[논문]Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes

Lee, Yongjae; Lee, Namil; Hwang, Soonkyu; Kim, Woori; Jeong, Yujin; Cho, Suhyung; Palsson, Bernhard O.; Cho, Byung-Kwan

doi:10.1038/s41597-020-00775-w

[해외논문] Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes 원문보기

Scientific data, v.7 = v.7 no.1, 2020년, pp.436 -

Lee, Yongjae (Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141 Republic of Korea) , Lee, Namil (Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141 Republic of Korea) , Hwang, Soonkyu (Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141 Republic of Korea) , Kim, Woori (Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141 Republic of Korea) , Jeong, Yujin (Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141 Republic of Korea) , Cho, Suhyung (Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141 Republic of Korea) , Palsson, Bernhard O. (Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA) , Cho, Byung-Kwan (Department of Biologi)

Abstract ▼ AI-Helper

Streptomyces species are gram-positive bacteria with GC-rich linear genomes and they serve as dominant reservoirs for producing clinically and industrially important secondary metabolites. Genome mining of Streptomyces revealed that each Streptomyces species typically encodes 20–50 secondary metabolite biosynthetic gene clusters (smBGCs), emphasizing their potential for novel compound discovery. Unfortunately, most of smBGCs are uncharacterized in terms of their products and regulation since they are silent under laboratory culture conditions. To translate the genomic potential of Streptomyces to practical applications, it is essential to understand the complex regulation of smBGC expression and to identify the underlying regulatory elements. To progress towards these goals, we applied two Next-Generation Sequencing methods, dRNA-Seq and Term-Seq, to industrially relevant Streptomyces species to reveal the 5´ and 3´ boundaries of RNA transcripts on a genome scale. This data provides a fundamental resource to aid our understanding of Streptomyces’ regulation of smBGC expression and to enhance their potential for secondary metabolite synthesis.Measurement(s)5´-ends of transcripts • 3´-ends of transcripts • RNA • TSS • transcription_termination_signalTechnology Type(s)dRNA-Seq • Term-Seq • RNA sequencingFactor Type(s)Streptomyces growth phaseSample Characteristic - OrganismStreptomyces avermitilis • Streptomyces clavuligerus • Streptomyces coelicolor • Streptomyces griseus • Streptomyces lividans • Streptomyces tsukubensis • Streptomyces venezuelaeMachine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13259393

참고문헌 (43)

1. Berdy J Bioactive microbial metabolites J Antibiot 2005 58 1 26 10.1038/ja.2005.1

상세보기
2. Demain AL Pharmaceutically active secondary metabolites of microorganisms Appl Microbiol Biotechnol 1999 52 455 463 10.1007/s002530051546 10570792

상세보기
3. Demain AL From natural products discovery to commercialization: a success story J Ind Microbiol Biotechnol 2006 33 486 495 10.1007/s10295-005-0076-x 16402247

상세보기
4. Silver LL Challenges of antibacterial discovery Clin Microbiol Rev 2011 24 71 109 10.1128/CMR.00030-10 21233508

상세보기
5. Bentley SD Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) Nature 2002 417 141 147 10.1038/417141a 12000953

상세보기
6. Nett M Ikeda H Moore BS Genomic basis for natural product biosynthetic diversity in the actinomycetes Nat Prod Rep 2009 26 1362 1384 10.1039/b817069j 19844637

상세보기
7. Ventola CL The antibiotic resistance crisis: part 1: causes and threats P T 2015 40 277 283 25859123
8. Challis GL Hopwood DA Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species Proc Natl Acad Sci USA 2003 100 Suppl 2 14555 14561 10.1073/pnas.1934677100 12970466

상세보기
9. Bibb MJ Regulation of secondary metabolism in streptomycetes Curr Opin Microbiol 2005 8 208 215 10.1016/j.mib.2005.02.016 15802254

상세보기
10. Bursy J Synthesis and uptake of the compatible solutes ectoine and 5-hydroxyectoine by Streptomyces coelicolor A3(2) in response to salt and heat stresses Appl Environ Microbiol 2008 74 7286 7296 10.1128/AEM.00768-08 18849444

상세보기
11. Lee, N. et al . Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus. ISME J , 10.1038/s41396-020-0594-6 (2020).
12. Bervoets I Charlier D Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology FEMS Microbiol Rev 2019 43 304 339 10.1093/femsre/fuz001 30721976

상세보기
13. Browning DF Busby SJ The regulation of bacterial transcription initiation Nat Rev Microbiol 2004 2 57 65 10.1038/nrmicro787 15035009

상세보기
14. Cho BK The transcription unit architecture of the Escherichia coli genome Nat Biotechnol 2009 27 1043 1049 10.1038/nbt.1582 19881496

상세보기
15. Dar D Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria Science 2016 352 aad9822 10.1126/science.aad9822 27120414

상세보기
16. Hwang S Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome Nucleic Acids Res 2019 47 6114 6129 10.1093/nar/gkz471 31131406

상세보기
17. Lee Y The Transcription Unit Architecture of Streptomyces lividans TK24 Front Microbiol 2019 10 2074 10.3389/fmicb.2019.02074 31555254

상세보기
18. Burg RW Avermectins, new family of potent anthelmintic agents: producing organism and fermentation Antimicrob Agents Chemother 1979 15 361 367 10.1128/aac.15.3.361 464561

상세보기
19. Paradkar A Clavulanic acid production by Streptomyces clavuligerus : biogenesis, regulation and strain improvement J Antibiot (Tokyo) 2013 66 411 420 10.1038/ja.2013.26 23612724

상세보기
20. Barreiro C Draft genome of Streptomyces tsukubaensis NRRL 18488, the producer of the clinically important immunosuppressant tacrolimus (FK506) J Bacteriol 2012 194 3756 3757 10.1128/JB.00692-12 22740677

상세보기
21. Waksman SA Streptomycin: background, isolation, properties, and utilization Science 1953 118 259 266 10.1126/science.118.3062.259 13089668

상세보기
22. Myronovskyi M Luzhetskyy A Heterologous production of small molecules in the optimized Streptomyces hosts Nat Prod Rep 2019 36 1281 1294 10.1039/c9np00023b 31453623

상세보기
23. Anne J Vrancken K Van Mellaert L Van Impe, J. & Bernaerts, K. Protein secretion biotechnology in Gram-positive bacteria with special emphasis on Streptomyces lividans Biochim Biophys Acta 2014 1843 1750 1761 10.1016/j.bbamcr.2013.12.023 24412306

상세보기
24. Jeong Y The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2) Nat Commun 2016 7 11605 10.1038/ncomms11605 27251447

상세보기
25. Dar D Sorek R High-resolution RNA 3′-ends mapping of bacterial Rho-dependent transcripts Nucleic Acids Res 2018 46 6797 6805 10.1093/nar/gky274 29669055

상세보기
26. Bailey TL MEME SUITE: tools for motif discovery and searching Nucleic Acids Res 2009 37 W202 208 10.1093/nar/gkp335 19458158

상세보기
27. Shine J Dalgarno L The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites Proc Natl Acad Sci USA 1974 71 1342 1346 10.1073/pnas.71.4.1342 4598299

상세보기
28. Morris DR Geballe AP Upstream open reading frames as regulators of mRNA translation Mol Cell Biol 2000 20 8635 8642 10.1128/mcb.20.23.8635-8642.2000 11073965

상세보기
29. Garst, A. D., Edwards, A. L. & Batey, R. T. Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol 3 , 10.1101/cshperspect.a003533 (2011).
30. Lee, Y. et al . Genome-scale determination of 5′ and 3′ boundaries of RNA transcripts in Streptomyces genomes. figshare 10.6084/m9.figshare.c.5044730 (2020).
31. Lalanne JB Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry Cell 2018 173 749 761 e738 10.1016/j.cell.2018.03.007 29606352

상세보기
32. 2020 NCBI Sequence Read Archive SRP158023
33. 2019 NCBI Sequence Read Archive SRP188290
34. 2019 NCBI Sequence Read Archive SRP103795
35. 2020 European Nucleotide Archive PRJEB40918
36. 2019 European Nucleotide Archive PRJEB31507
37. 2020 European Nucleotide Archive PRJEB36379
38. 2020 NCBI Sequence Read Archive SRX6937123
39. 2020 NCBI Sequence Read Archive SRX6937124
40. 2016 NCBI Sequence Read Archive SRP058830
41. 2019 European Nucleotide Archive PRJEB34219
42. 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 10.1101/gr.8.3.175 9521921

상세보기
43. Blin K antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline Nucleic Acids Res 2019 47 W81 W87 10.1093/nar/gkz310 31032519

상세보기

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