Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology
Fernandes de Brito L, Irla M, Kalinowski J, Wendisch VF (2017)
BMC Genomics 18(1): 846.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Einrichtung
Abstract / Bemerkung
Background
The plant growth promoting rhizobacterium Paenibacillus riograndensis SBR5 is a promising candidate to serve as crop inoculant. Despite its potential in providing environmental and economic benefits, the species P. riograndensis is poorly characterized. Here, we performed for the first time a detailed transcriptome analysis of P. riograndensis SBR5 using RNA-seq technology.
Results
RNA was isolated from P. riograndensis SBR5 cultivated under 15 different growth conditions and combined together in order to analyze an RNA pool representing a large set of expressed genes. The resultant total RNA was used to generate 2 different libraries, one enriched in 5′-ends of the primary transcripts and the other representing the whole transcriptome. Both libraries were sequenced and analyzed to identify the conserved sequences of ribosome biding sites and translation start motifs, and to elucidate operon structures present in the transcriptome of P. riograndensis. Sequence analysis of the library enriched in 5′-ends of the primary transcripts was used to identify 1082 transcription start sites (TSS) belonging to novel transcripts and allowed us to determine a promoter consensus sequence and regulatory sequences in 5′ untranslated regions including riboswitches. A putative thiamine pyrophosphate dependent riboswitch upstream of the thiamine biosynthesis gene thiC was characterized by translational fusion to a fluorescent reporter gene and shown to function in P. riograndensis SBR5.
Conclusions
Our RNA-seq analysis provides insight into the P. riograndensis SBR5 transcriptome at the systems level and will be a valuable basis for differential RNA-seq analysis of this bacterium.
Stichworte
Paenibacillus riograndensis;
RNA sequencing;
Transcriptional start sites;
Promoter motifs;
Ribosome biding sites;
Operon structures;
Thiamine pyrophosphate riboswitch Paenibacillus sonchi
Erscheinungsjahr
2017
Zeitschriftentitel
BMC Genomics
Band
18
Ausgabe
1
Art.-Nr.
846
ISSN
1471-2164
eISSN
1471-2164
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2914662
Zitieren
Fernandes de Brito L, Irla M, Kalinowski J, Wendisch VF. Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology. BMC Genomics. 2017;18(1): 846.
Fernandes de Brito, L., Irla, M., Kalinowski, J., & Wendisch, V. F. (2017). Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology. BMC Genomics, 18(1), 846. doi:10.1186/s12864-017-4235-z
Fernandes de Brito, Luciana, Irla, Marta, Kalinowski, Jörn, and Wendisch, Volker F. 2017. “Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology”. BMC Genomics 18 (1): 846.
Fernandes de Brito, L., Irla, M., Kalinowski, J., and Wendisch, V. F. (2017). Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology. BMC Genomics 18:846.
Fernandes de Brito, L., et al., 2017. Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology. BMC Genomics, 18(1): 846.
L. Fernandes de Brito, et al., “Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology”, BMC Genomics, vol. 18, 2017, : 846.
Fernandes de Brito, L., Irla, M., Kalinowski, J., Wendisch, V.F.: Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology. BMC Genomics. 18, : 846 (2017).
Fernandes de Brito, Luciana, Irla, Marta, Kalinowski, Jörn, and Wendisch, Volker F. “Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology”. BMC Genomics 18.1 (2017): 846.
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2019-09-06T09:18:53Z
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a273ce30c9078819e91a43a683d9dc81
Daten bereitgestellt von European Bioinformatics Institute (EBI)
2 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Function of L-Pipecolic Acid as Compatible Solute in Corynebacterium glutamicum as Basis for Its Production Under Hyperosmolar Conditions.
Pérez-García F, Brito LF, Wendisch VF., Front Microbiol 10(), 2019
PMID: 30858843
Pérez-García F, Brito LF, Wendisch VF., Front Microbiol 10(), 2019
PMID: 30858843
Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq.
Laass S, Monzon VA, Kliemt J, Hammelmann M, Pfeiffer F, Förstner KU, Soppa J., PLoS One 14(4), 2019
PMID: 31039177
Laass S, Monzon VA, Kliemt J, Hammelmann M, Pfeiffer F, Förstner KU, Soppa J., PLoS One 14(4), 2019
PMID: 31039177
72 References
Daten bereitgestellt von Europe PubMed Central.
AUTHOR UNKNOWN, 0
Isolation of bacteria of the genus Paenibacillus from soil and springs of the valley of geysers (Kamchatka)
Andreeva I, Morozov I, Pechurkina N, Morozova O, Ryabchikova E, Saranina I., 2010
Andreeva I, Morozov I, Pechurkina N, Morozova O, Ryabchikova E, Saranina I., 2010
Diversity and plant growth promoting evaluation abilities of bacteria isolated from sugarcane cultivated in the South of Brazil
Beneduzi A, Bruno B. Lisboa , Fernanda Moreira , Jose Ivo Baldani , Luciane Maria P. Passaglia , Luciano K. Vargas , Pedro B. Costa , Rodrigo Favreto ., Agric., Ecosyst. Environ., Appl. Soil Ecol. 63(), 2013
PMID: IND500606026
Beneduzi A, Bruno B. Lisboa , Fernanda Moreira , Jose Ivo Baldani , Luciane Maria P. Passaglia , Luciano K. Vargas , Pedro B. Costa , Rodrigo Favreto ., Agric., Ecosyst. Environ., Appl. Soil Ecol. 63(), 2013
PMID: IND500606026
AUTHOR UNKNOWN, 0
Systematic 16S rRNA gene sequencing of atypical clinical isolates identified 27 new bacterial species associated with humans.
Drancourt M, Berger P, Raoult D., J. Clin. Microbiol. 42(5), 2004
PMID: 15131188
Drancourt M, Berger P, Raoult D., J. Clin. Microbiol. 42(5), 2004
PMID: 15131188
Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus.
Ash C, Priest FG, Collins MD., Antonie Van Leeuwenhoek 64(3-4), 1993
PMID: 8085788
Ash C, Priest FG, Collins MD., Antonie Van Leeuwenhoek 64(3-4), 1993
PMID: 8085788
Comparative genomic analysis of N2-fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes.
Xie JB, Du Z, Bai L, Tian C, Zhang Y, Xie JY, Wang T, Liu X, Chen X, Cheng Q, Chen S, Li J., PLoS Genet. 10(3), 2014
PMID: 24651173
Xie JB, Du Z, Bai L, Tian C, Zhang Y, Xie JY, Wang T, Liu X, Chen X, Cheng Q, Chen S, Li J., PLoS Genet. 10(3), 2014
PMID: 24651173
AUTHOR UNKNOWN, 0
Paenibacillus riograndensis sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Triticum aestivum.
Beneduzi A, Costa PB, Parma M, Melo IS, Bodanese-Zanettini MH, Passaglia LM., Int. J. Syst. Evol. Microbiol. 60(Pt 1), 2009
PMID: 19648317
Beneduzi A, Costa PB, Parma M, Melo IS, Bodanese-Zanettini MH, Passaglia LM., Int. J. Syst. Evol. Microbiol. 60(Pt 1), 2009
PMID: 19648317
Alternative nitrogenase and pseudogenes: unique features of the Paenibacillus riograndensis nitrogen fixation system.
Fernandes Gde C, Trarbach LJ, de Campos SB, Beneduzi A, Passaglia LM., Res. Microbiol. 165(7), 2014
PMID: 24956360
Fernandes Gde C, Trarbach LJ, de Campos SB, Beneduzi A, Passaglia LM., Res. Microbiol. 165(7), 2014
PMID: 24956360
Bach E, Dubal G, Carvalho G, De B, Maria L, Passaglia P., 2016
Complete genome sequence of Paenibacillus riograndensis SBR5(T), a Gram-positive diazotrophic rhizobacterium.
Brito LF, Bach E, Kalinowski J, Ruckert C, Wibberg D, Passaglia LM, Wendisch VF., J. Biotechnol. 207(), 2015
PMID: 25959170
Brito LF, Bach E, Kalinowski J, Ruckert C, Wibberg D, Passaglia LM, Wendisch VF., J. Biotechnol. 207(), 2015
PMID: 25959170
Genomic and transcriptomic analysis of carbohydrate utilization by Paenibacillus sp. JDR-2: systems for bioprocessing plant polysaccharides.
Sawhney N, Crooks C, Chow V, Preston JF, St John FJ., BMC Genomics 17(), 2016
PMID: 26912334
Sawhney N, Crooks C, Chow V, Preston JF, St John FJ., BMC Genomics 17(), 2016
PMID: 26912334
Genome-wide transcriptome profiling of nitrogen fixation in Paenibacillus sp. WLY78.
Shi HW, Wang LY, Li XX, Liu XM, Hao TY, He XJ, Chen SF., BMC Microbiol. 16(), 2016
PMID: 26931570
Shi HW, Wang LY, Li XX, Liu XM, Hao TY, He XJ, Chen SF., BMC Microbiol. 16(), 2016
PMID: 26931570
Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique.
Pfeifer-Sancar K, Mentz A, Ruckert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24341750
Pfeifer-Sancar K, Mentz A, Ruckert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24341750
Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape.
Irla M, Neshat A, Brautaset T, Ruckert C, Kalinowski J, Wendisch VF., BMC Genomics 16(), 2015
PMID: 25758049
Irla M, Neshat A, Brautaset T, Ruckert C, Kalinowski J, Wendisch VF., BMC Genomics 16(), 2015
PMID: 25758049
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.
Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, Croucher NJ, Pickard DJ, Maskell DJ, Parkhill J, Choudhary J, Thomson NR, Dougan G., PLoS Genet. 5(7), 2009
PMID: 19609351
Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, Croucher NJ, Pickard DJ, Maskell DJ, Parkhill J, Choudhary J, Thomson NR, Dougan G., PLoS Genet. 5(7), 2009
PMID: 19609351
Genome sequence of the polymyxin-producing plant-probiotic rhizobacterium Paenibacillus polymyxa E681.
Kim JF, Jeong H, Park SY, Kim SB, Park YK, Choi SK, Ryu CM, Hur CG, Ghim SY, Oh TK, Kim JJ, Park CS, Park SH., J. Bacteriol. 192(22), 2010
PMID: 20851896
Kim JF, Jeong H, Park SY, Kim SB, Park YK, Choi SK, Ryu CM, Hur CG, Ghim SY, Oh TK, Kim JJ, Park CS, Park SH., J. Bacteriol. 192(22), 2010
PMID: 20851896
Complete genome sequence of Paenibacillus polymyxa SC2, a strain of plant growth-promoting Rhizobacterium with broad-spectrum antimicrobial activity.
Ma M, Wang C, Ding Y, Li L, Shen D, Jiang X, Guan D, Cao F, Chen H, Feng R, Wang X, Ge Y, Yao L, Bing X, Yang X, Li J, Du B., J. Bacteriol. 193(1), 2010
PMID: 21037012
Ma M, Wang C, Ding Y, Li L, Shen D, Jiang X, Guan D, Cao F, Chen H, Feng R, Wang X, Ge Y, Yao L, Bing X, Yang X, Li J, Du B., J. Bacteriol. 193(1), 2010
PMID: 21037012
Complete genome sequence of Paenibacillus beijingensis 7188(T) (=DSM 24997(T)), a novel rhizobacterium from jujube garden soil.
Kwak Y, Shin JH., J. Biotechnol. 206(), 2015
PMID: 25937453
Kwak Y, Shin JH., J. Biotechnol. 206(), 2015
PMID: 25937453
Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine.
Sudarsan N, Cohen-Chalamish S, Nakamura S, Emilsson GM, Breaker RR., Chem. Biol. 12(12), 2005
PMID: 16356850
Sudarsan N, Cohen-Chalamish S, Nakamura S, Emilsson GM, Breaker RR., Chem. Biol. 12(12), 2005
PMID: 16356850
Magnesium aminoclay-based transformation of Paenibacillus riograndensis and Paenibacillus polymyxa and development of tools for gene expression.
Brito LF, Irla M, Walter T, Wendisch VF., Appl. Microbiol. Biotechnol. 101(2), 2016
PMID: 27878581
Brito LF, Irla M, Walter T, Wendisch VF., Appl. Microbiol. Biotechnol. 101(2), 2016
PMID: 27878581
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead B, Trapnell C, Pop M, Salzberg SL., Genome Biol. 10(3), 2009
PMID: 19261174
Langmead B, Trapnell C, Pop M, Salzberg SL., Genome Biol. 10(3), 2009
PMID: 19261174
ReadXplorer--visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
PMID: 24790157
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
PMID: 24790157
Infernal 1.1: 100-fold faster RNA homology searches.
Nawrocki EP, Eddy SR., Bioinformatics 29(22), 2013
PMID: 24008419
Nawrocki EP, Eddy SR., Bioinformatics 29(22), 2013
PMID: 24008419
Rfam: updates to the RNA families database.
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18953034
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18953034
Rfam: an RNA family database.
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR., Nucleic Acids Res. 31(1), 2003
PMID: 12520045
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR., Nucleic Acids Res. 31(1), 2003
PMID: 12520045
Proven and potential involvement of vitamins in interactions of plants with plant growth-promoting bacteria—an overview
Palacios OA, Bashan Y, de-Bashan LE., Biol. Fertil. Soils 50(3), 2014
PMID: IND500739177
Palacios OA, Bashan Y, de-Bashan LE., Biol. Fertil. Soils 50(3), 2014
PMID: IND500739177
ARNold: a web tool for the prediction of Rho-independent transcription terminators.
Naville M, Ghuillot-Gaudeffroy A, Marchais A, Gautheret D., RNA Biol 8(1), 2011
PMID: 21282983
Naville M, Ghuillot-Gaudeffroy A, Marchais A, Gautheret D., RNA Biol 8(1), 2011
PMID: 21282983
ViennaRNA Package 2.0.
Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL., Algorithms Mol Biol 6(), 2011
PMID: 22115189
Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL., Algorithms Mol Biol 6(), 2011
PMID: 22115189
Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR.
Ao W, Gaudet J, Kent WJ, Muttumu S, Mango SE., Science 305(5691), 2004
PMID: 15375261
Ao W, Gaudet J, Kent WJ, Muttumu S, Mango SE., Science 305(5691), 2004
PMID: 15375261
WebLogo: a sequence logo generator.
Crooks GE, Hon G, Chandonia JM, Brenner SE., Genome Res. 14(6), 2004
PMID: 15173120
Crooks GE, Hon G, Chandonia JM, Brenner SE., Genome Res. 14(6), 2004
PMID: 15173120
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B., Nat. Methods 5(7), 2008
PMID: 18516045
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B., Nat. Methods 5(7), 2008
PMID: 18516045
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Sambrook J., 2001
Studies on transformation of Escherichia coli with plasmids.
Hanahan D., J. Mol. Biol. 166(4), 1983
PMID: 6345791
Hanahan D., J. Mol. Biol. 166(4), 1983
PMID: 6345791
Nucleotide sequence, expression and transcriptional analysis of the Corynebacterium glutamicum gltA gene encoding citrate synthase.
Eikmanns BJ, Thum-Schmitz N, Eggeling L, Ludtke KU, Sahm H., Microbiology (Reading, Engl.) 140 ( Pt 8)(), 1994
PMID: 7522844
Eikmanns BJ, Thum-Schmitz N, Eggeling L, Ludtke KU, Sahm H., Microbiology (Reading, Engl.) 140 ( Pt 8)(), 1994
PMID: 7522844
Programming biological operating systems: genome design, assembly and activation.
Gibson DG., Nat. Methods 11(5), 2014
PMID: 24781325
Gibson DG., Nat. Methods 11(5), 2014
PMID: 24781325
Riboswitches as antibacterial drug targets.
Blount KF, Breaker RR., Nat. Biotechnol. 24(12), 2006
PMID: 17160062
Blount KF, Breaker RR., Nat. Biotechnol. 24(12), 2006
PMID: 17160062
Complete genome sequence of Bacillus methanolicus MGA3, a thermotolerant amino acid producing methylotroph.
Irla M, Neshat A, Winkler A, Albersmeier A, Heggeset TM, Brautaset T, Kalinowski J, Wendisch VF, Ruckert C., J. Biotechnol. 188(), 2014
PMID: 25152427
Irla M, Neshat A, Winkler A, Albersmeier A, Heggeset TM, Brautaset T, Kalinowski J, Wendisch VF, Ruckert C., J. Biotechnol. 188(), 2014
PMID: 25152427
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts.
Schwientek P, Neshat A, Kalinowski J, Klein A, Ruckert C, Schneiker-Bekel S, Wendler S, Stoye J, Puhler A., J. Biotechnol. 190(), 2014
PMID: 24642337
Schwientek P, Neshat A, Kalinowski J, Klein A, Ruckert C, Schneiker-Bekel S, Wendler S, Stoye J, Puhler A., J. Biotechnol. 190(), 2014
PMID: 24642337
Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes.
Zheng X, Hu GQ, She ZS, Zhu H., BMC Genomics 12(), 2011
PMID: 21749696
Zheng X, Hu GQ, She ZS, Zhu H., BMC Genomics 12(), 2011
PMID: 21749696
The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.
Shine J, Dalgarno L., Proc. Natl. Acad. Sci. U.S.A. 71(4), 1974
PMID: 4598299
Shine J, Dalgarno L., Proc. Natl. Acad. Sci. U.S.A. 71(4), 1974
PMID: 4598299
The influence of ribosome-binding-site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo.
Vellanoweth RL, Rabinowitz JC., Mol. Microbiol. 6(9), 1992
PMID: 1375309
Vellanoweth RL, Rabinowitz JC., Mol. Microbiol. 6(9), 1992
PMID: 1375309
An analysis of initiation codon utilization in the Domain Bacteria - concerns about the quality of bacterial genome annotation.
Villegas A, Kropinski AM., Microbiology (Reading, Engl.) 154(Pt 9), 2008
PMID: 18757789
Villegas A, Kropinski AM., Microbiology (Reading, Engl.) 154(Pt 9), 2008
PMID: 18757789
Compilation and analysis of Escherichia coli promoter DNA sequences.
Hawley DK, McClure WR., Nucleic Acids Res. 11(8), 1983
PMID: 6344016
Hawley DK, McClure WR., Nucleic Acids Res. 11(8), 1983
PMID: 6344016
Effect of mutations in the "extended -10" motif of three Bacillus subtilis sigmaA-RNA polymerase-dependent promoters.
Camacho A, Salas M., J. Mol. Biol. 286(3), 1999
PMID: 10024443
Camacho A, Salas M., J. Mol. Biol. 286(3), 1999
PMID: 10024443
Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA.
Helmann JD., Nucleic Acids Res. 23(13), 1995
PMID: 7630711
Helmann JD., Nucleic Acids Res. 23(13), 1995
PMID: 7630711
The riboswitch control of bacterial metabolism.
Nudler E, Mironov AS., Trends Biochem. Sci. 29(1), 2004
PMID: 14729327
Nudler E, Mironov AS., Trends Biochem. Sci. 29(1), 2004
PMID: 14729327
Riboswitches: the oldest mechanism for the regulation of gene expression?
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS., Trends Genet. 20(1), 2004
PMID: 14698618
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS., Trends Genet. 20(1), 2004
PMID: 14698618
The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria.
Grundy FJ, Henkin TM., Mol. Microbiol. 30(4), 1998
PMID: 10094622
Grundy FJ, Henkin TM., Mol. Microbiol. 30(4), 1998
PMID: 10094622
Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA.
McDaniel BA, Grundy FJ, Artsimovitch I, Henkin TM., Proc. Natl. Acad. Sci. U.S.A. 100(6), 2003
PMID: 12626738
McDaniel BA, Grundy FJ, Artsimovitch I, Henkin TM., Proc. Natl. Acad. Sci. U.S.A. 100(6), 2003
PMID: 12626738
The T box and S box transcription termination control systems.
Grundy FJ, Henkin TM., Front. Biosci. 8(), 2003
PMID: 12456320
Grundy FJ, Henkin TM., Front. Biosci. 8(), 2003
PMID: 12456320
Transcription attenuation: a highly conserved regulatory strategy used by bacteria.
Merino E, Yanofsky C., Trends Genet. 21(5), 2005
PMID: 15851059
Merino E, Yanofsky C., Trends Genet. 21(5), 2005
PMID: 15851059
Comparative genomic analysis of T-box regulatory systems in bacteria.
Vitreschak AG, Mironov AA, Lyubetsky VA, Gelfand MS., RNA 14(4), 2008
PMID: 18359782
Vitreschak AG, Mironov AA, Lyubetsky VA, Gelfand MS., RNA 14(4), 2008
PMID: 18359782
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR., Proc. Natl. Acad. Sci. U.S.A. 101(17), 2004
PMID: 15096624
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR., Proc. Natl. Acad. Sci. U.S.A. 101(17), 2004
PMID: 15096624
Riboswitches in eubacteria sense the second messenger cyclic di-GMP.
Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR., Science 321(5887), 2008
PMID: 18635805
Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR., Science 321(5887), 2008
PMID: 18635805
Structural insights into recognition of c-di-AMP by the ydaO riboswitch.
Gao A, Serganov A., Nat. Chem. Biol. 10(9), 2014
PMID: 25086507
Gao A, Serganov A., Nat. Chem. Biol. 10(9), 2014
PMID: 25086507
Thiamin biosynthesis in prokaryotes.
Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon AP, Taylor S, Campobasso N, Chiu HJ, Kinsland C, Reddick JJ, Xi J., Arch. Microbiol. 171(5), 1999
PMID: 10382260
Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon AP, Taylor S, Campobasso N, Chiu HJ, Kinsland C, Reddick JJ, Xi J., Arch. Microbiol. 171(5), 1999
PMID: 10382260
Novel TPP-riboswitch activators bypass metabolic enzyme dependency.
Lunse CE, Scott FJ, Suckling CJ, Mayer G., Front Chem 2(), 2014
PMID: 25121086
Lunse CE, Scott FJ, Suckling CJ, Mayer G., Front Chem 2(), 2014
PMID: 25121086
Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation.
Chauvier A, Picard-Jean F, Berger-Dancause JC, Bastet L, Naghdi MR, Dube A, Turcotte P, Perreault J, Lafontaine DA., Nat Commun 8(), 2017
PMID: 28071751
Chauvier A, Picard-Jean F, Berger-Dancause JC, Bastet L, Naghdi MR, Dube A, Turcotte P, Perreault J, Lafontaine DA., Nat Commun 8(), 2017
PMID: 28071751
Bacterial antisense RNAs: how many are there, and what are they doing?
Thomason MK, Storz G., Annu. Rev. Genet. 44(), 2010
PMID: 20707673
Thomason MK, Storz G., Annu. Rev. Genet. 44(), 2010
PMID: 20707673
Root exudates as mediators of mineral acquisition in low-nutrient environments
Dakora FD, Phillips DA., 2002
Dakora FD, Phillips DA., 2002
A nomenclature for all signal recognition particle RNAs.
Zwieb C, van Nues RW, Rosenblad MA, Brown JD, Samuelsson T., RNA 11(1), 2005
PMID: 15611297
Zwieb C, van Nues RW, Rosenblad MA, Brown JD, Samuelsson T., RNA 11(1), 2005
PMID: 15611297
Iron deficiency resistance mechanisms enlightened by gene expression analysis in Paenibacillus riograndensis SBR5.
Sperb ER, Tadra-Sfeir MZ, Sperotto RA, Fernandes Gde C, Pedrosa Fde O, de Souza EM, Passaglia LM., Res. Microbiol. 167(6), 2016
PMID: 27130283
Sperb ER, Tadra-Sfeir MZ, Sperotto RA, Fernandes Gde C, Pedrosa Fde O, de Souza EM, Passaglia LM., Res. Microbiol. 167(6), 2016
PMID: 27130283
A single amino acid mutation in Spo0A results in sporulation deficiency of Paenibacillus polymyxa SC2.
Hou X, Yu X, Du B, Liu K, Yao L, Zhang S, Selin C, Fernando WG, Wang C, Ding Y., Res. Microbiol. 167(6), 2016
PMID: 27208661
Hou X, Yu X, Du B, Liu K, Yao L, Zhang S, Selin C, Fernando WG, Wang C, Ding Y., Res. Microbiol. 167(6), 2016
PMID: 27208661
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information.
Sierro N, Makita Y, de Hoon M, Nakai K., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17962296
Sierro N, Makita Y, de Hoon M, Nakai K., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17962296
Kinetics of Nif gene expression in a nitrogen-fixing bacterium.
Poza-Carrion C, Jimenez-Vicente E, Navarro-Rodriguez M, Echavarri-Erasun C, Rubio LM., J. Bacteriol. 196(3), 2013
PMID: 24244007
Poza-Carrion C, Jimenez-Vicente E, Navarro-Rodriguez M, Echavarri-Erasun C, Rubio LM., J. Bacteriol. 196(3), 2013
PMID: 24244007
Changes in gene expression during nitrogen starvation in Anabaena variabilis ATCC 29413.
Wealand JL, Myers JA, Hirschberg R., J. Bacteriol. 171(3), 1989
PMID: 2493442
Wealand JL, Myers JA, Hirschberg R., J. Bacteriol. 171(3), 1989
PMID: 2493442
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