1
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Rodriguez-Algarra F, Evans DM, Rakyan VK. Ribosomal DNA copy number variation associates with hematological profiles and renal function in the UK Biobank. CELL GENOMICS 2024; 4:100562. [PMID: 38749448 PMCID: PMC11228893 DOI: 10.1016/j.xgen.2024.100562] [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: 08/09/2023] [Revised: 11/19/2023] [Accepted: 04/21/2024] [Indexed: 06/15/2024]
Abstract
The phenotypic impact of genetic variation of repetitive features in the human genome is currently understudied. One such feature is the multi-copy 47S ribosomal DNA (rDNA) that codes for rRNA components of the ribosome. Here, we present an analysis of rDNA copy number (CN) variation in the UK Biobank (UKB). From the first release of UKB whole-genome sequencing (WGS) data, a discovery analysis in White British individuals reveals that rDNA CN associates with altered counts of specific blood cell subtypes, such as neutrophils, and with the estimated glomerular filtration rate, a marker of kidney function. Similar trends are observed in other ancestries. A range of analyses argue against reverse causality or common confounder effects, and all core results replicate in the second UKB WGS release. Our work demonstrates that rDNA CN is a genetic influence on trait variance in humans.
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Affiliation(s)
| | - David M Evans
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia; MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Vardhman K Rakyan
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
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2
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Watase GJ, Yamashita YM. RNA polymerase II-mediated rDNA transcription mediates rDNA copy number expansion in Drosophila. PLoS Genet 2024; 20:e1011136. [PMID: 38758955 PMCID: PMC11139327 DOI: 10.1371/journal.pgen.1011136] [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: 01/11/2024] [Revised: 05/30/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024] Open
Abstract
Ribosomal DNA (rDNA), which encodes ribosomal RNA, is an essential but unstable genomic element due to its tandemly repeated nature. rDNA's repetitive nature causes spontaneous intrachromatid recombination, leading to copy number (CN) reduction, which must be counteracted by a mechanism that recovers CN to sustain cells' viability. Akin to telomere maintenance, rDNA maintenance is particularly important in cell types that proliferate for an extended time period, most notably in the germline that passes the genome through generations. In Drosophila, the process of rDNA CN recovery, known as 'rDNA magnification', has been studied extensively. rDNA magnification is mediated by unequal sister chromatid exchange (USCE), which generates a sister chromatid that gains the rDNA CN by stealing copies from its sister. However, much remains elusive regarding how germ cells sense rDNA CN to decide when to initiate magnification, and how germ cells balance between the need to generate DNA double-strand breaks (DSBs) to trigger USCE vs. avoiding harmful DSBs. Recently, we identified an rDNA-binding Zinc-finger protein Indra as a factor required for rDNA magnification, however, the underlying mechanism of action remains unknown. Here we show that Indra is a negative regulator of rDNA magnification, balancing the need of rDNA magnification and repression of dangerous DSBs. Mechanistically, we show that Indra is a repressor of RNA polymerase II (Pol II)-dependent transcription of rDNA: Under low rDNA CN conditions, Indra protein amount is downregulated, leading to Pol II-mediated transcription of rDNA. This results in the expression of rDNA-specific retrotransposon, R2, which we have shown to facilitate rDNA magnification via generation of DBSs at rDNA. We propose that differential use of Pol I and Pol II plays a critical role in regulating rDNA CN expansion only when it is necessary.
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Affiliation(s)
- George J. Watase
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Chuo-ku, Kumamoto-shi, Kumamoto, JAPAN
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Yukiko M. Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Massachusetts Institute of Technology, Department of Biology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
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3
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Jiang S, Cai Z, Wang Y, Zeng C, Zhang J, Yu W, Su C, Zhao S, Chen Y, Shen Y, Ma Y, Cai Y, Dai J. High plasticity of ribosomal DNA organization in budding yeast. Cell Rep 2024; 43:113742. [PMID: 38324449 DOI: 10.1016/j.celrep.2024.113742] [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: 07/20/2023] [Revised: 12/12/2023] [Accepted: 01/19/2024] [Indexed: 02/09/2024] Open
Abstract
In eukaryotic genomes, rDNA generally resides as a highly repetitive and dynamic structure, making it difficult to study. Here, a synthetic rDNA array on chromosome III in budding yeast was constructed to serve as the sole source of rRNA. Utilizing the loxPsym site within each rDNA repeat and the Cre recombinase, we were able to reduce the copy number to as few as eight copies. Additionally, we constructed strains with two or three rDNA arrays and found that the presence of multiple arrays did not affect the formation of a single nucleolus. Although alteration of the position and number of rDNA arrays did impact the three-dimensional genome structure, the additional rDNA arrays had no deleterious influence on cell growth or transcriptomes. Overall, this study sheds light on the high plasticity of rDNA organization and opens up opportunities for future rDNA engineering.
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Affiliation(s)
- Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Zelin Cai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wang
- BGI Research, BGI, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Cheng Zeng
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiaying Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; School of Mechanical Engineering and Automation, Beihang University, Beijing 100191, China
| | - Wenfei Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenghao Su
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shijun Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, BGI, Shenzhen 518083, China
| | - Yue Shen
- BGI Research, BGI, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, 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 518120, China; College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Road, Shenzhen 518055, China.
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4
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Azbarova AV, Knorre DA. Role of Mitochondrial DNA in Yeast Replicative Aging. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1997-2006. [PMID: 38462446 DOI: 10.1134/s0006297923120040] [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: 08/23/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 03/12/2024]
Abstract
Despite the diverse manifestations of aging across different species, some common aging features and underlying mechanisms are shared. In particular, mitochondria appear to be among the most vulnerable systems in both metazoa and fungi. In this review, we discuss how mitochondrial dysfunction is related to replicative aging in the simplest eukaryotic model, the baker's yeast Saccharomyces cerevisiae. We discuss a chain of events that starts from asymmetric distribution of mitochondria between mother and daughter cells. With age, yeast mother cells start to experience a decrease in mitochondrial transmembrane potential and, consequently, a decrease in mitochondrial protein import efficiency. This induces mitochondrial protein precursors in the cytoplasm, the loss of mitochondrial DNA (mtDNA), and at the later stages - cell death. Interestingly, yeast strains without mtDNA can have either increased or decreased lifespan compared to the parental strains with mtDNA. The direction of the effect depends on their ability to activate compensatory mechanisms preventing or mitigating negative consequences of mitochondrial dysfunction. The central role of mitochondria in yeast aging and death indicates that it is one of the most complex and, therefore, deregulation-prone systems in eukaryotic cells.
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Affiliation(s)
- Aglaia V Azbarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Dmitry A Knorre
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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5
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Yamashita YM. Asymmetric Stem Cell Division and Germline Immortality. Annu Rev Genet 2023; 57:181-199. [PMID: 37552892 DOI: 10.1146/annurev-genet-022123-040039] [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] [Indexed: 08/10/2023]
Abstract
Germ cells are the only cell type that is capable of transmitting genetic information to the next generation, which has enabled the continuation of multicellular life for the last 1.5 billion years. Surprisingly little is known about the mechanisms supporting the germline's remarkable ability to continue in this eternal cycle, termed germline immortality. Even unicellular organisms age at a cellular level, demonstrating that cellular aging is inevitable. Extensive studies in yeast have established the framework of how asymmetric cell division and gametogenesis may contribute to the resetting of cellular age. This review examines the mechanisms of germline immortality-how germline cells reset the aging of cells-drawing a parallel between yeast and multicellular organisms.
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Affiliation(s)
- Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
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6
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Blokhina Y, Buchwalter A. Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562830. [PMID: 37904963 PMCID: PMC10614900 DOI: 10.1101/2023.10.18.562830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ribosomal DNA (rDNA) genes encode the structural RNAs of the ribosome and are present in hundreds of copies in mammalian genomes. Age-linked DNA hypermethylation throughout the rDNA constitutes a robust "methylation clock" that accurately reports age, yet the consequences of hypermethylation on rDNA function are unknown. We confirmed that pervasive hypermethylation of rDNA occurs during mammalian aging and senescence while rDNA copy number remains stable. We found that DNA methylation is exclusively found on the promoters and gene bodies of inactive rDNA. To model the effects of age-linked methylation on rDNA function, we directed de novo DNA methylation to the rDNA promoter or gene body with a nuclease-dead Cas9 (dCas9) - DNA methyltransferase fusion enzyme in human cells. Hypermethylation at each target site had no detectable effect on rRNA transcription, nucleolar morphology, or cellular growth rate. Instead, human UBF and Pol I remain bound to rDNA promoters in the presence of increased DNA methylation. These data suggest that promoter methylation is not sufficient to impair transcription of the human rDNA and imply that the human rDNA transcription machinery may be resilient to age-linked rDNA hypermethylation.
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Affiliation(s)
- Yana Blokhina
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco
- present address: NewLimit, South San Francisco, CA
| | - Abigail Buchwalter
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco
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7
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Enkhbaatar T, Skoneczny M, Stępień K, Mołoń M, Skoneczna A. Live while the DNA lasts. The role of autophagy in DNA loss and survival of diploid yeast cells during chronological aging. Aging (Albany NY) 2023; 15:9965-9983. [PMID: 37815879 PMCID: PMC10599738 DOI: 10.18632/aging.205102] [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: 06/13/2023] [Accepted: 09/06/2023] [Indexed: 10/12/2023]
Abstract
Aging is inevitable and affects all cell types, thus yeast cells are often used as a model in aging studies. There are two approaches to studying aging in yeast: replicative aging, which describes the proliferative potential of cells, and chronological aging, which is used for studying post-mitotic cells. While analyzing the chronological lifespan (CLS) of diploid Saccharomyces cerevisiae cells, we discovered a remarkable phenomenon: ploidy reduction during aging progression. To uncover the mechanism behind this unusual process we used yeast strains undergoing a CLS assay, looking for various aging parameters. Cell mortality, regrowth ability, autophagy induction and cellular DNA content measurements indicated that during the CLS assay, dying cells lost their DNA, and only diploids survived. We demonstrated that autophagy was responsible for the gradual loss of DNA. The nucleophagy marker activation at the start of the CLS experiment correlated with the significant drop in cell viability. The activation of piecemeal microautophagy of nucleus (PMN) markers appeared to accompany the chronological aging process until the end. Our findings emphasize the significance of maintaining at least one intact copy of the genome for the survival of post-mitotic diploid cells. During chronological aging, cellular components, including DNA, are exposed to increasing stress, leading to DNA damage and fragmentation in aging cells. We propose that PMN-dependent clearance of damaged DNA from the nucleus helps prevent genome rearrangements. However, as long as one copy of the genome can be rebuilt, cells can still survive.
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Affiliation(s)
- Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Karolina Stępień
- Institute of Medical Sciences, Rzeszów University, Rzeszów 35-959, Poland
| | - Mateusz Mołoń
- Institute of Biology, Rzeszów University, Rzeszów 35-601, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
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8
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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.
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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
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9
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Wang H, Li Q, Zhang Z, Ayepa E, Xiang Q, Yu X, Zhao K, Zou L, Gu Y, Li X, Chen Q, Zhang X, Yang Y, Jin X, Yin H, Liu ZL, Tang T, Liu B, Ma M. Discovery of new strains for furfural degradation using adaptive laboratory evolution in Saccharomyces cerevisiae. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132090. [PMID: 37480608 DOI: 10.1016/j.jhazmat.2023.132090] [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: 04/24/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023]
Abstract
In industrial production, the excessive discharge of furfural can pose harm to soil microorganisms, aquatic animals and plants, as well as humans. Therefore, it is crucial to develop efficient and cost-effective methods for degrading furfural in the environment. Currently, the use of Saccharomyces cerevisiae for furfural degradation in water has shown effectiveness, but there is a need to explore improved efficiency and tolerance in S. cerevisiae for this purpose. In this study, we isolated and evolved highly efficient furfural degradation strains, namely YBA_08 and F60C. These strains exhibited remarkable capabilities, degrading 59% and 99% furfural in the YPD medium after 72 h of incubation, significantly higher than the 31% achieved by the model strain S288C. Through analysis of the efficient degradation mechanism in the evolutionary strain F60C, we discovered a 326% increase in the total amount of NADH and NADPH. This increase likely promotes faster furfural degradation through intracellular aldehyde reductases. Moreover, the decrease in NADPH content led to a 406% increase in glutathione content at the background level, which protects cells from damage caused by reactive oxygen species. Mutations and differential expression related to cell cycle and cell wall synthesis were observed, enabling cell survival in the presence of furfural and facilitating rapid furfural degradation and growth recovery. Based on these findings, it is speculated that strains YBA_08 and F60C have the potential to contribute to furfural degradation in water and the production of furfuryl alcohol, ethanol, and FDCA in biorefinery processes.
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Affiliation(s)
- Hanyu Wang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China; College of Life Science, Leshan Normal University, Leshan, Sichuan 614000, China; Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan 614000, China
| | - Qian Li
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Zhengyue Zhang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Ellen Ayepa
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Quanju Xiang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Xiumei Yu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Ke Zhao
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Likou Zou
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Yunfu Gu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Qiang Chen
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Xiaoping Zhang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Yaojun Yang
- College of Life Science, Leshan Normal University, Leshan, Sichuan 614000, China; Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan 614000, China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, Zhejiang 311300, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Z Lewis Liu
- The US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 N University Street, Peoria, IL 61604, USA
| | - Tianle Tang
- Key Laboratory of Tropical Transitional Medicine of Ministry of Education, Hainan Medical University, No.3 Xueyuan Road, Haikou, Hainan 571199, China.
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, Zhejiang 311300, China; Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 413 90 Göteburg, Sweden.
| | - Menggen Ma
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China; Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China.
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10
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López-Gil L, Pascual-Ahuir A, Proft M. Genomic Instability and Epigenetic Changes during Aging. Int J Mol Sci 2023; 24:14279. [PMID: 37762580 PMCID: PMC10531692 DOI: 10.3390/ijms241814279] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Aging is considered the deterioration of physiological functions along with an increased mortality rate. This scientific review focuses on the central importance of genomic instability during the aging process, encompassing a range of cellular and molecular changes that occur with advancing age. In particular, this revision addresses the genetic and epigenetic alterations that contribute to genomic instability, such as telomere shortening, DNA damage accumulation, and decreased DNA repair capacity. Furthermore, the review explores the epigenetic changes that occur with aging, including modifications to histones, DNA methylation patterns, and the role of non-coding RNAs. Finally, the review discusses the organization of chromatin and its contribution to genomic instability, including heterochromatin loss, chromatin remodeling, and changes in nucleosome and histone abundance. In conclusion, this review highlights the fundamental role that genomic instability plays in the aging process and underscores the need for continued research into these complex biological mechanisms.
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Affiliation(s)
- Lucía López-Gil
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain;
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, Jaime Roig 11, 46010 Valencia, Spain
| | - Amparo Pascual-Ahuir
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain;
| | - Markus Proft
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, Jaime Roig 11, 46010 Valencia, Spain
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11
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Horkai D, Hadj-Moussa H, Whale AJ, Houseley J. Dietary change without caloric restriction maintains a youthful profile in ageing yeast. PLoS Biol 2023; 21:e3002245. [PMID: 37643155 PMCID: PMC10464975 DOI: 10.1371/journal.pbio.3002245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 07/12/2023] [Indexed: 08/31/2023] Open
Abstract
Caloric restriction increases lifespan and improves ageing health, but it is unknown whether these outcomes can be separated or achieved through less severe interventions. Here, we show that an unrestricted galactose diet in early life minimises change during replicative ageing in budding yeast, irrespective of diet later in life. Average mother cell division rate is comparable between glucose and galactose diets, and lifespan is shorter on galactose, but markers of senescence and the progressive dysregulation of gene expression observed on glucose are minimal on galactose, showing that these are not intrinsic aspects of replicative ageing but rather associated processes. Respiration on galactose is critical for minimising hallmarks of ageing, and forced respiration during ageing on glucose by overexpression of the mitochondrial biogenesis factor Hap4 also has the same effect though only in a fraction of cells. This fraction maintains Hap4 activity to advanced age with low senescence and a youthful gene expression profile, whereas other cells in the same population lose Hap4 activity, undergo dramatic dysregulation of gene expression and accumulate fragments of chromosome XII (ChrXIIr), which are tightly associated with senescence. Our findings support the existence of two separable ageing trajectories in yeast. We propose that a complete shift to the healthy ageing mode can be achieved in wild-type cells through dietary change in early life without caloric restriction.
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Affiliation(s)
- Dorottya Horkai
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | | | - Alex J. Whale
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
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Sultanov D, Hochwagen A. Varying strength of selection contributes to the intragenomic diversity of rRNA genes. Nat Commun 2022; 13:7245. [PMID: 36434003 PMCID: PMC9700816 DOI: 10.1038/s41467-022-34989-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
Abstract
Ribosome biogenesis in eukaryotes is supported by hundreds of ribosomal RNA (rRNA) gene copies that are encoded in the ribosomal DNA (rDNA). The multiple copies of rRNA genes are thought to have low sequence diversity within one species. Here, we present species-wide rDNA sequence analysis in Saccharomyces cerevisiae that challenges this view. We show that rDNA copies in this yeast are heterogeneous, both among and within isolates, and that many variants avoided fixation or elimination over evolutionary time. The sequence diversity landscape across the rDNA shows clear functional stratification, suggesting different copy-number thresholds for selection that contribute to rDNA diversity. Notably, nucleotide variants in the most conserved rDNA regions are sufficiently deleterious to exhibit signatures of purifying selection even when present in only a small fraction of rRNA gene copies. Our results portray a complex evolutionary landscape that shapes rDNA sequence diversity within a single species and reveal unexpectedly strong purifying selection of multi-copy genes.
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Affiliation(s)
- Daniel Sultanov
- grid.137628.90000 0004 1936 8753Department of Biology, New York University, New York, NY 10003 USA
| | - Andreas Hochwagen
- grid.137628.90000 0004 1936 8753Department of Biology, New York University, New York, NY 10003 USA
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Multifarious Translational Regulation during Replicative Aging in Yeast. J Fungi (Basel) 2022; 8:jof8090938. [PMID: 36135663 PMCID: PMC9500732 DOI: 10.3390/jof8090938] [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: 05/22/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Protein synthesis is strictly regulated during replicative aging in yeast, but global translational regulation during replicative aging is poorly characterized. To conduct ribosome profiling during replicative aging, we collected a large number of dividing aged cells using a miniature chemostat aging device. Translational efficiency, defined as the number of ribosome footprints normalized to transcript abundance, was compared between young and aged cells for each gene. We identified more than 700 genes with changes greater than twofold during replicative aging. Increased translational efficiency was observed in genes involved in DNA repair and chromosome organization. Decreased translational efficiency was observed in genes encoding ribosome components, transposon Ty1 and Ty2 genes, transcription factor HAC1 gene associated with the unfolded protein response, genes involved in cell wall synthesis and assembly, and ammonium permease genes. Our results provide a global view of translational regulation during replicative aging, in which the pathways involved in various cell functions are translationally regulated and cause diverse phenotypic changes.
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A feedback mechanism controls rDNA copy number evolution in yeast independently of natural selection. PLoS One 2022; 17:e0272878. [PMID: 36048821 PMCID: PMC9436098 DOI: 10.1371/journal.pone.0272878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/27/2022] [Indexed: 11/19/2022] Open
Abstract
Ribosomal DNA (rDNA) is the genetic loci that encodes rRNA in eukaryotes. It is typically arranged as tandem repeats that vary in copy number within the same species. We have recently shown that rDNA repeats copy number in the yeast Saccharomyces cerevisiae is controlled by cell volume via a feedback circuit that senses cell volume by means of the concentration of the free upstream activator factor (UAF). The UAF strongly binds the rDNA gene promoter, but is also able to repress SIR2 deacetylase gene transcription that, in turn, represses rDNA amplification. In this way, the cells with a smaller DNA copy number than what is optimal evolve to increase that copy number until they reach a number that sequestrates free UAF and provokes SIR2 derepression that, in turn, blocks rDNA amplification. Here we propose a mathematical model to show that this evolutionary process can amplify rDNA repeats independently of the selective advantage of yeast cells having bigger or smaller rDNA copy numbers. We test several variants of this process and show that it can explain the observed experimental results independently of natural selection. These results predict that an autoregulated feedback circuit may, in some instances, drive to non Darwinian deterministic evolution for a limited time period.
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The long and short of rDNA and yeast replicative aging. Proc Natl Acad Sci U S A 2022; 119:e2205124119. [PMID: 35658078 DOI: 10.1073/pnas.2205124119] [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
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