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Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.

Reinkensmeier J, Schlüter JP, Giegerich R, Becker A - Genes (Basel) (2011)

Bottom Line: This approach resulted in 39 RNA family models (RFMs) which showed various taxonomic distribution patterns.Whereas the majority of RFMs was restricted to Sinorhizobium species or the Rhizobiaceae, members of a few RFMs were more widely distributed in the Rhizobiales.Access to this data is provided via the RhizoGATE portal [1,2].

View Article: PubMed Central - PubMed

Affiliation: Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany. jreinken@cebitec.uni-bielefeld.de.

ABSTRACT
Post-transcriptional regulation by trans-encoded sRNAs, for example via base-pairing with target mRNAs, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. Several studies based on computational and RNA-seq approaches identified approximately 180 trans-encoded sRNAs in Sinorhizobium meliloti. The initial point of this report is a set of 52 trans-encoded sRNAs derived from the former studies. Sequence homology combined with structural conservation analyses were applied to elucidate the occurrence and distribution of conserved trans-encoded sRNAs in the order of Rhizobiales. This approach resulted in 39 RNA family models (RFMs) which showed various taxonomic distribution patterns. Whereas the majority of RFMs was restricted to Sinorhizobium species or the Rhizobiaceae, members of a few RFMs were more widely distributed in the Rhizobiales. Access to this data is provided via the RhizoGATE portal [1,2].

No MeSH data available.


Structural, functional and genomic features of RFMSmelC289. (a) Alignment of presumed functional hairpin loops and (b) consensus secondary structure of identified relatives of SmelC289. Base pairs are colored as in Figure 4a; (c) Microsynteny pattern of RFMSmelC289. Illustration as in Figure 4c.
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f6-genes-02-00925: Structural, functional and genomic features of RFMSmelC289. (a) Alignment of presumed functional hairpin loops and (b) consensus secondary structure of identified relatives of SmelC289. Base pairs are colored as in Figure 4a; (c) Microsynteny pattern of RFMSmelC289. Illustration as in Figure 4c.

Mentions: Except for RNA3 of S. medicae WSM419, all relatives of SmelC289 are located next to a prolyl-tRNA synthetase gene (Figure 6c, Table S1). In case of RNA11, RNA13, RNA14, RNA15, RNA17, RNA19, RNA20, and RNA21 of the Brucellaceae, the prolyl-tRNA synthetase gene is indeed located adjacent to the corresponding sRNA genes, but these sRNA genes are overlapped in antisense by one or two presumably misannotated, small hypothetical genes. For 18 RFMs, overlapping genes were predicted of which the majority is annotated as hypothetical and thus their function and existence remain in question.


Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.

Reinkensmeier J, Schlüter JP, Giegerich R, Becker A - Genes (Basel) (2011)

Structural, functional and genomic features of RFMSmelC289. (a) Alignment of presumed functional hairpin loops and (b) consensus secondary structure of identified relatives of SmelC289. Base pairs are colored as in Figure 4a; (c) Microsynteny pattern of RFMSmelC289. Illustration as in Figure 4c.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927594&req=5

f6-genes-02-00925: Structural, functional and genomic features of RFMSmelC289. (a) Alignment of presumed functional hairpin loops and (b) consensus secondary structure of identified relatives of SmelC289. Base pairs are colored as in Figure 4a; (c) Microsynteny pattern of RFMSmelC289. Illustration as in Figure 4c.
Mentions: Except for RNA3 of S. medicae WSM419, all relatives of SmelC289 are located next to a prolyl-tRNA synthetase gene (Figure 6c, Table S1). In case of RNA11, RNA13, RNA14, RNA15, RNA17, RNA19, RNA20, and RNA21 of the Brucellaceae, the prolyl-tRNA synthetase gene is indeed located adjacent to the corresponding sRNA genes, but these sRNA genes are overlapped in antisense by one or two presumably misannotated, small hypothetical genes. For 18 RFMs, overlapping genes were predicted of which the majority is annotated as hypothetical and thus their function and existence remain in question.

Bottom Line: This approach resulted in 39 RNA family models (RFMs) which showed various taxonomic distribution patterns.Whereas the majority of RFMs was restricted to Sinorhizobium species or the Rhizobiaceae, members of a few RFMs were more widely distributed in the Rhizobiales.Access to this data is provided via the RhizoGATE portal [1,2].

View Article: PubMed Central - PubMed

Affiliation: Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany. jreinken@cebitec.uni-bielefeld.de.

ABSTRACT
Post-transcriptional regulation by trans-encoded sRNAs, for example via base-pairing with target mRNAs, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. Several studies based on computational and RNA-seq approaches identified approximately 180 trans-encoded sRNAs in Sinorhizobium meliloti. The initial point of this report is a set of 52 trans-encoded sRNAs derived from the former studies. Sequence homology combined with structural conservation analyses were applied to elucidate the occurrence and distribution of conserved trans-encoded sRNAs in the order of Rhizobiales. This approach resulted in 39 RNA family models (RFMs) which showed various taxonomic distribution patterns. Whereas the majority of RFMs was restricted to Sinorhizobium species or the Rhizobiaceae, members of a few RFMs were more widely distributed in the Rhizobiales. Access to this data is provided via the RhizoGATE portal [1,2].

No MeSH data available.