1
|
Lujan SA, Garbacz MA, Liberti SE, Burkholder AB, Kunkel TA. Instability throughout the Saccharomyces cerevisiae genome resulting from Pms1 endonuclease deficiency. Nucleic Acids Res 2024; 52:9574-9585. [PMID: 39016170 PMCID: PMC11381345 DOI: 10.1093/nar/gkae616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/25/2024] [Accepted: 07/06/2024] [Indexed: 07/18/2024] Open
Abstract
The endonuclease activity of Pms1 directs mismatch repair by generating a nick in the newly replicated DNA strand. Inactivating Pms2, the human homologue of yeast Pms1, increases the chances of colorectal and uterine cancers. Here we use whole genome sequencing to show that loss of this endonuclease activity, via the pms1-DE variant, results in strong mutator effects throughout the Saccharomyces cerevisiae genome. Mutation rates are strongly increased for mutations resulting from all types of single-base substitutions and for a wide variety of single- and multi-base indel mutations. Rates for these events are further increased in strains combining pms1-DE with mutator variants of each of the three major leading and lagging strand replicases. In all cases, mutation rates, spectra, biases, and context preferences are statistically indistinguishable from strains with equivalent polymerases but lacking initial mismatch recognition due to deletion of MSH2. This implies that, across the nuclear genome, strand discrimination via the Pms1 endonuclease is as important for MMR as is initial mismatch recognition by Msh2 heterodimers.
Collapse
Affiliation(s)
- Scott A Lujan
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, NC 27709, USA
| | - Marta A Garbacz
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, NC 27709, USA
- Currently Marta A. Garbacz works at Exact Sciences Corporation, Torrey Pines Science Park, La Jolla, CA 92037, USA
| | | | - Adam B Burkholder
- Office of Environmental Science Cyberinfrastructure, NIH/NIEHS, DHHS. Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, NC 27709, USA
| |
Collapse
|
2
|
Wang P, Jiang W, Lai T, Liu Q, Shen Y, Ye B, Wu D. Germline variants in acquired aplastic anemia: current knowledge and future perspectives. Haematologica 2024; 109:2778-2789. [PMID: 38988263 PMCID: PMC11367197 DOI: 10.3324/haematol.2023.284312] [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: 09/16/2023] [Accepted: 04/09/2024] [Indexed: 07/12/2024] Open
Abstract
Aplastic anemia (AA) is a disease characterized by failure of hematopoiesis, bone marrow aplasia, and pancytopenia. It can be inherited or acquired. Although acquired AA is believed to be immune-mediated and random, new evidence suggests an underlying genetic predisposition. Besides confirmed genomic mutations that contribute to inherited AA (such as pathogenic mutations of TERT and TERC), germline variants, often in heterozygous states, also play a not negligible role in the onset and progression of acquired AA. These variants, associated with inherited bone marrow failure syndromes and inborn errors of immunity, contribute to the disease, possibly through mechanisms including gene homeostasis, DNA repair, and immune injury. This article explores the nuanced association between acquired AA and germline variants, detailing the clinical significance of germline variants in diagnosing and managing this condition. More work is encouraged to better understand the role of immunogenic pathogenic variants and whether somatic mutations participate as secondary "hits" in the development of bone marrow failure.
Collapse
Affiliation(s)
- Peicheng Wang
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang
| | - Wanzhi Jiang
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang
| | - Tianyi Lai
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang
| | - Qi Liu
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang
| | - Yingying Shen
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China; National Traditional Chinese Medicine Clinical Research Base (Hematology), Hangzhou, Zhejiang
| | - Baodong Ye
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China; National Traditional Chinese Medicine Clinical Research Base (Hematology), Hangzhou, Zhejiang.
| | - Dijiong Wu
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China; National Traditional Chinese Medicine Clinical Research Base (Hematology), Hangzhou, Zhejiang, China; Department of Oncology and Hematology, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine affiliated to Zhejiang Chinese Medicine University, Wenzhou, Zhejiang.
| |
Collapse
|
3
|
Joshi S, Dash S, Vijayan N, Nishant KT. Irc20 modulates LOH frequency and distribution in S. cerevisiae. DNA Repair (Amst) 2024; 141:103727. [PMID: 39098164 DOI: 10.1016/j.dnarep.2024.103727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/04/2024] [Accepted: 07/09/2024] [Indexed: 08/06/2024]
Abstract
Loss of Heterozygosity (LOH) due to mitotic recombination is frequently associated with the development of various cancers (e.g. retinoblastoma). LOH is also an important source of genetic diversity, especially in organisms where meiosis is infrequent. Irc20 is a putative helicase, and E3 ubiquitin ligase involved in DNA double-strand break repair pathway. We analyzed genome-wide LOH events, gross chromosomal changes, small insertion-deletions and single nucleotide mutations in eleven S. cerevisiae mutation accumulation lines of irc20∆, which underwent 50 mitotic bottlenecks. LOH enhancement in irc20∆ was small (1.6 fold), but statistically significant as compared to the wild type. Short (≤ 1 kb) and long (> 10 kb) LOH tracts were significantly enhanced in irc20∆. Both interstitial and terminal LOH events were also significantly enhanced in irc20∆ compared to the wild type. LOH events in irc20∆ were more telomere proximal and away from centromeres compared to the wild type. Gross chromosomal changes, single nucleotide mutations and in-dels were comparable between irc20∆ and wild type. Locus based and genome-wide analysis of meiotic recombination showed that meiotic crossover frequencies are not altered in irc20∆. These results suggest Irc20 primarily regulates mitotic recombination and does not affect meiotic crossovers. Our results suggest that the IRC20 gene is important for regulating LOH frequency and distribution.
Collapse
Affiliation(s)
- Sameer Joshi
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Suman Dash
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Nikilesh Vijayan
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Koodali T Nishant
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India; Center for High-Performance Computing, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India.
| |
Collapse
|
4
|
Cheng L, Zhao S, Li T, Hou S, Luo Z, Xu J, Yu W, Jiang S, Monti M, Schindler D, Zhang W, Hou C, Ma Y, Cai Y, Boeke JD, Dai J. Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae. Nat Commun 2024; 15:770. [PMID: 38278805 PMCID: PMC10817965 DOI: 10.1038/s41467-023-44511-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/13/2023] [Indexed: 01/28/2024] Open
Abstract
Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. However, the potential of SCRaMbLE to study genomic rearrangements is currently hindered, because a strain containing all 16 synthetic chromosomes is not yet available. Here, we construct SparLox83R, a yeast strain containing 83 loxPsym sites distributed across all 16 chromosomes. SCRaMbLE of SparLox83R produces versatile genome-wide genomic rearrangements, including inter-chromosomal events. Moreover, when combined with synthetic chromosomes, SCRaMbLE of hetero-diploids with SparLox83R leads to increased diversity of genomic rearrangements and relatively faster evolution of traits compared to hetero-diploids only with wild-type chromosomes. Analysis of the SCRaMbLEd strain with increased tolerance to nocodazole demonstrates that genomic rearrangements can perturb the transcriptome and 3D genome structure and consequently impact phenotypes. In summary, a genome with sparsely distributed loxPsym sites can serve as a powerful tool for studying the consequence of genomic rearrangements and accelerating strain engineering in Saccharomyces cerevisiae.
Collapse
Grants
- 32030004, 32150025 National Natural Science Foundation of China (National Science Foundation of China)
- 32001042 National Natural Science Foundation of China (National Science Foundation of China)
- 32101184 National Natural Science Foundation of China (National Science Foundation of China)
- 32122050 National Natural Science Foundation of China (National Science Foundation of China)
- 2021359 Youth Innovation Promotion Association of the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS)
- National Key R&D Program of China (2022YFF1201800,2018YFA0900100), Guangdong Natural Science Funds for Distinguished Young Scholar (2021B1515020060), Guangdong Provincial Key Laboratory of Synthetic Genomics (2023B1212060054), Bureau of International Cooperation, Chinese Academy of Sciences (172644KYSB20180022), Shenzhen Science and Technology Program (KQTD20180413181837372, KQTD20200925153547003), Innovation Program of Chinese Academy of Agricultural Science and Shenzhen Outstanding Talents Training Fund.
- Guandong Basic and Applied Basic Research Foundation (2023A1515030285)
- UK Biotechnology and Biological Sciences Research Council (BBSRC) grants BB/M005690/1, BB/P02114X/1 and BB/W014483/1, Royal Society Newton Advanced Fellowship (NAF\R2\180590) and a Volkswagen Foundation “Life? Initiative” Grant (Ref. 94 771)
- US NSF grants MCB-1026068, MCB-1443299, MCB-1616111 and MCB-1921641
Collapse
Affiliation(s)
- Li Cheng
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shijun Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianyi Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Shenzhen Lianghe Biotechnology Co., Ltd., Shenzhen, China
| | - Sha Hou
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhouqing Luo
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jinsheng Xu
- Department of Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenfei Yu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuangying Jiang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Marco Monti
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Chunhui Hou
- China State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yingxin Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yizhi Cai
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
| | - Junbiao Dai
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Rd, Shenzhen, 518055, Guangdong, China.
| |
Collapse
|
5
|
Kozmin SG, Dominska M, Zheng DQ, Petes TD. Splitting the yeast centromere by recombination. Nucleic Acids Res 2024; 52:690-707. [PMID: 37994724 PMCID: PMC10810202 DOI: 10.1093/nar/gkad1110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023] Open
Abstract
Although fusions between the centromeres of different human chromosomes have been observed cytologically in cancer cells, since the centromeres are long arrays of satellite sequences, the details of these fusions have been difficult to investigate. We developed methods of detecting recombination within the centromeres of the yeast Saccharomyces cerevisiae (intercentromere recombination). These events occur at similar rates (about 10-8/cell division) between two active or two inactive centromeres. We mapped the breakpoints of most of the recombination events to a region of 43 base pairs of uninterrupted homology between the two centromeres. By whole-genome DNA sequencing, we showed that most (>90%) of the events occur by non-reciprocal recombination (gene conversion/break-induced replication). We also found that intercentromere recombination can involve non-homologous chromosome, generating whole-arm translocations. In addition, intercentromere recombination is associated with very frequent chromosome missegregation. These observations support the conclusion that intercentromere recombination generally has negative genetic consequences.
Collapse
Affiliation(s)
- Stanislav G Kozmin
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | | | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| |
Collapse
|
6
|
Zhu YX, He M, Li KJ, Wang YK, Qian N, Wang ZF, Sheng H, Sui Y, Zhang DD, Zhang K, Qi L, Zheng DQ. Novel insights into the effects of 5-hydroxymethfurural on genomic instability and phenotypic evolution using a yeast model. Appl Environ Microbiol 2024; 90:e0164923. [PMID: 38108644 PMCID: PMC10807415 DOI: 10.1128/aem.01649-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/06/2023] [Indexed: 12/19/2023] Open
Abstract
5-Hydroxymethfurural (5-HMF) is naturally found in a variety of foods and beverages and represents a main inhibitor in the lignocellulosic hydrolysates used for fermentation. This study investigated the impact of 5-HMF on the genomic stability and phenotypic plasticity of the yeast Saccharomyces cerevisiae. Using next-generation sequencing technology, we examined the genomic alterations of diploid S. cerevisiae isolates that were subcultured on a medium containing 1.2 g/L 5-HMF. We found that in 5-HMF-treated cells, the rates of chromosome aneuploidy, large deletions/duplications, and loss of heterozygosity were elevated compared with that in untreated cells. 5-HMF exposure had a mild impact on the rate of point mutations but altered the mutation spectrum. Contrary to what was observed in untreated cells, more monosomy than trisomy occurred in 5-HMF-treated cells. The aneuploidy mutant with monosomic chromosome IX was more resistant to 5-HMF than the diploid parent strain because of the enhanced activity of alcohol dehydrogenase. Finally, we found that overexpression of ADH6 and ZWF1 effectively stabilized the yeast genome under 5-HMF stress. Our findings not only elucidated the global effect of 5-HMF on the genomic integrity of yeast but also provided novel insights into how chromosomal instability drives the environmental adaptability of eukaryotic cells.IMPORTANCESingle-cell microorganisms are exposed to a range of stressors in both natural and industrial settings. This study investigated the effects of 5-hydroxymethfurural (5-HMF), a major inhibitor found in baked foods and lignocellulosic hydrolysates, on the chromosomal instability of yeast. We examined the mechanisms leading to the distinct patterns of 5-HMF-induced genomic alterations and discovered that chromosomal loss, typically viewed as detrimental to cell growth under most conditions, can contribute to yeast tolerance to 5-HMF. Our results increased the understanding of how specific stressors stimulate genomic plasticity and environmental adaptation in yeast.
Collapse
Affiliation(s)
- Ying-Xuan Zhu
- Hainan Institute of Zhejiang University, Zhejiang University, Sanya, China
- Ocean College, Zhejiang University, Zhoushan, China
| | - Min He
- Hainan Institute of Zhejiang University, Zhejiang University, Sanya, China
| | - Ke-Jing Li
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ye-Ke Wang
- College of Life Science, Zhejiang University, Hangzhou, China
| | - Ning Qian
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ze-Fei Wang
- Hainan Institute of Zhejiang University, Zhejiang University, Sanya, China
| | - Huan Sheng
- Ocean College, Zhejiang University, Zhoushan, China
| | - Yang Sui
- Ocean College, Zhejiang University, Zhoushan, China
| | | | - Ke Zhang
- College of Life Science, Zhejiang University, Hangzhou, China
| | - Lei Qi
- Ocean College, Zhejiang University, Zhoushan, China
| | - Dao-Qiong Zheng
- Hainan Institute of Zhejiang University, Zhejiang University, Sanya, China
- Ocean College, Zhejiang University, Zhoushan, China
| |
Collapse
|
7
|
Al Zouabi L, Stefanutti M, Roumeliotis S, Le Meur G, Boumard B, Riddiford N, Rubanova N, Bohec M, Gervais L, Servant N, Bardin AJ. Molecular underpinnings and environmental drivers of loss of heterozygosity in Drosophila intestinal stem cells. Cell Rep 2023; 42:113485. [PMID: 38032794 DOI: 10.1016/j.celrep.2023.113485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/29/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023] Open
Abstract
During development and aging, genome mutation leading to loss of heterozygosity (LOH) can uncover recessive phenotypes within tissue compartments. This phenomenon occurs in normal human tissues and is prevalent in pathological genetic conditions and cancers. While studies in yeast have defined DNA repair mechanisms that can promote LOH, the predominant pathways and environmental triggers in somatic tissues of multicellular organisms are not well understood. Here, we investigate mechanisms underlying LOH in intestinal stem cells in Drosophila. Infection with the pathogenic bacteria, Erwinia carotovora carotovora 15, but not Pseudomonas entomophila, increases LOH frequency. Using whole genome sequencing of somatic LOH events, we demonstrate that they arise primarily via mitotic recombination. Molecular features and genetic evidence argue against a break-induced replication mechanism and instead support cross-over via double Holliday junction-based repair. This study provides a mechanistic understanding of mitotic recombination, an important mediator of LOH, and its effects on stem cells in vivo.
Collapse
Affiliation(s)
- Lara Al Zouabi
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Marine Stefanutti
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Spyridon Roumeliotis
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Gwenn Le Meur
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Benjamin Boumard
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Nick Riddiford
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Natalia Rubanova
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France; Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, PSL Research University, INSERM U900, 75005 Paris, France
| | - Mylène Bohec
- ICGex Next-Generation Sequencing Platform, Institut Curie, PSL Research University, 75005 Paris, France
| | - Louis Gervais
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Nicolas Servant
- Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, PSL Research University, INSERM U900, 75005 Paris, France
| | - Allison J Bardin
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France.
| |
Collapse
|
8
|
Overton MS, Guy SE, Chen X, Martsul A, Carolino K, Akbari OS, Meyer JR, Kryazhimskiy S. Upper Bound on the Mutational Burden Imposed by a CRISPR-Cas9 Gene-Drive Element. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569142. [PMID: 38076841 PMCID: PMC10705488 DOI: 10.1101/2023.11.28.569142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
CRISPR-Cas9 gene drives (CCGDs) are powerful tools for genetic control of wild populations, useful for eradication of disease vectors, conservation of endangered species and other applications. However, Cas9 alone and in a complex with gRNA can cause double-stranded DNA breaks at off-target sites, which could increase the mutational load and lead to loss of heterozygosity (LOH). These undesired effects raise potential concerns about the long-term evolutionary safety of CCGDs, but the magnitude of these effects is unknown. To estimate how the presence of a CCGD or a Cas9 alone in the genome affects the rates of LOH events and de novo mutations, we carried out a mutation accumulation experiment in yeast Saccharomyces cerevisiae. Despite its substantial statistical power, our experiment revealed no detectable effect of CCGD or Cas9 alone on the genome-wide rates of mutations or LOH events, suggesting that these rates are affected by less than 30%. Nevertheless, we found that Cas9 caused a slight but significant shift towards more interstitial and fewer terminal LOH events, and the CCGD caused a significant difference in the distribution of LOH events on Chromosome V. Taken together, our results show that these genetic elements impose a weak and likely localized additional mutational burden in the yeast model. Although the mutagenic effects of CCGDs need to be further evaluated in other systems, our results suggest that the effect of CCGDs on off-target mutation rates and genetic diversity may be acceptable.
Collapse
Affiliation(s)
- Michael S. Overton
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Sean E. Guy
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- Current address: Bionano Genomics, San Diego, CA 92121
| | - Xingsen Chen
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- Current address: Department of Entomology, University of Arizona, Tucson, Arizona, USA
| | - Alena Martsul
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- Current address: Illumina Inc., San Diego, CA 92122
| | - Krypton Carolino
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Omar S. Akbari
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin R. Meyer
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| |
Collapse
|
9
|
Crandall JG, Fisher KJ, Sato TK, Hittinger CT. Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism. PLoS Biol 2023; 21:e3001909. [PMID: 37943740 PMCID: PMC10635434 DOI: 10.1371/journal.pbio.3001909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 10/06/2023] [Indexed: 11/12/2023] Open
Abstract
Ploidy is an evolutionarily labile trait, and its variation across the tree of life has profound impacts on evolutionary trajectories and life histories. The immediate consequences and molecular causes of ploidy variation on organismal fitness are frequently less clear, although extreme mating type skews in some fungi hint at links between cell type and adaptive traits. Here, we report an unusual recurrent ploidy reduction in replicate populations of the budding yeast Saccharomyces eubayanus experimentally evolved for improvement of a key metabolic trait, the ability to use maltose as a carbon source. We find that haploids have a substantial, but conditional, fitness advantage in the absence of other genetic variation. Using engineered genotypes that decouple the effects of ploidy and cell type, we show that increased fitness is primarily due to the distinct transcriptional program deployed by haploid-like cell types, with a significant but smaller contribution from absolute ploidy. The link between cell-type specification and the carbon metabolism adaptation can be traced to the noncanonical regulation of a maltose transporter by a haploid-specific gene. This study provides novel mechanistic insight into the molecular basis of an environment-cell type fitness interaction and illustrates how selection on traits unexpectedly linked to ploidy states or cell types can drive karyotypic evolution in fungi.
Collapse
Affiliation(s)
- Johnathan G. Crandall
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kaitlin J. Fisher
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
10
|
Del Olmo V, Mixão V, Fotedar R, Saus E, Al Malki A, Księżopolska E, Nunez-Rodriguez JC, Boekhout T, Gabaldón T. Origin of fungal hybrids with pathogenic potential from warm seawater environments. Nat Commun 2023; 14:6919. [PMID: 37903766 PMCID: PMC10616089 DOI: 10.1038/s41467-023-42679-4] [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: 05/30/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Hybridisation is a common event in yeasts often leading to genomic variability and adaptation. The yeast Candida orthopsilosis is a human-associated opportunistic pathogen belonging to the Candida parapsilosis species complex. Most C. orthopsilosis clinical isolates are hybrids resulting from at least four independent crosses between two parental lineages, of which only one has been identified. The rare presence or total absence of parentals amongst clinical isolates is hypothesised to be a consequence of a reduced pathogenicity with respect to their hybrids. Here, we sequence and analyse the genomes of environmental C. orthopsilosis strains isolated from warm marine ecosystems. We find that a majority of environmental isolates are hybrids, phylogenetically closely related to hybrid clinical isolates. Furthermore, we identify the missing parental lineage, thus providing a more complete overview of the genomic evolution of this species. Additionally, we discover phenotypic differences between the two parental lineages, as well as between parents and hybrids, under conditions relevant for pathogenesis. Our results suggest a marine origin of C. orthopsilosis hybrids, with intrinsic pathogenic potential, and pave the way to identify pre-existing environmental adaptations that rendered hybrids more prone than parental lineages to colonise and infect the mammalian host.
Collapse
Affiliation(s)
- Valentina Del Olmo
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Verónica Mixão
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, P.O Box 20022, Doha, Qatar
| | - Ester Saus
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amina Al Malki
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, P.O Box 20022, Doha, Qatar
| | - Ewa Księżopolska
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Juan Carlos Nunez-Rodriguez
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Teun Boekhout
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Toni Gabaldón
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain.
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain.
- , Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
| |
Collapse
|
11
|
Sharp NP, Smith DR, Driscoll G, Sun K, Vickerman CM, Martin SCT. Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast. Genome Biol Evol 2023; 15:evad179. [PMID: 37847861 PMCID: PMC10581546 DOI: 10.1093/gbe/evad179] [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] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
The ribosomal DNA array in Saccharomyces cerevisiae consists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that unselected mutations elsewhere in the genome can disrupt copy number maintenance. In consequence, copy number generally declines gradually, consistent with a previously proposed model of rDNA maintenance where a downward mutational bias is normally compensated by mechanisms that increase copy number when it is low. This pattern holds across ploidy levels and strains in the standard lab environment but differs under some stressful conditions. We identify several alleles, gene categories, and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself are distinct from the rest of the genome and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.
Collapse
Affiliation(s)
- Nathaniel P Sharp
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Denise R Smith
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gregory Driscoll
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kexin Sun
- Present address: Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Sterling C T Martin
- Present address: Department of Biology, Washington University, St. Louis, Missouri, USA
| |
Collapse
|
12
|
Balarezo-Cisneros LN, Timouma S, Hanak A, Currin A, Valle F, Delneri D. High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries. Commun Biol 2023; 6:918. [PMID: 37679437 PMCID: PMC10484914 DOI: 10.1038/s42003-023-05285-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Kazachstania bulderi is a non-conventional yeast species able to grow efficiently on glucose and δ-gluconolactone at low pH. These unique traits make K. bulderi an ideal candidate for use in sustainable biotechnology processes including low pH fermentations and the production of green chemicals including organic acids. To accelerate strain development with this species, detailed information of its genetics is needed. Here, by employing long read sequencing we report a high-quality phased genome assembly for three strains of K. bulderi species, including the type strain. The sequences were assembled into 12 chromosomes with a total length of 14 Mb, and the genome was fully annotated at structural and functional levels, including allelic and structural variants, ribosomal array and mating type locus. This high-quality reference genome provides a resource to advance our fundamental knowledge of biotechnologically relevant non-conventional yeasts and to support the development of genetic tools for manipulating such strains towards their use as production hosts in biotechnological processes.
Collapse
Affiliation(s)
| | - Soukaina Timouma
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Alistair Hanak
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew Currin
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | - Daniela Delneri
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| |
Collapse
|
13
|
Qi L, Zhu YX, Wang YK, Tang XX, Li KJ, He M, Sui Y, Wang PM, Zheng DQ, Zhang K. Nonlethal Furfural Exposure Causes Genomic Alterations and Adaptability Evolution in Saccharomyces cerevisiae. Microbiol Spectr 2023; 11:e0121623. [PMID: 37395645 PMCID: PMC10434202 DOI: 10.1128/spectrum.01216-23] [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: 03/20/2023] [Accepted: 06/09/2023] [Indexed: 07/04/2023] Open
Abstract
Furfural is a major inhibitor found in lignocellulosic hydrolysate, a promising feedstock for the biofermentation industry. In this study, we aimed to investigate the potential impact of this furan-derived chemical on yeast genome integrity and phenotypic evolution by using genetic screening systems and high-throughput analyses. Our results showed that the rates of aneuploidy, chromosomal rearrangements (including large deletions and duplications), and loss of heterozygosity (LOH) increased by 50-fold, 23-fold, and 4-fold, respectively, when yeast cells were cultured in medium containing a nonlethal dose of furfural (0.6 g/L). We observed significantly different ratios of genetic events between untreated and furfural-exposed cells, indicating that furfural exposure induced a unique pattern of genomic instability. Furfural exposure also increased the proportion of CG-to-TA and CG-to-AT base substitutions among point mutations, which was correlated with DNA oxidative damage. Interestingly, although monosomy of chromosomes often results in the slower growth of yeast under spontaneous conditions, we found that monosomic chromosome IX contributed to the enhanced furfural tolerance. Additionally, terminal LOH events on the right arm of chromosome IV, which led to homozygosity of the SSD1 allele, were associated with furfural resistance. This study sheds light on the mechanisms underlying the influence of furfural on yeast genome integrity and adaptability evolution. IMPORTANCE Industrial microorganisms are often exposed to multiple environmental stressors and inhibitors during their application. This study demonstrates that nonlethal concentrations of furfural in the culture medium can significantly induce genome instability in the yeast Saccharomyces cerevisiae. Notably, furfural-exposed yeast cells displayed frequent chromosome aberrations, indicating the potent teratogenicity of this inhibitor. We identified specific genomic alterations, including monosomic chromosome IX and loss of heterozygosity of the right arm of chromosome IV, that confer furfural tolerance to a diploid S. cerevisiae strain. These findings enhance our understanding of how microorganisms evolve and adapt to stressful environments and offer insights for developing strategies to improve their performance in industrial applications.
Collapse
Affiliation(s)
- Lei Qi
- Donghai Laboratory, Zhoushan, China
- Ocean College, Zhejiang University, Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | | | - Ye-Ke Wang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | | | - Ke-Jing Li
- Ocean College, Zhejiang University, Zhoushan, China
| | - Min He
- Ocean College, Zhejiang University, Zhoushan, China
| | - Yang Sui
- Donghai Laboratory, Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Pin-Mei Wang
- Donghai Laboratory, Zhoushan, China
- Ocean College, Zhejiang University, Zhoushan, China
| | - Dao-Qiong Zheng
- Donghai Laboratory, Zhoushan, China
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ke Zhang
- College of Life Science, Zhejiang University, Hangzhou, China
| |
Collapse
|
14
|
Smukowski Heil C. Loss of Heterozygosity and Its Importance in Evolution. J Mol Evol 2023; 91:369-377. [PMID: 36752826 PMCID: PMC10276065 DOI: 10.1007/s00239-022-10088-8] [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: 09/14/2022] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
Loss of heterozygosity (LOH) is a mitotic recombination event that converts heterozygous loci to homozygous loci. This mutation event is widespread in organisms that have asexual reproduction like budding yeasts, and is also an important and frequent mutation event in tumorigenesis. Mutation accumulation studies have demonstrated that LOH occurs at a rate higher than the point mutation rate, and can impact large portions of the genome. Laboratory evolution experiments of heterozygous yeasts have revealed that LOH often unmasks beneficial recessive alleles that can confer large fitness advantages. Here, I highlight advances in understanding dominance, fitness, and phenotypes in laboratory evolved heterozygous yeast strains. I discuss best practices for detecting LOH in intraspecific and interspecific evolved clones and populations. Utilizing heterozygous strain backgrounds in laboratory evolution experiments offers an opportunity to advance our understanding of this important mutation type in shaping adaptation and genome evolution in wild, domesticated, and clinical populations.
Collapse
Affiliation(s)
- Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
| |
Collapse
|
15
|
Kadyrova LY, Mieczkowski PA, Kadyrov FA. Genome-wide contributions of the MutSα- and MutSβ-dependent DNA mismatch repair pathways to the maintenance of genetic stability in S. cerevisiae. J Biol Chem 2023; 299:104705. [PMID: 37059180 DOI: 10.1016/j.jbc.2023.104705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/07/2023] [Accepted: 04/08/2023] [Indexed: 04/16/2023] Open
Abstract
The DNA mismatch repair (MMR) system is a major DNA repair system that suppresses inherited and sporadic cancers in humans. In eukaryotes the MutSα-dependent and MutSβ-dependent MMR pathways correct DNA polymerase errors. Here, we investigated these two pathways on a whole-genome level in S. cerevisiae. We found that inactivation of MutSα-dependent MMR by deletion of the MSH6 gene increases the genome-wide mutation rate by ∼17-fold, and loss of MutSβ-dependent MMR via deletion of MSH3 elevates the genome-wide mutation rate by ∼4-fold. We also found that MutSα-dependent MMR does not show a preference for protecting coding or noncoding DNA from mutations, whereas MutSβ-dependent MMR preferentially protects noncoding DNA from mutations. The most frequent mutations in the msh6Δ strain are C>T transitions, whereas 1-6-bp deletions are the most common genetic alterations in the msh3Δ strain. Strikingly, MutSα-dependent MMR is more important than MutSβ-dependent MMR for protection from 1-bp insertions, while MutSβ-dependent MMR has a more critical role in the defense against 1-bp deletions and 2-6-bp indels. We also determined that a mutational signature of yeast MSH6 loss is similar to mutational signatures of human MMR deficiency. Furthermore, our analysis showed that compared to other 5'-NCN-3' trinucleotides, 5'-GCA-3' trinucleotides are at the highest risk of accumulating C>T transitions at the central position in the msh6Δ cells and that the presence of a G/A base at the -1 position is important for the efficient MutSα-dependent suppression of C>T transitions. Our results highlight key differences between the roles of the MutSα-dependent and MutSβ-dependent MMR pathways.
Collapse
Affiliation(s)
- Lyudmila Y Kadyrova
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Farid A Kadyrov
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| |
Collapse
|
16
|
Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements. PLoS Genet 2023; 19:e1010590. [PMID: 36701275 PMCID: PMC9879454 DOI: 10.1371/journal.pgen.1010590] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/21/2022] [Indexed: 01/27/2023] Open
Abstract
Although homologous recombination between transposable elements can drive genomic evolution in yeast by facilitating chromosomal rearrangements, the details of the underlying mechanisms are not fully clarified. In the genome of the yeast Saccharomyces cerevisiae, the most common class of transposon is the retrotransposon Ty1. Here, we explored how Cas9-induced double-strand breaks (DSBs) directed to Ty1 elements produce genomic alterations in this yeast species. Following Cas9 induction, we observed a significant elevation of chromosome rearrangements such as deletions, duplications and translocations. In addition, we found elevated rates of mitotic recombination, resulting in loss of heterozygosity. Using Southern analysis coupled with short- and long-read DNA sequencing, we revealed important features of recombination induced in retrotransposons. Almost all of the chromosomal rearrangements reflect the repair of DSBs at Ty1 elements by non-allelic homologous recombination; clustered Ty elements were hotspots for chromosome rearrangements. In contrast, a large proportion (about three-fourths) of the allelic mitotic recombination events have breakpoints in unique sequences. Our analysis suggests that some of the latter events reflect extensive processing of the broken ends produced in the Ty element that extend into unique sequences resulting in break-induced replication. Finally, we found that haploid and diploid strain have different preferences for the pathways used to repair double-stranded DNA breaks. Our findings demonstrate the importance of DNA lesions in retrotransposons in driving genome evolution.
Collapse
|
17
|
López-Cortegano E, Craig RJ, Chebib J, Balogun EJ, Keightley PD. Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii. Genome Res 2023; 33:45-60. [PMID: 36617667 PMCID: PMC9977147 DOI: 10.1101/gr.276957.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Genetic variation originates from several types of spontaneous mutation, including single-nucleotide substitutions, short insertions and deletions (indels), and larger structural changes. Structural mutations (SMs) drive genome evolution and are thought to play major roles in evolutionary adaptation, speciation, and genetic disease, including cancers. Sequencing of mutation accumulation (MA) lines has provided estimates of rates and spectra of single-nucleotide and indel mutations in many species, yet the rate of new SMs is largely unknown. Here, we use long-read sequencing to determine the full mutation spectrum in MA lines derived from two strains (CC-1952 and CC-2931) of the green alga Chlamydomonas reinhardtii The SM rate is highly variable between strains and between MA lines, and SMs represent a substantial proportion of all mutations in both strains (CC-1952 6%; CC-2931 12%). The SM spectra differ considerably between the two strains, with almost all inversions and translocations occurring in CC-2931 MA lines. This variation is associated with heterogeneity in the number and type of active transposable elements (TEs), which comprise major proportions of SMs in both strains (CC-1952 22%; CC-2931 38%). In CC-2931, a Crypton and a previously undescribed type of DNA element have caused 71% of chromosomal rearrangements, whereas in CC-1952, a Dualen LINE is associated with 87% of duplications. Other SMs, notably large duplications in CC-2931, are likely products of various double-strand break repair pathways. Our results show that diverse types of SMs occur at substantial rates, and support prominent roles for SMs and TEs in evolution.
Collapse
Affiliation(s)
- Eugenio López-Cortegano
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Rory J Craig
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- California Institute for Quantitative Biosciences, UC Berkeley, Berkeley, California 94720, USA
| | - Jobran Chebib
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Eniolaye J Balogun
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario ON M5S 3B2, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga ON L5L 1C6, Canada
| | - Peter D Keightley
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| |
Collapse
|
18
|
Rizzo M, Soisangwan N, Vega-Estevez S, Price RJ, Uyl C, Iracane E, Shaw M, Soetaert J, Selmecki A, Buscaino A. Stress combined with loss of the Candida albicans SUMO protease Ulp2 triggers selection of aneuploidy via a two-step process. PLoS Genet 2022; 18:e1010576. [PMID: 36574460 PMCID: PMC9829183 DOI: 10.1371/journal.pgen.1010576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/09/2023] [Accepted: 12/16/2022] [Indexed: 12/29/2022] Open
Abstract
A delicate balance between genome stability and instability ensures genome integrity while generating genetic diversity, a critical step for evolution. Indeed, while excessive genome instability is harmful, moderated genome instability can drive adaptation to novel environments by maximising genetic variation. Candida albicans, a human fungal pathogen that colonises different parts of the human body, adapts rapidly and frequently to different hostile host microenvironments. In this organism, the ability to generate large-scale genomic variation is a key adaptative mechanism triggering dangerous infections even in the presence of antifungal drugs. Understanding how fitter novel karyotypes are selected is key to determining how C. albicans and other microbial pathogens establish infections. Here, we identified the SUMO protease Ulp2 as a regulator of C. albicans genome integrity through genetic screening. Deletion of ULP2 leads to increased genome instability, enhanced genome variation and reduced fitness in the absence of additional stress. The combined stress caused by the lack of ULP2 and antifungal drug treatment leads to the selection of adaptive segmental aneuploidies that partially rescue the fitness defects of ulp2Δ/Δ cells. Short and long-read genomic sequencing demonstrates that these novel genotypes are selected via a two-step process leading to the formation of novel chromosomal fragments with breakpoints at microhomology regions and DNA repeats.
Collapse
Affiliation(s)
- Marzia Rizzo
- University of Kent, School of Biosciences, Kent Fungal Group, Canterbury Kent, United Kingdom
| | - Natthapon Soisangwan
- University of Minnesota, Department of Microbiology and Immunology, Minneapolis, Minnesota, United States of America
| | - Samuel Vega-Estevez
- University of Kent, School of Biosciences, Kent Fungal Group, Canterbury Kent, United Kingdom
| | | | - Chloe Uyl
- University of Kent, School of Biosciences, Kent Fungal Group, Canterbury Kent, United Kingdom
| | - Elise Iracane
- University of Kent, School of Biosciences, Kent Fungal Group, Canterbury Kent, United Kingdom
| | - Matt Shaw
- University of Kent, School of Biosciences, Kent Fungal Group, Canterbury Kent, United Kingdom
| | - Jan Soetaert
- Blizard Advanced Light Microscopy (BALM), Queen Mary University of London, United Kingdom
| | - Anna Selmecki
- University of Minnesota, Department of Microbiology and Immunology, Minneapolis, Minnesota, United States of America
| | - Alessia Buscaino
- University of Kent, School of Biosciences, Kent Fungal Group, Canterbury Kent, United Kingdom
- * E-mail:
| |
Collapse
|
19
|
Melde RH, Bao K, Sharp NP. Recent insights into the evolution of mutation rates in yeast. Curr Opin Genet Dev 2022; 76:101953. [PMID: 35834945 PMCID: PMC9491374 DOI: 10.1016/j.gde.2022.101953] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 02/08/2023]
Abstract
Mutation is the origin of all genetic variation, good and bad. The mutation process can evolve in response to mutations, positive or negative selection, and genetic drift, but how these forces contribute to mutation-rate variation is an unsolved problem at the heart of genetics research. Mutations can be challenging to measure, but genome sequencing and other tools have allowed for the collection of larger and more detailed datasets, particularly in the yeast-model system. We review key hypotheses for the evolution of mutation rates and describe recent advances in understanding variation in mutational properties within and among yeast species. The multidimensional spectrum of mutations is increasingly recognized as holding valuable clues about how this important process evolves.
Collapse
Affiliation(s)
- Robert H Melde
- Department of Genetics, University of Wisconsin-Madison, USA.
| | - Kevin Bao
- Department of Genetics, University of Wisconsin-Madison, USA
| | - Nathaniel P Sharp
- Department of Genetics, University of Wisconsin-Madison, USA. https://twitter.com/@sharpnath
| |
Collapse
|
20
|
Ban S, El-Sharkawy I, Zhao J, Fei Z, Xu K. An apple somatic mutation of delayed fruit maturation date is primarily caused by a retrotransposon insertion-associated large deletion. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1609-1625. [PMID: 35861682 DOI: 10.1111/tpj.15911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/03/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Somatic mutations may alter important traits in tree fruits, such as fruit color, size and maturation date. Autumn Gala (AGala), a somatic mutation from apple cultivar Gala, matures 4 weeks later than Gala. To understand the mechanisms underlying the delayed maturation, RNA-seq analyses were conducted with fruit sampled at 13 (Gala) and 16 (AGala) time-points during their growth and development. Weighted gene co-expression network analysis (WGCNA) of 23 372 differentially expressed genes resulted in 25 WGCNA modules. Of these, modules 1 (r = -0.98, P = 2E-21) and 2 (r = -0.52, P = 0.004), which were suppressed in AGala, were correlated with fruit maturation date. Surprisingly, 77 of the 152 member genes in module 1 were harbored in a 2.8-Mb genomic region on chromosome 6 that was deleted and replaced by a 10.7-kb gypsy-like retrotransposon (Gy-36) from chromosome 7 in AGala. Among the 77 member genes, MdACT7 was the most suppressed (by 10.5-fold) in AGala due to a disruptive 2.5-kb insertion in coding sequence. Moreover, MdACT7 is the exclusive apple counterpart of Arabidopsis ACT7 known of essential roles in plant development, and the functional allele MdACT7, which was lost to the deletion in AGala, was associated with early fruit maturation in 268 apple accessions. Overexpressing alleles MdACT7 and Mdact7 in an Arabidopsis act7 line showed that MdACT7 largely rescued its stunted growth and delayed initial flowering while Mdact7 did not. Therefore, the 2.8-Mb hemizygous deletion is largely genetically causal for fruit maturation delay in AGala, and the total loss of MdACT7 might have contributed to the phenotype.
Collapse
Affiliation(s)
- Seunghyun Ban
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, New York, USA
| | - Islam El-Sharkawy
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, New York, USA
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York, USA
- US Department of Agriculture, Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, New York, USA
| |
Collapse
|
21
|
Sui Y, Epstein A, Dominska M, Zheng DQ, Petes T, Klein H. Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides. Nucleic Acids Res 2022; 50:6890-6902. [PMID: 35748861 PMCID: PMC9262587 DOI: 10.1093/nar/gkac536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022] Open
Abstract
Ribonucleotides can be incorporated into DNA during replication by the replicative DNA polymerases. These aberrant DNA subunits are efficiently recognized and removed by Ribonucleotide Excision Repair, which is initiated by the heterotrimeric enzyme RNase H2. While RNase H2 is essential in higher eukaryotes, the yeast Saccharomyces cerevisiae can survive without RNase H2 enzyme, although the genome undergoes mutation, recombination and other genome instability events at an increased rate. Although RNase H2 can be considered as a protector of the genome from the deleterious events that can ensue from recognition and removal of embedded ribonucleotides, under conditions of high ribonucleotide incorporation and retention in the genome in a RNase H2-negative strain, sudden introduction of active RNase H2 causes massive DNA breaks and genome instability in a condition which we term 'ribodysgenesis'. The DNA breaks and genome instability arise solely from RNase H2 cleavage directed to the ribonucleotide-containing genome. Survivors of ribodysgenesis have massive loss of heterozygosity events stemming from recombinogenic lesions on the ribonucleotide-containing DNA, with increases of over 1000X from wild-type. DNA breaks are produced over one to two divisions and subsequently cells adapt to RNase H2 and ribonucleotides in the genome and grow with normal levels of genome instability.
Collapse
Affiliation(s)
- Yang Sui
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan 316021, China,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anastasiya Epstein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dao-Qiong Zheng
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan 316021, China,Hainan Institute of Zhejiang University, Sanya 572000, China,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hannah L Klein
- To whom correspondence should be addressed. Tel: +1 212 263 5778;
| |
Collapse
|
22
|
Gong FL, Han J, Li S. MULTI-SCULPT: Multiplex Integration via Selective, CRISPR-Mediated, Ultralong Pathway Transformation in Yeast for Plant Natural Product Synthesis. ACS Synth Biol 2022; 11:2484-2495. [PMID: 35737816 DOI: 10.1021/acssynbio.2c00135] [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] [Indexed: 12/22/2022]
Abstract
Yeast has been a versatile model host for complex and valuable natural product biosynthesis via the reconstruction of heterologous biosynthetic pathways. Recent advances in natural product pathway elucidation have uncovered many large and complicated plant pathways that contain 10-30 genes for the biosynthesis of structurally complex, valuable natural products. However, the ability to reconstruct ultralong pathways efficiently in yeast does not match the increasing demand for valuable plant natural product biomanufacturing. Here, we developed a one-pot, multigene pathway integration method in yeast, named MULTI-SCULPT for multiplex integration via selective, CRISPR-mediated, ultralong pathway transformation. Leveraging multilocus genomic disruption via CRISPR/Cas9, newly developed native and synthetic genetic parts, and fine-tuned gene integration and characterization methods, we managed to integrate 21 DNA inserts that contain a 12-gene plant isoflavone biosynthetic pathway into yeast with a 90-100% success rate in 12 days. This method enables fast and efficient ultralong biosynthetic pathway integration and can allow for the fast iterative integration of even longer pathways in the future. Ultimately, this method will accelerate combinatorial optimization of elucidated plant natural product pathways and accelerate putative pathway characterization heterologously.
Collapse
Affiliation(s)
- Franklin Leyang Gong
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jianing Han
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Sijin Li
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
23
|
Heasley LR, Argueso JL. Bursts of Genomic Instability Potentiate Phenotypic and Genomic Diversification in Saccharomyces cerevisiae. Front Genet 2022; 13:912851. [PMID: 35783258 PMCID: PMC9247159 DOI: 10.3389/fgene.2022.912851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
How microbial cells leverage their phenotypic potential to survive in a changing environment is a complex biological problem, with important implications for pathogenesis and species evolution. Stochastic phenotype switching, a particularly fascinating adaptive approach observed in numerous species across the tree of life, introduces phenotypic diversity into a population through mechanisms which have remained difficult to define. Here we describe our investigations into the mechanistic basis of colony morphology phenotype switching which occurs in populations of a pathogenic isolate of Saccharomyces cerevisiae, YJM311. We observed that clonal populations of YJM311 cells produce variant colonies that display altered morphologies and, using whole genome sequence analysis, discovered that these variant clones harbored an exceptional collection of karyotypes newly altered by de novo structural genomic variations (SVs). Overall, our analyses indicate that copy number alterations, more often than changes in allelic identity, provide the causative basis of this phenotypic variation. Individual variants carried between 1 and 16 de novo copy number variations, most of which were whole chromosomal aneuploidies. Notably, we found that the inherent stability of the diploid YJM311 genome is comparable to that of domesticated laboratory strains, indicating that the collections of SVs harbored by variant clones did not arise by a chronic chromosomal instability (CIN) mechanism. Rather, our data indicate that these variant clones acquired such complex karyotypic configurations simultaneously, during stochastic and transient episodes of punctuated systemic genomic instability (PSGI). Surprisingly, we found that the majority of these highly altered variant karyotypes were propagated with perfect fidelity in long-term passaging experiments, demonstrating that high aneuploidy burdens can often be conducive with prolonged genomic integrity. Together, our results demonstrate that colony morphology switching in YJM311 is driven by a stochastic process in which genome stability and plasticity are integrally coupled to phenotypic heterogeneity. Consequently, this system simultaneously introduces both phenotypic and genomic variation into a population of cells, which can, in turn perpetuate population diversity for many generations thereafter.
Collapse
|
24
|
Wang WY, Cai HQ, Qu SY, Lin WH, Liang CC, Liu H, Xie ZX, Yuan YJ. Genomic Variation-Mediating Fluconazole Resistance in Yeast. Biomolecules 2022; 12:biom12060845. [PMID: 35740970 PMCID: PMC9221393 DOI: 10.3390/biom12060845] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
Fungal infections pose a serious and growing threat to public health. These infections can be treated with antifungal drugs by killing hazardous fungi in the body. However, the resistance can develop over time when fungi are exposed to antifungal drugs by generating genomic variations, including mutation, aneuploidy, and loss of heterozygosity. The variations could reduce the binding affinity of a drug to its target or block the pathway through which drugs exert their activity. Here, we review genomic variation-mediating fluconazole resistance in the yeast Candida, with the hope of highlighting the functional consequences of genomic variations for the antifungal resistance.
Collapse
|
25
|
Avecilla G, Chuong JN, Li F, Sherlock G, Gresham D, Ram Y. Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics. PLoS Biol 2022; 20:e3001633. [PMID: 35622868 PMCID: PMC9140244 DOI: 10.1371/journal.pbio.3001633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/14/2022] [Indexed: 11/24/2022] Open
Abstract
The rate of adaptive evolution depends on the rate at which beneficial mutations are introduced into a population and the fitness effects of those mutations. The rate of beneficial mutations and their expected fitness effects is often difficult to empirically quantify. As these 2 parameters determine the pace of evolutionary change in a population, the dynamics of adaptive evolution may enable inference of their values. Copy number variants (CNVs) are a pervasive source of heritable variation that can facilitate rapid adaptive evolution. Previously, we developed a locus-specific fluorescent CNV reporter to quantify CNV dynamics in evolving populations maintained in nutrient-limiting conditions using chemostats. Here, we use CNV adaptation dynamics to estimate the rate at which beneficial CNVs are introduced through de novo mutation and their fitness effects using simulation-based likelihood-free inference approaches. We tested the suitability of 2 evolutionary models: a standard Wright-Fisher model and a chemostat model. We evaluated 2 likelihood-free inference algorithms: the well-established Approximate Bayesian Computation with Sequential Monte Carlo (ABC-SMC) algorithm, and the recently developed Neural Posterior Estimation (NPE) algorithm, which applies an artificial neural network to directly estimate the posterior distribution. By systematically evaluating the suitability of different inference methods and models, we show that NPE has several advantages over ABC-SMC and that a Wright-Fisher evolutionary model suffices in most cases. Using our validated inference framework, we estimate the CNV formation rate at the GAP1 locus in the yeast Saccharomyces cerevisiae to be 10-4.7 to 10-4 CNVs per cell division and a fitness coefficient of 0.04 to 0.1 per generation for GAP1 CNVs in glutamine-limited chemostats. We experimentally validated our inference-based estimates using 2 distinct experimental methods-barcode lineage tracking and pairwise fitness assays-which provide independent confirmation of the accuracy of our approach. Our results are consistent with a beneficial CNV supply rate that is 10-fold greater than the estimated rates of beneficial single-nucleotide mutations, explaining the outsized importance of CNVs in rapid adaptive evolution. More generally, our study demonstrates the utility of novel neural network-based likelihood-free inference methods for inferring the rates and effects of evolutionary processes from empirical data with possible applications ranging from tumor to viral evolution.
Collapse
Affiliation(s)
- Grace Avecilla
- Department of Biology, New York University, New York, New York, United States of America
- Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Julie N. Chuong
- Department of Biology, New York University, New York, New York, United States of America
- Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Fangfei Li
- Department of Genetics, Stanford University, California, Stanford, United States of America
| | - Gavin Sherlock
- Department of Genetics, Stanford University, California, Stanford, United States of America
| | - David Gresham
- Department of Biology, New York University, New York, New York, United States of America
- Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
26
|
Global genomic instability caused by reduced expression of DNA polymerase ε in yeast. Proc Natl Acad Sci U S A 2022; 119:e2119588119. [PMID: 35290114 PMCID: PMC8944251 DOI: 10.1073/pnas.2119588119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceAlthough most studies of the genetic regulation of genome stability involve an analysis of mutations within the coding sequences of genes required for DNA replication or DNA repair, recent studies in yeast show that reduced levels of wild-type enzymes can also produce a mutator phenotype. By whole-genome sequencing and other methods, we find that reduced levels of the wild-type DNA polymerase ε in yeast greatly increase the rates of mitotic recombination, aneuploidy, and single-base mutations. The observed pattern of genome instability is different from those observed in yeast strains with reduced levels of the other replicative DNA polymerases, Pol α and Pol δ. These observations are relevant to our understanding of cancer and other diseases associated with genetic instability.
Collapse
|
27
|
Tutaj H, Pirog A, Tomala K, Korona R. Genome-scale patterns in the loss of heterozygosity incidence in Saccharomyces cerevisiae. Genetics 2022; 221:6536968. [PMID: 35212738 PMCID: PMC9071580 DOI: 10.1093/genetics/iyac032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/17/2022] [Indexed: 02/07/2023] Open
Abstract
Former studies have established that loss of heterozygosity can be a key driver of sequence evolution in unicellular eukaryotes and tissues of metazoans. However, little is known about whether the distribution of loss of heterozygosity events is largely random or forms discernible patterns across genomes. To initiate our experiments, we introduced selectable markers to both arms of all chromosomes of the budding yeast. Subsequent extensive assays, repeated over several genetic backgrounds and environments, provided a wealth of information on the genetic and environmental determinants of loss of heterozygosity. Three findings stand out. First, the number of loss of heterozygosity events per unit time was more than 25 times higher for growing than starving cells. Second, loss of heterozygosity was most frequent when regions of homology around a recombination site were identical, about a half-% sequence divergence was sufficient to reduce its incidence. Finally, the density of loss of heterozygosity events was highly dependent on the genome's physical architecture. It was several-fold higher on short chromosomal arms than on long ones. Comparably large differences were seen within a single arm where regions close to a centromere were visibly less affected than regions close, though usually not strictly adjacent, to a telomere. We suggest that the observed uneven distribution of loss of heterozygosity events could have been caused not only by an uneven density of initial DNA damages. Location-depended differences in the mode of DNA repair, or its effect on fitness, were likely to operate as well.
Collapse
Affiliation(s)
- Hanna Tutaj
- Institute of Environmental Sciences, Jagiellonian University, 30-387 Cracow, Poland
| | - Adrian Pirog
- Institute of Environmental Sciences, Jagiellonian University, 30-387 Cracow, Poland
| | - Katarzyna Tomala
- Institute of Environmental Sciences, Jagiellonian University, 30-387 Cracow, Poland
| | - Ryszard Korona
- Institute of Environmental Sciences, Jagiellonian University, 30-387 Cracow, Poland,Corresponding author: Institute of Environmental Sciences, Jagiellonian University, Gronostajowa Street 7, 30-387 Krakow, Poland.
| |
Collapse
|
28
|
Potapova NA, Kondrashov AS, Mirkin SM. Characteristics and possible mechanisms of formation of microinversions distinguishing human and chimpanzee genomes. Sci Rep 2022; 12:591. [PMID: 35022450 PMCID: PMC8755829 DOI: 10.1038/s41598-021-04621-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/28/2021] [Indexed: 12/02/2022] Open
Abstract
Genomic inversions come in various sizes. While long inversions are relatively easy to identify by aligning high-quality genome sequences, unambiguous identification of microinversions is more problematic. Here, using a set of extra stringent criteria to distinguish microinversions from other mutational events, we describe microinversions that occurred after the divergence of humans and chimpanzees. In total, we found 59 definite microinversions that range from 17 to 33 nucleotides in length. In majority of them, human genome sequences matched exactly the reverse-complemented chimpanzee genome sequences, implying that the inverted DNA segment was copied precisely. All these microinversions were flanked by perfect or nearly perfect inverted repeats pointing to their key role in their formation. Template switching at inverted repeats during DNA replication was previously discussed as a possible mechanism for the microinversion formation. However, many of definite microinversions found by us cannot be easily explained via template switching owing to the combination of the short length and imperfect nature of their flanking inverted repeats. We propose a novel, alternative mechanism that involves repair of a double-stranded break within the inverting segment via microhomology-mediated break-induced replication, which can consistently explain all definite microinversion events.
Collapse
Affiliation(s)
- Nadezhda A Potapova
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia, 127051.
| | - Alexey S Kondrashov
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
| |
Collapse
|
29
|
Michelotti LA, Sun S, Heitman J, James TY. Clonal evolution in serially passaged Cryptococcus neoformans × deneoformans hybrids reveals a heterogenous landscape of genomic change. Genetics 2022; 220:iyab142. [PMID: 34849836 PMCID: PMC8733418 DOI: 10.1093/genetics/iyab142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/25/2021] [Indexed: 11/14/2022] Open
Abstract
Cryptococcus neoformans × deneoformans hybrids (also known as serotype AD hybrids) are basidiomycete yeasts that are common in a clinical setting. Like many hybrids, the AD hybrids are largely locked at the F1 stage and are mostly unable to undergo normal meiotic reproduction. However, these F1 hybrids, which display a high (∼10%) sequence divergence are known to genetically diversify through mitotic recombination and aneuploidy, and this diversification may be adaptive. In this study, we evolved a single AD hybrid genotype in six diverse environments by serial passaging and then used genome resequencing of evolved clones to determine evolutionary mechanisms of adaptation. The evolved clones generally increased fitness after passaging, accompanied by an average of 3.3 point mutations, 2.9 loss of heterozygosity (LOH) events, and 0.7 trisomic chromosomes per clone. LOH occurred through nondisjunction of chromosomes, crossing over consistent with break-induced replication, and gene conversion, in that order of prevalence. The breakpoints of these recombination events were significantly associated with regions of the genome with lower sequence divergence between the parents and clustered in sub-telomeric regions, notably in regions that had undergone introgression between the two parental species. Parallel evolution was observed, particularly through repeated homozygosity via nondisjunction, yet there was little evidence of environment-specific parallel change for either LOH, aneuploidy, or mutations. These data show that AD hybrids have both a remarkable genomic plasticity and yet are challenged in the ability to recombine through sequence divergence and chromosomal rearrangements, a scenario likely limiting the precision of adaptive evolution to novel environments.
Collapse
Affiliation(s)
- Lucas A Michelotti
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
30
|
Jinks-Robertson S, Petes TD. Mitotic recombination in yeast: what we know and what we don't know. Curr Opin Genet Dev 2021; 71:78-85. [PMID: 34311384 PMCID: PMC8671248 DOI: 10.1016/j.gde.2021.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022]
Abstract
Saccharomyces cerevisiae is at the forefront of defining the major recombination mechanisms/models that repair targeted double-strand breaks during mitosis. Each of these models predicts specific molecular intermediates as well as genetic outcomes. Recent use of single-nucleotide polymorphisms to track the exchange of sequences in recombination products has provided an unprecedented level of detail about the corresponding intermediates and the extents to which different mechanisms are utilized. This approach also has revealed complexities that are not predicted by canonical models, suggesting that modifications to these models are needed. Current data are consistent with the initiation of most inter-homolog spontaneous mitotic recombination events by a double-strand break. In addition, the sister chromatid is preferred over the homolog as a repair template.
Collapse
Affiliation(s)
- Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States.
| |
Collapse
|
31
|
Uncovering bleomycin-induced genomic alterations and underlying mechanisms in yeast. Appl Environ Microbiol 2021; 88:e0170321. [PMID: 34731050 DOI: 10.1128/aem.01703-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bleomycin (BLM) is a widely used chemotherapeutic drug. BLM-treated cells showed an elevated rate of mutations, but the underlying mechanisms remained unclear. In this study, the global genomic alterations in BLM-treated cells were explored in the yeast Saccharomyces cerevisiae. Using genetic assay and whole-genome sequencing, we found that the mutation rate could be greatly elevated in S. cerevisiae cells that underwent ZeocinTM (a BLM member) treatment. One-base deletion and T to G substitution at the 5'-GT-3' motif was the most striking signature of ZeocinTM-induced mutations. This was mainly the result of translesion DNA synthesis involving Rev1 and polymerase ζ. ZeocinTM treatment led to the frequent loss of heterozygosity and chromosomal rearrangements in the diploid strains. The breakpoints of recombination events were significantly associated with certain chromosomal elements. Lastly, we identified multiple genomic alterations that contributed to BLM resistance in the ZeocinTM-treated mutants. Overall, this study provides new insights into the genotoxicity and evolutional effects of BLM. Importance Bleomycin is an antitumor antibiotic that can mutate genomic DNA. Using yeast models in combination with genome sequencing, the mutational signatures of ZeocinTM (a member of the bleomycin family) are disclosed. Translesion-synthesis polymerases are crucial for the viability of ZeocinTM-treated yeast cells at the sacrifice of a higher mutation rate. We also confirmed that multiple genomic alterations were associated with the improved resistance to ZeocinTM, providing novel insights into how bleomycin resistance is developed in cells.
Collapse
|
32
|
Chovanec P, Yin Y. A mapping platform for mitotic crossover by single-cell multi-omics. Methods Enzymol 2021; 661:183-204. [PMID: 34776212 DOI: 10.1016/bs.mie.2021.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mitotic crossovers have the potential to cause large-scale genome rearrangements. Here, we describe high-throughput, single-cell, whole-genome sequencing methods for mapping crossovers genome-wide at scale. The methods are generalizable to various eukaryotes and to other end points requiring high-throughput, high-coverage single cell sequencing.
Collapse
Affiliation(s)
- Peter Chovanec
- Department of Human Genetics, University of California, Los Angeles, CA, Unites States
| | - Yi Yin
- Department of Human Genetics, University of California, Los Angeles, CA, Unites States.
| |
Collapse
|
33
|
Kubiak-Szymendera M, Pryszcz LP, Białas W, Celińska E. Epigenetic Response of Yarrowia lipolytica to Stress: Tracking Methylation Level and Search for Methylation Patterns via Whole-Genome Sequencing. Microorganisms 2021; 9:microorganisms9091798. [PMID: 34576693 PMCID: PMC8471669 DOI: 10.3390/microorganisms9091798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is a common, but not universal, epigenetic modification that plays an important role in multiple cellular processes. While definitely settled for numerous plant, mammalian, and bacterial species, the genome methylation in different fungal species, including widely studied and industrially-relevant yeast species, Yarrowia lipolytica, is still a matter of debate. In this paper, we report a differential DNA methylation level in the genome of Y. lipolytica subjected to sequential subculturing and to heat stress conditions. To this end, we adopted repeated batch bioreactor cultivations of Y. lipolytica subjected to thermal stress in specific time intervals. To analyze the variation in DNA methylation between stressed and control cultures, we (a) quantified the global DNA methylation status using an immuno-assay, and (b) studied DNA methylation patterns through whole-genome sequencing. Primarily, we demonstrated that 5 mC modification can be detected using a commercial immuno-assay, and that the modifications are present in Y. lipolytica’s genome at ~0.5% 5 mC frequency. On the other hand, we did not observe any changes in the epigenetic response of Y. lipolytica to heat shock (HS) treatment. Interestingly, we identified a general phenomenon of decreased 5 mC level in Y. lipolytica’s genome in the stationary phase of growth, when compared to a late-exponential epigenome. While this study provides an insight into the subculturing stress response and adaptation to the stress at epigenetic level by Y. lipolytica, it also leaves an open question of inability to detect any genomic DNA methylation level (either in CpG context or context-less) through whole-genome sequencing. The results of ONT sequencing, suggesting that 5 mC modification is either rare or non-existent in Y. lipolytica genome, are contradicted with the results of the immunoassay.
Collapse
Affiliation(s)
- Monika Kubiak-Szymendera
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Leszek P. Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
- Correspondence:
| |
Collapse
|
34
|
Fisher KJ, Vignogna RC, Lang GI. Overdominant Mutations Restrict Adaptive Loss of Heterozygosity at Linked Loci. Genome Biol Evol 2021; 13:6345346. [PMID: 34363476 PMCID: PMC8382679 DOI: 10.1093/gbe/evab181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2021] [Indexed: 12/29/2022] Open
Abstract
Loss of heterozygosity is a common mode of adaptation in asexual diploid populations. Because mitotic recombination frequently extends the full length of a chromosome arm, the selective benefit of loss of heterozygosity may be constrained by linked heterozygous mutations. In a previous laboratory evolution experiment with diploid yeast, we frequently observed homozygous mutations in the WHI2 gene on the right arm of Chromosome XV. However, when heterozygous mutations arose in the STE4 gene, another common target on Chromosome XV, loss of heterozygosity at WHI2 was not observed. Here, we show that mutations at WHI2 are partially dominant and that mutations at STE4 are overdominant. We test whether beneficial heterozygous mutations at these two loci interfere with one another by measuring loss of heterozygosity at WHI2 over 1,000 generations for ∼300 populations that differed initially only at STE4 and WHI2. We show that the presence of an overdominant mutation in STE4 reduces, but does not eliminate, loss of heterozygosity at WHI2. By sequencing 40 evolved clones, we show that populations with linked overdominant and partially dominant mutations show less parallelism at the gene level, more varied evolutionary outcomes, and increased rates of aneuploidy. Our results show that the degree of dominance and the phasing of heterozygous beneficial mutations can constrain loss of heterozygosity along a chromosome arm, and that conflicts between partially dominant and overdominant mutations can affect evolutionary outcomes.
Collapse
Affiliation(s)
- Kaitlin J Fisher
- Department of Biological Sciences, Lehigh University, USA.,Laboratory of Genetics, University of Wisconsin-Madison, USA
| | | | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, USA
| |
Collapse
|
35
|
Kiktev DA, Dominska M, Zhang T, Dahl J, Stepchenkova EI, Mieczkowski P, Burgers PM, Lujan S, Burkholder A, Kunkel TA, Petes TD. The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe-S cluster in DNA polymerase δ. Nucleic Acids Res 2021; 49:5623-5636. [PMID: 34019669 PMCID: PMC8191807 DOI: 10.1093/nar/gkab371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/22/2021] [Accepted: 05/16/2021] [Indexed: 11/12/2022] Open
Abstract
Iron-sulfur clusters (4Fe–4S) exist in many enzymes concerned with DNA replication and repair. The contribution of these clusters to enzymatic activity is not fully understood. We identified the MET18 (MMS19) gene of Saccharomyces cerevisiae as a strong mutator on GC-rich genes. Met18p is required for the efficient insertion of iron-sulfur clusters into various proteins. met18 mutants have an elevated rate of deletions between short flanking repeats, consistent with increased DNA polymerase slippage. This phenotype is very similar to that observed in mutants of POL3 (encoding the catalytic subunit of Pol δ) that weaken binding of the iron-sulfur cluster. Comparable mutants of POL2 (Pol ϵ) do not elevate deletions. Further support for the conclusion that met18 strains result in impaired DNA synthesis by Pol δ are the observations that Pol δ isolated from met18 strains has less bound iron and is less processive in vitro than the wild-type holoenzyme.
Collapse
Affiliation(s)
- Denis A Kiktev
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tony Zhang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joseph Dahl
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Elena I Stepchenkova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, St. Petersburg, Russia.,Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, St. Petersburg, Russia
| | - Piotr Mieczkowski
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Scott Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Adam Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| |
Collapse
|
36
|
Dutta A, Dutreux F, Schacherer J. Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds. eLife 2021; 10:70339. [PMID: 34159898 PMCID: PMC8245132 DOI: 10.7554/elife.70339] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022] Open
Abstract
The dynamics and diversity of the appearance of genetic variants play an essential role in the evolution of the genome and the shaping of biodiversity. Recent population-wide genome sequencing surveys have highlighted the importance of loss of heterozygosity (LOH) events and have shown that they are a neglected part of the genetic diversity landscape. To assess the extent, variability, and spectrum, we explored the accumulation of LOH events in 169 heterozygous diploid Saccharomyces cerevisiae mutation accumulation lines across nine genetic backgrounds. In total, we detected a large set of 22,828 LOH events across distinct genetic backgrounds with a heterozygous level ranging from 0.1% to 1%. LOH events are very frequent with a rate consistently much higher than the mutation rate, showing their importance for genome evolution. We observed that the interstitial LOH (I-LOH) events, resulting in internal short LOH tracts, were much frequent (n = 19,660) than the terminal LOH (T-LOH) events, that is, tracts extending to the end of the chromosome (n = 3168). However, the spectrum, the rate, and the fraction of the genome under LOH vary across genetic backgrounds. Interestingly, we observed that the more the ancestors were heterozygous, the more they accumulated T-LOH events. In addition, frequent short I-LOH tracts are a signature of the lines derived from hybrids with low spore fertility. Finally, we found lines showing almost complete homozygotization during vegetative progression. Overall, our results highlight that the variable dynamics of the LOH accumulation across distinct genetic backgrounds might lead to rapid differential genome evolution during vegetative growth.
Collapse
Affiliation(s)
- Abhishek Dutta
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Fabien Dutreux
- 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
| |
Collapse
|
37
|
Bulankova P, Sekulić M, Jallet D, Nef C, van Oosterhout C, Delmont TO, Vercauteren I, Osuna-Cruz CM, Vancaester E, Mock T, Sabbe K, Daboussi F, Bowler C, Vyverman W, Vandepoele K, De Veylder L. Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms. Curr Biol 2021; 31:3221-3232.e9. [PMID: 34102110 DOI: 10.1016/j.cub.2021.05.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/17/2021] [Accepted: 05/06/2021] [Indexed: 01/31/2023]
Abstract
Diatoms, an evolutionarily successful group of microalgae, display high levels of intraspecific genetic variability in natural populations. However, the contribution of various mechanisms generating such diversity is unknown. Here we estimated the genetic micro-diversity within a natural diatom population and mapped the genomic changes arising within clonally propagated diatom cell cultures. Through quantification of haplotype diversity by next-generation sequencing and amplicon re-sequencing of selected loci, we documented a rapid accumulation of multiple haplotypes accompanied by the appearance of novel protein variants in cell cultures initiated from a single founder cell. Comparison of the genomic changes between mother and daughter cells revealed copy number variation and copy-neutral loss of heterozygosity leading to the fixation of alleles within individual daughter cells. The loss of heterozygosity can be accomplished by recombination between homologous chromosomes. To test this hypothesis, we established an endogenous readout system and estimated that the frequency of interhomolog mitotic recombination was under standard growth conditions 4.2 events per 100 cell divisions. This frequency is increased under environmental stress conditions, including treatment with hydrogen peroxide and cadmium. These data demonstrate that copy number variation and mitotic recombination between homologous chromosomes underlie clonal variability in diatom populations. We discuss the potential adaptive evolutionary benefits of the plastic response in the interhomolog mitotic recombination rate, and we propose that this may have contributed to the ecological success of diatoms.
Collapse
Affiliation(s)
- Petra Bulankova
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.
| | - Mirna Sekulić
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Denis Jallet
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, 31077 Toulouse, France
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
| | - Ilse Vercauteren
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Cristina Maria Osuna-Cruz
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Emmelien Vancaester
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Koen Sabbe
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Fayza Daboussi
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, 31077 Toulouse, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Wim Vyverman
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Lieven De Veylder
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.
| |
Collapse
|
38
|
Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair. Cells 2021; 10:cells10051224. [PMID: 34067668 PMCID: PMC8156620 DOI: 10.3390/cells10051224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on Saccharomyces cerevisiae and human tumors. Well-studied organisms include Drosophila melanogaster and Mus musculus, while less genetically tractable species include great apes and long-lived trees. A variety of techniques have been developed to gather mutation rates, either per generation or per cell division. Generational rates are described through whole-organism mutation accumulation experiments and through offspring–parent sequencing, or they have been identified by descent. Rates per somatic cell division have been estimated from cell line mutation accumulation experiments, from systemic variant allele frequencies, and from widely spaced samples with known cell divisions per unit of tissue growth. The latter methods are also used to estimate generational mutation rates for large organisms that lack dedicated germlines, such as trees and hyphal fungi. Mechanistic studies involving genetic manipulation of MMR genes prior to mutation rate determination are thus far confined to yeast, Arabidopsis thaliana, Caenorhabditis elegans, and one chicken cell line. A great deal of work in wild-type organisms has begun to establish a sound baseline, but far more work is needed to uncover the variety of MMR across eukaryotes. Nonetheless, the few MMR studies reported to date indicate that MMR contributes 100-fold or more to genome stability, and they have uncovered insights that would have been impossible to obtain using reporter gene assays.
Collapse
|
39
|
Gorkovskiy A, Verstrepen KJ. The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi. Genes (Basel) 2021; 12:699. [PMID: 34066718 PMCID: PMC8150848 DOI: 10.3390/genes12050699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/12/2023] Open
Abstract
Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV.
Collapse
Affiliation(s)
- Anton Gorkovskiy
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| |
Collapse
|
40
|
Origin, Regulation, and Fitness Effect of Chromosomal Rearrangements in the Yeast Saccharomyces cerevisiae. Int J Mol Sci 2021; 22:ijms22020786. [PMID: 33466757 PMCID: PMC7830279 DOI: 10.3390/ijms22020786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/02/2021] [Accepted: 01/11/2021] [Indexed: 11/16/2022] Open
Abstract
Chromosomal rearrangements comprise unbalanced structural variations resulting in gain or loss of DNA copy numbers, as well as balanced events including translocation and inversion that are copy number neutral, both of which contribute to phenotypic evolution in organisms. The exquisite genetic assay and gene editing tools available for the model organism Saccharomyces cerevisiae facilitate deep exploration of the mechanisms underlying chromosomal rearrangements. We discuss here the pathways and influential factors of chromosomal rearrangements in S. cerevisiae. Several methods have been developed to generate on-demand chromosomal rearrangements and map the breakpoints of rearrangement events. Finally, we highlight the contributions of chromosomal rearrangements to drive phenotypic evolution in various S. cerevisiae strains. Given the evolutionary conservation of DNA replication and recombination in organisms, the knowledge gathered in the small genome of yeast can be extended to the genomes of higher eukaryotes.
Collapse
|
41
|
Hundreds of thousands of cell generations reveal a treasure chest of genome alterations. Proc Natl Acad Sci U S A 2020; 117:31567-31569. [PMID: 33199644 DOI: 10.1073/pnas.2021185117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|