Bioinformatics and molecular approaches to detect NRPS genes involved in the biosynthesis of kurstakin from Bacillus thuringiensis

Applied Microbiology and Biotechnology

Volumn 92, Issue 3, 2011, Pages 571-581

  Abderrahmani, Ahmed ^a,b   Tapi, Arthur ^a   Nateche, Farida ^b   Chollet, Marlène ^a   Leclère, Valérie ^a   Wathelet, Bernard ^c   Hacene, Hocine ^b   Jacques, Philippe ^a  

^a UNIV LILLE   (France)

^b UNIVERSITY OF SCIENCES AND TECHNOLOGY HOUARI BOUMEDIENE   (Algeria)

^c UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Bacillus thuringiensis; Kurstakins; MALDI ToF; Nonribosomal lipopeptides; PCR; Spreading

Indexed keywords

BACILLUS THURINGIENSIS; KURSTAKINS; LIPOPEPTIDES; MALDI-TOF; PCR; SPREADING;

BACILLI; BACILLUS CEREUS; BACTERIOLOGY; BIOCHEMISTRY; BIOINFORMATICS; BIOSYNTHESIS; DESORPTION; INDUCTIVELY COUPLED PLASMA; MASS SPECTROMETRY; OCEAN HABITATS; POLYMERASE CHAIN REACTION;

GENES;

BACTERIAL ENZYME; KURSTAKIN; LIPOPEPTIDE; NONRIBOSOMAL PEPTIDE SYNTHETASE; PEPTIDE SYNTHASE; UNCLASSIFIED DRUG;

ANTIMICROBIAL ACTIVITY; BACTERIUM; BIOINFORMATICS; DESORPTION; DETECTION METHOD; GENE EXPRESSION; GENETIC ENGINEERING; MOLECULAR ANALYSIS; PEPTIDE; POLYMERASE CHAIN REACTION;

ALGERIA; ANTIMICROBIAL ACTIVITY; ARTICLE; BACILLUS CEREUS; BACILLUS THURINGIENSIS; BACTERIAL CELL; BIOINFORMATICS; BIOSYNTHESIS; GENE SEQUENCE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION;

ALGERIA; BACILLUS CEREUS; BACILLUS THURINGIENSIS; BIOSYNTHETIC PATHWAYS; COMPUTATIONAL BIOLOGY; DNA PRIMERS; GENE LIBRARY; LIPOPEPTIDES; OPERON; PEPTIDE SYNTHASES; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

ALGERIA;

BACILLUS CEREUS; BACILLUS THURINGIENSIS;

EID: 82355169760     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-011-3453-6     Document Type: Article

References (31)

1. MZ Ansari G Yadav RS Gokhale D Mohanty 2004 NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases Nucleic Acids Res 32 405 413 10.1093/nar/gkh359
2. BO Bachmann J Ravel 2009 Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data Methods Enzymol 458 181 217 10.1016/S0076-6879(09)04808-3 1:CAS:528: DC%2BD1MXpsFejs7c%3D
3. SB Bumpus BS Evans PM Thomas I Ntai NL Kelleher 2009 A proteomics approach to discovering natural products and their biosynthetic pathways Nat Biotechnol 27 951 956 10.1038/nbt.1565 1:CAS:528:DC%2BD1MXhtFGjt73J
4. S Caboche M Pupin V Leclère A Fontaine P Jacques G Kucherov 2008 NORINE: a database of nonribosomal peptides Nucleic Acids Res 36 D326 D331 10.1093/nar/gkm792 1:CAS:528:DC%2BD1cXhtVWjs7s%3D
5. S Caboche M Pupin V Leclère P Jacques G Kucherov 2009 Structural pattern matching of nonribosomal peptides BMC Struct Biol 18 9 15
6. J Chauffaux M Marchal N Gilois I Jehanno C Buisson 1997 Recherche de souches de Bacillus thuringiensis dans différents biotopes à travers le monde Can J Microbiol 43 337 343 10.1139/m97-047
7. XH Chen A Koumoutsi R Scholz K Schneider J Vate R Süssmuth J Piel R Borriss 2009 Genome analysis of Bacillus amyloliquefaciens FZB42 reveals its potential for biocontrol of plant pathogens J Biotechnol 140 27 37 10.1016/j.jbiotec.2008.10.011 1:CAS:528:DC%2BD1MXjtFOjtLg%3D
8. RA De Maagd A Bravo N Crickmore 2001 How Bacillus thuringiensis has evolved specific toxins to colonize the insect world Trends Genet 17 193 199 10.1016/S0168-9525(01)02237-5
9. Y Hathout YP Ho V Ryzhov P Demirev C Fenselau 2000 Kurstakins: a new class of lipopeptides isolated from Bacillus thuringiensis J Nat Prod 63 1492 1496 10.1021/np000169q 1:CAS:528:DC%2BD3cXmsVCqsb4%3D
10. H Hofte HR Whiteley 1989 Insecticidal crystal proteins of Bacillus thuringiensis Microbiol Rev 53 242 255 1:CAS:528:DyaL1MXltFajt78%3D
11. 2 with a Mu d(lac) element for ecological studies Appl Environ Microbiol 56 1046 1052 1:CAS:528:DyaK3cXkt1SktLc%3D
12. PI Kim H Bai D Bai H Chae S Chung Y Kim R Park YT Chi 2004 Purification and characterization of a lipopeptide produced by Bacillus thuringiensis CMB26 J Appl Microbiol 97 942 949 10.1111/j.1365-2672.2004.02356.x 1:CAS:528: DC%2BD2cXhtVahtLzI
13. A Kotoujansky M Lemattre P Boistard 1982 Utilization of a thermosensitive episome bearing transposon Tn10 to isolate Hfr donor strains of Erwinia carotovora subsp. chrysanthemi J Bacteriol 150 122 131 1:CAS:528: DyaL38XhvFChtL0%3D
14. V Leclère M Béchet A Adam JS Guez B Wathelet M Ongena P Thonart F Gancel M Chollet-Imbert Ph Jacques 2005 Mycosubtilin overproduction by Bacillus subtilis BBG100 enhances the organism's antagonistic and biocontrol activities Appl Environ Microbiol 71 4577 4584 10.1128/AEM.71.8.4577-4584.2005
15. V Leclère R Marti M Bechet P Fickers P Jacques 2006 The lipopeptides mycosubtilin and surfactin enhance spreading of Bacillus subtilis strains by their surface-active properties Arch Microbiol 186 475 483 10.1007/s00203-006-0163-z
16. YK Lee SB Kim CS Park JG Kim HM Oh BD Yoon HS Kim 2005 Chromosomal integration of sfp gene in Bacillus subtilis to enhance bioavailability of hydrophobic liquids Appl Microbiol Biotechnol 67 789 794 10.1007/s00253-004- 1847-4 1:CAS:528:DC%2BD2MXltlChsro%3D
17. F Leenders TH Stein B Kablitz P Franke J Vater 1999 Rapid typing of Bacillus subtilis strains by their secondary metabolites using matrix-assisted laser desorption/ionization mass spectrometry of intact cells Rapid Commun Mass Spectrom 13 943 949 10.1002/(SICI)1097-0231(19990530)13:10<943::AID- RCM591>3.0.CO;2-0 1:CAS:528:DyaK1MXjsVyntbc%3D
18. MA Marahiel LO Essen 2009 Nonribosomal peptide synthetases mechanistic and structural aspects of essential domains Methods Enzymol 458 337 351 10.1016/S0076-6879(09)04813-7 1:CAS:528:DC%2BD1MXpsFejsLo%3D
19. JJ May TM Wendrich MA Marahiel 2001 The dhb operon of Bacillus subtilis encodes the biosynthetic template for the catecholic siderophore 2,3-dihydroxybenzoate-glycine-threonine trimeric ester bacillibactin J Biol Chem 276 7209 7217 10.1074/jbc.M009140200 1:CAS:528:DC%2BD3MXislyisr0%3D
20. AL Moyne TE Cleveland S Tuzun 2004 Molecular characterization and analysis of the operon encoding the antifungal lipopeptide bacillomycin D FEMS Microbiol Lett 234 43 49 10.1111/j.1574-6968.2004.tb09511.x 1:CAS:528: DC%2BD2cXjsVensbc%3D
21. SB Needleman CD Wunsch 1970 A general method applicable to the search for similarities in the amino acid sequence of two proteins J Mol Biol 48 443 453 10.1016/0022-2836(70)90057-4 1:CAS:528:DyaE3cXktVShu74%3D
22. V Nihorimbere P Fickers P Thonart M Ongena 2009 Ecological fitness of Bacillus subtilis BGS3 regarding production of the surfactin lipopeptide in the rhizosphere Env Microbiol Reports 1 124 130 10.1111/j.1758-2229.2009.00017.x 1:CAS:528:DC%2BD1MXotlaktr4%3D
23. M Ongena P Jacques 2008 Bacillus lipopeptides: versatile weapons for plant disease biocontrol Trends Microbiol 16 116 125 10.1016/j.tim.2007.12.009
24. M Ongena E Jourdan A Adam M Paquot A Brans B Joris JL Arpigny P Thonart 2007 Surfactin and fengycin lipopeptides of Bacillus subtilis as elicitors of induced systemic resistance in plants Environ Microbiol 9 1084 1090 10.1111/j.1462-2920.2006.01202.x 1:CAS:528:DC%2BD2sXktlOrtbo%3D
25. NP Price AP Rooney JL Swezey E Perry FM Cohan 2007 Mass spectrometric analyses of lipopeptides from Bacillus strains isolated from diverse geographical locations FEMS Microbiol Lett 271 83 89 10.1111/j.1574-6968.2007. 00702.x 1:CAS:528:DC%2BD2sXlslSlsL8%3D
26. C Rausch T Weber O Kohlbacher W Wohlleben DH Huson 2005 Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVM) Nucleic Acids Res 33 5799 5808 10.1093/nar/gki885 1:CAS:528:DC%2BD2MXht1OmsbjI
27. Read TD, Akmal A, Bishop-Lilly K, Chen PE, Cook C, Kiley MP, Lentz S, Mateczun A, Nagarajan N, Nolan N, Osborne BI, Pop M, Sozhamannan S, Stewart AC, Sulakvelidze A, Thomason B, Willner K, Zwick ME (2009) Annotation of the Bacillus thuringiensis serovar pondicheriensis BGSC 4BA1 genome. Direct Submission in Genbank databases, NCBI, USA
28. A Tapi M Chollet-Imbert B Scherens P Jacques 2010 New approach for the detection of non ribosomal peptide synthetase genes in Bacillus strains by polymerase chain reaction Appl Microbiol Biotechnol 85 1521 1531 10.1007/s00253-009-2176-4 1:CAS:528:DC%2BC3cXmvVGrtg%3D%3D
29. CC Tseng SD Bruner RM Kohli MA Marahiel CT Walsh SA Sieber 2002 Characterization of the surfactin synthetase C-terminal thioesterase domain as a cyclic depsipeptide synthase Biochem 41 13350 13351 10.1021/bi026592a 1:CAS:528:DC%2BD38XnvVOjsbo%3D
30. N Vanittanakom W Loeffler U Koch G Jung 1986 Fengycin a novel antifungal lipopeptide antibiotic produced by Bacillus subtilis F-29-3 J Antibiot 39 888 901 1:CAS:528:DyaL28XltlSns7Y%3D
31. J Vater B Kablitz C Wilde P Franke N Mehta SS Cameotra 2002 Matrix-assisted laser desorption ionization-time of flight mass spectrometry of lipopeptide biosurfactants in whole cells and culture filtrates of Bacillus subtilis C-1 isolated from petroleum sludge Appl Environ Microbiol 68 6210 6219 10.1128/AEM.68.12.6210-6219.2002 1:CAS:528:DC%2BD38Xptlartb4%3D