scholarly journals Stem-Loop Structures within mRNA Coding Sequences Activate Translation Initiation and Mediate Control by Small Regulatory RNAs

2017 ◽  
Vol 68 (1) ◽  
pp. 158-170.e3 ◽  
Author(s):  
Jonathan Jagodnik ◽  
Claude Chiaruttini ◽  
Maude Guillier
Keyword(s):  
Translation Initiation ◽  
Stem Loop ◽  
Coding Sequences ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas

scholarly journals Trans-Acting Effectors Versus RNA Cis-Elements: A Tightly Knit Regulatory Mesh

2020 ◽  
Vol 11 ◽  
Author(s):  
Marie-Claude Carrier ◽  
Evelyne Ng Kwan Lim ◽  
Gabriel Jeannotte ◽  
Eric Massé
Keyword(s):  
Translation Initiation ◽  
Translation Regulation ◽  
Sequence Motifs ◽  
Cis Elements ◽  
Rna Structures ◽  
Mechanistic Studies ◽  
Small Regulatory Rnas ◽  
Environmental Variations ◽  
Regulatory Rnas ◽  
Rna Transcript

Prokaryotic organisms often react instantly to environmental variations to ensure their survival. They can achieve this by rapidly and specifically modulating translation, the critical step of protein synthesis. The translation machinery responds to an array of cis-acting elements, located on the RNA transcript, which dictate the fate of mRNAs. These cis-encoded elements, such as RNA structures or sequence motifs, interact with a variety of regulators, among them small regulatory RNAs. These small regulatory RNAs (sRNAs) are especially effective at modulating translation initiation through their interaction with cis-encoded mRNA elements. Here, through selected examples of canonical and non-canonical regulatory events, we demonstrate the intimate connection between mRNA cis-encoded features and sRNA-dependent translation regulation. We also address how sRNA-based mechanistic studies can drive the discovery of new roles for cis-elements. Finally, we briefly overview the challenges of using translation regulation by synthetic regulators as a tool.

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 Novel start codons introduce novel coding sequences in the human genomes

2020 ◽  
Author(s):  
He Zhang ◽  
Yang Xie
Keyword(s):  
Translation Initiation ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Human Populations ◽  
The Novel ◽  
Coding Sequences ◽  
Human Genomes ◽  
High Level ◽  
Selection Signal ◽  
Human Specific

AbstractStart-gain mutations can introduce novel start codons and generate novel coding sequences that may affect the function of genes. In this study, we systematically investigated the novel start codons that were either polymorphic or fixed in the human genomes. 829 polymorphic start-gain SNVs were identified in the human populations, and the novel start codons introduced by these SNVs have significantly higher activity in translation initiation. Some of these start-gain SNVs were reported to be associated with phenotypes and diseases in previous studies. By comparative genomic analysis, we found 26 human-specific start codons that were fixed after the divergence between the human and chimpanzee, and high-level translation initiation activity was observed on them. The negative selection signal was detected in the novel coding sequences introduced by these human-specific start codons, indicating the important function of these novel coding sequences. This study reveals start-gain mutations are keeping appearing in the human genomes during the evolution and may be important sources altering the function of genes which may further affect the phenotypes or cause diseases.

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 Distinct Poly(rC) Binding Protein KH Domain Determinants for Poliovirus Translation Initiation and Viral RNA Replication

2002 ◽  
Vol 76 (23) ◽  
pp. 12008-12022 ◽  
Author(s):  
Brandon L. Walter ◽  
Todd B. Parsley ◽  
Ellie Ehrenfeld ◽  
Bert L. Semler
Keyword(s):  
Translation Initiation ◽  
Rna Synthesis ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Replication ◽  
Viral Rna ◽  
Host Protein ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure

ABSTRACT The limited coding capacity of picornavirus genomic RNAs necessitates utilization of host cell factors in the completion of an infectious cycle. One host protein that plays a role in both translation initiation and viral RNA synthesis is poly(rC) binding protein 2 (PCBP2). For picornavirus RNAs containing type I internal ribosome entry site (IRES) elements, PCBP2 binds the major stem-loop structure (stem-loop IV) in the IRES and is essential for translation initiation. Additionally, the binding of PCBP2 to the 5′-terminal stem-loop structure (stem-loop I or cloverleaf) in concert with viral protein 3CD is required for initiation of RNA synthesis directed by poliovirus replication complexes. PCBP1, a highly homologous isoform of PCBP2, binds to poliovirus stem-loop I with an affinity similar to that of PCBP2; however, PCBP1 has reduced affinity for stem-loop IV. Using a dicistronic poliovirus RNA, we were able to functionally uncouple translation and RNA replication in PCBP-depleted extracts. Our results demonstrate that PCBP1 rescues RNA replication but is not able to rescue translation initiation. We have also generated mutated versions of PCBP2 containing site-directed lesions in each of the three RNA-binding domains. Specific defects in RNA binding to either stem-loop I and/or stem-loop IV suggest that these domains may have differential functions in translation and RNA replication. These predictions were confirmed in functional assays that allow separation of RNA replication activities from translation. Our data have implications for differential picornavirus template utilization during viral translation and RNA replication and suggest that specific PCBP2 domains may have distinct roles in these activities.

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).

Sign in / Sign up

Export Citation Format

Share Document