메뉴 건너뛰기




Volumn 6, Issue 1, 2012, Pages 1-10

Complete genome sequence of Paenibacillus sp. strain JDR-2

Author keywords

Aerobic; Gram positive; Mesophile; Paenibacillus; Xylan; Xylanolytic

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; HEMICELLULOSE;

EID: 84859133189     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2374349     Document Type: Article
Times cited : (14)

References (42)
  • 1
    • 33144487406 scopus 로고    scopus 로고
    • Microbial strategies for the depolymerization of glucuronoxylan: Leads to the biotechnological applications of endoxylanases
    • eds S.D. Mansfield and J. N. Saddler. ACS Symposium Series No. 855. Ch 12
    • Preston JF, Hurlbert JC, Rice JD, Ragunathan A, St. John FJ. Microbial Strategies for the Depolymerization of Glucuronoxylan: Leads to the Biotechnological Applications of Endoxylanases in Application of Enzymes to Lignocellulosics, eds S.D. Mansfield and J. N. Saddler. ACS Symposium Series No. 855. Ch 12. pp191-210. 2003.
    • (2003) Application of Enzymes to Lignocellulosics , pp. 191-210
    • Preston, J.F.1    Hurlbert, J.C.2    Rice, J.D.3    Ragunathan, A.4    John, F.J.5
  • 2
    • 33144486522 scopus 로고    scopus 로고
    • Paenibacillus sp. strain JDR-2 and XynA1: A novel system for methylglucuronoxylan utilization
    • PubMed
    • StJohn FJ, Rice J, Preston J. Paenibacillus sp. strain JDR-2 and XynA1: a novel system for methylglucuronoxylan utilization. Appl Environ Microbiol 2006; 72:1496-1506. PubMed http://dx.doi.org/10.1128/AEM.72.2.1496-1506.2006
    • (2006) Appl Environ Microbiol , vol.72 , pp. 1496-1506
    • Stjohn, F.J.1    Rice, J.2    Preston, J.3
  • 3
    • 37449009285 scopus 로고    scopus 로고
    • Structure, function, and regulation of the aldouronate utilization gene cluster from Paenibacillus sp. strain JDR-2
    • PubMed
    • Chow V, Nong G, Preston J. Structure, function, and regulation of the aldouronate utilization gene cluster from Paenibacillus sp. strain JDR-2. J Bacteriol 2007; 189:8863-8870. PubMed http://dx.doi.org/10.1128/JB.01141-07
    • (2007) J Bacteriol , vol.189 , pp. 8863-8870
    • Chow, V.1    Nong, G.2    Preston, J.3
  • 4
    • 67649622092 scopus 로고    scopus 로고
    • Aldouronate utilization in Paenibacillus sp. strain JDR-2: Physiological and enzymatic evidence for coupling of extracellular depolymerization and intracellular metabolism
    • PubMed
    • Nong G, Rice J, Chow V, Preston J. Aldouronate utilization in Paenibacillus sp. strain JDR-2: Physiological and enzymatic evidence for coupling of extracellular depolymerization and intracellular metabolism. Appl Environ Microbiol 2009; 75:4410-4418. PubMed http://dx.doi.org/10.1128/AEM.02354-08
    • (2009) Appl Environ Microbiol , vol.75 , pp. 4410-4418
    • Nong, G.1    Rice, J.2    Chow, V.3    Preston, J.4
  • 5
    • 78650143650 scopus 로고    scopus 로고
    • Complete genome sequence of Paenibacillus polymyxa SC2, a strain of plant growth-promoting Rhizobacterium with broad-spectrum antimicrobial activity
    • PubMed
    • Ma M, Wang C, Ding Y, Li L, Shen D, Jiang X, Guan D, Cao F, Chen H, Feng R, et al. Complete genome sequence of Paenibacillus polymyxa SC2, a strain of plant growth-promoting Rhizobacterium with broad-spectrum antimicrobial activity. J Bacteriol 2011; 193:311-312. PubMed http://dx.doi.org/10.1128/JB.01234-10
    • (2011) J Bacteriol , vol.193 , pp. 311-312
    • Ma, M.1    Wang, C.2    Ding, Y.3    Li, L.4    Shen, D.5    Jiang, X.6    Guan, D.7    Cao, F.8    Chen, H.9    Feng, R.10
  • 6
    • 78049417954 scopus 로고    scopus 로고
    • Genome sequence of the polymyxin-producing plant-probiotic rhizobacterium Paenibacillus polymyxa E681
    • PubMed
    • Kim JF, Jeong H, Park SY, Kim SB, Park YK, Choi SK, Ryu CM, Hur CG, Ghim SY, Oh TK, et al. Genome sequence of the polymyxin-producing plant-probiotic rhizobacterium Paenibacillus polymyxa E681. J Bacteriol 2010; 192:6103-6104. PubMed http://dx.doi.org/10.1128/JB.00983-10
    • (2010) J Bacteriol , vol.192 , pp. 6103-6104
    • Kim, J.F.1    Jeong, H.2    Park, S.Y.3    Kim, S.B.4    Park, Y.K.5    Choi, S.K.6    Ryu, C.M.7    Hur, C.G.8    Ghim, S.Y.9    Oh, T.K.10
  • 7
    • 78650133443 scopus 로고    scopus 로고
    • Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments
    • PubMed
    • Sirota-Madi A, Olender T, Helman Y, Ingham C, Brainis I, Roth D, Hagi E, Brodsky L, Leshkowitz D, Galatenko V, et al. Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments. BMC Genomics 2010; 11:710. PubMed http://dx.doi.org/10.1186/1471-2164-11-710
    • (2010) BMC Genomics , vol.11 , pp. 710
    • Sirota-Madi, A.1    Olender, T.2    Helman, Y.3    Ingham, C.4    Brainis, I.5    Roth, D.6    Hagi, E.7    Brodsky, L.8    Leshkowitz, D.9    Galatenko, V.10
  • 8
    • 69549114509 scopus 로고    scopus 로고
    • The innate immune and systemic response in honey bees to a bacterial pathogen, Paenibacillus Larvae
    • PubMed
    • Chan QW, Melathopoulos AP, Pernal SF, Foster LJ. The innate immune and systemic response in honey bees to a bacterial pathogen, Paenibacillus larvae. BMC Genomics 2009; 10:387. PubMed http://dx.doi.org/10.1186/1471-2164-10-387
    • (2009) BMC Genomics , vol.10 , pp. 387
    • Chan, Q.W.1    Melathopoulos, A.P.2    Pernal, S.F.3    Foster, L.J.4
  • 9
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24:1596-1599. PubMed http://dx.doi.org/10.1093/molbev/msm092
    • (2007) Mol Biol Evol , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 10
    • 34249910658 scopus 로고    scopus 로고
    • Use of PCR-targeted mutagenesis to disrupt production of fusaricidin-type antifungal antibiotics in Paenibacillus Polymyxa
    • PubMed
    • Li J, Beatty PK, Shah S, Jensen SE. Use of PCR-targeted mutagenesis to disrupt production of fusaricidin-type antifungal antibiotics in Paenibacillus polymyxa. Appl Environ Microbiol 2007; 73:3480-3489. PubMed http://dx.doi.org/10.1128/AEM.02662-06
    • (2007) Appl Environ Microbiol , vol.73 , pp. 3480-3489
    • Li, J.1    Beatty, P.K.2    Shah, S.3    Jensen, S.E.4
  • 12
    • 0025300402 scopus 로고
    • Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
    • PubMed
    • 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 http://dx.doi.org/10.1073/pnas.87.12.4576
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 4576-4579
    • Woese, C.R.1    Kandler, O.2    Wheelis, M.L.3
  • 13
    • 0344278514 scopus 로고
    • The Higher Taxa, or, a Place for Everything...?
    • Holt JG, First Edition, The Williams and Wilkins Co., Baltimore
    • Murray RGE. The Higher Taxa, or, a Place for Everything...? In: Holt JG (ed), Bergey's Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co., Baltimore, 1984, p. 31-34.
    • (1984) Bergey's Manual of Systematic Bacteriology , vol.1 , pp. 31-34
    • Murray, R.G.E.1
  • 14
    • 0000685441 scopus 로고    scopus 로고
    • The Road Map to the Manual
    • Garrity GM, Boone DR, Castenholz RW, Second Edition, Springer, New York
    • Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
    • (2001) Bergey's Manual of Systematic Bacteriology , vol.1 , pp. 119-169
    • Garrity, G.M.1    Holt, J.G.2
  • 15
    • 80054899466 scopus 로고    scopus 로고
    • Bacilli class nov
    • De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB, Second Edition, Springer-Verlag, New York
    • Ludwig W, Schleifer KH, Whitman WB. Class I. Bacilli class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 19-20.
    • (2009) Bergey's Manual of Systematic Bacteriology , vol.3 , pp. 19-20
    • Ludwig, W.1    Schleifer, K.H.2    Whitman, W.B.3    Class, I.4
  • 16
    • 80053365349 scopus 로고    scopus 로고
    • List of new names and new combinations previously effectively but not validly, published. List no. 132
    • Euzéby J. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469-472. http://dx.doi.org/10.1099/ijs.0.022855-0
    • (2010) Int J Syst Evol Microbiol , vol.60 , pp. 469-472
    • Euzéby, J.1
  • 17
    • 84865212442 scopus 로고
    • Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Second Edition, Masson et Cie, Paris
    • Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1-692.
    • (1953) Dictionnaire Des Bactéries Pathogènes , pp. 1-692
    • Prévot, A.R.1
  • 19
    • 78649797844 scopus 로고    scopus 로고
    • Family IV. Paenibacillaceae fam. nov
    • De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB, Second Edition, Springer-Verlag, New York
    • De Vos P, Ludwig W, Schleifer KH, Whitman WB. Family IV. Paenibacillaceae fam. nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 269.
    • (2009) Bergey's Manual of Systematic Bacteriology , vol.3 , pp. 269
    • de Vos, P.1    Ludwig, W.2    Schleifer, K.H.3    Whitman, W.B.4
  • 21
    • 0043034491 scopus 로고
    • Validation List no. 51. Validation of the publication of new names and new combinations previously effectively published outside the IJSB
    • Murray RGE, ed. Validation List no. 51. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1994; 44:852. http://dx.doi.org/10.1099/00207713-44-4-852
    • (1994) Int J Syst Bacteriol , vol.44 , pp. 852
    • Murray, R.G.E.1
  • 22
    • 0345516032 scopus 로고    scopus 로고
    • Taxonomic note: Necessary correction of specific and subspecific epithets according to Rules 12c and 13b of the International Code of Nomenclature of Bacteria (1990 Revision)
    • Euzéby JP. Taxonomic note: necessary correction of specific and subspecific epithets according to Rules 12c and 13b of the International Code of Nomenclature of Bacteria (1990 Revision). Int J Syst Bacteriol 1998; 48:1073-1075. http://dx.doi.org/10.1099/00207713-48-3-1073
    • (1998) Int J Syst Bacteriol , vol.48 , pp. 1073-1075
    • Euzéby, J.P.1
  • 23
    • 0034108445 scopus 로고    scopus 로고
    • What is the type species of the genus Paenibacillus? Request for an Opinion
    • PubMed
    • Tindall BJ. What is the type species of the genus Paenibacillus? Request for an Opinion. Int J Syst Evol Microbiol 2000; 50:939-940. PubMed http://dx.doi.org/10.1099/00207713-50-2-939
    • (2000) Int J Syst Evol Microbiol , vol.50 , pp. 939-940
    • Tindall, B.J.1
  • 24
    • 13244287867 scopus 로고    scopus 로고
    • 1994 is Paenibacillus polymyxa. Opinion 77. Judicial Commission of the International Committee on Systematics of Prokaryotes
    • The type species of the genus Paenibacillus Ash et al, PubMed
    • Trüper HG. The type species of the genus Paenibacillus Ash et al. 1994 is Paenibacillus polymyxa. Opinion 77. Judicial Commission of the International Committee on Systematics of Prokaryotes. Int J Syst Evol Microbiol 2005; 55:513. PubMed
    • (2005) Int J Syst Evol Microbiol , vol.55 , pp. 513
    • Trüper, H.G.1
  • 27
    • 84859135328 scopus 로고    scopus 로고
    • MIDI. MIS Operating Manual. MIDI, Inc., Newark, DE 19713 2002
    • MIDI. MIS Operating Manual. MIDI, Inc., Newark, DE 19713; 2002.
  • 29
    • 84859135327 scopus 로고    scopus 로고
    • DOE Joint Genome Institute
    • DOE Joint Genome Institute. http://www.jgi.doe.gov
  • 30
    • 84859121099 scopus 로고    scopus 로고
    • The Phred/Phrap/Consed software package
    • The Phred/Phrap/Consed software package. http://www.phrap.com
  • 31
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • PubMed
    • Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8:186-194. PubMed
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 32
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • PubMed
    • Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8:175-185. PubMed
    • (1998) Genome Res , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 33
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • PubMed
    • Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998; 8:195-202. PubMed
    • (1998) Genome Res , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 35
    • 84859151332 scopus 로고    scopus 로고
    • Integrated Microbial Genome portal of JGI
    • Integrated Microbial Genome portal of JGI. http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_ oid=644736396
  • 36
    • 84859151338 scopus 로고    scopus 로고
    • NCBI
    • NCBI. http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve& dopt=Overview&list_uids=1609.
  • 37
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • PubMed
    • Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1    Chen, G.L.2    Locascio, P.F.3    Land, M.L.4    Larimer, F.W.5    Hauser, L.J.6
  • 39
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • PubMed
    • Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed http://dx.doi.org/10.1093/nar/25.5.955
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 41
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • PubMed
    • Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567-580. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 42
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3.0
    • PubMed
    • Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783-795. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028
    • (2004) J Mol Biol , vol.340 , pp. 783-795
    • Bendtsen, J.D.1    Nielsen, H.2    von Heijne, G.3    Brunak, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.