A broadening world of bacterial small RNAs

Liu, Jane M.; Camilli, Andrew

doi:10.1016/j.mib.2009.11.004

Cited by 74 publications

(61 citation statements)

References 50 publications

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“…Small noncoding RNAs transcribed in the IGRs of the prokaryotic genomes play an important role in metabolism regulation (11), and they can act as regulators of gene expression in all prokaryotes in which they have been studied. They are often defined as noncoding transcripts that act in trans to control the translation or stability of their target mRNA (11,46). However, recent reports show that they could act in a significantly different way: in cis-acting chromosomally encoded antisense small noncoding RNAs or even as regulatory and translated RNAs (4,46).…”

Section: Discussionmentioning

confidence: 99%

Effect of Periodontal Pathogens on the Metatranscriptome of a Healthy Multispecies Biofilm Model

Frias-Lopez

Duran-Pinedo²

2012

J Bacteriol

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Oral bacterial biofilms are highly complex microbial communities with up to 700 different bacterial taxa. We report here the use of metatranscriptomic analysis to study patterns of community gene expression in a multispecies biofilm model composed of species found in healthy oral biofilms (Actinomyces naeslundii, Lactobacillus casei, Streptococcus mitis, Veillonella parvula, and Fusobacterium nucleatum) and the same biofilm plus the periodontopathogens Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans. The presence of the periodontopathogens altered patterns in gene expression, and data indicate that transcription of protein-encoding genes and small noncoding RNAs is stimulated. In the healthy biofilm hypothetical proteins, transporters and transcriptional regulators were upregulated while chaperones and cell division proteins were downregulated. However, when the pathogens were present, chaperones were highly upregulated, probably due to increased levels of stress. We also observed a significant upregulation of ABC transport systems and putative transposases. Changes in Clusters of Orthologous Groups functional categories as well as gene set enrichment analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that in the absence of pathogens, only sets of proteins related to transport and secondary metabolism were upregulated, while in the presence of pathogens, proteins related to growth and division as well as a large portion of transcription factors were upregulated. Finally, we identified several small noncoding RNAs whose predicted targets were genes differentially expressed in the open reading frame libraries. These results show the importance of pathogens controlling gene expression of a healthy oral community and the usefulness of metatranscriptomic techniques to study gene expression profiles in complex microbial community models.

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Section: Discussionmentioning

confidence: 99%

Effect of Periodontal Pathogens on the Metatranscriptome of a Healthy Multispecies Biofilm Model

Frias-Lopez

Duran-Pinedo²

2012

J Bacteriol

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“…They interfere with translation or alter transcript stability and thus can regulate the expression of the corresponding genes positively or negatively. Thereby, sRNAs constitute important mediators of posttranscriptional gene regulation in bacteria (Papenfort and Vogel, 2009;Waters and Storz, 2009;Liu and Camilli, 2010). Certainly, control of the initiation of translation and stability-based mechanisms are not mutually exclusive and can appear simultaneously.…”

Section: Mechanism Of Psrr1 Posttranscriptional Regulationmentioning

confidence: 99%

The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria

Dienst²,

et al. 2014

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Little is known so far about RNA regulators of photosynthesis in plants, algae, or cyanobacteria. The small RNA PsrR1 (formerly SyR1) has been discovered in Synechocystis sp PCC 6803 and appears to be widely conserved within the cyanobacterial phylum. Expression of PsrR1 is induced shortly after a shift from moderate to high-light conditions. Artificial overexpression of PsrR1 led to a bleaching phenotype under moderate light growth conditions. Advanced computational target prediction suggested that several photosynthesis-related mRNAs could be controlled by PsrR1, a finding supported by the results of transcriptome profiling experiments upon pulsed overexpression of this small RNA in Synechocystis sp PCC 6803. We confirmed the interaction between PsrR1 and the ribosome binding regions of the psaL, psaJ, chlN, and cpcA mRNAs by mutational analysis in a heterologous reporter system. Focusing on psaL as a specific target, we show that the psaL mRNA is processed by RNase E only in the presence of PsrR1. Furthermore, we provide evidence for a posttranscriptional regulation of psaL by PsrR1 in the wild type at various environmental conditions and analyzed the consequences of PsrR1-based regulation on photosystem I. In summary, computational and experimental data consistently establish the small RNA PsrR1 as a regulatory factor controlling photosynthetic functions.

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“…The majority of sRNAs, the trans-encoded sRNAs, require the protein Hfq, an RNA chaperone necessary for the formation of limited base-pairing interactions with target mRNAs. 5,6 A second class of sRNAs, the cis-encoded antisense RNAs, regulates the expression of genes located directly on the opposite strand. These sRNAs do not require Hfq for action and form extensive base-pairing with their target mRNA without the requirement for any co-factor.…”

Section: Introductionmentioning

confidence: 99%

The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress inE. coli

Gerstle¹,

Klätschke²,

Hahn³

et al. 2012

RNA Biology

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A broadening world of bacterial small RNAs

Cited by 74 publications

References 50 publications

Effect of Periodontal Pathogens on the Metatranscriptome of a Healthy Multispecies Biofilm Model

Effect of Periodontal Pathogens on the Metatranscriptome of a Healthy Multispecies Biofilm Model

The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria

The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress inE. coli

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