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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.


Workflow of thermodynamic matcher construction.
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f2-genes-02-00925: Workflow of thermodynamic matcher construction.

Mentions: Figure 2 gives an overview of the TDM construction process. Here, we start from a transcript that has a well-defined secondary structure. First, we create a graphical description of this structure, using the Locomotif editor. The graphics can be annotated with size constraints for structural components, and with required sequence motifs. The graphics is then compiled by locomotif into a TDM. We use the TDM to scan other bacterial genomes in order to find subsequences that fold well into the described structure motif. The assessment of candidates is used to adapt the design of the TDM to be more restrictive or more relaxed.


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

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

Workflow of thermodynamic matcher construction.
© Copyright Policy
Related In: Results  -  Collection

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

f2-genes-02-00925: Workflow of thermodynamic matcher construction.
Mentions: Figure 2 gives an overview of the TDM construction process. Here, we start from a transcript that has a well-defined secondary structure. First, we create a graphical description of this structure, using the Locomotif editor. The graphics can be annotated with size constraints for structural components, and with required sequence motifs. The graphics is then compiled by locomotif into a TDM. We use the TDM to scan other bacterial genomes in order to find subsequences that fold well into the described structure motif. The assessment of candidates is used to adapt the design of the TDM to be more restrictive or more relaxed.

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.