Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T)

Standards in Genomic Sciences

Volumn 1, Issue 1, 2009, Pages 54-62

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

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

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

^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

Dry soil; Flexible rods; Gram negative; Heparinase producer; Mesophile; Sphingobacteriaceae; Strictly aerobic

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDETES; NEGIBACTERIA; PEDOBACTER; PEDOBACTER HEPARINUS; SPHINGOBACTERIACEAE;

EID: 77957104084     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.22138     Document Type: Article

References (24)

1. Korn ED, Payza AN. The degradation of heparin by bacterial enzymes. I. Adaptation and lyophilized cells. J Biol Chem 1956; 223:853-858 PMID:13385232
2. Christensen P. Description and taxonomic status of Cytophaga heparina (Payza and Korn) comb. nov. (basionym: Flavobacterium heparinum Payza and Korn 1956) Int J Syst Bacteriol 1980; 30:473-475 doi:10.1099/00207713-30-2-473
3. Takeuchi M, Yokota A. Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum. J Gen Appl Microbiol 1992; 38:465-482 doi:10.2323/jgam.38.465
4. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K, Joubert JJ. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 1998; 48:165-177 PMID:9542086 doi:10.1099/00207713-48-1-165
5. Yoon MH, Ten LN, Im WT, Lee ST. Pedobacter panaciterrae sp. nov., isolated from soil in South Korea. Int J Syst Evol Microbiol 2007; 57:381-386 PMID:17267983 doi:10.1099/ijs.0.64693-0
6. de Boer W, Wagenaar AM, Klein Gunnewiek PJ, van Veen JA. In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria. FEMS Microbiol Ecol 2007; 59:177-185 PMID:17233750 doi:10.1111/j.15746941.2006.00197.x
7. Carrero-Colon M, Nakatsu CH, Konopka A. Effect of nutrient periodicity on microbial community dynamics. Appl Environ Microbiol 2006; 72:3175 MID:16672455 doi:10.1128/AEM.72.5.31753183.2006
8. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452 MID:11934745 doi:10.1093/bioinformatics/18.3. 452
9. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552
10. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008; 57:758 MID:18853362 doi:10.1080/10635150802429642
11. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475 MID:17981842 doi:10.1093/nar/gkm884
12. Galliher PM, Cooney CL, Langer R, Linhardt RJ. Heparinase production by Flavobacterium heparinum. Appl Environ Microbiol 1981; 41:360-365 PMID:7235692
13. Dietrich CP, Silva ME, Michelacci YM. Sequential degradation of heparin in Flavobacterium heparinum. Purification and properties of five enzymes involved in heparin degradation. J Biol Chem 1973; 248:6408-6415 PMID:4730325
14. Blain F, Tkalec AL, Shao Z, Poulin C, Pedneault M, Gu K, Eggimann B, Zimmermann J, Su H. Expression system for high levels of GAG lyase gene expression and study of the hepA upstream region in Flavobacterium hepari0num. J Bacteriol 2002; 184:3242 MID:12029040 doi:10.1128/JB.184.12.32423252.2002
15. Huang W, Matte A, Li Y, Kim YS, Linhardt RJ, Su H, Cygler M. Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution. J Mol Biol 1999; 294:1257 MID:10600383 doi:10.1006/jmbi.1999.3292
16. Shaya D, Tocilj A, Li Y, Myette J, Venkataraman G, Sasisekharan R, Cygler M. Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product. J Biol Chem 2006; 281:15525 MID:16565082 doi:10.1074/jbc.M512055200
17. 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 MID:18464787 doi:10.1038/nbt1360
18. Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzéby J, Tindall BJ. Taxonomic Outline of the Bacteria and Archaea. Michigan State University Board of Trustees; 2007 www.taxonomicoutline.org
19. Biological Agents: Technical rules for biological agents TRBA 466
20. 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 unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29 PMID:10802651 doi:10.1038/75556
21. Han CS, Chain P. Finishing repeat regions automatically with Dupfinisher CSREA Press. In: Arabnia AR, Valafar H, editors. Proceedings of the 2006 international conference on bioinformatics & computational biology; 2006 June 26-29. CSREA Press. p 141-146
22. Anonymous. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. Oak Ridge Pedobacter heparinus type strain (HIM 762-3T) National Laboratory and University of see 2009
23. Pati A. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes (In preparation 2009).
24. Markowitz V, Mavromatis K, Ivanova N, Chen IM, Chu K, Palaniappan K, Szeto E, Anderson I, Lykidis A, Kyrpides N. Expert Review of Functional Annotations for Microbial Genomes. Bioinformatics 2009 in press