationships. Front. Microbiol. 3:327. http://dx.doi.org/10.3389/fmicb.2012.00327.
6. Shu QL, Jiao NZ. 2008. Different Planctomycetes diversity patterns in latitudinal surface seawater of the open sea and in sediment. J. Microbiol. 46:154-159. http://dx.doi.org/10.1007/s12275-008-0002-9.
7. Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Medigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MSM, Wagner M, Le Paslier D. 2006. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440:790-794. http://dx.doi.org/10.1038/nature04647.
8. Bebear C, de Barbeyrac B. 2009. Genital Chlamydia trachomatis infections. Clin. Microbiol. Infect. 15:4-10. http://dx.doi.org/10.1111/j.1469 -0691.2008.02647.x.
9. Corsaro D, Greub G. 2006. Pathogenic potential of novel chlamydiae and diagnostic approaches to infections due to these obligate intracellular bacteria. Clin. Microbiol. Rev. 19:283-297. http://dx.doi.org/10.1128/CMR.19.2.283-297.2006.
10. Horn M. 2008. Chlamydiae as symbionts in eukaryotes. Annu. Rev. Microbiol. 62:113-131. http://dx.doi.org/10.1146/annurev.micro.62.081307.162818.
11. Zwart G, Crump BC, Agterveld MPKV, Hagen F, Han SK. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28:141-155. http: //dx.doi.org/10.3354/ame028141.
12. Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N. 2011. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol. Biochem. 43: 1450-1455. http://dx.doi.org/10.1016/j.soilbio.2011.03.012.
13. Santarella-Mellwig R, Franke J, Jaedicke A, Gorjanacz M, Bauer U, Budd A, Mattaj IW, Devos DP. 2010. The compartmentalized bacteria of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum have membrane coat-like proteins. PLoS Biol. 8:e1000281. http://dx.doi.org/10.1371/journal.pbio.1000281.
14. Devos DP, Reynaud EG. 2010. Evolution. Intermediate steps. Science 330:1187-1188. http://dx.doi.org/10.1126/science.1196720.
15. Fuerst JA, Sagulenko E. 2011. Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat. Rev. Microbiol. 9:403-413. http://dx.doi.org/10.1038/nrmicro2578.
16. Fuchsman CA, Rocap G. 2006. Whole-genome reciprocal BLAST analysis reveals that Planctomycetes do not share an unusually large number of genes with Eukarya and Archaea. Appl. Environ. Microbiol. 72:6841- 6844. http://dx.doi.org/10.1128/AEM.00429-06.
17. McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM. 2011. Planctomycetes and eukaryotes: a case of analogy not homology. Bioessays 33:810-817. http://dx.doi.org/10.1002/bies.201100045.
18. Budd A, Devos DP. 2012. Evaluating the evolutionary origins of unexpected character distributions within the bacterial Planctomycetes- Verrucomicrobia-Chlamydiae superphylum. Front. Microbiol. 3:401. http://dx.doi.org/10.3389/fmicb.2012.00401.
19. Forterre P. 2011. A new fusion hypothesis for the origin of Eukarya: better than previous ones, but probably also wrong. Res. Microbiol. 162:77-91. http://dx.doi.org/10.1016/j.resmic.2010.10.005.
20. Fuerst JA, Sagulenko E. 2012. Keys to eukaryality: planctomycetes and ancestral evolution of cellular complexity. Front. Microbiol. 3:167. http: //dx.doi.org/10.3389/fmicb.2012.00167.
21. Nakamura Y, Cochrane G, Karsch-Mizrachi I. 2013. The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 41:D21- 24. http://dx.doi.org/10.1093/nar/gks1084.
22. Pruitt KD, Tatusova T, Maglott DR. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35:D61-D65. http://dx.doi.org/10.1093/nar/gkl842.
23. Rattei T, Tischler P, Gotz S, Jehl MA, Hoser J, Arnold R, Conesa A, Mewes HW. 2010. SIMAP-a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Res. 38:D223-226. http://dx.doi.org/10.1093/nar/gkp949.
24. Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. 2012. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 40:D284-289. http://dx.doi.org /10.1093/nar/gkr1060.
25. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. http: //dx.doi.org/10.1093/nar/25.17.3389.
26. Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, Rokhsar D, Dubchak I. 2012. The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res. 40:D26-32. http://dx.doi.org/10.1093 /nar/gkr947.
27. Marchler-Bauer A, Zheng CJ, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Lu SN, Marchler GH, Song JS, Thanki N, Yamashita RA, Zhang DC, Bryant SH. 2013. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 41:D348-D352. http://dx.doi.org/10.1093/nar /gks1243.
28. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. http://dx.doi.org/10.1093/nar/gkh340.
29. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739. http://dx.doi.org/10.1093/molbev/msr121.
30. Sneath PHA, Sokal RR. 1973. Numerical taxonomy; the principles and practice of numerical classification. W. H. Freeman, San Francisco, CA.
31. Price MN, Dehal PS, Arkin AP. 2010. FastTree 2-approximately maximum- likelihood trees for large alignments. PLoS One 5:e9490. http://dx.doi.org/10.1371/journal.pone.0009490.
32. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
33. Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximumlikelihood approach. Mol. Biol. Evol. 18:691-699. http://dx.doi.org/10.1093/oxfordjournals.molbev.a003851.
34. Letunic I, Bork P. 2007. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127-128. http://dx.doi.org/10.1093/bioinformatics/btl529.
35. Schlesner H. 1987. Verrucomicrobium spinosum gen. nov., sp. nov.-a fimbriated prosthecate bacterium. Syst. Appl. Microbiol. 10:54-56. http: //dx.doi.org/10.1016/S0723-2020(87)80010-3.
36. Schlesner H. 1994. The development of media suitable for the microorganisms morphologically resembling Planctomyces spp., Pirellula spp., and other Planctomycetales from various aquatic habitats using dilute media. Syst. Appl. Microbiol. 17:135-145. http://dx.doi.org/10.1016 /S0723-2020(11)80042-1.
37. Thellin O, Zorzi W, Lakaye B, De Borman B, Coumans B, Hennen G, Grisar T, Igout A, Heinen E. 1999. Housekeeping genes as internal standards: use and limits. J. Biotechnol. 75:291-295. http://dx.doi.org/10.1016/S0168-1656(99)00163-7.
38. Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang CG, Dandekar T, Hentschel U. 2011. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J. 5:61-70. http://dx.doi.org/10.1038/ismej.2010.95.
39. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FSL. 2010. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26:1608-1615. http://dx.doi.org/10.1093/bioinformatics/btq249.
40. Harrison SC. 1991. A structural taxonomy of DNA-binding domains. Nature 353:715-719. http://dx.doi.org/10.1038/353715a0.
41. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. 2009. InterPro: the integrative protein signature database. Nucleic Acids Res. 37:D211-D215. http://dx.doi.org/10.1093/nar/gkn785.
42. Horn M, Collingro A, Schmitz-Esser S, Beier CL, Purkhold U, Fartmann B, Brandt P, Nyakatura GJ, Droege M, Frishman D, Rattei T, Mewes HW, Wagner M. 2004. Illuminating the evolutionary history of chlamydiae. Science 304:728-730. http://dx.doi.org/10.1126/science.1096330.
43. Sixt BS, Heinz C, Pichler P, Heinz E, Montanaro J, Op den Camp HJM, Ammerer G, Mechtler K, Wagner M, Horn M. 2011. Proteomic analysis reveals a virtually complete set of proteins for translation and energy generation in elementary bodies of the amoeba symbiont Protochlamydia amoebophila. Proteomics 11:1868-1892. http://dx.doi.org/10.1002/pmic.201000510.
44. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC. 2008. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 36:D534-D538. http://dx.doi.org/10.1093/nar/gkm869.
45. Rattei T, Tischler P, Arnold R, Hamberger F, Krebs J, Krumsiek J, Wachinger B, Stumpflen V, Mewes W. 2008. SIMAP-structuring the network of protein similarities. Nucleic Acids Res. 36:D289-D292. http: //dx.doi.org/10.1093/nar/gkm963.
46. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410. http://dx.doi.org/10.1016/S0022-2836(05)80360-2.
47. Lagkouvardos I, Weinmaier T, Lauro FM, Cavicchioli R, Rattei T, Horn M. 15 August 2013. Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the chlamydiae. ISME J. (Epub ahead of print.) http://dx.doi.org/10.1038/ismej.2013.142.
48. Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: A sequence logo generator. Genome Res. 14:1188-1190. http://dx.doi.org /10.1101/gr.849004.
49. Zhang Y. 2008. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40. http://dx.doi.org/10.1186/1471-2105-9-40.
50. Xu D, Zhang Y. 2012. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 80:1715-1735. http://dx.doi.org/10.1002/prot.24065.