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Biba DA, Wolf YI, Koonin EV, Rochman ND. Balance between asymmetric allocation and repair of somatic damage in unicellular life forms as an ancient form of r/K selection. Proc Natl Acad Sci U S A 2024; 121:e2400008121. [PMID: 38787879 PMCID: PMC11145259 DOI: 10.1073/pnas.2400008121] [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: 01/01/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Over the course of multiple divisions, cells accumulate diverse nongenetic, somatic damage including misfolded and aggregated proteins and cell wall defects. If the rate of damage accumulation exceeds the rate of dilution through cell growth, a dedicated mitigation strategy is required to prevent eventual population collapse. Strategies for somatic damage control can be divided into two categories, asymmetric allocation and repair, which are not, in principle, mutually exclusive. We explore a mathematical model to identify the optimal strategy, maximizing the total cell number, over a wide range of environmental and physiological conditions. The optimal strategy is primarily determined by extrinsic, damage-independent mortality and the physiological model for damage accumulation that can be either independent (linear) or increasing (exponential) with respect to the prior accumulated damage. Under the linear regime, the optimal strategy is either exclusively repair or asymmetric allocation, whereas under the exponential regime, the optimal strategy is a combination of asymmetry and repair. Repair is preferred when extrinsic mortality is low, whereas at high extrinsic mortality, asymmetric damage allocation becomes the strategy of choice. We hypothesize that at an early stage of life evolution, optimization over repair and asymmetric allocation of somatic damage gave rise to r and K selection strategists.
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Affiliation(s)
- Dmitry A. Biba
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
- Oak Ridge Institute for Science and Education, Oak Ridge, TN37830
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
| | - Nash D. Rochman
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
- Institute for Implementation Science in Population Health, City University of New York, New York, NY10027
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy City, University of New York, New York, NY10027
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Biba DA, Wolf YI, Koonin EV, Rochman ND. Unicellular life balances asymmetric allocation and repair of somatic damage representing the origin of r/K selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568103. [PMID: 38076808 PMCID: PMC10705550 DOI: 10.1101/2023.11.21.568103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Over the course of multiple divisions, cells accumulate diverse non-genetic, somatic damage including misfolded and aggregated proteins and cell wall defects. If the rate of damage accumulation exceeds the rate of dilution through cell growth, a dedicated mitigation strategy is required to prevent eventual population collapse. Strategies for somatic damage control can be divided into two categories, asymmetric allocation and repair, which are not, in principle, mutually exclusive. Through mathematical modelling, we identify the optimal strategy, maximizing the total cell number, over a wide range of environmental and physiological conditions. The optimal strategy is primarily determined by extrinsic (damage-independent) mortality and the physiological model for damage accumulation that can be either independent (linear) or increasing (exponential) with respect to the prior accumulated damage. Under the linear regime, the optimal strategy is either exclusively repair or asymmetric allocation whereas under the exponential regime, the optimal strategy is mixed. Repair is preferred when extrinsic mortality is low, whereas at high extrinsic mortality, asymmetric damage allocation becomes the strategy of choice. We hypothesize that optimization over somatic damage repair and asymmetric allocation in early cellular life forms gave rise to the r and K selection strategies.
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Affiliation(s)
- Dmitry A. Biba
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Nash D. Rochman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
- Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY), New York, NY, USA
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York (CUNY), New York, NY, USA
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Time-resolved microfluidics unravels individual cellular fates during double-strand break repair. BMC Biol 2022; 20:269. [PMID: 36464673 PMCID: PMC9720956 DOI: 10.1186/s12915-022-01456-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/31/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Double-strand break repair (DSBR) is a highly regulated process involving dozens of proteins acting in a defined order to repair a DNA lesion that is fatal for any living cell. Model organisms such as Saccharomyces cerevisiae have been used to study the mechanisms underlying DSBR, including factors influencing its efficiency such as the presence of distinct combinations of microsatellites and endonucleases, mainly by bulk analysis of millions of cells undergoing repair of a broken chromosome. Here, we use a microfluidic device to demonstrate in yeast that DSBR may be studied at a single-cell level in a time-resolved manner, on a large number of independent lineages undergoing repair. RESULTS We used engineered S. cerevisiae cells in which GFP is expressed following the successful repair of a DSB induced by Cas9 or Cpf1 endonucleases, and different genetic backgrounds were screened to detect key events leading to the DSBR efficiency. Per condition, the progenies of 80-150 individual cells were analyzed over 24 h. The observed DSBR dynamics, which revealed heterogeneity of individual cell fates and their contributions to global repair efficacy, was confronted with a coupled differential equation model to obtain repair process rates. Good agreement was found between the mathematical model and experimental results at different scales, and quantitative comparisons of the different experimental conditions with image analysis of cell shape enabled the identification of three types of DSB repair events previously not recognized: high-efficacy error-free, low-efficacy error-free, and low-efficacy error-prone repair. CONCLUSIONS Our analysis paves the way to a significant advance in understanding the complex molecular mechanism of DSB repair, with potential implications beyond yeast cell biology. This multiscale and multidisciplinary approach more generally allows unique insights into the relation between in vivo microscopic processes within each cell and their impact on the population dynamics, which were inaccessible by previous approaches using molecular genetics tools alone.
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Mojumdar A, Mair N, Adam N, Cobb JA. Changes in DNA double-strand break repair during aging correlate with an increase in genomic mutations. J Mol Biol 2022; 434:167798. [PMID: 35998703 DOI: 10.1016/j.jmb.2022.167798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/24/2022]
Abstract
A double -strand break (DSB) is one of the most deleterious forms of DNA damage. In eukaryotic cells, two main repair pathways have evolved to repair DSBs, homologous recombination (HR) and non-homologous end-joining (NHEJ). HR is the predominant pathway of repair in the unicellular eukaryotic organism, S. cerevisiae. However, during replicative aging the relative use of HR and NHEJ shifts in favor of end-joining repair. By monitoring repair events in the HO-DSB system, we find that early in replicative aging there is a decrease in the association of long-range resection factors, Dna2-Sgs1 and Exo1 at the break site and a decrease in DNA resection. Subsequently, as aging progressed, the recovery of Ku70 at DSBs decreased and the break site associated with the nuclear pore complex at the nuclear periphery, which is the location where DSB repair occurs through alternative pathways that are more mutagenic. End-bridging remained intact as HR and NHEJ declined, but eventually it too became disrupted in cells at advanced replicative age. In all, our work provides insight into the molecular changes in DSB repair pathway during replicative aging. HR first declined, resulting in a transient increase in the NHEJ. However, with increased cellular divisions, Ku70 recovery at DSBs and NHEJ subsequently declined. In wild type cells of advanced replicative age, there was a high frequency of repair products with genomic deletions and microhomologies at the break junction, events not observed in young cells which repaired primarily by HR.
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Affiliation(s)
- Aditya Mojumdar
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine; University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Nicola Mair
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine; University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Nancy Adam
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine; University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Jennifer A Cobb
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine; University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada.
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Schnitzer B, Österberg L, Skopa I, Cvijovic M. Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing. PLoS Comput Biol 2022; 18:e1010261. [PMID: 35797415 PMCID: PMC9295998 DOI: 10.1371/journal.pcbi.1010261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/19/2022] [Accepted: 05/31/2022] [Indexed: 11/18/2022] Open
Abstract
The accumulation of protein damage is one of the major drivers of replicative ageing, describing a cell’s reduced ability to reproduce over time even under optimal conditions. Reactive oxygen and nitrogen species are precursors of protein damage and therefore tightly linked to ageing. At the same time, they are an inevitable by-product of the cell’s metabolism. Cells are able to sense high levels of reactive oxygen and nitrogen species and can subsequently adapt their metabolism through gene regulation to slow down damage accumulation. However, the older or damaged a cell is the less flexibility it has to allocate enzymes across the metabolic network, forcing further adaptions in the metabolism. To investigate changes in the metabolism during replicative ageing, we developed an multi-scale mathematical model using budding yeast as a model organism. The model consists of three interconnected modules: a Boolean model of the signalling network, an enzyme-constrained flux balance model of the central carbon metabolism and a dynamic model of growth and protein damage accumulation with discrete cell divisions. The model can explain known features of replicative ageing, like average lifespan and increase in generation time during successive division, in yeast wildtype cells by a decreasing pool of functional enzymes and an increasing energy demand for maintenance. We further used the model to identify three consecutive metabolic phases, that a cell can undergo during its life, and their influence on the replicative potential, and proposed an intervention span for lifespan control.
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Affiliation(s)
- Barbara Schnitzer
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Linnea Österberg
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Iro Skopa
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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Kowald A, Kirkwood TBL. Senolytics and the compression of late-life mortality. Exp Gerontol 2021; 155:111588. [PMID: 34637949 DOI: 10.1016/j.exger.2021.111588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 01/01/2023]
Abstract
Senescent cells play an important role in mammalian ageing and in the etiology of age-related diseases. Treatment of mice with senolytics - drugs that selectively remove senescent cells - causes an extension of median lifespan but has little effect on maximum lifespan. Postponement of some mortality to later ages, without a corresponding increase in maximum mortality, can be termed 'compression of mortality'. When we fit the standard Gompertz mortality model to the survival data following senolytic treatment, we find an increase in the slope parameter, commonly described as the 'actuarial ageing rate'. These observations raise important questions about the actions of senolytic treatments and their effects on health and survival, which are not yet sufficiently understood. To explore how the survival data from senolytics experiments might be explained, we combine a recent exploration of the evolutionary basis of cellular senescence with theoretical consideration of the molecular processes that might be involved. We perform numerical simulations of senescent cell accumulation and senolytic treatment in an ageing population. The simulations suggest that while senolytics diminish the burden of senescent cells, they may also impair the general repair capacity of the organism, leading to a faster accumulation post-treatment of new senescent cells. Our results suggest a framework to address the benefits and possible side effects of senolytic therapies, with the potential to aid in the design of optimal treatment regimens.
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Affiliation(s)
- Axel Kowald
- UK National Innovation Centre for Ageing, The Catalyst, 3 Science Square, Newcastle University, Newcastle upon Tyne NE4 5TG, UK; Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research (IBIMA), Rostock, Germany.
| | - Thomas B L Kirkwood
- UK National Innovation Centre for Ageing, The Catalyst, 3 Science Square, Newcastle University, Newcastle upon Tyne NE4 5TG, UK; Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark.
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