Codon bias and the folding dynamics of the cystic fibrosis transmembrane conductance regulator

Bartoszewski, Rafał; Króliczewski, Jarosław; Piotrowski, Arkadiusz; Janaszak-Jasiecka, Anna; Bartoszewska, Sylwia; Vecchio-Pagán, Briana; Fu, Lianwu; Sobolewska, Aleksandra; Matalon, Sadis; Cutting, Garry R.; Rowe, Steven M.; Collawn, James F.

doi:10.1186/s11658-016-0025-x

Cited by 37 publications

(32 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The results were expressed as the mean ± standard deviation (SD). Statistical significance among means was determined using the Student’s t-test (two samples, paired and unpaired) [ 17 ]. Analyzes were performed with Dell Statistica version 13 (Dell Inc., 2016).…”

Section: Methodsmentioning

confidence: 99%

miR-200b downregulates CFTR during hypoxia in human lung epithelial cells

et al. 2017

Self Cite

View full text Add to dashboard Cite

BackgroundHypoxic conditions induce the expression of hypoxia-inducible factors (HIFs) that allow cells to adapt to the changing conditions and alter the expression of a number of genes including the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is a low abundance mRNA in airway epithelial cells even during normoxic conditions, but during hypoxia its mRNA expression decreases even further.MethodsIn the current studies, we examined the kinetics of hypoxia-induced changes in CFTR mRNA and protein levels in two human airway epithelial cell lines, Calu-3 and 16HBE14o-, and in normal primary bronchial epithelial cells. Our goal was to examine the posttranscriptional modifications that affected CFTR expression during hypoxia. We utilized in silico predictive protocols to establish potential miRNAs that could potentially regulate CFTR message stability and identified miR-200b as a candidate molecule.ResultsAnalysis of each of the epithelial cell types during prolonged hypoxia revealed that CFTR expression decreased after 12 h during a time when miR-200b was continuously upregulated. Furthermore, manipulation of the miRNA levels during normoxia and hypoxia using miR-200b mimics and antagomirs decreased and increased CFTR mRNA levels, respectively, and thus established that miR-200b downregulates CFTR message levels during hypoxic conditions.ConclusionThe data suggest that miR-200b may be a suitable target for modulating CFTR levels in vivo.Electronic supplementary materialThe online version of this article (10.1186/s11658-017-0054-0) contains supplementary material, which is available to authorized users.

show abstract

Section: Methodsmentioning

confidence: 99%

miR-200b downregulates CFTR during hypoxia in human lung epithelial cells

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…where the time separation provided by the pause allows completion of the folding without interruption, thus avoiding problems in protein folding and aggregation [26][27][28][29]. Codon usage may also alter the final folded structure of the encoded protein and affect the efficiency of protein transportation [30,31].…”

Section: Introductionmentioning

confidence: 99%

Protein surface charge effect on 3D domain swapping in cells for c-type cytochromes

Yang

Yamanaka

Nagao

et al. 2019

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

View full text Add to dashboard Cite

“…The effect of codon usage and mRNA structural changes in protein translation rates and how they can affect protein structure and function is beginning to be studied. Bartoszewski et al (2016) stated that these synonymous mutations can alter the translational kinetics and protein folding and/or function and the mechanism of how this occurs is based on a model in which codon usage modulates the translational rate by introducing pauses caused by nonoptimal or rare codons or by introducing changes in the mRNA structure, which influences co-translational folding. Parmley et al (2006) showed that silent mutations affected stability of the secondary structure of the mRNA in mammals.…”

Section: Discussionmentioning

confidence: 99%

HSF1 and HSPA6 as functional candidate genes associated with heat tolerance in Angus cattle

et al. 2018

View full text Add to dashboard Cite

The purpose of this study was to access and characterize single nucleotide polymorphisms (SNP) located within the HSF1 and HSPA6 candidate genes for adaptability in Angus breed raised in subtropical climate. Samples of DNA from 20 animals representing extreme phenotypes for adaptability traits were obtained. Sequence variations in the candidate genes were described by sequencing target regions. We identified 12 SNP located in the HSF1 gene. Moreover, four of the six SNP found in the HSPA6 gene cause amino acid substitutions in protein-coding regions. We also identified a representative SNP (called tag SNP) in a region of the HSF1 gene with high linkage disequilibrium (r 2 = 0.87) that may represent 11 SNP located in this gene. Minor allele frequency observed for the SNP ranged from 0.10 to 0.50 and 0.02 to 0.21 for the HSF1 and the HSPA6 genes, respectively. Overall, almost all SNP analyzed showed significant deviation from the Hardy-Weinberg Equilibrium and half of the loci had heterozygosity greater than 0.50. The data suggest that there is sequence variability in these genes that could be exploited by breeding programs. There is genetic variation in HSF1 and HSPA6 genes in this populations of Angus breed, which is fundamental to obtain response to selection.

show abstract

Codon bias and the folding dynamics of the cystic fibrosis transmembrane conductance regulator

Cited by 37 publications

References 58 publications

miR-200b downregulates CFTR during hypoxia in human lung epithelial cells

miR-200b downregulates CFTR during hypoxia in human lung epithelial cells

Protein surface charge effect on 3D domain swapping in cells for c-type cytochromes

HSF1 and HSPA6 as functional candidate genes associated with heat tolerance in Angus cattle

Contact Info

Product

Resources

About