scholarly journals Distinct tmRNA sequence elements facilitate RNase R engagement on rescued ribosomes for selective nonstop mRNA decay

2014 ◽  
Vol 42 (17) ◽  
pp. 11192-11202 ◽  
Author(s):  
Krithika Venkataraman ◽  
Hina Zafar ◽  
A. Wali Karzai
Keyword(s):  
Mrna Decay ◽  
Rnase R ◽  
Nonstop Mrna Decay ◽  
Sequence Elements

scholarly journals tmRNA determinants required for facilitating nonstop mRNA decay

RNA ◽  
2006 ◽  
Vol 12 (12) ◽  
pp. 2187-2198 ◽  
Author(s):  
P. Mehta ◽  
J. Richards ◽  
A. W. Karzai
Keyword(s):  
Mrna Decay ◽  
Nonstop Mrna Decay

MOLECULAR BIOLOGY: Skiing Toward Nonstop mRNA Decay

Science ◽  
2002 ◽  
Vol 295 (5563) ◽  
pp. 2221-2222 ◽  
Author(s):  
L. E. Maquat
Keyword(s):  
Molecular Biology ◽  
Mrna Decay ◽  
Nonstop Mrna Decay

A functional involvement of ABCE1, eukaryotic ribosome recycling factor, in nonstop mRNA decay in Drosophila melanogaster cells

Biochimie ◽  
2014 ◽  
Vol 106 ◽  
pp. 10-16 ◽  
Author(s):  
Isao Kashima ◽  
Masaki Takahashi ◽  
Yoshifumi Hashimoto ◽  
Eri Sakota ◽  
Yoshikazu Nakamura ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Mrna Decay ◽  
Ribosome Recycling Factor ◽  
Eukaryotic Ribosome ◽  
Nonstop Mrna Decay ◽  
Functional Involvement

scholarly journals In vivo 3′-to-5′ exoribonuclease targetomes of Streptococcus pyogenes

2018 ◽  
Vol 115 (46) ◽  
pp. 11814-11819 ◽  
Author(s):  
Anne-Laure Lécrivain ◽  
Anaïs Le Rhun ◽  
Thibaud T. Renault ◽  
Rina Ahmed-Begrich ◽  
Karin Hahnke ◽  
...  
Keyword(s):  
Streptococcus Pyogenes ◽  
Mrna Decay ◽  
Regulatory Elements ◽  
Culture Conditions ◽  
Rnase R ◽  
Control Of Gene Expression ◽  
Genome Wide ◽  
Standard Culture ◽  
Distinct Features

mRNA decay plays an essential role in the control of gene expression in bacteria. Exoribonucleases (exoRNases), which trim transcripts starting from the 5′ or 3′ end, are particularly important to fully degrade unwanted transcripts and renew the pool of nucleotides available in the cell. While recent techniques have allowed genome-wide identification of ribonuclease (RNase) targets in bacteria in vivo, none of the 3′-to-5′ exoRNase targetomes (i.e., global processing sites) have been studied so far. Here, we report the targetomes of YhaM, polynucleotide phosphorylase (PNPase), and RNase R of the human pathogen Streptococcus pyogenes. We determined that YhaM is an unspecific enzyme that trims a few nucleotides and targets the majority of transcript ends, generated either by transcription termination or by endonucleolytic activity. The molecular determinants for YhaM-limited processivity are yet to be deciphered. We showed that PNPase clears the cell from mRNA decay fragments produced by endoribonucleases (endoRNases) and is the major 3′-to-5′ exoRNase for RNA turnover in S. pyogenes. In particular, PNPase is responsible for the degradation of regulatory elements from 5′ untranslated regions. However, we observed little RNase R activity in standard culture conditions. Overall, our study sheds light on the very distinct features of S. pyogenes 3′-to-5′ exoRNases.

Chapter 17 Studying tmRNA‐Mediated Surveillance and Nonstop mRNA Decay

2008 ◽  
pp. 329-358 ◽  
Author(s):  
Thomas Sundermeier ◽  
Zhiyun Ge ◽  
Jamie Richards ◽  
Daniel Dulebohn ◽  
A. Wali Karzai
Keyword(s):  
Mrna Decay ◽  
Nonstop Mrna Decay

scholarly journals Genetic interactions between [PSI+] and nonstop mRNA decay affect phenotypic variation

2005 ◽  
Vol 102 (29) ◽  
pp. 10244-10249 ◽  
Author(s):  
M. A. Wilson ◽  
S. Meaux ◽  
R. Parker ◽  
A. van Hoof
Keyword(s):  
Phenotypic Variation ◽  
Mrna Decay ◽  
Genetic Interactions ◽  
Nonstop Mrna Decay

scholarly journals Nonsense mRNA suppression via nonstop decay

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Joshua A Arribere ◽  
Andrew Z Fire
Keyword(s):  
Mrna Decay ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Nonsense Mediated Decay ◽  
Stop Codons ◽  
Nonstop Mrna Decay ◽  
Rna Fragments ◽  
Nonsense Mediated Mrna Decay ◽  
Key Steps

Nonsense-mediated mRNA decay is the process by which mRNAs bearing premature stop codons are recognized and cleared from the cell. While considerable information has accumulated regarding recognition of the premature stop codon, less is known about the ensuing mRNA suppression. During the characterization of a second, distinct translational surveillance pathway (nonstop mRNA decay), we trapped intermediates in nonsense mRNA degradation. We present data in support of a model wherein nonsense-mediated decay funnels into the nonstop decay pathway in Caenorhabditis elegans. Specifically, our results point to SKI-exosome decay and pelota-based ribosome removal as key steps facilitating suppression and clearance of prematurely-terminated translation complexes. These results suggest a model in which premature stop codons elicit nucleolytic cleavage, with the nonstop pathway disengaging ribosomes and degrading the resultant RNA fragments to suppress ongoing expression.

scholarly journals NONU-1 encodes a conserved endonuclease required for mRNA translation surveillance

2019 ◽  
Author(s):  
Marissa L. Glover ◽  
A. Max. Burroughs ◽  
Thea A. Egelhofer ◽  
Makena N. Pule ◽  
L. Aravind ◽  
...  
Keyword(s):  
Mrna Decay ◽  
Domain Architecture ◽  
Mrna Translation ◽  
Mrna Levels ◽  
Mechanistic Studies ◽  
C Elegans ◽  
Endonucleolytic Cleavage ◽  
Nonstop Mrna Decay ◽  
Unknown Factor ◽  
Cellular Translation

ABSTRACTCellular translation surveillance rescues ribosomes that stall on problematic mRNAs. During translation surveillance, endonucleolytic cleavage of the problematic mRNA is a critical step in rescuing stalled ribosomes. However, the nuclease(s) responsible remain unknown. Here we identify NONU-1 as a novel endoribonuclease required for translation surveillance pathways including No-Go and Nonstop mRNA Decay. We show that: (1) NONU-1 reduces Nonstop and No-Go mRNA levels; (2) NONU-1 contains an Smr RNase domain required for mRNA decay and with properties similar to the unknown endonuclease; and (3) the domain architecture and catalytic residues of NONU-1 are conserved throughout metazoans and eukaryotes, respectively. We extend our results inC. elegansto homologous factors inS. cerevisiae, showing conservation of function of the NONU-1 protein across billions of years of evolution. Our work establishes the identity of a previously unknown factor critical to translation surveillance and will inform mechanistic studies at the intersection of translation and mRNA decay.

scholarly journals A small segment of the MAT alpha 1 transcript promotes mRNA decay in Saccharomyces cerevisiae: a stimulatory role for rare codons.

1993 ◽  
Vol 13 (9) ◽  
pp. 5141-5148 ◽  
Author(s):  
G Caponigro ◽  
D Muhlrad ◽  
R Parker
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mrna Decay ◽  
Decay Rates ◽  
Coding Region ◽  
Rapid Decay ◽  
Small Segment ◽  
Rare Codons ◽  
Discrete Sequence ◽  
Chimeric Transcripts ◽  
Sequence Elements

Differences in decay rates of eukaryotic transcripts can be determined by discrete sequence elements within mRNAs. Through the analysis of chimeric transcripts and internal deletions, we have identified a 65-nucleotide segment of the MAT alpha 1 mRNA coding region, termed the MAT alpha 1 instability element, that is sufficient to confer instability to a stable PGK1 reporter transcript and that accelerates turnover of the unstable MAT alpha 1 mRNA. This 65-nucleotide element is composed of two parts, one located within the 5' 33 nucleotides and the second located in the 3' 32 nucleotides. The first part, which can be functionally replaced by sequences containing rare codons, is unable to promote rapid decay by itself but can enhance the action of the 3' 32 nucleotides (positions 234 to 266 in the MAT alpha 1 mRNA) in accelerating turnover. A second portion of the MAT alpha 1 mRNA (nucleotides 265 to 290) is also sufficient to destabilize the PGK1 reporter transcript when positioned 3' of rare codons, suggesting that the 3' half of the MAT alpha 1 instability element is functionally reiterated within the MAT alpha 1 mRNA. The observation that rare codons are part of the 65-nucleotide MAT alpha 1 instability element suggests possible mechanisms through which translation and mRNA decay may be linked.

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