scholarly journals RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R

2006 ◽  
Vol 34 (20) ◽  
pp. 5923-5931 ◽  
Author(s):  
Victoria Portnoy ◽  
Gadi Schuster
Keyword(s):  
Rnase R ◽  
Rna Polyadenylation

scholarly journals Decreased Expression of Stable RNA Can Alleviate the Lethality Associated with RNase E Deficiency in Escherichia coli

2017 ◽  
Vol 199 (8) ◽  
Author(s):  
P. Himabindu ◽  
K. Anupama
Keyword(s):  
Escherichia Coli ◽  
Mrna Degradation ◽  
Gram Negative Bacteria ◽  
Rrna Processing ◽  
Rnase E ◽  
Rnase R ◽  
Content Type ◽  
E Coli ◽  
Rrna Species ◽  
Rna Levels

ABSTRACT The endoribonuclease RNase E participates in mRNA degradation, rRNA processing, and tRNA maturation in Escherichia coli, but the precise reasons for its essentiality are unclear and much debated. The enzyme is most active on RNA substrates with a 5′-terminal monophosphate, which is sensed by a domain in the enzyme that includes residue R169; E. coli also possesses a 5′-pyrophosphohydrolase, RppH, that catalyzes conversion of 5′-terminal triphosphate to 5′-terminal monophosphate on RNAs. Although the C-terminal half (CTH), beyond residue approximately 500, of RNase E is dispensable for viability, deletion of the CTH is lethal when combined with an R169Q mutation or with deletion of rppH. In this work, we show that both these lethalities can be rescued in derivatives in which four or five of the seven rrn operons in the genome have been deleted. We hypothesize that the reduced stable RNA levels under these conditions minimize the need of RNase E to process them, thereby allowing for its diversion for mRNA degradation. In support of this hypothesis, we have found that other conditions that are known to reduce stable RNA levels also suppress one or both lethalities: (i) alterations in relA and spoT, which are expected to lead to increased basal ppGpp levels; (ii) stringent rpoB mutations, which mimic high intracellular ppGpp levels; and (iii) overexpression of DksA. Lethality suppression by these perturbations was RNase R dependent. Our work therefore suggests that its actions on the various substrates (mRNA, rRNA, and tRNA) jointly contribute to the essentiality of RNase E in E. coli. IMPORTANCE The endoribonuclease RNase E is essential for viability in many Gram-negative bacteria, including Escherichia coli. Different explanations have been offered for its essentiality, including its roles in global mRNA degradation or in the processing of several tRNA and rRNA species. Our work suggests that, rather than its role in the processing of any one particular substrate, its distributed functions on all the different substrates (mRNA, rRNA, and tRNA) are responsible for the essentiality of RNase E in E. coli.

scholarly journals The emerging role of circular RNAs in breast cancer

2019 ◽  
Vol 39 (6) ◽  
Author(s):  
Si-ying Zhou ◽  
Wei Chen ◽  
Su-jin Yang ◽  
Zi-han Xu ◽  
Jia-hua Hu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cell Invasion ◽  
Clinical Characteristics ◽  
Circular Rnas ◽  
Rnase R ◽  
New Class ◽  
Regulatory Rnas ◽  
And Function

AbstractBreast cancer (BCa) is one of the most frequently diagnosed cancers and leading cause of cancer deaths among females worldwide. Circular RNAs (circRNAs) are a new class of endogenous regulatory RNAs characterized by circular shape resulting from covalently closed continuous loops that are capable of regulating gene expression at transcription or post-transcription levels. With the unique structures, circRNAs are resistant to exonuclease RNase R and maintain stability more easily than linear RNAs. Recently, an increasing number of circRNAs are discovered and reported to show different expression in BCa and these dysregulated circRNAs were correlated with patients’ clinical characteristics and grade in the progression of BCa. CircRNAs participate in the bioprocesses of carcinogenesis of BCa, including cell proliferation, apoptosis, cell cycle, tumorigenesis, vascularization, cell invasion, migration as well as metastasis. Here we concentrated on biogenesis and function of circRNAs, summarized their implications in BCa and discussed their potential as diagnostic and therapeutic targets for BCa.

The role of RNase R in trans-translation and ribosomal quality control

Biochimie ◽  
2015 ◽  
Vol 114 ◽  
pp. 113-118 ◽  
Author(s):  
Susana Domingues ◽  
Ricardo N. Moreira ◽  
José M. Andrade ◽  
Ricardo F. dos Santos ◽  
Cátia Bárria ◽  
...  
Keyword(s):  
Quality Control ◽  
Rnase R ◽  
In Trans

scholarly journals Merkel Cell Polyomavirus Encodes Circular RNAs (circRNAs) Enabling a Dynamic circRNA/microRNA/mRNA Regulatory Network

mBio ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. e03059-20
Author(s):  
Bizunesh Abere ◽  
Hongzhao Zhou ◽  
Jinghui Li ◽  
Simon Cao ◽  
Tuna Toptan ◽  
...  
Keyword(s):  
Viral Replication ◽  
Rna Sequencing ◽  
Regulatory Network ◽  
T Antigen ◽  
Merkel Cell Polyomavirus ◽  
Circular Rnas ◽  
Merkel Cell ◽  
Rnase R ◽  
Early Region ◽  
Human Dna

ABSTRACTViral noncoding RNAs have acquired increasing prominence as important regulators of infection and mediators of pathogenesis. Circular RNAs (circRNAs) generated by backsplicing events have been identified in several oncogenic human DNA viruses. Here, we show that Merkel cell polyomavirus (MCV), the etiologic cause of ∼80% of Merkel cell carcinomas (MCCs), also expresses circular RNAs. By RNase R-resistant RNA sequencing, four putative circRNA backsplice junctions (BSJs) were identified from the MCV early region (ER). The most abundantly expressed MCV circRNA, designated circMCV-T, is generated through backsplicing of all of ER exon II to form a 762-nucleotide (nt) circular RNA molecule. Curiously, circMCV-T, as well as two other less abundantly expressed putative MCV circRNAs, overlaps in a complementary fashion with the MCV microRNA (miRNA) locus that encodes MCV-miR-M1. circMCV-T is consistently detected in concert with linear T antigen transcripts throughout infection, suggesting a crucial role for this RNA molecule in the regulatory functions of the early region, known to be vital for viral replication. Knocking out the hairpin structure of MCV-miR-M1 in genomic early region expression constructs and using a new high-efficiency, recombinase-mediated, recircularized MCV molecular clone demonstrates that circMCV-T levels decrease in the presence of MCV-miR-M1, underscoring the interplay between MCV circRNA and miRNA. Furthermore, circMCV-T partially reverses the known inhibitory effect of MCV-miR-M1 on early gene expression. RNase R-resistant RNA sequencing of lytic rat polyomavirus 2 (RatPyV2) identified an analogously located circRNA, stipulating a crucial, conserved regulatory function of this class of RNA molecules in the family of polyomaviruses.IMPORTANCE Covalently closed circular RNAs were recently described in the human DNA tumor viruses Epstein-Barr virus (EBV), Kaposi’s sarcoma-associated herpesvirus (KSHV), and human papillomavirus (HPV). Here, we show that MCV, another DNA tumor virus, generates circRNAs from its early regulatory region in concert with T antigen linear transcripts. MCV circMCV-T interacts with another MCV noncoding RNA, miR-M1, to functionally modulate early region transcript expression important for viral replication and long-term episomal persistence. This work describes a dynamic regulatory network integrating circRNA/miRNA/mRNA biomolecules and underscores the intricate functional modulation between several classes of polyomavirus-encoded RNAs in the control of viral replication.

scholarly journals Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

RNA ◽  
2011 ◽  
Vol 17 (4) ◽  
pp. 761-772 ◽  
Author(s):  
P. J. Shepard ◽  
E.-A. Choi ◽  
J. Lu ◽  
L. A. Flanagan ◽  
K. J. Hertel ◽  
...  
Keyword(s):  
Dynamic Landscape ◽  
Rna Polyadenylation

scholarly journals Landscape of RNA polyadenylation inE. coli

2016 ◽  
pp. gkw894 ◽  
Author(s):  
Alexandre Maes ◽  
Céline Gracia ◽  
Nicolas Innocenti ◽  
Kaiyang Zhang ◽  
Erik Aurell ◽  
...  
Keyword(s):  
Rna Polyadenylation

scholarly journals Insights into How RNase R Degrades Structured RNA: Analysis of the Nuclease Domain

2009 ◽  
Vol 387 (3) ◽  
pp. 570-583 ◽  
Author(s):  
Helen A. Vincent ◽  
Murray P. Deutscher
Keyword(s):  
Rnase R ◽  
Rna Analysis ◽  
Nuclease Domain

scholarly journals Maturation-specific polyadenylation and translational control: diversity of cytoplasmic polyadenylation elements, influence of poly(A) tail size, and formation of stable polyadenylation complexes.

1990 ◽  
Vol 10 (11) ◽  
pp. 5634-5645 ◽  
Author(s):  
J Paris ◽  
J D Richter
Keyword(s):  
Complex Formation ◽  
Oocyte Maturation ◽  
Translational Control ◽  
Untranslated Regions ◽  
Stable Complex ◽  
Mobility Shift ◽  
Cytoplasmic Polyadenylation ◽  
Egg Extracts ◽  
Gel Mobility Shift ◽  
Rna Polyadenylation

Early embryonic development in Xenopus laevis is programmed in part by maternally derived mRNAs, many of which are translated at the completion of meiosis (oocyte maturation). Polysomal recruitment of at least one of these mRNAs, G10, is regulated by cytoplasmic poly(A) elongation which, in turn, is dependent upon the cytoplasmic polyadenylation element (CPE) UUUUUUAUAAAG and the hexanucleotide AAUAAA (L. L. McGrew, E. Dworkin-Rastl, M. B. Dworkin, and J. D. Richter, Genes Dev. 3:803-815, 1989). We have investigated whether sequences similar to the G10 RNA CPE that are present in other RNAs could also be responsible for maturation-specific polyadenylation. B4 RNA, which encodes a histone H1-like protein, requires a CPE of the sequence UUUUUAAU as well as the polyadenylation hexanucleotide. The 3' untranslated regions of Xenopus c-mos RNA and mouse HPRT RNA also contain U-rich CPEs since they confer maturation-specific polyadenylation when fused to Xenopus B-globin RNA. Polyadenylation of B4 RNA, which occurs very early during maturation, is limited to 150 residues, and it is this number that is required for polysomal recruitment. To investigate the possible diversity of factors and/or affinities that might control polyadenylation, egg extracts that faithfully adenylate exogenously added RNA were used in competition experiments. At least one factor is shared by B4 and G10 RNAs, although it has a much greater affinity for B4 RNA. Additional experiments demonstrate that an intact CPE and hexanucleotide are both required to compete for the polyadenylation apparatus. Gel mobility shift assays show that two polyadenylation complexes are formed on B4 RNA. Optimal complex formation requires an intact CPE and hexanucleotide but not ongoing adenylation. These data, plus additional RNA competition studies, suggest that stable complex formation is enhanced by an interaction of the trans-acting factors that bind the CPE and polyadenylation hexanucleotide.

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