ArticleBMC genomics2010
Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 45 citations in OpenAlex.
- Identification of sigma factor 54-regulated small non-coding RNAs by employing genome-wide and transcriptome-based methods in rhizobium strains.3 Biotech · 2022Article
- Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria.Microorganisms · 2020Review
- Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia.High-throughput · 2018Review
- An account of evolutionary specialization: the AbcR small RNAs in the Rhizobiales.Molecular microbiology · 2018Review
- Article
- A Genome-Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis inFrontiers in microbiology · 2017Article
- The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Thermodynamic matchers for the construction of the cuckoo RNA family.RNA biology · 2015Article
- RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock.BMC genomics · 2014Article
- Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region.RNA biology · 2014Article
- COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.Nucleic acids research · 2014Article
- Riboregulators and the role of Hfq in photosynthetic bacteria.RNA biology · 2014Review
- Riboregulation in plant-associated α-proteobacteria.RNA biology · 2014Review
- Canonical and non-canonical EcfG sigma factors control the general stress response in Rhizobium etli.MicrobiologyOpen · 2013Article
- Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308.Molecular microbiology · 2012Article
- Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens.RNA biology · 2012Article
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- Article
- Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing.BMC plant biology · 2011Article
- Small RNAs in the genus Clostridium.mBio · 2011Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNon-coding RNAs (ncRNAs) play a crucial role in the intricate regulation of bacterial gene expression, allowing bacteria to quickly adapt to changing environments. In the past few years, a growing number of regulatory RNA elements have been predicted by computational methods, mostly in well-studied gamma-proteobacteria but lately in several alpha-proteobacteria as well. Here, we have compared an extensive compilation of these non-coding RNA predictions to intergenic expression data of a whole-genome high-resolution tiling array in the soil-dwelling alpha-proteobacterium Rhizobium etli.
resultsExpression of 89 candidate ncRNAs was detected, both on the chromosome and on the six megaplasmids encompassing the R. etli genome. Of these, 11 correspond to functionally well characterized ncRNAs, 12 were previously identified in other alpha-proteobacteria but are as yet uncharacterized and 66 were computationally predicted earlier but had not been experimentally identified and were therefore classified as novel ncRNAs. The latter comprise 17 putative sRNAs and 49 putative cis-regulatory ncRNAs. A selection of these candidate ncRNAs was validated by RT-qPCR, Northern blotting and 5' RACE, confirming the existence of 4 ncRNAs. Interestingly, individual transcript levels of numerous ncRNAs varied during free-living growth and during interaction with the eukaryotic host plant, pointing to possible ncRNA-dependent regulation of these specialized processes.
conclusionsOur data support the practical value of previous ncRNA prediction algorithms and significantly expand the list of candidate ncRNAs encoded in the intergenic regions of R. etli and, by extension, of alpha-proteobacteria. Moreover, we show high-resolution tiling arrays to be suitable tools for studying intergenic ncRNA transcription profiles across the genome. The differential expression levels of some of these ncRNAs may indicate a role in adaptation to changing environmental conditions.
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