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Qiao X, Kong N, Sun S, Li X, Jiang C, Luo C, Wang L, Song L. Polymorphisms in the cysteine dioxygenase gene and their association with taurine content in the Pacific oyster Crassostrea gigas. Comp Biochem Physiol B Biochem Mol Biol 2024; 273:110981. [PMID: 38642610 DOI: 10.1016/j.cbpb.2024.110981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
The Pacific oyster Crassostrea gigas is rich in taurine, which is crucial for its adaptation to the fluctuating intertidal environment and presents significant potential in improving taurine nutrition and boosting immunity in humans. Cysteine dioxygenase (CDO) is a key enzyme involved in the initial step of taurine biosynthesis and plays a crucial role in regulating taurine content in the body. In the present study, polymorphisms of CDO gene in C. gigas (CgCDO) and their association with taurine content were evaluated in 198 individuals. A total of 24 single nucleotide polymorphism (SNP) loci were identified in the exonic region of CgCDO gene by direct sequencing. Among these SNPs, c.279G>A and c.287C>A were found to be significantly associated with taurine content, with the GG and AA genotype at the two loci exhibiting enhanced taurine accumulation (p < 0.05). Haplotype analysis revealed that the 279GG/287AA haplotype had the highest taurine content of 29.24 mg/g, while the 279AA/287CC haplotype showed the lowest taurine content of 21.19 mg/g. These results indicated that the SNPs of CgCDO gene could influence the taurine content in C. gigas and have potential applications in the selective breeding of high-taurine varieties.
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Affiliation(s)
- Xin Qiao
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Ning Kong
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China.
| | - Shiqing Sun
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Xiang Li
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Chunyu Jiang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Cong Luo
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
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Fang WW, Kong XL, Yang JY, Tao NN, Li YM, Wang TT, Li YY, Han QL, Zhang YZ, Hu JJ, Li HC, Liu Y. PE/PPE mutations in the transmission of Mycobacterium tuberculosis in China revealed by whole genome sequencing. BMC Microbiol 2024; 24:206. [PMID: 38858614 PMCID: PMC11163795 DOI: 10.1186/s12866-024-03352-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/26/2024] [Indexed: 06/12/2024] Open
Abstract
OBJECTIVE This study aims to examine the impact of PE/PPE gene mutations on the transmission of Mycobacterium tuberculosis (M. tuberculosis) in China. METHODS We collected the whole genome sequencing (WGS) data of 3202 M. tuberculosis isolates in China from 2007 to 2018 and investigated the clustering of strains from different lineages. To evaluate the potential role of PE/PPE gene mutations in the dissemination of the pathogen, we employed homoplastic analysis to detect homoplastic single nucleotide polymorphisms (SNPs) within these gene regions. Subsequently, logistic regression analysis was conducted to analyze the statistical association. RESULTS Based on nationwide M. tuberculosis WGS data, it has been observed that the majority of the M. tuberculosis burden in China is caused by lineage 2 strains, followed by lineage 4. Lineage 2 exhibited a higher number of transmission clusters, totaling 446 clusters, of which 77 were cross-regional clusters. Conversely, there were only 52 transmission clusters in lineage 4, of which 9 were cross-regional clusters. In the analysis of lineage 2 isolates, regression results showed that 4 specific gene mutations, PE4 (position 190,394; c.46G > A), PE_PGRS10 (839,194; c.744 A > G), PE16 (1,607,005; c.620T > G) and PE_PGRS44 (2,921,883; c.333 C > A), were significantly associated with the transmission of M. tuberculosis. Mutations of PE_PGRS10 (839,334; c.884 A > G), PE_PGRS11 (847,613; c.1455G > C), PE_PGRS47 (3,054,724; c.811 A > G) and PPE66 (4,189,930; c.303G > C) exhibited significant associations with the cross-regional clusters. A total of 13 mutation positions showed a positive correlation with clustering size, indicating a positive association. For lineage 4 strains, no mutations were found to enhance transmission, but 2 mutation sites were identified as risk factors for cross-regional clusters. These included PE_PGRS4 (338,100; c.974 A > G) and PPE13 (976,897; c.1307 A > C). CONCLUSION Our results indicate that some PE/PPE gene mutations can increase the risk of M. tuberculosis transmission, which might provide a basis for controlling the spread of tuberculosis.
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Affiliation(s)
- Wei-Wei Fang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Xiang-Long Kong
- Shandong Artificial Intelligence Institute, Qilu University of Technology & Shandong Academy of Sciences, Jinan, Shandong, PR China
| | - Jie-Yu Yang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Ning-Ning Tao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
| | - Ya-Meng Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Ting-Ting Wang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
| | - Ying-Ying Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Qi-Lin Han
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Yu-Zhen Zhang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Jin-Jiang Hu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Huai-Chen Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China.
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Diniz CHDP, Henrique T, Stefanini ACB, De Castro TB, Tajara EH. Cetuximab chemotherapy resistance: Insight into the homeostatic evolution of head and neck cancer (Review). Oncol Rep 2024; 51:80. [PMID: 38639184 PMCID: PMC11056821 DOI: 10.3892/or.2024.8739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
The complex evolution of genetic alterations in cancer that occurs in vivo is a selective process involving numerous factors and mechanisms. Chemotherapeutic agents that prevent the growth and spread of cancer cells induce selective pressure, leading to rapid artificial selection of resistant subclones. This rapid evolution is possible because antineoplastic drugs promote alterations in tumor‑cell metabolism, thus creating a bottleneck event. The few resistant cells that survive in this new environment obtain differential reproductive success that enables them to pass down the newly selected resistant gene pool. The present review aims to summarize key findings of tumor evolution, epithelial‑mesenchymal transition and resistance to cetuximab therapy in head and neck squamous cell carcinoma.
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Affiliation(s)
- Carlos Henrique De Paula Diniz
- Department of Molecular Biology, School of Medicine of São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, SP 15090-000, Brazil
| | - Tiago Henrique
- Department of Molecular Biology, School of Medicine of São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, SP 15090-000, Brazil
| | - Ana Carolina B. Stefanini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, SP 15090-000, Brazil
- Department of Experimental Research, Albert Einstein Education and Research Israeli Institute, IIEPAE, São Paulo, SP 05652-900, Brazil
| | - Tialfi Bergamin De Castro
- Department of Molecular Biology, School of Medicine of São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, SP 15090-000, Brazil
- Microbial Pathogenesis Department, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA
| | - Eloiza H. Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, SP 15090-000, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP 05508-090, Brazil
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Li M, Zhang Y, Zhou P, Miao Y, Li S, Jiang L. Mutational analysis of pulmonary large cell neuroendocrine carcinoma: APC gene mutations identify a good prognostic factor. Lung Cancer 2024; 192:107825. [PMID: 38795461 DOI: 10.1016/j.lungcan.2024.107825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 05/28/2024]
Abstract
Pulmonary large cell neuroendocrine carcinoma (LCNEC) is a highly aggressive neoplasm with biological heterogeneity. Mutations in multiple genes have been identified in LCNEC. However, associations between gene alterations, histopathological characteristics, and prognosis remain ambiguous. Here, we investigated the clinicopathologic, immunohistochemical, and genomic characteristics of 19 patients with LCNEC and 9 patients with atypical carcinoid (AC). We revealed high mutation frequencies of TP53 (89.5 %), RB1 (42.1 %), APC (31.6 %), and MCL1 (31.6 %) in LCNEC, while genetic alterations were rarely found in AC. APC alterations mainly occurred to the exon 16 and were only identified in LCNEC with wild-type RB1. The 19 LCNEC were further subgrouped into APC wild-type (LCNEC-APCMT, 6/19) and APC-mutated (LCNEC-APCWT, 13/19) subgroups. In comparison with LCNEC-APCWT, LCNEC-APCMT displayed lower TMB (median: 12.64 vs 4.20, P = 0.045), and relatively mild cytologic atypia. In addition, LCNEC-APCMT distinguished itself from AC and LCNEC-APCWT by obviously downregulated expression of neuroendocrine markers (CD56 and Syn, P < 0.01) and significantly altered expression of genes downstream of APC (β-catenin migrating into the cytoplasm and nucleus, P < 0.001; c-Myc upregulating, P = 0.005). The OS of LCNEC-APCMT was numerically intermediate between AC and LCNEC-APCWT. We first proposed that APC alterations were common in LCNEC with wild-type RB1 and that LCNEC-APCMT was associated with lower TMB and better OS in comparison with LCNEC-APCWT.
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Affiliation(s)
- Mengqian Li
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
| | - Ying Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
| | - Ping Zhou
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
| | - Yuqing Miao
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
| | - Shuang Li
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
| | - Lili Jiang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
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Osugi A, Tamaru A, Yoshiyama T, Iwamoto T, Mitarai S, Murase Y. Mycobacterium tuberculosis is less likely to acquire pathogenic mutations during latent infection than during active disease. Microbiol Spectr 2024:e0428923. [PMID: 38786200 DOI: 10.1128/spectrum.04289-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024] Open
Abstract
Most people infected with Mycobacterium tuberculosis (Mtb) are believed to be in a state of latent tuberculosis (TB) infection (LTBI). Although LTBI is asymptomatic and not infectious, there is a risk of developing active disease even decades after infection. Here, to characterize mutations acquired during LTBI, we collected and analyzed Mtb genomes from seven Japanese patient pairs, each pair consisting of two active TB patients whose starting dates of developing active disease were >3 years apart; one had a high suspicion of LTBI before developing active disease, whereas the other did not. Thereafter, we compared these genomes with those of longitudinal sample pairs within a host of chronic active TB infections combined with public data. The bacterial populations in patients with LTBI were genetically more homogeneous and accumulated single nucleotide polymorphisms (SNPs) slower than those from active disease. Moreover, the lower proportion of nonsynonymous SNPs indicated weaker selective pressures during LTBI than active disease. Finally, the different mutation spectrums indicated different mutators between LTBI and active disease. These results suggest that the likelihood of the acquisition of mutations responsible for antibiotic resistance and increased virulence was lower in the Mtb population from LTBI than active disease.IMPORTANCEControlling latent tuberculosis (TB) infection (LTBI) activation is an effective strategy for TB elimination, where understanding Mycobacterium tuberculosis (Mtb) dynamics within the host plays an important role. Previous studies on chronic active disease reported that Mtb accumulated genomic mutations within the host, possibly resulting in acquired drug resistance and increased virulence. However, several reports suggest that fewer mutations accumulate during LTBI than during the active disease, but the associated risk is largely unknown. Here, we analyzed the genomic dynamics of Mtb within the host during LTBI. Our results statistically suggest that Mtb accumulates mutations during LTBI, but most mutations are under low selective pressures, which induce mutations responsible for drug resistance and virulence. Thus, we propose that LTBI acts as a source for new TB disease rather than as a period for in-host genome evolution.
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Affiliation(s)
- Asami Osugi
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
| | - Aki Tamaru
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Takashi Yoshiyama
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
| | | | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
- Basic Mycobacteriology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yoshiro Murase
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
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Xiao Y, Wang N, Jin X, Liu A, Zhang Z. Clinical relevance of SCN and CyN induced by ELANE mutations: a systematic review. Front Immunol 2024; 15:1349919. [PMID: 38840904 PMCID: PMC11150597 DOI: 10.3389/fimmu.2024.1349919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
Introduction According to the PRISMA criteria, a systematic review has been conducted to investigate the clinical relevance between patients with severe congenital neutropenia (SCN) and cyclic congenital neutropenia (CyN) induced by ELANE mutations. Methods We have searched PubMed, EMBASE, Web of Science, Scopus, Cochrane, CNKI, Wanfang Medicine, and VIP for ELANE mutation related literature published from 1997 to 2022. Using Microsoft Excel collect and organize data, SPSS 25, GraphPad Prism 8.0.1, and Omap analyze and plot statistical. Compare the gender, age, geography, mutation sites, infection characteristics, treatment, and other factors of SCN and CyN patients induced by ELANE mutations, with a focus on exploring the relationship between genotype and clinical characteristics, genotype and prognosis. Results This study has included a total of 467 patients with SCN and 90 patients with CyN. The onset age of SCN and CyN are both less than 1 year old, and the onset and diagnosis age of SCN are both younger than CyN. The mutation of ELANE gene is mainly missense mutation, and hot spot mutations include S126L, P139L, G214R, c.597+1G>A. The high-frequency mutations with severe outcomes are A57V, L121H, L121P, c.597+1G>A, c.597+1G>T, S126L, C151Y, C151S, G214R, C223X. Respiratory tract, skin and mucosa are the most common infection sites, Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli are the most common. Discussion Patients with refractory G-CSF are more likely to develop severe outcomes. The commonly used pre-treatment schemes for transplantation are Bu-Cy-ATG and Flu-Bu-ATG. The prognosis of transplantation is mostly good, but the risk of GVHD is high. Systematic Review Registration https://www.crd.york.ac.uk/PROSPERO/. PROSPERO, identifier CRD42023434656.
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Affiliation(s)
- Yufan Xiao
- Department of Rheumatology and Immunology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Nandi Wang
- Department of Rheumatology and Immunology, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Xinghao Jin
- Department of Rheumatology and Immunology, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Anna Liu
- Department of Rheumatology and Immunology, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Zhiyong Zhang
- Department of Rheumatology and Immunology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, Chongqing, China
- National Clinical Research Center for Child Health and Disorders, Children’s Hospital of Chongqing Medical University, Chongqing, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children’s Hospital of Chongqing Medical University, Chongqing, China
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Zhong T, Wu H, Hu J, Liu Y, Zheng Y, Li N, Sun Z, Yin XF, He QY, Sun X. Two synonymous single-nucleotide polymorphisms promoting fluoroquinolone resistance of Escherichia coli in the environment. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133849. [PMID: 38432089 DOI: 10.1016/j.jhazmat.2024.133849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
Single-nucleotide polymorphism (SNP) is one of the core mechanisms that respond to antibiotic resistance of Escherichia coli (E. coli), which is a major issue in environmental pollution. A specific type of SNPs, synonymous SNPs, have been generally considered as the "silent" SNPs since they do not change the encoded amino acid. However, the impact of synonymous SNPs on mRNA splicing, nucleo-cytoplasmic export, stability, and translation was gradually discovered in the last decades. Figuring out the mechanism of synonymous SNPs in regulating antibiotic resistance is critical to improve antimicrobial therapy strategies in clinics and biological treatment strategies of antibiotic-resistant E. coli-polluted materials. With our newly designed antibiotic resistant SNPs prediction algorithm, Multilocus Sequence Type based Identification for Phenotype-single nucleotide polymorphism Analysis (MIPHA), and in vivo validation, we identified 2 important synonymous SNPs 522 G>A and 972 C>T, located at hisD gene, which was previously predicted as a fluoroquinolone resistance-related gene without a detailed mechanism in the E. coli samples with environmental backgrounds. We first discovered that hisD causes gyrA mutation via the upregulation of sbmC and its downstream gene umuD. Moreover, those 2 synonymous SNPs of hisD cause its own translational slowdown and further reduce the expression levels of sbmC and its downstream gene umuD, making the fluoroquinolone resistance determining region of gyrA remains unmutated, ultimately causing the bacteria to lose their ability to resist drugs. This study provided valuable insight into the role of synonymous SNPs in mediating antibiotic resistance of bacteria and a new perspective for the treatment of environmental pollution caused by drug-resistant bacteria.
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Affiliation(s)
- Tairan Zhong
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Haiming Wu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jiehua Hu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Yun Liu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Yundan Zheng
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Nan Li
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zhenghua Sun
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xing-Feng Yin
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.
| | - Xuesong Sun
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.
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Ślesak I, Ślesak H. From cyanobacteria and cyanophages to chloroplasts: the fate of the genomes of oxyphototrophs and the genes encoding photosystem II proteins. THE NEW PHYTOLOGIST 2024; 242:1055-1067. [PMID: 38439684 DOI: 10.1111/nph.19633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/02/2024] [Indexed: 03/06/2024]
Abstract
Chloroplasts are the result of endosymbiosis of cyanobacterial organisms with proto-eukaryotes. The psbA, psbD and psbO genes are present in all oxyphototrophs and encode the D1/D2 proteins of photosystem II (PSII) and PsbO, respectively. PsbO is a peripheral protein that stabilizes the O2-evolving complex in PSII. Of these genes, psbA and psbD remained in the chloroplastic genome, while psbO was transferred to the nucleus. The genomes of selected cyanobacteria, chloroplasts and cyanophages carrying psbA and psbD, respectively, were analysed. The highest density of genes and coding sequences (CDSs) was estimated for the genomes of cyanophages, cyanobacteria and chloroplasts. The synonymous mutation rate (rS) of psbA and psbD in chloroplasts remained almost unchanged and is lower than that of psbO. The results indicate that the decreasing genome size in chloroplasts is more similar to the genome reduction observed in contemporary endosymbiotic organisms than in streamlined genomes of free-living cyanobacteria. The rS of atpA, which encodes the α-subunit of ATP synthase in chloroplasts, suggests that psbA and psbD, and to a lesser extent psbO, are ancient and conservative and arose early in the evolution of oxygenic photosynthesis. The role of cyanophages in the evolution of oxyphototrophs and chloroplastic genomes is discussed.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Halina Ślesak
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
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Serra Moncadas L, Hofer C, Bulzu PA, Pernthaler J, Andrei AS. Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis. Nat Commun 2024; 15:3421. [PMID: 38653968 PMCID: PMC11039613 DOI: 10.1038/s41467-024-47767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.
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Affiliation(s)
- Lucas Serra Moncadas
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Cyrill Hofer
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Adrian-Stefan Andrei
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.
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10
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Knaga S, Kasperek K, Luchowska A, Drabik K, Próchniak T, Zięba G, Batkowska J. The relationship between lysozyme gene polymorphism and quality changes during the storage of eggs derived from 2 commercial strains of Japanese quail. Poult Sci 2024; 103:103792. [PMID: 38729073 PMCID: PMC11103425 DOI: 10.1016/j.psj.2024.103792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/08/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
During the storage irreversible changes occur in eggs that result in a deterioration of their quality. The most significant changes affect the albumen. One of the major proteins of albumen present in egg white is lysozyme, which protects the embryo from microorganisms. This enzyme also contributes to the qualitative characteristics of albumen. It is possible that its polymorphism also affects the quality and stability of the obtained raw material that is, table eggs. Therefore, the aim of this study was to assess the potential effect of polymorphism in the lysozyme gene and protein on the quality changes during the storage of eggs derived from 2 genetic strains of Japanese quail belonging to various utility types. Eggs from selected females of laying and meat-type breeds were stored for 14 wk. During this period the egg quality traits were evaluated 10 times. DNA was isolated from each female and all exons of the lysozyme gene had been sequenced. In total, fourteen SNPs' and one 4-bp indel mutation were identified in exons and adjacent intronic sequences, among which SNP1 (1:32140723) resulted in a substitution of lysine with glutamine (Q21K). The results showed that SNP1 (strain S22), as well as the SNP2, SNP5, SNP7, SNP8, SNP10, SNP11, SNP12 and SNP13 were significantly associated with breaking strength during egg storage in both investigated Japanese quail strains. Furthermore, a 3 haplotype blocks containing nine SNPs (2, 5, 6, 7, 8, 10, 11, 12 and 13) were identified. These blocks displayed 8 distinct haplotypes that had significant association with breaking strength at all storage time points where egg quality analyses were performed. The study also revealed significant effects of breed and storage time on the egg quality traits. These results provide new insights into the genetic basis of egg quality during storage and could be incorporated into the breeding programs involving these strains.
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Affiliation(s)
- S Knaga
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Bydgoszcz 85-084, Poland
| | - K Kasperek
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, Lublin 20-950, Poland
| | - A Luchowska
- Student Research Circle of Dentofacial Orthopedics and Orthodontics, Poznan University of Medical Sciences, Poznan 60-812, Poland
| | - K Drabik
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, Lublin 20-950, Poland
| | - T Próchniak
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, Lublin 20-950, Poland
| | - G Zięba
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, Lublin 20-950, Poland
| | - J Batkowska
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, Lublin 20-950, Poland.
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11
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Sun J, Li M, Sun H, Lin Z, Shi B, Jia Z. Genetic association and functional validation of ZFP36L2 in non-syndromic orofacial cleft subtypes. J Hum Genet 2024; 69:139-144. [PMID: 38321215 DOI: 10.1038/s10038-024-01222-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Non-syndromic orofacial cleft (NSOC) is one of the most common craniofacial malformations with complex etiology. This study aimed to explore the role of specific SNPs in ZFP36L2 and its functional relevance in zebrafish models. METHODS We analyzed genetic data of the Chinese Han population from two previous GWAS, comprising of 2512 cases and 2255 controls. Based on the Hardy-Weinberg Equilibrium (HWE) and minor allele frequency (MAF), SNPs in the ZFP36L2 were selected for association analysis. In addition, zebrafish models were used to clarify the in-situ expression pattern of zfp36l2 and the impact of its Morpholino-induced knockdown. RESULTS Via association analysis, rs7933 in ZFP36L2 was significantly associated with various non-syndromic cleft lip-only subtypes, potentially conferring a protective effect. Zebrafish embryos showed elevated expression of zfp36l2 in the craniofacial region during critical stages of oral cavity formation. Furthermore, Morpholino-induced knockdown of zfp36l2 led to craniofacial abnormalities, including cleft lip, which was partially rescued by the addition of zfp36l2 mRNA. CONCLUSION Our findings highlight the significance of ZFP36L2 in the etiology of NSOC, supported by both human genetic association data and functional studies in zebrafish. These results pave the way for further exploration of targeted interventions for craniofacial malformations.
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Affiliation(s)
- Jialin Sun
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Mujia Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Huaqin Sun
- SCU-CUHK Joint Laboratory for Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyuan Lin
- SCU-CUHK Joint Laboratory for Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
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12
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Chen S, Navickas A, Goodarzi H. Translational adaptation in breast cancer metastasis and emerging therapeutic opportunities. Trends Pharmacol Sci 2024; 45:304-318. [PMID: 38453522 DOI: 10.1016/j.tips.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/09/2024]
Abstract
Breast cancer's tendency to metastasize poses a critical barrier to effective treatment, making it a leading cause of mortality among women worldwide. A growing body of evidence is showing that translational adaptation is emerging as a key mechanism enabling cancer cells to thrive in the dynamic tumor microenvironment (TME). Here, we systematically summarize how breast cancer cells utilize translational adaptation to drive metastasis, highlighting the intricate regulation by specific translation machinery and mRNA attributes such as sequences and structures, along with the involvement of tRNAs and other trans-acting RNAs. We provide an overview of the latest findings and emerging concepts in this area, discussing their potential implications for therapeutic strategies in breast cancer.
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Affiliation(s)
- Siyu Chen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Albertas Navickas
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
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13
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Chen Y, Ma S, Ku H, Huangfu B, Wang K, Du C, Zhang M. Contiguous identity between entire coding regions of transgenic and native genes rather than special regions is essential for a strong co-suppression. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112016. [PMID: 38311253 DOI: 10.1016/j.plantsci.2024.112016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
The discovery of co-suppression in plants has greatly boosted the study of gene silencing mechanisms, but its triggering mechanism has remained a mystery. In this study, we explored its possible trigger mechanism by using Fatty acid desaturase 2 (FAD2) and Fatty acid elongase 1 (FAE1) strong co-suppression systems. Analysis of small RNAs in FAD2 co-suppression lines showed that siRNAs distributed throughout the coding region of FAD2 with an accumulated peak. However, mutations of the peak siRNA-matched site and siRNA derived site had not alleviated the co-suppression of its transgenic lines. Synthetic FAD2 (AtFAD2sm), which has synonymous mutations in the entire coding region, failed to trigger any co-suppression. Furthermore, 5' and 3' portions of AtFAD2 and AtFAD2sm were swapped to form two hybrid genes, AtFAD2-3sm and AtFAD2-5sm. 80 % and 92 % of their transgenic lines exhibited co-suppression, respectively. Finally, FAE1s with different degrees of the continuous sequence identity compared with AtFAE1 were tested in their Arabidopsis transgenic lines, and the results showed the co-suppression frequency was reduced as their continuous sequence identity stepped down. This work suggests that contiguous identity between the entire coding regions of transgenic and native genes rather than a special region is essential for a strong co-suppression.
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Affiliation(s)
- Yangyang Chen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shijie Ma
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, Anhui Province, China.
| | - Hangkai Ku
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Bingyuan Huangfu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Chang Du
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China; College of Life Sciences, South China Normal University, Guangzhou, Guangdong 610631, China.
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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14
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Jiang Y, Li H, Li Z, Du S, Zhang R, Zhao Y, Christiani DC, Shen S, Chen F. A cross-trait study of lung cancer and its related respiratory diseases based on large-scale exome sequencing population. Transl Lung Cancer Res 2024; 13:512-525. [PMID: 38601445 PMCID: PMC11002514 DOI: 10.21037/tlcr-24-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/27/2024] [Indexed: 04/12/2024]
Abstract
Background Genome-wide association studies (GWASs) explain the genetic susceptibility between diseases and common variants. Nevertheless, with the appearance of large-scale sequencing profiles, we could explore the rare coding variants in disease pathogenesis. Methods We estimated the genetic correlation of nine respiratory diseases and lung cancer in the UK Biobank (UKB) by linkage disequilibrium score regression (LDSC). Then, we performed exome-wide association studies at single-variant level and gene-level for lung cancer and lung cancer-related respiratory diseases using the whole-exome sequencing (WES) data of 427,934 European participants. Cross-trait meta-analysis was conducted by association analysis based on subsets (ASSET) to identify the pleiotropic variants, while in-silico functional analysis was performed to explore their function. Causal mediation analysis was used to explore whether these pleiotropic variants lead to lung cancer is mediated by affecting the chronic respiratory diseases. Results Five respiratory diseases [emphysema, pneumonia, asthma, chronic obstructive pulmonary disease (COPD), and fibrosis] were genetically correlated with lung cancer. We identified 102 significant independent variants at single-variant levels for lung cancer and five lung cancer-related diseases. 15:78590583:G>A (missense variant in CHRNA5) was shared in lung cancer, emphysema, and COPD. Meanwhile, 14 significant genes and 87 suggestive genes were identified in gene-based association tests, including HSD3B7 (lung cancer), SRSF2 (pneumonia), TNXB (asthma), TERT (fibrosis), MOSPD3 (emphysema). Based on the cross-trait meta-analysis, we detected 145 independent pleiotropic variants. We further identified abundant pathways with significant enrichment effects, demonstrating that these pleiotropic genes were functional. Meanwhile, the proportion of mediation effects of these variants ranged from 6 to 23 (emphysema: 23%; COPD: 20%; pneumonia: 20%; fibrosis: 7%; asthma: 6%) through these five respiratory diseases to the incidence of lung cancer. Conclusions The identified shared genetic variants, genes, biological pathways, and potential intermediate causal pathways provide a basis for further exploration of the relationship between lung cancer and respiratory diseases.
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Affiliation(s)
- Yunke Jiang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Hongru Li
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zaiming Li
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Sha Du
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Yang Zhao
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing, China
| | - David C. Christiani
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Pulmonary and Critical Care Division, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sipeng Shen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing, China
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing, China
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15
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Klim J, Zielenkiewicz U, Kaczanowski S. Loss-of-function mutations are main drivers of adaptations during short-term evolution. Sci Rep 2024; 14:7128. [PMID: 38532077 DOI: 10.1038/s41598-024-57694-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
We noticed that during short-term experimental evolution and carcinogenesis, mutations causing gene inactivation (i.e., nonsense mutations or frameshifts) are frequent. Our meta-analysis of 65 experiments using modified dN/dS statistics indicated that nonsense mutations are adaptive in different experimental conditions and we empirically confirmed this prediction. Using yeast S. cerevisiae as a model we show that fixed or highly frequent gene loss-of-function mutations are almost exclusively adaptive in the majority of experiments.
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Affiliation(s)
- Joanna Klim
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Urszula Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Szymon Kaczanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
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16
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Ren G, Gu X, Zhang L, Gong S, Song S, Chen S, Chen Z, Wang X, Li Z, Zhou Y, Li L, Yang J, Lai F, Dang Y. Ribosomal frameshifting at normal codon repeats recodes functional chimeric proteins in human. Nucleic Acids Res 2024; 52:2463-2479. [PMID: 38281188 PMCID: PMC10954444 DOI: 10.1093/nar/gkae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
Ribosomal frameshifting refers to the process that ribosomes slip into +1 or -1 reading frame, thus produce chimeric trans-frame proteins. In viruses and bacteria, programmed ribosomal frameshifting can produce essential trans-frame proteins for viral replication or regulation of other biological processes. In humans, however, functional trans-frame protein derived from ribosomal frameshifting is scarcely documented. Combining multiple assays, we show that short codon repeats could act as cis-acting elements that stimulate ribosomal frameshifting in humans, abbreviated as CRFS hereafter. Using proteomic analyses, we identified many putative CRFS events from 32 normal human tissues supported by trans-frame peptides positioned at codon repeats. Finally, we show a CRFS-derived trans-frame protein (HDAC1-FS) functions by antagonizing the activities of HDAC1, thus affecting cell migration and apoptosis. These data suggest a novel type of translational recoding associated with codon repeats, which may expand the coding capacity of mRNA and diversify the regulation in human.
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Affiliation(s)
- Guiping Ren
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Xiaoqian Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Lu Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Shimin Gong
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Shuang Song
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Shunkai Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Zhenjing Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Xiaoyan Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Zhanbiao Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Yingshui Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Longxi Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Jiao Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Fan Lai
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650021, China
- Southwest United Graduate School, Kunming650092, China
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Nkurikiyimfura O, Waheed A, Fang H, Yuan X, Chen L, Wang YP, Lu G, Zhan J, Yang L. Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene. BMC Ecol Evol 2024; 24:36. [PMID: 38494489 PMCID: PMC10946160 DOI: 10.1186/s12862-024-02223-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/11/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Sequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous mutation, synonymous mutations are generally considered to be selectively neutral but accumulating evidence suggests they also contribute to species adaptation by regulating the flow of genetic information and the development of functional traits. In this study, we analysed sequence characteristics of ATP6, a housekeeping gene from 139 Phytophthora infestans isolates, and compared the fitness components including metabolic rate, temperature sensitivity, aggressiveness, and fungicide tolerance among synonymous mutations. RESULTS We found that the housekeeping gene exhibited low genetic variation and was represented by two major synonymous mutants at similar frequency (0.496 and 0.468, respectively). The two synonymous mutants were generated by a single nucleotide substitution but differed significantly in fitness as well as temperature-mediated spatial distribution and expression. The synonymous mutant ending in AT was more common in cold regions and was more expressed at lower experimental temperature than the synonymous mutant ending in GC and vice versa. CONCLUSION Our results are consistent with the argument that synonymous mutations can modulate the adaptive evolution of species including pathogens and have important implications for sustainable disease management, especially under climate change.
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Affiliation(s)
- Oswald Nkurikiyimfura
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Abdul Waheed
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Hanmei Fang
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaoxian Yuan
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lixia Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yan-Ping Wang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, Sichuan, 611130, China
| | - Guodong Lu
- Department of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden.
| | - Lina Yang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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Li Y, Li Y, Liu Y, Kong X, Tao N, Hou Y, Wang T, Han Q, Zhang Y, Long F, Li H. Iron-related gene mutations driving global Mycobacterium tuberculosis transmission revealed by whole-genome sequencing. BMC Genomics 2024; 25:249. [PMID: 38448842 PMCID: PMC10916221 DOI: 10.1186/s12864-024-10152-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Iron plays a crucial role in the growth of Mycobacterium tuberculosis (M. tuberculosis). However, the precise regulatory mechanism governing this system requires further elucidation. Additionally, limited studies have examined the impact of gene mutations related to iron on the transmission of M. tuberculosis globally. This research aims to investigate the correlation between mutations in iron-related genes and the worldwide transmission of M. tuberculosis. RESULTS A total of 13,532 isolates of M. tuberculosis were included in this study. Among them, 6,104 (45.11%) were identified as genomic clustered isolates, while 8,395 (62.04%) were classified as genomic clade isolates. Our results showed that a total of 12 single nucleotide polymorphisms (SNPs) showed a positive correlation with clustering, such as Rv1469 (ctpD, C758T), Rv3703c (etgB, G1122T), and Rv3743c (ctpJ, G676C). Additionally, seven SNPs, including Rv0104 (T167G, T478G), Rv0211 (pckA, A302C), Rv0283 (eccB3, C423T), Rv1436 (gap, G654T), ctpD C758T, and etgB C578A, demonstrated a positive correlation with transmission clades across different countries. Notably, our findings highlighted the positive association of Rv0104 T167G, pckA A302C, eccB3 C423T, ctpD C758T, and etgB C578A with transmission clades across diverse regions. Furthermore, our analysis identified 78 SNPs that exhibited significant associations with clade size. CONCLUSIONS Our study reveals the link between iron-related gene SNPs and M. tuberculosis transmission, offering insights into crucial factors influencing the pathogenicity of the disease. This research holds promise for targeted strategies in prevention and treatment, advancing research and interventions in this field.
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Affiliation(s)
- Yameng Li
- Clinical Department of Integrated Traditional Chinese and Western Medicine , The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, 250014, Jinan, Shandong, People's Republic of China
| | - Yifan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), 250031, Jinan, Shandong, People's Republic of China
| | - Yao Liu
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, People's Republic of China
| | - Xianglong Kong
- Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), 250011, Jinan, Shandong, People's Republic of China
| | - Ningning Tao
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, People's Republic of China
| | - Yawei Hou
- Institute of Chinese Medical Literature and Culture of Shandong University of Traditional Chinese Medicine, 250355, Jinan, Shandong, People's Republic of China
| | - Tingting Wang
- Clinical Department of Integrated Traditional Chinese and Western Medicine , The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, 250014, Jinan, Shandong, People's Republic of China
| | - Qilin Han
- Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, People's Republic of China
| | - Yuzhen Zhang
- Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, People's Republic of China
| | - Fei Long
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), 250031, Jinan, Shandong, People's Republic of China.
| | - Huaichen Li
- Clinical Department of Integrated Traditional Chinese and Western Medicine , The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, 250014, Jinan, Shandong, People's Republic of China.
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, People's Republic of China.
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19
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Sakamoto F, Kanamori S, Díaz LM, Cádiz A, Ishii Y, Yamaguchi K, Shigenobu S, Nakayama T, Makino T, Kawata M. Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards. Ecol Evol 2024; 14:e11117. [PMID: 38455144 PMCID: PMC10920033 DOI: 10.1002/ece3.11117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Understanding the genetic basis for adapting to thermal environments is important due to serious effects of global warming on ectothermic species. Various genes associated with thermal adaptation in lizards have been identified mainly focusing on changes in gene expression or the detection of positively selected genes using coding regions. Only a few comprehensive genome-wide analyses have included noncoding regions. This study aimed to identify evolutionarily conserved and accelerated genomic regions using whole genomes of eight Anolis lizard species that have repeatedly adapted to similar thermal environments in multiple lineages. Evolutionarily conserved genomic regions were extracted as regions with overall sequence conservation (regions with fewer base substitutions) across all lineages compared with the neutral model. Genomic regions that underwent accelerated evolution in the lineage of interest were identified as those with more base substitutions in the target branch than in the entire background branch. Conserved elements across all branches were relatively abundant in "intergenic" genomic regions among noncoding regions. Accelerated regions (ARs) of each lineage contained a significantly greater proportion of noncoding RNA genes than the entire multiple alignment. Common genes containing ARs within 5 kb of their vicinity in lineages with similar thermal habitats were identified. Many genes associated with circadian rhythms and behavior were found in hot-open and cool-shaded habitat lineages. These genes might play a role in contributing to thermal adaptation and assist future studies examining the function of genes involved in thermal adaptation via genome editing.
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Affiliation(s)
- Fuku Sakamoto
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | | | - Luis M. Díaz
- National Museum of Natural History of CubaHavanaCuba
| | - Antonio Cádiz
- Faculty of BiologyUniversity of HavanaHavanaCuba
- Present address:
Department of BiologyUniversity of MiamiCoral GablesFloridaUSA
| | - Yuu Ishii
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | | | - Shuji Shigenobu
- Trans‐Omics FacilityNational Institute for Basic BiologyOkazakiJapan
- Department of Basic Biology, School of Life ScienceThe Graduate University for Advanced Studies, SOKENDAIOkazakiJapan
| | - Takuro Nakayama
- Division of Life Sciences, Center for Computational SciencesUniversity of TsukubaTsukubaJapan
| | - Takashi Makino
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Masakado Kawata
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
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20
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Rimkute I, Chaimongkol N, Woods KD, Nagata BM, Darko S, Gudbole S, Henry AR, Sosnovtsev SV, Olia AS, Verardi R, Bok K, Todd JP, Woodward R, Kwong PD, Douek DC, Alves DA, Green KY, Roederer M. A non-human primate model for human norovirus infection. Nat Microbiol 2024; 9:776-786. [PMID: 38321182 DOI: 10.1038/s41564-023-01585-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/12/2023] [Indexed: 02/08/2024]
Abstract
Norovirus infection can cause gastrointestinal disease in humans. Development of therapies and vaccines against norovirus have been limited by the lack of a suitable and reliable animal model. Here we established rhesus macaques as an animal model for human norovirus infection. We show that rhesus macaques are susceptible to oral infection with human noroviruses from two different genogroups. Variation in duration of virus shedding (days to weeks) between animals, evolution of the virus over the time of infection, induction of virus-specific adaptive immune responses, susceptibility to reinfection and preferential replication of norovirus in the jejunum of rhesus macaques was similar to infection reported in humans. We found minor pathological signs and changes in epithelial cell surface glycosylation patterns in the small intestine during infection. Detection of viral protein and RNA in intestinal biopsies confirmed the presence of the virus in chromogranin A-expressing epithelial cells, as it does in humans. Thus, rhesus macaques are a promising non-human primate model to evaluate vaccines and therapeutics against norovirus disease.
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Affiliation(s)
- Inga Rimkute
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Natthawan Chaimongkol
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kamron D Woods
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Bianca M Nagata
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, USA
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sucheta Gudbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Stanislav V Sosnovtsev
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Karin Bok
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - John-Paul Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ruth Woodward
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Derron A Alves
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, USA
| | - Kim Y Green
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
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21
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Love AM, Nair NU. Specific codons control cellular resources and fitness. SCIENCE ADVANCES 2024; 10:eadk3485. [PMID: 38381824 PMCID: PMC10881034 DOI: 10.1126/sciadv.adk3485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
As cellular engineering progresses from simply overexpressing proteins to imparting complex phenotypes through multigene expression, judicious appropriation of cellular resources is essential. Since codon use is degenerate and biased, codons may control cellular resources at a translational level. We investigate how partitioning transfer RNA (tRNA) resources by incorporating dissimilar codon usage can drastically alter interdependence of expression level and burden on the host. By isolating the effect of individual codons' use during translation elongation while eliminating confounding factors, we show that codon choice can trans-regulate fitness of the host and expression of other heterologous or native genes. We correlate specific codon usage patterns with host fitness and derive a coding scheme for multigene expression called the Codon Health Index (CHI, χ). This empirically derived coding scheme (χ) enables the design of multigene expression systems that avoid catastrophic cellular burden and is robust across several proteins and conditions.
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Affiliation(s)
- Aaron M. Love
- Manus Bio, Waltham, MA 02453, USA
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, USA
| | - Nikhil U. Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, USA
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22
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Rech J, Schett G, Tufan A, Kuemmerle-Deschner JB, Özen S, Tascilar K, Geck L, Krickau T, Cohen E, Welzel T, Kuehn M, Vetterli M. Patient Experiences and Challenges in the Management of Autoinflammatory Diseases-Data from the International FMF & AID Global Association Survey. J Clin Med 2024; 13:1199. [PMID: 38592017 PMCID: PMC10931825 DOI: 10.3390/jcm13051199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/03/2024] [Accepted: 02/13/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Autoinflammatory diseases (AIDs) are rare, mostly genetic diseases that affect the innate immune system and are associated with inflammatory symptoms. Both paediatric and adult patients face daily challenges related to their disease, diagnosis and subsequent treatment. For this reason, a survey was developed in collaboration between the FMF & AID Global Association and the Erlangen Center for Periodic Systemic Autoinflammatory Diseases. METHODS The aim of the survey was to collect the personal assessment of affected patients with regard to their current status in terms of diagnostic timeframes, the interpretation of genetic tests, the number of misdiagnoses, and pain and fatigue despite treatment. RESULTS In total, data from 1043 AID patients (829 adults and 214 children/adolescents) from 52 countries were collected and analyzed. Familial Mediterranean fever (FMF) (521/50%) and Behçet's disease (311/30%) were the most frequently reported diseases. The average time to diagnosis was 3 years for children/adolescents and 14 years for adults. Prior to the diagnosis of autoinflammatory disease, patients received several misdiagnoses, including psychosomatic disorders. The vast majority of patients reported that genetic testing was available (92%), but only 69% were tested. A total of 217 patients reported that no increase in acute-phase reactants was detected during their disease episodes. The intensity of pain and fatigue was measured in AID patients and found to be high. A total of 88% of respondents received treatment again, while 8% reported no treatment. CONCLUSIONS AID patients, particularly adults, suffer from significant delays in diagnosis, misdiagnosis, and a variety of symptoms, including pain and fatigue. Based on the results presented, raising awareness of these diseases in the wider medical community is crucial to improving patient care and quality of life.
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Affiliation(s)
- Jürgen Rech
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (G.S.); (K.T.); (L.G.)
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany;
- Center for Rare Diseases Erlangen (ZSEER), Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Georg Schett
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (G.S.); (K.T.); (L.G.)
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany;
- Center for Rare Diseases Erlangen (ZSEER), Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Abdurrahman Tufan
- Division of Rheumatology, Department of Internal Medicine, Gazi University Ankara, 06560 Ankara, Turkey;
| | - Jasmin B. Kuemmerle-Deschner
- Division of Pediatric Rheumatology, Autoinflammation Reference Center Tübingen, Department of Pediatrics, University Hospital Tübingen, 72016 Tübingen, Germany;
| | - Seza Özen
- Department of Pediatric Rheumatology, Hacettepe University, 06100 Ankara, Turkey;
| | - Koray Tascilar
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (G.S.); (K.T.); (L.G.)
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany;
- Center for Rare Diseases Erlangen (ZSEER), Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Leonie Geck
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (G.S.); (K.T.); (L.G.)
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany;
- Center for Rare Diseases Erlangen (ZSEER), Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Tobias Krickau
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany;
- Center for Rare Diseases Erlangen (ZSEER), Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Department of Paediatrics, Friedrich-Alexander University (FAU), Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Ellen Cohen
- FMF & AID Global Association, 8306 Zurich, Switzerland; (E.C.); (M.V.)
| | - Tatjana Welzel
- Pediatric Rheumatology, University Children’s Hospital Basel (UKBB), University of Basel, 4001 Basel, Switzerland;
| | | | - Malena Vetterli
- FMF & AID Global Association, 8306 Zurich, Switzerland; (E.C.); (M.V.)
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23
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Abid R, Nisar H, Chaudhary SU, Hamid M, Sahibzada KI, Firdous S, Mudassar M, Sadaf S. Association of epilepsy and neurological impairments with homozygous recessive missense mutations found in the genes responsible for ganglioside biosynthesis ( ST3GAL5) and calcium voltage-gated channels ( CACNA1H) - insights through molecular dynamic simulations. J Biomol Struct Dyn 2024:1-12. [PMID: 38356142 DOI: 10.1080/07391102.2024.2314751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
With over 2.2 million cases, the incidence rate of epilepsy in Pakistan is far higher than the rest of the world due primarily to the frequent, traditionally imposed cousin marriages. In the present study, comprehensive whole exome sequencing (WES) analyses of a three-generation family with four affected members presenting 'unexplained' childhood absence epilepsy (CAE), seizures and dementia, was performed in a quest to identify heritable, epilepsy-causal gene variants to better aid in carrier screening and genetic counselling. The WES data was generated, analyzed, and validated through Sanger's sequencing, molecular dynamic simulation (MDS) analysis, and molecular mechanics with generalized Born and surface area solvation (MM/GBSA) studies. Two homozygous recessive, missense mutations in ST3GAL5 (c.311A > G, p. His104Arg) and CACNA1H (c.6230G > A, p. Arg2077His) genes, earlier regarded as benign or of uncertain significance, have been identified as a potential etiology. Comparative MDS and free binding energy calculations revealed substantial structural perturbations in mutant forms of ST3GAL5 leading to decreased binding and reduced catalytic activity of the p.His104Arg and two other functional variants (p.Val74Glu and p.Arg288Ter) when compared with wild type. Our findings reinforce that WES analyses may uncover 'hidden', heritable variants and together with MDS and MM/GBSA may provide plausible clues to answer the unexplained causes of epilepsy for an effective management and better patient outcome. Further, revisit of epilepsy-associated mutational landscape in population context is imperative as the variants with 'benign' tags may turn out to be 'non-benign', when exist in combination with other benign.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rizwan Abid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Haseeb Nisar
- Department of Life-Sciences, University of Management and Technology, Lahore, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics & Engineering Research Laboratory, Department of Life-Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Maham Hamid
- Biomedical Informatics & Engineering Research Laboratory, Department of Life-Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Kashif Iqbal Sahibzada
- Department of Health Professional Technologies, The University of Lahore, Lahore, Pakistan
| | - Safia Firdous
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Lahore, Pakistan
| | | | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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24
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Liang J, Tang M, Chen L, Wang W, Liang X. Oxidative stress resistance prompts pyrroloquinoline quinone biosynthesis in Hyphomicrobium denitrificans H4-45. Appl Microbiol Biotechnol 2024; 108:204. [PMID: 38349428 PMCID: PMC10864529 DOI: 10.1007/s00253-024-13053-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/15/2024]
Abstract
Pyrroloquinoline quinone (PQQ) is a natural antioxidant with diverse applications in food and pharmaceutical industries. A lot of effort has been devoted toward the discovery of PQQ high-producing microbial species and characterization of biosynthesis, but it is still challenging to achieve a high PQQ yield. In this study, a combined strategy of random mutagenesis and adaptive laboratory evolution (ALE) with fermentation optimization was applied to improve PQQ production in Hyphomicrobium denitrificans H4-45. A mutant strain AE-9 was obtained after nearly 400 generations of UV-LiCl mutagenesis, followed by an ALE process, which was conducted with a consecutive increase of oxidative stress generated by kanamycin, sodium sulfide, and potassium tellurite. In the flask culture condition, the PQQ production in mutant strain AE-9 had an 80.4% increase, and the cell density increased by 14.9% when compared with that of the initial strain H4-45. Moreover, batch and fed-batch fermentation processes were optimized to further improve PQQ production by pH control strategy, methanol and H2O2 feed flow, and segmented fermentation process. Finally, the highest PQQ production and productivity of the mutant strain AE-9 reached 307 mg/L and 4.26 mg/L/h in a 3.7-L bioreactor, respectively. Whole genome sequencing analysis showed that genetic mutations in the ftfL gene and thiC gene might contribute to improving PQQ production by enhancing methanol consumption and cell growth in the AE-9 strain. Our study provided a systematic strategy to obtain a PQQ high-producing mutant strain and achieve high production of PQQ in fermentation. These practical methods could be applicable to improve the production of other antioxidant compounds with uncleared regulation mechanisms. KEY POINTS: • Improvement of PQQ production by UV-LiCl mutagenesis combined with adaptive laboratory evolution (ALE) and fermentation optimization. • A consecutive increase of oxidative stress could be used as the antagonistic factor for ALE to enhance PQQ production. • Mutations in the ftfL gene and thiC gene indicated that PQQ production might be increased by enhancing methanol consumption and cell growth.
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Affiliation(s)
- Jiale Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Mingjie Tang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Lang Chen
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Wenjie Wang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
| | - Xinle Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
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25
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Zurita AMI, Kyriazis CC, Lohmueller KE. The impact of non-neutral synonymous mutations when inferring selection on non-synonymous mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579314. [PMID: 38370782 PMCID: PMC10871344 DOI: 10.1101/2024.02.07.579314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The distribution of fitness effects (DFE) describes the proportions of new mutations that have different effects on reproductive fitness. Accurate measurements of the DFE are important because the DFE is a fundamental parameter in evolutionary genetics and has implications for our understanding of other phenomena like complex disease or inbreeding depression. Current computational methods to infer the DFE for nonsynonymous mutations from natural variation first estimate demographic parameters from synonymous variants to control for the effects of demography and background selection. Then, conditional on these parameters, the DFE is then inferred for nonsynonymous mutations. This approach relies on the assumption that synonymous variants are neutrally evolving. However, some evidence points toward synonymous mutations having measurable effects on fitness. To test whether selection on synonymous mutations affects inference of the DFE of nonsynonymous mutations, we simulated several possible models of selection on synonymous mutations using SLiM and attempted to recover the DFE of nonsynonymous mutations using Fit∂a∂i, a common method for DFE inference. Our results show that the presence of selection on synonymous variants leads to incorrect inferences of recent population growth. Furthermore, under certain parameter combinations, inferences of the DFE can have an inflated proportion of highly deleterious nonsynonymous mutations. However, this bias can be eliminated if the correct demographic parameters are used for DFE inference instead of the biased ones inferred from synonymous variants. Our work demonstrates how unmodeled selection on synonymous mutations may affect downstream inferences of the DFE.
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Affiliation(s)
- Aina Martinez I Zurita
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Kirk E Lohmueller
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
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26
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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] [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.
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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
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Ports BL, Jensen-Seaman MI. Convergent rates of protein evolution identify novel targets of sexual selection in primates. Evolution 2024; 78:364-377. [PMID: 37864838 PMCID: PMC10834059 DOI: 10.1093/evolut/qpad188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 10/23/2023]
Abstract
Sexual selection is the differential reproductive success of individuals, resulting from competition for mates, mate choice, or success in fertilization. In primates, this selective pressure often leads to the development of exaggerated traits which play a role in sexual competition and successful reproduction. In order to gain insight into the mechanisms driving the development of sexually selected traits, we used an unbiased genome-wide approach across 21 primate species to correlate individual rates of protein evolution to relative testes size and sexual dimorphism in body size, 2 anatomical hallmarks of sexual selection in mammals. Among species with presumed high levels of sperm competition, we detected strong conservation of testes-specific proteins responsible for spermatogenesis and ciliary form and function. In contrast, we identified accelerated evolution of female reproductive proteins expressed in the vagina, cervix, and fallopian tubes in these same species. Additionally, we found accelerated protein evolution in lymphoid tissue, indicating that adaptive immune functions may also be influenced by sexual selection. This study demonstrates the distinct complexity of sexual selection in primates revealing contrasting patterns of protein evolution between male and female reproductive tissues.
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Affiliation(s)
- Bri L Ports
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA, United States
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28
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Dhar D, Mehanovic S, Moss W, Miller CL. Sequences at gene segment termini inclusive of untranslated regions and partial open reading frames play a critical role in mammalian orthoreovirus S gene packaging. PLoS Pathog 2024; 20:e1012037. [PMID: 38394338 PMCID: PMC10917250 DOI: 10.1371/journal.ppat.1012037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Mammalian orthoreovirus (MRV) is a prototypic member of the Spinareoviridae family and has ten double-stranded RNA segments. One copy of each segment must be faithfully packaged into the mature virion, and prior literature suggests that nucleotides (nts) at the terminal ends of each gene likely facilitate their packaging. However, little is known about the precise packaging sequences required or how the packaging process is coordinated. Using a novel approach, we have determined that 200 nts at each terminus, inclusive of untranslated regions (UTR) and parts of the open reading frame (ORF), are sufficient for packaging S gene segments (S1-S4) individually and together into replicating virus. Further, we mapped the minimal sequences required for packaging the S1 gene segment into a replicating virus to 25 5' nts and 50 3' nts. The S1 UTRs, while not sufficient, were necessary for efficient packaging, as mutations of the 5' or 3' UTRs led to a complete loss of virus recovery. Using a second novel assay, we determined that 50 5' nts and 50 3' nts of S1 are sufficient to package a non-viral gene segment into MRV. The 5' and 3' termini of the S1 gene are predicted to form a panhandle structure and specific mutations within the stem of the predicted panhandle region led to a significant decrease in viral recovery. Additionally, mutation of six nts that are conserved across the three major serotypes of MRV that are predicted to form an unpaired loop in the S1 3' UTR, led to a complete loss of viral recovery. Overall, our data provide strong experimental proof that MRV packaging signals lie at the terminal ends of the S gene segments and offer support that the sequence requirements for efficient packaging of the S1 segment include a predicted panhandle structure and specific sequences within an unpaired loop in the 3' UTR.
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Affiliation(s)
- Debarpan Dhar
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Samir Mehanovic
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Walter Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Cathy L. Miller
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
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29
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Mello AC, Leao D, Dias L, Colombelli F, Recamonde-Mendoza M, Turchetto-Zolet AC, Matte U. Broken silence: 22,841 predicted deleterious synonymous variants identified in the human exome through computational analysis. Genet Mol Biol 2024; 46:e20230125. [PMID: 38259032 PMCID: PMC10804382 DOI: 10.1590/1678-4685-gmb-2023-0125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 12/10/2023] [Indexed: 01/24/2024] Open
Abstract
Synonymous single nucleotide variants (sSNVs) do not alter the primary structure of a protein, thus it was previously accepted that they were neutral. Recently, several studies demonstrated their significance to a range of diseases. Still, variant prioritization strategies lack focus on sSNVs. Here, we identified 22,841 deleterious synonymous variants in 125,748 human exomes using two in silico predictors (SilVA and CADD). While 98.2% of synonymous variants are classified as neutral, 1.8% are predicted to be deleterious, yielding an average of 9.82 neutral and 0.18 deleterious sSNVs per exome. Further investigation of prediction features via Heterogeneous Ensemble Feature Selection revealed that impact on amino acid sequence and conservation carry the most weight for a deleterious prediction. Thirty nine detrimental sSNVs are not rare and are located on disease associated genes. Ten distinct putatively non-deleterious sSNVs are likely to be under positive selection in the North-Western European and East Asian populations. Taken together our analysis gives voice to the so-called silent mutations as we propose a robust framework for evaluating the deleteriousness of sSNVs in variant prioritization studies.
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Affiliation(s)
- Ana Carolina Mello
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa
Experimental, Laboratório de Células, Tecidos e Genes, Porto Alegre, RS,
Brazil
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Delva Leao
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Ciências Biológicas: Bioquímica, Porto Alegre, RS, Brazil
| | - Luis Dias
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa
Experimental, Laboratório de Células, Tecidos e Genes, Porto Alegre, RS,
Brazil
| | - Felipe Colombelli
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de
Informática, Porto Alegre, RS, Brazil
| | - Mariana Recamonde-Mendoza
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de
Informática, Porto Alegre, RS, Brazil
| | - Andreia Carina Turchetto-Zolet
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de
Genética, Porto Alegre, RS, Brazil
| | - Ursula Matte
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa
Experimental, Laboratório de Células, Tecidos e Genes, Porto Alegre, RS,
Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de
Genética, Porto Alegre, RS, Brazil
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30
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Oelschlaeger P. Molecular Mechanisms and the Significance of Synonymous Mutations. Biomolecules 2024; 14:132. [PMID: 38275761 PMCID: PMC10813300 DOI: 10.3390/biom14010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Synonymous mutations result from the degeneracy of the genetic code. Most amino acids are encoded by two or more codons, and mutations that change a codon to another synonymous codon do not change the amino acid in the gene product. Historically, such mutations have been considered silent because they were assumed to have no to very little impact. However, research in the last few decades has produced several examples where synonymous mutations play important roles. These include optimizing expression by enhancing translation initiation and accelerating or decelerating translation elongation via codon usage and mRNA secondary structures, stabilizing mRNA molecules and preventing their breakdown before translation, and faulty protein folding or increased degradation due to enhanced ubiquitination and suboptimal secretion of proteins into the appropriate cell compartments. Some consequences of synonymous mutations, such as mRNA stability, can lead to different outcomes in prokaryotes and eukaryotes. Despite these examples, the significance of synonymous mutations in evolution and in causing disease in comparison to nonsynonymous mutations that do change amino acid residues in proteins remains controversial. Whether the molecular mechanisms described by which synonymous mutations affect organisms can be generalized remains poorly understood and warrants future research in this area.
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Affiliation(s)
- Peter Oelschlaeger
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
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31
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Li J, Li C, Xu W. Liver cancer-specific mutations in functional domains of ADAR2 lead to the elevation of coding and non-coding RNA editing in multiple tumor-related genes. Mol Genet Genomics 2024; 299:1. [PMID: 38170228 DOI: 10.1007/s00438-023-02091-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/17/2023] [Indexed: 01/05/2024]
Abstract
Mutation is the major cause of phenotypic innovations. Apart from DNA mutations, the alteration on RNA such as the ADAR-mediated A-to-I RNA editing could also shape the phenotype. These two layers of variations have not been systematically combined to study their collective roles in cancers. We collected the high-quality transcriptomes of ten hepatocellular carcinoma (HCC) and the matched control samples. We systematically identified HCC-specific mutations in the exonic regions and profiled the A-to-I RNA editome in each sample. All ten HCC samples had mutations in the CDS of ADAR2 gene (dsRNA-binding domain or catalytic domain). The consequence of these mutations converged to the elevation of ADAR2 efficiency as reflected by the global increase of RNA editing levels in HCC. The up-regulated editing sites (UES) were enriched in the CDS and UTR of oncogenes and tumor suppressor genes (TSG), indicating the possible roles of these target genes in HCC oncogenesis. We present the mutation-ADAR2-UES-oncogene/TSG-HCC axis that explains how mutations at different layers would finally lead to abnormal phenotype. In the light of central dogma, our work provides novel insights into how to fully take advantage of the transcriptome data to decipher the consequence of mutations.
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Affiliation(s)
- Jian Li
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Chaowei Li
- Department of PET/CT, The Second Clinical Medical College of Qingdao University (Qingdao Center Hospital), Qingdao, 266042, China
| | - Wengui Xu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
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32
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Jiang D, Zhang J. Ascertainment Bias in the Genomic Test of Positive Selection on Regulatory Sequences. Mol Biol Evol 2024; 41:msad284. [PMID: 38149460 PMCID: PMC10766478 DOI: 10.1093/molbev/msad284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/12/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2023] Open
Abstract
Evolution of gene expression mediated by cis-regulatory changes is thought to be an important contributor to organismal adaptation, but identifying adaptive cis-regulatory changes is challenging due to the difficulty in knowing the expectation under no positive selection. A new approach for detecting positive selection on transcription factor binding sites (TFBSs) was recently developed, thanks to the application of machine learning in predicting transcription factor (TF) binding affinities of DNA sequences. Given a TFBS sequence from a focal species and the corresponding inferred ancestral sequence that differs from the former at n sites, one can predict the TF-binding affinities of many n-step mutational neighbors of the ancestral sequence and obtain a null distribution of the derived binding affinity, which allows testing whether the binding affinity of the real derived sequence deviates significantly from the null distribution. Applying this test genomically to all experimentally identified binding sites of 3 TFs in humans, a recent study reported positive selection for elevated binding affinities of TFBSs. Here, we show that this genomic test suffers from an ascertainment bias because, even in the absence of positive selection for strengthened binding, the binding affinities of known human TFBSs are more likely to have increased than decreased in evolution. We demonstrate by computer simulation that this bias inflates the false positive rate of the selection test. We propose several methods to mitigate the ascertainment bias and show that almost all previously reported positive selection signals disappear when these methods are applied.
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Affiliation(s)
- Daohan Jiang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Present address: Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Ma J, Nie Y, Zhang L, Xu Y. The evolutionary mechanism and function analysis of two subgroups of histamine-producing and non-histamine-producing Tetragenococcus halophilus. Food Res Int 2024; 176:113744. [PMID: 38163696 DOI: 10.1016/j.foodres.2023.113744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/07/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024]
Abstract
Tetragenococcus halophilus is a halophilic bacterium that existed in the fermentation of soy sauce and miso for flavor production and probiotic benefits. However, it is composed of two subgroups, histamine-producing and non-histamine-producing, with the former causing histamine accumulation and offering risks to food safety. Exploring the evolutionary mechanisms and physiological function of histamine-biosynthesis is of significance for understanding the formative mechanism of T. halophilus's strain-specificity and is helpful for microbial control. Using systematic genomic analysis, we found that plasmid acquisition and loss is the evolutionary form resulting in the two subgroups of T. halophilus. Two plasmids, plasmid α with 30 kb and plasmid β with 4 kb existed in histamine-producing T. halophilus. We investigated the whole genetic information and proposed their genetic function in both two plasmids. The acquisition of histamine-producing plasmid enhanced the acid tolerance of histamine-producing T. halophilus but did not affect salt tolerance. More interestingly, we found that the existence of plasmid will promote the co-culture growth of T. halophilus. This study deepens our understanding of the formative mechanism of microbial species diversity, and provides our knowledge of the physiological function of histamine-producing plasmids.
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Affiliation(s)
- Jinjin Ma
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Yao Nie
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Lijie Zhang
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
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Liu Q, Cai YD, Ma L, Liu H, Linghu T, Guo S, Wei S, Song F, Tian L, Cai W, Li H. Relaxed purifying selection pressure drives accelerated and dynamic gene rearrangements in thrips (Insecta: Thysanoptera) mitochondrial genomes. Int J Biol Macromol 2023; 253:126742. [PMID: 37689283 DOI: 10.1016/j.ijbiomac.2023.126742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/06/2023] [Accepted: 08/26/2023] [Indexed: 09/11/2023]
Abstract
Insect mitochondrial genomes (mitogenome) generally present a typical gene order, which is considered as the ancestral arrangement. All sequenced mitogenomes in the Thysanoptera display high levels of gene rearrangement. Due to limited number of thrips mitogenomes sequenced, how gene rearrangement may be shaped by evolution remain unclear. Here, we analyzed 33 thrips mitogenomes, including 14 newly sequenced. These mitogenomes were diverse in organization, nucleotides substitution and gene arrangements. We found 28 highly rearranged gene orders with the breakpoints of gene rearrangements from 25 to 33. Reconstruction of the ancestors mitochondrial gene arrangements states indicated that Tubulifera have more complex pathways than Terebrantia in the gene order evolution. Molecular calibration estimated that divergence of two suborders occurred in the middle Triassic while the radiation of thrips was associated with the arose and flourish of angiosperm. Our evolutionary hypothesis testing suggests that relaxation of selection pressure enabled the early phase of Thysanoptera evolution, followed by a stronger selective pressure fixed diversification. Our analyses found gene inversion increases the nonsynonymous substitution rates and provide an evolutionary hypothesis driving the diverse gene orders.
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Affiliation(s)
- Qiaoqiao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hangrui Liu
- Department of Physics and Astronomy, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Tianye Linghu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shaokun Guo
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests of Ministry of Agriculture and Rural Affairs, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shujun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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Matkarimov BT, Saparbaev MK. Chargaff's second parity rule lies at the origin of additive genetic interactions in quantitative traits to make omnigenic selection possible. PeerJ 2023; 11:e16671. [PMID: 38107580 PMCID: PMC10725672 DOI: 10.7717/peerj.16671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/22/2023] [Indexed: 12/19/2023] Open
Abstract
Background Francis Crick's central dogma provides a residue-by-residue mechanistic explanation of the flow of genetic information in living systems. However, this principle may not be sufficient for explaining how random mutations cause continuous variation of quantitative highly polygenic complex traits. Chargaff's second parity rule (CSPR), also referred to as intrastrand DNA symmetry, defined as near-exact equalities G ≈ C and A ≈ T within a single DNA strand, is a statistical property of cellular genomes. The phenomenon of intrastrand DNA symmetry was discovered more than 50 years ago; at present, it remains unclear what its biological role is, what the mechanisms are that force cellular genomes to comply strictly with CSPR, and why genomes of certain noncellular organisms have broken intrastrand DNA symmetry. The present work is aimed at studying a possible link between intrastrand DNA symmetry and the origin of genetic interactions in quantitative traits. Methods Computational analysis of single-nucleotide polymorphisms in human and mouse populations and of nucleotide composition biases at different codon positions in bacterial and human proteomes. Results The analysis of mutation spectra inferred from single-nucleotide polymorphisms observed in murine and human populations revealed near-exact equalities of numbers of reverse complementary mutations, indicating that random genetic variations obey CSPR. Furthermore, nucleotide compositions of coding sequences proved to be statistically interwoven via CSPR because pyrimidine bias at the 3rd codon position compensates purine bias at the 1st and 2nd positions. Conclusions According to Fisher's infinitesimal model, we propose that accumulation of reverse complementary mutations results in a continuous phenotypic variation due to small additive effects of statistically interwoven genetic variations. Therefore, additive genetic interactions can be inferred as a statistical entanglement of nucleotide compositions of separate genetic loci. CSPR challenges the neutral theory of molecular evolution-because all random mutations participate in variation of a trait-and provides an alternative solution to Haldane's dilemma by making a gene function diffuse. We propose that CSPR is symmetry of Fisher's infinitesimal model and that genetic information can be transferred in an implicit contactless manner.
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Affiliation(s)
- Bakhyt T. Matkarimov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- L.N.Gumilev Eurasian National University, Astana, Kazakhstan
| | - Murat K. Saparbaev
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Yang B, Cheng Z, Luo L, Cheng K, Gan S, Shi Y, Liu C, Wang D. Comparative analysis of codon usage patterns of Plasmodium helical interspersed subtelomeric (PHIST) proteins. Front Microbiol 2023; 14:1320060. [PMID: 38156001 PMCID: PMC10752978 DOI: 10.3389/fmicb.2023.1320060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023] Open
Abstract
Background Plasmodium falciparum is a protozoan parasite that causes the most severe form of malaria in humans worldwide, which is predominantly found in sub-Saharan Africa, where it is responsible for the majority of malaria-related deaths. Plasmodium helical interspersed subtelomeric (PHIST) proteins are a family of proteins, with a conserved PHIST domain, which are typically located at the subtelomeric regions of the Plasmodium falciparum chromosomes and play crucial roles in the interaction between the parasite and its human host, such as cytoadherence, immune evasion, and host cell remodeling. However, the specific utilization of synonymous codons by PHIST proteins in Plasmodium falciparum is still unknown. Methods Codon usage bias (CUB) refers to the unequal usage of synonymous codons during translation, resulting in over- or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact various cellular processes, including protein expression levels and genetic variation. To investigate this, the CUB of 88 PHIST protein coding sequences (CDSs) from 5 subgroups were analyzed in this study. Results The results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis identified a higher occurrence of AT-ended codons (AGA and UUA) in PHIST proteins of Plasmodium falciparum. The average effective number of codons (ENC) for these PHIST proteins was 36.69, indicating a weak codon preference among them, as it was greater than 35. Additionally, the correlation analysis among codon base composition (GC1, GC2, GC3, GCs), codon adaptation index (CAI), codon bias index (CBI), frequency of optimal codons (FOP), ENC, general average hydropathicity (GRAVY), aromaticity (AROMO), length of synonymous codons (L_sym), and length of amino acids (L_aa) revealed the influence of base composition and codon usage indices on codon usage bias, with GC1 having a significant impact in this study. Furthermore, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis provided additional evidence that natural selection plays a crucial role in determining codon bias in PHIST proteins. Conclusion In conclusion, this study has enhanced our understanding of the characteristics of codon usage and genetic evolution in PHIST proteins, thereby providing data foundation for further research on antimalarial drugs or vaccines.
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Affiliation(s)
- Baoling Yang
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Ziwen Cheng
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Like Luo
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Kuo Cheng
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Shengqi Gan
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Yuyi Shi
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Che Liu
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Dawei Wang
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
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Wang L, Lin N, Zhang Y, Guo S, Liu C, Lin C, Zeng Y, Wu W, Guo J, Zhu C, Zhan F, Ou Q, Xun Z. A novel TRIM22 gene polymorphism promotes the response to PegIFNα therapy through cytokine-cytokine receptor interaction signaling pathway in chronic hepatitis B. Microbiol Spectr 2023; 11:e0224723. [PMID: 37882560 PMCID: PMC10715138 DOI: 10.1128/spectrum.02247-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/08/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Pegylated interferon alfa (PegIFNα) has limited efficacy in the treatment of chronic hepatitis B (CHB). Although many biomarkers related to hepatitis B virus (HBV) have been proposed to stratify patients, the response rate to PegIFNα is still unsatisfactory. Herein, our data suggest that the single-nucleotide polymorphism (SNP) rs10838543 in TRIM22 potentiates a positive clinical response to PegIFNα treatment in patients with hepatitis B e antigen-positive CHB by increasing the levels of IFNL1, CCL3, and CCL5. These observations can help guide treatment decisions for patients with CHB to improve the response rate to PegIFNα.
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Affiliation(s)
- Long Wang
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- The First Clinical College, Fujian Medical University , Fuzhou, Fujian, China
| | - Ni Lin
- The First Clinical College, Fujian Medical University , Fuzhou, Fujian, China
| | - Yanfang Zhang
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- The First Clinical College, Fujian Medical University , Fuzhou, Fujian, China
| | - Shaoying Guo
- The First Clinical College, Fujian Medical University , Fuzhou, Fujian, China
| | - Can Liu
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- The First Clinical College, Fujian Medical University , Fuzhou, Fujian, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
| | - Caorui Lin
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
| | - Yongbin Zeng
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
| | - Wennan Wu
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
| | - Jianhui Guo
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
| | - Chenggong Zhu
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- The First Clinical College, Fujian Medical University , Fuzhou, Fujian, China
| | - Fuguo Zhan
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
| | - Qishui Ou
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- The First Clinical College, Fujian Medical University , Fuzhou, Fujian, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
| | - Zhen Xun
- Department of Laboratory Medicine, Fujian Key Laboratory of Laboratory Medicine, Gene Diagnosis Research Center, Fujian Clinical Research Center for Clinical Immunology Laboratory Test, The First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
- The First Clinical College, Fujian Medical University , Fuzhou, Fujian, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University , Fuzhou, Fujian, China
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Bajaj P, Bhasin M, Varadarajan R. Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene. BMC Genomics 2023; 24:732. [PMID: 38049728 PMCID: PMC10694988 DOI: 10.1186/s12864-023-09817-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/18/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Single synonymous codon mutations typically have only minor or no effects on gene function. Here, we estimate the effects on cell growth of ~ 200 single synonymous codon mutations in an operonic context by mutating almost all positions of ccdB, the 101-residue long cytotoxin of the ccdAB Toxin-Antitoxin (TA) operon to most degenerate codons. Phenotypes were assayed by transforming the mutant library into CcdB sensitive and resistant E. coli strains, isolating plasmid pools, and subjecting them to deep sequencing. Since autoregulation is a hallmark of TA operons, phenotypes obtained for ccdB synonymous mutants after transformation in a RelE toxin reporter strain followed by deep sequencing provided information on the amount of CcdAB complex formed. RESULTS Synonymous mutations in the N-terminal region involved in translation initiation showed the strongest non-neutral phenotypic effects. We observe an interplay of numerous factors, namely, location of the codon, codon usage, t-RNA abundance, formation of anti-Shine Dalgarno sequences, predicted transcript secondary structure, and evolutionary conservation in determining phenotypic effects of ccdB synonymous mutations. Incorporation of an N-terminal, hyperactive synonymous mutation, in the background of the single synonymous codon mutant library sufficiently increased translation initiation, such that mutational effects on either folding or termination of translation became more apparent. Introduction of putative pause sites not only affects the translational rate, but might also alter the folding kinetics of the protein in vivo. CONCLUSION In summary, the study provides novel insights into diverse mechanisms by which synonymous mutations modulate gene function. This information is useful in optimizing heterologous gene expression in E. coli and understanding the molecular bases for alteration in gene expression that arise due to synonymous mutations.
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Affiliation(s)
- Priyanka Bajaj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
- Present address: Department of Bioengineering and Therapeutic Sciences, University of CA - San Francisco, San Francisco, CA, 94158, USA
| | - Munmun Bhasin
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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Xu Y, Bush SJ, Yang X, Xu L, Wang B, Ye K. Evolutionary analysis of conserved non-coding elements subsequent to whole-genome duplication in opium poppy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1804-1824. [PMID: 37706612 DOI: 10.1111/tpj.16466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
Whole-genome duplication (WGD) leads to the duplication of both coding and non-coding sequences within an organism's genome, providing an abundant supply of genetic material that can drive evolution, ultimately contributing to plant adaptation and speciation. Although non-coding sequences contain numerous regulatory elements, they have been understudied compared to coding sequences. In order to address this gap, we explored the evolutionary patterns of regulatory sequences, coding sequences and transcriptomes using conserved non-coding elements (CNEs) as regulatory element proxies following the recent WGD event in opium poppy (Papaver somniferum). Our results showed similar evolutionary patterns in subgenomes of regulatory and coding sequences. Specifically, the biased or unbiased retention of coding sequences reflected the same pattern as retention levels in regulatory sequences. Further, the divergence of gene expression patterns mediated by regulatory element variations occurred at a more rapid pace than that of gene coding sequences. However, gene losses were purportedly dependent on relaxed selection pressure in coding sequences. Specifically, the rapid evolution of tissue-specific benzylisoquinoline alkaloid production in P. somniferum was associated with regulatory element changes. The origin of a novel stem-specific ACR, which utilized ancestral cis-elements as templates, is likely to be linked to the evolutionary trajectory behind the transition of the PSMT1-CYP719A21 cluster from high levels of expression solely in P. rhoeas root tissue to its elevated expression in P. somniferum stem tissue. Our findings demonstrate that rapid regulatory element evolution can contribute to the emergence of new phenotypes and provide valuable insights into the high evolvability of regulatory elements.
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Affiliation(s)
- Yu Xu
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Stephen J Bush
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xinyi Yang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Linfeng Xu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Kai Ye
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Louros N, Schymkowitz J, Rousseau F. Mechanisms and pathology of protein misfolding and aggregation. Nat Rev Mol Cell Biol 2023; 24:912-933. [PMID: 37684425 DOI: 10.1038/s41580-023-00647-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
Despite advances in machine learning-based protein structure prediction, we are still far from fully understanding how proteins fold into their native conformation. The conventional notion that polypeptides fold spontaneously to their biologically active states has gradually been replaced by our understanding that cellular protein folding often requires context-dependent guidance from molecular chaperones in order to avoid misfolding. Misfolded proteins can aggregate into larger structures, such as amyloid fibrils, which perpetuate the misfolding process, creating a self-reinforcing cascade. A surge in amyloid fibril structures has deepened our comprehension of how a single polypeptide sequence can exhibit multiple amyloid conformations, known as polymorphism. The assembly of these polymorphs is not a random process but is influenced by the specific conditions and tissues in which they originate. This observation suggests that, similar to the folding of native proteins, the kinetics of pathological amyloid assembly are modulated by interactions specific to cells and tissues. Here, we review the current understanding of how intrinsic protein conformational propensities are modulated by physiological and pathological interactions in the cell to shape protein misfolding and aggregation pathology.
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Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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Li Y, Kong X, Li Y, Tao N, Wang T, Li Y, Hou Y, Zhu X, Han Q, Zhang Y, An Q, Liu Y, Li H. Association between fatty acid metabolism gene mutations and Mycobacterium tuberculosis transmission revealed by whole genome sequencing. BMC Microbiol 2023; 23:379. [PMID: 38041005 PMCID: PMC10691062 DOI: 10.1186/s12866-023-03072-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Fatty acid metabolism greatly promotes the virulence and pathogenicity of Mycobacterium tuberculosis (M.tb). However, the regulatory mechanism of fatty acid metabolism in M.tb remains to be elucidated, and limited evidence about the effects of gene mutations in fatty acid metabolism on the transmission of M.tb was reported. RESULTS Overall, a total of 3193 M.tb isolates were included in the study, of which 1596 (50%) were genomic clustered isolates. Most of the tuberculosis isolates belonged to lineage2(n = 2744,85.93%), followed by lineage4(n = 439,13.75%) and lineage3(n = 10,0.31%).Regression results showed that the mutations of gca (136,605, 317G > C, Arg106Pro; OR, 22.144; 95% CI, 2.591-189.272), ogt(1,477,346, 286G > C ,Gly96Arg; OR, 3.893; 95%CI, 1.432-10.583), and rpsA (1,834,776, 1235 C > T, Ala412Val; OR, 3.674; 95% CI, 1.217-11.091) were significantly associated with clustering; mutations in gca and rpsA were also significantly associated with clustering of lineage2. Mutation in arsA(3,001,498, 885 C > G, Thr295Thr; OR, 6.278; 95% CI, 2.508-15.711) was significantly associated with cross-regional clusters. We also found that 20 mutation sites were positively correlated with cluster size, while 11 fatty acid mutation sites were negatively correlated with cluster size. CONCLUSION Our research results suggested that mutations in genes related to fatty acid metabolism were related to the transmission of M.tb. This research could help in the future control of the transmission of M.tb.
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Affiliation(s)
- Yameng Li
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Xianglong Kong
- Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250011, Shandong, People's Republic of China
| | - Yifan Li
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, 250031, Shandong, People's Republic of China
| | - Ningning Tao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China
| | - Tingting Wang
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Yingying Li
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Yawei Hou
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Xuehan Zhu
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, People's Republic of China
| | - Qilin Han
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, People's Republic of China
| | - Yuzhen Zhang
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, People's Republic of China
| | - Qiqi An
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China.
| | - Huaichen Li
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China.
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China.
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Papkou A, Garcia-Pastor L, Escudero JA, Wagner A. A rugged yet easily navigable fitness landscape. Science 2023; 382:eadh3860. [PMID: 37995212 DOI: 10.1126/science.adh3860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/29/2023] [Indexed: 11/25/2023]
Abstract
Fitness landscape theory predicts that rugged landscapes with multiple peaks impair Darwinian evolution, but experimental evidence is limited. In this study, we used genome editing to map the fitness of >260,000 genotypes of the key metabolic enzyme dihydrofolate reductase in the presence of the antibiotic trimethoprim, which targets this enzyme. The resulting landscape is highly rugged and harbors 514 fitness peaks. However, its highest peaks are accessible to evolving populations via abundant fitness-increasing paths. Different peaks share large basins of attraction that render the outcome of adaptive evolution highly contingent on chance events. Our work shows that ruggedness need not be an obstacle to Darwinian evolution but can reduce its predictability. If true in general, the complexity of optimization problems on realistic landscapes may require reappraisal.
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Affiliation(s)
- Andrei Papkou
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Lucia Garcia-Pastor
- Departamento de Sanidad Animal and VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - José Antonio Escudero
- Departamento de Sanidad Animal and VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, NM, USA
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Wang D, Yang B. Analysis of codon usage bias of thioredoxin in apicomplexan protozoa. Parasit Vectors 2023; 16:431. [PMID: 37990340 PMCID: PMC10664530 DOI: 10.1186/s13071-023-06002-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/06/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Apicomplexan protozoa are a diverse group of obligate intracellular parasites causing many diseases that affect humans and animals, such as malaria, toxoplasmosis, and cryptosporidiosis. Apicomplexan protozoa possess unique thioredoxins (Trxs) that have been shown to regulate various cellular processes including metabolic redox regulation, parasite survival, and host immune evasion. However, it is still unknown how synonymous codons are used by apicomplexan protozoa Trxs. METHODS Codon usage bias (CUB) is the unequal usage of synonymous codons during translation which leads to the over- or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact a variety of cellular processes including protein expression levels and genetic variation. This study analyzed the CUB of 32 Trx coding sequences (CDS) from 11 apicomplexan protozoa. RESULTS The results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in Cryptosporidium spp. and Plasmodium spp., while the Eimeria spp., Babesia spp., Hammondia hammondi, Neospora caninum, and Toxoplasma gondii tended to end in G/C. The average effective number of codon (ENC) value of these apicomplexan protozoa is 46.59, which is > 35, indicating a weak codon preference among apicomplexan protozoa Trxs. Furthermore, the correlation analysis among codon base composition (GC1, GC2, GC3, GCs), codon adaptation index (CAI), codon bias index (CBI), frequency of optimal codons (FOP), ENC, general average hydropathicity (GRAVY), aromaticity (AROMO), length of synonymous codons (L_sym), and length of amino acids (L_aa) indicated the influence of base composition and codon usage indices on CUB. Additionally, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis further demonstrated that natural selection plays an important role in apicomplexan protozoa Trxs codon bias. CONCLUSIONS In conclusion, this study increased the understanding of codon usage characteristics and genetic evolution of apicomplexan protozoa Trxs, which expanded new ideas for vaccine and drug research.
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Affiliation(s)
- Dawei Wang
- Jinzhou Medical University, Jinzhou, 121000, Liaoning Province, China
| | - Baoling Yang
- Jinzhou Medical University, Jinzhou, 121000, Liaoning Province, China.
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Chamchoy K, Sudsumrit S, Wongwigkan J, Petmitr S, Songdej D, Adams ER, Edwards T, Leartsakulpanich U, Boonyuen U. Molecular characterization of G6PD mutations identifies new mutations and a high frequency of intronic variants in Thai females. PLoS One 2023; 18:e0294200. [PMID: 37967096 PMCID: PMC10651042 DOI: 10.1371/journal.pone.0294200] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/26/2023] [Indexed: 11/17/2023] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked enzymopathy caused by mutations in the G6PD gene. A medical concern associated with G6PD deficiency is acute hemolytic anemia induced by certain foods, drugs, and infections. Although phenotypic tests can correctly identify hemizygous males, as well as homozygous and compound heterozygous females, heterozygous females with a wide range of G6PD activity may be misclassified as normal. This study aimed to develop multiplex high-resolution melting (HRM) analyses to enable the accurate detection of G6PD mutations, especially among females with heterozygous deficiency. Multiplex HRM assays were developed to detect six G6PD variants, i.e., G6PD Gaohe (c.95A>G), G6PD Chinese-4 (c.392G>T), G6PD Mahidol (c.487G>A), G6PD Viangchan (c.871G>A), G6PD Chinese-5 (c.1024C>T), and G6PD Union (c.1360C>T) in two reactions. The assays were validated and then applied to genotype G6PD mutations in 248 Thai females. The sensitivity of the HRM assays developed was 100% [95% confidence interval (CI): 94.40%-100%] with a specificity of 100% (95% CI: 88.78%-100%) for detecting these six mutations. The prevalence of G6PD deficiency was estimated as 3.63% (9/248) for G6PD deficiency and 31.05% (77/248) for intermediate deficiency by phenotypic assay. The developed HRM assays identified three participants with normal enzyme activity as heterozygous for G6PD Viangchan. Interestingly, a deletion in intron 5 nucleotide position 637/638 (c.486-34delT) was also detected by the developed HRM assays. G6PD genotyping revealed a total of 12 G6PD genotypes, with a high prevalence of intronic variants. Our results suggested that HRM analysis-based genotyping is a simple and reliable approach for detecting G6PD mutations, and could be used to prevent the misdiagnosis of heterozygous females by phenotypic assay. This study also sheds light on the possibility of overlooking intronic variants, which could affect G6PD expression and contribute to enzyme deficiency.
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Affiliation(s)
- Kamonwan Chamchoy
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Sirapapha Sudsumrit
- 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
| | - Songsak Petmitr
- 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, United Kingdom
| | - Thomas Edwards
- Centre for Drugs and Diagnostics Research, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Usa Boonyuen
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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45
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Zhang Z, Tong F, Chen C, Zhang T, Qian G, Yang X, Huang X, Yang R, Zhao Z. Long-term follow-up of children with carbamoyl phosphate synthase 1 deficiency detected in newborn screening. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:721-726. [PMID: 37986659 PMCID: PMC10764181 DOI: 10.3724/zdxbyxb-2023-0359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/05/2023] [Indexed: 11/22/2023]
Abstract
OBJECTIVES To investigate genotype-phenotype characteristics and long-term prognosis of neonatal carbamoyl phosphate synthetase 1 (CPS1) deficiency among children through newborn screening in Zhejiang province. METHODS The clinical and follow-up data of children with CPS1 deficiency detected through neonatal screening and confirmed by tandem mass spectrometry and genetic testing in Zhejiang Province Newborn Disease Screening Center from September 2013 to August 2023 were retrospectively analyzed. RESULTS A total of 4 056 755 newborns were screened and 6 cases of CPS1 deficiency were diagnosed through phenotypic and genetic testing. Ten different variations of CPS1 genewere identified in genetic testing, including 2 known pathogenic variations (c.2359C>T and c.1549+1G>T) and 8 unreported variations (c.3405-1G>T, c.2372C>T, c.1436C>T, c.2228T>C, c.2441G>A, c.3031G>A, c.3075T>C and c.390-403del). All patients had decreased citrulline levels (2.72-6.21 μmol/L), and varying degrees of elevated blood ammonia. The patients received restricted natural protein intake (special formula), arginine and supportive therapy after diagnosis, and were followed-up for a period ranging from 9 months to 10 years. Three patients experienced hyperammonemia, and one patient each had attention deficit hyperactivity disorder, transient facial twitching and increased muscle tone. One patient died, while the other five surviving patients had normal scores of the Ages & Stages Questionnaires (ASQ) and Griffiths Development Scales up to the present time; 4 cases had combined height or weight lag and one case was normal in height and weight. CONCLUSIONS Low citrulline levels and hyperammonemia are common in CPS1 deficiency patients in Zhejiang. Most gene variants identified were specific to individual families, and no hotspot mutations were found. Early diagnosis through newborn screening and following standardized treatment can significantly improve the prognosis of the patients.
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Affiliation(s)
- Zhanming Zhang
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China.
| | - Fan Tong
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Chi Chen
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Ting Zhang
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Guling Qian
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Xin Yang
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Xinwen Huang
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Rulai Yang
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Zhengyan Zhao
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China.
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46
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Mani S, Tlusty T. Gene birth in a model of non-genic adaptation. BMC Biol 2023; 21:257. [PMID: 37957718 PMCID: PMC10644530 DOI: 10.1186/s12915-023-01745-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Over evolutionary timescales, genomic loci can switch between functional and non-functional states through processes such as pseudogenization and de novo gene birth. Particularly, de novo gene birth is a widespread process, and many examples continue to be discovered across diverse evolutionary lineages. However, the general mechanisms that lead to functionalization are poorly understood, and estimated rates of de novo gene birth remain contentious. Here, we address this problem within a model that takes into account mutations and structural variation, allowing us to estimate the likelihood of emergence of new functions at non-functional loci. RESULTS Assuming biologically reasonable mutation rates and mutational effects, we find that functionalization of non-genic loci requires the realization of strict conditions. This is in line with the observation that most de novo genes are localized to the vicinity of established genes. Our model also provides an explanation for the empirical observation that emerging proto-genes are often lost despite showing signs of adaptation. CONCLUSIONS Our work elucidates the properties of non-genic loci that make them fertile for adaptation, and our results offer mechanistic insights into the process of de novo gene birth.
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Affiliation(s)
- Somya Mani
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Republic of Korea.
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Departments of Physics and Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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47
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Dyakonova VE. DNA Instability in Neurons: Lifespan Clock and Driver of Evolution. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1719-1731. [PMID: 38105193 DOI: 10.1134/s0006297923110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/19/2023] [Accepted: 09/20/2023] [Indexed: 12/19/2023]
Abstract
In the last ten years, the discovery of neuronal DNA postmitotic instability has changed the theoretical landscape in neuroscience and, more broadly, biology. In 2003, A. M. Olovnikov suggested that neuronal DNA is the "initial substrate of aging". Recent experimental data have significantly increased the likelihood of this hypothesis. How does neuronal DNA accumulate damage and in what genome regions? What factors contribute to this process and how are they associated with aging and lifespan? These questions will be discussed in the review. In the course of Metazoan evolution, the instability of neuronal DNA has been accompanied by searching for the pathways to reduce the biological cost of brain activity. Various processes and activities, such as sleep, evolutionary increase in the number of neurons in the vertebrate brain, adult neurogenesis, distribution of neuronal activity, somatic polyploidy, and RNA editing in cephalopods, can be reconsidered in the light of the trade-off between neuronal plasticity and DNA instability in neurons. This topic is of considerable importance for both fundamental neuroscience and translational medicine.
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Affiliation(s)
- Varvara E Dyakonova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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48
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Campero-Basaldua C, González J, García JA, Ramírez E, Hernández H, Aguirre B, Torres-Ramírez N, Márquez D, Sánchez NS, Gómez-Hernández N, Torres-Machorro AL, Riego-Ruiz L, Scazzocchio C, González A. Neo-functionalization in Saccharomyces cerevisiae: a novel Nrg1-Rtg3 chimeric transcriptional modulator is essential to maintain mitochondrial DNA integrity. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231209. [PMID: 37920568 PMCID: PMC10618058 DOI: 10.1098/rsos.231209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 11/04/2023]
Abstract
In Saccharomyces cerevisiae, the transcriptional repressor Nrg1 (Negative Regulator of Glucose-repressed genes) and the β-Zip transcription factor Rtg3 (ReTroGrade regulation) mediate glucose repression and signalling from the mitochondria to the nucleus, respectively. Here, we show a novel function of these two proteins, in which alanine promotes the formation of a chimeric Nrg1/Rtg3 regulator that represses the ALT2 gene (encoding an alanine transaminase paralog of unknown function). An NRG1/NRG2 paralogous pair, resulting from a post-wide genome small-scale duplication event, is present in the Saccharomyces genus. Neo-functionalization of only one paralog resulted in the ability of Nrg1 to interact with Rtg3. Both nrg1Δ and rtg3Δ single mutant strains were unable to use ethanol and showed a typical petite (small) phenotype on glucose. Neither of the wild-type genes complemented the petite phenotype, suggesting irreversible mitochondrial DNA damage in these mutants. Neither nrg1Δ nor rtg3Δ mutant strains expressed genes encoded by any of the five polycistronic units transcribed from mitochondrial DNA in S. cerevisiae. This, and the direct measurement of the mitochondrial DNA gene complement, confirmed that irreversible damage of the mitochondrial DNA occurred in both mutant strains, which is consistent with the essential role of the chimeric Nrg1/Rtg3 regulator in mitochondrial DNA maintenance.
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Affiliation(s)
- Carlos Campero-Basaldua
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - James González
- Laboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Janeth Alejandra García
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Edgar Ramírez
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Hugo Hernández
- Departamento de Biología, Facultad de Química, UNAM, México City, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Beatriz Aguirre
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Nayeli Torres-Ramírez
- Laboratorio de Microscopía Electrónica Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Dariel Márquez
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Norma Silvia Sánchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Nicolás Gómez-Hernández
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, SLP, México
| | - Ana Lilia Torres-Machorro
- Laboratorio de Biología Celular, Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias ‘Ismael Cosío Villegas', Tlalpan, Mexico
| | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, SLP, México
| | - Claudio Scazzocchio
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
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49
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Hegelmeyer NK, Parkin LA, Previti ML, Andrade J, Utama R, Sejour RJ, Gardin J, Muller S, Ketchum S, Yurovsky A, Futcher B, Goodwin S, Ueberheide B, Seeliger JC. Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. mBio 2023; 14:e0084123. [PMID: 37787543 PMCID: PMC10653884 DOI: 10.1128/mbio.00841-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/16/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine for Mtb. We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is one of the first reports that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.
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Affiliation(s)
- Nuri K. Hegelmeyer
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Lia A. Parkin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Mary L. Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Joshua Andrade
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Richard J. Sejour
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Justin Gardin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Stephanie Muller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Steven Ketchum
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Alisa Yurovsky
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jessica C. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
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50
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Pentz JT, MacGillivray K, DuBose JG, Conlin PL, Reinhardt E, Libby E, Ratcliff WC. Evolutionary consequences of nascent multicellular life cycles. eLife 2023; 12:e84336. [PMID: 37889142 PMCID: PMC10611430 DOI: 10.7554/elife.84336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/08/2023] [Indexed: 10/28/2023] Open
Abstract
A key step in the evolutionary transition to multicellularity is the origin of multicellular groups as biological individuals capable of adaptation. Comparative work, supported by theory, suggests clonal development should facilitate this transition, although this hypothesis has never been tested in a single model system. We evolved 20 replicate populations of otherwise isogenic clonally reproducing 'snowflake' yeast (Δace2/∆ace2) and aggregative 'floc' yeast (GAL1p::FLO1 /GAL1p::FLO1) with daily selection for rapid growth in liquid media, which favors faster cell division, followed by selection for rapid sedimentation, which favors larger multicellular groups. While both genotypes adapted to this regime, growing faster and having higher survival during the group-selection phase, there was a stark difference in evolutionary dynamics. Aggregative floc yeast obtained nearly all their increased fitness from faster growth, not improved group survival; indicating that selection acted primarily at the level of cells. In contrast, clonal snowflake yeast mainly benefited from higher group-dependent fitness, indicating a shift in the level of Darwinian individuality from cells to groups. Through genome sequencing and mathematical modeling, we show that the genetic bottlenecks in a clonal life cycle also drive much higher rates of genetic drift-a result with complex implications for this evolutionary transition. Our results highlight the central role that early multicellular life cycles play in the process of multicellular adaptation.
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Affiliation(s)
| | - Kathryn MacGillivray
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of TechnologyAtlantaUnited States
| | - James G DuBose
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Peter L Conlin
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Emma Reinhardt
- Department of Biology, University of North Carolina at Chapel HillChapel HillUnited States
| | | | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
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