A novel docking domain interface model predicting recombination between homoeologous modular biosynthetic gene clusters

Journal of Industrial Microbiology and Biotechnology

Volumn 38, Issue 9, 2011, Pages 1295-1304

  Starcevic, Antonio ^a,b   Diminic, Janko ^b   Zucko, Jurica ^a,b   Elbekali, Mouhsine ^a   Schlosser, Tobias ^a   Lisfi, Mohamed ^a   Vukelic, Ana ^b   Long, Paul F ^c   Hranueli, Daslav ^b   Cullum, John ^a  

^a Rheinland Pfälzische Technische Universität Kaiserslautern Landau   (Germany)

^b UNIVERSITY OF ZAGREB   (Croatia)

^c KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

Bacillus; Chi sequence; Non ribosomal peptide synthetase; Polyketide synthase; Streptomyces

Indexed keywords

DOCKING PROTEIN; KETOSYNTHASE; POLYKETIDE SYNTHASE; UNCLASSIFIED DRUG;

ADENYLATION; ARTICLE; BACTERIAL STRAIN; BIOSYNTHESIS; CHROMOSOME; EVOLUTION; GENE CLUSTER; GENETIC RECOMBINATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; STREPTOMYCES;

GENES, BACTERIAL; MODELS, GENETIC; PEPTIDE SYNTHASES; POLYKETIDE SYNTHASES; PROTEIN STRUCTURE, TERTIARY; RECOMBINATION, GENETIC; STREPTOMYCES; SUBSTRATE SPECIFICITY;

STREPTOMYCES;

EID: 80052468396     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-010-0909-0     Document Type: Article

References (38)

1. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 403 410 2231712 1:CAS:528:DyaK3MXitVGmsA%3D%3D
2. S Anand MV Prasad G Yadav N Kumar J Shehara MZ Ansari D Mohanty 2010 SBSPKS: structure based sequence analysis of polyketide synthases Nucleic Acids Res 38 suppl W487 W496 20444870 10.1093/nar/gkq340 1:CAS:528: DC%2BC3cXotVSru7k%3D
3. MJ Bibb PR Findlay MW Johnson 1984 The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein coding sequences Gene 30 157 166 6096212 10.1016/0378-1119(84)90116-1 1:CAS:528:DyaL2MXls12itA%3D%3D (Pubitemid 15201773)
4. I Biswas E Maguin SD Ehrlich A Gruss 1995 A 7-base-pair sequence protects DNA from exonucleolytic degradation in Lactococcus lactis Proc Natl Acad Sci USA 92 2244 2248 7892255 10.1073/pnas.92.6.2244 1:CAS:528:DyaK2MXksVCqtbg%3D
5. T Brautaset ON Sekurova H Sletta TE Ellingsen AR Strøm S Valla SB Zotchev 2000 Biosynthesis of the polyene antifungal antibiotic nystatin in Streptomyces noursei ATCC 11455: analysis of the gene cluster and deduction of the biosynthetic pathway Chem Biol 7 395 403 10873841 10.1016/S1074-5521(00) 00120-4 1:CAS:528:DC%2BD3cXktl2nsLk%3D (Pubitemid 30400042)
6. TJ Buchholz TW Geders FE Bartley 3rd KA Reynolds JL Smith DH Sherman 2009 Structural basis for binding specificity between subclasses of modular polyketide synthase docking domains ACS Chem Biol 4 41 52 19146481 10.1021/cb8002607 1:CAS:528:DC%2BD1MXjt1ajsA%3D%3D
7. Caboche S, Pupin M, Leclère V, Fontaine A, Jacques P, Kucherov G (2008) NORINE: a database of nonribosomal peptides. Nucleic Acids Res 36(Database issue):D326-D331
8. P Caffrey S Lynch E Flood S Finnan M Oliynyk 2001 Amphotericin biosynthesis in Streptomyces nodosus: deductions from analysis of polyketide synthase and late genes Chem Biol 8 713 723 11451671 10.1016/S1074-5521(01) 00046-1 1:CAS:528:DC%2BD3MXltVGju7s%3D (Pubitemid 32632537)
9. YA Chan AM Podevels BM Kevanya MG Thomas 2009 Biosynthesis of polyketide synthase extender units Nat Prod Rep 26 90 114 19374124 10.1039/b801658p 1:CAS:528:DC%2BD1cXhsFWju7vJ
10. CW Chen CH Huang HH Lee HH Tsai R Kirby 2002 Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes Trends Genet 18 522 529 12350342 10.1016/S0168-9525(02)02752-X 1:CAS:528:DC%2BD38Xnt1CqsLY%3D (Pubitemid 35287027)
11. A Datta M Hendrix M Lipsitch S Jinks-Robertson 1997 Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast Proc Natl Acad Sci USA 94 9757 9762 9275197 10.1073/pnas.94.18.9757 1:CAS:528:DyaK2sXlvVWhu7o%3D (Pubitemid 27408136)
12. D Denapaite A Paravić Radičević B Čajavec IS Hunter D Hranueli J Cullum 2005 Persistence of the chromosome end regions at low copy number in mutant strains of Streptomyces rimosus and S. lividans Food Technol Biotechnol 43 9 17 1:CAS:528:DC%2BD2MXktFGgsL8%3D (Pubitemid 40422154)
13. S Donadio P Monciardini M Sosio 2007 Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics Nat Prod Rep 24 1073 1109 17898898 10.1039/b514050c 1:CAS:528:DC%2BD2sXht1ygt7vP (Pubitemid 47493391)
14. S Egan P Wiener D Kallifidas EM Wellington 2001 Phylogeny of Streptomyces species and evidence for horizontal transfer of entire and partial antibiotic gene clusters Antonie Van Leeuwenhoek 79 127 133 11519998 10.1023/A: 1010296220929 1:CAS:528:DC%2BD3MXmslWkt7w%3D (Pubitemid 32747122)
15. MA Fischbach CT Walsh 2006 Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms Chem Rev 106 3468 3496 16895337 10.1021/cr0503097 1:CAS:528:DC%2BD28XmvFCqurw%3D (Pubitemid 44376945)
16. MA Fischbach CT Walsh J Clardy 2008 The evolution of gene collectives: how natural selection drives chemical innovation Proc Natl Acad Sci USA 105 4601 4608 18216259 10.1073/pnas.0709132105 1:CAS:528:DC%2BD1cXktlSrtrs%3D (Pubitemid 351753784)
17. B Gravius D Glocker J Pigac K Pandža D Hranueli J Cullum 1994 The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its interactions with the chromosome Microbiology 140 2271 2277 7952179 10.1099/13500872-140-9-2271 1:CAS:528:DyaK2cXmsVOrsrc%3D (Pubitemid 24297031)
18. DA Hopwood 2006 Soil to genomics: the Streptomyces chromosome Annu Rev Genet 40 1 23 16761950 10.1146/annurev.genet.40.110405.090639 1:CAS:528:DC%2BD2sXnslGq (Pubitemid 44956777)
19. D Hranueli J Cullum B Basrak P Goldstein PF Long 2005 Plasticity of the Streptomyces genome-evolution and engineering of new antibiotics Curr Med Chem 12 1697 1704 16022666 10.2174/0929867054367176 1:CAS:528:DC%2BD2MXlsFerurY%3D (Pubitemid 40895009)
20. TW Huang CW Chen 2006 A recA null mutation may be generated in Streptomyces coelicolor J Bacteriol 188 6771 6779 16980478 10.1128/JB.00951-06 1:CAS:528:DC%2BD28XhtVCgs7nF (Pubitemid 44497888)
21. H Jenke-Kodama E Dittmann 2009 Bioinformatic perspectives on NRPS/PKS megasynthases: advances and challenges Nat Prod Rep 26 874 883 19554239 10.1039/b810283j 1:CAS:528:DC%2BD1MXns1Srsrw%3D
22. AT Keatinge-Clay 2007 A tylosin ketoreductase reveals how chirality is determined in polyketides Chem Biol 14 898 908 17719489 10.1016/j.chembiol.2007. 07.009 1:CAS:528:DC%2BD2sXpsFehsrk%3D (Pubitemid 47268779)
23. C Khosla S Kapur DE Cane 2009 Revisiting the modularity of modular polyketide synthases Curr Opin Chem Biol 13 135 143 19217343 10.1016/j.cbpa.2008.12.018 1:CAS:528:DC%2BD1MXlsVektr0%3D
24. H Kinashi M Shimaji-Murayama T Hanafusa 1992 Integration of SCP1, a giant linear plasmid, into the Streptomyces coelicolor chromosome Gene 115 35 41 1319377 10.1016/0378-1119(92)90537-Y 1:CAS:528:DyaK38XltVGluro%3D
25. K Kurosawa I Ghiviriga TG Sambandan PA Lessard JE Barbara C Rha AJ Sinskey 2008 Rhodostreptomycins, antibiotics biosynthesized following horizontal gene transfer from Streptomyces padanus to Rhodococcus fascians J Am Chem Soc 130 1126 1127 18179219 10.1021/ja077821p 1:CAS:528:DC%2BD1cXivFyqtA%3D%3D (Pubitemid 351170977)
26. S Mochizuki K Hiratsu M Suwa T Ishii F Sugino K Yamada H Kinashi 2003 The large linear plasmid pSLA2-L of Streptomyces rochei has an unusually condensed gene organization for secondary metabolism Mol Microbiol 48 1501 1510 12791134 10.1046/j.1365-2958.2003.03523.x 1:CAS:528:DC%2BD3sXkvFCmtLs%3D (Pubitemid 36751057)
27. Y Nakamura Y Nishio K Ikeo T Gojobori 2003 The genome stability in Corynebacterium species due to lack of the recombinational repair system Gene 317 149 155 14604803 10.1016/S0378-1119(03)00653-X 1:CAS:528: DC%2BD3sXosFyis74%3D (Pubitemid 37356929)
28. 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 5420325 10.1016/0022-2836(70)90057-4 1:CAS:528:DyaE3cXktVShu74%3D
29. S Pandza G Biuković A Paravić A Dadbin J Cullum D Hranueli 1998 Recombination between the linear plasmid pPZG101 and the linear chromosome of Streptomyces rimosus can lead to exchange of ends Mol Microbiol 28 1165 1176 9680206 10.1046/j.1365-2958.1998.00877.x 1:CAS:528:DyaK1cXktl2jt7c%3D (Pubitemid 28293540)
30. EP Rocha E Cornet B Michel 2005 Comparative and evolutionary analysis of the bacterial homologous recombination systems PLoS Genet 1 e15 16132081 10.1371/journal.pgen.0010015
31. ES Sattely MA Fischbach CT Walsh 2008 Total biosynthesis: in vitro reconstitution of polyketide and nonribosomal peptide pathways Nat Prod Rep 25 757 793 18663394 10.1039/b801747f 1:CAS:528:DC%2BD1cXptVCms74%3D
32. P Shen HV Huang 1986 Homologous recombination in Escherichia coli: dependence on substrate length and homology Genetics 112 441 457 3007275 1:CAS:528:DyaL28XhsVaqt7g%3D
33. A Starcevic J Cullum M Jaspars D Hranueli PF Long 2007 Predicting the nature and timing of epimerisation on a modular polyketide synthase Chembiochem 8 28 31 17133646 10.1002/cbic.200600399 1:CAS:528:DC%2BD2sXhtFCnu7k%3D (Pubitemid 46121566)
34. A Starcevic J Zucko J Simunkovic PF Long J Cullum D Hranueli 2008 ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures Nucleic Acids Res 36 6882 6892 18978015 10.1093/nar/gkn685 1:CAS:528:DC%2BD1cXhsVCgtrnL
35. R Uno Y Nakayama K Arakawa M Tomita 2000 The orientation bias of Chi sequences is a general tendency of G-rich oligomers Gene 259 207 215 11163978 10.1016/S0378-1119(00)00430-3 1:CAS:528:DC%2BD3MXitV2luw%3D%3D (Pubitemid 32119252)
36. M Wei S Wang G Shang 2010 Biosynthetic pathways and engineering for bioactive natural products Curr Org Chem 14 1433 1446 10.2174/138527210791616759 1:CAS:528:DC%2BC3cXhtlCqur3I
37. M Yamasaki H Kinashi 2004 Two chimeric chromosomes of Streptomyces coelicolor A3(2) generated by single crossover of the wild-type chromosome and linear plasmid scp1 J Bacteriol 186 6553 6559 15375137 10.1128/JB.186.19.6553- 6559.2004 1:CAS:528:DC%2BD2cXotVynu7s%3D (Pubitemid 39258138)
38. J Zucko A Starcevic J Diminic M Elbekali M Lisfi PF Long J Cullum D Hranueli 2010 From DNA sequences to chemical structures-methods for mining microbial genomic and metagenomic datasets for new natural products Food Technol Biotechnol 48 234 242 1:CAS:528:DC%2BC3cXpvVKqtL0%3D