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.

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).

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

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.

scholarly journals GW182 Proteins Restrict Extracellular Vesicle-Mediated Export of MicroRNAs in Mammalian Cancer Cells

2021 ◽  
Vol 41 (5) ◽  
Author(s):  
Souvik Ghosh ◽  
Kamalika Mukherjee ◽  
Yogaditya Chakrabarty ◽  
Susanta Chatterjee ◽  
Bartika Ghoshal ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Mammalian Cells ◽  
Extracellular Vesicle ◽  
Human Cells ◽  
Negative Regulator ◽  
Interacting Protein ◽  
Processing Bodies ◽  
Target Mrnas ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas

ABSTRACT MicroRNAs (miRNAs) are small regulatory RNAs of relatively long half-life in non-proliferative human cells. However, in cancer cells the half-lives of miRNAs are comparatively short. To understand the mechanism of rapid miRNA turnover in cancer cells, we explored the effect of target mRNAs on the abundance of the miRNAs that repress them. We have noted an accelerated extracellular vesicle (EV)-mediated export of miRNAs in presence of their target mRNAs in mammalian cells, and this target-driven miRNA-export process is retarded by Ago2-interacting protein GW182B. The GW182 group of proteins are localized to GW182 bodies or RNA processing bodies in mammalian cells, and GW182B-dependent retardation of miRNA export depends on GW body integrity and is independent of the HuR protein-mediated auxiliary pathway of miRNA export. Our data thus support the existence of a HuR-independent pathway of miRNA export in human cells that can be targeted in MDA-MB-231 cancer cells, to increase the level of cellular let-7a, a known negative regulator of cancer growth.

scholarly journals Two GacA-Dependent Small RNAs Modulate the Quorum-Sensing Response in Pseudomonas aeruginosa

2006 ◽  
Vol 188 (16) ◽  
pp. 6026-6033 ◽  
Author(s):  
Elisabeth Kay ◽  
Bérénice Humair ◽  
Valérie Dénervaud ◽  
Kathrin Riedel ◽  
Stéphanie Spahr ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Small Rnas ◽  
Homoserine Lactone ◽  
Two Component System ◽  
Bond Forming ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Chitin Binding Protein ◽  
Biofilm Development

ABSTRACT In Pseudomonas aeruginosa, the GacS/GacA two-component system positively controls the quorum-sensing machinery and the expression of extracellular products via two small regulatory RNAs, RsmY and RsmZ. An rsmY rsmZ double mutant and a gacA mutant were similarly impaired in the synthesis of the quorum-sensing signal N-butanoyl-homoserine lactone, the disulfide bond-forming enzyme DsbA, and the exoproducts hydrogen cyanide, pyocyanin, elastase, chitinase (ChiC), and chitin-binding protein (CbpD). Both mutants showed increased swarming ability, azurin release, and early biofilm development.

scholarly journals Structure of anEscherichia coliHfq:RNA complex at 0.97 Å resolution

2014 ◽  
Vol 70 (11) ◽  
pp. 1492-1497 ◽  
Author(s):  
Eike C. Schulz ◽  
Orsolya Barabas
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Binding Site ◽  
Small Rnas ◽  
Target Genes ◽  
Rna Binding ◽  
Base Pairing ◽  
Rna Chaperone ◽  
Target Mrnas ◽  
Rna Interaction

In bacteria, small RNAs (sRNAs) silence or activate target genes through base pairing with the mRNA, thereby modulating its translation. A central player in this process is the RNA chaperone Hfq, which facilitates the annealing of sRNAs with their target mRNAs. Hfq has two RNA-binding surfaces that recognize A-rich and U-rich sequences, and is believed to bind an sRNA–mRNA pair simultaneously. However, how Hfq promotes annealing remains unclear. Here, the crystal structure ofEscherichia coliHfq is presented in complex with U6-RNA bound to its proximal binding site at 0.97 Å resolution, revealing the Hfq–RNA interaction in exceptional detail.

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.

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 A Cluster of Four Homologous Small RNAs Modulates C1Metabolism and the Pyruvate Dehydrogenase Complex in Rhodobacter sphaeroides under Various Stress Conditions

2015 ◽  
Vol 197 (10) ◽  
pp. 1839-1852 ◽  
Author(s):  
Fabian Billenkamp ◽  
Tao Peng ◽  
Bork A. Berghoff ◽  
Gabriele Klug
Keyword(s):  
Oxidative Stress ◽  
Rhodobacter Sphaeroides ◽  
Pyruvate Dehydrogenase ◽  
Small Rnas ◽  
Pyruvate Dehydrogenase Complex ◽  
Oxygen Species ◽  
Content Type ◽  
Target Mrnas ◽  
Regulatory Rnas ◽  
Dehydrogenase Complex

ABSTRACTIn bacteria, regulatory RNAs play an important role in the regulation and balancing of many cellular processes and stress responses. Among these regulatory RNAs,trans-encoded small RNAs (sRNAs) are of particular interest since one sRNA can lead to the regulation of multiple target mRNAs. In the purple bacteriumRhodobacter sphaeroides, several sRNAs are induced by oxidative stress. In this study, we focused on the functional characterization of four homologous sRNAs that are cotranscribed with the gene for the conserved hypothetical protein RSP_6037, a genetic arrangement described for only a few sRNAs until now. Each of the four sRNAs is characterized by two stem-loops that carry CCUCCUCCC motifs in their loops. They are induced under oxidative stress, as well as by various other stress conditions, and were therefore renamed here sRNAs CcsR1 to CcsR4 (CcsR1–4) forconservedCCUCCUCCC motifstress-inducedRNAs 1 to 4. Increased CcsR1–4 expression decreases the expression of genes involved in C1metabolism or encoding components of the pyruvate dehydrogenase complex either directly by binding to their target mRNAs or indirectly. One of the CcsR1–4 target mRNAs encodes the transcriptional regulator FlhR, an activator of glutathione-dependent methanol/formaldehyde metabolism. Downregulation of this glutathione-dependent pathway increases the pool of glutathione, which helps to counteract oxidative stress. The FlhR-dependent downregulation of the pyruvate dehydrogenase complex reduces a primary target of reactive oxygen species and reduces aerobic electron transport, a main source of reactive oxygen species. Our findings reveal a previously unknown strategy used by bacteria to counteract oxidative stress.IMPORTANCEPhototrophic organisms have to cope with photo-oxidative stress due to the function of chlorophylls as photosensitizers for the formation of singlet oxygen. Our study assigns an important role in photo-oxidative stress resistance to a cluster of four homologous sRNAs in the anoxygenic phototrophic bacteriumRhodobacter sphaeroides. We reveal a function of these regulatory RNAs in the fine-tuning of C1metabolism. A model that relates oxidative stress defense to C1metabolism is presented.

scholarly journals Small Toxic Proteins and the Antisense RNAs That Repress Them

2008 ◽  
Vol 72 (4) ◽  
pp. 579-589 ◽  
Author(s):  
Elizabeth M. Fozo ◽  
Matthew R. Hemm ◽  
Gisela Storz
Keyword(s):  
Amino Acids ◽  
Small Rna ◽  
Small Rnas ◽  
Short Length ◽  
Type I ◽  
Practical Applications ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Rna Genes ◽  
Toxic Proteins

SUMMARY There has been a great expansion in the number of small regulatory RNAs identified in bacteria. Some of these small RNAs repress the synthesis of potentially toxic proteins. Generally the toxin proteins are hydrophobic and less than 60 amino acids in length, and the corresponding antitoxin small RNA genes are antisense to the toxin genes or share long stretches of complementarity with the target mRNAs. Given their short length, only a limited number of these type I toxin-antitoxin loci have been identified, but it is predicted that many remain to be found. Already their characterization has given insights into regulation by small RNAs, has suggested functions for the small toxic proteins at the cell membrane, and has led to practical applications for some of the type I toxin-antitoxin loci.

scholarly journals Compensatory sequence variation between trans-species small RNAs and their target sites

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Nathan R Johnson ◽  
Claude W dePamphilis ◽  
Michael J Axtell
Keyword(s):  
Small Rnas ◽  
Synonymous Site ◽  
Protein Coding ◽  
Coding Regions ◽  
Target Sites ◽  
Site Variation ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Multiple Species ◽  
Multiple Variants

Trans-species small regulatory RNAs (sRNAs) are delivered to host plants from diverse pathogens and parasites and can target host mRNAs. How trans-species sRNAs can be effective on diverse hosts has been unclear. Multiple species of the parasitic plant Cuscuta produce trans-species sRNAs that collectively target many host mRNAs. Confirmed target sites are nearly always in highly conserved, protein-coding regions of host mRNAs. Cuscuta trans-species sRNAs can be grouped into superfamilies that have variation in a three-nucleotide period. These variants compensate for synonymous-site variation in host mRNAs. By targeting host mRNAs at highly conserved protein-coding sites, and simultaneously expressing multiple variants to cover synonymous-site variation, Cuscuta trans-species sRNAs may be able to successfully target multiple homologous mRNAs from diverse hosts.

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