1
|
Boonyuen U, Jacob BAC, Wongwigkan J, Chamchoy K, Singha-Art N, Pengsuk N, Songdej D, Adams ER, Edwards T, Chamnanchanunt S, Amran SI, Latif NA, Louis NE, Chandran S. Genetic analysis and molecular basis of G6PD deficiency among malaria patients in Thailand: implications for safe use of 8-aminoquinolines. Malar J 2024; 23:38. [PMID: 38308253 PMCID: PMC10835850 DOI: 10.1186/s12936-024-04864-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/27/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND It was hypothesized that glucose-6-phosphate dehydrogenase (G6PD) deficiency confers a protective effect against malaria infection, however, safety concerns have been raised regarding haemolytic toxicity caused by radical cure with 8-aminoquinolines in G6PD-deficient individuals. Malaria elimination and control are also complicated by the high prevalence of G6PD deficiency in malaria-endemic areas. Hence, accurate identification of G6PD deficiency is required to identify those who are eligible for malaria treatment using 8-aminoquinolines. METHODS The prevalence of G6PD deficiency among 408 Thai participants diagnosed with malaria by microscopy (71), and malaria-negative controls (337), was assessed using a phenotypic test based on water-soluble tetrazolium salts. High-resolution melting (HRM) curve analysis was developed from a previous study to enable the detection of 15 common missense, synonymous and intronic G6PD mutations in Asian populations. The identified mutations were subjected to biochemical and structural characterisation to understand the molecular mechanisms underlying enzyme deficiency. RESULTS Based on phenotypic testing, the prevalence of G6PD deficiency (< 30% activity) was 6.13% (25/408) and intermediate deficiency (30-70% activity) was found in 15.20% (62/408) of participants. Several G6PD genotypes with newly discovered double missense variants were identified by HRM assays, including G6PD Gaohe + Viangchan, G6PD Valladolid + Viangchan and G6PD Canton + Viangchan. A significantly high frequency of synonymous (c.1311C>T) and intronic (c.1365-13T>C and c.486-34delT) mutations was detected with intermediate to normal enzyme activity. The double missense mutations were less catalytically active than their corresponding single missense mutations, resulting in severe enzyme deficiency. While the mutations had a minor effect on binding affinity, structural instability was a key contributor to the enzyme deficiency observed in G6PD-deficient individuals. CONCLUSIONS With varying degrees of enzyme deficiency, G6PD genotyping can be used as a complement to phenotypic screening to identify those who are eligible for 8-aminoquinolines. The information gained from this study could be useful for management and treatment of malaria, as well as for the prevention of unanticipated reactions to certain medications and foods in the studied population.
Collapse
Affiliation(s)
- Usa Boonyuen
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Beatriz Aira C Jacob
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jutamas Wongwigkan
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kamonwan Chamchoy
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Natsamon Singha-Art
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Natnicha Pengsuk
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Duantida Songdej
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Emily R Adams
- Centre for Drugs and Diagnostics Research, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas Edwards
- Centre for Drugs and Diagnostics Research, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Supat Chamnanchanunt
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Syazwani Itri Amran
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Nurriza Ab Latif
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Naveen Eugene Louis
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Shamini Chandran
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| |
Collapse
|
2
|
Karakostis K, Malbert-Colas L, Thermou A, Vojtesek B, Fåhraeus R. The DNA damage sensor ATM kinase interacts with the p53 mRNA and guides the DNA damage response pathway. Mol Cancer 2024; 23:21. [PMID: 38263180 PMCID: PMC10804554 DOI: 10.1186/s12943-024-01933-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND The ATM kinase constitutes a master regulatory hub of DNA damage and activates the p53 response pathway by phosphorylating the MDM2 protein, which develops an affinity for the p53 mRNA secondary structure. Disruption of this interaction prevents the activation of the nascent p53. The link of the MDM2 protein-p53 mRNA interaction with the upstream DNA damage sensor ATM kinase and the role of the p53 mRNA in the DNA damage sensing mechanism, are still highly anticipated. METHODS The proximity ligation assay (PLA) has been extensively used to reveal the sub-cellular localisation of the protein-mRNA and protein-protein interactions. ELISA and co-immunoprecipitation confirmed the interactions in vitro and in cells. RESULTS This study provides a novel mechanism whereby the p53 mRNA interacts with the ATM kinase enzyme and shows that the L22L synonymous mutant, known to alter the secondary structure of the p53 mRNA, prevents the interaction. The relevant mechanistic roles in the DNA Damage Sensing pathway, which is linked to downstream DNA damage response, are explored. Following DNA damage (double-stranded DNA breaks activating ATM), activated MDMX protein competes the ATM-p53 mRNA interaction and prevents the association of the p53 mRNA with NBS1 (MRN complex). These data also reveal the binding domains and the phosphorylation events on ATM that regulate the interaction and the trafficking of the complex to the cytoplasm. CONCLUSION The presented model shows a novel interaction of ATM with the p53 mRNA and describes the link between DNA Damage Sensing with the downstream p53 activation pathways; supporting the rising functional implications of synonymous mutations altering secondary mRNA structures.
Collapse
Affiliation(s)
- Konstantinos Karakostis
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France.
- Institut de Biotecnologia I de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.
| | - Laurence Malbert-Colas
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France
| | - Aikaterini Thermou
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Robin Fåhraeus
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France.
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic.
- Department of Medical Biosciences, Umeå University, Umeå, 90185, Sweden.
| |
Collapse
|
3
|
Rao Y, Ahmed N, Pritchard J, O'Brien EP. Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer. BMC Bioinformatics 2023; 24:462. [PMID: 38062391 PMCID: PMC10704839 DOI: 10.1186/s12859-023-05521-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Synonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutations might be enriched in cancer has been explored in several recent studies. However, none of these studies control for all three types of mutational heterogeneity (patient, histology, and gene) that are known to affect the accurate identification of non-synonymous cancer-associated genes. Our goal is to adopt the current standard for non-synonymous mutations in an investigation of synonymous mutations. RESULTS Here, we create an algorithm, MutSigCVsyn, an adaptation of MutSigCV, to identify cancer-associated genes that are enriched for synonymous mutations based on a non-coding background model that takes into account the mutational heterogeneity across these levels. Using MutSigCVsyn, we first analyzed 2572 cancer whole-genome samples from the Pan-cancer Analysis of Whole Genomes (PCAWG) to identify non-synonymous cancer drivers as a quality control. Indicative of the algorithm accuracy we find that 58.6% of these candidate genes were also found in Cancer Census Gene (CGC) list, and 66.2% were found within the PCAWG cancer driver list. We then applied it to identify 30 putative cancer-associated genes that are enriched for synonymous mutations within the same samples. One of the promising gene candidates is the B cell lymphoma 2 (BCL-2) gene. BCL-2 regulates apoptosis by antagonizing the action of proapoptotic BCL-2 family member proteins. The synonymous mutations in BCL2 are enriched in its anti-apoptotic domain and likely play a role in cancer cell proliferation. CONCLUSION Our study introduces MutSigCVsyn, an algorithm that accounts for mutational heterogeneity at patient, histology, and gene levels, to identify cancer-associated genes that are enriched for synonymous mutations using whole genome sequencing data. We identified 30 putative candidate genes that will benefit from future experimental studies on the role of synonymous mutations in cancer biology.
Collapse
Affiliation(s)
- Yiyun Rao
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Nabeel Ahmed
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA
- Moderna, Inc., Cambridge, USA
| | - Justin Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, State College, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| |
Collapse
|
4
|
Wang Z, Wang C, Zhang Y, Liu S, Cheng Y, Wang S, Xia P, Hao L. Porcine IGF-1R synonymous mutations in the extracellular domain affect proliferation and differentiation of skeletal muscle cells. Gene 2023; 854:147098. [PMID: 36496177 DOI: 10.1016/j.gene.2022.147098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Miniature pigs are considered ideal organ donors for xenotransplantation in humans, but the mechanism underlying their dwarfism remains to be elucidated. IGF-1R is a crucial factor in body size formation in mammals, including skeletal muscle formation and development. The extracellular domain (ECD) binds to the ligand, a phenomenon that results in the activation of downstream pathways. METHODS In this study, the coding sequences of two IGF-1R ECD haplotypes of the large Landrace (LP) pig and the small Bama Xiang (BM) pig were cloned into pcDNA3.1 vectors to generate pcDNA3.1-LP and pcDNA3.1-BM. The two recombinant vectors were then transfected into skeletal muscle cells. RESULTS IGF-1R transcript was found to be expressed at higher levels in the pcDNA3.1-LP group than in the pcDNA3.1-BM group. The IGF-1R ECD from LP promoted cell proliferation and CyclinD1 expression, and promoted the phosphorylation of protein kinase B (to yield p-AKT). Moreover, the IGF-1R ECD from LP increased cell differentiation and the expression of myogenic determination factor (MyoD). CONCLUSION Our data indicated that the IGF-1R ECD haplotypes between pig breeds with different body sizes affect IGF-1R expression, in turn affecting the proliferation and differentiation of skeletal muscle cells by activating downstream signalling pathways.
Collapse
Affiliation(s)
- Zhaoguo Wang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Chunli Wang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Ying Zhang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Songcai Liu
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China.
| | - Yunyun Cheng
- Ministry of Health Key Laboratory of Radiobiology, College of Public Health, Jilin University, Changchun, Jilin 130061, China
| | - Siyao Wang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Peijun Xia
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Linlin Hao
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China.
| |
Collapse
|
5
|
Wong JLC, David S, Sanchez-Garrido J, Woo JZ, Low WW, Morecchiato F, Giani T, Rossolini GM, Beis K, Brett SJ, Clements A, Aanensen DM, Rouskin S, Frankel G. Recurrent emergence of Klebsiella pneumoniae carbapenem resistance mediated by an inhibitory ompK36 mRNA secondary structure. Proc Natl Acad Sci U S A 2022; 119:e2203593119. [PMID: 36095213 DOI: 10.1073/pnas.2203593119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Outer membrane porins in Gram-negative bacteria facilitate antibiotic influx. In Klebsiella pneumoniae, modifications in the porin OmpK36 are implicated in increasing resistance to carbapenems. An analysis of large K. pneumoniae genome collections, encompassing major healthcare-associated clones, revealed the recurrent emergence of a synonymous cytosine-to-thymine transition at position 25 (25c > t) in ompK36. We show that the 25c > t transition increases carbapenem resistance through depletion of OmpK36 from the outer membrane. The mutation attenuates K. pneumoniae in a murine pneumonia model, which accounts for its limited clonal expansion observed by phylogenetic analysis. However, in the context of carbapenem treatment, the 25c > t transition tips the balance toward treatment failure, thus accounting for its recurrent emergence. Mechanistically, the 25c > t transition mediates an intramolecular messenger RNA (mRNA) interaction between a uracil encoded by 25t and the first adenine within the Shine-Dalgarno sequence. This specific interaction leads to the formation of an RNA stem structure, which obscures the ribosomal binding site thus disrupting translation. While mutations reducing OmpK36 expression via transcriptional silencing are known, we uniquely demonstrate the repeated selection of a synonymous ompK36 mutation mediating translational suppression in response to antibiotic pressure.
Collapse
|
6
|
Ran X, Xiao J, Cheng F, Wang T, Teng H, Sun Z. Pan-cancer analyses of synonymous mutations based on tissue-specific codon optimality. Comput Struct Biotechnol J 2022; 20:3567-3580. [PMID: 35860410 PMCID: PMC9287186 DOI: 10.1016/j.csbj.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/22/2022] [Accepted: 07/03/2022] [Indexed: 11/24/2022] Open
Abstract
Developed tissue-specific codon optimality in 29 human tissues. Applied these to analyze synonymous mutations in ∼10,000 tumor and normal samples. Synonymous mutations frequently increase optimal codons in most cancer types. Synonymous mutations frequently increase optimal codons cell cycle-related genes. Frequency of optimal codon gain relates to proliferation, DDR deficiency, and survival.
Codon optimality has been demonstrated to be an important determinant of mRNA stability and expression levels in multiple model organisms and human cell lines. However, tissue-specific codon optimality has not been developed to investigate how codon optimality is usually perturbed by somatic synonymous mutations in human cancers. Here, we determined tissue-specific codon optimality in 29 human tissues based on mRNA expression data from the Genotype-Tissue Expression project. We found that optimal codons were associated with differentiation, whereas non-optimal codons were correlated with proliferation. Furthermore, codons biased toward differentiation displayed greater tissue specificity in codon optimality, and the tissue specificity of codon optimality was primarily present in amino acids with high degeneracy of the genetic code. By applying tissue-specific codon optimality to somatic synonymous mutations in 8532 tumor samples across 24 cancer types and to those in 416 normal cells across six human tissues, we found that synonymous mutations frequently increased optimal codons in tumor cells and cancer-related genes (e.g., genes involved in cell cycle). Furthermore, an elevated frequency of optimal codon gain was found to promote tumor cell proliferation in three cancer types characterized by DNA damage repair deficiency and could act as a prognostic biomarker for patients with triple-negative breast cancer. In summary, this study profiled tissue-specific codon optimality in human tissues, revealed alterations in codon optimality caused by synonymous mutations in human cancers, and highlighted the non-negligible role of optimal codon gain in tumorigenesis and therapeutics.
Collapse
Affiliation(s)
- Xia Ran
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyuan Xiao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Fang Cheng
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Tao Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Kaifu District, Changsha, Hunan 410078, China
| | - Huajing Teng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| |
Collapse
|
7
|
Hassanin A. Variation in synonymous nucleotide composition among genomes of sarbecoviruses and consequences for the origin of COVID-19. Gene X 2022; 835:146641. [PMID: 35700806 PMCID: PMC9200079 DOI: 10.1016/j.gene.2022.146641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/19/2022] [Accepted: 06/02/2022] [Indexed: 11/26/2022] Open
Abstract
The subgenus Sarbecovirus includes two human viruses, SARS-CoV and SARS-CoV-2, respectively responsible for the SARS epidemic and COVID-19 pandemic, as well as many bat viruses and two pangolin viruses. Here, the synonymous nucleotide composition (SNC) of Sarbecovirus genomes was analysed by examining third codon-positions, dinucleotides, and degenerate codons. The results show evidence for the eight following groups: (i) SARS-CoV related coronaviruses (SCoVrC including many bat viruses from China), (ii) SARS-CoV-2 related coronaviruses (SCoV2rC; including five bat viruses from Cambodia, Thailand and Yunnan), (iii) pangolin sarbecoviruses, (iv) three bat sarbecoviruses showing evidence of recombination between SCoVrC and SCoV2rC genomes, (v) two highly divergent bat sarbecoviruses from Yunnan, (vi) the bat sarbecovirus from Japan, (vii) the bat sarbecovirus from Bulgaria, and (viii) the bat sarbecovirus from Kenya. All these groups can be diagnosed by specific nucleotide compositional features except the one concerned by recombination between SCoVrC and SCoV2rC. In particular, SCoV2rC genomes have less cytosines and more uracils at third codon-positions than other sarbecoviruses, whereas the genomes of pangolin sarbecoviruses show more adenines at third codon-positions. I suggest that taxonomic differences in the imbalanced nucleotide pools available in host cells during viral replication can explain the eight groups of SNC here detected among Sarbecovirus genomes. A related effect due to hibernating bats and their latitudinal distribution is also discussed. I conclude that the two independent host switches from Rhinolophus bats to pangolins resulted in convergent mutational constraints and that SARS-CoV-2 emerged directly from a horseshoe bat sarbecovirus.
Collapse
Affiliation(s)
- Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, EPHE, MNHN, UA, Paris, France.
| |
Collapse
|
8
|
Chu D, Wei L. Context-dependent and -independent selection on synonymous mutations revealed by 1,135 genomes of Arabidopsis thaliana. BMC Ecol Evol 2021; 21:68. [PMID: 33910528 PMCID: PMC8079846 DOI: 10.1186/s12862-021-01792-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 04/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Synonymous mutations do not alter the amino acids and therefore are regarded as neutral for a long time. However, they do change the tRNA adaptation index (tAI) of a particular codon (independent of its context), affecting the tRNA availability during translation. They could also change the isoaccepting relationship with its neighboring synonymous codons in particular context, which again affects the local translation process. Evidence of selection pressure on synonymous mutations has emerged. RESULTS The proposed selection patterns on synonymous mutations are never formally and systematically tested in plant species. We fully take advantage of the SNP data from 1,135 A. thaliana lines, and found that the synonymous mutations that increase tAI or the isoaccepting mutations in isoaccepting codon context tend to have higher derived allele frequencies (DAF) compared to other synonymous mutations of the opposite effects. CONCLUSIONS Synonymous mutations are not strictly neutral. The synonymous mutations that increase tAI or the isoaccepting mutations in isoaccepting codon context are likely to be positively selected. We propose the concept of context-dependent and -independent selection on synonymous mutations. These concepts broaden our knowledge of the functional consequences of synonymous mutations, and should be appealing to phytologists and evolutionary biologists.
Collapse
Affiliation(s)
- Duan Chu
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian, Beijing, China
| | - Lai Wei
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian, Beijing, China.
| |
Collapse
|
9
|
Li Q, Li J, Yu CP, Chang S, Xie LL, Wang S. Synonymous mutations that regulate translation speed might play a non-negligible role in liver cancer development. BMC Cancer 2021; 21:388. [PMID: 33836673 PMCID: PMC8033552 DOI: 10.1186/s12885-021-08131-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/30/2021] [Indexed: 01/11/2023] Open
Abstract
Background Synonymous mutations do not change the protein sequences. Automatically, they have been regarded as neutral events and are ignored in the mutation-based cancer studies. However, synonymous mutations will change the codon optimality, resulting in altered translational velocity. Methods We fully utilized the transcriptome and translatome of liver cancer and normal tissue from ten patients. We profiled the mutation spectrum and examined the effect of synonymous mutations on translational velocity. Results Synonymous mutations that increase the codon optimality significantly enhanced the translational velocity, and were enriched in oncogenes. Meanwhile, synonymous mutations decreasing codon optimality slowed down translation, and were enriched in tumor suppressor genes. These synonymous mutations significantly contributed to the translational changes in tumor samples compared to normal samples. Conclusions Synonymous mutations might play a role in liver cancer development by altering codon optimality and translational velocity. Synonymous mutations should no longer be ignored in the genome-wide studies.
Collapse
Affiliation(s)
- Qun Li
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jian Li
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chun-Peng Yu
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shuai Chang
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ling-Ling Xie
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Song Wang
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China.
| |
Collapse
|
10
|
Mboumba Bouassa RS, Pere H, Mossoro-Kpinde CD, Roques P, Gody JC, Moussa S, Veyer D, Gresenguet G, Charpentier C, Jenabian MA, Djoba Siawaya JF, Belec L. Purifying Selection in Human Immunodeficiency Virus-1 pol Gene in Perinatally Human Immunodeficiency Virus-1-Infected Children Harboring Discordant Immunological Response and Virological Nonresponse to Long-Term Antiretroviral Therapy. J Clin Med Res 2020; 12:369-376. [PMID: 32587653 PMCID: PMC7295550 DOI: 10.14740/jocmr4157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/23/2020] [Indexed: 11/11/2022] Open
Abstract
Background Biological monitoring of antiretroviral treatment (ART) in human immunodeficiency virus (HIV)-infected pediatric population remains challenging. The aim of the present study was to assess the long-term HIV-1 genetic diversity in pol gene in HIV-1-infected children in virological failure under antiretroviral regimen adapted according to the successive World Health Organization (WHO) guidelines for resource-constrained settings. Methods HIV-1 diversity in pol gene was assessed in HIV-1-infected children and adolescents born from HIV-infected mothers (median age at follow-up: 13.8 years) in virological failure (VF+) despite long-term regimen recommended by the WHO. The numbers of nonsynonymous substitutions per potential nonsynonymous site (dN) and of synonymous substitutions at potential synonymous sites (dS) in HIV-1 pol gene and the dN/dS ratios were used to estimate the selective pressure on circulating HIV-1. Results The immunological responses to ART basically corresponded to: 1) Full therapeutic failure with immunological (I-) and virological nonresponses in one-quarter (24.6%) of study children ((I-, VF+) subgroup); 2) Discordant immunovirological responses with paradoxical high CD4 T cell counts (I+) and high HIV-1 RNA load in the remaining cohort patients (75.4%) ((I+, VF+) subgroup). The mean dS was 1.8-fold higher in (I+, VF+) than (I-, VF+) subgroup (25.9 ± 18.4 vs. 14.3 ± 10.8). In the (I+, VF+) subgroup, the mean dS was 1.6-fold higher than the mean dN. Finally, the mean dN/dS ratio was 2.1-fold lower in (I+, VF+) than (I-, VF+) subgroup (0.6 ± 0.3 vs. 1.3 ± 0.7), indicating purifying selection in the immunovirological discordant (I+, VF+) subgroup and positive selection in the immunovirological failure (I-, VF+) subgroup. Conclusions Children and adolescents in immunovirological therapeutic failure harbor positive selection of HIV-1 strains favoring diversifying in pol-encoded amino acids. In contrast, children with persistent discordant immunovirological responses show accumulation of mutations and purifying selection in pol gene sequences, indicating limited genetic evolution and likely suggesting genetic adaptation of viruses to host functional constraints.
Collapse
Affiliation(s)
- Ralph-Sydney Mboumba Bouassa
- Laboratoire de Virologie, Hopital Europeen Georges Pompidou, Assistance Publique-Hopitaux de Paris (AP-HP) and Universite de Paris, Paris Sorbonne Cite, Paris, France.,Ecole Doctorale Regionale en Infectiologie Tropicale, Franceville, Gabon
| | - Helene Pere
- Laboratoire de Virologie, Hopital Europeen Georges Pompidou, Assistance Publique-Hopitaux de Paris (AP-HP) and Universite de Paris, Paris Sorbonne Cite, Paris, France.,Universite de Paris, Paris Sorbonne Cite, Paris, France
| | - Christian Diamant Mossoro-Kpinde
- Faculte des Sciences de la Sante, Universite de Bangui, Bangui, Central African Republic.,Laboratoire National de Biologie Clinique et de Sante Publique, Bangui, Central African Republic
| | - Pierre Roques
- Commissariat a l'Energie Atomique (CEA)-Universite Paris-Saclay; INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie Francois-Jacob (IBJF), Fontenay-aux-Roses, France
| | - Jean Chrysostome Gody
- Faculte des Sciences de la Sante, Universite de Bangui, Bangui, Central African Republic.,Complexe Pediatrique, Bangui, Central African Republic
| | - Sandrine Moussa
- Institut Pasteur de Bangui, Bangui, Central African Republic
| | - David Veyer
- Laboratoire de Virologie, Hopital Europeen Georges Pompidou, Assistance Publique-Hopitaux de Paris (AP-HP) and Universite de Paris, Paris Sorbonne Cite, Paris, France
| | - Gerard Gresenguet
- Faculte des Sciences de la Sante, Universite de Bangui, Bangui, Central African Republic.,Unite de Recherches et d'Intervention sur les Maladies Sexuellement Transmissibles et le SIDA, Departement de Sante Publique, Faculte des Sciences de la Sante de Bangui, Central African Republic
| | - Charlotte Charpentier
- IAME, UMR 1137, INSERM, Universite Paris Diderot, Sorbonne Paris Cite, AP-HP, Laboratoire de Virologie, Hopital Bichat, AP-HP, Paris, France
| | - Mohammad-Ali Jenabian
- Departement des Sciences Biologiques et Centre de Recherche BioMed, Universite du Quebec a Montreal (UQAM), Montreal, QC, Canada
| | - Joel Fleury Djoba Siawaya
- Ecole Doctorale Regionale en Infectiologie Tropicale, Franceville, Gabon.,Laboratory Medicine, Mother and Child University Hospital Jeanne Ebori, Libreville, Gabon
| | - Laurent Belec
- Laboratoire de Virologie, Hopital Europeen Georges Pompidou, Assistance Publique-Hopitaux de Paris (AP-HP) and Universite de Paris, Paris Sorbonne Cite, Paris, France.,Ecole Doctorale Regionale en Infectiologie Tropicale, Franceville, Gabon.,Universite de Paris, Paris Sorbonne Cite, Paris, France
| |
Collapse
|
11
|
Wang C, Liu S, Wu Q, Cheng Y, Feng T, Song J, Yang R, Geng H, Lu G, Wang S, Hao L. Porcine IGF-1R synonymous mutations in the intracellular domain affect cell proliferation and alter kinase activity. Int J Biol Macromol 2020; 152:147-153. [PMID: 32109480 DOI: 10.1016/j.ijbiomac.2020.02.281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 01/04/2023]
Abstract
Miniature pigs are regarded as ideal organ donors for xenotransplantation into humans. Elucidating the formation mechanism of miniature pigs is important. The insulin-like growth factor 1 receptor (IGF-1R) is crucial in the regulation of cell proliferation and organismal growth. According to our previous research, the IGF-1R expression levels between large and miniature pigs showed different profiles in liver and muscle tissues. Here, five synonymous mutations of IGF-1R in the coding sequence (CDS) of intracellular domain (ICD) between large and miniature pigs were analysed by constructing expression vectors of two haplotypes and named pcDNA3.1-LP (with the CDS of IGF-1R ICD of Large White pigs, LP group) and pcDNA3.1-BM (with the CDS of IGF-1R ICD of Bama Xiang pigs, BM group). The IGF-1R of the BM group was expressed lower than that of the LP group in transcription, translation and autophosphorylation levels. The IGF-1R of the BM group also down-regulated the protein levels of p-AKT/p-ERK than that of the LP group. PK-15 and C2C12 cell proliferation were detected to further understand the function of the haplotype. Results showed that the proliferation viability of PK-15 and C2C12 cells weakened in the BM group. Moreover, the mRNA and protein stabilities of the BM group were higher than those of the LP group. Our data indicated that two haplotypes of IGF-1R CDS in ICD between large and miniature pigs altered IGF-1R expression and down-regulated AKT and ERK signalling pathways at translation levels, resulting in an inhibitory effect on PK-15 and C2C12 cell proliferation.
Collapse
Affiliation(s)
- Chunli Wang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Songcai Liu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China; Five-Star Animal Health Pharmaceutical Factory of Jilin Province, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Qingyan Wu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Yunyun Cheng
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Tianqi Feng
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Jie Song
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Rui Yang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Hongwei Geng
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Guanhong Lu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Siyao Wang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Linlin Hao
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China.
| |
Collapse
|
12
|
Abstract
Background Synonymous mutations are able to change the tAI (tRNA adaptation index) of a codon and consequently affect the local translation rate. Intuitively, one may hypothesize that those synonymous mutations which increase the tAI values are favored by natural selection. Results We use the maize (Zea mays) genome to test our assumption. The first supporting evidence is that the tAI-increasing synonymous mutations have higher fixed-to-polymorphic ratios than the tAI-decreasing ones. Next, the DAF (derived allele frequency) or MAF (minor allele frequency) of the former is significantly higher than the latter. Moreover, similar results are obtained when we investigate CAI (codon adaptation index) instead of tAI. Conclusion The synonymous mutations in the maize genome are not strictly neutral. The tAI-increasing mutations are positively selected while those tAI-decreasing ones undergo purifying selection. This selection force might be weak but should not be automatically ignored.
Collapse
Affiliation(s)
- Duan Chu
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China
| | - Lai Wei
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China.
| |
Collapse
|
13
|
Abstract
Synonymous mutations do not change the amino acid but do change the synonymous codon usage. In genomes of different organisms, the gene conversion process is biased toward GC, which is irrespective of mutation bias. In the coding region, this trend is especially obvious and it is possibly caused by the preference on G/C-ending codons over the A/T-ending ones. If the G/C-ending codons are advantageous, then the synonymous mutations that change A/T to G/C would be "optimal" compared to the opposite ones. In theory, one should observe signals of positive selection on these optimal synonymous mutations. The recently released single-nucleotide polymorphism (SNP) data from the 1001 genome project of Arabidopsis thaliana provided researchers with an unprecedented opportunity to verify this assumption. I fully take advantage of the SNP data from 1,135 A thaliana lines and came to the conclusion that synonymous mutations in natural populations are not strictly neutral: the synonymous mutations that increase GC content (from A/T to G/C) tend to have higher derived allele frequencies (DAFs) and, therefore, are likely to be positively selected. My current study broadens our knowledge of the selection patterns of synonymous mutations and should be appealing to evolutionary biologists. One sentence summary: In 1135 genomes of Arabidopsis thaliana, the synonymous mutations that increase the GC content tend to have higher derived allele frequencies (DAFs) and are likely to be positively selected.
Collapse
Affiliation(s)
- Lai Wei
- College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
14
|
Abstract
Background Non-synonymous mutations altering tumor suppressor genes and oncogenes are widely studied. However, synonymous mutations, which do not alter the protein sequence, are rarely investigated in melanoma genome studies. Methods We explored the role of somatic synonymous mutations in melanoma samples from TCGA (The Cancer Genome Atlas). The pathogenic synonymous mutation and neutral synonymous mutation data were used to assess the significance of pathogenic synonymous mutations in melanoma likely to affect genetic regulatory elements using Fisher’s exact test. Poisson distribution probabilities of each gene were used to mine the genes with multiple potential functional synonymous mutations affecting regulatory elements. Results Concentrating on five types of genetic regulatory functions, we found that the mutational patterns of pathogenic synonymous mutations are mostly involved in exonic splicing regulators in near-splicing sites or inside DNase I hypersensitivity sites or non-optimal codon. Moreover, the sites of miRNA binding alteration exhibit a significantly lower rate of evolution than other sites. Finally, 12 genes were hit by recurrent potentially functional synonymous mutations, which showed statistical significance in the pathogenic mutations. Among them, nine genes (DNAH5, ADCY8, GRIN2A, KSR2, TECTA, RIMS2, XKR6, MYH1, SCN10A) have been reported to be mutated in melanoma, and other three genes (SLC9A2, CASR, SLC8A3) have a great potential to impact melanoma. Conclusion These findings confirm the functional consequences of somatic synonymous mutations in melanoma, emphasizing the significance of research in future studies.
Collapse
Affiliation(s)
- Di Zhang
- College of information science and engineering, Shaoguan University, Shaoguan, Guangdong, China.,Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China
| | - Junfeng Xia
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China.
| |
Collapse
|
15
|
Abstract
Background Synonymous mutations have been identified to play important roles in cancer development, although they do not modify the protein sequences. However, relatively little research has specifically delineated the functionality of synonymous mutations in cancer. Results We investigated the nucleotide-based and amino acid-based features of synonymous mutations across 15 cancer types from The Cancer Genome Atlas (TCGA), and revealed novel driver candidates by identifying hotspot mutations. Firstly, synonymous mutations were analyzed between TCGA and 1000 Genomes Project at nucleotide and amino acid levels. We found that C:G → T:A transitions were the most frequent single-base substitutions, and leucine underwent the largest number of synonymous mutations in TCGA due to prevalent C → T transition, which induced the transformation between optimal and non-optimal codons. Next, 97 synonymous hotspot mutations in 86 genes were nominated as candidate drivers with potential cancer risk by considering the mutational rates across different sequence contexts. We observed that non-CpG-island GC transition sequence context was positively selected across most of cancer types, and different sequence contexts under which hotspot mutations occur could be significance for genetic differences and functional features. We also found that the hotspots were more conserved than neutral mutations of hotspot-mutation-containing-genes and frequently happened at leucine. In addition, we mapped hotspots, neutral and non-hotspot mutations of hotspot-mutation-containing-genes to their respective protein domains and found ion transport domain was the most frequent one, which could mediate the cell interaction and had relevant implication for tumor therapy. And the signatures of synonymous hotspots were qualitatively similar with those of harmful missense variants. Conclusions We illustrated the preferences of cancer associated synonymous mutations, especially hotspots, and laid the groundwork for understanding the synonymous mutations act as drivers in cancer.
Collapse
Affiliation(s)
- Yannan Bin
- Institutes of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Xiaojuan Wang
- Institutes of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Le Zhao
- Institutes of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Pengbo Wen
- Institutes of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Junfeng Xia
- Institutes of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China.
| |
Collapse
|
16
|
Chu D, Wei L. Parsing the synonymous mutations in the maize genome: isoaccepting mutations are more advantageous in regions with codon co-occurrence bias. BMC Plant Biol 2019; 19:422. [PMID: 31610786 PMCID: PMC6791113 DOI: 10.1186/s12870-019-2050-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Synonymous mutations do not change amino acids but do sometimes change the tRNAs (anticodons) that decode a particular codon. An isoaccepting codon is a synonymous codon that shares the same tRNA. If a mutated codon could base pair with the same anticodon as the original, the mutation is termed an isoaccepting mutation. An interesting but less-studied type of codon bias is codon co-occurrence bias. There is a trend to cluster the isoaccepting codons in the genome. The proposed advantage of codon co-occurrence bias is that the tRNA released from the ribosome E site could be quickly recharged and subsequently decode the following isoaccepting codons. This advantage would enhance translation efficiency. In plant species, whether there are signals of positive selection on isoaccepting mutations in the codon co-occurred regions has not been studied. RESULTS We termed polymorphic mutations in coding regions using publicly available RNA-seq data in maize (Zea mays). Next, we classified all synonymous mutations into three categories according to the context, i.e., the relationship between the focal codon and the previous codon, as follows: isoaccepting, nonisoaccepting and nonsynonymous. We observed higher fractions of isoaccepting mutations in the isoaccepting context. If we looked at the minor allele frequency (MAF) spectrum, the isoaccepting mutations have a higher MAF in the isoaccepting context than that in other regions, and accordingly, the nonisoaccepting mutations have a higher MAF in the nonisoaccepting context. CONCLUSION Our results indicate that in regions with codon co-occurrence bias, natural selection maintains this pattern by suppressing the nonisoaccepting mutations. However, if the consecutive codons are nonisoaccepting, mutations tend to switch these codons to become isoaccepting. Our study demonstrates that the codon co-occurrence bias in the maize genome is selectively maintained by natural selection and that the advantage of this trend could potentially be the rapid recharging and reuse of tRNAs to increase translation efficiency.
Collapse
Affiliation(s)
- Duan Chu
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China
| | - Lai Wei
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China.
| |
Collapse
|
17
|
Batista RL, Rodrigues ADS, Nishi MY, Gomes NL, Faria JAD, Moraes DRD, Carvalho LR, Costa EMF, Domenice S, Mendonca BB. A recurrent synonymous mutation in the human androgen receptor gene causing complete androgen insensitivity syndrome. J Steroid Biochem Mol Biol 2017; 174:14-16. [PMID: 28743543 DOI: 10.1016/j.jsbmb.2017.07.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/18/2017] [Indexed: 12/14/2022]
Abstract
Androgen insensitivity syndrome (AIS) is the most common cause of 46,XY disorders of sex development (46,XY DSD). This syndrome is an X-linked inheritance disease and it is caused by mutations in the human androgen receptor (AR) gene. Non-synonymous point AR mutations are frequently described in this disease, including in the complete phenotype. We present a novel synonymous mutation in the human AR gene (c.1530C > T) in four 46,XY patients from two unrelated families associated with complete androgen insensitivity syndrome (CAIS). The analysis of mRNA from testis showed that synonymous AR mutation changed the natural exon 1 donor splice site, with deletion of the last 92 nucleotides of the AR exon 1 leading to a premature stop codon 12 positions ahead resulting in a truncate AR protein. Linkage analyses suggested a probable founder effect for this mutation. In conclusion, we described the first synonymous AR mutation associated with CAIS phenotype, reinforcing the disease-causing role of synonymous mutations.
Collapse
Affiliation(s)
- Rafael Loch Batista
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia e Metabologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
| | - Andresa di Santi Rodrigues
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia e Metabologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mirian Yumie Nishi
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia e Metabologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Nathalia Lisboa Gomes
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia e Metabologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - José Antonio Diniz Faria
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia e Metabologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Daniela Rodrigues de Moraes
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia e Metabologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Luciani Renata Carvalho
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia e Metabologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Elaine Maria Frade Costa
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia e Metabologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Sorahia Domenice
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia e Metabologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Berenice Bilharinho Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia e Metabologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
18
|
Bartoszewski R, Króliczewski J, Piotrowski A, Jasiecka AJ, Bartoszewska S, Vecchio-Pagan B, Fu L, Sobolewska A, Matalon S, Cutting GR, Rowe SM, Collawn JF. Codon bias and the folding dynamics of the cystic fibrosis transmembrane conductance regulator. Cell Mol Biol Lett 2016; 21:23. [PMID: 28536625 PMCID: PMC5415761 DOI: 10.1186/s11658-016-0025-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/13/2016] [Indexed: 12/20/2022] Open
Abstract
Synonymous or silent mutations are often overlooked in genetic analyses for disease-causing mutations unless they are directly associated with potential splicing defects. More recent studies, however, indicate that some synonymous single polynucleotide polymorphisms (sSNPs) are associated with changes in protein expression, and in some cases, protein folding and function. The impact of codon usage and mRNA structural changes on protein translation rates and how they can affect protein structure and function is just beginning to be appreciated. Examples are given here that demonstrate how synonymous mutations alter the translational kinetics and protein folding and/or function. The mechanism for 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, and this in turn influences co-translational folding. Two examples of this include the multidrug resistance protein (p-glycoprotein) and the cystic fibrosis transmembrane conductance regulator gene (CFTR). CFTR is also used here as a model to illustrate how synonymous mutations can be examined using in silico predictive methods to identify which sSNPs have the potential to change protein structure. The methodology described here can be used to help identify "non-silent" synonymous mutations in other genes.
Collapse
Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Jaroslaw Króliczewski
- Laboratory of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Arkadiusz Piotrowski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Anna Janaszak Jasiecka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Briana Vecchio-Pagan
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Lianwu Fu
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
| | - Aleksandra Sobolewska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Sadis Matalon
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, USA.,Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
| | - Garry R Cutting
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Steven M Rowe
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Departments of Medicine and Pediatrics, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
| | - James F Collawn
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
| |
Collapse
|
19
|
Pizzo L, Iriarte A, Alvarez-Valin F, Marín M. Conservation of CFTR codon frequency through primates suggests synonymous mutations could have a functional effect. Mutat Res 2015; 775:19-25. [PMID: 25839760 DOI: 10.1016/j.mrfmmm.2015.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 02/05/2015] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
Cystic fibrosis is an inherited chronic disease that affects the lungs and digestive system, with a prevalence of about 1:3000 people. Cystic fibrosis is caused by mutations in CFTR gene, which lead to a defective function of the chloride channel, the cystic fibrosis transmembrane conductance regulator (CFTR). Up-to-date, more than 1900 mutations have been reported in CFTR. However for an important proportion of them, their functional effects and the relation to disease are still not understood. Many of these mutations are silent (or synonymous), namely they do not alter the encoded amino acid. These synonymous mutations have been considered as neutral to protein function. However, more recent evidence in bacterial and human proteins has put this concept under revision. With the aim of understanding possible functional effects of synonymous mutations in CFTR, we analyzed human and primates CFTR codon usage and divergence patterns. We report the presence of regions enriched in rare and frequent codons. This spatial pattern of codon preferences is conserved in primates, but this cannot be explained by sequence conservation alone. In sum, the results presented herein suggest a functional implication of these regions of the gene that may be maintained by purifying selection acting to preserve a particular codon usage pattern along the sequence. Overall these results support the idea that several synonymous mutations in CFTR may have functional importance, and could be involved in the disease.
Collapse
Affiliation(s)
- Lucilla Pizzo
- Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Andrés Iriarte
- Dpto. de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Dpto. de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, IIBCE, Montevideo, Uruguay; Dpto. de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, IIBCE, Montevideo, Uruguay
| | - Fernando Alvarez-Valin
- Sección Biomatemática, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Mónica Marín
- Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| |
Collapse
|
20
|
Fernández-Calero T, Astrada S, Alberti A, Horjales S, Arnal JF, Rovira C, Bollati-Fogolín M, Flouriot G, Marin M. The transcriptional activities and cellular localization of the human estrogen receptor alpha are affected by the synonymous Ala87 mutation. J Steroid Biochem Mol Biol 2014; 143:99-104. [PMID: 24607813 DOI: 10.1016/j.jsbmb.2014.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 02/19/2014] [Accepted: 02/21/2014] [Indexed: 10/25/2022]
Abstract
Until recently, synonymous mutations (which do not change amino acids) have been much neglected. Some evidence suggests that this kind of mutations could affect mRNA secondary structure or stability, translation kinetics and protein structure. To explore deeper the role of synonymous mutations, we studied their consequence on the functional activity of the estrogen receptor alpha (ERα). The ERα is a ligand-inducible transcription factor that orchestrates pleiotropic cellular effects, at both genomic and non-genomic levels in response to estrogens. In this work we analyzed in transient transfection experiments, the activity of ERα carrying the synonymous mutation Ala87, a polymorphism involving about 5-10% of the population. In comparison to the wild type receptor, our results show that ERαA87 mutation reduces the transactivation efficiency of ERα on an ERE reporter gene while its expression level remains similar. This mutation enhances 4-OHT-induced transactivation of ERα on an AP1 reporter gene. Finally, the mutation affects the subcellular localization of ERα in a cell type specific manner. It enhances the cytoplasmic location of ERα without significant changes in non-genomic effects of E2. The functional alteration of the ERαA87 determined in this work highlights the relevance of synonymous mutations for biomedical and pharmacological points of view.
Collapse
Affiliation(s)
- Tamara Fernández-Calero
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay; Bioinformatics Unit, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay.
| | - Soledad Astrada
- Cell Biology Unit, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Alvaro Alberti
- Cell Biology Unit, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Sofía Horjales
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Jean Francois Arnal
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1048, Institute of Metabolic and Cardiovascular Diseases, University of Toulouse 3, Toulouse, France
| | - Carlos Rovira
- Department of Oncology and CREATE Health Strategic Centre for Clinical Cancer Research, Lund University, BMC, 221 84 Lund, Sweden
| | | | - Gilles Flouriot
- University of Rennes 1, Institut de Recherche en Santé, Environnement et Travail, IRSET, INSERM U1085, Team TREC, Biosit, Rennes, France
| | - Mónica Marin
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| |
Collapse
|
21
|
Tsukuda M, Miyazaki K. Directed evolution study unveiling key sequence factors that affect translation efficiency in Escherichia coli. J Biosci Bioeng 2013; 116:540-5. [PMID: 23790548 DOI: 10.1016/j.jbiosc.2013.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/08/2013] [Accepted: 05/08/2013] [Indexed: 11/23/2022]
Abstract
Synonymous mutations in protein coding genes significantly impact translation efficiency. We synthesized a pair of genes encoding green fluorescent protein that were separated by 160 synonymous mutations to investigate key factors that affect translation efficiency. One sequence was optimized for Escherichia coli (GFP(Eco)) and the other for Bacillus subtilis (GFP(Bsu)). When the genes were expressed in E. coli, GFP(Eco) fluoresced 12-fold stronger than GFP(Bsu), confirming the suboptimal nature of the GFP(Bsu) gene. We then employed directed evolution to improve the expression of GFP(Bsu). Random mutagenesis and DNA shuffling was used to generate mutant libraries, which were screened for fluorescence. A variant showing 6-fold fluorescence enhancement was identified, which contained a single mutation (G10A) in a rare codon for Gly-4. However, the substitution generated another type of rare codon, AGA, for Arg, suggesting that the improvement was caused by a factor other than the rare codon. We next applied saturation mutagenesis to Gly-4. The darkest variant contained a GGG codon (GFP(Bsu)-G) for Gly-4. Taking the location of the mutation into account, we hypothesized that destabilization of the mRNA secondary structure around the initiation codon improved the expression. We then randomized the nucleotide triplet in 5'-untranslated region (5'UTR) of GFP(Bsu), which is complementary to the Gly-4 codon. A variant showing 6-fold fluorescence enhancement was identified, which exhibited a destabilized secondary structure. When this 5'UTR sequence was combined with GFP(Bsu)-G, 22-fold fluorescent improvement was achieved. Collectively, the stability of the mRNA secondary structure around the initiation codon predominantly affected the translation efficiency.
Collapse
|