Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011

Valverde C, Livny J, Schlüter J-P, Reinkensmeier J, Becker A, Parisi G (2008)
BMC Genomics 9(1): 416.

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Background: Small non-coding RNAs (sRNAs) have emerged as ubiquitous regulatory elements in bacteria and other life domains. However, few sRNAs have been identified outside several well-studied species of gamma-proteobacteria and thus relatively little is known about the role of RNA-mediated regulation in most other bacterial genera. Here we have conducted a computational prediction of putative sRNA genes in intergenic regions (IgRs) of the symbiotic alpha-proteobacterium S. meliloti 1021 and experimentally confirmed the expression of dozens of these candidate loci in the closely related strain S. meliloti 2011. Results: Our first sRNA candidate compilation was based mainly on the output of the sRNAPredictHT algorithm. A thorough manual sequence analysis of the curated list rendered an initial set of 18 IgRs of interest, from which 14 candidates were detected in strain 2011 by Northern blot and/or microarray analysis. Interestingly, the intracellular transcript levels varied in response to various stress conditions. We developed an alternative computational method to more sensitively predict sRNA-encoding genes and score these predicted genes based on several features to allow identification of the strongest candidates. With this novel strategy, we predicted 60 chromosomal independent transcriptional units that, according to our annotation, represent strong candidates for sRNA-encoding genes, including most of the sRNAs experimentally verified in this work and in two other contemporary studies. Additionally, we predicted numerous candidate sRNA genes encoded in megaplasmids pSymA and pSymB. A significant proportion of the chromosomal- and megaplasmid- borne putative sRNA genes were validated by microarray analysis in strain 2011. Conclusion: Our data extend the number of experimentally detected S. meliloti sRNAs and significantly expand the list of putative sRNA-encoding IgRs in this and closely related alpha-proteobacteria. In addition, we have developed a computational method that proved useful to predict sRNA-encoding genes in S. meliloti. We anticipate that this predictive approach can be flexibly implemented in many other bacterial species.
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BMC Genomics
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9
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1
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416
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Valverde C, Livny J, Schlüter J-P, Reinkensmeier J, Becker A, Parisi G. Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics. 2008;9(1):416.
Valverde, C., Livny, J., Schlüter, J. - P., Reinkensmeier, J., Becker, A., & Parisi, G. (2008). Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics, 9(1), 416. doi:10.1186/1471-2164-9-416
Valverde, C., Livny, J., Schlüter, J. - P., Reinkensmeier, J., Becker, A., and Parisi, G. (2008). Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics 9, 416.
Valverde, C., et al., 2008. Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics, 9(1), p 416.
C. Valverde, et al., “Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011”, BMC Genomics, vol. 9, 2008, pp. 416.
Valverde, C., Livny, J., Schlüter, J.-P., Reinkensmeier, J., Becker, A., Parisi, G.: Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics. 9, 416 (2008).
Valverde, Claudio, Livny, Jonathan, Schlüter, Jan-Philip, Reinkensmeier, Jan, Becker, Anke, and Parisi, Gustavo. “Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011”. BMC Genomics 9.1 (2008): 416.
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41 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

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Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J, Hess WR, Fischer HM, Evguenieva-Hackenberg E., RNA Biol 9(1), 2012
PMID: 22258152
A survey of sRNA families in α-proteobacteria.
del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N, Jiménez-Zurdo JI., RNA Biol 9(2), 2012
PMID: 22418845
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.
Reinkensmeier J, Schlüter JP, Giegerich R, Becker A., Genes (Basel) 2(4), 2011
PMID: 24710299
Proteomic alterations explain phenotypic changes in Sinorhizobium meliloti lacking the RNA chaperone Hfq.
Barra-Bily L, Fontenelle C, Jan G, Flechard M, Trautwetter A, Pandey SP, Walker GC, Blanco C., J Bacteriol 192(6), 2010
PMID: 20081032
The Sinorhizobium meliloti RNA chaperone Hfq mediates symbiosis of S. meliloti and alfalfa.
Barra-Bily L, Pandey SP, Trautwetter A, Blanco C, Walker GC., J Bacteriol 192(6), 2010
PMID: 20081033
The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon metabolism and the symbiotic interaction with alfalfa.
Torres-Quesada O, Oruezabal RI, Peregrina A, Jofré E, Lloret J, Rivilla R, Toro N, Jiménez-Zurdo JI., BMC Microbiol 10(), 2010
PMID: 20205931
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.
Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR., Genome Biol 11(3), 2010
PMID: 20230605
Role of the Sinorhizobium meliloti global regulator Hfq in gene regulation and symbiosis.
Gao M, Barnett MJ, Long SR, Teplitski M., Mol Plant Microbe Interact 23(4), 2010
PMID: 20192823
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.
Schlüter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jänicke S, Becker JD, Giegerich R, Becker A., BMC Genomics 11(), 2010
PMID: 20398411
sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes.
Sridhar J, Sambaturu N, Sabarinathan R, Ou HY, Deng Z, Sekar K, Rafi ZA, Rajakumar K., PLoS One 5(8), 2010
PMID: 20700540
RNase J is involved in the 5'-end maturation of 16S rRNA and 23S rRNA in Sinorhizobium meliloti.
Madhugiri R, Evguenieva-Hackenberg E., FEBS Lett 583(14), 2009
PMID: 19540834
Regulatory RNAs in prokaryotes: here, there and everywhere.
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PMID: 19732342
Expression of small RNAs in Rhizobiales and protection of a small RNA and its degradation products by Hfq in Sinorhizobium meliloti.
Voss B, Hölscher M, Baumgarth B, Kalbfleisch A, Kaya C, Hess WR, Becker A, Evguenieva-Hackenberg E., Biochem Biophys Res Commun 390(2), 2009
PMID: 19800865
Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides.
Berghoff BA, Glaeser J, Sharma CM, Vogel J, Klug G., Mol Microbiol 74(6), 2009
PMID: 19906181

75 References

Daten bereitgestellt von Europe PubMed Central.

Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria.
Yuan ZC, Zaheer R, Morton R, Finan TM., Nucleic Acids Res. 34(9), 2006
PMID: 16717279
Regulatory Sequence Analysis Tools
AUTHOR UNKNOWN, 0
NCBI Entrez Genome. Bacteria Complete Chromosome List
AUTHOR UNKNOWN, 0
Identification of cyanobacterial non-coding RNAs by comparative genome analysis.
Axmann IM, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR., Genome Biol. 6(9), 2005
PMID: 16168080
Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli.
Kawano M, Reynolds AA, Miranda-Rios J, Storz G., Nucleic Acids Res. 33(3), 2005
PMID: 15718303
Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021.
Capela D, Barloy-Hubler F, Gouzy J, Bothe G, Ampe F, Batut J, Boistard P, Becker A, Boutry M, Cadieu E, Dreano S, Gloux S, Godrie T, Goffeau A, Kahn D, Kiss E, Lelaure V, Masuy D, Pohl T, Portetelle D, Puhler A, Purnelle B, Ramsperger U, Renard C, Thebault P, Vandenbol M, Weidner S, Galibert F., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
PMID: 11481430
Isolation and characterization of alfalfa-nodulating rhizobia present in acidic soils of central argentina and uruguay
del Papa MF , Balague LJ, Sowinski SC, Wegener C, Segundo E, Abarca FM, Toro N, Niehaus K, P hler A , Aguilar OM, Martinez-Drets G, Lagares A., Appl. Environ. Microbiol. 65(4), 1999
PMID: 10103231
6S RNA regulates E. coli RNA polymerase activity.
Wassarman KM, Storz G., Cell 101(6), 2000
PMID: 10892648
6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.
Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR., RNA 11(5), 2005
PMID: 15811922
6S RNA: a small RNA regulator of transcription.
Wassarman KM., Curr. Opin. Microbiol. 10(2), 2007
PMID: 17383220
Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria.
Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR., Genome Biol. 6(8), 2005
PMID: 16086852
A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome.
Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB., BioSystems 65(2-3), 2002
PMID: 12069726
RNA families database
AUTHOR UNKNOWN, 0
Detection of low-level promoter activity within open reading frame sequences of Escherichia coli.
Kawano M, Storz G, Rao BS, Rosner JL, Martin RG., Nucleic Acids Res. 33(19), 2005
PMID: 16260475
RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria.
Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A, Wagner EG., Nucleic Acids Res. 31(22), 2003
PMID: 14602901
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
Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri.
Kulkarni PR, Cui X, Williams JW, Stevens AM, Kulkarni RV., Nucleic Acids Res. 34(11), 2006
PMID: 16822857
In search of RNase P RNA from microbial genomes.
Li Y, Altman S., RNA 10(10), 2004
PMID: 15337843
Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis.
Vitreschak AG, Lyubetskaya EV, Shirshin MA, Gelfand MS, Lyubetsky VA., FEMS Microbiol. Lett. 234(2), 2004
PMID: 15135544

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