메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch

Author keywords

actinobacteria; Erythromycin; Metabolic switch; RNA sequencing; Saccharopolyspora erythraea

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME;

EID: 84872175708     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-15     Document Type: Article
Times cited : (18)

References (51)
  • 1
    • 15744383448 scopus 로고    scopus 로고
    • Regulation of secondary metabolism in streptomycetes
    • Bibb MJ. Regulation of secondary metabolism in streptomycetes. Curr Opin Microbiol 2005, 8(2):208-215.
    • (2005) Curr Opin Microbiol , vol.8 , Issue.2 , pp. 208-215
    • Bibb, M.J.1
  • 3
    • 83155163762 scopus 로고    scopus 로고
    • Toward improvement of erythromycin A production in an industrial Saccharopolyspora erythraea strain via facilitation of genetic manipulation with an artificial attB site for specific recombination
    • Wu J, Zhang Q, Deng W, Qian J, Zhang S, Liu W. Toward improvement of erythromycin A production in an industrial Saccharopolyspora erythraea strain via facilitation of genetic manipulation with an artificial attB site for specific recombination. Appl Environ Microbiol 2011, 77(21):7508-7516.
    • (2011) Appl Environ Microbiol , vol.77 , Issue.21 , pp. 7508-7516
    • Wu, J.1    Zhang, Q.2    Deng, W.3    Qian, J.4    Zhang, S.5    Liu, W.6
  • 4
    • 77954701883 scopus 로고    scopus 로고
    • Quantitative proteomics analysis of Streptomyces coelicolor development demonstrates that onset of secondary metabolism coincides with hypha differentiation
    • Manteca A, Sanchez J, Jung HR, Schwammle V, Jensen ON. Quantitative proteomics analysis of Streptomyces coelicolor development demonstrates that onset of secondary metabolism coincides with hypha differentiation. Mol Cell Proteomics 2010, 9(7):1423-1436.
    • (2010) Mol Cell Proteomics , vol.9 , Issue.7 , pp. 1423-1436
    • Manteca, A.1    Sanchez, J.2    Jung, H.R.3    Schwammle, V.4    Jensen, O.N.5
  • 12
    • 45549088326 scopus 로고    scopus 로고
    • The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
    • Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing. Science 2008, 320(5881):1344-1349.
    • (2008) Science , vol.320 , Issue.5881 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 13
    • 0024276903 scopus 로고
    • When polymerases collide: Replication and the transcriptional organization of the E. coli chromosome
    • Brewer BJ. When polymerases collide: Replication and the transcriptional organization of the E. coli chromosome. Cell 1988, 53(5):679-686.
    • (1988) Cell , vol.53 , Issue.5 , pp. 679-686
    • Brewer, B.J.1
  • 14
    • 33845653671 scopus 로고    scopus 로고
    • Soil to genomics: the Streptomyces chromosome
    • Hopwood DA. Soil to genomics: the Streptomyces chromosome. Annu Rev Genet 2006, 40:1-23.
    • (2006) Annu Rev Genet , vol.40 , pp. 1-23
    • Hopwood, D.A.1
  • 16
  • 17
    • 84859768479 scopus 로고    scopus 로고
    • Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
    • Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 2012, 28(8):1086-1092.
    • (2012) Bioinformatics , vol.28 , Issue.8 , pp. 1086-1092
    • Schulz, M.H.1    Zerbino, D.R.2    Vingron, M.3    Birney, E.4
  • 18
    • 34547582418 scopus 로고    scopus 로고
    • CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
    • Kong L, Zhang Y, Ye Z-Q, Liu X-Q, Zhao S-Q, Wei L, Gao G. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 2007, 35(suppl 2):W345-W349.
    • (2007) Nucleic Acids Res , vol.35 , Issue.SUPPL. 2
    • Kong, L.1    Zhang, Y.2    Ye, Z.-Q.3    Liu, X.-Q.4    Zhao, S.-Q.5    Wei, L.6    Gao, G.7
  • 20
    • 32644436271 scopus 로고    scopus 로고
    • Cytological and biochemical evidence for an early cell dismantling event in surface cultures of Streptomyces antibioticus
    • Manteca A, Fernandez M, Sanchez J. Cytological and biochemical evidence for an early cell dismantling event in surface cultures of Streptomyces antibioticus. Res Microbiol 2006, 157(2):143-152.
    • (2006) Res Microbiol , vol.157 , Issue.2 , pp. 143-152
    • Manteca, A.1    Fernandez, M.2    Sanchez, J.3
  • 21
    • 84875803284 scopus 로고    scopus 로고
    • The transcriptome of Streptomyces coelicolor: RNA-seq and RNA immunoprecipitation identify substrates for RNase III
    • Published ahead of print
    • Gatewood ML, Bralley P, Weil MR, Jones GH. The transcriptome of Streptomyces coelicolor: RNA-seq and RNA immunoprecipitation identify substrates for RNase III. J Bacteriol 2012, Published ahead of print.
    • (2012) J Bacteriol
    • Gatewood, M.L.1    Bralley, P.2    Weil, M.R.3    Jones, G.H.4
  • 22
    • 77949376180 scopus 로고    scopus 로고
    • RNA degradation and the regulation of antibiotic synthesis in Streptomyces
    • Jones GH. RNA degradation and the regulation of antibiotic synthesis in Streptomyces. Future Microbiol 2010, 5(3):419-429.
    • (2010) Future Microbiol , vol.5 , Issue.3 , pp. 419-429
    • Jones, G.H.1
  • 23
    • 77956281182 scopus 로고    scopus 로고
    • Structural and operational complexity of the Geobacter sulfurreducens genome
    • Qiu Y, Cho BK, Park YS, Lovley D, Palsson BO, Zengler K. Structural and operational complexity of the Geobacter sulfurreducens genome. Genome Res 2010, 20(9):1304-1311.
    • (2010) Genome Res , vol.20 , Issue.9 , pp. 1304-1311
    • Qiu, Y.1    Cho, B.K.2    Park, Y.S.3    Lovley, D.4    Palsson, B.O.5    Zengler, K.6
  • 24
    • 84855475577 scopus 로고    scopus 로고
    • Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site
    • Hatoum-Aslan A, Maniv I, Marraffini LA. Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site. Proc Natl Acad Sci U S A 2011, 108(52):21218-21222.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , Issue.52 , pp. 21218-21222
    • Hatoum-Aslan, A.1    Maniv, I.2    Marraffini, L.A.3
  • 26
    • 83355162664 scopus 로고    scopus 로고
    • Signals and regulators that govern Streptomyces development
    • McCormick JR, Flärdh K. Signals and regulators that govern Streptomyces development. FEMS Microbiol Rev 2012, 36:1.
    • (2012) FEMS Microbiol Rev , vol.36 , pp. 1
    • McCormick, J.R.1    Flärdh, K.2
  • 27
    • 77957345958 scopus 로고    scopus 로고
    • Regulation of a novel gene cluster involved in secondary metabolite production in Streptomyces coelicolor
    • Hindra, Pak P, Elliot MA. Regulation of a novel gene cluster involved in secondary metabolite production in Streptomyces coelicolor. J Bacteriol 2010, 192(19):4973-4982.
    • (2010) J Bacteriol , vol.192 , Issue.19 , pp. 4973-4982
    • Hindra1    Pak, P.2    Elliot, M.A.3
  • 28
    • 75149138294 scopus 로고    scopus 로고
    • Regulation of morphological differentiation in S. coelicolor by RNase III (AbsB) cleavage of mRNA encoding the AdpA transcription factor
    • Xu W, Huang J, Lin R, Shi J, Cohen SN. Regulation of morphological differentiation in S. coelicolor by RNase III (AbsB) cleavage of mRNA encoding the AdpA transcription factor. Mol Microbiol 2010, 75(3):781-791.
    • (2010) Mol Microbiol , vol.75 , Issue.3 , pp. 781-791
    • Xu, W.1    Huang, J.2    Lin, R.3    Shi, J.4    Cohen, S.N.5
  • 32
    • 84863895769 scopus 로고    scopus 로고
    • Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae
    • Harigaya Y, Parker R. Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2012, 109(29):11764-11769.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , Issue.29 , pp. 11764-11769
    • Harigaya, Y.1    Parker, R.2
  • 34
    • 57349093477 scopus 로고    scopus 로고
    • The endonuclease activity of RNase III is required for the regulation of antibiotic production by Streptomyces coelicolor
    • Gravenbeek ML, Jones GH. The endonuclease activity of RNase III is required for the regulation of antibiotic production by Streptomyces coelicolor. Microbiology 2008, 154(Pt 11):3547-3555.
    • (2008) Microbiology , vol.154 , Issue.PART 11 , pp. 3547-3555
    • Gravenbeek, M.L.1    Jones, G.H.2
  • 35
    • 84857157480 scopus 로고    scopus 로고
    • PpGpp magic beyond RNA polymerase
    • Dalebroux ZD, Swanson MS. ppGpp magic beyond RNA polymerase. Nat Rev Microbiol 2012, 10(3):203-212.
    • (2012) Nat Rev Microbiol , vol.10 , Issue.3 , pp. 203-212
    • Dalebroux, Z.D.1    Swanson, M.S.2
  • 36
    • 77956533718 scopus 로고    scopus 로고
    • (p)ppGpp inhibits polynucleotide phosphorylase from streptomyces but not from Escherichia coli and increases the stability of bulk mRNA in Streptomyces coelicolor
    • Gatewood ML, Jones GH. (p)ppGpp inhibits polynucleotide phosphorylase from streptomyces but not from Escherichia coli and increases the stability of bulk mRNA in Streptomyces coelicolor. J Bacteriol 2010, 192(17):4275-4280.
    • (2010) J Bacteriol , vol.192 , Issue.17 , pp. 4275-4280
    • Gatewood, M.L.1    Jones, G.H.2
  • 37
    • 77954837414 scopus 로고    scopus 로고
    • Guanosine 5'-diphosphate 3'-diphosphate (ppGpp) as a negative modulator of polynucleotide phosphorylase activity in a 'rare' actinomycete
    • Siculella L, Damiano F, di Summa R, Tredici SM, Alduina R, Gnoni GV, Alifano P. Guanosine 5'-diphosphate 3'-diphosphate (ppGpp) as a negative modulator of polynucleotide phosphorylase activity in a 'rare' actinomycete. Mol Microbiol 2010, 77(3):716-729.
    • (2010) Mol Microbiol , vol.77 , Issue.3 , pp. 716-729
    • Siculella, L.1    Damiano, F.2    di Summa, R.3    Tredici, S.M.4    Alduina, R.5    Gnoni, G.V.6    Alifano, P.7
  • 38
    • 64949203863 scopus 로고    scopus 로고
    • Phenotypes and gene expression profiles of Saccharopolyspora erythraea rifampicin-resistant (rif) mutants affected in erythromycin production
    • Carata E, Peano C, Tredici SM, Ferrari F, Tala A, Corti G, Bicciato S, De Bellis G, Alifano P. Phenotypes and gene expression profiles of Saccharopolyspora erythraea rifampicin-resistant (rif) mutants affected in erythromycin production. Microb Cell Fact 2009, 8:18.
    • (2009) Microb Cell Fact , vol.8 , pp. 18
    • Carata, E.1    Peano, C.2    Tredici, S.M.3    Ferrari, F.4    Tala, A.5    Corti, G.6    Bicciato, S.7    De Bellis, G.8    Alifano, P.9
  • 39
    • 84867574100 scopus 로고    scopus 로고
    • Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production
    • Licona-Cassani C, Marcellin E, Quek LE, Jacob S, Nielsen LK. Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production. Antonie Van Leeuwenhoek 2012, 102(3):493-502.
    • (2012) Antonie Van Leeuwenhoek , vol.102 , Issue.3 , pp. 493-502
    • Licona-Cassani, C.1    Marcellin, E.2    Quek, L.E.3    Jacob, S.4    Nielsen, L.K.5
  • 40
    • 36849034573 scopus 로고    scopus 로고
    • Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy
    • Hu G, Llinas M, Li J, Preiser PR, Bozdech Z. Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350.
    • (2007) BMC Bioinformatics , vol.8 , pp. 350
    • Hu, G.1    Llinas, M.2    Li, J.3    Preiser, P.R.4    Bozdech, Z.5
  • 41
    • 84875805352 scopus 로고    scopus 로고
    • DSN Normalization Sample Prep Guide
    • DSN Normalization Sample Prep Guide Pilot Release DSN Normalization Sample Prep Guide.
    • Pilot Release
  • 42
    • 80053019485 scopus 로고    scopus 로고
    • Regulation by Small RNAs in Bacteria: Expanding Frontiers
    • Storz G, Vogel J, Wassarman Karen M. Regulation by Small RNAs in Bacteria: Expanding Frontiers. Mol Cell 2011, 43(6):880-891.
    • (2011) Mol Cell , vol.43 , Issue.6 , pp. 880-891
    • Storz, G.1    Vogel, J.2    Wassarman Karen, M.3
  • 43
    • 84875809907 scopus 로고    scopus 로고
    • Directional mRNA-Seq Library Prep
    • Directional mRNA-Seq Library Prep Pre-Release Protocol Directional mRNA-Seq Library Prep.
    • Pre-Release Protocol
  • 45
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760.
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 46
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25.
    • (2009) Genome Biol , vol.10 , Issue.3
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.4
  • 47
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359.
    • (2012) Nat Methods , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 50
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    • Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010, 11:94.
    • (2010) BMC Bioinformatics , vol.11 , pp. 94
    • Bullard, J.H.1    Purdom, E.2    Hansen, K.D.3    Dudoit, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.