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Pan J, Williams E, Sung W, Lynch M, Long H. The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:20-27. [PMID: 33791681 PMCID: PMC8009600 DOI: 10.1007/s42995-020-00060-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Mutation is a primary source of genetic variation that is used to power evolution. Many studies, however, have shown that most mutations are deleterious and, as a result, extremely low mutation rates might be beneficial for survival. Using a mutation accumulation experiment, an unbiased method for mutation study, we found an extremely low base-substitution mutation rate of 5.94 × 10-11 per nucleotide site per cell division (95% Poisson confidence intervals: 4.65 × 10-11, 7.48 × 10-11) and indel mutation rate of 8.25 × 10-12 per site per cell division (95% confidence intervals: 3.96 × 10-12, 1.52 × 10-11) in the bacterium Photorhabdus luminescens ATCC29999. The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction. It has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the effective population size (drift-barrier hypothesis) and we found that the effective population size of this bacterium is significantly greater than most other bacteria. This finding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fidelity can evolve within organisms that maintain large effective population sizes.
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Affiliation(s)
- Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Emily Williams
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85281 USA
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223 USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85281 USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
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2
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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Aston E, Channon A, Belavkin RV, Gifford DR, Krašovec R, Knight CG. Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover. Sci Rep 2017; 7:15519. [PMID: 29138394 PMCID: PMC5686101 DOI: 10.1038/s41598-017-14628-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/02/2017] [Indexed: 01/22/2023] Open
Abstract
The critical mutation rate (CMR) determines the shift between survival-of-the-fittest and survival of individuals with greater mutational robustness ("flattest"). We identify an inverse relationship between CMR and sequence length in an in silico system with a two-peak fitness landscape; CMR decreases to no more than five orders of magnitude above estimates of eukaryotic per base mutation rate. We confirm the CMR reduces exponentially at low population sizes, irrespective of peak radius and distance, and increases with the number of genetic crossovers. We also identify an inverse relationship between CMR and the number of genes, confirming that, for a similar number of genes to that for the plant Arabidopsis thaliana (25,000), the CMR is close to its known wild-type mutation rate; mutation rates for additional organisms were also found to be within one order of magnitude of the CMR. This is the first time such a simulation model has been assigned input and produced output within range for a given biological organism. The decrease in CMR with population size previously observed is maintained; there is potential for the model to influence understanding of populations undergoing bottleneck, stress, and conservation strategy for populations near extinction.
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Affiliation(s)
- Elizabeth Aston
- School of Computing and Mathematics, Keele University, Keele, Staffordshire, UK.
| | - Alastair Channon
- School of Computing and Mathematics, Keele University, Keele, Staffordshire, UK
| | - Roman V Belavkin
- School of Engineering and Information Sciences, Middlesex University, London, UK
| | - Danna R Gifford
- Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Rok Krašovec
- Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Christopher G Knight
- Faculty of Science and Engineering, The University of Manchester, Manchester, UK
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Swings T, Van den Bergh B, Wuyts S, Oeyen E, Voordeckers K, Verstrepen KJ, Fauvart M, Verstraeten N, Michiels J. Adaptive tuning of mutation rates allows fast response to lethal stress in Escherichia coli. eLife 2017; 6. [PMID: 28460660 PMCID: PMC5429094 DOI: 10.7554/elife.22939] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
While specific mutations allow organisms to adapt to stressful environments, most changes in an organism's DNA negatively impact fitness. The mutation rate is therefore strictly regulated and often considered a slowly-evolving parameter. In contrast, we demonstrate an unexpected flexibility in cellular mutation rates as a response to changes in selective pressure. We show that hypermutation independently evolves when different Escherichia coli cultures adapt to high ethanol stress. Furthermore, hypermutator states are transitory and repeatedly alternate with decreases in mutation rate. Specifically, population mutation rates rise when cells experience higher stress and decline again once cells are adapted. Interestingly, we identified cellular mortality as the major force driving the quick evolution of mutation rates. Together, these findings show how organisms balance robustness and evolvability and help explain the prevalence of hypermutation in various settings, ranging from emergence of antibiotic resistance in microbes to cancer relapses upon chemotherapy.
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Affiliation(s)
- Toon Swings
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Sander Wuyts
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Eline Oeyen
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Karin Voordeckers
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium.,VIB Laboratory for Genetics and Genomics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Kevin J Verstrepen
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium.,VIB Laboratory for Genetics and Genomics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium.,Smart Systems and Emerging Technologies Unit, Imec (Interuniversity Micro-Electronics Centre), Leuven, Belgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
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Abstract
Mutations are the ultimate source of variation used for evolutionary adaptation, while also being predominantly deleterious and a source of genetic disorders. Understanding the rate of insertion-deletion mutations (indels) is essential to understanding evolutionary processes, especially in coding regions, where such mutations can disrupt production of essential proteins. Using direct estimates of indel rates from 14 phylogenetically diverse eukaryotic and bacterial species, along with measures of standing variation in such species, we obtain results that imply an inverse relationship of mutation rate and effective population size. These results, which corroborate earlier observations on the base-substitution mutation rate, appear most compatible with the hypothesis that natural selection reduces mutation rates per effective genome to the point at which the power of random genetic drift (approximated by the inverse of effective population size) becomes overwhelming. Given the substantial differences in DNA metabolism pathways that give rise to these two types of mutations, this consistency of results raises the possibility that refinement of other molecular and cellular traits may be inversely related to species-specific levels of random genetic drift.
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The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway. G3-GENES GENOMES GENETICS 2016; 6:2157-63. [PMID: 27194804 PMCID: PMC4938668 DOI: 10.1534/g3.116.030130] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mycobacterium smegmatis is a bacterium that is naturally devoid of known postreplicative DNA mismatch repair (MMR) homologs, mutS and mutL, providing an opportunity to investigate how the mutation rate and spectrum has evolved in the absence of a highly conserved primary repair pathway. Mutation accumulation experiments of M. smegmatis yielded a base-substitution mutation rate of 5.27 × 10−10 per site per generation, or 0.0036 per genome per generation, which is surprisingly similar to the mutation rate in MMR-functional unicellular organisms. Transitions were found more frequently than transversions, with the A:T→G:C transition rate significantly higher than the G:C→A:T transition rate, opposite to what is observed in most studied bacteria. We also found that the transition-mutation rate of M. smegmatis is significantly lower than that of other naturally MMR-devoid or MMR-knockout organisms. Two possible candidates that could be responsible for maintaining high DNA fidelity in this MMR-deficient organism are the ancestral-like DNA polymerase DnaE1, which contains a highly efficient DNA proofreading histidinol phosphatase (PHP) domain, and/or the existence of a uracil-DNA glycosylase B (UdgB) homolog that might protect the GC-rich M. smegmatis genome against DNA damage arising from oxidation or deamination. Our results suggest that M. smegmatis has a noncanonical Dam (DNA adenine methylase) methylation system, with target motifs differing from those previously reported. The mutation features of M. smegmatis provide further evidence that genomes harbor alternative routes for improving replication fidelity, even in the absence of major repair pathways.
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Ness RW, Morgan AD, Vasanthakrishnan RB, Colegrave N, Keightley PD. Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii. Genome Res 2015; 25:1739-49. [PMID: 26260971 PMCID: PMC4617969 DOI: 10.1101/gr.191494.115] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 07/30/2015] [Indexed: 12/17/2022]
Abstract
Describing the process of spontaneous mutation is fundamental for understanding the genetic basis of disease, the threat posed by declining population size in conservation biology, and much of evolutionary biology. Directly studying spontaneous mutation has been difficult, however, because new mutations are rare. Mutation accumulation (MA) experiments overcome this by allowing mutations to build up over many generations in the near absence of natural selection. Here, we sequenced the genomes of 85 MA lines derived from six genetically diverse strains of the green alga Chlamydomonas reinhardtii. We identified 6843 new mutations, more than any other study of spontaneous mutation. We observed sevenfold variation in the mutation rate among strains and that mutator genotypes arose, increasing the mutation rate approximately eightfold in some replicates. We also found evidence for fine-scale heterogeneity in the mutation rate, with certain sequence motifs mutating at much higher rates, and clusters of multiple mutations occurring at closely linked sites. There was little evidence, however, for mutation rate heterogeneity between chromosomes or over large genomic regions of 200 kbp. We generated a predictive model of the mutability of sites based on their genomic properties, including local GC content, gene expression level, and local sequence context. Our model accurately predicted the average mutation rate and natural levels of genetic diversity of sites across the genome. Notably, trinucleotides vary 17-fold in rate between the most and least mutable sites. Our results uncover a rich heterogeneity in the process of spontaneous mutation both among individuals and across the genome.
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Affiliation(s)
- Rob W Ness
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Labs, King's Buildings, Edinburgh EH9 3JT, Scotland
| | - Andrew D Morgan
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Labs, King's Buildings, Edinburgh EH9 3JT, Scotland
| | | | - Nick Colegrave
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Labs, King's Buildings, Edinburgh EH9 3JT, Scotland
| | - Peter D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Labs, King's Buildings, Edinburgh EH9 3JT, Scotland
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Synthetic microbial ecosystems for biotechnology. Biotechnol Lett 2014; 36:1141-51. [PMID: 24563311 DOI: 10.1007/s10529-014-1480-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/31/2014] [Indexed: 12/11/2022]
Abstract
Most highly controlled and specific applications of microorganisms in biotechnology involve pure cultures. Maintaining single strain cultures is important for industry as contaminants can reduce productivity and lead to longer "down-times" during sterilisation. However, microbes working together provide distinct advantages over pure cultures. They can undertake more metabolically complex tasks, improve efficiency and even expand applications to open systems. By combining rapidly advancing technologies with ecological theory, the use of microbial ecosystems in biotechnology will inevitably increase. This review provides insight into the use of synthetic microbial communities in biotechnology by applying the engineering paradigm of measure, model, manipulate and manufacture, and illustrate the emerging wider potential of the synthetic ecology field. Systems to improve biofuel production using microalgae are also discussed.
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Rétaux S, Casane D. Evolution of eye development in the darkness of caves: adaptation, drift, or both? EvoDevo 2013; 4:26. [PMID: 24079393 PMCID: PMC3849642 DOI: 10.1186/2041-9139-4-26] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 08/05/2013] [Indexed: 11/10/2022] Open
Abstract
Animals inhabiting the darkness of caves are generally blind and de-pigmented, regardless of the phylum they belong to. Survival in this environment is an enormous challenge, the most obvious being to find food and mates without the help of vision, and the loss of eyes in cave animals is often accompanied by an enhancement of other sensory apparatuses. Here we review the recent literature describing developmental biology and molecular evolution studies in order to discuss the evolutionary mechanisms underlying adaptation to life in the dark. We conclude that both genetic drift (neutral hypothesis) and direct and indirect selection (selective hypothesis) occurred together during the loss of eyes in cave animals. We also identify some future directions of research to better understand adaptation to total darkness, for which integrative analyses relying on evo-devo approaches associated with thorough ecological and population genomic studies should shed some light.
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Affiliation(s)
- Sylvie Rétaux
- DECA group, Neurobiology & Development Laboratory, CNRS, Gif sur Yvette, France
| | - Didier Casane
- LEGS, CNRS, Gif sur Yvette and Université Paris Diderot, Sorbonne Paris Cité, France
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