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Genes (Basel). 2011 Nov 18;2(4):925-56. doi: 10.3390/genes2040925.

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

Author information

1
Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany. jreinken@cebitec.uni-bielefeld.de.
2
Institute of Biology III, Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79102 Freiburg, Germany. jan-philip.schlueter@biologie.uni-freiburg.de.
3
Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany. robert@techfak.uni-bielefeld.de.
4
Institute of Biology III, Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79102 Freiburg, Germany. anke.becker@uni-freiburg.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].

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