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Ushijima Y, Naruse S, Ishikawa Y, Kawashima N, Sanada M, Nakashima M, Kim JH, Terakura S, Kihara R, Watamoto K, Nishiyama T, Kitamura K, Matsushita T, Kiyoi H. Initiating-clone analysis in patients with acute myeloid leukemia secondary to essential thrombocythemia. Sci Rep 2024; 14:15906. [PMID: 38987297 PMCID: PMC11237009 DOI: 10.1038/s41598-024-66461-8] [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: 02/12/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
Most of essential thrombocythemia (ET) patients have the clone harboring a mutation in one of the JAK2, CALR, or MPL gene, and these clones generally acquire additional mutations at transformation to acute myeloid leukemia (AML). However, the proliferation of triple-negative clones has sometimes been observed at AML transformation. To clarify the clonal evolution of ET to AML, we analyzed paired samples at ET and AML transformation in eight patients. We identified that JAK2-unmutated AML clones proliferated at AML transformation in three patients in whom the JAK2-mutated clone was dominant at ET. In two patients, TET2-mutated, but not JAK2-mutated, clones might be common initiating clones for ET and transformed AML. In a patient with JAK2-mutated ET, SMARCC2, UBR4, and ZNF143, but not JAK2, -mutated clones proliferated at AML transformation. Precise analysis using single-cell sorted CD34+/CD38- fractions suggested that ET clone with JAK2-mutated and AML clone with TP53 mutation was derived from the common clone with these mutations. Although further study is required to clarify the biological significance of SMARCC2, UBR4, and ZNF143 mutations during disease progression of ET and AML transformation, the present results demonstrate the possibility of a common initial clone involved in both ET and transformed AML.
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Affiliation(s)
- Yoko Ushijima
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Tsurumai-Cho 65, Showa-Ku, Nagoya, 466-8550, Japan
| | - Seara Naruse
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Tsurumai-Cho 65, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yuichi Ishikawa
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Tsurumai-Cho 65, Showa-Ku, Nagoya, 466-8550, Japan.
| | - Naomi Kawashima
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Tsurumai-Cho 65, Showa-Ku, Nagoya, 466-8550, Japan
| | - Masashi Sanada
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Marie Nakashima
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Tsurumai-Cho 65, Showa-Ku, Nagoya, 466-8550, Japan
| | - Jeong Hui Kim
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Tsurumai-Cho 65, Showa-Ku, Nagoya, 466-8550, Japan
| | - Seitaro Terakura
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Tsurumai-Cho 65, Showa-Ku, Nagoya, 466-8550, Japan
| | - Rika Kihara
- Department of Hematology and Oncology, Konan Kosei Hospital, Konan, Japan
- Department of Hematology, Komaki City Hospital, Komaki, Japan
| | - Koichi Watamoto
- Department of Hematology, Komaki City Hospital, Komaki, Japan
| | - Takahiro Nishiyama
- Division of Hematology, Ichinomiya Municipal Hospital, Ichinomiya, Japan
| | - Kunio Kitamura
- Division of Hematology, Ichinomiya Municipal Hospital, Ichinomiya, Japan
| | - Tadashi Matsushita
- Department of Transfusion Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Tsurumai-Cho 65, Showa-Ku, Nagoya, 466-8550, Japan.
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Lee CL, Chuang CK, Chiu HC, Chang YH, Tu YR, Lo YT, Lin HY, Lin SP. Application of whole exome sequencing in the diagnosis of muscular disorders: a study of Taiwanese pediatric patients. Front Genet 2024; 15:1365729. [PMID: 38818036 PMCID: PMC11137626 DOI: 10.3389/fgene.2024.1365729] [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: 01/04/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Background Muscular dystrophies and congenital myopathies encompass various inherited muscular disorders that present diagnostic challenges due to clinical complexity and genetic heterogeneity. Methods This study aimed to investigate the use of whole exome sequencing (WES) in diagnosing muscular disorders in pediatric patients in Taiwan. Out of 161 pediatric patients suspected to have genetic/inherited myopathies, 115 received a molecular diagnosis through conventional tests, single gene testing, and gene panels. The remaining 46 patients were divided into three groups: Group 1 (multiplex ligation-dependent probe amplification-negative Duchenne muscular dystrophy) with three patients (6.5%), Group 2 (various forms of muscular dystrophies) with 21 patients (45.7%), and Group 3 (congenital myopathies) with 22 patients (47.8%). Results WES analysis of these groups found pathogenic variants in 100.0% (3/3), 57.1% (12/21), and 68.2% (15/22) of patients in Groups 1 to 3, respectively. WES had a diagnostic yield of 65.2% (30 patients out of 46), detecting 30 pathogenic or potentially pathogenic variants across 28 genes. Conclusion WES enables the diagnosis of rare diseases with symptoms and characteristics similar to congenital myopathies and muscular dystrophies, such as muscle weakness. Consequently, this approach facilitates targeted therapy implementation and appropriate genetic counseling.
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Affiliation(s)
- Chung-Lin Lee
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, Taipei, Taiwan
- Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
| | - Chih-Kuang Chuang
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- College of Medicine, Fu-Jen Catholic University, Taipei, Taiwan
| | - Huei-Ching Chiu
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
| | - Ya-Hui Chang
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yuan-Rong Tu
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yun-Ting Lo
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
| | - Hsiang-Yu Lin
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, Taipei, Taiwan
- Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Shuan-Pei Lin
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, Taipei, Taiwan
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
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3
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Gaikani HK, Stolar M, Kriti D, Nislow C, Giaever G. From beer to breadboards: yeast as a force for biological innovation. Genome Biol 2024; 25:10. [PMID: 38178179 PMCID: PMC10768129 DOI: 10.1186/s13059-023-03156-9] [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: 02/14/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
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Affiliation(s)
- Hamid Kian Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Monika Stolar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
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Arshad M, Noor N, Iqbal Z, Jaleel H. In silico analysis of missense SNPs in TNFR1a and their possible therapeutic or pathogenic role in immune diseases. Hum Immunol 2023; 84:609-617. [PMID: 37748952 DOI: 10.1016/j.humimm.2023.09.003] [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: 05/19/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
Abstract
Tumor necrosis factor alpha (TNFa) is an inflammatory cytokine that is involved in the pathogenesis of various inflammatory disorders including rheumatoid arthritis. TNF-alpha receptor I (TNFR1a) is one of the receptors TNFa binds with for its activation. Any variation in this receptor might affect the role of TNFa in successive events. Amino acid residue substitutions might happen in TNFR1a through non-synonymous single nucleotide polymorphisms (nsSNPs) which may alter the functioning of TNFa, hence, identifying any such substitutions is of paramount significance. In this study, six nsSNPs at five different evolutionary conserved regions are predicted to be detrimental to the structure and/or function of TNFR1a by using numerous computational tools. Their 3D models are also proposed in this study. Besides, they were found to reduce the stability and affect the molecular mechanisms of this protein. Two contrasting possibilities might happen because of these substitutions. One, they might reduce the production of TNFa which is overexpressed in inflammatory diseases, hence can play therapeutic role in such diseases. Second, they might possibly hinder the apoptosis to occur which can effectuate the uncontrolled division of cells, hence can be pathogenic in diseases like cancer. Further investigations on these nsSNPs using animal models and at cellular level will open doors to understand the underlying mechanisms behind various diseases.
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Affiliation(s)
- Maria Arshad
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik, Iceland.
| | - Nabeel Noor
- Shalamar Medical & Dental College, Lahore, Pakistan
| | - Zunair Iqbal
- Shalamar Medical & Dental College, Lahore, Pakistan
| | - Hadiqa Jaleel
- Department of Research & Innovation, Shalamar Institute of Health Sciences, Lahore, Pakistan
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5
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Robinson D, Vanacloig-Pedros E, Cai R, Place M, Hose J, Gasch AP. Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast. G3 (BETHESDA, MD.) 2023; 13:jkad159. [PMID: 37481264 PMCID: PMC10542507 DOI: 10.1093/g3journal/jkad159] [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: 05/11/2023] [Revised: 05/11/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Variation in gene copy number can alter gene expression and influence downstream phenotypes; thus copy-number variation provides a route for rapid evolution if the benefits outweigh the cost. We recently showed that genetic background significantly influences how yeast cells respond to gene overexpression, revealing that the fitness costs of copy-number variation can vary substantially with genetic background in a common-garden environment. But the interplay between copy-number variation tolerance and environment remains unexplored on a genomic scale. Here, we measured the tolerance to gene overexpression in four genetically distinct Saccharomyces cerevisiae strains grown under sodium chloride stress. Overexpressed genes that are commonly deleterious during sodium chloride stress recapitulated those commonly deleterious under standard conditions. However, sodium chloride stress uncovered novel differences in strain responses to gene overexpression. West African strain NCYC3290 and North American oak isolate YPS128 are more sensitive to sodium chloride stress than vineyard BC187 and laboratory strain BY4743. Consistently, NCYC3290 and YPS128 showed the greatest sensitivities to overexpression of specific genes. Although most genes were deleterious, hundreds were beneficial when overexpressed-remarkably, most of these effects were strain specific. Few beneficial genes were shared between the sodium chloride-sensitive isolates, implicating mechanistic differences behind their sodium chloride sensitivity. Transcriptomic analysis suggested underlying vulnerabilities and tolerances across strains, and pointed to natural copy-number variation of a sodium export pump that likely contributes to strain-specific responses to overexpression of other genes. Our results reveal extensive strain-by-environment interactions in the response to gene copy-number variation, raising important implications for the accessibility of copy-number variation-dependent evolutionary routes under times of stress.
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Affiliation(s)
- DeElegant Robinson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53704, USA
| | - Elena Vanacloig-Pedros
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53704, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53704, USA
| | - Ruoyi Cai
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53704, USA
| | - Michael Place
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53704, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53704, USA
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53704, USA
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53704, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53704, USA
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53704, USA
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Yu G, Liu Y, Li Z, Deng S, Wu Z, Zhang X, Chen W, Yang J, Chen X, Yang JR. Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect. Nat Commun 2023; 14:5853. [PMID: 37730811 PMCID: PMC10511511 DOI: 10.1038/s41467-023-41550-w] [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: 08/23/2022] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
The transcriptional intermediates of RNAs fold into secondary structures with multiple regulatory roles, yet the details of such cotranscriptional RNA folding are largely unresolved in eukaryotes. Here, we present eSPET-seq (Structural Probing of Elongating Transcripts in eukaryotes), a method to assess the cotranscriptional RNA folding in Saccharomyces cerevisiae. Our study reveals pervasive structural transitions during cotranscriptional folding and overall structural similarities between nascent and mature RNAs. Furthermore, a combined analysis with genome-wide R-loop and mutation rate approximations provides quantitative evidence for the antimutator effect of nascent RNA folding through competitive inhibition of the R-loops, known to facilitate transcription-associated mutagenesis. Taken together, we present an experimental evaluation of cotranscriptional folding in eukaryotes and demonstrate the antimutator effect of nascent RNA folding. These results suggest genome-wide coupling between the processing and transmission of genetic information through RNA folding.
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Affiliation(s)
- Gongwang Yu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yao Liu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zizhang Li
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shuyun Deng
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zhuoxing Wu
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiaoyu Zhang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Wenbo Chen
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Junnan Yang
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiaoshu Chen
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China.
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Kovuri P, Yadav A, Sinha H. Role of genetic architecture in phenotypic plasticity. Trends Genet 2023; 39:703-714. [PMID: 37173192 DOI: 10.1016/j.tig.2023.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023]
Abstract
Phenotypic plasticity, the ability of an organism to display different phenotypes across environments, is widespread in nature. Plasticity aids survival in novel environments. Herein, we review studies from yeast that allow us to start uncovering the genetic architecture of phenotypic plasticity. Genetic variants and their interactions impact the phenotype in different environments, and distinct environments modulate the impact of genetic variants and their interactions on the phenotype. Because of this, certain hidden genetic variation is expressed in specific genetic and environmental backgrounds. A better understanding of the genetic mechanisms of phenotypic plasticity will help to determine short- and long-term responses to selection and how wide variation in disease manifestation occurs in human populations.
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Affiliation(s)
- Purnima Kovuri
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, India; Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai, India; Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India
| | - Anupama Yadav
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, India; Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai, India; Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India.
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8
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Rezvannejad E, Mousavizadeh S. Identification genetic variations in some heat shock protein genes of Tali goat breed and study their structural and functional effects on relevant proteins. Vet Med Sci 2023; 9:2247-2259. [PMID: 37530404 PMCID: PMC10508551 DOI: 10.1002/vms3.1231] [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: 10/06/2022] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Animals of different regions have adapted to adverse environmental conditions by modifying their phenotypic and genotypic characteristics in the long run. OBJECTIVES In this study, the effect of genetic variations of 10 heat shock protein (HSP) genes (HSP70A4, HSP70A9, HSP40C17, HSP40C27, HSP90AA1, HSP90AB1, HSPB7, HSPB11, HSPD1 and HSPE1) on the three-dimensional protein structure and function of proteins in Tali goat (a tropical breed) were studied and were compared with Saanen goat (as a sensitive breed). METHODS A pooled DNA of 15 samples from blood was sequenced and mapped to the goat reference sequence. The bioinformatics analysis was used to identify nsSNPs in the Tali breed and was compared with the Saanen goat. Four online bioinformatics tools (Sorting Intolerant from Tolerant, Protein Variation Effect Analyzer, Polymorphism Phenotyping version2 and Single Nucleotide Polymorphism Database and Gene Ontology) showed three deleterious missense nsSNPs and seven natural missense SNPs in these HSPs genes of Tali goat. RESULTS Out of 10 reported nsSNPs, 5 nsSNPs in HSP70A4, 1 nsSNP inHSP70A9, 2 nsSNPs in HSP40C17, 1 nsSNP in HSP40C27 and 1 nsSNP in HSPD1 were detected. ConSurf tools showed that the majority of the predicted nsSNPs occur in conserved sites. Moreover, several post-translational modification (PTM) predictors computed the probability of post-translation change of nsSNPs. The putative phosphorylation and glycosylation sites in HSPs proteins were substitutions rs669769139 and rs666336692 of the Tali goat breed. CONCLUSION These results on the effect of type of genetic variants on the function of HSP proteins will assist to predict the resistance to hard conditions in goat breeds. Considering that the identified SNPid rs669769139 (S248) which is located on the N-terminal ATPase domain of HSP70A4 is a PTM site with a highly conserved score and a natural substitution on changing the stability and benign protein that can affect the functional and structural characterization of HSPs protein for adaptation to the local climate.
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Affiliation(s)
- Elham Rezvannejad
- Department of Biotechnology, Institute of Sciences and High Technology and Environmental SciencesGraduate University of Advanced TechnologyKermanIran
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9
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Robinson D, Vanacloig-Pedros E, Cai R, Place M, Hose J, Gasch AP. Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540375. [PMID: 37503218 PMCID: PMC10369901 DOI: 10.1101/2023.05.11.540375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Variation in gene copy number can alter gene expression and influence downstream phenotypes; thus copy-number variation (CNV) provides a route for rapid evolution if the benefits outweigh the cost. We recently showed that genetic background significantly influences how yeast cells respond to gene over-expression (OE), revealing that the fitness costs of CNV can vary substantially with genetic background in a common-garden environment. But the interplay between CNV tolerance and environment remains unexplored on a genomic scale. Here we measured the tolerance to gene OE in four genetically distinct Saccharomyces cerevisiae strains grown under sodium chloride (NaCl) stress. OE genes that are commonly deleterious during NaCl stress recapitulated those commonly deleterious under standard conditions. However, NaCl stress uncovered novel differences in strain responses to gene OE. West African strain NCYC3290 and North American oak isolate YPS128 are more sensitive to NaCl stress than vineyard BC187 and laboratory strain BY4743. Consistently, NCYC3290 and YPS128 showed the greatest sensitivities to gene OE. Although most genes were deleterious, hundreds were beneficial when overexpressed - remarkably, most of these effects were strain specific. Few beneficial genes were shared between the NaCl-sensitive isolates, implicating mechanistic differences behind their NaCl sensitivity. Transcriptomic analysis suggested underlying vulnerabilities and tolerances across strains, and pointed to natural CNV of a sodium export pump that likely contributes to strain-specific responses to OE of other genes. Our results reveal extensive strain-by-environment interaction in the response to gene CNV, raising important implications for the accessibility of CNV-dependent evolutionary routes under times of stress.
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Affiliation(s)
- DeElegant Robinson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison WI 53704
| | - Elena Vanacloig-Pedros
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison WI 53704
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison WI 53704
| | - Ruoyi Cai
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison WI 53704
| | - Michael Place
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison WI 53704
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison WI 53704
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison WI 53704
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison WI 53704
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison WI 53704
- Department of Medical Genetics, University of Wisconsin-Madison, Madison WI 53704
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Shinwari K, Wu Y, Rehman HM, Xiao N, Bolkov M, Tuzankina I, Chereshnev V. In-silico assessment of high-risk non-synonymous SNPs in ADAMTS3 gene associated with Hennekam syndrome and their impact on protein stability and function. BMC Bioinformatics 2023; 24:251. [PMID: 37322437 DOI: 10.1186/s12859-023-05361-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
Hennekam Lymphangiectasia-Lymphedema Syndrome 3 (HKLLS3) is a rare genetical disorder caused by mutations in a few genes including ADAMTS3. It is characterized by lymphatic dysplasia, intestinal lymphangiectasia, severe lymphedema and distinctive facial appearance. Up till now, no extensive studies have been conducted to elucidate the mechanism of the disease caused by various mutations. As a preliminary investigation of HKLLS3, we sorted out the most deleterious nonsynonymous single nucleotide polymorphisms (nsSNPs) that might affect the structure and function of ADAMTS3 protein by using a variety of in silico tools. A total of 919 nsSNPs in the ADAMTS3 gene were identified. 50 nsSNPs were predicted to be deleterious by multiple computational tools. 5 nsSNPs (G298R, C567Y, A370T, C567R and G374S) were found to be the most dangerous and can be associated with the disease as predicted by different bioinformatics tools. Modelling of the protein shows it can be divided into segments 1, 2 and 3, which are connected by short loops. Segment 3 mainly consists of loops without substantial secondary structures. With prediction tools and molecular dynamics simulation, some SNPs were found to significantly destabilize the protein structure and disrupt the secondary structures, especially in segment 2. The deleterious effects of mutations in segment 1 are possibly not from destabilization but from other factors such as the change in phosphorylation as suggested by post-translational modification (PTM) studies. This is the first-ever study of ADAMTS3 gene polymorphism, and the predicted nsSNPs in ADAMST3, some of which have not been reported yet in patients, will serve for diagnostic purposes and further therapeutic implications in Hennekam syndrome, contributing to better diagnosis and treatment.
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Affiliation(s)
- Khyber Shinwari
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia.
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia.
| | - Yurong Wu
- Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Ningkun Xiao
- Department of Psychology, Ural Federal University, Yekaterinburg, Russia
| | - Mikhail Bolkov
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
| | - Irina Tuzankina
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
| | - Valery Chereshnev
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
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11
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Xu D, Shao Q, Zhou C, Mahmood A, Zhang J. In Silico Analysis of nsSNPs of Human KRAS Gene and Protein Modeling Using Bioinformatic Tools. ACS OMEGA 2023; 8:13362-13370. [PMID: 37065036 PMCID: PMC10099408 DOI: 10.1021/acsomega.3c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
The KRAS gene belongs to the RAS family and codes for 188 amino acid residues of KRAS protein, with a molecular mass of 21.6 kD. Non-synonymous single-nucleotide polymorphisms (nsSNPs) have been identified within the coding region in which some are associated with different diseases. However, structural changes are not well defined yet. In this study, we first categorized SNPs in the KRAS coding area and then used computational methods to determine their impact on the protein structure and stability. In addition, the three-dimensional model of KRAS was taken from the Protein Data Bank for structural modeling. Furthermore, genomic data were extracted from a variety of sources, including the 1000 Genome Project, dbSNPs, and ENSEMBLE, and assessed through in silico methods. Based on various tools used in this study, 10 out of 48 missense SNPs with rsIDs were found deleterious. The substitution of alanine for proline at position 146 pushed several residues toward the center of the protein. Arginine instead of leucine has a minor effect on protein structure and stability. In addition, the substitution of proline for leucine at the 34th position disrupted the structure and led to a bigger size than the wild-type protein, hence interrupting the protein interaction. Using the well-intended computational approach and applying several bioinformatic tools, we characterized and identified most damaging nsSNPs and further explored the structural dynamics and stability of KRAS protein.
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Affiliation(s)
- Duoduo Xu
- Oncology
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325000, China
| | - Qiqi Shao
- Department
of Nursing, Central Health Center of Zeya
Town, Ouhai District, Wenzhou 325000, China
| | - Chen Zhou
- Ultrasonography
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325099, China
| | - Arif Mahmood
- Center
for Medical Genetics and Hunan Key Laboratory of Medical Genetics,
School of Life Sciences, Central South University, Changsha 410078, Hunan, China
| | - Jizhou Zhang
- Oncology
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325000, China
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12
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Bedrat A. UGDR: a generic pipeline to detect recombined regions in polyploid and complex hybrid yeast genomes. BMC Bioinformatics 2022; 23:555. [PMID: 36544090 PMCID: PMC9773435 DOI: 10.1186/s12859-022-05113-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION In eukaryotes, homologous recombination between the parental genomes frequently occurs during the evolutionary conserved process of meiosis, generating the genetic diversity transmitted by the gametes. The genome-wide determination of the frequency and location of the recombination events can now be efficiently performed by genotyping the offspring's polymorphic markers. However, genotyping recombination in complex hybrid genomes with existing methods remains challenging because of their strain and ploidy specificity and the degree of diversity and complexity of the parental genomes, especially in [Formula: see text] polyploids. RESULTS We present UGDR, a pipeline to genotype the polymorphisms of complex hybrid yeast genomes. It is based on optimal mapping strategies of NGS reads, comparative analyses of the allelic ratio variation and read depth coverage. We tested the UGDR pipeline with sequencing reads from recombined hybrid diploid yeast strains and various clinical strains exhibiting different degrees of ploidy. UGDR allows to plot the markers distribution and recombination profile per chromosome. CONCLUSION UGDR detects and plots recombination events in haploids and polyploid yeasts, which facilitates the discovery and understanding of the yeast genetic recombination map and identify new out-performing recombinants.
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Affiliation(s)
- Amina Bedrat
- grid.418596.70000 0004 0639 6384Institut Curie, UPMC University, Paris, France ,Meiogenix, 27 Rue du Chemin Vert, Paris, France ,grid.30760.320000 0001 2111 8460Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, USA
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13
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Fareed MM, Dutta K, Dandekar T, Tarabonda H, Skorb EV, Shityakov S. In silico investigation of nonsynonymous single nucleotide polymorphisms in BCL2 apoptosis regulator gene to design novel protein-based drugs against cancer. J Cell Biochem 2022; 123:2044-2056. [PMID: 36146908 DOI: 10.1002/jcb.30330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/04/2022] [Accepted: 09/10/2022] [Indexed: 12/24/2022]
Abstract
BCL2 apoptosis regulator gene encodes Bcl-2 pro-survival protein, which plays an important role to evade apoptosis in various cancers. Moreover, single nucleotide polymorphisms (SNPs) in the BCL2 gene can be nonsynonymous (nsSNPs), which might affect the protein stability and probably its function. Therefore, we implement cutting-edge computational techniques based on the Spherical Polar Fourier and Monte-Carlo algorithms to investigate the impact of these SNPs on the B cell lymphoma-2 (Bcl-2) stability and therapeutic potential of protein-based molecules to inhibit this protein. As a result, we identified two nsSNPs (Q118R and R129C) to be deleterious and highly conserved, having a negative effect on protein stability. Additionally, molecular docking and molecular dynamics simulations confirmed the decreased binding affinity of mutated Bcl-2 variants to bind three-helix bundle protein inhibitor as these mutations occurred in the protein-protein binding site. Overall, this computational approach investigating nsSNPs provides a useful basis for designing novel molecules to inhibit Bcl-2 pro-survival pathway in malignant cells.
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Affiliation(s)
- Muhammad Mazhar Fareed
- Department of Computer Science, School of Science and Engineering, Università degli studi di Verona, Verona, Italy
| | - Kunal Dutta
- Department of Human Physiology, Vidyasagar University, Midnapore, West Bengal, India
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Herman Tarabonda
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russia
| | - Ekaterina V Skorb
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russia
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russia
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14
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Huang YS, Hsu C, Chune YC, Liao IC, Wang H, Lin YL, Hwu WL, Lee NC, Lai F. Diagnosis of a Single-Nucleotide Variant in Whole-Exome Sequencing Data for Patients With Inherited Diseases: Machine Learning Study Using Artificial Intelligence Variant Prioritization. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2022; 3:e37701. [PMID: 38935959 PMCID: PMC11168239 DOI: 10.2196/37701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/29/2022] [Accepted: 08/22/2022] [Indexed: 06/29/2024]
Abstract
BACKGROUND In recent years, thanks to the rapid development of next-generation sequencing (NGS) technology, an entire human genome can be sequenced in a short period. As a result, NGS technology is now being widely introduced into clinical diagnosis practice, especially for diagnosis of hereditary disorders. Although the exome data of single-nucleotide variant (SNV) can be generated using these approaches, processing the DNA sequence data of a patient requires multiple tools and complex bioinformatics pipelines. OBJECTIVE This study aims to assist physicians to automatically interpret the genetic variation information generated by NGS in a short period. To determine the true causal variants of a patient with genetic disease, currently, physicians often need to view numerous features on every variant manually and search for literature in different databases to understand the effect of genetic variation. METHODS We constructed a machine learning model for predicting disease-causing variants in exome data. We collected sequencing data from whole-exome sequencing (WES) and gene panel as training set, and then integrated variant annotations from multiple genetic databases for model training. The model built ranked SNVs and output the most possible disease-causing candidates. For model testing, we collected WES data from 108 patients with rare genetic disorders in National Taiwan University Hospital. We applied sequencing data and phenotypic information automatically extracted by a keyword extraction tool from patient's electronic medical records into our machine learning model. RESULTS We succeeded in locating 92.5% (124/134) of the causative variant in the top 10 ranking list among an average of 741 candidate variants per person after filtering. AI Variant Prioritizer was able to assign the target gene to the top rank for around 61.1% (66/108) of the patients, followed by Variant Prioritizer, which assigned it for 44.4% (48/108) of the patients. The cumulative rank result revealed that our AI Variant Prioritizer has the highest accuracy at ranks 1, 5, 10, and 20. It also shows that AI Variant Prioritizer presents better performance than other tools. After adopting the Human Phenotype Ontology (HPO) terms by looking up the databases, the top 10 ranking list can be increased to 93.5% (101/108). CONCLUSIONS We successfully applied sequencing data from WES and free-text phenotypic information of patient's disease automatically extracted by the keyword extraction tool for model training and testing. By interpreting our model, we identified which features of variants are important. Besides, we achieved a satisfactory result on finding the target variant in our testing data set. After adopting the HPO terms by looking up the databases, the top 10 ranking list can be increased to 93.5% (101/108). The performance of the model is similar to that of manual analysis, and it has been used to help National Taiwan University Hospital with a genetic diagnosis.
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Affiliation(s)
- Yu-Shan Huang
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei City, Taiwan
| | - Ching Hsu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei City, Taiwan
| | - Yu-Chang Chune
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei City, Taiwan
| | - I-Cheng Liao
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei City, Taiwan
| | - Hsin Wang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei City, Taiwan
| | - Yi-Lin Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei City, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics, National Taiwan University Hospital, Taipei City, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei City, Taiwan
| | - Feipei Lai
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei City, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei City, Taiwan
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15
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Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast. Nat Ecol Evol 2022; 6:763-773. [PMID: 35484218 DOI: 10.1038/s41559-022-01730-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/10/2022] [Indexed: 01/05/2023]
Abstract
Deleterious mutations are generally considered to be irrelevant for morphological evolution. However, they could be compensated by conditionally beneficial mutations, thereby providing access to new adaptive paths. Here we use high-dimensional phenotyping of laboratory-evolved budding yeast lineages to demonstrate that new cellular morphologies emerge exceptionally rapidly as a by-product of gene loss and subsequent compensatory evolution. Unexpectedly, the capacities for invasive growth, multicellular aggregation and biofilm formation also spontaneously evolve in response to gene loss. These multicellular phenotypes can be achieved by diverse mutational routes and without reactivating the canonical regulatory pathways. These ecologically and clinically relevant traits originate as pleiotropic side effects of compensatory evolution and have no obvious utility in the laboratory environment. The extent of morphological diversity in the evolved lineages is comparable to that of natural yeast isolates with diverse genetic backgrounds and lifestyles. Finally, we show that both the initial gene loss and subsequent compensatory mutations contribute to new morphologies, with their synergistic effects underlying specific morphological changes. We conclude that compensatory evolution is a previously unrecognized source of morphological diversity and phenotypic novelties.
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16
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Bakerlee CW, Nguyen Ba AN, Shulgina Y, Rojas Echenique JI, Desai MM. Idiosyncratic epistasis leads to global fitness-correlated trends. Science 2022; 376:630-635. [PMID: 35511982 PMCID: PMC10124986 DOI: 10.1126/science.abm4774] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Epistasis can markedly affect evolutionary trajectories. In recent decades, protein-level fitness landscapes have revealed extensive idiosyncratic epistasis among specific mutations. By contrast, other work has found ubiquitous and apparently nonspecific patterns of global diminishing-returns and increasing-costs epistasis among mutations across the genome. Here, we used a hierarchical CRISPR gene drive system to construct all combinations of 10 missense mutations from across the genome in budding yeast and measured their fitness in six environments. We show that the resulting fitness landscapes exhibit global fitness-correlated trends but that these trends emerge from specific idiosyncratic interactions. We thus provide experimental validation of recent theoretical work arguing that fitness-correlated trends can emerge as the generic consequence of idiosyncratic epistasis.
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Affiliation(s)
- Christopher W Bakerlee
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Quantitative Biology Initiative, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Alex N Nguyen Ba
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Quantitative Biology Initiative, Harvard University, Cambridge, MA, USA.,Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Yekaterina Shulgina
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jose I Rojas Echenique
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Quantitative Biology Initiative, Harvard University, Cambridge, MA, USA.,NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA, USA.,Department of Physics, Harvard University, Cambridge, MA, USA
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17
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Shinwari K, Rehman HM, Liu G, Bolkov MA, Tuzankina IA, Chereshnev VA. Novel Disease-Associated Missense Single-Nucleotide Polymorphisms Variants Predication by Algorithms Tools and Molecular Dynamics Simulation of Human TCIRG1 Gene Causing Congenital Neutropenia and Osteopetrosis. Front Mol Biosci 2022; 9:879875. [PMID: 35573728 PMCID: PMC9095858 DOI: 10.3389/fmolb.2022.879875] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022] Open
Abstract
T Cell Immune Regulator 1, ATPase H + Transporting V0 Subunit A3 (TCIRG1 gene provides instructions for making one part, the a3 subunit, of a large protein complex known as a vacuolar H + -ATPase (V-ATPase). V-ATPases are a group of similar complexes that act as pumps to move positively charged hydrogen atoms (protons) across membranes. Single amino acid changes in highly conserved areas of the TCIRG1 protein have been linked to autosomal recessive osteopetrosis and severe congenital neutropenia. We used multiple computational approaches to classify disease-prone single nucleotide polymorphisms (SNPs) in TCIRG1. We used molecular dynamics analysis to identify the deleterious nsSNPs, build mutant protein structures, and assess the impact of mutation. Our results show that fifteen nsSNPs (rs199902030, rs200149541, rs372499913, rs267605221, rs374941368, rs375717418, rs80008675, rs149792489, rs116675104, rs121908250, rs121908251, rs121908251, rs149792489 and rs116675104) variants are likely to be highly deleterious mutations as by incorporating them into wild protein they destabilize the wild protein structure and function. They are also located in the V-ATPase I domain, which may destabilize the structure and impair TCIRG1 protein activation, as well as reduce its ATPase effectiveness. These mutants have not yet been identified in patients suffering from CN and osteopetrosis while (G405R, R444L, and D517N) reported in our study are already associated with osteopetrosis. Mutation V52L reported in our study was identified in a patient suspected for CN. Finally, these mutants can help to further understand the broad pool of illness susceptibilities associated with TCIRG1 catalytic kinase domain activation and aid in the development of an effective treatment for associated diseases.
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Affiliation(s)
- Khyber Shinwari
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- *Correspondence: Khyber Shinwari,
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Alnoorians Group of Institutes, Shad Bagh, Lahore, Pakistan
| | - Guojun Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Mikhail A. Bolkov
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Irina A. Tuzankina
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Valery. A. Chereshnev
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
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18
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Ali MZ, Farid A, Ahmad S, Muzammal M, Mohaini MA, Alsalman AJ, Al Hawaj MA, Alhashem YN, Alsaleh AA, Almusalami EM, Maryam M, Khan MA. In Silico Analysis Identified Putative Pathogenic Missense nsSNPs in Human SLITRK1 Gene. Genes (Basel) 2022; 13:672. [PMID: 35456478 PMCID: PMC9030497 DOI: 10.3390/genes13040672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 02/04/2023] Open
Abstract
Human DNA contains several variations, which can affect the structure and normal functioning of a protein. These variations could be single nucleotide polymorphisms (SNPs) or insertion-deletions (InDels). SNPs, as opposed to InDels, are more commonly present in DNA and may cause genetic disorders. In the current study, several bioinformatic tools were used to prioritize the pathogenic variants in the SLITRK1 gene. Out of all of the variants, 16 were commonly predicted to be pathogenic by these tools. All the variants had very low frequency, i.e., <0.0001 in the global population. The secondary structure of all filtered variants was predicted, but no structural change was observed at the site of variation in any variant. Protein stability analysis of these variants was then performed, which determined a decrease in protein stability of 10 of the variants. Amino acid conservation analysis revealed that all the amino acids were highly conserved, indicating their structural and functional importance. Protein 3D structure of wildtype SLITRK1 and all of its variants was predicted using I-TASSER, and the effect of variation on 3D structure of the protein was observed using the Missense3D tool, which presented the probable structural loss in three variants, i.e., Asn529Lys, Leu496Pro and Leu94Phe. The wildtype SLITRK1 protein and these three variants were independently docked with their close interactor protein PTPRD, and remarkable differences were observed in the docking sites of normal and variants, which will ultimately affect the functional activity of the SLITRK1 protein. Previous studies have shown that mutations in SLITRK1 are involved in Tourette syndrome. The present study may assist a molecular geneticist in interpreting the variant pathogenicity in research as well as diagnostic setup.
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Affiliation(s)
- Muhammad Zeeshan Ali
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Arshad Farid
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Safeer Ahmad
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Muhammad Muzammal
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Mohammed Al Mohaini
- Basic Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Al Ahsa 31982, Saudi Arabia;
- King Abdullah International Medical Research Center, Al Ahsa 31982, Saudi Arabia
| | - Abdulkhaliq J. Alsalman
- Department of Clinical Pharmacy, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia;
| | - Maitham A. Al Hawaj
- Department of Pharmacy Practice, College of Clinical Pharmacy, King Faisal University, Al Ahsa 31982, Saudi Arabia;
| | - Yousef N. Alhashem
- Clinical Laboratory Sciences Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia; (Y.N.A.); (A.A.A.)
| | - Abdulmonem A. Alsaleh
- Clinical Laboratory Sciences Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia; (Y.N.A.); (A.A.A.)
| | | | - Mahpara Maryam
- Department of Zoology, Government College No.1, Dera Ismail Khan 29111, Pakistan;
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
- Department of Human Genetics, Sidra Medical and Research Centre, Doha 26999, Qatar
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19
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Targa A, Larrimore KE, Wong CK, Chong YL, Fung R, Lee J, Choi H, Rancati G. Non-genetic and genetic rewiring underlie adaptation to hypomorphic alleles of an essential gene. EMBO J 2021; 40:e107839. [PMID: 34528284 PMCID: PMC8561638 DOI: 10.15252/embj.2021107839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/05/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Adaptive evolution to cellular stress is a process implicated in a wide range of biological and clinical phenomena. Two major routes of adaptation have been identified: non-genetic changes, which allow expression of different phenotypes in novel environments, and genetic variation achieved by selection of fitter phenotypes. While these processes are broadly accepted, their temporal and epistatic features in the context of cellular evolution and emerging drug resistance are contentious. In this manuscript, we generated hypomorphic alleles of the essential nuclear pore complex (NPC) gene NUP58. By dissecting early and long-term mechanisms of adaptation in independent clones, we observed that early physiological adaptation correlated with transcriptome rewiring and upregulation of genes known to interact with the NPC; long-term adaptation and fitness recovery instead occurred via focal amplification of NUP58 and restoration of mutant protein expression. These data support the concept that early phenotypic plasticity allows later acquisition of genetic adaptations to a specific impairment. We propose this approach as a genetic model to mimic targeted drug therapy in human cells and to dissect mechanisms of adaptation.
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Affiliation(s)
- Altea Targa
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Katherine E Larrimore
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Cheng Kit Wong
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Yu Lin Chong
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Ronald Fung
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Joseph Lee
- Department of MedicineYong Loo Lin School of MedicineNUS and National University Health SystemSingaporeSingapore
| | - Hyungwon Choi
- Department of MedicineYong Loo Lin School of MedicineNUS and National University Health SystemSingaporeSingapore
| | - Giulia Rancati
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
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20
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Alam MS, Saleh MA, Mozibullah M, Riham AT, Solayman M, Gan SH. Computational algorithmic and molecular dynamics study of functional and structural impacts of non-synonymous single nucleotide polymorphisms in human DHFR gene. Comput Biol Chem 2021; 95:107587. [PMID: 34710812 DOI: 10.1016/j.compbiolchem.2021.107587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/21/2021] [Accepted: 10/01/2021] [Indexed: 11/26/2022]
Abstract
Human dihydrofolate reductase (DHFR) is a conserved enzyme that is central to folate metabolism and is widely targeted in pathogenic diseases as well as cancers. Although studies have reported the fact that genetic mutations in DHFR leads to a rare autosomal recessive inborn error of folate metabolism and drug resistance, there is a lack of an extensive study on how the deleterious non-synonymous SNPs (nsSNPs) disrupt its phenotypic effects. In this study, we aim at discovering the structural and functional consequences of nsSNPs in DHFR by employing a combined computational approach consisting of ten recently developed in silico tools for identification of damaging nsSNPs and molecular dynamics (MD) simulation for getting deeper insights into the magnitudes of damaging effects. Our study revealed the presence of 12 most deleterious nsSNPs affecting the native phenotypic effects, with three (R71T, G118D, Y122D) identified in the co-factor and ligand binding active sites. MD simulations also suggested that these three SNPs particularly Y122D, alter the overall structural flexibility and dynamics of the native DHFR protein which can provide more understandings into the crucial roles of these mutants in influencing the loss of DHFR function.
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Affiliation(s)
- Md Shahed Alam
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Abu Saleh
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Mozibullah
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Ashik Tanvir Riham
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Solayman
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia.
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia
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21
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Pathogenic genetic variants from highly connected cancer susceptibility genes confer the loss of structural stability. Sci Rep 2021; 11:19264. [PMID: 34584144 PMCID: PMC8479081 DOI: 10.1038/s41598-021-98547-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/25/2021] [Indexed: 01/09/2023] Open
Abstract
Genetic polymorphisms in DNA damage repair and tumor suppressor genes have been associated with increasing the risk of several types of cancer. Analyses of putative functional single nucleotide polymorphisms (SNP) in such genes can greatly improve human health by guiding choice of therapeutics. In this study, we selected nine genes responsible for various cancer types for gene enrichment analysis and found that BRCA1, ATM, and TP53 were more enriched in connectivity. Therefore, we used different computational algorithms to classify the nonsynonymous SNPs which are deleterious to the structure and/or function of these three proteins. The present study showed that the major pathogenic variants (V1687G and V1736G of BRCA1, I2865T and V2906A of ATM, V216G and L194H of TP53) might have a greater impact on the destabilization of the proteins. To stabilize the high-risk SNPs, we performed mutation site-specific molecular docking analysis and validated using molecular dynamics (MD) simulation and molecular mechanics/Poisson Boltzmann surface area (MM/PBSA) studies. Additionally, SNPs of untranslated regions of these genes affecting miRNA binding were characterized. Hence, this study will assist in developing precision medicines for cancer types related to these polymorphisms.
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Computational analysis of missense variants in MMP2 gene linked with Winchester syndrome and Nodulosis-Arthropathy-Osteolysis reveals structural shift in protein-protein and protein-ligand complexes. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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23
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Comprehensive characterization of the single nucleotide polymorphisms located in the isocitrate dehydrogenase isoform 1 and 2 genes using in silico approach. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Shih CH, Fay J. Cis-regulatory variants affect gene expression dynamics in yeast. eLife 2021; 10:e68469. [PMID: 34369376 PMCID: PMC8367379 DOI: 10.7554/elife.68469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022] Open
Abstract
Evolution of cis-regulatory sequences depends on how they affect gene expression and motivates both the identification and prediction of cis-regulatory variants responsible for expression differences within and between species. While much progress has been made in relating cis-regulatory variants to expression levels, the timing of gene activation and repression may also be important to the evolution of cis-regulatory sequences. We investigated allele-specific expression (ASE) dynamics within and between Saccharomyces species during the diauxic shift and found appreciable cis-acting variation in gene expression dynamics. Within-species ASE is associated with intergenic variants, and ASE dynamics are more strongly associated with insertions and deletions than ASE levels. To refine these associations, we used a high-throughput reporter assay to test promoter regions and individual variants. Within the subset of regions that recapitulated endogenous expression, we identified and characterized cis-regulatory variants that affect expression dynamics. Between species, chimeric promoter regions generate novel patterns and indicate constraints on the evolution of gene expression dynamics. We conclude that changes in cis-regulatory sequences can tune gene expression dynamics and that the interplay between expression dynamics and other aspects of expression is relevant to the evolution of cis-regulatory sequences.
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Affiliation(s)
- Ching-Hua Shih
- Department of Biology, University of RochesterRochesterUnited States
| | - Justin Fay
- Department of Biology, University of RochesterRochesterUnited States
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25
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Klim J, Zielenkiewicz U, Skoneczny M, Skoneczna A, Kurlandzka A, Kaczanowski S. Genetic interaction network has a very limited impact on the evolutionary trajectories in continuous culture-grown populations of yeast. BMC Ecol Evol 2021; 21:99. [PMID: 34039270 PMCID: PMC8157726 DOI: 10.1186/s12862-021-01830-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/19/2021] [Indexed: 11/30/2022] Open
Abstract
Background The impact of genetic interaction networks on evolution is a fundamental issue. Previous studies have demonstrated that the topology of the network is determined by the properties of the cellular machinery. Functionally related genes frequently interact with one another, and they establish modules, e.g., modules of protein complexes and biochemical pathways. In this study, we experimentally tested the hypothesis that compensatory evolutionary modifications, such as mutations and transcriptional changes, occur frequently in genes from perturbed modules of interacting genes. Results Using Saccharomyces cerevisiae haploid deletion mutants as a model, we investigated two modules lacking COG7 or NUP133, which are evolutionarily conserved genes with many interactions. We performed laboratory evolution experiments with these strains in two genetic backgrounds (with or without additional deletion of MSH2), subjecting them to continuous culture in a non-limiting minimal medium. Next, the evolved yeast populations were characterized through whole-genome sequencing and transcriptome analyses. No obvious compensatory changes resulting from inactivation of genes already included in modules were identified. The supposedly compensatory inactivation of genes in the evolved strains was only rarely observed to be in accordance with the established fitness effect of the genetic interaction network. In fact, a substantial majority of the gene inactivations were predicted to be neutral in the experimental conditions used to determine the interaction network. Similarly, transcriptome changes during continuous culture mostly signified adaptation to growth conditions rather than compensation of the absence of the COG7, NUP133 or MSH2 genes. However, we noticed that for genes whose inactivation was deleterious an upregulation of transcription was more common than downregulation. Conclusions Our findings demonstrate that the genetic interactions and the modular structure of the network described by others have very limited effects on the evolutionary trajectory following gene deletion of module elements in our experimental conditions and has no significant impact on short-term compensatory evolution. However, we observed likely compensatory evolution in functionally related (albeit non-interacting) genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01830-9.
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Affiliation(s)
- Joanna Klim
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Urszula Zielenkiewicz
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Anna Kurlandzka
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Szymon Kaczanowski
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.
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26
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Brion C, Caradec C, Pflieger D, Friedrich A, Schacherer J. Pervasive Phenotypic Impact of a Large Nonrecombining Introgressed Region in Yeast. Mol Biol Evol 2021; 37:2520-2530. [PMID: 32359150 PMCID: PMC7475044 DOI: 10.1093/molbev/msaa101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To explore the origin of the diversity observed in natural populations, many studies have investigated the relationship between genotype and phenotype. In yeast species, especially in Saccharomyces cerevisiae, these studies are mainly conducted using recombinant offspring derived from two genetically diverse isolates, allowing to define the phenotypic effect of genetic variants. However, large genomic variants such as interspecies introgressions are usually overlooked even if they are known to modify the genotype–phenotype relationship. To have a better insight into the overall phenotypic impact of introgressions, we took advantage of the presence of a 1-Mb introgressed region, which lacks recombination and contains the mating-type determinant in the Lachancea kluyveri budding yeast. By performing linkage mapping analyses in this species, we identified a total of 89 loci affecting growth fitness in a large number of conditions and 2,187 loci affecting gene expression mostly grouped into two major hotspots, one being the introgressed region carrying the mating-type locus. Because of the absence of recombination, our results highlight the presence of a sexual dimorphism in a budding yeast for the first time. Overall, by describing the phenotype–genotype relationship in the Lachancea kluyveri species, we expanded our knowledge on how genetic characteristics of large introgression events can affect the phenotypic landscape.
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Affiliation(s)
- Christian Brion
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - David Pflieger
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
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27
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Klim J, Zielenkiewicz U, Kurlandzka A, Kaczanowski S. The Adaptive Landscape of Genetic Interaction Network Has No Impact on Yeast Adaptive Evolution. Front Genet 2021; 12:640501. [PMID: 33815476 PMCID: PMC8013701 DOI: 10.3389/fgene.2021.640501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Joanna Klim
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Urszula Zielenkiewicz
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Kurlandzka
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Szymon Kaczanowski
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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28
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Charoensuk C, Thamtarana PJ, Chanprasert C, Tangjittipokin W, Shirakawa J, Togashi Y, Orime K, Songprakhon P, Chaichana C, Abubakar Z, Ouying P, Sujjitjoon J, Doria A, Plengvidhya N, Yenchitsomanus PT. Autosomal dominant diabetes associated with a novel ZYG11A mutation resulting in cell cycle arrest in beta-cells. Mol Cell Endocrinol 2021; 522:111126. [PMID: 33321115 DOI: 10.1016/j.mce.2020.111126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 01/20/2023]
Abstract
Diabetes is a genetically heterogeneous disease, for which we are aiming to identify causative genes. Here, we report a missense mutation (c.T1424C:p.L475P) in ZYG11A identified by exome sequencing as segregating with hyperglycemia in a Thai family with autosomal dominant diabetes. ZYG11A functions as a target recruitment subunit of an E3 ubiquitin ligase complex that plays an important role in the regulation of cell cycle. We demonstrate an increase in cells arrested at G2/mitotic phase among beta-cells deficient for ZYG11A or overexpressing L475P-ZYG11A, which is associated with a decreased growth rate. This is the first evidence linking a ZYG11A mutation to hyperglycemia, and suggesting ZYG11A as a cell cycle regulator required for beta-cell growth. Since most family members were either overweight or obese, but only mutation carriers developed hyperglycemia, our data also suggests the ZYG11A mutation as a genetic factor predisposing obese individuals to beta-cell failure in maintenance of glucose homeostasis.
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Affiliation(s)
- Chutima Charoensuk
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Prapaporn Jungtrakoon Thamtarana
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Chutima Chanprasert
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Watip Tangjittipokin
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Jun Shirakawa
- Laboratory of Diabetes and Metabolic Disorders, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, 371-8512, Japan; Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Yu Togashi
- Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Kazuki Orime
- Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Pucharee Songprakhon
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Chartchai Chaichana
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Zuroida Abubakar
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Paweena Ouying
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Jatuporn Sujjitjoon
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Alessandro Doria
- Section on Genetics and Epidemiology, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nattachet Plengvidhya
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Division of Endocrinology and Metabolism, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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29
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Molecular and evolutionary processes generating variation in gene expression. Nat Rev Genet 2020; 22:203-215. [PMID: 33268840 DOI: 10.1038/s41576-020-00304-w] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/18/2022]
Abstract
Heritable variation in gene expression is common within and between species. This variation arises from mutations that alter the form or function of molecular gene regulatory networks that are then filtered by natural selection. High-throughput methods for introducing mutations and characterizing their cis- and trans-regulatory effects on gene expression (particularly, transcription) are revealing how different molecular mechanisms generate regulatory variation, and studies comparing these mutational effects with variation seen in the wild are teasing apart the role of neutral and non-neutral evolutionary processes. This integration of molecular and evolutionary biology allows us to understand how the variation in gene expression we see today came to be and to predict how it is most likely to evolve in the future.
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30
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Soltani I, Bahia W, Radhouani A, Mahdhi A, Ferchichi S, Almawi WY. Comprehensive in-silico analysis of damage associated SNPs in hOCT1 affecting Imatinib response in chronic myeloid leukemia. Genomics 2020; 113:755-766. [PMID: 33075481 DOI: 10.1016/j.ygeno.2020.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/18/2020] [Accepted: 10/05/2020] [Indexed: 12/22/2022]
Abstract
Non-synonymous single nucleotide polymorphisms (nsSNPs) in hOCT1 (encoded by SLC22A1 gene) are expected to affect Imatinib uptake in chronic myeloid leukemia (CML). In this study, sequence homology-based genetic analysis of a set of 270 coding SNPs identified 18 nsSNPs to be putatively damaging/deleterious using eight different algorithms. Subsequently, based on conservation of amino acid residues, stability analysis, posttranscriptional modifications, and solvent accessibility analysis, the possible structural-functional relationship was established for high-confidence nsSNPs. Furthermore, based on the modeling results, some dissimilarities of mutant type amino acids from wild-type amino acids such as size, charge, interaction and hydrophobicity were revealed. Three highly deleterious mutations consisting of P283L, G401S and R402G in SLC22A1 gene that may alter the protein structure, function and stability were identified. These results provide a filtered data to explore the effect of uncharacterized nsSNP and find their association with Imatinib resistance in CML.
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Affiliation(s)
- Ismael Soltani
- Molecular and Cellular Hematology Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.
| | - Wael Bahia
- Research Unit of Clinical and Molecular Biology, Department of Biochemistry, Faculty of Pharmacy of Monastir, University of Monastir, Tunisia
| | - Assala Radhouani
- Faculty of Medicine, University of Tunis El Manar, Tunis, Tunisia
| | - Abdelkarim Mahdhi
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, University of Monastir, Tunisia
| | - Salima Ferchichi
- Research Unit of Clinical and Molecular Biology, Department of Biochemistry, Faculty of Pharmacy of Monastir, University of Monastir, Tunisia
| | - Wassim Y Almawi
- Faculty of Sciences, El Manar University, Tunis, Tunisia; College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
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31
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Hossain MS, Roy AS, Islam MS. In silico analysis predicting effects of deleterious SNPs of human RASSF5 gene on its structure and functions. Sci Rep 2020; 10:14542. [PMID: 32884013 PMCID: PMC7471297 DOI: 10.1038/s41598-020-71457-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 07/17/2020] [Indexed: 11/09/2022] Open
Abstract
Ras association domain-containing protein 5 (RASSF5), one of the prospective biomarkers for tumors, generally plays a crucial role as a tumor suppressor. As deleterious effects can result from functional differences through SNPs, we sought to analyze the most deleterious SNPs of RASSF5 as well as predict the structural changes associated with the mutants that hamper the normal protein-protein interactions. We adopted both sequence and structure based approaches to analyze the SNPs of RASSF5 protein. We also analyzed the putative post translational modification sites as well as the altered protein-protein interactions that encompass various cascades of signals. Out of all the SNPs obtained from the NCBI database, only 25 were considered as highly deleterious by six in silico SNP prediction tools. Among them, upon analyzing the effect of these nsSNPs on the stability of the protein, we found 17 SNPs that decrease the stability. Significant deviation in the energy minimization score was observed in P350R, F321L, and R277W. Besides this, docking analysis confirmed that P350R, A319V, F321L, and R277W reduce the binding affinity of the protein with H-Ras, where P350R shows the most remarkable deviation. Protein-protein interaction analysis revealed that RASSF5 acts as a hub connecting two clusters consisting of 18 proteins and alteration in the RASSF5 may lead to disassociation of several signal cascades. Thus, based on these analyses, our study suggests that the reported functional SNPs may serve as potential targets for different proteomic studies, diagnosis and therapeutic interventions.
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Affiliation(s)
- Md Shahadat Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Arpita Singha Roy
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Sajedul Islam
- Department of Biochemistry and Biotechnology, University of Barishal, Barishal, Bangladesh.
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32
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Humble E, Dobrynin P, Senn H, Chuven J, Scott AF, Mohr DW, Dudchenko O, Omer AD, Colaric Z, Lieberman Aiden E, Al Dhaheri SS, Wildt D, Oliaji S, Tamazian G, Pukazhenthi B, Ogden R, Koepfli KP. Chromosomal-level genome assembly of the scimitar-horned oryx: Insights into diversity and demography of a species extinct in the wild. Mol Ecol Resour 2020; 20:1668-1681. [PMID: 32365406 DOI: 10.1111/1755-0998.13181] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/09/2020] [Accepted: 04/24/2020] [Indexed: 01/04/2023]
Abstract
Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a large-scale and long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.
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Affiliation(s)
- Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Pavel Dobrynin
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA.,Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Helen Senn
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Justin Chuven
- Terrestrial & Marine Biodiversity Sector, Environment Agency, Abu Dhabi, United Arab Emirates
| | - Alan F Scott
- Genetic Resources Core Facility, McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David W Mohr
- Genetic Resources Core Facility, McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | | | - David Wildt
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Shireen Oliaji
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Gaik Tamazian
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia
| | - Budhan Pukazhenthi
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
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33
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Ravishankar A, Pupo A, Gallagher JEG. Resistance Mechanisms of Saccharomyces cerevisiae to Commercial Formulations of Glyphosate Involve DNA Damage Repair, the Cell Cycle, and the Cell Wall Structure. G3 (BETHESDA, MD.) 2020; 10:2043-2056. [PMID: 32299824 PMCID: PMC7263678 DOI: 10.1534/g3.120.401183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/13/2020] [Indexed: 12/16/2022]
Abstract
The use of glyphosate-based herbicides is widespread and despite their extensive use, their effects are yet to be deciphered completely. The additives in commercial formulations of glyphosate, though labeled inert when used individually, have adverse effects when used in combination with other additives along with the active ingredient. As a species, Saccharomyces cerevisiae has a wide range of resistance to glyphosate-based herbicides. To investigate the underlying genetic differences between sensitive and resistant strains, global changes in gene expression were measured, when yeast were exposed to a glyphosate-based herbicide (GBH). Expression of genes involved in numerous pathways crucial to the cell's functioning, such as DNA replication, MAPK signaling, meiosis, and cell wall synthesis changed. Because so many diverse pathways were affected, these strains were then subjected to in-lab-evolutions (ILE) to select mutations that confer increased resistance. Common fragile sites were found to play a role in adaptation to resistance to long-term exposure of GBHs. Copy number increased in approximately 100 genes associated with cell wall proteins, mitochondria, and sterol transport. Taking ILE and transcriptomic data into account it is evident that GBHs affect multiple biological processes in the cell. One such component is the cell wall structure which acts as a protective barrier in alleviating the stress caused by exposure to inert additives in GBHs. Sed1, a GPI-cell wall protein, plays an important role in tolerance of a GBH. Hence, a detailed study of the changes occurring at the genome and transcriptome levels is essential to better understand the effects of an environmental stressor such as a GBH, on the cell as a whole.
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Affiliation(s)
| | - Amaury Pupo
- Department of Biology, West Virginia University
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34
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Non-tandem repeat polymorphisms at microsatellite loci in wine yeast species. Mol Genet Genomics 2020; 295:685-693. [DOI: 10.1007/s00438-020-01652-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/07/2020] [Indexed: 10/24/2022]
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Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination. PLoS Genet 2020; 16:e1008632. [PMID: 32084126 PMCID: PMC7055915 DOI: 10.1371/journal.pgen.1008632] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 03/04/2020] [Accepted: 01/27/2020] [Indexed: 01/04/2023] Open
Abstract
Transposable elements constitute a large fraction of most eukaryotic genomes. Insertion of mobile DNA sequences typically has deleterious effects on host fitness, and thus diverse mechanisms have evolved to control mobile element proliferation. Mobility of the Ty1 retrotransposon in Saccharomyces yeasts is regulated by copy number control (CNC) mediated by a self-encoded restriction factor derived from the Ty1 gag capsid gene that inhibits virus-like particle function. Here, we survey a panel of wild and human-associated strains of S. cerevisiae and S. paradoxus to investigate how genomic Ty1 content influences variation in Ty1 mobility. We observe high levels of mobility for a tester element with a gag sequence from the canonical Ty1 subfamily in permissive strains that either lack full-length Ty1 elements or only contain full-length copies of the Ty1' subfamily that have a divergent gag sequence. In contrast, low levels of canonical Ty1 mobility are observed in restrictive strains carrying full-length Ty1 elements containing a canonical gag sequence. Phylogenomic analysis of full-length Ty1 elements revealed that Ty1' is the ancestral subfamily present in wild strains of S. cerevisiae, and that canonical Ty1 in S. cerevisiae is a derived subfamily that acquired gag from S. paradoxus by horizontal transfer and recombination. Our results provide evidence that variation in the ability of S. cerevisiae and S. paradoxus strains to repress canonical Ty1 transposition via CNC is regulated by the genomic content of different Ty1 subfamilies, and that self-encoded forms of transposon control can spread across species boundaries by horizontal transfer.
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Groß C, Derks M, Megens HJ, Bosse M, Groenen MAM, Reinders M, de Ridder D. pCADD: SNV prioritisation in Sus scrofa. Genet Sel Evol 2020; 52:4. [PMID: 32033531 PMCID: PMC7006094 DOI: 10.1186/s12711-020-0528-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/28/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by predicting their consequence. Due to experimental difficulties to evaluate variants that do not cause an amino-acid substitution, other prioritization methods are needed. For human genomes, the prediction of deleterious genomic variants has taken a step forward with the introduction of the combined annotation dependent depletion (CADD) method. In theory, this approach can be applied to any species. Here, we present pCADD (p for pig), a model to score single nucleotide variants (SNVs) in pig genomes. RESULTS To evaluate whether pCADD captures sites with biological meaning, we used transcripts from miRNAs and introns, sequences from genes that are specific for a particular tissue, and the different sites of codons, to test how well pCADD scores differentiate between functional and non-functional elements. Furthermore, we conducted an assessment of examples of non-coding and coding SNVs, which are causal for changes in phenotypes. Our results show that pCADD scores discriminate between functional and non-functional sequences and prioritize functional SNVs, and that pCADD is able to score the different positions in a codon relative to their redundancy. Taken together, these results indicate that based on pCADD scores, regions with biological relevance can be identified and distinguished according to their rate of adaptation. CONCLUSIONS We present the ability of pCADD to prioritize SNVs in the pig genome with respect to their putative deleteriousness, in accordance to the biological significance of the region in which they are located. We created scores for all possible SNVs, coding and non-coding, for all autosomes and the X chromosome of the pig reference sequence Sscrofa11.1, proposing a toolbox to prioritize variants and evaluate sequences to highlight new sites of interest to explain biological functions that are relevant to animal breeding.
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Affiliation(s)
- Christian Groß
- Delft Bioinformatics Lab, University of Technology Delft, 2600GA, Delft, The Netherlands. .,Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands.
| | - Martijn Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Marcel Reinders
- Delft Bioinformatics Lab, University of Technology Delft, 2600GA, Delft, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
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Nomura T. Recombination-induced revertant mosaicism in ichthyosis with confetti and loricrin keratoderma. J Dermatol Sci 2019; 97:94-100. [PMID: 31928837 DOI: 10.1016/j.jdermsci.2019.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 12/26/2019] [Accepted: 12/26/2019] [Indexed: 01/23/2023]
Abstract
Revertant mosaicism refers to a condition in which a pathogenic germline mutation is spontaneously corrected in somatic cells, resulting in the presence of two or more cell populations with different genotypes in an organism arising from a single fertilized egg. If the revertant cells are clonally expanded due to a survival advantage over the surrounding mutant cells, patients benefit from this self-healing phenomenon which leads to the development of milder-than-expected clinical phenotypes; in genetic skin diseases, patients with revertant mosaicism present with small islands of healthy skin. To date, revertant mosaicism has been reported in ∼50 genetic diseases involving the skin, blood, liver, muscle, and brain. In this review, I briefly summarize current knowledge on revertant mosaicism in two particular skin diseases, ichthyosis with confetti (IWC) and loricrin keratoderma (LK), both of which develop numerous revertant skin patches. Notably, homologous recombination (HR) is the only mechanism underlying the reversion of pathogenic mutations in IWC and LK, and this was identified following the analysis of ∼50 revertant epidermis samples. All the samples showed long-tract loss of heterozygosity (LOH) that originated at regions centromeric to pathogenic mutations and extended to the telomere of the mutation-harboring chromosomes. Elucidating the molecular mechanisms underlying revertant mosaicism in IWC and LK-especially how mutant proteins induce long-tract LOH-would potentially expand the possibility of manipulating HR to induce the reversion of disease-causing mutations and help devising novel therapies not only for IWC and LK but also for other intractable genetic diseases.
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Affiliation(s)
- Toshifumi Nomura
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
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Tanwar H, Kumar DT, Doss CGP, Zayed H. Bioinformatics classification of mutations in patients with Mucopolysaccharidosis IIIA. Metab Brain Dis 2019; 34:1577-1594. [PMID: 31385193 PMCID: PMC6858298 DOI: 10.1007/s11011-019-00465-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/08/2019] [Indexed: 02/06/2023]
Abstract
Mucopolysaccharidosis (MPS) IIIA, also known as Sanfilippo syndrome type A, is a severe, progressive disease that affects the central nervous system (CNS). MPS IIIA is inherited in an autosomal recessive manner and is caused by a deficiency in the lysosomal enzyme sulfamidase, which is required for the degradation of heparan sulfate. The sulfamidase is produced by the N-sulphoglucosamine sulphohydrolase (SGSH) gene. In MPS IIIA patients, the excess of lysosomal storage of heparan sulfate often leads to mental retardation, hyperactive behavior, and connective tissue impairments, which occur due to various known missense mutations in the SGSH, leading to protein dysfunction. In this study, we focused on three mutations (R74C, S66W, and R245H) based on in silico pathogenic, conservation, and stability prediction tool studies. The three mutations were further subjected to molecular dynamic simulation (MDS) analysis using GROMACS simulation software to observe the structural changes they induced, and all the mutants exhibited maximum deviation patterns compared with the native protein. Conformational changes were observed in the mutants based on various geometrical parameters, such as conformational stability, fluctuation, and compactness, followed by hydrogen bonding, physicochemical properties, principal component analysis (PCA), and salt bridge analyses, which further validated the underlying cause of the protein instability. Additionally, secondary structure and surrounding amino acid analyses further confirmed the above results indicating the loss of protein function in the mutants compared with the native protein. The present results reveal the effects of three mutations on the enzymatic activity of sulfamidase, providing a molecular explanation for the cause of the disease. Thus, this study allows for a better understanding of the effect of SGSH mutations through the use of various computational approaches in terms of both structure and functions and provides a platform for the development of therapeutic drugs and potential disease treatments.
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Affiliation(s)
- Himani Tanwar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - D Thirumal Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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Islam MJ, Khan AM, Parves MR, Hossain MN, Halim MA. Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation. Sci Rep 2019; 9:16426. [PMID: 31712642 PMCID: PMC6848484 DOI: 10.1038/s41598-019-52308-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/09/2019] [Indexed: 02/08/2023] Open
Abstract
Serine-threonine kinase11 (STK11) is a tumor suppressor gene which plays a key role in regulating cell growth and apoptosis. It is widely known as a multitasking kinase and engaged in cell polarity, cell cycle arrest, chromatin remodeling, energy metabolism, and Wnt signaling. The substitutions of single amino acids in highly conserved regions of the STK11 protein are associated with Peutz-Jeghers syndrome (PJS), which is an autosomal dominant inherited disorder. The abnormal function of the STK11 protein is still not well understood. In this study, we classified disease susceptible single nucleotide polymorphisms (SNPs) in STK11 by using different computational algorithms. We identified the deleterious nsSNPs, constructed mutant protein structures, and evaluated the impact of mutation by employing molecular docking and molecular dynamics analysis. Our results show that W239R and W308C variants are likely to be highly deleterious mutations found in the catalytic kinase domain, which may destabilize structure and disrupt the activation of the STK11 protein as well as reduce its catalytic efficiency. The W239R mutant is likely to have a greater impact on destabilizing the protein structure compared to the W308C mutant. In conclusion, these mutants can help to further realize the large pool of disease susceptibilities linked with catalytic kinase domain activation of STK11 and assist to develop an effective drug for associated diseases.
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Affiliation(s)
- Md Jahirul Islam
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy's Lake, Khulshi- 4202, Chittagong, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh
| | - Md Rimon Parves
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy's Lake, Khulshi- 4202, Chittagong, Bangladesh
| | - Md Nayeem Hossain
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh.
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Multiple Changes Underlie Allelic Divergence of CUP2 Between Saccharomyces Species. G3-GENES GENOMES GENETICS 2019; 9:3595-3600. [PMID: 31519745 PMCID: PMC6829129 DOI: 10.1534/g3.119.400616] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Under the model of micromutationism, phenotypic divergence between species is caused by accumulation of many small-effect changes. While mapping the causal changes to single nucleotide resolution could be difficult for diverged species, genetic dissection via chimeric constructs allows us to evaluate whether a large-effect gene is composed of many small-effect nucleotide changes. In a previously described non-complementation screen, we found an allele difference of CUP2, a copper-binding transcription factor, underlies divergence in copper resistance between Saccharomyces cerevisiae and S. uvarum. Here, we tested whether the allele effect of CUP2 was caused by multiple nucleotide changes. By analyzing chimeric constructs containing four separate regions in the CUP2 gene, including its distal promoter, proximal promoter, DNA binding domain and transcriptional activation domain, we found that all four regions of the S. cerevisiae allele conferred copper resistance, with the proximal promoter showing the largest effect, and that both additive and epistatic effects are likely involved. These findings support a model of multiple changes underlying evolution and suggest an important role of both protein coding and cis-regulatory changes in evolution.
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Arifuzzaman M, Mitra S, Das R, Hamza A, Absar N, Dash R. In silico analysis of nonsynonymous single-nucleotide polymorphisms (nsSNPs) of the SMPX gene. Ann Hum Genet 2019; 84:54-71. [PMID: 31583691 DOI: 10.1111/ahg.12350] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/06/2019] [Accepted: 08/08/2019] [Indexed: 02/06/2023]
Abstract
Mutations in the SMPX gene can disrupt the regular activity of the SMPX protein, which is involved in the hearing process. Recent reports showing a link between nonsynonymous single-nucleotide polymorphisms (nsSNPs) in SMPX and hearing loss, thus classifying deleterious SNPs in SMPX will be an uphill task before designing a more extensive population study. In this study, damaging nsSNPs of SMPX from the dbSNP database were identified by using 13 bioinformatics tools. Initially, the impact of nsSNPs in the SMPX gene were evaluated through different in silico predictors; and the deleterious convergent changes were analyzed by energy-minimization-guided residual network analysis. In addition, the pathogenic effects of mutations in SMPX-mediated protein-protein interactions were also characterized by structural modeling and binding energy calculations. A total of four mutations (N19D, A29T, K54N, and S71L) were found to be highly deleterious by all the tools, which are located at highly conserved regions. Furthermore, all four mutants showed structural alterations, and the communities of amino acids for mutant proteins were readily changed, compared to the wild-type. Among them, A29T (rs772775896) was revealed as the most damaging nsSNP, which caused significant structural deviation of the SMPX protein, as a result reducing the binding affinity to other functional partners. These findings reflect the computational insights into the deleterious role of nsSNPs in SMPX, which might be helpful for subjecting wet-lab confirmatory analysis.
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Affiliation(s)
- Md Arifuzzaman
- College of Pharmacy, Yeungnam University, Gyeongbuk, Republic of Korea
| | - Sarmistha Mitra
- Plasma Bioscience Research Center, Plasma-Bio Display, Kwangwoon University, Seoul, Republic of Korea
| | - Raju Das
- Department of Biochemistry and Biotechnology, University of Science & Technology Chittagong, Chittagong, Bangladesh
| | - Amir Hamza
- Department of Biochemistry, Hallym University, Gangwon, Republic of Korea
| | - Nurul Absar
- Department of Biochemistry and Biotechnology, University of Science & Technology Chittagong, Chittagong, Bangladesh
| | - Raju Dash
- Department of Anatomy, Dongguk University Graduate School of Medicine, Gyeongju, Republic of Korea
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James TY, Michelotti LA, Glasco AD, Clemons RA, Powers RA, James ES, Simmons DR, Bai F, Ge S. Adaptation by Loss of Heterozygosity in Saccharomyces cerevisiae Clones Under Divergent Selection. Genetics 2019; 213:665-683. [PMID: 31371407 PMCID: PMC6781901 DOI: 10.1534/genetics.119.302411] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/29/2019] [Indexed: 01/14/2023] Open
Abstract
Loss of heterozygosity (LOH) is observed during vegetative growth and reproduction of diploid genotypes through mitotic crossovers, aneuploidy caused by nondisjunction, and gene conversion. We aimed to test the role that LOH plays during adaptation of two highly heterozygous Saccharomyces cerevisiae genotypes to multiple environments over a short time span in the laboratory. We hypothesized that adaptation would be observed through parallel LOH events across replicate populations. Using genome resequencing of 70 clones, we found that LOH was widespread with 5.2 LOH events per clone after ∼500 generations. The most common mode of LOH was gene conversion (51%) followed by crossing over consistent with either break-induced replication or double Holliday junction resolution. There was no evidence that LOH involved nondisjunction of whole chromosomes. We observed parallel LOH in both an environment-specific and environment-independent manner. LOH largely involved recombining existing variation between the parental genotypes, but also was observed after de novo, presumably beneficial, mutations occurred in the presence of canavanine, a toxic analog of arginine. One highly parallel LOH event involved the ENA salt efflux pump locus on chromosome IV, which showed repeated LOH to the allele from the European parent, an allele originally derived by introgression from S. paradoxus Using CRISPR-engineered LOH we showed that the fitness advantage provided by this single LOH event was 27%. Overall, we found extensive evidence that LOH could be adaptive and is likely to be a greater source of initial variation than de novo mutation for rapid evolution of diploid genotypes.
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Affiliation(s)
- Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Lucas A Michelotti
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Alexander D Glasco
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Rebecca A Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Robert A Powers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Ellen S James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - D Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Fengyan Bai
- Institute of Microbiology, Chinese Academy of Sciences, State Key Laboratory of Mycology, Chaoyang District, Beijing 100101, China
| | - Shuhua Ge
- Technology Development and Transfer Center, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100029, China
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Computational analysis of high-risk SNPs in human CHK2 gene responsible for hereditary breast cancer: A functional and structural impact. PLoS One 2019; 14:e0220711. [PMID: 31398194 PMCID: PMC6688789 DOI: 10.1371/journal.pone.0220711] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/22/2019] [Indexed: 12/18/2022] Open
Abstract
Nowadays CHK2 mutation is studied frequently in hereditary breast and ovarian cancer patients in addition to BRCA1/BRCA2. CHK2 is a tumor suppressor gene that encodes a serine/threonine kinase, also involved in pathways such as DNA repair, cell cycle regulation and apoptosis in response to DNA damage. CHK2 is a well-studied moderate penetrance gene that correlates with third high risk susceptibility gene with an increased risk for breast cancer. Hence before planning large population study, it is better to scrutinize putative functional SNPs of CHK2 using different computational tools. In this study, we have used various computational approaches to identify nsSNPs which are deleterious to the structure and/or function of CHK2 protein that might be causing this disease. Computational analysis was performed by different in silico tools including SIFT, Align GVGD, SNAP-2, PROVEAN, Poly-Phen-2, PANTHER, PhD-SNP, MUpro, iPTREE-STAB, Consurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, Verify-3D, FT Site, COACH and PyMol. Out of 78 nsSNP of human CHK2 gene, seven nsSNPs were predicted functionally most significant SNPs. Among these seven nsSNP, p.Arg160Gly, p.Gly210Arg and p.Ser415Phe are highly conserved residues with conservation score of 9 and three nsSNP were predicted to be involved in post translational modification. The p.Arg160Gly and p.Gly210Arg may interfere in phosphopeptide binding site on FHA conserved domain. The p.Ser415Phe may interfere in formation of activation loop of protein-kinase domain and might interfere in interactions of CHK2 with ligand. The study concludes that mutation of serine to phenylalanine at position 415 is a major mutation in native CHK2 protein which might contribute to its malfunction, ultimately causing disease. This is the first comprehensive study, where CHK2 gene variants are analyzed using in silico tools hence it will be of great help while considering large scale studies and also in developing precision medicines related to these polymorphisms in the era of personalized medicine.
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Akhtar M, Jamal T, Jamal H, Din JU, Jamal M, Arif M, Arshad M, Jalil F. Identification of most damaging nsSNPs in human CCR6 gene: In silico analyses. Int J Immunogenet 2019; 46:459-471. [PMID: 31364806 DOI: 10.1111/iji.12449] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/05/2019] [Accepted: 06/12/2019] [Indexed: 12/30/2022]
Abstract
Single nucleotide polymorphisms in CCR6 (C-C chemokine receptor type 6) gene have been found to be the possible cause of many diseases like rheumatoid arthritis, psoriasis, lupus nephritis and systemic sclerosis and other autoimmune diseases. Therefore, identification of structurally and functionally important polymorphisms in CCR6 is important in order to study its potential malfunctioning and discovering therapeutic targets. Several bioinformatics tools were used to identify most damaging nsSNPs that might be vital for CCR6 structure and function. The in silico tools included PROVEAN, SIFT, SNP&GO and PolyPhen2 followed by I-Mutant MutPred and ConSurf. Phyre2 and I-TASSER were used for protein 3-D Modelling while gene-gene interaction was predicted by STRING and GeneMANIA. Our study suggested that three nsSNPs rs1376162684, rs751102128 and rs1185426631 are the most damaging in CCR6 gene while 7 missense SNPs rs1438637216, rs139697820, rs768420505, rs1282264186, rs1394647982, rs769360638 and rs1263402382 are found to revert into stop codons. Prediction of post-transcriptional modifications highlighted the significance of rs1376162684 because it effected potential phosphorylation site. Gene-gene interactions showed relation of CCR6 with other genes depicting its importance in several pathways and co-expressions. In future, studying diseases related to CCR6 should include investigation of these 10 nsSNPs. Being the first of its type, this study also proposes future perspectives that will help in precision medicines. For such purposes, CCR6 proteins from patients of autoimmune diseases should be explored. Animal models can also be of significance find out the effects of CCR6 in diseases.
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Affiliation(s)
- Mehran Akhtar
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Tazkira Jamal
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | | | - Jalal Ud Din
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Arif
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Maria Arshad
- Attaur Rahman School of Applied Biosciences, NUST, Islamabad, Pakistan
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
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Peltier E, Friedrich A, Schacherer J, Marullo P. Quantitative Trait Nucleotides Impacting the Technological Performances of Industrial Saccharomyces cerevisiae Strains. Front Genet 2019; 10:683. [PMID: 31396264 PMCID: PMC6664092 DOI: 10.3389/fgene.2019.00683] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/01/2019] [Indexed: 11/13/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae is certainly the prime industrial microorganism and is related to many biotechnological applications including food fermentations, biofuel production, green chemistry, and drug production. A noteworthy characteristic of this species is the existence of subgroups well adapted to specific processes with some individuals showing optimal technological traits. In the last 20 years, many studies have established a link between quantitative traits and single-nucleotide polymorphisms found in hundreds of genes. These natural variations constitute a pool of QTNs (quantitative trait nucleotides) that modulate yeast traits of economic interest for industry. By selecting a subset of genes functionally validated, a total of 284 QTNs were inventoried. Their distribution across pan and core genome and their frequency within the 1,011 Saccharomyces cerevisiae genomes were analyzed. We found that 150 of the 284 QTNs have a frequency lower than 5%, meaning that these variants would be undetectable by genome-wide association studies (GWAS). This analysis also suggests that most of the functional variants are private to a subpopulation, possibly due to their adaptive role to specific industrial environment. In this review, we provide a literature survey of their phenotypic impact and discuss the opportunities and the limits of their use for industrial strain selection.
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Affiliation(s)
- Emilien Peltier
- Department Sciences du vivant et de la sante, Université de Bordeaux, UR Œnologie EA 4577, Bordeaux, France
- Biolaffort, Bordeaux, France
| | - Anne Friedrich
- Department Micro-organismes, Génomes, Environnement, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Department Micro-organismes, Génomes, Environnement, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Philippe Marullo
- Department Sciences du vivant et de la sante, Université de Bordeaux, UR Œnologie EA 4577, Bordeaux, France
- Biolaffort, Bordeaux, France
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Pontes A, Čadež N, Gonçalves P, Sampaio JP. A Quasi-Domesticate Relic Hybrid Population of Saccharomyces cerevisiae × S. paradoxus Adapted to Olive Brine. Front Genet 2019; 10:449. [PMID: 31191600 PMCID: PMC6548830 DOI: 10.3389/fgene.2019.00449] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/30/2019] [Indexed: 11/13/2022] Open
Abstract
The adaptation of the yeast Saccharomyces cerevisiae to man-made environments for the fermentation of foodstuffs and beverages illustrates the scientific, social, and economic relevance of microbe domestication. Here we address a yet unexplored aspect of S. cerevisiae domestication, that of the emergence of lineages harboring some domestication signatures but that do not fit completely in the archetype of a domesticated yeast, by studying S. cerevisiae strains associated with processed olives, namely table olives, olive brine, olive oil, and alpechin. We confirmed earlier observations that reported that the Olives population results from a hybridization between S. cerevisiae and S. paradoxus. We concluded that the olive hybrids form a monophyletic lineage and that the S. cerevisiae progenitor belonged to the wine population of this species. We propose that homoploid hybridization gave rise to a diploid hybrid genome, which subsequently underwent the loss of most of the S. paradoxus sub-genome. Such a massive loss of heterozygosity was probably driven by adaptation to the new niche. We observed that olive strains are more fit to grow and survive in olive brine than control S. cerevisiae wine strains and that they appear to be adapted to cope with the presence of NaCl in olive brine through expansion of copy number of ENA genes. We also investigated whether the S. paradoxus HXT alleles retained by the Olives population were likely to contribute to the observed superior ability of these strains to consume sugars in brine. Our experiments indicate that sugar consumption profiles in the presence of NaCl are different between members of the Olives and Wine populations and only when cells are cultivated in nutritional conditions that support adaptation of their proteome to the high salt environment, which suggests that the observed differences are due to a better overall fitness of olives strains in the presence of high NaCl concentrations. Although relic olive hybrids exhibit several characteristics of a domesticated lineage, tangible benefits to humans cannot be associated with their phenotypes. These strains can be seen as a case of adaptation without positive or negative consequences to humans, that we define as a quasi-domestication.
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Affiliation(s)
- Ana Pontes
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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García-Ríos E, Nuévalos M, Barrio E, Puig S, Guillamón JM. A new chromosomal rearrangement improves the adaptation of wine yeasts to sulfite. Environ Microbiol 2019; 21:1771-1781. [PMID: 30859719 DOI: 10.1111/1462-2920.14586] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/05/2019] [Accepted: 03/06/2019] [Indexed: 11/27/2022]
Abstract
Sulfite-generating compounds are widely used during winemaking as preservatives because of its antimicrobial and antioxidant properties. Thus, wine yeast strains have developed different genetic strategies to increase its sulfite resistance. The most efficient sulfite detoxification mechanism in Saccharomyces cerevisiae uses a plasma membrane protein called Ssu1 to efflux sulfite. In wine yeast strains, two chromosomal translocations (VIIItXVI and XVtXVI) involving the SSU1 promoter region have been shown to upregulate SSU1 expression and, as a result, increase sulfite tolerance. In this study, we have identified a novel chromosomal rearrangement that triggers wine yeast sulfite adaptation. An inversion in chromosome XVI (inv-XVI) probably due to sequence microhomology, which involves SSU1 and GCR1 regulatory regions, increases the expression of SSU1 and the sulfite resistance of a commercial wine yeast strain. A detailed dissection of this chimeric SSU1 promoter indicates that both the removed SSU1 promoter sequence and the relocated GCR1 sequence contribute to SSU1 upregulation and sulfite tolerance. However, no relevant function has been attributed to the SSU1-promoter-binding transcription factor Fzf1. These results unveil a new genomic event that confers an evolutive advantage to wine yeast strains.
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Affiliation(s)
- Estéfani García-Ríos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - Marcos Nuévalos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain.,Departament de Genètica, Universitat de València, Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
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Fay JC, Liu P, Ong GT, Dunham MJ, Cromie GA, Jeffery EW, Ludlow CL, Dudley AM. A polyploid admixed origin of beer yeasts derived from European and Asian wine populations. PLoS Biol 2019; 17:e3000147. [PMID: 30835725 PMCID: PMC6400334 DOI: 10.1371/journal.pbio.3000147] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/30/2019] [Indexed: 11/18/2022] Open
Abstract
Strains of Saccharomyces cerevisiae used to make beer, bread, and wine are genetically and phenotypically distinct from wild populations associated with trees. The origins of these domesticated populations are not always clear; human-associated migration and admixture with wild populations have had a strong impact on S. cerevisiae population structure. We examined the population genetic history of beer strains and found that ale strains and the S. cerevisiae portion of allotetraploid lager strains were derived from admixture between populations closely related to European grape wine strains and Asian rice wine strains. Similar to both lager and baking strains, ale strains are polyploid, providing them with a passive means of remaining isolated from other populations and providing us with a living relic of their ancestral hybridization. To reconstruct their polyploid origin, we phased the genomes of two ale strains and found ale haplotypes to both be recombinants between European and Asian alleles and to also contain novel alleles derived from extinct or as yet uncharacterized populations. We conclude that modern beer strains are the product of a historical melting pot of fermentation technology.
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Affiliation(s)
- Justin C. Fay
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- Department of Genetics, Washington University, St. Louis, Missouri, United States of America
- * E-mail:
| | - Ping Liu
- Department of Genetics, Washington University, St. Louis, Missouri, United States of America
| | - Giang T. Ong
- Department of Genome Sciences, Seattle, Washington, United States of America
| | - Maitreya J. Dunham
- Department of Genome Sciences, Seattle, Washington, United States of America
| | - Gareth A. Cromie
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Eric W. Jeffery
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Catherine L. Ludlow
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Aimée M. Dudley
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
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Identification and structural characterization of deleterious non-synonymous single nucleotide polymorphisms in the human SKP2 gene. Comput Biol Chem 2019; 79:127-136. [PMID: 30802828 DOI: 10.1016/j.compbiolchem.2019.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 01/27/2019] [Accepted: 02/13/2019] [Indexed: 12/17/2022]
Abstract
In SCF (Skp, Cullin, F-box) ubiquitin-protein ligase complexes, S-phase kinase 2 (SKP2) is one of the major players of F-box family, that is responsible for the degradation of several important cell regulators and tumor suppressor proteins. Despite of having significant evidence for the role of SKP2 on tumorgenesis, there is a lack of available data regarding the effect of non-synonymous polymorphisms. In this communication, the structural and functional consequences of non-synonymous single nucleotide polymorphisms (nsSNPs) of SKP2 have been reported by employing various computational approaches and molecular dynamics simulation. Initially, several computational tools like SIFT, PolyPhen-2, PredictSNP, I-Mutant 2.0 and ConSurf have been implicated in this study to explore the damaging SNPs. In total of 172 nsSNPs, 5 nsSNPs were identified as deleterious and 3 of them were predicted to be decreased the stability of protein. Guided from ConSurf analysis, P101L (rs761253702) and Y346C (rs755010517) were categorized as the highly conserved and functional disrupting mutations. Therefore, these mutations were subjected to three dimensional model building and molecular dynamics simulation study for the detailed structural consequences upon the mutations. The study revealed that P101L and Y346C mutations increased the flexibility and changed the structural dynamics. As both these mutations are located in the most functional regions of SKP2 protein, these computational insights might be helpful to consider these nsSNPs for wet-lab confirmatory analysis as well as in rationalizing future population based studies and structure based drug design against SKP2.
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Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum ( Sorghum bicolor). Genetics 2019; 211:1075-1087. [PMID: 30622134 PMCID: PMC6404259 DOI: 10.1534/genetics.118.301742] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/22/2018] [Indexed: 11/18/2022] Open
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. Valluru et al. identify putative deleterious mutations among ∼5.5M segregating variants of 229 diverse sorghum... Sorghum (Sorghum bicolor L.) is a major food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. The lack of recombination, drift, and the coupling with favorable loci impede the removal of deleterious mutations from the genome by selection. To study how deleterious variants impact phenotypes, we identified putative deleterious mutations among ∼5.5 M segregating variants of 229 diverse biomass sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that ∼33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups. Across racial groups, the mutation burden correlated negatively with biomass, plant height, specific leaf area (SLA), and tissue starch content (TSC), suggesting that deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly one-half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (average of 3.1% across all stages). There is no advantage in total heritable variance for SLA and TSC. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, these results suggest that incorporating putatively deleterious variants into genomic models slightly improves prediction accuracy because of extensive linkage. Knowledge of deleterious variants could be leveraged for sorghum breeding through either genome editing and/or conventional breeding that focuses on the selection of progeny with fewer deleterious alleles.
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