Key players in regulatory RNA realm of bacteria

Mahendran, Gowthami; Jayasinghe, Oshadhi T.; Thavakumaran, Dhanushika; Arachchilage, Gayan Mirihana; Silva, Gayathri N.

doi:10.1016/j.bbrep.2022.101276

Cited by 6 publications

(3 citation statements)

References 180 publications

(279 reference statements)

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“…The 6S RNA in E. coli and Bacillus subtilis activates the transcription of stationary phase genes via the inhibition of exponential-phase RNA polymerase holoenzyme, while enabling the accumulation and activity of the stationary-phase RNA polymerase holoenzyme [90][91][92]. Specifically, 6S RNA forms a binding interaction with σ A (σ 70 ) RNA polymerase, thereby impeding DNA binding and repressing transcription initiated by σ A -dependent promoters during the stationary phase.…”

Section: The 6s Rna and Tmrna Mediated Regulationmentioning

confidence: 99%

Molecular Markers and Regulatory Networks in Solventogenic Clostridium Species: Metabolic Engineering Conundrum

Olorunsogbon,

Okonkwo,

Ezeji

2024

Fermentation

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Solventogenic Clostridium species are important for establishing the sustainable industrial bioproduction of fuels and important chemicals such as acetone and butanol. The inherent versatility of these species in substrate utilization and the range of solvents produced during acetone butanol–ethanol (ABE) fermentation make solventogenic Clostridium an attractive choice for biotechnological applications such as the production of fuels and chemicals. The functional qualities of these microbes have thus been identified to be related to complex regulatory networks that play essential roles in modulating the metabolism of this group of bacteria. Yet, solventogenic Clostridium species still struggle to consistently achieve butanol concentrations exceeding 20 g/L in batch fermentation, primarily due to the toxic effects of butanol on the culture. Genomes of solventogenic Clostridium species have a relatively greater prevalence of genes that are intricately controlled by various regulatory molecules than most other species. Consequently, the use of genetic or metabolic engineering strategies that do not consider the underlying regulatory mechanisms will not be effective. Several regulatory factors involved in substrate uptake/utilization, sporulation, solvent production, and stress responses (Carbon Catabolite Protein A, Spo0A, AbrB, Rex, CsrA) have been identified and characterized. In this review, the focus is on newly identified regulatory factors in solventogenic Clostridium species, the interaction of these factors with previously identified molecules, and potential implications for substrate utilization, solvent production, and resistance/tolerance to lignocellulose-derived microbial inhibitory compounds. Taken together, this review is anticipated to highlight the challenges impeding the re-industrialization of ABE fermentation, and inspire researchers to generate innovative strategies for overcoming these obstacles.

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Section: The 6s Rna and Tmrna Mediated Regulationmentioning

confidence: 99%

Molecular Markers and Regulatory Networks in Solventogenic Clostridium Species: Metabolic Engineering Conundrum

Olorunsogbon,

Okonkwo,

Ezeji

2024

Fermentation

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“…Moreover, the discovery of a variety of novel regulatory non‐coding RNAs through RNA‐seq has rekindled interest in RNase III. Non‐coding regulatory RNAs are part of the riboregulation network and were not only described in bacteria (in bacteria called sRNAs) but also in numerous other organisms (reviewed in Jørgensen et al, 2020; Mahendran et al, 2022; Papenfort & Melamed, 2023; Storz et al, 2011). sRNAs can exert their regulatory effects on gene expression by specific base pairing with their target mRNAs, and thereby form RNA–RNA duplexes, which are often recognised by RNase III as a substrate (Lioliou et al, 2012; McKellar et al, 2022; Mediati et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

RNase III participates in control of quorum sensing, pigmentation and oxidative stress resistance in Rhodobacter sphaeroides

Börner,

Friedrich,

Klug

2023

Molecular Microbiology

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RNase III is a dsRNA‐specific endoribonuclease, highly conserved in bacteria and eukarya. In this study, we analysed the effects of inactivation of RNase III on the transcriptome and the phenotype of the facultative phototrophic α‐proteobacterium Rhodobacter sphaeroides. RNA‐seq revealed an unexpectedly high amount of genes with increased expression located directly downstream to the rRNA operons. Chromosomal insertion of additional transcription terminators restored wild type‐like expression of the downstream genes, indicating that RNase III may modulate the rRNA transcription termination in R. sphaeroides. Furthermore, we identified RNase III as a major regulator of quorum‐sensing autoinducer synthesis in R. sphaeroides. It negatively controls the expression of the autoinducer synthase CerI by reducing cerI mRNA stability. In addition, RNase III inactivation caused altered resistance against oxidative stress and impaired formation of photosynthetically active pigment‐protein complexes. We also observed an increase in the CcsR small RNAs that were previously shown to promote resistance to oxidative stress. Taken together, our data present interesting insights into RNase III‐mediated regulation and expand the knowledge on the function of this important enzyme in bacteria.

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“…Small non-coding RNAs (sRNAs) are a type of RNA that regulate the expression of their target genes in response to environmental changes [ 13 ]. Many sRNAs play a major role in global gene regulatory networks and always modulate the gene expression of numerous targets at a post-transcriptional level by base pairing with mRNA targets [ 14 , 15 , 16 ].…”

Section: Introductionmentioning

confidence: 99%

RyhB in Avian Pathogenic Escherichia coli Regulates the Expression of Virulence-Related Genes and Contributes to Meningitis Development in a Mouse Model

Meng

Chen

Wang

et al. 2022

IJMS

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Avian pathogenic Escherichia coli (APEC) is an important member of extraintestinal pathogenic Escherichia coli (ExPEC). It shares similar pathogenic strategies with neonatal meningitis E. coli (NMEC) and may threaten human health due to its potential zoonosis. RyhB is a small non-coding RNA that regulates iron homeostasis in E. coli. However, it is unclear whether RyhB regulates meningitis occurrence. To investigate the function of RyhB in the development of meningitis, we constructed the deletion mutant APEC XM∆ryhB and the complemented mutant APEC XM∆ryhB/pryhB, established a mouse meningitis model and evaluated the role of RyhB in virulence of APEC. The results showed that the deletion of ryhB decreased biofilm formation, adhesion to the brain microvascular endothelial cell line bEnd.3 and serum resistance. RNA-seq data showed that the expression of multiple virulence-related genes changed in the ryhB deletion mutant in the presence of duck serum. Deletion of ryhB reduced the clinical symptoms of mice, such as opisthotonus, diarrhea and neurological signs, when challenged with APEC. Compared with the mice infected with the wild-type APEC, fewer histopathological lesions were observed in the brain of mice infected with the ryhB deletion mutant APEC XM∆ryhB. The bacterial loads in the tissues and the relative expression of cytokines (IL-1β, IL-6, and TNF-α) in the brain significantly decreased when challenged with the APEC XM∆ryhB. The expressions of tight junction proteins (claudin-5, occludin and ZO-1) were not reduced in the brain of mice infected with APEC XM∆ryhB; that is, the blood-brain barrier permeability of mice was not significantly damaged. In conclusion, RyhB contributes to the pathogenicity of APEC XM in the meningitis-causing process by promoting biofilm formation, adhesion to endothelial cells, serum resistance and virulence-related genes expression.

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Key players in regulatory RNA realm of bacteria

Cited by 6 publications

References 180 publications

Molecular Markers and Regulatory Networks in Solventogenic Clostridium Species: Metabolic Engineering Conundrum

Molecular Markers and Regulatory Networks in Solventogenic Clostridium Species: Metabolic Engineering Conundrum

RNase III participates in control of quorum sensing, pigmentation and oxidative stress resistance in Rhodobacter sphaeroides

RyhB in Avian Pathogenic Escherichia coli Regulates the Expression of Virulence-Related Genes and Contributes to Meningitis Development in a Mouse Model

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