Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica

FEMS Microbiology Letters

Volumn 236, Issue 2, 2004, Pages 333-340

  Studholme, David J ^a   Fuerst, John A ^b   Bateman, Alex ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Planctomycete; Protein domain; Proteome analysis; Secretion; Sequence motif; Signal peptide

Indexed keywords

BACTERIAL PROTEIN; SIGNAL PEPTIDE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL CELL; BACTERIAL GENOME; BACTERIAL STRAIN; CARBOXY TERMINAL SEQUENCE; CELL COMPARTMENTALIZATION; CELL FUNCTION; CELL LINEAGE; CELL SURFACE; CLUSTER ANALYSIS; CYTOLOGY; GENE DUPLICATION; MOLECULAR BIOLOGY; NONHUMAN; PHYLUM; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; RHODOPIRELLULA BALTICA; SECRETORY CELL; SEQUENCE ANALYSIS; TRANSPORT KINETICS;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BACTERIA; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; MOLECULAR SEQUENCE DATA; PROTEIN SORTING SIGNALS; PROTEIN STRUCTURE, TERTIARY; PROTEOME; SEQUENCE ALIGNMENT;

PLANCTOMYCETES; RHODOPIRELLULA BALTICA;

EID: 3142602706     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.femsle.2004.06.007     Document Type: Article

References (32)

1. Fuerst J.A. The planctomycetes - emerging models for microbial ecology, evolution and cell biology. Microbiology. 141:1995;1493-1506
2. Lindsay M.R., Webb R.I., Fuerst J.A. Pirellulosomes: a new type of membrane-bounded cell compartment in planctomycete bacteria of the genus Pirellula. Microbiology. 143:1997;739-748
3. Schlesner, H., Rendsmann, C., Tindall, B.J., Gade, D., Rabus, R., Pfeiffer, S., Hirsch, P. (2004). Taxonomic heterogeneity within the Planctomycetales as derived by DNA-DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov., and emended description of the genus Pirellula. Int. J. Syst. Envol. Microbiol., in press. Available from 10.1099/ijs.0.63113-0
4. Fuerst J.A., Webb R.I. Membrane-bounded nucleoid in the eubacterium Gemmata obscuriglobus. Proc. Natl. Acad. Sci. USA. 88:1991;8184-8188
5. Lindsay M.R., Webb R.I., Strous M., Jetten M.S., Butler M.K., Forde R.J., Fuerst J.A. Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell. Archives of Microbiology. 175:2001;413-429
6. Brochier C., Philippe H. Phylogeny: a non-hyperthermophilic ancestor for bacteria. Nature. 417:2002;244
7. Glockner F.O., Kube M., Bauer M., Teeling H., Lombardot T., Ludwig W., Gade D., Beck A., Borzym K., Heitmann K., Rabus R., Schlesner H., Amann R., Reinhardt R. Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proc. Natl. Acad. Sci. USA. 100:2003;8298-8303
8. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L., Studholme D.J., Yeats C., Eddy S.R. The Pfam protein families database. Nucleic Acids Res. 32:2004;D138-D141
9. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410
10. Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:2002;3059-3066
11. Eddy S.R. Profile hidden Markov models. Bioinformatics. 14:1998;755-763
12. Apweiler R., Bairoch A., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R, Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., Yeh L.S. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32:2004;D115-D119
13. Hulo N., Sigrist C.J., Le Saux V., Langendijk-Genevaux P.S., Bordoli L., Gattiker A., De Castro E., Bucher P., Bairoch A. Recent improvements to the PROSITE database. Nucleic Acids Res. 32:2004;D134-D137
14. Tam R., Saier M.H. Jr. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol. Rev. 57:1993;320-346
15. Berks B.C., Palmer T., Sargent F. The Tat protein translocation pathway and its role in microbial physiology. Adv. Microb. Physiol. 47:2003;187-254
16. Bayer E.A., Shimon L.J., Shoham Y., Lamed R. Cellulosomes - structure and ultrastructure. J. Struct. Biol. 124:1998;221-234
17. Schwarz E.M., Benzer S. Calx, a Na-Ca exchanger gene of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA. 94:1997;10249-10254
18. Wheelock M.J., Johnson K.R. Cadherins as modulators of cellular phenotype. Annu. Rev. Cell. Dev. Biol. 19:2003;207-235
19. Lawler J., Hynes R.O. The structure of human thrombospondin, an adhesive glycoprotein with multiple calcium-binding sites and homologies with several different proteins. J. Cell. Biol. 103:1986;1635-1648
20. Schlesner H. Pirella marina sp.nov., a budding, peptidoglycan-less bacterium from brackish water. Syst. Appl. Microbiol. 8:1986;177-180
21. Schlesner H. 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. 17:1994;135-145
22. Staley J.T. Budding bacteria of the Pasteuria-Blastobacter group. Can. J. Microbiol. 19:1973;609-614
23. Tekniepe B.L., Schmidt J.M., Starr M.P. Life cycle of a budding and appendaged bacterium belonging to morphotype IV of the Blastocaulis-Planctomyces group. Curr. Microbiol. 5:1981;1-6
24. Butler M.K., Wang J., Webb R.I., Fuerst J.A. Molecular and ultrastructural confirmation of classification of ATCC 35122 as a strain of Pirellula staleyi. Int. J. Syst. Evol. Microbiol. 52:2002;1663-1667
25. Schlesner H., Hirsch P. Assignment of ATCC27377 to Pirella gen. Nov. as Pirella staleyi comb. Nov. Int. J. Syst. Bacteriol. 34:1984;492-495
26. Baumgartner S., Hofmann K., Chiquet-Ehrismann R., Bucher P. The discoidin domain family revisited: new members from prokaryotes and a homology-based fold prediction. Protein Sci. 7:1998;1626-1631
27. Helmann J.D. The extracytoplasmic function (ECF) sigma factors. Adv. Microb. Physiol. 46:2002;47-110
28. Teeling H., Lombardot T., Bauer M., Ludwig W., Glöckner F.O. Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees. IJSEM. 54:2004;791-801
29. Ward N.L., Rainey F.A., Hedlund B.P., Staley J.T., Ludwig W., Stackebrandt E. Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny. Int.J. Syst. Evol. Microbiol. 50:2000;1965-1972
30. Letunic I, Copley R.R, Schmidt S., Ciccarelli F.D., Doerks T., Schultz J., Ponting C.P., Bork P. SMART 4.0: towards genomic data integration. Nucleic Acids Res. 32:2004;D142-D144
31. Nielsen H., Engelbrecht J., Brunak S., von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1997;1-6
32. Clamp M., Cuff J., Searle S.M., Barton G.J. The Jalview Java alignment editor. Bioinformatics. 20:2004;426-427