Diversity and Versatility in Small RNA-Mediated Regulation in Bacterial Pathogens

Bacterial gene expression is under the control of a large set of molecules acting at multiple levels. In addition to the transcription factors (TFs) already known to be involved in global regulation of gene expression, small regulatory RNAs (sRNAs) are emerging as major players in gene regulatory networks, where they allow environmental adaptation and fitness. Developments in high-throughput screening have enabled their detection in the entire bacterial kingdom. These sRNAs influence a plethora of biological processes, including but not limited to outer membrane synthesis, metabolism, TF regulation, transcription termination, virulence, and antibiotic resistance and persistence. Almost always noncoding, they regulate target genes at the post-transcriptional level, usually through base-pair interactions with mRNAs, alone or with the help of dedicated chaperones. There is growing evidence that sRNA-mediated mechanisms of actions are far more diverse than initially thought, and that they go beyond the so-called cis- and trans-encoded classifications. These molecules can be derived and processed from 5' untranslated regions (UTRs), coding or non-coding sequences, and even from 3' UTRs. They usually act within the bacterial cytoplasm, but recent studies showed sRNAs in extracellular vesicles, where they influence host cell interactions. In this review, we highlight the various functions of sRNAs in bacterial pathogens, and focus on the increasing examples of widely diverse regulatory mechanisms that might compel us to reconsider what constitute the sRNA.

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Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1517140113 ◽

2016 ◽

Vol 113 (13) ◽

pp. E1835-E1843 ◽

Cited By ~ 8

Author(s):

Mina Fazlollahi ◽

Ivor Muroff ◽

Eunjee Lee ◽

Helen C. Causton ◽

Harmen J. Bussemaker

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Gene Regulatory Networks ◽

Regulatory Networks ◽

Target Genes ◽

Regulation Of Gene Expression ◽

Nonsynonymous Mutation ◽

Gene Regulatory ◽

Genetic Modulators

Regulation of gene expression by transcription factors (TFs) is highly dependent on genetic background and interactions with cofactors. Identifying specific context factors is a major challenge that requires new approaches. Here we show that exploiting natural variation is a potent strategy for probing functional interactions within gene regulatory networks. We developed an algorithm to identify genetic polymorphisms that modulate the regulatory connectivity between specific transcription factors and their target genes in vivo. As a proof of principle, we mapped connectivity quantitative trait loci (cQTLs) using parallel genotype and gene expression data for segregants from a cross between two strains of the yeast Saccharomyces cerevisiae. We identified a nonsynonymous mutation in the DIG2 gene as a cQTL for the transcription factor Ste12p and confirmed this prediction empirically. We also identified three polymorphisms in TAF13 as putative modulators of regulation by Gcn4p. Our method has potential for revealing how genetic differences among individuals influence gene regulatory networks in any organism for which gene expression and genotype data are available along with information on binding preferences for transcription factors.

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Dam and its role in pathogenicity of Salmonella enterica

The Journal of Infection in Developing Countries ◽

10.3855/jidc.465 ◽

2009 ◽

Vol 3 (07) ◽

pp. 484-490 ◽

Cited By ~ 9

Author(s):

Mónica N. Giacomodonato ◽

Sebastián H. Sarnacki ◽

Mariángeles Noto Llana ◽

M. Cristina Cerquetti

Keyword(s):

Gene Expression ◽

Animal Models ◽

Salmonella Enterica ◽

Bacterial Pathogens ◽

General Strategy ◽

Essential Factor ◽

Bacterial Gene ◽

Bacterial Gene Expression ◽

Dam Methylation

Dam methylation is an essential factor involved in the virulence of an increasing number of bacterial pathogens including Salmonella enterica. Lack of Dam methylation causes severe attenuation in animal models. It has been proposed that dysregulation of Dam activity is potentially a general strategy for the generation of vaccines against bacterial pathogens. In this review, we focus our attention on the role of methylation by Dam protein in regulating bacterial gene expression and virulence in Salmonella enterica.

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Transcriptome Analysis of Insulin Signaling-Associated Transcription Factors in C. elegans Reveal Their Genome-Wide Target Genes Specificity and Complexity

International Journal of Molecular Sciences ◽

10.3390/ijms222212462 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12462

Author(s):

Neha Kaushik ◽

Soumya Rastogi ◽

Sonia Verma ◽

Deepak Pandey ◽

Ashutosh Halder ◽

...

Keyword(s):

Transcription Factors ◽

Insulin Signaling ◽

Regulatory Networks ◽

Target Genes ◽

Regulation Of Gene Expression ◽

Large Set ◽

Sequencing Analysis ◽

Experimental Conditions ◽

Functional Annotations ◽

C Elegans

Insulin/IGF-1-like signaling (IIS) plays a crucial, conserved role in development, growth, reproduction, stress tolerance, and longevity. In Caenorhabditis elegans, the enhanced longevity under reduced insulin signaling (rIIS) is primarily regulated by the transcription factors (TFs) DAF-16/FOXO, SKN-1/Nrf-1, and HSF1/HSF-1. The specific and coordinated regulation of gene expression by these TFs under rIIS has not been comprehensively elucidated. Here, using RNA-sequencing analysis, we report a systematic study of the complexity of TF-dependent target gene interactions during rIIS under analogous genetic and experimental conditions. We found that DAF-16 regulates only a fraction of the C. elegans transcriptome but controls a large set of genes under rIIS; SKN-1 and HSF-1 show the opposite trend. Both of the latter TFs function as activators and repressors to a similar extent, while DAF-16 is predominantly an activator. For expression of the genes commonly regulated by TFs under rIIS conditions, DAF-16 is the principal determining factor, dominating over the other two TFs, irrespective of whether they activate or repress these genes. The functional annotations and regulatory networks presented in this study provide novel insights into the complexity of the gene regulatory networks downstream of the IIS pathway that controls diverse phenotypes, including longevity.

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Microarray Analysis of Bacterial Gene Expression: Towards the Regulome

Comparative and Functional Genomics ◽

10.1002/cfg.193 ◽

2002 ◽

Vol 3 (4) ◽

pp. 352-354 ◽

Cited By ~ 3

Author(s):

Sharon L. Kendall ◽

Farahnaz Movahedzadeh ◽

Andreas Wietzorrek ◽

Neil G. Stoker

Keyword(s):

Gene Expression ◽

Microarray Analysis ◽

Type Strain ◽

Regulatory Networks ◽

Wild Type Strain ◽

Microarray Technology ◽

Wild Type ◽

Bacterial Gene ◽

Bacterial Gene Expression

Microarray technology allows co-regulated genes to be identified. In order to identify genes that are controlled by specific regulators, gene expression can be compared in mutant and wild-type bacteria. However, there are a number of pitfalls with this approach; in particular, the regulator may not be active under the conditions in which the wild-type strain is cultured. Once co-regulated genes have been identified, proteinbinding motifs can be identified. By combining these data with a map of promoters, or operons (the operome), the regulatory networks in the cell (the regulome) can start to be built up.

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Small RNA Mcr11 regulates genes involved in the central metabolism ofMycobacterium tuberculosisand requires 3’ sequence along with the transcription factor AbmR for stable expression

10.1101/616912 ◽

2019 ◽

Author(s):

Roxie C. Girardin ◽

Kathleen A. McDonough

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Target Genes ◽

Ectopic Expression ◽

Etiologic Agent ◽

Stable Expression ◽

Central Metabolism ◽

Bacterial Gene ◽

Bacterial Gene Expression ◽

Sequence Elements

AbstractMycobacterium tuberculosis(Mtb), the etiologic agent of tuberculosis, must adapt to host-associated environments during infection by modulating gene expression. Small regulatory RNAs (sRNAs) are key regulators of bacterial gene expression, but their roles in Mtb are not well understood. Here, we address the expression and function of the Mtb sRNA Mcr11, which is associated with slow bacterial growth and latent infections in mice. We found, by using biochemical and genetic approaches, that the AbmR transcription factor and an extended region of native sequence 3’ to themcr11gene enhance production of mature Mcr11. Additionally, we found that expression of Mcr11 was unstable in the saprophyteMycobacterium smegmatis, which lacks anmcr11orthologue. Bioinformatic analyses used to predict regulatory targets of Mcr11 identified 9-11 nucleotide regions immediately upstream of Rv3282 andlipBwith potential for direct base-pairing with Mcr11.mcr11-dependent regulation of Rv3282,lipB,Rv2216 andpknAwas demonstrated using qRT-PCR in wild type versusmcr11-deleted Mtb and found to be responsive to the presence of fatty acids. These studies establish that Mcr11 has roles in regulating growth and central metabolism in Mtb that warrant further investigation. In addition, our finding that multiple factors are required for production of stable, mature Mcr11 emphasizes the need to study mechanisms of sRNA expression and stability in TB complex mycobacteria to understand their roles in TB pathogenesis.Author SummaryBacterial pathogens must continuously modulate their gene expression in response to changing conditions to successfully infect and survive within their hosts. Transcription factors are well known regulators of gene expression, but there is growing recognition that small RNAs (sRNAs) also have critically important roles in bacterial gene regulation. Many sRNAs have been identified inM. tuberculosis(Mtb), but little is known about their expression, regulatory targets or roles in Mtb biology. In this study, we found that the Mtb sRNA Mcr11, which is expressed at high levels in slowly replicating Mtb and during mouse infection, regulates expression of several target genes involved in central metabolism. Importantly, we also discovered thatmcr11has unexpected requirements for stable expression in mycobacteria. In particular, we identified RNA sequence elements immediately downstream ofmcr11that enhance transcription termination and production of mature Mcr11 RNA in TB-complex mycobacteria. Meanwhile, ectopic expression of Mcr11 was unstable in a non-pathogenic strain of mycobacteria, suggesting that factors specific to pathogenic mycobacteria are required for the stable production of Mcr11. These studies identify sRNA stability as a new frontier for understanding gene expression in Mtb.

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