Quantitative correlation between mRNA secondary structure around the region downstream of the initiation codon and translational efficiency inEscherichia coli

2009 ◽  
Vol 104 (3) ◽  
pp. 611-616 ◽  
Author(s):  
Sang Woo Seo ◽  
Jina Yang ◽  
Gyoo Yeol Jung
Keyword(s):  
Secondary Structure ◽  
Initiation Codon ◽  
Translational Efficiency ◽  
Inescherichia Coli ◽  
Mrna Secondary Structure ◽  
Quantitative Correlation

scholarly journals Widespread positive selection for mRNA secondary structure at synonymous sites in domesticated yeast

2019 ◽  
Author(s):  
Minghao Yu ◽  
Wenna Guo ◽  
Qiang Wang ◽  
Jian-Qun Chen
Keyword(s):  
Secondary Structure ◽  
Positive Selection ◽  
Yeast Genome ◽  
Cellular Respiration ◽  
Translational Efficiency ◽  
Mrna Secondary Structure ◽  
Frequency Spectra ◽  
Mrna Structure ◽  
Synonymous Sites ◽  
Selection For

AbstractmRNA secondary structure assumes a critical role in gene regulation, especially for translational efficiency. Previous studies have a growing appreciation of purifying selection for the conserved mRNA structure across lineages of different species. However, the effect of mRNA structure on positive evolution remains unclear. Here, we construct a large-scale dataset of single nucleotide polymorphisms (SNPs) at synonymous sites in the population of Saccharomyces cerevisiae, combined with the experimental assessment of mRNA structure, and perform empirical population genetics data analysis through unfolded site-frequency spectra. Our results suggest that functional mRNA stem drives faster evolution of increasing GC contents itself with the purpose of regulating translational speed, which is greatly influenced by length. At the synonymous site without codon usage bias, this kind of positive selection still exists. Furthermore, mRNA secondary structure is subject to positive selection widespread among the yeast genome, particularly related to mitochondria activities, which is possibly aimed to achieve a balance between cellular respiration and alcoholic fermentation precisely at a non-protein level. It is conducive to the adaption of the dramatic environment alterations from wild to man-made environments during the domestication.

The involvement of mRNA secondary structure in protein synthesis

1987 ◽  
Vol 65 (6) ◽  
pp. 576-581 ◽  
Author(s):  
Jerry Pelletier ◽  
Nahum Sonenberg
Keyword(s):  
Secondary Structure ◽  
Translation Initiation ◽  
Binding Proteins ◽  
Atp Hydrolysis ◽  
Mrna Translation ◽  
Noncoding Region ◽  
Translational Efficiency ◽  
Mrna Secondary Structure ◽  
Complex Process ◽  
Eukaryotic Mrnas

Translation initiation in eukaryotes is a complex process involving many factors. A key step in this process is the binding of mRNA to the 43S preinitiation complex. This is generally the rate-limiting step in translation initiation and consequently a major determinant of mRNA translational efficiency. The primary and secondary structure of the mRNA 5′ noncoding region have been implicated in modulating translational efficiency. Translational efficiency was shown to be inversely proportional to the degree of secondary structure at the mRNA 5′ noncoding region. Furthermore, it was shown that cap-binding proteins that interact with the 5′ cap structure (m7GpppN) of eukaryotic mRNAs are involved in the "unwinding" of the mRNA secondary structure, in an ATP hydrolysis mediated event, to facilitate ribosome binding. Thus, cap-binding proteins can potentially regulate mRNA translation. Here, we discuss the available data supporting the notion that eukaryotic 5′ mRNA secondary structure plays an important role in translation initiation and the possible regulation of this process.

scholarly journals Hypertrophic cardiomyopathy MYH7 mutation R723G alters mRNA secondary structure

2020 ◽  
Vol 52 (1) ◽  
pp. 15-19
Author(s):  
J. Rose ◽  
T. Kraft ◽  
B. Brenner ◽  
J. Montag
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
Secondary Structure ◽  
Experimental Evidence ◽  
Point Mutation ◽  
Shape Analysis ◽  
Allelic Imbalance ◽  
Mrna Secondary Structure ◽  
Wild Type ◽  
Mrna Structure

Point mutation R723G in the MYH7 gene causes hypertrophic cardiomyopathy (HCM). Heterozygous patients with this mutation exhibit a comparable allelic imbalance of the MYH7 gene. On average 67% of the total MYH7 mRNA are derived from the MYH7R723G-allele and 33% from the MYH7WT allele. Mechanisms underlying mRNA allelic imbalance are largely unknown. We suggest that a different mRNA lifetime of the alleles may cause the allelic drift in R723G patients. A potent regulator of mRNA lifetime is its secondary structure. To test for alterations in the MYH7R723G mRNA structure we used selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) analysis. We show significantly different SHAPE reactivity of wild-type and MYH7R723G RNA, which is in accordance with bioinformatically predicted structures. Thus, we provide the first experimental evidence for mRNA secondary structure alterations by the HCM point mutation. We assume that this may result in a prolonged lifetime of MYH7R723G mRNA in vivo and subsequently in the determined allelic imbalance.

scholarly journals Regulation of Translational Efficiency by Disparate5′-UTRs of PPARγSplice Variants

PPAR Research ◽  
2009 ◽  
Vol 2009 ◽  
pp. 1-8 ◽  
Author(s):  
Shawn McClelland ◽  
Roopali Shrivastava ◽  
Jheem D. Medh
Keyword(s):  
Secondary Structure ◽  
Posttranscriptional Regulation ◽  
Protein A ◽  
Firefly Luciferase ◽  
Translational Efficiency ◽  
Protein Levels ◽  
Gene Assay ◽  
Firefly Luciferase Gene

The PPAR-γgene encodes for at least 7 unique transcripts due to alternative splicing of five exons in the5′-untranslated region (UTR). The translated region is encoded by exons 1–6, which are identical in all isoforms. This study investigated the role of the5′-UTR in regulating the efficiency with which the message is translated to protein. A coupledin vitrotranscription-translation assay demonstrated that PPAR-γ1, -γ2, and -γ5 are efficiently translated, whereas PPAR-γ4 and -γ7 are poorly translated. Anin vivoreporter gene assay using each5′-UTR upstream of the firefly luciferase gene showed that the5′-UTRs for PPAR-γ1, -γ2, and -γ4 enhanced translation, whereas the5′-UTRs for PPAR-γ5 and -γ7 inhibited translation. Models of RNA secondary structure, obtained by the mfold software, were used to explain the mechanism of regulation by each5′-UTR. In general, it was found that the translational efficiency was inversely correlated with the stability of the mRNA secondary structure, the presence of base-pairing in the consensus Kozak sequence, the number of start codons in the5′-UTR, and the length of the5′-UTR. A better understanding of posttranscriptional regulation of translation will allow modulation of protein levels without altering transcription.

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