Assembling the Current Pieces: The Puzzle of RNA-Mediated Regulation in Staphylococcus aureus

The success of the major opportunistic human Staphylococcus aureus relies on the production of numerous virulence factors, which allow rapid colonization and dissemination in any tissues. Indeed, regulation of its virulence is multifactorial, and based on the production of transcriptional factors, two-component systems (TCS) and small regulatory RNAs (sRNAs). Advances in high-throughput sequencing technologies have unveiled the existence of hundreds of potential RNAs with regulatory functions, but only a fraction of which have been validated in vivo. These discoveries have modified our thinking and understanding of bacterial physiology and virulence fitness by placing sRNAs, alongside transcriptional regulators, at the center of complex and intertwined regulatory networks that allow S. aureus to rapidly adapt to the environmental cues present at infection sites. In this review, we describe the recently acquired knowledge of characterized regulatory RNAs in S. aureus that are associated with metal starvation, nutrient availability, stress responses and virulence. These findings highlight the importance of sRNAs for the comprehension of S. aureus infection processes while raising questions about the interplay between these key regulators and the pathways they control.

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Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover

Plants ◽

10.3390/plants10020267 ◽

2021 ◽

Vol 10 (2) ◽

pp. 267

Author(s):

Axel J. Giudicatti ◽

Ariel H. Tomassi ◽

Pablo A. Manavella ◽

Agustin L. Arce

Keyword(s):

Small Rna ◽

Stress Responses ◽

Cellular Localization ◽

Mirna Biogenesis ◽

Small Rna Sequencing ◽

Sequencing Data ◽

Extensive Analysis ◽

Small Regulatory Rnas ◽

Regulatory Rnas ◽

Argonaute 1

MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to stabilize and protect the molecule and to assemble a functional RNA-induced silencing complex (RISC). A specific machinery controls miRNA turnover to ensure the silencing release of targeted-genes in given circumstances. The trimming and tailing of miRNAs are fundamental modifications related to their turnover and, hence, to their action. In order to gain a better understanding of these modifications, we analyzed Arabidopsis thaliana small RNA sequencing data from a diversity of mutants, related to miRNA biogenesis, action, and turnover, and from different cellular fractions and immunoprecipitations. Besides confirming the effects of known players in these pathways, we found increased trimming and tailing in miRNA biogenesis mutants. More importantly, our analysis allowed us to reveal the importance of ARGONAUTE 1 (AGO1) loading, slicing activity, and cellular localization in trimming and tailing of miRNAs.

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Stem-loops direct precise processing of 3′ UTR-derived small RNA MicL

10.1101/341578 ◽

2018 ◽

Author(s):

Taylor B Updegrove ◽

Andrew B Kouse ◽

Katarzyna J Bandyra ◽

Gisela Storz

Keyword(s):

Small Rna ◽

Cleavage Site ◽

Differential Sensitivity ◽

Rnase E ◽

Small Regulatory Rnas ◽

Regulatory Rnas ◽

Derivatives Of

AbstractIncreasing numbers of 3′UTR-derived small, regulatory RNAs (sRNAs) are being discovered in bacteria, most generated by cleavage from longer transcripts. The enzyme required for these cleavages has been reported to be RNase E, the major endoribonuclease in enterica bacteria. Previous studies investigating RNase E have come to a range of different conclusions regarding the determinants for RNase E processing. To understand the sequence and structure determinants for the precise processing of the 3′ UTR-derived sRNAs, we examined the cleavage of multiple mutant and chimeric derivatives of the 3′ UTR-derived MicL sRNA in vivo and in vitro. Our results revealed that tandem stem-loops 3′ to the cleavage site define optimal, correctly-positioned cleavage of MicL and likely other similar sRNAs. Moreover, our assays of MicL, ArcZ and CpxQ showed that sRNAs exhibit differential sensitivity to RNase E, likely a consequence of a hierarchy of sRNA features recognized by the endonuclease.

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DualSeqDB: the host–pathogen dual RNA sequencing database for infection processes

Nucleic Acids Research ◽

10.1093/nar/gkaa890 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D687-D693

Author(s):

Javier Macho Rendón ◽

Benjamin Lang ◽

Marc Ramos Llorens ◽

Gian Gaetano Tartaglia ◽

Marc Torrent Burgas

Keyword(s):

Pathogenic Bacteria ◽

High Throughput Sequencing ◽

Homo Sapiens ◽

Cell Types ◽

Natural Hosts ◽

Host Infection ◽

Infection Processes ◽

Different Strains

Abstract Despite antibiotic resistance being a matter of growing concern worldwide, the bacterial mechanisms of pathogenesis remain underexplored, restraining our ability to develop new antimicrobials. The rise of high-throughput sequencing technology has made available a massive amount of transcriptomic data that could help elucidate the mechanisms underlying bacterial infection. Here, we introduce the DualSeqDB database, a resource that helps the identification of gene transcriptional changes in both pathogenic bacteria and their natural hosts upon infection. DualSeqDB comprises nearly 300 000 entries from eight different studies, with information on bacterial and host differential gene expression under in vivo and in vitro conditions. Expression data values were calculated entirely from raw data and analyzed through a standardized pipeline to ensure consistency between different studies. It includes information on seven different strains of pathogenic bacteria and a variety of cell types and tissues in Homo sapiens, Mus musculus and Macaca fascicularis at different time points. We envisage that DualSeqDB can help the research community in the systematic characterization of genes involved in host infection and help the development and tailoring of new molecules against infectious diseases. DualSeqDB is freely available at http://www.tartaglialab.com/dualseq.

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Use of Aptamer Tagging to Identify In Vivo Protein Binding Partners of Small Regulatory RNAs

Bacterial Regulatory RNA ◽

10.1007/978-1-61779-949-5_11 ◽

2012 ◽

pp. 177-200 ◽

Cited By ~ 2

Author(s):

Colin P. Corcoran ◽

Renate Rieder ◽

Dimitri Podkaminski ◽

Benjamin Hofmann ◽

Jörg Vogel

Keyword(s):

Protein Binding ◽

Binding Partners ◽

Small Regulatory Rnas ◽

Regulatory Rnas

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Mechanisms by Which Small RNAs Affect Bacterial Activity

Journal of Dental Research ◽

10.1177/0022034519876898 ◽

2019 ◽

Vol 98 (12) ◽

pp. 1315-1323

Author(s):

L. Lei ◽

Y. Yang ◽

S. Wu ◽

X. Ma ◽

...

Keyword(s):

Stress Responses ◽

Small Rnas ◽

Environmental Changes ◽

Expression Profiles ◽

Bacterial Flora ◽

Oral Disease ◽

Bacterial Gene ◽

Bacterial Physiology ◽

Cellular Processes ◽

Regulatory Rnas

The oral cavity contains a distinct habitat that supports diverse bacterial flora. Recent observations have provided additional evidence that sRNAs are key regulators of bacterial physiology and pathogenesis. These sRNAs have been divided into 5 functional groups: cis-encoded RNAs, trans-encoded RNAs, RNA regulators of protein activity, bacterial CRISPR (clustered regularly interspaced short palindromic repeat) RNAs, and a novel category of miRNA-size small RNAs (msRNAs). In this review, we discuss a critical group of key commensal and opportunistic oral pathogens. In general, supragingival bacterial sRNAs function synergistically to fine-tune the regulation of cellular processes and stress responses in adaptation to environmental changes. Particularly in the cariogenic bacteria Streptococcus mutans, both the antisense vicR RNA and msRNA1657 can impede the metabolism of bacterial exopolysaccharides, prevent biofilm formation, and suppress its cariogenicity. In Enterococcus faecalis, selected sRNAs control the expression of proteins involved in diverse cellular processes and stress responses. In subgingival plaques, sRNAs from periodontal pathogens can function as novel bacterial signaling molecules that mediate bacterial-human interactions in periodontal homeostasis. In Porphyromonas gingivalis, the expression profiles of putative sRNA101 and sRNA42 were found to respond to hemin availability after hemin starvation. Regarding Aggregatibacter actinomycetemcomitans (previously Actinobacillus actinomycetemcomitans), a major periodontal pathogen associated with aggressive periodontitis, the predicted sRNAs interact with several virulence genes, including those encoding leukotoxin and cytolethal distending toxin. Furthermore, in clinical isolates, these associated RNAs could be explored not only as potential biomarkers for oral disease monitoring but also as alternative types of regulators for drug design. Thus, this emerging subspecialty of bacterial regulatory RNAs could reshape our understanding of bacterial gene regulation from their key roles of endogenous regulatory RNAs to their activities in pathologic processes.

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Identification and Profiling of Conserved MicroRNAs in Different Developmental Stages of Crown Imperial (Fritillaria Imperialis L.) using High-throughput Sequencing

10.21203/rs.3.rs-707079/v1 ◽

2021 ◽

Author(s):

Fereshteh Ahmadi Teshniz ◽

Behrouz Shiran ◽

Sadegh Mousavi-Fard ◽

Hossein Fallahi ◽

Bojana Banović Đeri

Keyword(s):

Plant Species ◽

Abiotic Stresses ◽

Regulatory Networks ◽

High Throughput Sequencing ◽

Developmental Stages ◽

Expression Patterns ◽

Practical Application ◽

Sequencing Technologies ◽

New Strategies ◽

Different Tissues

Abstract Novel strategies for improvement of plants’ ornamental and other properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. These are two major reasons why more studies are needed before envisioned new strategies may take their course in practical application domain. This research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. Among identified conserved miRNA families in crown imperial, miR166, miR169 and miR396 families were the most abundant ones. The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles these miRNAs have in growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.

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Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq

10.1101/2021.08.13.456236 ◽

2021 ◽

Author(s):

Kumari Kavita ◽

Aixia Zhang ◽

Chin-Hsien Tai ◽

Nadim Majdalani ◽

Gisela Storz ◽

...

Keyword(s):

Escherichia Coli ◽

Rna Binding ◽

Class Ii ◽

Rna Chaperone ◽

Terminal Domain ◽

C Terminus ◽

Bacterial Rna ◽

Small Regulatory Rnas ◽

Regulatory Rnas

Hfq, a bacterial RNA chaperone, stabilizes small regulatory RNAs (sRNAs) and facilitates sRNA base-pairing with target mRNAs. Hfq has a conserved N-terminal domain and a poorly conserved disordered C-terminal domain (CTD). In a transcriptome-wide examination of the effects of a chromosomal CTD deletion (Hfq1-65), the Escherichia coli mutant was most defective for the accumulation of sRNAs that bind the proximal and distal faces of Hfq (Class II sRNAs), but other sRNAs also were affected. There were only modest effects on the levels of mRNAs, suggesting little disruption of sRNA-dependent regulation. However, cells expressing Hfq lacking the CTD deletion in combination with a weak distal face mutation were defective for the function of the Class II sRNA ChiX and repression of mutS, both dependent upon distal face RNA binding. Loss of the region between amino acids 66-72 was critical for this defect. The CTD region beyond amino acid 72 was not necessary for distal face-dependent regulation, but was needed for functions associated with the Hfq rim, seen most clearly in combination with a rim mutant. Our results suggest that the C-terminus collaborates in various ways with different binding faces of Hfq, leading to distinct outcomes for individual sRNAs.

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A novel computational approach for genome-wide prediction of small RNAs in bacteria

10.1101/011668 ◽

2014 ◽

Author(s):

Lei Li ◽

Hoi Shan Kwan

Keyword(s):

Small Rnas ◽

Computational Prediction ◽

Transcriptional Regulators ◽

Structural Features ◽

Extensive Study ◽

Bacterial Physiology ◽

Genome Wide ◽

Small Regulatory Rnas ◽

Regulatory Rnas ◽

Window Approach

Small regulatory RNAs (sRNAs) are the most abundant post-transcriptional regulators in bacteria. They serve ubiquitous roles that control nearly every aspects of bacterial physiology. Identification of important features from sRNAs sequences will guide the computational prediction of new sRNA sequences for a better understanding of the pervasive sRNA-mediated regulation in bacteria. In this study, we have performed systematic analyses of many sequence and structural features that are possibly related to sRNA properties and identified a subset of significant features that effectively discriminate sRNAs sequences from random sequences. we then used a neural network model that integrated these subfeatures on unlabeled testing datasets, and it had achieved a 92.2% recall and 89.8% specificity. Finally, we applied this prediction model for genome-wide identification of sRNAs-encoded genes using a sliding-window approach. We recovered multiple known sRNAs and hundreds of predicted new sRNAs. These candidate novel sRNAs deserve extensive study to better understand the sRNA-mediated regulatory network in bacteria.

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Microprocessor dynamics shows co- and post-transcriptional processing of pri-miRNAs

10.1101/097311 ◽

2016 ◽

Author(s):

Annita Louloupi ◽

Evgenia Ntini ◽

Julia Liz ◽

Ulf Andersson Ørom

Keyword(s):

Mirna Biogenesis ◽

Intact Cells ◽

Step Process ◽

Mirna Processing ◽

In Vivo Kinetics ◽

Small Regulatory Rnas ◽

Regulatory Rnas ◽

Kinetics Of ◽

Over Time

AbstractmiRNAs are small regulatory RNAs involved in the regulation of translation of target transcripts. miRNA biogenesis is a multi-step process starting with the cleavage of the primary miRNA transcript in the nucleus by the Microprocessor complex. Endogenous processing of pri-miRNAs is challenging to study and the in vivo kinetics of this process is not known. Here, we present a method for determining the processing kinetics of pri-miRNAs within intact cells over time using a pulse-chase approach to obtain nascent RNA within a 1-hour window after labeling with bromouridine. We show, that pri-miRNAs exhibit different processing kinetics ranging from fast over intermediate to slow processing and provide evidence that pri-miRNA processing can occur both co-transcriptionally and post-transcriptionally.

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