Thermodynamic matchers for the construction of the cuckoo RNA family

Reinkensmeier J, Giegerich R (2015)
RNA Biology 12(2): 197-207.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Abstract / Bemerkung
RNA family models describe classes of functionally related, non-coding RNAs based on sequence and structure conservation. The most important method for modeling RNA families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous RNAs. However, the performance of covariance models in finding remote homologs is poor for RNA families with high sequence conservation, while for families with high structure but low sequence conservation, these models are difficult to built in the first place. A complementary approach to RNA family modeling involves the use of thermodynamic matchers. Thermodynamic matchers are RNA folding programs, based on the established thermodynamic model, but tailored to a specific structural motif. As thermodynamic matchers focus on structure and folding energy, they unfold their potential in discovering homologs, when high structure conservation is paired with low sequence conservation. In contrast to covariance models, construction of thermodynamic matchers does not require an input alignment, but requires human design decisions and experimentation, and hence, model construction is more laborious. Here we report a case study on an RNA family that was constructed by means of thermodynamic matchers. It starts from a set of known but structurally different members of the same RNA family. The consensus secondary structure of this family consists of 2 to 4 adjacent hairpins. Each hairpin loop carries the same motif, CCUCCUCCC, while the stems show high variability in their nucleotide content. The present study describes (1) a novel approach for the integration of the structurally varying family into a single RNA family model by means of the thermodynamic matcher methodology, and (2) provides the results of homology searches that were conducted with this model in a wide spectrum of bacterial species.
Stichworte
small; homology search; family model; alphaproteobacteria; cuckoo RNA; RNA; structural RNA; thermodynamic matcher
Erscheinungsjahr
2015
Zeitschriftentitel
RNA Biology
Band
12
Ausgabe
2
Seite(n)
197-207
ISSN
1547-6286
Page URI
https://pub.uni-bielefeld.de/record/2733607

Zitieren

Reinkensmeier J, Giegerich R. Thermodynamic matchers for the construction of the cuckoo RNA family. RNA Biology. 2015;12(2):197-207.
Reinkensmeier, J., & Giegerich, R. (2015). Thermodynamic matchers for the construction of the cuckoo RNA family. RNA Biology, 12(2), 197-207. doi:10.1080/15476286.2015.1017206
Reinkensmeier, Jan, and Giegerich, Robert. 2015. “Thermodynamic matchers for the construction of the cuckoo RNA family”. RNA Biology 12 (2): 197-207.
Reinkensmeier, J., and Giegerich, R. (2015). Thermodynamic matchers for the construction of the cuckoo RNA family. RNA Biology 12, 197-207.
Reinkensmeier, J., & Giegerich, R., 2015. Thermodynamic matchers for the construction of the cuckoo RNA family. RNA Biology, 12(2), p 197-207.
J. Reinkensmeier and R. Giegerich, “Thermodynamic matchers for the construction of the cuckoo RNA family”, RNA Biology, vol. 12, 2015, pp. 197-207.
Reinkensmeier, J., Giegerich, R.: Thermodynamic matchers for the construction of the cuckoo RNA family. RNA Biology. 12, 197-207 (2015).
Reinkensmeier, Jan, and Giegerich, Robert. “Thermodynamic matchers for the construction of the cuckoo RNA family”. RNA Biology 12.2 (2015): 197-207.

4 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

A conserved α-proteobacterial small RNA contributes to osmoadaptation and symbiotic efficiency of rhizobia on legume roots.
Robledo M, Peregrina A, Millán V, García-Tomsig NI, Torres-Quesada O, Mateos PF, Becker A, Jiménez-Zurdo JI., Environ Microbiol 19(7), 2017
PMID: 28401641

41 References

Daten bereitgestellt von Europe PubMed Central.

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
Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog.
Willkomm DK, Minnerup J, Huttenhofer A, Hartmann RK., Nucleic Acids Res. 33(6), 2005
PMID: 15814812
RNA-Seq: a revolutionary tool for transcriptomics.
Wang Z, Gerstein M, Snyder M., Nat. Rev. Genet. 10(1), 2009
PMID: 19015660
Rfam 11.0: 10 years of RNA families.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23125362
RNA sequence analysis using covariance models.
Eddy SR, Durbin R., Nucleic Acids Res. 22(11), 1994
PMID: 8029015
Infernal 1.1: 100-fold faster RNA homology searches.
Nawrocki EP, Eddy SR., Bioinformatics 29(22), 2013
PMID: 24008419

Mitchison G., 1998
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
Overlapping alternative sigma factor regulons in the response to singlet oxygen in Rhodobacter sphaeroides.
Nuss AM, Glaeser J, Berghoff BA, Klug G., J. Bacteriol. 192(10), 2010
PMID: 20304993
Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides.
Berghoff BA, Glaeser J, Sharma CM, Zobawa M, Lottspeich F, Vogel J, Klug G., Mol. Microbiol. 80(6), 2011
PMID: 21535243
Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.
del Val C, Rivas E, Torres-Quesada O, Toro N, Jimenez-Zurdo JI., Mol. Microbiol. 66(5), 2007
PMID: 17971083
Fast and reliable prediction of noncoding RNAs.
Washietl S, Hofacker IL, Stadler PF., Proc. Natl. Acad. Sci. U.S.A. 102(7), 2005
PMID: 15665081
Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011.
Valverde C, Livny J, Schluter JP, Reinkensmeier J, Becker A, Parisi G., BMC Genomics 9(), 2008
PMID: 18793445
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.
Schluter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Janicke S, Becker JD, Giegerich R, Becker A., BMC Genomics 11(), 2010
PMID: 20398411
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021.
Schluter JP, Reinkensmeier J, Barnett MJ, Lang C, Krol E, Giegerich R, Long SR, Becker A., BMC Genomics 14(), 2013
PMID: 23497287
High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs.
Livny J, Teonadi H, Livny M, Waldor MK., PLoS ONE 3(9), 2008
PMID: 18787707
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.
Reinkensmeier J, Schluter JP, Giegerich R, Becker A., Genes (Basel) 2(4), 2011
PMID: 24710299
Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens.
Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F., RNA Biol 9(4), 2012
PMID: 22336765
A survey of sRNA families in α-proteobacteria.
del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N, Jimenez-Zurdo JI., RNA Biol 9(2), 2012
PMID: 22418845
The quest for orthologs: finding the corresponding gene across genomes.
Kuzniar A, van Ham RC, Pongor S, Leunissen JA., Trends Genet. 24(11), 2008
PMID: 18819722
Regulation by small RNAs in bacteria: expanding frontiers.
Storz G, Vogel J, Wassarman KM., Mol. Cell 43(6), 2011
PMID: 21925377
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation.
Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P., Nucleic Acids Res. 37(21), 2009
PMID: 19786493
Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism.
Boisset S, Geissmann T, Huntzinger E, Fechter P, Bendridi N, Possedko M, Chevalier C, Helfer AC, Benito Y, Jacquier A, Gaspin C, Vandenesch F, Romby P., Genes Dev. 21(11), 2007
PMID: 17545468
Small RNA sX13: a multifaceted regulator of virulence in the plant pathogen Xanthomonas.
Schmidtke C, Abendroth U, Brock J, Serrania J, Becker A, Bonas U., PLoS Pathog. 9(9), 2013
PMID: 24068933
A variable homopolymeric G-repeat defines small RNA-mediated posttranscriptional regulation of a chemotaxis receptor in Helicobacter pylori.
Pernitzsch SR, Tirier SM, Beier D, Sharma CM., Proc. Natl. Acad. Sci. U.S.A. 111(4), 2014
PMID: 24474799
Comparative analysis of RNA families reveals distinct repertoires for each domain of life.
Hoeppner MP, Gardner PP, Poole AM., PLoS Comput. Biol. 8(11), 2012
PMID: 23133357
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
Mathews DH, Sabina J, Zuker M, Turner DH., J. Mol. Biol. 288(5), 1999
PMID: 10329189
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
Thermodynamic matchers: strengthening the significance of RNA folding energies.
Hochsmann T, Hochsmann M, Giegerich R., Comput Syst Bioinformatics Conf (), 2006
PMID: 17369630
RNAMotif, an RNA secondary structure definition and search algorithm.
Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R., Nucleic Acids Res. 29(22), 2001
PMID: 11713323
Faster computation of exact RNA shape probabilities.
Janssen S, Giegerich R., Bioinformatics 26(5), 2010
PMID: 20080511
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549
Locomotif: from graphical motif description to RNA motif search.
Reeder J, Reeder J, Giegerich R., Bioinformatics 23(13), 2007
PMID: 17646322
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.
Sauthoff G, Mohl M, Janssen S, Giegerich R., Bioinformatics 29(5), 2013
PMID: 23355290
Yield grammar analysis and product optimization in a domain-specific language for dynamic programming
Giegerich R., 2014
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.
Janssen S, Schudoma C, Steger G, Giegerich R., BMC Bioinformatics 12(), 2011
PMID: 22051375
Abstract folding space analysis based on helices.
Huang J, Backofen R, Voß B., RNA 18(12), 2012
PMID: 23104999
Proteinortho: detection of (co-)orthologs in large-scale analysis.
Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ., BMC Bioinformatics 12(), 2011
PMID: 21526987
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 25779873
PubMed | Europe PMC

Suchen in

Google Scholar