Regulatory RNAs and target mRNA decay in prokaryotes

Lalaouna, David; Simoneau-Roy, Maxime; Lafontaine, Daniel A.; Massé, Éric

doi:10.1016/j.bbagrm.2013.02.013

Cited by 128 publications

(101 citation statements)

References 78 publications

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“…Cis-encoding antisense RNAs are fully complementary to targets, whereas trans-encoding RNAs show only partial complementarity. These trans-acting sRNAs have the potential to regulate multiple targets and one mRNA can be regulated by more than one sRNA [109,110]. A key helper protein that is required for the activity of the trans-encoded sRNAs, is the RNA chaperone protein Hfq (for review see Ref.…”

Section: Translation Regulation By Srnasmentioning

confidence: 99%

Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics

et al. 2015

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Section: Translation Regulation By Srnasmentioning

confidence: 99%

Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics

et al. 2015

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“…Moreover, it was recently reported that small RNAs expressed by a plant fungus regulate cellular gene expression using the host cell's own RNAi machinery and thereby contribute to the pathogenicity of this fungus [10]. In contrast, prokaryotes are not believed to express miRNAs, although they do express a wide array of small, non-coding RNAs (sRNAs) that regulate a diverse set of physiological processes inside the bacterial cell [11], [12]. For example, bacterial sRNAs form ribonucleoproteins that control cellular functions ranging from protein secretion to the recognition of foreign nucleic acids [13]–[15].…”

Section: Introductionmentioning

confidence: 99%

Search for MicroRNAs Expressed by Intracellular Bacterial Pathogens in Infected Mammalian Cells

et al. 2014

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MicroRNAs are expressed by all multicellular organisms and play a critical role as post-transcriptional regulators of gene expression. Moreover, different microRNA species are known to influence the progression of a range of different diseases, including cancer and microbial infections. A number of different human viruses also encode microRNAs that can attenuate cellular innate immune responses and promote viral replication, and a fungal pathogen that infects plants has recently been shown to express microRNAs in infected cells that repress host cell immune responses and promote fungal pathogenesis. Here, we have used deep sequencing of total expressed small RNAs, as well as small RNAs associated with the cellular RNA-induced silencing complex RISC, to search for microRNAs that are potentially expressed by intracellular bacterial pathogens and translocated into infected animal cells. In the case of Legionella and Chlamydia and the two mycobacterial species M. smegmatis and M. tuberculosis, we failed to detect any bacterial small RNAs that had the characteristics expected for authentic microRNAs, although large numbers of small RNAs of bacterial origin could be recovered. However, a third mycobacterial species, M. marinum, did express an ∼23-nt small RNA that was bound by RISC and derived from an RNA stem-loop with the characteristics expected for a pre-microRNA. While intracellular expression of this candidate bacterial microRNA was too low to effectively repress target mRNA species in infected cultured cells in vitro, artificial overexpression of this potential bacterial pre-microRNA did result in the efficient repression of a target mRNA. This bacterial small RNA therefore represents the first candidate microRNA of bacterial origin.

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“…36,37 Moreover, there is a burgeoning list of examples that RNase activity can be modulated by adaptor proteins, and a plethora of small noncoding RNAs have been discovered which can confer target selectivity to prokaryotic RNases. 38 Furthermore, the cellular localization of the RNA-degrading complexes seems to vary under different environmental conditions, and a fascinating new observation of spatial distribution patterns of the microbial mRNA species strongly suggests that microbes organize mRNA decay in time and space. 39,40 Our knowledge about the environmental signals and regulators that control mRNA decay is still in its infancy, but recent studies have undoubtedly shown that 'regulated ribolysis' is a crucial control mechanism for the expression of virulence factors in enteric pathogens.…”

Section: Cmentioning

confidence: 99%

RNA-based mechanisms of virulence control in Enterobacteriaceae

2016

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Enteric pathogens of the family Enterobacteriaceae colonize various niches within animals and humans in which they compete with intestinal commensals and are attacked by the host immune system. To survive these hostile environments they possess complex, multilayer regulatory networks that coordinate the control of virulence factors, host-adapted metabolic functions and stress resistance. An important part of these intricate control networks are RNA-based control systems that enable the pathogen to fine-tune its responses. Recent next-generation sequencing approaches revealed a large repertoire of conserved and species-specific riboregulators, including numerous cis-and trans-acting non-coding RNAs, sensory RNA elements (RNA thermometers, riboswitches), regulatory RNA-binding proteins and RNA degrading enzymes which regulate colonization factors, toxins, host defense processes and virulence-relevant physiological and metabolic processes. All of which are important cues for pathogens to sense and respond to fluctuating conditions during the infection. This review covers infection-relevant riboregulators of E. coli, Salmonella, Shigella and Yersinia, highlights their versatile regulatory mechanisms, complex target regulons and functions, and discusses emerging topics and future challenges to fully understand and exploit RNA-based control to combat bacterial infections.

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Regulatory RNAs and target mRNA decay in prokaryotes

Cited by 128 publications

References 78 publications

Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics

Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics

Search for MicroRNAs Expressed by Intracellular Bacterial Pathogens in Infected Mammalian Cells

RNA-based mechanisms of virulence control in Enterobacteriaceae

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