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: 846.

Download
OA 1.17 MB
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Volltext vorhanden für diesen Nachweis
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.
Erscheinungsjahr
Zeitschriftentitel
BMC Genomics
Band
18
Art.-Nr.
846
eISSN
Finanzierungs-Informationen
Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
PUB-ID

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: 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, 846. doi:10.1186/s12864-017-4235-z
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: 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 (2017): 846.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2017-11-08T16:50:15Z

1 Zitation in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

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
Diversity and plant growth promoting evaluation abilities of bacteria isolated from sugarcane cultivated in the South of Brazil
Beneduzi A, Moreira F, Costa PB, Vargas LK, Lisboa BB, Favreto R, Baldani JI, Passaglia LMP., Agric., Ecosyst. Environ., Appl. Soil Ecol. 63(), 2013
PMID: IND500606026

AUTHOR UNKNOWN, 0
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

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
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

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
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
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
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
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
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
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
Trimmomatic: a flexible trimmer for Illumina sequence data.
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
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
Infernal 1.1: 100-fold faster RNA homology searches.
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
Rfam: an RNA family database.
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR., Nucleic Acids Res. 31(1), 2003
PMID: 12520045
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
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
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
WebLogo: a sequence logo generator.
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
Basic local alignment search tool.
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
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
Riboswitches as antibacterial drug targets.
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
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
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
Compilation and analysis of Escherichia coli promoter DNA sequences.
Hawley DK, McClure WR., Nucleic Acids Res. 11(8), 1983
PMID: 6344016
The riboswitch control of bacterial metabolism.
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
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
The T box and S box transcription termination control systems.
Grundy FJ, Henkin TM., Front. Biosci. 8(), 2003
PMID: 12456320
Comparative genomic analysis of T-box regulatory systems in bacteria.
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
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
Structural insights into recognition of c-di-AMP by the ydaO riboswitch.
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
Novel TPP-riboswitch activators bypass metabolic enzyme dependency.
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
Bacterial antisense RNAs: how many are there, and what are they doing?
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
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
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
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
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
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
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

AUTHOR UNKNOWN, 0

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 29100491
PubMed | Europe PMC

Suchen in

Google Scholar