TY  - JOUR
A1  - Hahn, Julia
A1  - Thalmann, Sebastian
A1  - Migur, Anzhela
A1  - Boeselager, Raphael Freiherr von
A1  - Kubatova, Nina
A1  - Kubareva, Elena
A1  - Schwalbe, Harald
A1  - Evguenieva-Hackenberg, Elena
T1  - Conserved small mRNA with an unique, extended Shine-Dalgarno sequence
T2  - RNA biology
N2  - Up to now, very small protein-coding genes have remained unrecognized in sequenced genomes. We identified an mRNA of 165 nucleotides (nt), which is conserved in Bradyrhizobiaceae and encodes a polypeptide with 14 amino acid residues (aa). The small mRNA harboring a unique Shine-Dalgarno sequence (SD) with a length of 17 nt was localized predominantly in the ribosome-containing P100 fraction of Bradyrhizobium japonicum USDA 110. Strong interaction between the mRNA and 30S ribosomal subunits was demonstrated by their co-sedimentation in sucrose density gradient. Using translational fusions with egfp, we detected weak translation and found that it is impeded by both the extended SD and the GTG start codon (instead of ATG). Biophysical characterization (CD- and NMR-spectroscopy) showed that synthesized polypeptide remained unstructured in physiological puffer. Replacement of the start codon by a stop codon increased the stability of the transcript, strongly suggesting additional posttranscriptional regulation at the ribosome. Therefore, the small gene was named rreB (ribosome-regulated expression in Bradyrhizobiaceae). Assuming that the unique ribosome binding site (RBS) is a hallmark of rreB homologs or similarly regulated genes, we looked for similar putative RBS in bacterial genomes and detected regions with at least 16 nt complementarity to the 3′-end of 16S rRNA upstream of sORFs in Caulobacterales, Rhizobiales, Rhodobacterales and Rhodospirillales. In the Rhodobacter/Roseobacter lineage of α-proteobacteria the corresponding gene (rreR) is conserved and encodes an 18 aa protein. This shows how specific RBS features can be used to identify new genes with presumably similar control of expression at the RNA level.
KW  - a-proteobacteria
KW  - Bradyrhizobium
KW  - ribosomal binding site
KW  - ribosome
KW  - RNA stability
KW  - Shine-Dalgarno
KW  - small gene
KW  - small protein
KW  - sORF
KW  - translation initiation region
Y1  - 2017
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/46877
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-468775
SN  - 1555-8584
SN  - 1547-6286
N1  - This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way
VL  - 14
IS  - 10
SP  - 1353
EP  - 1363
PB  - Taylor & Francis
CY  - Philadelphia, Pa.
ER  -