Complete genome sequence of Haliangium ochraceum type strain (SMP-2 T)

Standards in Genomic Sciences

Volumn 2, Issue 1, 2010, Pages 96-106

  Ivanova, Natalia ^a   Daum, Chris ^a   Lang, Elke ^b   Abt, Birte ^b   Kopitz, Markus ^b   Saunders, Elizabeth ^c   Lapidus, Alla ^a   Lucas, Susan ^a   del Rio, Tijana Glavina ^a   Nolan, Matt ^a   Tice, Hope ^a   Copeland, Alex ^a   Cheng, Jan Fang ^a   Chen, Feng ^a   Bruce, David ^a,c   Goodwin, Lynne ^a,c   Pitluck, Sam ^a   Mavromatis, Konstantinos ^a   Pati, Amrita ^a   Mikhailova, Natalia ^a   Chen, Amy ^d   Palaniappan, Krishna ^d   Land, Miriam ^a,e   Hauser, Loren ^a,e   Chang, Yun Juan ^a,e   Jeffries, Cynthia D ^a,e   Detter, John C ^a,c   Brettin, Thomas ^a,c   Rohde, Manfred ^f   Göker, Markus ^b   Bristow, Jim ^a   Markowitz, Victor ^d   Eisen, Jonathan A ^a,g   Hugenholtz, Philip ^a   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^b   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

^f HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Aerobic; Decomposition of bacterial and yeast cells; Fruiting bodies; GEBA; Gliding; Gram negative; Mesophile; Moderately halophilic; Myxobacteria; Myxococcales

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); COCCOIDEA; HALIANGIACEAE; HALIANGIUM; HALIANGIUM OCHRACEUM; MYXOCOCCALES; NEGIBACTERIA;

EID: 78751547656     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.69.1277     Document Type: Article

References (41)

1. Fudou R, Jojima Y, Iizuka T, Yamanaka S. Haliangium ochraceum gen. nov., sp. nov. and Haliangium tepidum sp. nov.: novel moderately halophilic myxobacteria isolated from coastal saline environments. J Gen Appl Microbiol 2002; 48:109-116 PubMed doi:10.2323/jgam.48.109
2. Iizuka T, Jojima Y, Fudou R, Yamanaka S. Isolation of myxobacteria from the marine environment. FEMS Microbiol Lett 1998; 169:317-322 PubMed doi:10.1111/j.1574-6968.1998.tb13335.x
3. Iizuka T, Jojima Y, Fudou R, Tokura M, Hiraishi A, Yamanaka S. Enhygromyxa salina gen. nov., sp. nov., a slightly halophilic myxobacterium isolated from the coastal areas of Japan. Syst Appl Microbiol 2003; 26:189-196 PubMed doi:10.1078/072320203322346038
4. Iizuka T, Jojima Y, Fudou R, Tokura M, Hiraishi A, Ahn JW, Yamanaka S. Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan. Int J Syst Evol Micro- biol 2003; 53:189-195 PubMed doi:10.1099/ijs.0.02418-0
5. Spröer C, Reichenbach H, Stackebrandt E. The correlation between morphological and phylogenetic classification of myxobacteria. Int J Syst Bacteriol 1999; 49:1255-1262 PubMed
6. Reichenbach H, Garrity GM, Brenner DJ, Krieg NR, Staley JT. Order VIII. Myxococcales Tchan, Pochon and Pre ́vot 1948, 398AL. In: Brenner DJ, Krieg NR, Staley JT, Eds. Bergey's Manual of Systematic Bacteriology, 2nd edn., Vol. 2 Part C. Springer, New York 2005: 1059-1072.
7. Euzéby J. Validation List No. 115. List of new names and new combinations previously effectively, but not validly published. Int J Syst Evol Microbiol 2007; 57:893-897 PubMed doi:10.1099/ijs.0.65207-0
8. Garrity GM, Bell JA, Lilburn TG. Taxonomic outline of the Procaryotes. In: Garrity GM, Boone DR, Castenholz RW, Eds. Bergey's Manual of Systematic Bacteriology, 2nd edn. Springer, New York 2004: 1-39.
9. Gerth K, Pradella S, Perlova O, Beyer S, Müller R. Myxobacteria: proficient producers of novel natural products with various biological activities -past and future biotechnological aspects with the focus on the genus Sorangium. J Biotechnol 2003; 106:233-253 PubMed doi:10.1016/j.jbiotec.2003.07.015
10. Kaiser D. Myxococcus - from single-cell polarity to complex multicellular patterns. Annu Rev Genet 2008; 42:109-130 PubMed doi:10.1146/annurev.genet.42.110807.091615
11. Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, et al. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Bio-technol 2007; 25:1281-1289 PubMed doi:10.1038/nbt1354
12. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452-464 PubMed doi:10.1093/bioinformatics/18.3.452
13. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552 PubMed
14. Stamatakis A, Hoover P, Rougemont J. A Rapid Bootstrap Algorithm for the RAxML Web Servers. Syst Biol 2008; 57:758-771 PubMed doi:10.1080/10635150802429642
15. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346-D354 PubMed doi:10.1093/nar/gkp848
16. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547 PubMed doi:10.1038/nbt1360
17. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579 PubMed doi:10.1073/pnas.87.12.4576
18. Garrity GM, Holt JG. The road map to the manual. In: Garrity GM, Boone DR, Castenholtz RW (eds), Bergey's Manual of Systematic Bacteriology, 2nd edition, Vol. 1, Springer, NY, 2001, p 119-169.
19. Kuever J, Rainey FA, Widdel F. Class IV. Delta- proteobacteria class nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, 2nd edition, Vol. 2, Part C, Springer, NY, 2005, p 922.
20. Tchan YT, Pochon J, Prévot AR. Etude de systématique bactérienne. VIII. Essai de classification des Cytophaga. Ann Inst Pasteur (Paris) 1948; 74:394-400.
21. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420.
22. Euzéby J. Validation List no. 115. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2007; 57:893-897 PubMed doi:10.1099/ijs.0.65207-0
23. Zhang YQ, Li YZ, Wang B, Wu ZH, Zhang CY, Gong X, Qiu ZJ, Zhang Y. Characteristics and living patterns of marine myxobacterial isolates. Appl Environ Microbiol 2005; 71:3331-3336. PubMed doi:10.1128/AEM.71.6.3331-3336.2005
24. Agents B. Technical rules for biological agents www.baua.de TRBA 466.
25. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the un-ification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29 PubMed doi:10.1038/75556
26. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
27. Berleman JE, Kirby JR. Deciphering the hunting strategy of a bacterial wolfpack. FEMS Microbiol Rev 2009; 33:942-957 PubMed doi:10.1111/j.1574-6976.2009.00185.x
28. Bode HB, Dickschat JS, Kroppenstedt RM, Schulz S, Müller R. Biosynthesis of isofatty acids in myxobacteria: iso-even fatty acids are derived by alpha-oxidation from isoodd fatty acids. J Am Chem Soc 2005; 127:532-533 PubMed doi:10.1021/ja043570y
29. Shimkets L, Dworkin M, Reichenbach H. The Myxobacteria. In: The Prokaryotes, Volume 7: Proteobacteria: Delta and Epsilon Subclasses. Deeply Rooting Bacteria (Eds Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E). Springer, New York 2006, 31-117.DOI10.1007/0-387-30747-8
30. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova N, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic en-cyclopedia of Bacteria and Archaea. Nature 2009; 462:1056-1060 PubMed doi:10.1038/nature08656
31. T). Stand Genomic Sci 2009; 1:12-20. doi:10.4056/sigs.761
32. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Genomics (In press)
33. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. Nat Methods (In press).
34. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278 PubMed doi:10.1093/bioinformatics/btp393
35. Bolten CJ, Heinzle E, Müller R, Wittmann C. Investigation of the central carbon metabolism of Sorangium cellulosum: metabolic network recon-struction and quantification of pathway fluxes. J Microbiol Biotechnol 2009; 19:23-36. PubMed
36. Goldman B, Bhat S, Shimkets LJ. Genome evolution and the emergence of fruiting body development in Myxococcus xanthus. PLoS ONE 2007; 2:e1329 PubMed doi:10.1371/journal.pone.0001329
37. Wenzel SC, Müller R. The impact of genomics on the exploitation of myxobacterial secondary metabolome. Nat Prod Rep 2009; 26:1385-1407 PubMed doi:10.1039/b817073h
38. Stevens TJ, Paoli M. RCC1-like repeat proteins: a pangenomic, structurally diverse new superfamily of beta-propeller domains. Proteins 2008; 70:378-387 PubMed doi:10.1002/prot.21521
39. Shih YL, Rothfield L. The bacterial cytoskeleton. Microbiol Mol Biol Rev 2006; 70:729-754.PubMed doi:10.1128/MMBR.00017-06
40. Komaki H, Fudou R, Iizuka T, Nakajima D, Oka-zaki K, Shibata D, Ojika M, Harayama S. PCR detection of type I polyketide synthase genes in myxobacteria. Appl Environ Microbiol 2008; 74:5571-5574 PubMed doi:10.1128/AEM.00224-08
41. Thomas SH, Wagner RD, Arakaki AK, Skolnick J, Kirby JR, Shimkets LJ, Sanford RA, Löffler FE. The mosaic genome of Anaeromyxobacter dehaloge-nans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PLoS ONE 2008; 3:e2103 PubMed doi:10.1371/journal.pone.0002103