Mechanistic study of base-pairing small regulatory RNAs in bacteria

Methods ◽  
2017 ◽  
Vol 117 ◽  
pp. 67-76 ◽  
Author(s):  
Jonathan Jagodnik ◽  
Anaïs Brosse ◽  
Thao Nguyen Le Lam ◽  
Claude Chiaruttini ◽  
Maude Guillier
Keyword(s):  
Mechanistic Study ◽  
Base Pairing ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas

scholarly journals Cis- and Trans-Encoded Small Regulatory RNAs in Bacillus subtilis

2021 ◽  
Vol 9 (9) ◽  
pp. 1865
Author(s):  
Sabine Brantl ◽  
Peter Müller
Keyword(s):  
Potential Role ◽  
Bacterial Species ◽  
Model Organism ◽  
Physiological Role ◽  
Base Pairing ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Rna Chaperones ◽  
Cis And Trans

Small regulatory RNAs (sRNAs) that act by base-pairing are the most abundant posttranscriptional regulators in all three kingdoms of life. Over the past 20 years, a variety of approaches have been employed to discover chromosome-encoded sRNAs in a multitude of bacterial species. However, although largely improved bioinformatics tools are available to predict potential targets of base-pairing sRNAs, it is still challenging to confirm these targets experimentally and to elucidate the mechanisms as well as the physiological role of their sRNA-mediated regulation. Here, we provide an overview of currently known cis- and trans-encoded sRNAs from B. subtilis with known targets and defined regulatory mechanisms and on the potential role of RNA chaperones that are or might be required to facilitate sRNA regulation in this important Gram-positive model organism.

scholarly journals Bacterial chaperone protein Hfq facilitates the annealing of sponge RNAs to small regulatory RNAs

2021 ◽  
Author(s):  
Ewelina M. Małecka ◽  
Daria Sobańska ◽  
Mikołaj Olejniczak
Keyword(s):  
Environmental Conditions ◽  
Small Rnas ◽  
Base Pairing ◽  
Biochemical Methods ◽  
Target Mrnas ◽  
Chaperone Protein ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Posttranscriptional Level

ABSTRACTBacterial small RNAs (sRNAs) in association with the chaperone protein Hfq regulate the expression of many target mRNAs. Since sRNAs’ action is crucial to engender a response to changing environmental conditions, their activity needs to be regulated. One such mechanism occurs at posttranscriptional level and involves sponge RNAs (or anti-sRNAs) which sequester sRNAs affecting their regulatory output. Both types of RNAs were identified on Hfq, but it is not known how Hfq interacts with RNA sponges and stimulates their base-pairing with sRNAs. Here, we used biochemical methods to demonstrate that anti-sRNAs resemble sRNAs by their structure and their modes of Hfq binding. Hfq facilitates sponge RNA annealing to sRNA, and each surface of the protein plays a particular role in the process. Moreover, we found that the efficiency of sponge RNA interactions with sRNAs can be improved, therefore, we propose that natural RNA sponges might not sequester sRNAs optimally.

Recent Research Advances in Small Regulatory RNAs in Streptococcus

2021 ◽  
Author(s):  
Zhi-Qiang Xiong ◽  
Ze-Xuan Lv ◽  
Xin Song ◽  
Xin-Xin Liu ◽  
Yong-Jun Xia ◽  
...  
Keyword(s):  
Small Regulatory Rnas ◽  
Regulatory Rnas

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

Plants ◽  
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.

scholarly journals An Interplay Between Small Regulatory RNAs Patterns Leaves

2007 ◽  
Vol 2 (6) ◽  
pp. 519-521 ◽  
Author(s):  
Fabio T.S. Nogueira ◽  
Marja C.P. Timmermans
Keyword(s):  
Small Regulatory Rnas ◽  
Regulatory Rnas

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

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.

scholarly journals Hfq and three Hfq-dependent small regulatory RNAs—MgrR, RyhB and McaS—coregulate the locus of enterocyte effacement in enteropathogenicEscherichia coli

2016 ◽  
Vol 75 (1) ◽  
pp. ftw113 ◽  
Author(s):  
Shantanu Bhatt ◽  
Marisa Egan ◽  
Jasmine Ramirez ◽  
Christian Xander ◽  
Valerie Jenkins ◽  
...  
Keyword(s):  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Enterocyte Effacement

MiR-302: The Multifunctional MicroRNA

2019 ◽  
Vol 3 (1) ◽  
pp. 01-02
Author(s):  
Shao Ying
Keyword(s):  
Protein Translation ◽  
Mature Mirnas ◽  
Mirna Precursor ◽  
Regulate Gene Expression ◽  
Cellular Processes ◽  
Target Mrnas ◽  
Complementary Sequences ◽  
Wide Range ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas

MicroRNAs (miRNAs) are short single-stranded noncoding RNAs (20- to 25-nucleotide (nt) long) representing a class of small regulatory RNAs. By inhibiting the translation of target mRNAs, miRNAs regulate gene expression posttranscriptionally and thus play an important role in a wide range of cellular processes. Currently, there are two known types of miRNAs: intergenic and intronic miRNAs. Biogenesis of an intergenic miRNA starts with the synthesis of a primary miRNA transcript (pri-miRNA) catalyzed by types-II or -III RNA polymerase (Pol-II/III). Pri-miRNAs are processed in the nucleus by the ribonuclease Drosha into a miRNA precursor (pre-miRNA) approximately 60-nt in length. After being transported into the cytoplasm, these pre-miRNAs are further processed into mature and functional miRNAs by the cytoplasmic ribonuclease Dicer. Mature miRNAs then associate with a number of proteins to form the RNA-induced silencing complex (RISC) that bind with target mRNAs having total or partial complementary sequences to the miRNAs and initiate the inhibition of subsequent protein translation via RNA interference (RNAi).

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