1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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:
| |
Collapse
|
4
|
Abstract
Ageing, death, and potential immortality lie at the heart of biology, but two seemingly incompatible paradigms coexist in different research communities and have done since the nineteenth century. The universal senescence paradigm sees senescence as inevitable in all cells. Damage accumulates. The potential immortality paradigm sees some cells as potentially immortal, especially unicellular organisms, germ cells and cancerous cells. Recent research with animal cells, yeasts and bacteria show that damaged cell constituents do in fact build up, but can be diluted by growth and cell division, especially by asymmetric cell division. By contrast, mammalian embryonic stem cells and many cancerous and 'immortalized' cell lines divide symmetrically, and yet replicate indefinitely. How do they acquire their potential immortality? I suggest they are rejuvenated by excreting damaged cell constituents in extracellular vesicles. If so, our understanding of cellular senescence, rejuvenation and potential immortality could be brought together in a new synthesis, which I call the cellular rejuvenation hypothesis: damaged cell constituents build up in all cells, but cells can be rejuvenated either by growth and cell division or, in 'immortal' cell lines, by excreting damaged cell constituents. In electronic supplementary material, appendix, I outline nine ways in which this hypothesis could be tested.
Collapse
|
5
|
Steiner UK. Senescence in Bacteria and Its Underlying Mechanisms. Front Cell Dev Biol 2021; 9:668915. [PMID: 34222238 PMCID: PMC8249858 DOI: 10.3389/fcell.2021.668915] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/14/2021] [Indexed: 12/11/2022] Open
Abstract
Bacteria have been thought to flee senescence by dividing into two identical daughter cells, but this notion of immortality has changed over the last two decades. Asymmetry between the resulting daughter cells after binary fission is revealed in physiological function, cell growth, and survival probabilities and is expected from theoretical understanding. Since the discovery of senescence in morphologically identical but physiologically asymmetric dividing bacteria, the mechanisms of bacteria aging have been explored across levels of biological organization. Quantitative investigations are heavily biased toward Escherichia coli and on the role of inclusion bodies—clusters of misfolded proteins. Despite intensive efforts to date, it is not evident if and how inclusion bodies, a phenotype linked to the loss of proteostasis and one of the consequences of a chain of reactions triggered by reactive oxygen species, contribute to senescence in bacteria. Recent findings in bacteria question that inclusion bodies are only deleterious, illustrated by fitness advantages of cells holding inclusion bodies under varying environmental conditions. The contributions of other hallmarks of aging, identified for metazoans, remain elusive. For instance, genomic instability appears to be age independent, epigenetic alterations might be little age specific, and other hallmarks do not play a major role in bacteria systems. What is surprising is that, on the one hand, classical senescence patterns, such as an early exponential increase in mortality followed by late age mortality plateaus, are found, but, on the other hand, identifying mechanisms that link to these patterns is challenging. Senescence patterns are sensitive to environmental conditions and to genetic background, even within species, which suggests diverse evolutionary selective forces on senescence that go beyond generalized expectations of classical evolutionary theories of aging. Given the molecular tool kits available in bacteria, the high control of experimental conditions, the high-throughput data collection using microfluidic systems, and the ease of life cell imaging of fluorescently marked transcription, translation, and proteomic dynamics, in combination with the simple demographics of growth, division, and mortality of bacteria, make the challenges surprising. The diversity of mechanisms and patterns revealed and their environmental dependencies not only present challenges but also open exciting opportunities for the discovery and deeper understanding of aging and its mechanisms, maybe beyond bacteria and aging.
Collapse
Affiliation(s)
- Ulrich Karl Steiner
- Evolutionary Demography Group, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
6
|
Koshy-Chenthittayil S, Archambault L, Senthilkumar D, Laubenbacher R, Mendes P, Dongari-Bagtzoglou A. Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review. Microorganisms 2021; 9:417. [PMID: 33671308 PMCID: PMC7922883 DOI: 10.3390/microorganisms9020417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/05/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
The human microbiome has been a focus of intense study in recent years. Most of the living organisms comprising the microbiome exist in the form of biofilms on mucosal surfaces lining our digestive, respiratory, and genito-urinary tracts. While health-associated microbiota contribute to digestion, provide essential nutrients, and protect us from pathogens, disturbances due to illness or medical interventions contribute to infections, some that can be fatal. Myriad biological processes influence the make-up of the microbiota, for example: growth, division, death, and production of extracellular polymers (EPS), and metabolites. Inter-species interactions include competition, inhibition, and symbiosis. Computational models are becoming widely used to better understand these interactions. Agent-based modeling is a particularly useful computational approach to implement the various complex interactions in microbial communities when appropriately combined with an experimental approach. In these models, each cell is represented as an autonomous agent with its own set of rules, with different rules for each species. In this review, we will discuss innovations in agent-based modeling of biofilms and the microbiota in the past five years from the biological and mathematical perspectives and discuss how agent-based models can be further utilized to enhance our comprehension of the complex world of polymicrobial biofilms and the microbiome.
Collapse
Affiliation(s)
- Sherli Koshy-Chenthittayil
- Center for Quantitative Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA; (S.K.-C.); (L.A.); (P.M.)
| | - Linda Archambault
- Center for Quantitative Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA; (S.K.-C.); (L.A.); (P.M.)
- Department of Oral Health and Diagnostic Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | | | | | - Pedro Mendes
- Center for Quantitative Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA; (S.K.-C.); (L.A.); (P.M.)
- Center for Cell Analysis and Modeling, Department of Cell Biology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Anna Dongari-Bagtzoglou
- Department of Oral Health and Diagnostic Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| |
Collapse
|
7
|
Abstract
Damage is an inevitable consequence of life. For unicellular organisms, this leads to a trade-off between allocating resources into damage repair or into growth coupled with segregation of damage upon cell division, i.e., aging and senescence. Few studies considered repair as an alternative to senescence. None considered biofilms, where the majority of unicellular organisms live, although fitness advantages in well-mixed systems often turn into disadvantages in spatially structured systems such as biofilms. We compared the fitness consequences of aging versus an adaptive repair mechanism based on sensing damage, using an individual-based model of a generic unicellular organism growing in biofilms. We found that senescence is not beneficial provided that growth is limited by substrate availability. Instead, it is useful as a stress response to deal with damage that failed to be repaired when (i) extrinsic mortality was high; (ii) a degree of multicellularity was present; and (iii) damage segregation was effective. The extent of senescence due to damage accumulation—or aging—is evidently evolvable as it differs hugely between species and is not universal, suggesting that its fitness advantages depend on life history and environment. In contrast, repair of damage is present in all organisms studied. Despite the fundamental trade-off between investing resources into repair or into growth, repair and segregation of damage have not always been considered alternatives. For unicellular organisms, unrepaired damage could be divided asymmetrically between daughter cells, leading to senescence of one and rejuvenation of the other. Repair of “unicells” has been predicted to be advantageous in well-mixed environments such as chemostats. Most microorganisms, however, live in spatially structured systems, such as biofilms, with gradients of environmental conditions and cellular physiology as well as a clonal population structure. To investigate whether this clonal structure might favor senescence by damage segregation (a division-of-labor strategy akin to the germline-soma division in multicellular organisms), we used an individual-based computational model and developed an adaptive repair strategy where cells respond to their current intracellular damage levels by investing into repair machinery accordingly. Our simulations showed that the new adaptive repair strategy was advantageous provided that growth was limited by substrate availability, which is typical for biofilms. Thus, biofilms do not favor a germline-soma-like division of labor between daughter cells in terms of damage segregation. We suggest that damage segregation is beneficial only when extrinsic mortality is high, a degree of multicellularity is present, and an active mechanism makes segregation effective. IMPORTANCE Damage is an inevitable consequence of life. For unicellular organisms, this leads to a trade-off between allocating resources into damage repair or into growth coupled with segregation of damage upon cell division, i.e., aging and senescence. Few studies considered repair as an alternative to senescence. None considered biofilms, where the majority of unicellular organisms live, although fitness advantages in well-mixed systems often turn into disadvantages in spatially structured systems such as biofilms. We compared the fitness consequences of aging versus an adaptive repair mechanism based on sensing damage, using an individual-based model of a generic unicellular organism growing in biofilms. We found that senescence is not beneficial provided that growth is limited by substrate availability. Instead, it is useful as a stress response to deal with damage that failed to be repaired when (i) extrinsic mortality was high; (ii) a degree of multicellularity was present; and (iii) damage segregation was effective.
Collapse
|
8
|
Schnitzer B, Borgqvist J, Cvijovic M. The synergy of damage repair and retention promotes rejuvenation and prolongs healthy lifespans in cell lineages. PLoS Comput Biol 2020; 16:e1008314. [PMID: 33044956 PMCID: PMC7598927 DOI: 10.1371/journal.pcbi.1008314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/30/2020] [Accepted: 09/04/2020] [Indexed: 01/29/2023] Open
Abstract
Damaged proteins are inherited asymmetrically during cell division in the yeast Saccharomyces cerevisiae, such that most damage is retained within the mother cell. The consequence is an ageing mother and a rejuvenated daughter cell with full replicative potential. Daughters of old and damaged mothers are however born with increasing levels of damage resulting in lowered replicative lifespans. Remarkably, these prematurely old daughters can give rise to rejuvenated cells with low damage levels and recovered lifespans, called second-degree rejuvenation. We aimed to investigate how damage repair and retention together can promote rejuvenation and at the same time ensure low damage levels in mother cells, reflected in longer health spans. We developed a dynamic model for damage accumulation over successive divisions in individual cells as part of a dynamically growing cell lineage. With detailed knowledge about single-cell dynamics and relationships between all cells in the lineage, we can infer how individual damage repair and retention strategies affect the propagation of damage in the population. We show that damage retention lowers damage levels in the population by reducing the variability across the lineage, and results in larger population sizes. Repairing damage efficiently in early life, as opposed to investing in repair when damage has already accumulated, counteracts accelerated ageing caused by damage retention. It prolongs the health span of individual cells which are moreover less prone to stress. In combination, damage retention and early investment in repair are beneficial for healthy ageing in yeast cell populations.
Collapse
Affiliation(s)
- Barbara Schnitzer
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Johannes Borgqvist
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
9
|
Barth E, Sieber P, Stark H, Schuster S. Robustness during Aging-Molecular Biological and Physiological Aspects. Cells 2020; 9:E1862. [PMID: 32784503 PMCID: PMC7465392 DOI: 10.3390/cells9081862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the process of aging is still an important challenge to enable healthy aging and to prevent age-related diseases. Most studies in age research investigate the decline in organ functionality and gene activity with age. The focus on decline can even be considered a paradigm in that field. However, there are certain aspects that remain surprisingly stable and keep the organism robust. Here, we present and discuss various properties of robust behavior during human and animal aging, including physiological and molecular biological features, such as the hematocrit, body temperature, immunity against infectious diseases and others. We examine, in the context of robustness, the different theories of how aging occurs. We regard the role of aging in the light of evolution.
Collapse
Affiliation(s)
- Emanuel Barth
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Patricia Sieber
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Heiko Stark
- Institute of Zoology and Evolutionary Research with Phyletic Museum, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Stefan Schuster
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany;
| |
Collapse
|
10
|
Lindberg RT, Collins S. Quality-quantity trade-offs drive functional trait evolution in a model microalgal 'climate change winner'. Ecol Lett 2020; 23:780-790. [PMID: 32067351 DOI: 10.1111/ele.13478] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/08/2019] [Accepted: 01/08/2020] [Indexed: 01/05/2023]
Abstract
Phytoplankton are the unicellular photosynthetic microbes that form the base of aquatic ecosystems, and their responses to global change will impact everything from food web dynamics to global nutrient cycles. Some taxa respond to environmental change by increasing population growth rates in the short-term and are projected to increase in frequency over decades. To gain insight into how these projected 'climate change winners' evolve, we grew populations of microalgae in ameliorated environments for several hundred generations. Most populations evolved to allocate a smaller proportion of carbon to growth while increasing their ability to tolerate and metabolise reactive oxygen species (ROS). This trade-off drives the evolution of traits that underlie the ecological and biogeochemical roles of phytoplankton. This offers evolutionary and a metabolic frameworks for understanding trait evolution in projected 'climate change winners' and suggests that short-term population booms have the potential to be dampened or reversed when environmental amelioration persists.
Collapse
Affiliation(s)
- Rasmus T Lindberg
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Sinéad Collins
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| |
Collapse
|
11
|
Synergistic effects of repair, resilience and retention of damage determine the conditions for replicative ageing. Sci Rep 2020; 10:1556. [PMID: 32005954 PMCID: PMC6994596 DOI: 10.1038/s41598-020-58444-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 01/15/2020] [Indexed: 12/31/2022] Open
Abstract
Accumulation of damaged proteins is a hallmark of ageing, occurring in organisms ranging from bacteria and yeast to mammalian cells. During cell division in Saccharomyces cerevisiae, damaged proteins are retained within the mother cell, resulting in an ageing mother while a new daughter cell exhibits full replicative potential. The cell-specific features determining the ageing remain elusive. It has been suggested that the replicative ageing is dependent on the ability of the cell to repair and retain pre-existing damage. To deepen the understanding of how these factors influence the life of individual cells, we developed and experimentally validated a dynamic model of damage accumulation accounting for replicative ageing on the single cell level. The model includes five essential properties: cell growth, damage formation, damage repair, cell division and cell death, represented in a theoretical framework describing the conditions allowing for replicative ageing, starvation, immortality or clonal senescence. We introduce the resilience to damage, which can be interpreted as the difference in volume between an old and a young cell. We show that the capacity to retain damage deteriorates with high age, that asymmetric division allows for retention of damage, and that there is a trade-off between retention and the resilience property. Finally, we derive the maximal degree of asymmetry as a function of resilience, proposing that asymmetric cell division is beneficial with respect to replicative ageing as it increases the lifespan of a given organism. The proposed model contributes to a deeper understanding of the ageing process in eukaryotic organisms.
Collapse
|
12
|
Schramm FD, Schroeder K, Jonas K. Protein aggregation in bacteria. FEMS Microbiol Rev 2020; 44:54-72. [PMID: 31633151 PMCID: PMC7053576 DOI: 10.1093/femsre/fuz026] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/17/2019] [Indexed: 02/07/2023] Open
Abstract
Protein aggregation occurs as a consequence of perturbations in protein homeostasis that can be triggered by environmental and cellular stresses. The accumulation of protein aggregates has been associated with aging and other pathologies in eukaryotes, and in bacteria with changes in growth rate, stress resistance and virulence. Numerous past studies, mostly performed in Escherichia coli, have led to a detailed understanding of the functions of the bacterial protein quality control machinery in preventing and reversing protein aggregation. However, more recent research points toward unexpected diversity in how phylogenetically different bacteria utilize components of this machinery to cope with protein aggregation. Furthermore, how persistent protein aggregates localize and are passed on to progeny during cell division and how their presence impacts reproduction and the fitness of bacterial populations remains a controversial field of research. Finally, although protein aggregation is generally seen as a symptom of stress, recent work suggests that aggregation of specific proteins under certain conditions can regulate gene expression and cellular resource allocation. This review discusses recent advances in understanding the consequences of protein aggregation and how this process is dealt with in bacteria, with focus on highlighting the differences and similarities observed between phylogenetically different groups of bacteria.
Collapse
Affiliation(s)
- Frederic D Schramm
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm 10691, Sweden
| | - Kristen Schroeder
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm 10691, Sweden
| | - Kristina Jonas
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm 10691, Sweden
| |
Collapse
|
13
|
Abstract
Longevity reflects the ability to maintain homeostatic conditions necessary for life as an organism ages. A long-lived organism must contend not only with environmental hazards but also with internal entropy and macromolecular damage that result in the loss of fitness during ageing, a phenomenon known as senescence. Although central to many of the core concepts in biology, ageing and longevity have primarily been investigated in sexually reproducing, multicellular organisms. However, growing evidence suggests that microorganisms undergo senescence, and can also exhibit extreme longevity. In this Review, we integrate theoretical and empirical insights to establish a unified perspective on senescence and longevity. We discuss the evolutionary origins, genetic mechanisms and functional consequences of microbial ageing. In addition to having biomedical implications, insights into microbial ageing shed light on the role of ageing in the origin of life and the upper limits to longevity.
Collapse
|
14
|
Ali Q, Dainese R, Cvijovic M. Adaptive damage retention mechanism enables healthier yeast population. J Theor Biol 2019; 473:52-66. [PMID: 30980870 DOI: 10.1016/j.jtbi.2019.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 03/04/2019] [Accepted: 04/08/2019] [Indexed: 11/29/2022]
Abstract
During cytokinesis in budding yeast (Saccharomyces cerevisiae) damaged proteins are distributed asymmetrically between the daughter and the mother cell. Retention of damaged proteins is a crucial mechanism ensuring a healthy daughter cell with full replicative potential and an ageing mother cell. However, the protein quality control (PQC) system is tuned for optimal reproduction success which suggests optimal health and size of the population, rather than long-term survival of the mother cell. Modelling retention of damage as an adaptable mechanism, we propose two damage retention strategies to find an optimal way of decreasing damage retention efficiency to maximize population size and minimize the damage in the individual yeast cell. A pedigree model is used to investigate the impact of small variations in the strategies over the whole population. These impacts are based on the altruistic effects of damage retention mechanism and are measured by a cost function whose minimum value provides the optimal health and size of the population. We showed that fluctuations in the cost function allow yeast cell to continuously vary its strategy, suggesting that optimal reproduction success is a local minimum of the cost function. Our results suggest that a rapid decrease in the efficiency of damage retention, at the time when the mother cell is almost exhausted, produces fewer daughters with high levels of damaged proteins. In addition, retaining more damage during the early divisions increases the number of healthy daughters in the population.
Collapse
Affiliation(s)
- Qasim Ali
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Chalmers tvärgata 3, SE-41296 Gothenburg, Sweden; Department of Mathematics, North Carolina State University, NC 27607, USA
| | - Riccardo Dainese
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Chalmers tvärgata 3, SE-41296 Gothenburg, Sweden; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marija Cvijovic
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Chalmers tvärgata 3, SE-41296 Gothenburg, Sweden.
| |
Collapse
|
15
|
Ogrodnik M, Salmonowicz H, Gladyshev VN. Integrating cellular senescence with the concept of damage accumulation in aging: Relevance for clearance of senescent cells. Aging Cell 2019; 18:e12841. [PMID: 30346102 PMCID: PMC6351832 DOI: 10.1111/acel.12841] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/31/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022] Open
Abstract
Understanding the aging process and ways to manipulate it is of major importance for biology and medicine. Among the many aging theories advanced over the years, the concept most consistent with experimental evidence posits the buildup of numerous forms of molecular damage as a foundation of the aging process. Here, we discuss that this concept integrates well with recent findings on cellular senescence, offering a novel view on the role of senescence in aging and age‐related disease. Cellular senescence has a well‐established role in cellular aging, but its impact on the rate of organismal aging is less defined. One of the most prominent features of cellular senescence is its association with macromolecular damage. The relationship between cell senescence and damage concerns both damage as a molecular signal of senescence induction and accelerated accumulation of damage in senescent cells. We describe the origin, regulatory mechanisms, and relevance of various damage forms in senescent cells. This view on senescent cells as carriers and inducers of damage puts new light on senescence, considering it as a significant contributor to the rise in organismal damage. Applying these ideas, we critically examine current evidence for a role of cellular senescence in aging and age‐related diseases. We also discuss the differential impact of longevity interventions on senescence burden and other types of age‐related damage. Finally, we propose a model on the role of aging‐related damage accumulation and the rate of aging observed upon senescent cell clearance.
Collapse
Affiliation(s)
- Mikolaj Ogrodnik
- Institute for Cell and Molecular Biosciences; Newcastle University Institute for Ageing; Newcastle upon Tyne UK
| | - Hanna Salmonowicz
- Institute for Cell and Molecular Biosciences; Newcastle University Institute for Ageing; Newcastle upon Tyne UK
| | - Vadim N. Gladyshev
- Division of Genetics; Department of Medicine; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
| |
Collapse
|
16
|
Dühring S, Ewald J, Germerodt S, Kaleta C, Dandekar T, Schuster S. Modelling the host-pathogen interactions of macrophages and Candida albicans using Game Theory and dynamic optimization. J R Soc Interface 2018; 14:rsif.2017.0095. [PMID: 28701506 PMCID: PMC5550964 DOI: 10.1098/rsif.2017.0095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/16/2017] [Indexed: 12/21/2022] Open
Abstract
The release of fungal cells following macrophage phagocytosis, called non-lytic expulsion, is reported for several fungal pathogens. On one hand, non-lytic expulsion may benefit the fungus in escaping the microbicidal environment of the phagosome. On the other hand, the macrophage could profit in terms of avoiding its own lysis and being able to undergo proliferation. To analyse the causes of non-lytic expulsion and the relevance of macrophage proliferation in the macrophage–Candida albicans interaction, we employ Evolutionary Game Theory and dynamic optimization in a sequential manner. We establish a game-theoretical model describing the different strategies of the two players after phagocytosis. Depending on the parameter values, we find four different Nash equilibria and determine the influence of the systems state of the host upon the game. As our Nash equilibria are a direct consequence of the model parameterization, we can depict several biological scenarios. A parameter region, where the host response is robust against the fungal infection, is determined. We further apply dynamic optimization to analyse whether macrophage mitosis is relevant in the host–pathogen interaction of macrophages and C. albicans. For this, we study the population dynamics of the macrophage–C. albicans interactions and the corresponding optimal controls for the macrophages, indicating the best macrophage strategy of switching from proliferation to attacking fungal cells.
Collapse
Affiliation(s)
- Sybille Dühring
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Jan Ewald
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Sebastian Germerodt
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Thomas Dandekar
- Biocenter, Department of Bioinformatics, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| |
Collapse
|
17
|
Koch C, Müller S. Personalized microbiome dynamics – Cytometric fingerprints for routine diagnostics. Mol Aspects Med 2018; 59:123-134. [DOI: 10.1016/j.mam.2017.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/26/2017] [Accepted: 06/28/2017] [Indexed: 02/06/2023]
|
18
|
Kreft JU, Plugge CM, Prats C, Leveau JHJ, Zhang W, Hellweger FL. From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality. Front Microbiol 2017; 8:2299. [PMID: 29230200 PMCID: PMC5711835 DOI: 10.3389/fmicb.2017.02299] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/07/2017] [Indexed: 01/04/2023] Open
Abstract
Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level. We review published models that explicitly consider genes and make predictions at the population or ecosystem level. The models can be grouped into three general approaches, i.e., metabolic flux, gene-centric and agent-based. We describe and contrast these approaches by applying them to a hypothetical ecosystem and discuss their strengths and weaknesses. An important distinguishing feature is how variation between individual cells (individuality) is handled. In microbial ecosystems, individual heterogeneity is generated by a number of mechanisms including stochastic interactions of molecules (e.g., gene expression), stochastic and deterministic cell division asymmetry, small-scale environmental heterogeneity, and differential transport in a heterogeneous environment. This heterogeneity can then be amplified and transferred to other cell properties by several mechanisms, including nutrient uptake, metabolism and growth, cell cycle asynchronicity and the effects of age and damage. For example, stochastic gene expression may lead to heterogeneity in nutrient uptake enzyme levels, which in turn results in heterogeneity in intracellular nutrient levels. Individuality can have important ecological consequences, including division of labor, bet hedging, aging and sub-optimality. Understanding the importance of individuality and the mechanism(s) underlying it for the specific microbial system and question investigated is essential for selecting the optimal modeling strategy.
Collapse
Affiliation(s)
- Jan-Ulrich Kreft
- Centre for Computational Biology, Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Clara Prats
- Department of Physics, School of Agricultural Engineering of Barcelona, Universitat Politècnica de Catalunya-BarcelonaTech, Castelldefels, Spain
| | - Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Ferdi L Hellweger
- Civil and Environmental Engineering Department, Marine and Environmental Sciences Department, Bioengineering Department, Northeastern University, Boston, MA, United States
| |
Collapse
|
19
|
Florea M. Aging and immortality in unicellular species. Mech Ageing Dev 2017; 167:5-15. [PMID: 28844968 DOI: 10.1016/j.mad.2017.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/21/2017] [Accepted: 08/13/2017] [Indexed: 12/22/2022]
Abstract
It has been historically thought that in conditions that permit growth, most unicellular species do not to age. This was particularly thought to be the case for symmetrically dividing species, as such species lack a clear distinction between the soma and the germline. Despite this, studies of the symmetrically dividing species Escherichia coli and Schizosaccharomyces pombe have recently started to challenge this notion. They indicate that E. coli and S. pombe do age, but only when subjected to environmental stress. If true, this suggests that aging may be widespread among microbial species in general, and that studying aging in microbes may inform other long-standing questions in aging. This review examines the recent evidence for and against replicative aging in symmetrically dividing unicellular organisms, the mechanisms that underlie aging, why aging evolved in these species, and how microbial aging fits into the context of other questions in aging.
Collapse
Affiliation(s)
- Michael Florea
- Graduate School of Arts and Sciences, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA.
| |
Collapse
|
20
|
Collins S. Growth rate evolution in improved environments under Prodigal Son dynamics. Evol Appl 2016; 9:1179-1188. [PMID: 27695525 PMCID: PMC5039330 DOI: 10.1111/eva.12403] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/06/2016] [Indexed: 01/17/2023] Open
Abstract
I use an individual-based model to investigate the evolution of cell division rates in asexual populations under chronic environmental enrichment. I show that maintaining increased growth rates over hundreds of generations following environmental improvement can be limited by increases in cellular damage associated with more rapid reproduction. In the absence of further evolution to either increase damage tolerance or decrease the cost of repair or rate of damage, environmental improvement does not reliably lead to long-term increases in reproductive rate in microbes. Here, more rapid cell division rates also increases damage, leading to selection for damage avoidance or repair, and a subsequent decrease in population growth, which I call Prodigal Son dynamics, because the consequences of 'living fast' force a return to ancestral growth rates. Understanding the conditions under which environmental enrichment is expected to sustainably increase cell division rates is important in applications that require rapid cell division (e.g. biofuel reactors) or seek to avoid the emergence of rapid cell division rates (controlling biofouling).
Collapse
Affiliation(s)
- Sinéad Collins
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
| |
Collapse
|
21
|
Vedel S, Nunns H, Košmrlj A, Semsey S, Trusina A. Asymmetric Damage Segregation Constitutes an Emergent Population-Level Stress Response. Cell Syst 2016; 3:187-198. [PMID: 27426983 DOI: 10.1016/j.cels.2016.06.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 04/05/2016] [Accepted: 06/16/2016] [Indexed: 01/15/2023]
Abstract
Asymmetric damage segregation (ADS) is a mechanism for increasing population fitness through non-random, asymmetric partitioning of damaged macromolecules at cell division. ADS has been reported across multiple organisms, though the measured effects on fitness of individuals are often small. Here, we introduce a cell-lineage-based framework that quantifies the population-wide effects of ADS and then verify our results experimentally in E. coli under heat and antibiotic stress. Using an experimentally validated mathematical model, we find that the beneficial effect of ADS increases with stress. In effect, low-damage subpopulations divide faster and amplify within the population acting like a positive feedback loop whose strength scales with stress. Analysis of protein aggregates shows that the degree of asymmetric inheritance is damage dependent in single cells. Together our results indicate that, despite small effects in single cell, ADS exerts a strong beneficial effect on the population level and arises from the redistribution of damage within a population, through both single-cell and population-level feedback.
Collapse
Affiliation(s)
- Søren Vedel
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark; Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark.
| | - Harry Nunns
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Szabolcs Semsey
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Ala Trusina
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark.
| |
Collapse
|
22
|
Günther S, Faust K, Schumann J, Harms H, Raes J, Müller S. Species-sorting and mass-transfer paradigms control managed natural metacommunities. Environ Microbiol 2016; 18:4862-4877. [DOI: 10.1111/1462-2920.13402] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/30/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Susanne Günther
- Department of Environmental Microbiology; Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
| | - Karoline Faust
- VIB Center for the Biology of Disease, KU Leuven, O&N 4; Herestraat 49 3000 Leuven Belgium
- Department of Microbiology and Immunology; KU Leuven, O&N 4; Herestraat 49 3000 Leuven Belgium
- Bioengineering Sciences; Vrije Universiteit Brussel; Pleinlaan 2 1050 Brussels Belgium
| | - Joachim Schumann
- Department of Environmental Microbiology; Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
| | - Hauke Harms
- Department of Environmental Microbiology; Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
| | - Jeroen Raes
- VIB Center for the Biology of Disease, KU Leuven, O&N 4; Herestraat 49 3000 Leuven Belgium
- Department of Microbiology and Immunology; KU Leuven, O&N 4; Herestraat 49 3000 Leuven Belgium
| | - Susann Müller
- Department of Environmental Microbiology; Helmholtz Centre for Environmental Research; Permoserstr. 15 04318 Leipzig Germany
| |
Collapse
|
23
|
Abstract
Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage-CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE).
Collapse
|
24
|
Chao L, Rang CU, Proenca AM, Chao JU. Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation. PLoS Comput Biol 2016; 12:e1004700. [PMID: 26761487 PMCID: PMC4711911 DOI: 10.1371/journal.pcbi.1004700] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/10/2015] [Indexed: 11/18/2022] Open
Abstract
Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother's old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother's old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington's genetic assimilation. Our model is able to quantify the evolution of the assimilation because it characterizes the fitness consequences of variation.
Collapse
Affiliation(s)
- Lin Chao
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Camilla Ulla Rang
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Audrey Menegaz Proenca
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, Brazil
| | - Jasper Ubirajara Chao
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| |
Collapse
|
25
|
Oliveira SMD, Neeli-Venkata R, Goncalves NSM, Santinha JA, Martins L, Tran H, Mäkelä J, Gupta A, Barandas M, Häkkinen A, Lloyd-Price J, Fonseca JM, Ribeiro AS. Increased cytoplasm viscosity hampers aggregate polar segregation inEscherichia coli. Mol Microbiol 2015; 99:686-99. [DOI: 10.1111/mmi.13257] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Samuel M. D. Oliveira
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Ramakanth Neeli-Venkata
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Nadia S. M. Goncalves
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - João A. Santinha
- UNINOVA; Instituto de Desenvolvimento de Novas Tecnologias; Campus FCT-UNL; 2829-516 Caparica Portugal
| | - Leonardo Martins
- UNINOVA; Instituto de Desenvolvimento de Novas Tecnologias; Campus FCT-UNL; 2829-516 Caparica Portugal
| | - Huy Tran
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Jarno Mäkelä
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Abhishekh Gupta
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Marilia Barandas
- UNINOVA; Instituto de Desenvolvimento de Novas Tecnologias; Campus FCT-UNL; 2829-516 Caparica Portugal
| | - Antti Häkkinen
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - Jason Lloyd-Price
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| | - José M. Fonseca
- UNINOVA; Instituto de Desenvolvimento de Novas Tecnologias; Campus FCT-UNL; 2829-516 Caparica Portugal
| | - Andre S. Ribeiro
- Laboratory of Biosystem Dynamics; Department of Signal Processing; Tampere University of Technology; 33101 Tampere Finland
| |
Collapse
|
26
|
Lade SJ, Coelho M, Tolić IM, Gross T. Fusion leads to effective segregation of damage during cell division: An analytical treatment. J Theor Biol 2015; 378:47-55. [PMID: 25934351 DOI: 10.1016/j.jtbi.2015.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/13/2015] [Accepted: 04/19/2015] [Indexed: 11/17/2022]
Abstract
High levels of cellular damage are associated with impairment of cellular function and cell death. Partitioning the damage into a fraction of cells in the population improves population fitness and survival. We have previously shown that protein aggregates, resulting from misfolded, damaged proteins, fuse with each other leading to damage partitioning during cell division. Here, using an analytical treatment of aggregate fusion in dividing cells we present analytical expressions for two measures of damage partition: aggregate mass partition asymmetry between two dividing cells and standard deviation of total aggregate mass across the population. The scaling laws obtained demonstrate how damage partition may generally depend on characteristics of the cellular processes, facilitating better understanding of damage segregation in biological cells.
Collapse
Affiliation(s)
- Steven J Lade
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.
| | - Miguel Coelho
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Iva M Tolić
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany; Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Thilo Gross
- Department of Engineering Mathematics, University of Bristol, BS8 1UB Bristol, UK
| |
Collapse
|
27
|
From protein damage to cell aging to population fitness in E. coli: Insights from a multi-level agent-based model. Ecol Modell 2015. [DOI: 10.1016/j.ecolmodel.2015.01.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|