The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island

Genome Biology and Evolution

Volumn 5, Issue 6, 2013, Pages 1165-1175

  Cruz Morales, Pablo ^a   Vijgenboom, Erik ^b   Iruegas Bocardo, Fernanda ^a   Girard, Geneviève ^b   Yáñez Guerra, Luis Alfonso ^a   Ramos Aboites, Hilda E ^a   Pernodet, Jean Luc ^c   Anné, Jozef ^d   Van Wezel, Gilles P ^b   Barona Gómez, Francisco ^a  

^a DEPARTAMENTO DE FÍSICA   (Mexico)

^b LEIDEN UNIVERSITY   (Netherlands)

^c UNIVERSITÉ PARIS SACLAY   (France)

^d REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

Author keywords

Bacterial next generation genome sequencing; Copper homeostasis; L F trna transferase; Peptide biosynthesis; Streptomyces comparative genomics

Indexed keywords

BACTERIAL RNA; COPPER; PEPTIDE; TRANSFER RNA;

BACTERIAL GENOME; GENE EXPRESSION REGULATION; GENETICS; GENOMIC ISLAND; METABOLISM; PROTEIN SYNTHESIS; STREPTOMYCES COELICOLOR; STREPTOMYCES LIVIDANS; ARTICLE; BACTERIAL NEXT-GENERATION GENOME SEQUENCING; COPPER HOMEOSTASIS; L/F TRNA TRANSFERASE; PEPTIDE SYNTHESIS; STREPTOMYCES COMPARATIVE GENOMICS;

COPPER; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; GENOMIC ISLANDS; PEPTIDES; PROTEIN BIOSYNTHESIS; RNA, BACTERIAL; RNA, TRANSFER; STREPTOMYCES COELICOLOR; STREPTOMYCES LIVIDANS;

BACTERIAL NEXT-GENERATION GENOME SEQUENCING; COPPER HOMEOSTASIS; L/F TRNA TRANSFERASE; PEPTIDE BIOSYNTHESIS; STREPTOMYCES COMPARATIVE GENOMICS;

EID: 84891598612     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt082     Document Type: Article

References (56)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
2. Anné J, et al. 2012. Recombinant protein production and streptomycetes. J Biotechnol. 158(4):159-167.
3. Aziz RK, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75.
4. Bachmann BO, Ravel J. 2009. Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods Enzymol. 458:181-217.
5. Bentley SD, et al. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417 (6885):141-147.
6. Blundell KL, Wilson MT, Svistunenko DA, Vijgenboom E, Worrall JA. 2013. Morphological development and cytochrome c oxidase activity in Streptomyces lividans are dependent on the action of a copper bound Sco protein. Open Biol. 3:120163.
7. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27(4):578-579.
8. Carver TJ, et al. 2005. ACT: the Artemis Comparison Tool. Bioinformatics 21(16):3422-3423.
9. Challis GL. 2008. Mining microbial genomes for new natural products and biosynthetic pathways. Microbiology 154(Pt 6):1555-1569.
10. Chen CW, Yu TW, Lin YS, Kieser HM, Hopwood DA. 1993. The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule. Mol Microbiol. 7(6):925-932.
11. D'Huys PJ, et al. 2012. Genome-scale metabolic flux analysis of Streptomyces lividans growing on a complex medium. J Biotechnol. 161(1):1-13.
12. Dwarakanath S, et al. 2012. Response to copper stress in Streptomyces lividans extends beyond genes under direct control of a copper-sensitive operon repressor protein (CsoR). J Biol Chem. 287(21):17833-17847.
13. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797.
14. Eichenseer C, Altenbuchner J. 1994. The very large amplifiable element AUD2 from Streptomyces lividans 66 has insertion sequence-like repeats at its ends. J Bacteriol. 176(22):7107-7112.
15. Fung AW, et al. 2011. An alternative mechanism for the catalysis of peptide bond formation by L/F transferase: substrate binding and orientation. J Mol Biol. 409(4):617-629.
16. Garg RP, Qian XL, Alemany LB, Moran S, Parry RJ. 2008. Investigations of valanimycin biosynthesis: elucidation of the role of seryl-tRNA. Proc Natl Acad Sci U S A. 105(18):6543-6547.
17. Gondry M, et al. 2009. Cyclodipeptide synthases are a family of tRNA-dependent peptide bond-forming enzymes. Nat Chem Biol. 5(6):414-420.
18. Hänel F, Krügel H, Fiedler G. 1989. Arsenical resistance of growth and phosphate control of antibiotic biosynthesis in Streptomyces. J Gen Microbiol. 135(3):583-591.
19. Hodgson DA. 2000. Primary metabolism and its control in streptomycetes: a most unusual group of bacteria. Adv Microb Physiol. 42:47-238.
20. Hopwood DA. 1999. Forty years of genetics with Streptomyces: from in vivo through in vitro to in silico. Microbiology 145(9):2183-2202.
21. Hopwood DA, Kieser T, Wright HM, Bibb MJ. 1983. Plasmids, recombination and chromosome mapping in Streptomyces lividans 66. J Gen Microbiol. 129(7):2257-2269.
22. Huang CH, et al. 2003. Linear plasmid SLP2 of Streptomyces lividans is a composite replicon. Mol Microbiol. 47(6):1563-1576.
23. Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
24. Husemann P, Stoye J. 2010. R2cat: Synteny plots and comparative assembly. Bioinformatics 26(4):570-571.
25. Jayapal KP, Lian W, Glod F, Sherman DH, Hu WS. 2007. Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans. BMC Genomics 8:229.
26. Keijser BJ, van Wezel GP, Canters GW, Kieser T, Vijgenboom E. 2000. The ram-dependence of Streptomyces lividans differentiation is bypassed by copper. J Mol Microbiol Biotechnol. 2:565-574.
27. Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA. 2000. Practical Streptomyces genetics. Norwich (UK): John Innes Foundation. p. 427-430.
28. Kinashi H. 2011. Giant linear plasmids in Streptomyces: a treasure trove of antibiotic biosynthetic clusters. J Antibiot (Tokyo). 64(1):19-25.
29. Koren S, et al. 2012. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol. 30(7):693-700.
30. Leibowitz MJ, Soffer RL. 1969. A soluble enzyme from Escherichia coli which catalyzes the transfer of leucine and phenylalanine from tRNA to acceptor proteins. Biochem Biophys Res Commun. 36(1):47-53.
31. Lewis RA, et al. 2010. Metabolic and evolutionary insights into the closelyrelated species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization. BMC Genomics 11:682.
32. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760.
33. Li H, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078-2079.
34. Li Y, Weissman KJ, Müller R. 2008. Myxochelin biosynthesis: direct evidence for two- and four-electron reduction of a carrier protein-bound thioester. J Am Chem Soc. 130(24):7554-7555.
35. Lin Y, et al. 2011. Draft genome of Streptomyces zinciresistens K42, a novel metal-resistant species isolated from copper-zinc mine tailings. J Bacteriol. (22): 6408-6409.
36. Lin YB. 2011. Streptomyces zinciresistens sp. nov., a zinc-resistant actinomycete isolated from soil from a copper and zinc mine. Int J Syst Evol Microbiol. 61(Pt 3):616-620.
37. Medema MH, et al. 2010. The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol Evol. 2:212-224.
38. Myers EW, et al. 2000. A whole-genome assembly of Drosophila. Science 287(5461):2196-2204.
39. Nakahara H, et al. 1985. Mercuric reductase enzymes from Streptomyces species and group B Streptococcus. J Gen Microbiol. 131(5):1053-1059.
40. Price-Whelan A, Dietrich LE, Newman DK. 2006. Rethinking "secondary" metabolism: physiological roles for phenazine antibiotics. Nat Chem Biol. 2(2):71-78.
41. Ravel J, Schrempf H, Hill RT. 1998. Mercury resistance is encoded by transferable giant linear plasmids in two Chesapeake bay Streptomyces strains. Appl Environ Microbiol. 64(9):3383-3388.
42. Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A. 106(45):19126-19131.
43. Rodríguez-Montelongo L, Volentini SI, Farías RN, Massa EM, Rapisarda VA. 2006. The Cu (II)-reductase NADH dehydrogenase-2 of Escherichia coli improves the bacterial growth in extreme copper concentrations and increases the resistance to the damage caused by copper and hydroperoxide. Arch Biochem Biophys. 451(1):1-7.
44. Sales CM, et al. 2011. Genome sequence of the 1, 4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190. J Bacteriol. 193(17):4549-4550.
45. Schwedock J, McCormick JR, Angert ER, Nodwell JR, Losick R. 1997. Assembly of the cell division protein FtsZ into ladder-like structures in the aerial hyphae of Streptomyces coelicolor. Mol Microbiol. 25(5):847-858.
46. Sedlmeier R, Altenbuchner J. 1992. Cloning and DNA sequence analysis of the mercury resistance genes of Streptomyces lividans. Mol Gen Genet. 236(1):76-85.
47. Tsai IJ, Otto TD, Berriman M. 2010. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol. 11(4):R41.
48. van Wezel GP, McDowall KJ. 2011. The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. Nat Prod Rep. 28(7):1311-1333.
49. Volff JN, Altenbuchner J. 1997. High-frequency transposition of IS1373, the insertion sequence delimiting the amplifiable element AUD2 of Streptomyces lividans. J Bacteriol. 179(17):5639-5642.
50. Wang L, et al. 2006. arsRBOCT arsenic resistance system encoded by linear plasmid pHZ227 in Streptomyces sp. Strain FR-008. Appl Environ Microbiol. 72(5):3738-3742.
51. Watanabe K, et al. 2007. Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase. Nature 449(7164):867-871.
52. Weaver D, et al. 2004. Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S.coelicolor A3(2) chromosome. Mol Microbiol. 51 (6):1535-1550.
53. Worrall JA, Vijgenboom E. 2010. Copper mining in Streptomyces: enzymes, natural products and development. Nat Prod Rep. 27(5):742-756.
54. Yim G, Wang HH, Davies J. 2007. Antibiotics as signalling molecules. Philos Trans R Soc Lond B Biol Sci. 362(1483):1195-1200.
55. Zhang W, Ntai I, Kelleher NL, Walsh CT. 2011. tRNA-dependent peptide bond formation by the transferase PacB in biosynthesis of the pacidamycin group of pentapeptidyl nucleoside antibiotics. Proc Natl Acad Sci U S A. 108(30):12249-12253.
56. Zhou X, et al. 2005. A novel DNA modification by sulphur. Mol Microbiol. 57(5):1428-1438.