scholarly journals On the role of mRNA secondary structure in bacterial translation

2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Claude Chiaruttini ◽  
Maude Guillier
Keyword(s):  
Secondary Structure ◽  
Mrna Secondary Structure ◽  
Bacterial Translation

scholarly journals mRNA structure regulates protein expression through changes in functional half-life

2019 ◽  
Vol 116 (48) ◽  
pp. 24075-24083 ◽  
Author(s):  
David M. Mauger ◽  
B. Joseph Cabral ◽  
Vladimir Presnyak ◽  
Stephen V. Su ◽  
David W. Reid ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Protein Expression ◽  
Codon Usage ◽  
Half Life ◽  
Order Structure ◽  
Messenger Rnas ◽  
Mrna Secondary Structure ◽  
Modified Nucleotides ◽  
Highly Correlated

Messenger RNAs (mRNAs) encode information in both their primary sequence and their higher order structure. The independent contributions of factors like codon usage and secondary structure to regulating protein expression are difficult to establish as they are often highly correlated in endogenous sequences. Here, we used 2 approaches, global inclusion of modified nucleotides and rational sequence design of exogenously delivered constructs, to understand the role of mRNA secondary structure independent from codon usage. Unexpectedly, highly expressed mRNAs contained a highly structured coding sequence (CDS). Modified nucleotides that stabilize mRNA secondary structure enabled high expression across a wide variety of primary sequences. Using a set of eGFP mRNAs with independently altered codon usage and CDS structure, we find that the structure of the CDS regulates protein expression through changes in functional mRNA half-life (i.e., mRNA being actively translated). This work highlights an underappreciated role of mRNA secondary structure in the regulation of mRNA stability.

scholarly journals mRNA secondary structure stability regulates bacterial translation insulation and re-initiation

2020 ◽  
Author(s):  
Yonatan Chemla ◽  
Michael Peeri ◽  
Mathias Luidor Heltberg ◽  
Jerry Eichler ◽  
Mogens Høgh Jensen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Secondary Structure ◽  
Structure Stability ◽  
Mrna Secondary Structure ◽  
Bacterial Genomes ◽  
Stop Codons ◽  
Factor Governing ◽  
Bacterial Translation ◽  
Main Factor

AbstractIn bacteria, translation re-initiation is crucial for synthesizing proteins encoded by genes that are organized into operons. The mechanisms regulating translation re-initiation remain, however, poorly understood. We now describe the ribosome termination structure (RTS), a conserved and stable mRNA secondary structure precisely localized downstream of stop codons, which serves as the main factor governing re-initiation efficiency in a synthetic Escherichia coli operon. We further report that in 95% of 128 analyzed bacterial genomes representing all phyla, this structure is selectively depleted when re-initiation is advantageous yet selectively enriched so as to insulate translation when re-initiation is deleterious.

scholarly journals mRNA structure regulates protein expression through changes in functional half-life

2019 ◽  
Author(s):  
David M. Mauger ◽  
B. Joseph Cabral ◽  
Vladimir Presnyak ◽  
Stephen V. Su ◽  
David W. Reid ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Protein Expression ◽  
Codon Usage ◽  
Half Life ◽  
High Expression ◽  
Order Structure ◽  
List Type ◽  
Mrna Secondary Structure ◽  
Modified Nucleotides

SummaryMessenger RNAs (mRNAs) encode information in both their primary sequence and their higher order structure. The independent contributions of factors like codon usage and secondary structure to regulating protein expression are difficult to establish as they are often highly correlated in endogenous sequences. Here, we used two approaches, global inclusion of modified nucleotides and rational sequence design of exogenously delivered constructs to understand the role of mRNA secondary structure independent from codon usage. Unexpectedly, highly-expressed mRNAs contained a highly-structured coding sequence (CDS). Modified nucleotides that stabilize mRNA secondary structure enabled high expression across a wide-variety of primary sequences. Using a set of eGFP mRNAs that independently altered codon usage and CDS structure, we find that the structure of the CDS regulates protein expression through changes in functional mRNA half-life (i.e. mRNA being actively translated). This work highlights an underappreciated role of mRNA secondary structure in the regulation of mRNA stability. [150 words]HighlightsProtein expression from modified mRNAs tends to follow the pattern m1 Ψ > U >mo5UProtein expression correlates with mRNA thermodynamic stability: Ψ≈ m1Ψ > U > mo5UA highly structured CDS correlates with high expressionIncreased structured mRNAs extend functional half-life

scholarly journals A possible universal role for mRNA secondary structure in bacterial translation revealed using a synthetic operon

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yonatan Chemla ◽  
Michael Peeri ◽  
Mathias Luidor Heltberg ◽  
Jerry Eichler ◽  
Mogens Høgh Jensen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Secondary Structure ◽  
Experimental Evidence ◽  
Translation Termination ◽  
Mrna Secondary Structure ◽  
Bacterial Genomes ◽  
Stop Codons ◽  
Synthetic Operon ◽  
Bacterial Translation

Abstract In bacteria, translation re-initiation is crucial for synthesizing proteins encoded by genes that are organized into operons. The mechanisms regulating translation re-initiation remain, however, poorly understood. We now describe the ribosome termination structure (RTS), a conserved and stable mRNA secondary structure localized immediately downstream of stop codons, and provide experimental evidence for its role in governing re-initiation efficiency in a synthetic Escherichia coli operon. We further report that RTSs are abundant, being associated with 18%–65% of genes in 128 analyzed bacterial genomes representing all phyla, and are selectively depleted when translation re-initiation is advantageous yet selectively enriched so as to insulate translation when re-initiation is deleterious. Our results support a potentially universal role for the RTS in controlling translation termination-insulation and re-initiation across bacteria.

RNA secondary structure dependence in METTL3–METTL14 mRNA methylation is modulated by the N-terminal domain of METTL3

2020 ◽  
Vol 402 (1) ◽  
pp. 89-98
Author(s):  
Nathalie Meiser ◽  
Nicole Mench ◽  
Martin Hengesbach
Keyword(s):  
Secondary Structure ◽  
Rna Binding ◽  
Specific Protein ◽  
Structure Dependence ◽  
Terminal Domain ◽  
Methylation Assay ◽  
A Site ◽  
Methylation Activity

AbstractN6-methyladenosine (m6A) is the most abundant modification in mRNA. The core of the human N6-methyltransferase complex (MTC) is formed by a heterodimer consisting of METTL3 and METTL14, which specifically catalyzes m6A formation within an RRACH sequence context. Using recombinant proteins in a site-specific methylation assay that allows determination of quantitative methylation yields, our results show that this complex methylates its target RNAs not only sequence but also secondary structure dependent. Furthermore, we demonstrate the role of specific protein domains on both RNA binding and substrate turnover, focusing on postulated RNA binding elements. Our results show that one zinc finger motif within the complex is sufficient to bind RNA, however, both zinc fingers are required for methylation activity. We show that the N-terminal domain of METTL3 alters the secondary structure dependence of methylation yields. Our results demonstrate that a cooperative effect of all RNA-binding elements in the METTL3–METTL14 complex is required for efficient catalysis, and that binding of further proteins affecting the NTD of METTL3 may regulate substrate specificity.

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