51
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Wang W, Wang T, Gao Y, Liang G, Pu Y, Zhang J. Model of neural development by differentiating human induced pluripotent stem cells into neural progenitor cells to study the neurodevelopmental toxicity of lead. Food Chem Toxicol 2023; 179:113947. [PMID: 37467947 DOI: 10.1016/j.fct.2023.113947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Lead (Pb) exposure causes immeasurable damage to multiple human systems, particularly the central nervous system (CNS). In this study, human induced pluripotent stem cells (hiPSCs) were differentiated into neural progenitor cells (NPCs) to investigate the neurotoxic effects of Pb. The hiPSCs were treated with 0, 0.5, 1.0, 2.5, 5.0 and 10.0 μmol/L Pb for 7 days, whereas embryoid bodies (EBs) and NPCs were treated with 0, 0.1, 0.5, and 1.0 μmol/L Pb for 7 days. Pb exposure disrupted the cell cycle and caused apoptosis in hiPSCs, EBs, and NPCs. Besides, Pb inhibited the differentiation of NPCs and EBs. Whole exome sequencing revealed 2509, 2413, and 1984 single nucleotide variants (SNVs) caused by Pb in hiPSCs, EBs, and NPCs, respectively. The common mutation sites in the exon region were mostly nonsynonymous mutations. We identified 18, 19, and 18 common deleterious mutations in hiPSCs, EBs, and NPCs, respectively. Additionally, Online Mendelian Inheritance in Man database analysis revealed 30, 20, and 13 genes related to CNS disorders in hiPSCs, EBs, and NPCs, respectively. Our findings suggest that this in vitro model may supplement animal models and be applied to the study of neurodevelopmental toxicity in the future.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Tong Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Yu Gao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Geyu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Juan Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, 210009, China; Jiangsu Institute for Sports and Health (JISH), Nanjing, 211100, China.
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52
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Lobinska G, Pilpel Y, Ram Y. Phenotype switching of the mutation rate facilitates adaptive evolution. Genetics 2023; 225:iyad111. [PMID: 37293818 PMCID: PMC10471227 DOI: 10.1093/genetics/iyad111] [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: 02/05/2023] [Revised: 02/05/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
The mutation rate plays an important role in adaptive evolution. It can be modified by mutator and anti-mutator alleles. Recent empirical evidence hints that the mutation rate may vary among genetically identical individuals: evidence from bacteria suggests that the mutation rate can be affected by expression noise of a DNA repair protein and potentially also by translation errors in various proteins. Importantly, this non-genetic variation may be heritable via a transgenerational epigenetic mode of inheritance, giving rise to a mutator phenotype that is independent from mutator alleles. Here, we investigate mathematically how the rate of adaptive evolution is affected by the rate of mutation rate phenotype switching. We model an asexual population with two mutation rate phenotypes, non-mutator and mutator. An offspring may switch from its parental phenotype to the other phenotype. We find that switching rates that correspond to so-far empirically described non-genetic systems of inheritance of the mutation rate lead to higher rates of adaptation on both artificial and natural fitness landscapes. These switching rates can maintain within the same individuals both a mutator phenotype and intermediary mutations, a combination that facilitates adaptation. Moreover, non-genetic inheritance increases the proportion of mutators in the population, which in turn increases the probability of hitchhiking of the mutator phenotype with adaptive mutations. This in turns facilitates the acquisition of additional adaptive mutations. Our results rationalize recently observed noise in the expression of proteins that affect the mutation rate and suggest that non-genetic inheritance of this phenotype may facilitate evolutionary adaptive processes.
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Affiliation(s)
- Gabriela Lobinska
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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53
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Liu W, Zuo S, Shao Y, Bi K, Zhao J, Huang L, Xu Z, Lian J. Retron-mediated multiplex genome editing and continuous evolution in Escherichia coli. Nucleic Acids Res 2023; 51:8293-8307. [PMID: 37471041 PMCID: PMC10450171 DOI: 10.1093/nar/gkad607] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/02/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
While there are several genome editing techniques available, few are suitable for dynamic and simultaneous mutagenesis of arbitrary targeted sequences in prokaryotes. Here, to address these limitations, we present a versatile and multiplex retron-mediated genome editing system (REGES). First, through systematic optimization of REGES, we achieve efficiency of ∼100%, 85 ± 3%, 69 ± 14% and 25 ± 14% for single-, double-, triple- and quadruple-locus genome editing, respectively. In addition, we employ REGES to generate pooled and barcoded variant libraries with degenerate RBS sequences to fine-tune the expression level of endogenous and exogenous genes, such as transcriptional factors to improve ethanol tolerance and biotin biosynthesis. Finally, we demonstrate REGES-mediated continuous in vivo protein evolution, by combining retron, polymerase-mediated base editing and error-prone transcription. By these case studies, we demonstrate REGES as a powerful multiplex genome editing and continuous evolution tool with broad applications in synthetic biology and metabolic engineering.
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Affiliation(s)
- Wenqian Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Siqi Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Youran Shao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ke Bi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiarun Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
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54
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Cebrián-Sastre E, Chiner-Oms A, Torres-Pérez R, Comas I, Oliveros JC, Blázquez J, Castañeda-García A. Selective Pressure by Rifampicin Modulates Mutation Rates and Evolutionary Trajectories of Mycobacterial Genomes. Microbiol Spectr 2023; 11:e0101723. [PMID: 37436169 PMCID: PMC10433840 DOI: 10.1128/spectrum.01017-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/16/2023] [Indexed: 07/13/2023] Open
Abstract
Resistance to the frontline antibiotic rifampicin constitutes a challenge to the treatment and control of tuberculosis. Here, we analyzed the mutational landscape of Mycobacterium smegmatis during long-term evolution with increasing concentrations of rifampicin, using a mutation accumulation assay combined with whole-genome sequencing. Antibiotic treatment enhanced the acquisition of mutations, doubling the genome-wide mutation rate of the wild-type cells. While antibiotic exposure led to extinction of almost all wild-type lines, the hypermutable phenotype of the ΔnucS mutant strain (noncanonical mismatch repair deficient) provided an efficient response to the antibiotic, leading to high rates of survival. This adaptative advantage resulted in the emergence of higher levels of rifampicin resistance, an accelerated acquisition of drug resistance mutations in rpoB (β RNA polymerase), and a wider diversity of evolutionary pathways that led to drug resistance. Finally, this approach revealed a subset of adaptive genes under positive selection with rifampicin that could be associated with the development of antibiotic resistance. IMPORTANCE Rifampicin is the most important first-line antibiotic against mycobacterial infections, including tuberculosis, one of the top causes of death worldwide. Acquisition of rifampicin resistance constitutes a major global public health problem that makes the control of the disease challenging. Here, we performed an experimental evolution assay under antibiotic selection to analyze the response and adaptation of mycobacteria, leading to the acquisition of rifampicin resistance. This approach explored the total number of mutations that arose in the mycobacterial genomes under long-term rifampicin exposure, using whole-genome sequencing. Our results revealed the effect of rifampicin at a genomic level, identifying different mechanisms and multiple pathways leading to rifampicin resistance in mycobacteria. Moreover, this study detected that an increase in the rate of mutations led to enhanced levels of drug resistance and survival. In summary, all of these results could be useful to understand and prevent the emergence of drug-resistant isolates in mycobacterial infections.
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Affiliation(s)
- E. Cebrián-Sastre
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - A. Chiner-Oms
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - R. Torres-Pérez
- Servicio de Bioinformática para Genómica y Proteómica. Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - I. Comas
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - J. C. Oliveros
- Servicio de Bioinformática para Genómica y Proteómica. Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - J. Blázquez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - A. Castañeda-García
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (CNM-ISCIII), Majadahonda (Madrid), Spain
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55
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Roig Molina FJ, Amaro González C, Alcaine Otín A, Carro Fernández J. Vibrio vulnificus mutation rate: an in vitro approach. Front Microbiol 2023; 14:1223293. [PMID: 37621400 PMCID: PMC10445137 DOI: 10.3389/fmicb.2023.1223293] [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: 05/15/2023] [Accepted: 07/13/2023] [Indexed: 08/26/2023] Open
Abstract
Vibrio vulnificus is a multi-host pathogenic species currently subdivided into five phylogenetic lineages (L) plus one pathovar with the ability to infect fish due to a transmissible virulence plasmid. This plasmid (or a fragment of it) has been transmitted between lineages within the species, contributing to the evolution of V. vulnificus. This study aimed to provide an experimental approximation to the V. vulnificus mutation rate by determining spontaneous mutation rates from bacterial cultures of representants of the different lineages by whole-genome sequencing. To this purpose, synonymous SNP differences, i.e., spontaneous mutation not subjected to the evolutive forces, between initial and final culture after serial growth were evaluated and used for mutation rate calculation.
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Affiliation(s)
- Francisco Jose Roig Molina
- Computing for Medical and Biological Applications Group, Facultad de Ciencias de la Salud, Universidad San Jorge, Zaragoza, Spain
| | - Carmen Amaro González
- Departamento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain
- Estructura de Investigación Interdisciplinar en Biotecnología y Biomedicina BIOTECMED, University of Valencia, Valencia, Spain
| | - Alejandro Alcaine Otín
- Computing for Medical and Biological Applications Group, Facultad de Ciencias de la Salud, Universidad San Jorge, Zaragoza, Spain
| | - Jesús Carro Fernández
- Computing for Medical and Biological Applications Group, Facultad de Ciencias de la Salud, Universidad San Jorge, Zaragoza, Spain
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56
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Birzu G, Muralidharan HS, Goudeau D, Malmstrom RR, Fisher DS, Bhaya D. Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543983. [PMID: 37333348 PMCID: PMC10274767 DOI: 10.1101/2023.06.06.543983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.
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Affiliation(s)
- Gabriel Birzu
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | | | - Danielle Goudeau
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rex R. Malmstrom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel S. Fisher
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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57
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Buko T, Tuczko N, Ishikawa T. DNA Data Storage. BIOTECH 2023; 12:44. [PMID: 37366792 DOI: 10.3390/biotech12020044] [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: 04/20/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
The demand for data storage is growing at an unprecedented rate, and current methods are not sufficient to accommodate such rapid growth due to their cost, space requirements, and energy consumption. Therefore, there is a need for a new, long-lasting data storage medium with high capacity, high data density, and high durability against extreme conditions. DNA is one of the most promising next-generation data carriers, with a storage density of 10¹⁹ bits of data per cubic centimeter, and its three-dimensional structure makes it about eight orders of magnitude denser than other storage media. DNA amplification during PCR or replication during cell proliferation enables the quick and inexpensive copying of vast amounts of data. In addition, DNA can possibly endure millions of years if stored in optimal conditions and dehydrated, making it useful for data storage. Numerous space experiments on microorganisms have also proven their extraordinary durability in extreme conditions, which suggests that DNA could be a durable storage medium for data. Despite some remaining challenges, such as the need to refine methods for the fast and error-free synthesis of oligonucleotides, DNA is a promising candidate for future data storage.
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Affiliation(s)
- Tomasz Buko
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
| | - Nella Tuczko
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
| | - Takao Ishikawa
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
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58
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Worthan SB, McCarthy RDP, Behringer MG. Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes. J Mol Evol 2023; 91:311-324. [PMID: 36752825 PMCID: PMC10276084 DOI: 10.1007/s00239-022-10087-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/21/2022] [Indexed: 02/09/2023]
Abstract
Following the completion of an adaptive evolution experiment, fitness evaluations are routinely conducted to assess the magnitude of adaptation. In doing so, proper consideration should be given when determining the appropriate methods as trade-offs may exist between accuracy and throughput. Here, we present three instances in which small changes in the framework or execution of fitness evaluations significantly impacted the outcomes. The first case illustrates that discrepancies in fitness conclusions can arise depending on the approach to evaluating fitness, the culture vessel used, and the sampling method. The second case reveals that variations in environmental conditions can occur associated with culture vessel material. Specifically, these subtle changes can greatly affect microbial physiology leading to changes in the culture pH and distorting fitness measurements. Finally, the last case reports that heterogeneity in CFU formation time can result in inaccurate fitness conclusions. Based on each case, considerations and recommendations are presented for future adaptive evolution experiments.
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Affiliation(s)
- Sarah B Worthan
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Robert D P McCarthy
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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59
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Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220055. [PMID: 37004719 PMCID: PMC10067271 DOI: 10.1098/rstb.2022.0055] [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: 11/01/2022] [Accepted: 02/16/2023] [Indexed: 04/04/2023] Open
Abstract
Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. We argue that empirical knowledge of mutational biases is likely to improve in the near future, and that this knowledge is readily applicable to the challenges of short-term prediction. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Alejandro V. Cano
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bryan L. Gitschlag
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Hana Rozhoňová
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Rockville, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M. McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joshua L. Payne
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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60
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Deng A, Wang T, Wang J, Li L, Wang X, Liu L, Wen T. Adaptive mechanisms of Bacillus to near space extreme environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 886:163952. [PMID: 37164076 DOI: 10.1016/j.scitotenv.2023.163952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023]
Abstract
Earth's near space is an extreme atmosphere environment with high levels of radiation, low atmospheric pressure and dramatic temperature fluctuations. The region is above the flight altitude of aircraft but below the orbit of satellites, which has special and Mars-like conditions for investigating the survival and evolution of life. Technical limitations including flight devices, payloads and technologies/methodologies hinder microbiological research in near space. In this study, we investigated microbial survival and adaptive strategies in near space using a scientific balloon fight mission and multi-omics analyses. Methods for sample preparation, storage, protector and vessel were optimized to prepare the exposed microbial samples. After 3 h 17 min of exposure at a float altitude of ~32 km, only Bacillus strains were alive with survival efficiencies of 0-10-6. Diverse mutants with significantly altered metabolites were generated, firstly proving that Earth's near space could be used as a new powerful microbial breeding platform. Multi-omics analyses of mutants revealed cascade changes at the genome, transcriptome and proteome levels. In response to environmental stresses, two mutants had similar proteome changes caused by different genomic mutations and mRNA expression levels. Metabolic network analysis combined with proteins' expression levels revealed that metabolic fluxes of EMP, PPP and purine synthesis-related pathways were significantly altered to increase/decrease inosine production. Further analysis showed that proteins related to translation, molecular chaperones, cell wall/membrane, sporulation, DNA replication/repair and anti-oxidation were significantly upregulated, enabling cells to efficiently repair DNA/protein damages and improve viability against environmental stress. Overall, these results revealed genetic and metabolic responses of Bacillus to the harsh conditions in near space, providing a research basis for bacterial adaptive mechanisms in extreme environments.
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Affiliation(s)
- Aihua Deng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Tiantian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyue Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lai Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueliang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Liu
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Tingyi Wen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid medical school, University of Chinese Academy of Sciences, Beijing 100049, China; China Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, China.
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61
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Sellés Vidal L, Isalan M, Heap JT, Ledesma-Amaro R. A primer to directed evolution: current methodologies and future directions. RSC Chem Biol 2023; 4:271-291. [PMID: 37034405 PMCID: PMC10074555 DOI: 10.1039/d2cb00231k] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Directed evolution is one of the most powerful tools for protein engineering and functions by harnessing natural evolution, but on a shorter timescale. It enables the rapid selection of variants of biomolecules with properties that make them more suitable for specific applications. Since the first in vitro evolution experiments performed by Sol Spiegelman in 1967, a wide range of techniques have been developed to tackle the main two steps of directed evolution: genetic diversification (library generation), and isolation of the variants of interest. This review covers the main modern methodologies, discussing the advantages and drawbacks of each, and hence the considerations for designing directed evolution experiments. Furthermore, the most recent developments are discussed, showing how advances in the handling of ever larger library sizes are enabling new research questions to be tackled.
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Affiliation(s)
- Lara Sellés Vidal
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
- School of Life Sciences, The University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
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62
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Honma H, Takahashi N, Arisue N, Sugishita T. Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T). Microb Genom 2023; 9. [PMID: 37083479 DOI: 10.1099/mgen.0.001003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Malarial parasites exhibit extensive genomic plasticity, which induces the antigen diversification and the development of antimalarial drug resistance. Only a few studies have examined the genome maintenance mechanisms of parasites. The study aimed at elucidating the impact of a mutation in a DNA mismatch repair gene on genome stability by maintaining the mutant and wild-type parasites through serial in vitro cultures for approximately 400 days and analysing the subsequent spontaneous mutations. A P513T mutant of the DNA mismatch repair protein PfMSH2-1 from Plasmodium falciparum 3D7 was created. The mutation did not influence the base substitution rate but significantly increased the insertion/deletion (indel) mutation rate in short tandem repeats (STRs) and minisatellite loci. STR mutability was affected by allele size, genomic category and certain repeat motifs. In the mutants, significant telomere healing and homologous recombination at chromosomal ends caused extensive gene loss and generation of chimeric genes, resulting in large-scale chromosomal alteration. Additionally, the mutant showed increased tolerance to N-methyl-N'-nitro-N-nitrosoguanidine, suggesting that PfMSH2-1 was involved in recognizing DNA methylation damage. This work provides valuable insights into the role of PfMSH2-1 in genome stability and demonstrates that the genomic destabilization caused by its dysfunction may lead to antigen diversification.
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Affiliation(s)
- Hajime Honma
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Nobuyuki Takahashi
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Nobuko Arisue
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Tomohiko Sugishita
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
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Bhawsinghka N, Burkholder A, Schaaper RM. Detection of DNA replication errors and 8-oxo-dGTP-mediated mutations in E. coli by Duplex DNA Sequencing. DNA Repair (Amst) 2023; 123:103462. [PMID: 36738688 PMCID: PMC9992157 DOI: 10.1016/j.dnarep.2023.103462] [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: 10/27/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
Mutation is a phenomenon inescapable for all life-forms, including bacteria. While bacterial mutation rates are generally low due to the operation of error-avoidance systems, sometimes they are elevated by many orders of magnitude. Such a state, known as a hypermutable state, can result from exposure to stress or to harmful environments. Studies of bacterial mutation frequencies and analysis of the precise types of mutations can provide insights into the mechanisms by which mutations occur and the possible involvement of error-avoidance pathways. Several approaches have been used for this, like reporter assays involving non-essential genes or mutation accumulation over multiple generations. However, these approaches give an indirect estimation, and a more direct approach for determining mutations is desirable. With the recent development of a DNA sequencing technique known as Duplex Sequencing, it is possible to detect rare variants in a population at a frequency of 1 in 107 base pairs or less. Here, we have applied Duplex Sequencing to study spontaneous mutations in E. coli. We also investigated the production of replication errors by using a mismatch-repair defective (mutL) strain as well as oxidative-stress associated mutations using a mutT-defective strain. For DNA from a wild-type strain we obtained mutant frequencies in the range of 10-7 to 10-8 depending on the specific base-pair substitution, but we argue that these mutants merely represent a background of the system, rather than mutations that occurred in vivo. In contrast, bona-fide in vivo mutations were identified for DNA from both the mutL and mutT strains, as indicated by specific increases in base substitutions that are fully consistent with their established in vivo roles. Notably, the data reproduce the specific context effects of in vivo mutations as well as the leading vs. lagging strand bias among DNA replication errors.
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Affiliation(s)
- Niketa Bhawsinghka
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Adam Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Roel M Schaaper
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
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64
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Seng R, Phunpang R, Saiprom N, Dulsuk A, Chewapreecha C, Thaipadungpanit J, Batty EM, Chantratita W, West TE, Chantratita N. Phenotypic and genetic alterations of Burkholderia pseudomallei in patients during relapse and persistent infections. Front Microbiol 2023; 14:1103297. [PMID: 36814569 PMCID: PMC9939903 DOI: 10.3389/fmicb.2023.1103297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/09/2023] [Indexed: 02/09/2023] Open
Abstract
The bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a severe tropical disease associated with high mortality and relapse and persistent infections. Treatment of melioidosis requires prolonged antibiotic therapy; however, little is known about relapse and persistent infections, particularly the phenotypic and genetic alterations of B. pseudomallei in patients. In this study, we performed pulsed-field gel electrophoresis (PFGE) to compare the bacterial genotype between the initial isolate and the subsequent isolate from each of 23 suspected recurrent and persistent melioidosis patients in Northeast Thailand. We used whole-genome sequencing (WGS) to investigate multilocus sequence types and genetic alterations of within-host strain pairs. We also investigated the bacterial phenotypes associated with relapse and persistent infections, including multinucleated giant cell (MNGC) formation efficiency and intracellular multiplication. We first identified 13 (1.2%) relapse, 7 (0.7%) persistent, and 3 (0.3%) reinfection patients from 1,046 survivors. Each of the 20 within-host strain pairs from patients with relapse and persistent infections shared the same genotype, suggesting that the subsequent isolates arise from the infecting isolate. Logistic regression analysis of clinical data revealed regimen and duration of oral antibiotic therapies as risk factors associated with relapse and persistent infections. WGS analysis demonstrated 17 within-host genetic alteration events in 6 of 20 paired isolates, including a relatively large deletion and 16 single-nucleotide polymorphism (stocktickerSNP) mutations distributed across 12 genes. In 1 of 20 paired isolates, we observed significantly increased cell-to-cell fusion and intracellular replication in the second isolate compared with the initial isolate from a patient with persistent infection. WGS analysis suggested that a non-synonymous mutation in the tssB-5 gene, which encoded an essential component of the type VI secretion system, may be associated with the increased intracellular replication and MNGC formation efficiency of the second isolate of the patient. This information provides insights into genetic and phenotypic alterations in B. pseudomallei in human melioidosis, which may represent a bacterial strategy for persistent and relapse infections.
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Affiliation(s)
- Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Adul Dulsuk
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Janjira Thaipadungpanit
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Elizabeth M. Batty
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - T. Eoin West
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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65
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López-Cortegano E, Craig RJ, Chebib J, Balogun EJ, Keightley PD. Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii. Genome Res 2023; 33:45-60. [PMID: 36617667 PMCID: PMC9977147 DOI: 10.1101/gr.276957.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Genetic variation originates from several types of spontaneous mutation, including single-nucleotide substitutions, short insertions and deletions (indels), and larger structural changes. Structural mutations (SMs) drive genome evolution and are thought to play major roles in evolutionary adaptation, speciation, and genetic disease, including cancers. Sequencing of mutation accumulation (MA) lines has provided estimates of rates and spectra of single-nucleotide and indel mutations in many species, yet the rate of new SMs is largely unknown. Here, we use long-read sequencing to determine the full mutation spectrum in MA lines derived from two strains (CC-1952 and CC-2931) of the green alga Chlamydomonas reinhardtii The SM rate is highly variable between strains and between MA lines, and SMs represent a substantial proportion of all mutations in both strains (CC-1952 6%; CC-2931 12%). The SM spectra differ considerably between the two strains, with almost all inversions and translocations occurring in CC-2931 MA lines. This variation is associated with heterogeneity in the number and type of active transposable elements (TEs), which comprise major proportions of SMs in both strains (CC-1952 22%; CC-2931 38%). In CC-2931, a Crypton and a previously undescribed type of DNA element have caused 71% of chromosomal rearrangements, whereas in CC-1952, a Dualen LINE is associated with 87% of duplications. Other SMs, notably large duplications in CC-2931, are likely products of various double-strand break repair pathways. Our results show that diverse types of SMs occur at substantial rates, and support prominent roles for SMs and TEs in evolution.
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Affiliation(s)
- Eugenio López-Cortegano
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Rory J Craig
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- California Institute for Quantitative Biosciences, UC Berkeley, Berkeley, California 94720, USA
| | - Jobran Chebib
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Eniolaye J Balogun
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario ON M5S 3B2, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga ON L5L 1C6, Canada
| | - Peter D Keightley
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
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Adaptive Laboratory Evolution of Microorganisms: Methodology and Application for Bioproduction. Microorganisms 2022; 11:microorganisms11010092. [PMID: 36677384 PMCID: PMC9864036 DOI: 10.3390/microorganisms11010092] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Adaptive laboratory evolution (ALE) is a useful experimental methodology for fundamental scientific research and industrial applications to create microbial cell factories. By using ALE, cells are adapted to the environment that researchers set based on their objectives through the serial transfer of cell populations in batch cultivations or continuous cultures and the fitness of the cells (i.e., cell growth) under such an environment increases. Then, omics analyses of the evolved mutants, including genome sequencing, transcriptome, proteome and metabolome analyses, are performed. It is expected that researchers can understand the evolutionary adaptation processes, and for industrial applications, researchers can create useful microorganisms that exhibit increased carbon source availability, stress tolerance, and production of target compounds based on omics analysis data. In this review article, the methodologies for ALE in microorganisms are introduced. Moreover, the application of ALE for the creation of useful microorganisms as cell factories has also been introduced.
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Fressatti Cardoso R, Martín-Blecua I, Pietrowski Baldin V, Meneguello JE, Valverde JR, Blázquez J, Castañeda-García A. Noncanonical Mismatch Repair Protein NucS Modulates the Emergence of Antibiotic Resistance in Mycobacterium abscessus. Microbiol Spectr 2022; 10:e0222822. [PMID: 36219122 PMCID: PMC9769700 DOI: 10.1128/spectrum.02228-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/22/2022] [Indexed: 01/06/2023] Open
Abstract
NucS/EndoMS-dependent noncanonical mismatch repair (MMR) ensures the stability of genomic DNA in mycobacteria and acts as a guardian of the genome by preventing the accumulation of point mutations. In order to address whether the inactivation of noncanonical MMR could increase the acquisition of drug resistance by mutation, a ΔnucS strain was constructed and explored in the emerging pathogen Mycobacterium abscessus. Deletion of nucS resulted in a mutator phenotype with increased acquisition of resistance to macrolides and aminoglycosides, the two main groups of antimycobacterial agents for M. abscessus treatment, and also to second-line drugs such as fluoroquinolones. Inactivation of the noncanonical MMR in M. abscessus led to increases of 10- to 22-fold in the appearance of spontaneous mutants resistant to the macrolide clarithromycin and the aminoglycosides amikacin, gentamicin, and apramycin, compared with the wild-type strain. Furthermore, emergence of fluoroquinolone (ciprofloxacin) resistance was detected in a nucS-deficient strain but not in a wild-type M. abscessus strain. Acquired drug resistance to macrolides and aminoglycosides was analyzed through sequencing of the 23S rRNA gene rrl and the 16S rRNA gene rrs from independent drug-resistant colonies of both strains. When the acquisition of clarithromycin resistance was examined, a different mutational profile was detected in the M. abscessus ΔnucS strain compared with the wild-type one. To summarize, M. abscessus requires the NucS-dependent noncanonical MMR pathway to prevent the emergence of drug-resistant isolates by mutation. To our knowledge, this is the first report that reveals the role of NucS in a human pathogen, and these findings have potential implications for the treatment of M. abscessus infections. IMPORTANCE Chronic infections caused by M. abscessus are an emerging challenge in public health, posing a substantial health and economic burden, especially in patients with cystic fibrosis. Treatment of M. abscessus infections with antibiotics is particularly challenging, as its complex drug resistance mechanisms, including constitutive resistance through DNA mutation, lead to high rates of treatment failure. To decipher the evolution of antibiotic resistance in M. abscessus, we studied NucS-dependent noncanonical MMR, a unique DNA repair pathway involved in genomic maintenance. Inactivation of NucS is linked to the increase of DNA mutations (hypermutation), which can confer drug resistance. Our analysis detected increased acquisition of mutations conferring resistance to first-line and second-line antibiotics. We believe that this study will improve the knowledge of how this pathogen could evolve into an untreatable infectious agent, and it uncovers a role for hypermutators in chronic infectious diseases under antibiotic pressure.
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Affiliation(s)
- Rosilene Fressatti Cardoso
- Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Isabel Martín-Blecua
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología CNB-CSIC, Madrid, Spain
| | - Vanessa Pietrowski Baldin
- Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Jean Eduardo Meneguello
- Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - José Ramón Valverde
- Departamento de Computación Científica, Centro Nacional de Biotecnología CNB-CSIC, Madrid, Spain
| | - Jesús Blázquez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología CNB-CSIC, Madrid, Spain
| | - Alfredo Castañeda-García
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología CNB-CSIC, Madrid, Spain
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68
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Genome stability during serial subculturing in hyperepidemic multidrug-resistant Klebsiella pneumoniae and Escherichia coli. J Glob Antimicrob Resist 2022; 31:152-161. [PMID: 36049731 DOI: 10.1016/j.jgar.2022.08.014] [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: 07/19/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Core-genome single nucleotide variant (cgSNV) analysis represents a powerful tool for epidemiological investigations of multidrug-resistant (MDR) bacteria. However, cgSNV thresholds to confirm whether isolates are the same clone are not formally defined. METHODS We implemented hybrid whole-genome sequencing to study the genomic changes of four MDR isolates belonging to hyperepidemic sequence types (STs) during 20 propagation steps (T20) on MacConkey and CHROMID(R) ESBL plates. The following strains were analyzed: Klebsiella pneumoniae AE-2247421 (OXA-48/NDM-1-producing, ST101), K. pneumoniae MCL-2017-2 (CTX-M-15-producing, ST307), Escherichia coli Ec-042 (OXA-181-producing, ST410), and E. coli Ec-050 (NDM-5-producing, ST167). The genome assembly at T5 and T20 was compared to that at time point zero (T0) and to two reference genomes. RESULTS At T20, AE-2247421 lost the IncL blaOXA-48-carrying plasmid when grown on CHROMID(R) ESBL plates, while a large fragment encompassing blaNDM-1 was lost from its IncC plasmid when grown on both plates. In contrast, no structural changes were noted for the other three strains. Regarding the cgSNVs, the following results were obtained at T5 and T20 (ranges considering the different agar plates and reference genomes): AE-2247421 (1-8 and 2-12 cgSNVs), MCL-2017-2 (both 1-2 cgSNVs), Ec-042 (both 0 cgSNVs), and Ec-050 (0-6 and 0-9 cgSNVs). CONCLUSION We showed that structural changes and accumulation of cgSNVs can occur in few propagation steps under laboratory conditions. These changes might also arise in the clinical context in a short time, especially under antibiotics treatment. This phenomenon should be carefully considered because it might affect the final interpretation of epidemiological genomic analyses.
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69
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Witzany C, Regoes RR, Igler C. Assessing the relative importance of bacterial resistance, persistence and hyper-mutation for antibiotic treatment failure. Proc Biol Sci 2022; 289:20221300. [PMID: 36350213 PMCID: PMC9653239 DOI: 10.1098/rspb.2022.1300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/18/2022] [Indexed: 08/01/2023] Open
Abstract
To curb the rising threat of antimicrobial resistance, we need to understand the routes to antimicrobial treatment failure. Bacteria can survive treatment by using both genetic and phenotypic mechanisms to diminish the effect of antimicrobials. We assemble empirical data showing that, for example, Pseudomonas aeruginosa infections frequently contain persisters, transiently non-growing cells unaffected by antibiotics (AB) and hyper-mutators, mutants with elevated mutation rates, and thus higher probability of genetic resistance emergence. Resistance, persistence and hyper-mutation dynamics are difficult to disentangle experimentally. Hence, we use stochastic population modelling and deterministic fitness calculations to investigate the relative importance of genetic and phenotypic mechanisms for immediate treatment failure and establishment of prolonged, chronic infections. We find that persistence causes 'hidden' treatment failure with very low cell numbers if antimicrobial concentrations prevent growth of genetically resistant cells. Persister cells can regrow after treatment is discontinued and allow for resistance evolution in the absence of AB. This leads to different mutational routes during treatment and relapse of an infection. By contrast, hyper-mutation facilitates resistance evolution during treatment, but rarely contributes to treatment failure. Our findings highlight the time and concentration dependence of different bacterial mechanisms to escape AB killing, which should be considered when designing 'failure-proof' treatments.
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Affiliation(s)
| | - Roland R. Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Claudia Igler
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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70
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Lieberman TD. Detecting bacterial adaptation within individual microbiomes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210243. [PMID: 35989602 PMCID: PMC9393564 DOI: 10.1098/rstb.2021.0243] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/17/2022] [Indexed: 12/11/2022] Open
Abstract
The human microbiome harbours a large capacity for within-person adaptive mutations. Commensal bacterial strains can stably colonize a person for decades, and billions of mutations are generated daily within each person's microbiome. Adaptive mutations emerging during health might be driven by selective forces that vary across individuals, vary within an individual, or are completely novel to the human population. Mutations emerging within individual microbiomes might impact the immune system, the metabolism of nutrients or drugs, and the stability of the community to perturbations. Despite this potential, relatively little attention has been paid to the possibility of adaptive evolution within complex human-associated microbiomes. This review discusses the promise of studying within-microbiome adaptation, the conceptual and technical limitations that may have contributed to an underappreciation of adaptive de novo mutations occurring within microbiomes to date, and methods for detecting recent adaptive evolution. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
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Affiliation(s)
- Tami D. Lieberman
- Department of Civil and Environmental Engineering, Institute for Medical Engineering and Science,Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Ragon Institute, Cambridge, MA, USA
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71
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Environmental complexity is more important than mutation in driving the evolution of latent novel traits in E. coli. Nat Commun 2022; 13:5904. [PMID: 36202805 PMCID: PMC9537139 DOI: 10.1038/s41467-022-33634-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022] Open
Abstract
Recent experiments show that adaptive Darwinian evolution in one environment can lead to the emergence of multiple new traits that provide no immediate benefit in this environment. Such latent non-adaptive traits, however, can become adaptive in future environments. We do not know whether mutation or environment-driven selection is more important for the emergence of such traits. To find out, we evolve multiple wild-type and mutator E. coli populations under two mutation rates in simple (single antibiotic) environments and in complex (multi-antibiotic) environments. We then assay the viability of evolved populations in dozens of new environments and show that all populations become viable in multiple new environments different from those they had evolved in. The number of these new environments increases with environmental complexity but not with the mutation rate. Genome sequencing demonstrates the reason: Different environments affect pleiotropic mutations differently. Our experiments show that the selection pressure provided by an environment can be more important for the evolution of novel traits than the mutational supply experienced by a wild-type and a mutator strain of E. coli. Novel traits without immediate fitness benefit evolve frequently but we don’t know whether mutation or environment-driven selection drives this evolution. Here, using experimental evolution of E. coli populations, the authors demonstrate the importance of selection in the evolution of latent novel traits.
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72
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Ba Q, Zhou J, Li J, Cheng S, Zhang X, Wang H. Mutagenic Characteristics of Six Heavy Metals in Escherichia coli: The Commonality and Specificity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13867-13877. [PMID: 36121417 PMCID: PMC9536316 DOI: 10.1021/acs.est.2c04785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/27/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
The history of long-term environmental exposure to heavy metals can be recorded in the genome as sporadic and specific mutations. Variable environments introduce diverse and adaptive mutations to organisms. To reveal the information hidden in genomes about environmental exposure to heavy metals, we performed long-term mutation accumulation (MA) experiments with Escherichia coli, analyzed genomes from 36 populations across 1650 generations with 6 heavy metal exposure regimes (arsenic, cadmium, chromium, copper, nickel, and lead), and inferred metal-specific evolution modes at the genomic level. All heavy metals induced genetic mutations with a mean rate of 3.459 × 10-9 per nucleotide per generation. The mutational spectrum exhibited distinct signatures; however, heavy metals also shared common mutation signatures prominently associated with all cancer types. The mutated genes showed an average similarity of 54.4% within the same exposure regime, whereas only 38.8% between exposure regimes. In terms of biological insights, mutated genes were enriched to fundamental cellular processes such as metabolism, motility, and transport. Our study elucidates the mutagenic commonality and specificity of environmental heavy metals, which are highly specific at mutational features and locus, but conserved at gene and functional levels, and may play crucial roles in the convergence of adaptation to heavy metals.
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Affiliation(s)
- Qian Ba
- State
Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell
Omics, School of Public Health, Shanghai
Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingqi Zhou
- State
Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell
Omics, School of Public Health, Shanghai
Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingquan Li
- State
Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell
Omics, School of Public Health, Shanghai
Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shujun Cheng
- State
Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell
Omics, School of Public Health, Shanghai
Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaokang Zhang
- School
of Public Health and Health Management, Gannan Medical University, Ganzhou 341000, China
| | - Hui Wang
- State
Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell
Omics, School of Public Health, Shanghai
Jiao Tong University School of Medicine, Shanghai 200025, China
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Suyal DC, Joshi D, Kumar S, Bhatt P, Narayan A, Giri K, Singh M, Soni R, Kumar R, Yadav A, Devi R, Kaur T, Kour D, Yadav AN. Himalayan Microbiomes for Agro-environmental Sustainability: Current Perspectives and Future Challenges. MICROBIAL ECOLOGY 2022; 84:643-675. [PMID: 34647148 DOI: 10.1007/s00248-021-01849-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
The Himalayas are one of the most mystical, yet least studied terrains of the world. One of Earth's greatest multifaceted and diverse montane ecosystems is also one of the thirty-four global biodiversity hotspots of the world. These are supposed to have been uplifted about 60-70 million years ago and support, distinct environments, physiography, a variety of orogeny, and great biological diversity (plants, animals, and microbes). Microbes are the pioneer colonizer of the Himalayas that are involved in various bio-geological cycles and play various significant roles. The applications of Himalayan microbiomes inhabiting in lesser to greater Himalayas have been recognized. The researchers explored the applications of indigenous microbiomes in both agricultural and environmental sectors. In agriculture, microbiomes from Himalayan regions have been suggested as better biofertilizers and biopesticides for the crops growing at low temperature and mountainous areas as they help in the alleviation of cold stress and other biotic stresses. Along with alleviation of low temperature, Himalayan microbes also have the capability to enhance plant growth by availing the soluble form of nutrients like nitrogen, phosphorus, potassium, zinc, and iron. These microbes have been recognized for producing plant growth regulators (abscisic acid, auxin, cytokinin, ethylene, and gibberellins). These microbes have been reported for bioremediating the diverse pollutants (pesticides, heavy metals, and xenobiotics) for environmental sustainability. In the current perspectives, present review provides a detailed discussion on the ecology, biodiversity, and adaptive features of the native Himalayan microbiomes in view to achieve agro-environmental sustainability.
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Affiliation(s)
- Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Sirmaur, Himachal Pradesh, India
| | - Divya Joshi
- Uttarakhand Pollution Control Board, Regional Office, Kashipur, Uttarakhand, India
| | - Saurabh Kumar
- Division of Crop Research, Research Complex for Eastern Region, Patna, Bihar, India
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Arun Narayan
- Forest Research Institute, Dehradun, 2480 06, India
| | - Krishna Giri
- Rain Forest Research Institute, Jorhat, 785 010, India
| | - Manali Singh
- Department of Biotechnology, Invertis Institute of Engineering and Technology (IIET), Invertis University, Bareilly, 243123, Uttar Pradesh, India
| | - Ravindra Soni
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwa Vidyalaya, Raipur, Chhattisgarh, India
| | - Rakshak Kumar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Ashok Yadav
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Rubee Devi
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Tanvir Kaur
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Divjot Kour
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.
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74
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Selveshwari S, Khaire KC, Kadam A, Dey S. The effect of migration and variation on populations of Escherichia coli adapting to complex fluctuating environments. J Evol Biol 2022; 35:1500-1507. [PMID: 36177784 DOI: 10.1111/jeb.14101] [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: 05/14/2022] [Revised: 07/17/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022]
Abstract
Migration, a critical evolutionary force, can have contrasting effects on adaptation. It can aid as well as impede adaptation. The effects of migration on microbial adaptation have been studied primarily in simple constant environments. Very little is known about the effects of migration on adaptation to complex, fluctuating environments. In our study, we subjected replicate populations of Escherichia coli, adapting to complex and unpredictably fluctuating environments to different proportions of clonal ancestral immigrants. Contrary to the results from simple/constant environments, the presence of clonal immigrants reduced all measured proxies of fitness. However, migration from a source population with a greater variance in fitness resulted in no change in fitness with respect to the no-migration control, except at the highest level of migration. Thus, the presence of variation in the immigrants could counter the adverse effects of migration in complex and unpredictably fluctuating environments. Our study demonstrates that the effects of migration are strongly dependent on the nature of the destination environment and the genetic makeup of immigrants. These results enhance our understanding of the influences of migrating populations, which could help better predict the consequences of migration.
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Affiliation(s)
- S Selveshwari
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Kaustubh Chandrakant Khaire
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Aditee Kadam
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Sutirth Dey
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
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75
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Mahilkar A, Raj N, Kemkar S, Saini S. Selection in a growing colony biases results of mutation accumulation experiments. Sci Rep 2022; 12:15470. [PMID: 36104390 PMCID: PMC9475022 DOI: 10.1038/s41598-022-19928-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022] Open
Abstract
Mutations provide the raw material for natural selection to act. Therefore, understanding the variety and relative frequency of different type of mutations is critical to understanding the nature of genetic diversity in a population. Mutation accumulation (MA) experiments have been used in this context to estimate parameters defining mutation rates, distribution of fitness effects (DFE), and spectrum of mutations. MA experiments can be performed with different effective population sizes. In MA experiments with bacteria, a single founder is grown to a size of a colony (~ 108). It is assumed that natural selection plays a minimal role in dictating the dynamics of colony growth. In this work, we simulate colony growth via a mathematical model, and use our model to mimic an MA experiment. We demonstrate that selection ensures that, in an MA experiment, fraction of all mutations that are beneficial is over-represented by a factor of almost two, and that the distribution of fitness effects of beneficial and deleterious mutations are inaccurately captured in an MA experiment. Given this, the estimate of mutation rates from MA experiments is non-trivial. We then perform an MA experiment with 160 lines of E. coli, and show that due to the effect of selection in a growing colony, the size and sector of a colony from which the experiment is propagated impacts the results. Overall, we demonstrate that the results of MA experiments need to be revisited taking into account the action of selection in a growing colony.
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Affiliation(s)
- Anjali Mahilkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Namratha Raj
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sharvari Kemkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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76
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McLean EK, Nye TM, Lowder FC, Simmons LA. The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria. Annu Rev Microbiol 2022; 76:461-480. [PMID: 35655343 PMCID: PMC9527769 DOI: 10.1146/annurev-micro-102521-014450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
During the essential processes of DNA replication and transcription, RNA-DNA hybrid intermediates are formed that pose significant risks to genome integrity when left unresolved. To manage RNA-DNA hybrids, all cells rely on RNase H family enzymes that specifically cleave the RNA portion of the many different types of hybrids that form in vivo. Recent experimental advances have provided new insight into how RNA-DNA hybrids form and the consequences to genome integrity that ensue when persistent hybrids remain unresolved. Here we review the types of RNA-DNA hybrids, including R-loops, RNA primers, and ribonucleotide misincorporations, that form during DNA replication and transcription and discuss how each type of hybrid can contribute to genome instability in bacteria. Further, we discuss how bacterial RNase HI, HII, and HIII and bacterial FEN enzymes contribute to genome maintenance through the resolution of hybrids.
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Affiliation(s)
- Emma K McLean
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
| | - Taylor M Nye
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
- Current affiliation: Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Frances C Lowder
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
| | - Lyle A Simmons
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
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77
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Keller P, Reiter MA, Kiefer P, Gassler T, Hemmerle L, Christen P, Noor E, Vorholt JA. Generation of an Escherichia coli strain growing on methanol via the ribulose monophosphate cycle. Nat Commun 2022; 13:5243. [PMID: 36068201 PMCID: PMC9448777 DOI: 10.1038/s41467-022-32744-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Methanol is a liquid with high energy storage capacity that holds promise as an alternative substrate to replace sugars in the biotechnology industry. It can be produced from CO2 or methane and its use does not compete with food and animal feed production. However, there are currently only limited biotechnological options for the valorization of methanol, which hinders its widespread adoption. Here, we report the conversion of the industrial platform organism Escherichia coli into a synthetic methylotroph that assimilates methanol via the energy efficient ribulose monophosphate cycle. Methylotrophy is achieved after evolution of a methanol-dependent E. coli strain over 250 generations in continuous chemostat culture. We demonstrate growth on methanol and biomass formation exclusively from the one-carbon source by 13C isotopic tracer analysis. In line with computational modeling, the methylotrophic E. coli strain optimizes methanol oxidation by upregulation of an improved methanol dehydrogenase, increasing ribulose monophosphate cycle activity, channeling carbon flux through the Entner-Doudoroff pathway and downregulating tricarboxylic acid cycle enzymes. En route towards sustainable bioproduction processes, our work lays the foundation for the efficient utilization of methanol as the dominant carbon and energy resource. Using one carbon compounds as feedstock is a promising approach in abating climate change. Here, the authors report the conversion of E. coli into a synthetic methylotroph that assimilates methanol via the ribulose monophosphate cycle and a set of distinctive mutations.
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Affiliation(s)
- Philipp Keller
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Michael A Reiter
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Thomas Gassler
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Lucas Hemmerle
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland.,Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Philipp Christen
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland.
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78
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Schmidt SBI, Rodríguez-Rojas A, Rolff J, Schreiber F. Biocides used as material preservatives modify rates of de novo mutation and horizontal gene transfer in bacteria. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129280. [PMID: 35714537 DOI: 10.1016/j.jhazmat.2022.129280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/20/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Antimicrobial resistance (AMR) is a global health problem with the environment being an important compartment for the evolution and transmission of AMR. Previous studies showed that de-novo mutagenesis and horizontal gene transfer (HGT) by conjugation or transformation - important processes underlying resistance evolution and spread - are affected by antibiotics, metals and pesticides. However, natural microbial communities are also frequently exposed to biocides used as material preservatives, but it is unknown if these substances induce mutagenesis and HGT. Here, we show that active substances used in material preservatives can increase rates of mutation and conjugation in a species- and substance-dependent manner, while rates of transformation are not increased. The bisbiguanide chlorhexidine digluconate, the quaternary ammonium compound didecyldimethylammonium chloride, the metal copper, the pyrethroid-insecticide permethrin, and the azole-fungicide propiconazole increase mutation rates in Escherichia coli, whereas no increases were identified for Bacillus subtilis and Acinetobacter baylyi. Benzalkonium chloride, chlorhexidine and permethrin increased conjugation in E. coli. Moreover, our results show a connection between the RpoS-mediated general stress and the RecA-linked SOS response with increased rates of mutation and conjugation, but not for all biocides. Taken together, our data show the importance of assessing the contribution of material preservatives on AMR evolution and spread.
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Affiliation(s)
- Selina B I Schmidt
- Division of Biodeterioration and Reference Organisms (4.1), Department of Materials and the Environment, Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 87, 12205 Berlin, Germany.
| | - Alexandro Rodríguez-Rojas
- Evolutionary Biology, Institute of Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany; Internal Medicine - Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
| | - Jens Rolff
- Evolutionary Biology, Institute of Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany.
| | - Frank Schreiber
- Division of Biodeterioration and Reference Organisms (4.1), Department of Materials and the Environment, Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 87, 12205 Berlin, Germany.
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79
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Henderson AL, Moreno A, Kram KE. Parallel Evolution towards Increased Motility in Long-Term Cultures of Escherichia coli, Even Though Motility was Not Required for Long-Term Survival. Microbiol Spectr 2022; 10:e0233021. [PMID: 35735986 PMCID: PMC9431438 DOI: 10.1128/spectrum.02330-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/31/2022] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli can survive for long periods in batch culture in the laboratory, where they experience a stressful and heterogeneous environment. During this incubation, E. coli acquires mutations that are selected in response to this environment, ultimately leading to evolved populations that are better adapted to these complex conditions, which can lead to a better understanding of evolutionary mechanisms. Mutations in regulatory genes often play a role in adapting to heterogeneous environments. To identify such mutations, we examined transcriptional differences during log phase growth in unaged cells compared to those that had been aged for 10 days and regrown. We identified expression changes in genes involved in motility and chemotaxis after adaptation to long-term cultures. We hypothesized that aged populations would also have phenotypic changes in motility and that motility may play a role in survival and adaptation to long-term cultures. While aged populations did show an increase in motility, this increase was not essential for survival in long-term cultures. We identified mutations in the regulatory gene sspA and other genes that may contribute to the observed differences in motility. Taken together, these data provide an overall picture of the role of mutations in regulatory genes for adaptation while underscoring that all changes that occur during evolution in stressful environments are not necessarily adaptive. IMPORTANCE Understanding how bacteria adapt in long-term cultures aids in both better treatment options for bacterial infections and gives insight into the mechanisms involved in bacterial evolution. In the past, it has been difficult to study these organisms in their natural environments. By using experimental evolution in heterogeneous and stressful laboratory conditions, we can more closely mimic natural environments and examine evolutionary mechanisms. One way to observe these mechanisms is to look at transcriptomic and genomic data from cells adapted to these complex conditions. Here, we found that although aged cells increase motility, this increase is not essential for survival in these conditions. These data emphasize that not all changes that occur due to evolutionary processes are adaptive, but these observations could still lead to hypotheses about the causative mutations. The information gained here allow us to make inferences about general mechanisms underlying phenotypic changes due to evolution.
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Affiliation(s)
- Autumn L. Henderson
- Department of Biology, California State University, Dominguez Hills, Carson, California, USA
| | - Angie Moreno
- Department of Biology, California State University, Dominguez Hills, Carson, California, USA
| | - Karin E. Kram
- Department of Biology, California State University, Dominguez Hills, Carson, California, USA
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80
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Determination of Mutation Rates with Two Symmetric and Asymmetric Mutation Types. Symmetry (Basel) 2022. [DOI: 10.3390/sym14081701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We revisit our earlier paper, with two of the coauthors, in which we proposed an unbiased and consistent estimator μ^n for an unknown mutation rate μ of microorganisms. Previously, we proved that the associated sequence of estimators μ^n converges to μ almost surely pointwise on a nonextinct set Ω0. Here, we show that this sequence converges also in the mean square with respect to conditional probability measure P0·=P·∩Ω0/PΩ0 and that, with respect to P0, the estimator is asymptotically unbiased. We further assume that a microorganism can mutate or turn to a different variant of one of the two types. In particular, it can mean that bacteria under attack by a virus or chemical agent are either perishing or surviving, turning them to stronger variant. We propose estimators for their respective types and show that they are a.s. pointwise and L2-consistent and asymptotically unbiased with respect to measure P0.
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81
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Rapid evolution of mutation rate and spectrum in response to environmental and population-genetic challenges. Nat Commun 2022; 13:4752. [PMID: 35963846 PMCID: PMC9376063 DOI: 10.1038/s41467-022-32353-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 07/26/2022] [Indexed: 11/15/2022] Open
Abstract
Ecological and demographic factors can significantly shape the evolution of microbial populations both directly and indirectly, as when changes in the effective population size affect the efficiency of natural selection on the mutation rate. However, it remains unclear how rapidly the mutation-rate responds evolutionarily to the entanglement of ecological and population-genetic factors over time. Here, we directly assess the mutation rate and spectrum of Escherichia coli clones isolated from populations evolving in response to 1000 days of different transfer volumes and resource-replenishment intervals. The evolution of mutation rates proceeded rapidly in response to demographic and/or environmental changes, with substantial bidirectional shifts observed as early as 59 generations. These results highlight the remarkable rapidity by which mutation rates are shaped in asexual lineages in response to environmental and population-genetic forces, and are broadly consistent with the drift-barrier hypothesis for the evolution of mutation rates, while also highlighting situations in which mutator genotypes may be promoted by positive selection. How rapidly the mutation rate responds evolutionarily to ecological and population-genetic factors over time is unclear. Here, the authors show that the evolution of mutation rates in E. coli proceeds rapidly in response to these factors with substantial bidirectional shifts.
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82
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Hall KM, Pursell ZF, Morici LA. The role of the Pseudomonas aeruginosa hypermutator phenotype on the shift from acute to chronic virulence during respiratory infection. Front Cell Infect Microbiol 2022; 12:943346. [PMID: 35937684 PMCID: PMC9355025 DOI: 10.3389/fcimb.2022.943346] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic respiratory infection (CRI) with Pseudomonas aeruginosa (Pa) presents many unique challenges that complicate treatment. One notable challenge is the hypermutator phenotype which is present in up to 60% of sampled CRI patient isolates. Hypermutation can be caused by deactivating mutations in DNA mismatch repair (MMR) genes including mutS, mutL, and uvrD. In vitro and in vivo studies have demonstrated hypermutator strains to be less virulent than wild-type Pa. However, patients colonized with hypermutators display poorer lung function and a higher incidence of treatment failure. Hypermutation and MMR-deficiency create increased genetic diversity and population heterogeneity due to elevated mutation rates. MMR-deficient strains demonstrate higher rates of mucoidy, a hallmark virulence determinant of Pa during CRI in cystic fibrosis patients. The mucoid phenotype results from simple sequence repeat mutations in the mucA gene made in the absence of functional MMR. Mutations in Pa are further increased in the absence of MMR, leading to microcolony biofilm formation, further lineage diversification, and population heterogeneity which enhance bacterial persistence and host immune evasion. Hypermutation facilitates the adaptation to the lung microenvironment, enabling survival among nutritional complexity and microaerobic or anaerobic conditions. Mutations in key acute-to-chronic virulence “switch” genes, such as retS, bfmS, and ampR, are also catalyzed by hypermutation. Consequently, strong positive selection for many loss-of-function pathoadaptive mutations is seen in hypermutators and enriched in genes such as lasR. This results in the characteristic loss of Pa acute infection virulence factors, including quorum sensing, flagellar motility, and type III secretion. Further study of the role of hypermutation on Pa chronic infection is needed to better inform treatment regimens against CRI with hypermutator strains.
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Affiliation(s)
- Kalen M. Hall
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Zachary F. Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Lisa A. Morici
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
- *Correspondence: Lisa A. Morici,
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83
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Ho AT, Hurst LD. Stop codon usage as a window into genome evolution: mutation, selection, biased gene conversion and the TAG paradox. Genome Biol Evol 2022; 14:6648529. [PMID: 35867377 PMCID: PMC9348620 DOI: 10.1093/gbe/evac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 11/16/2022] Open
Abstract
Protein coding genes terminate with one of three stop codons (TAA, TGA, or TAG) that, like synonymous codons, are not employed equally. With TGA and TAG having identical nucleotide content, analysis of their differential usage provides an unusual window into the forces operating on what are ostensibly functionally identical residues. Across genomes and between isochores within the human genome, TGA usage increases with G + C content but, with a common G + C → A + T mutation bias, this cannot be explained by mutation bias-drift equilibrium. Increased usage of TGA in G + C-rich genomes or genomic regions is also unlikely to reflect selection for the optimal stop codon, as TAA appears to be universally optimal, probably because it has the lowest read-through rate. Despite TAA being favored by selection and mutation bias, as with codon usage bias G + C pressure is the prime determinant of between-species TGA usage trends. In species with strong G + C-biased gene conversion (gBGC), such as mammals and birds, the high usage and conservation of TGA is best explained by an A + T → G + C repair bias. How to explain TGA enrichment in other G + C-rich genomes is less clear. Enigmatically, across bacterial and archaeal species and between human isochores TAG usage is mostly unresponsive to G + C pressure. This unresponsiveness we dub the TAG paradox as currently no mutational, selective, or gBGC model provides a well-supported explanation. That TAG does increase with G + C usage across eukaryotes makes the usage elsewhere yet more enigmatic. We suggest resolution of the TAG paradox may provide insights into either an unknown but common selective preference (probably at the DNA/RNA level) or an unrecognized complexity to the action of gBGC.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, UK
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84
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Toll-Riera M, Olombrada M, Castro-Giner F, Wagner A. A limit on the evolutionary rescue of an Antarctic bacterium from rising temperatures. SCIENCE ADVANCES 2022; 8:eabk3511. [PMID: 35857489 PMCID: PMC9286510 DOI: 10.1126/sciadv.abk3511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Climate change is gradual, but it can also cause brief extreme heat waves that can exceed the upper thermal limit of any one organism. To study the evolutionary potential of upper thermal tolerance, we evolved the cold-adapted Antarctic bacterium Pseudoalteromonas haloplanktis to survive at 30°C, beyond its ancestral thermal limit. This high-temperature adaptation occurred rapidly and in multiple populations. It involved genomic changes that occurred in a highly parallel fashion and mitigated the effects of protein misfolding. However, it also confronted a physiological limit, because populations failed to grow beyond 30°C. Our experiments aimed to facilitate evolutionary rescue by using a small organism with large populations living at temperatures several degrees below their upper thermal limit. Larger organisms with smaller populations and living at temperatures closer to their upper thermal tolerances are even more likely to go extinct during extreme heat waves.
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Affiliation(s)
- Macarena Toll-Riera
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Miriam Olombrada
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, NM, USA
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa
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85
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Chakrabartty I, Khan M, Mahanta S, Chopra H, Dhawan M, Choudhary OP, Bibi S, Mohanta YK, Emran TB. Comparative overview of emerging RNA viruses: Epidemiology, pathogenesis, diagnosis and current treatment. Ann Med Surg (Lond) 2022; 79:103985. [PMID: 35721786 PMCID: PMC9188442 DOI: 10.1016/j.amsu.2022.103985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
From many decades, emerging infections have threatened humanity. The pandemics caused by different CoVs have already claimed and will continue to claim millions of lives. The SARS, Ebola, MERS epidemics and the most recent emergence of COVID-19 pandemic have threatened populations across borders. Since a highly pathogenic CoV has been evolved into the human population in the twenty-first century known as SARS, scientific advancements and innovative methods to tackle these viruses have increased in order to improve response preparedness towards the unpredictable threat posed by these rapidly emerging pathogens. Recently published review articles on SARS-CoV-2 have mainly focused on its pathogenesis, epidemiology and available treatments. However, in this review, we have done a systematic comparison of all three CoVs i.e., SARS, MERS and SARS-CoV-2 along with Ebola and Zika in terms of their epidemiology, virology, clinical features and current treatment strategies. This review focuses on important emerging RNA viruses starting from Zika, Ebola and the CoVs which include SARS, MERS and SARS-CoV-2. Each of these viruses has been elaborated on the basis of their epidemiology, virulence, transmission and treatment. However, special attention has been given to SARS-CoV-2 and the disease caused by it i.e., COVID-19 due to current havoc caused worldwide. At the end, insights into the current understanding of the lessons learned from previous epidemics to combat emerging CoVs have been described. The travel-related viral spread, the unprecedented nosocomial outbreaks and the high case-fatality rates associated with these highly transmissible and pathogenic viruses highlight the need for new prophylactic and therapeutic actions which include but are not limited to clinical indicators, contact tracing, and laboratory investigations as important factors that need to be taken into account in order to arrive at the final conclusion. Recently published review articles on SARS-CoV-2 have mainly focused on its pathogenesis, epidemiology and available treatments. The pandemics caused by different CoVs have already claimed and will continue to claim millions of lives. This review focuses on important emerging RNA viruses starting from Zika, Ebola and the CoVs which include SARS, MERS and SARS-CoV-2. Globally, numerous studies and researchers have recently started fighting this virus.
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Affiliation(s)
- Ishani Chakrabartty
- Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), 9th Mile, Techno City, Baridua, Ri-Bhoi 793101, Meghalaya, India
| | - Maryam Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P, India
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology (NIELIT), Guwahati Centre Guwahati, 781008, Assam, India
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.,Trafford College, Altrincham, Manchester, WA14 5PQ, UK
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, India
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan.,Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Yugal Kishore Mohanta
- Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), 9th Mile, Techno City, Baridua, Ri-Bhoi 793101, Meghalaya, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
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86
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Patlán-Vázquez AG, Ayala-García VM, Vallin C, Cortés J, Vásquez-Morales SG, Robleto EA, Nudler E, Pedraza-Reyes M. Dynamics of Mismatch and Alternative Excision-Dependent Repair in Replicating Bacillus subtilis DNA Examined Under Conditions of Neutral Selection. Front Microbiol 2022; 13:866089. [PMID: 35847079 PMCID: PMC9280176 DOI: 10.3389/fmicb.2022.866089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Spontaneous DNA deamination is a potential source of transition mutations. In Bacillus subtilis, EndoV, a component of the alternative excision repair pathway (AER), counteracts the mutagenicity of base deamination-induced mispairs. Here, we report that the mismatch repair (MMR) system, MutSL, prevents the harmful effects of HNO2, a deaminating agent of Cytosine (C), Adenine (A), and Guanine (G). Using Maximum Depth Sequencing (MDS), which measures mutagenesis under conditions of neutral selection, in B. subtilis strains proficient or deficient in MutSL and/or EndoV, revealed asymmetric and heterogeneous patterns of mutations in both DNA template strands. While the lagging template strand showed a higher frequency of C → T substitutions; G → A mutations, occurred more frequently in the leading template strand in different genetic backgrounds. In summary, our results unveiled a role for MutSL in preventing the deleterious effects of base deamination and uncovered differential patterns of base deamination processing by the AER and MMR systems that are influenced by the sequence context and the replicating DNA strand.
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Affiliation(s)
- Adriana G. Patlán-Vázquez
- Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico
| | | | - Carmen Vallin
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jonathan Cortés
- Biological Research Center, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Suria G. Vásquez-Morales
- Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico
| | - Eduardo A. Robleto
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Evgeny Nudler
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, United States
| | - Mario Pedraza-Reyes
- Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico
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87
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A 16 th century Escherichia coli draft genome associated with an opportunistic bile infection. Commun Biol 2022; 5:599. [PMID: 35710940 PMCID: PMC9203756 DOI: 10.1038/s42003-022-03527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli – one of the most characterized bacteria and a major public health concern – remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16th century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past. Ancient DNA from an Italian mummy’s gallstone provides insight into opportunistic E. coli infection.
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88
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Zhang M, Holowko MB, Hayman Zumpe H, Ong CS. Machine Learning Guided Batched Design of a Bacterial Ribosome Binding Site. ACS Synth Biol 2022; 11:2314-2326. [PMID: 35704784 PMCID: PMC9295160 DOI: 10.1021/acssynbio.2c00015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optimization of gene expression levels is an essential part of the organism design process. Fine control of this process can be achieved by engineering transcription and translation control elements, including the ribosome binding site (RBS). Unfortunately, the design of specific genetic parts remains challenging because of the lack of reliable design methods. To address this problem, we have created a machine learning guided Design-Build-Test-Learn (DBTL) cycle for the experimental design of bacterial RBSs to demonstrate how small genetic parts can be reliably designed using relatively small, high-quality data sets. We used Gaussian Process Regression for the Learn phase of the cycle and the Upper Confidence Bound multiarmed bandit algorithm for the Design of genetic variants to be tested in vivo. We have integrated these machine learning algorithms with laboratory automation and high-throughput processes for reliable data generation. Notably, by Testing a total of 450 RBS variants in four DBTL cycles, we have experimentally validated RBSs with high translation initiation rates equaling or exceeding our benchmark RBS by up to 34%. Overall, our results show that machine learning is a powerful tool for designing RBSs, and they pave the way toward more complicated genetic devices.
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Affiliation(s)
- Mengyan Zhang
- Machine Learning and Artificial Intelligence Future Science Platform, CSIRO, Canberra, ACT 2601, Australia.,Department of Computer Science, Australian National University, Canberra, ACT 2601, Australia.,Data61, CSIRO, Canberra, ACT 2601, Australia
| | - Maciej Bartosz Holowko
- Synthetic Biology Future Science Platform, CSIRO, Canberra, ACT 2601, Australia.,Land and Water, CSIRO, Canberra, ACT 2601, Australia
| | - Huw Hayman Zumpe
- Synthetic Biology Future Science Platform, CSIRO, Canberra, ACT 2601, Australia.,Land and Water, CSIRO, Canberra, ACT 2601, Australia
| | - Cheng Soon Ong
- Machine Learning and Artificial Intelligence Future Science Platform, CSIRO, Canberra, ACT 2601, Australia.,Department of Computer Science, Australian National University, Canberra, ACT 2601, Australia.,Data61, CSIRO, Canberra, ACT 2601, Australia
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89
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Marciano DC, Wang C, Hsu TK, Bourquard T, Atri B, Nehring RB, Abel NS, Bowling EA, Chen TJ, Lurie PD, Katsonis P, Rosenberg SM, Herman C, Lichtarge O. Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli. Nat Commun 2022; 13:3189. [PMID: 35680894 PMCID: PMC9184624 DOI: 10.1038/s41467-022-30889-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/24/2022] [Indexed: 11/08/2022] Open
Abstract
Since antibiotic development lags, we search for potential drug targets through directed evolution experiments. A challenge is that many resistance genes hide in a noisy mutational background as mutator clones emerge in the adaptive population. Here, to overcome this noise, we quantify the impact of mutations through evolutionary action (EA). After sequencing ciprofloxacin or colistin resistance strains grown under different mutational regimes, we find that an elevated sum of the evolutionary action of mutations in a gene identifies known resistance drivers. This EA integration approach also suggests new antibiotic resistance genes which are then shown to provide a fitness advantage in competition experiments. Moreover, EA integration analysis of clinical and environmental isolates of antibiotic resistant of E. coli identifies gene drivers of resistance where a standard approach fails. Together these results inform the genetic basis of de novo colistin resistance and support the robust discovery of phenotype-driving genes via the evolutionary action of genetic perturbations in fitness landscapes.
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Affiliation(s)
- David C Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Teng-Kuei Hsu
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas Bourquard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benu Atri
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Clara Analytics Inc., 451 El Camino Real #201, Santa Clara, CA, 95050, USA
| | - Ralf B Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth A Bowling
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Taylor J Chen
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pamela D Lurie
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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90
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Abstract
Ecotypic diversification and its associated cooperative behaviors are frequently observed in natural microbial populations whose access to resources is often sporadic. However, the extent to which fluctuations in resource availability influence the emergence of cooperative ecotypes is not fully understood. To determine how exposure to repeated resource limitation affects the establishment and long-term maintenance of ecotypes in a structured environment, we followed 32 populations of Escherichia coli evolving to either 1-day or 10-day feast/famine cycles for 900 days. Population-level analysis revealed that compared to populations evolving to 1-day cycles, 10-day populations evolved increased biofilm density, higher parallelism in mutational targets, and increased mutation rates. As previous investigations of evolution in structured environments have identified biofilm formation as the earliest observable phenotype associated with diversification of ecotypes, we revived cultures midway through the evolutionary process and conducted additional genomic, transcriptional, and phenotypic analyses of clones isolated from these evolving populations. We found not only that 10-day feast/famine cycles support multiple ecotypes but also that these ecotypes exhibit cooperative behavior. Consistent with the black queen hypothesis, or evolution of cooperation by gene loss, transcriptomic evidence suggests the evolution of bidirectional cross-feeding behaviors based on essential resources. These results provide insight into how analogous cooperative relationships may emerge in natural microbial communities. IMPORTANCE Despite regular feast and famine conditions representing an environmental pressure that is commonly encountered by microbial communities, the evolutionary outcomes of repeated cycles of feast and famine have been less studied. By experimentally evolving initially isogenic Escherichia coli populations to 10-day feast/famine cycles, we observed rapid diversification into ecotypes with evidence of bidirectional cross-feeding on costly resources and frequency-dependent fitness. Although unidirectional cross-feeding has been repeatedly observed to evolve in laboratory culture, most investigations of bidirectional cooperative behaviors in microbial populations have been conducted in engineered communities. This work demonstrates the de novo evolution of black queen relationships in a microbial population originating from a single ancestor, providing a model for investigation of the eco-evolutionary processes leading to mutualistic cooperation.
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91
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Foster-Nyarko E, Pallen MJ. The microbial ecology of Escherichia coli in the vertebrate gut. FEMS Microbiol Rev 2022; 46:fuac008. [PMID: 35134909 PMCID: PMC9075585 DOI: 10.1093/femsre/fuac008] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
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Affiliation(s)
- Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, United Kingdom
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92
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Ellington AJ, Reisch CR. Efficient and Iterative Retron-Mediated in vivo Recombineering in E. coli. Synth Biol (Oxf) 2022; 7:ysac007. [PMID: 35673614 PMCID: PMC9165427 DOI: 10.1093/synbio/ysac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/22/2022] [Accepted: 05/02/2022] [Indexed: 11/28/2022] Open
Abstract
Recombineering is an important tool in gene editing, enabling fast, precise and highly specific in vivo modification of microbial genomes. Oligonucleotide-mediated recombineering via the in vivo production of single-stranded DNA can overcome the limitations of traditional recombineering methods that rely on the exogenous delivery of editing templates. By modifying a previously reported plasmid-based system for fully in vivo single-stranded DNA recombineering, we demonstrate iterative editing of independent loci by utilizing a temperature-sensitive origin of replication for easy curing of the editing plasmid from recombinant cells. Optimization of the promoters driving the expression of the system’s functional components, combined with targeted counterselection against unedited cells with Cas9 nuclease, enabled editing efficiencies of 90–100%. The addition of a dominant-negative mutL allele to the system allowed single-nucleotide edits that were otherwise unachievable due to mismatch repair. Finally, we tested alternative recombinases and found that efficiency significantly increased for some targets. Requiring only a single cloning step for retargeting, our system provides an easy-to-use method for rapid, efficient construction of desired mutants.
Graphical Abstract
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Affiliation(s)
- Adam J Ellington
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL 32611-7011, USA
| | - Christopher R Reisch
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL 32611-7011, USA
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93
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Pan J, Li W, Ni J, Wu K, Konigsberg I, Rivera CE, Tincher C, Gregory C, Zhou X, Doak TG, Lee H, Wang Y, Gao X, Lynch M, Long H. Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica. Mol Biol Evol 2022; 39:msac081. [PMID: 35446958 PMCID: PMC9040049 DOI: 10.1093/molbev/msac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Because errors at the DNA level power pathogen evolution, a systematic understanding of the rate and molecular spectra of mutations could guide the avoidance and treatment of infectious diseases. We thus accumulated tens of thousands of spontaneous mutations in 768 repeatedly bottlenecked lineages of 18 strains from various geographical sites, temporal spread, and genetic backgrounds. Entailing over ∼1.36 million generations, the resultant data yield an average mutation rate of ∼0.0005 per genome per generation, with a significant within-species variation. This is one of the lowest bacterial mutation rates reported, giving direct support for a high genome stability in this pathogen resulting from high DNA-mismatch-repair efficiency and replication-machinery fidelity. Pathogenicity genes do not exhibit an accelerated mutation rate, and thus, elevated mutation rates may not be the major determinant for the diversification of toxin and secretion systems. Intriguingly, a low error rate at the transcript level is not observed, suggesting distinct fidelity of the replication and transcription machinery. This study urges more attention on the most basic evolutionary processes of even the best-known human pathogens and deepens the understanding of their genome evolution.
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Affiliation(s)
- Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Weiyi Li
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Kun Wu
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Iain Konigsberg
- Division of Biomedical Informatics & Personalized Medicine, Department of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Caitlyn E. Rivera
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Clayton Tincher
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Colin Gregory
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Xia Zhou
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Thomas G. Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Heewook Lee
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ 85281, USA
| | - Yan Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, No. 72 Binhai Road, Qingdao, Shandong Province 266237, China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
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94
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Khedkar S, Smyshlyaev G, Letunic I, Maistrenko OM, Coelho LP, Orakov A, Forslund SK, Hildebrand F, Luetge M, Schmidt TSB, Barabas O, Bork P. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. Nucleic Acids Res 2022; 50:3155-3168. [PMID: 35323968 PMCID: PMC8989519 DOI: 10.1093/nar/gkac163] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/30/2022] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal.
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Affiliation(s)
- Supriya Khedkar
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Georgy Smyshlyaev
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Ivica Letunic
- Biobyte solutions GmbH, Bothestr 142, 69117 Heidelberg, Germany
| | - Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Askarbek Orakov
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Sofia K Forslund
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, Berlin, Germany.,Experimental and Clinical Research Center, Charité-Universitätsmedizin and Max-Delbrück Center, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Falk Hildebrand
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Mechthild Luetge
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Thomas S B Schmidt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Orsolya Barabas
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Yonsei Frontier Lab (YFL), Yonsei University, Seoul 03722, South Korea
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95
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Xu H, Dai C, Tang Y, Xu X, Umego EC, He R, Ma H. The selective breeding and mutagenesis mechanism of high-yielding surfactin Bacillus subtilis strains with atmospheric and room temperature plasma. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:1851-1861. [PMID: 34464473 DOI: 10.1002/jsfa.11521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/05/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Surfactin, a good biological surfactant, is derived from the metabolites of microorganisms. However, the ability of natural strains to produce surfactin is low, and so the presented study aimed to use a novel mutagenesis technology to increase their yields. RESULTS Atmospheric and room temperature plasma (ARTP) was used to conduct mutation breeding of Bacillus subtilis CICC 10721, and a mutant strain M45 with a higher surfactin yield of 34.2% and a stable subculture was screened out. From the fermentation kinetics study, it was found that the maximum cell dry weight, maximum growth rate and surfactin synthesis parameters of the mutant strain M45 were all greater than that of the original strain. Scanning electron microscope and laser scanning confocal microscope observations showed that the spore morphology changed after ARTP treating, and the intracellular Ca2+ concentration of the mutant increased. Genome resequencing analysis showed that 66 single nucleotide poymorphism non-synonymous mutation sites occurred in M45, and the identification results of the fermentation broth extract from M45 showed that it is composed of C12 -C16 surfactin. CONCLUSION ARTP mutagenesis was found to change the morphology of bacteria, membrane permeability and genes related to the synthesis and secretion of surfactin. The present study provides a basis for industrial production of surfactin and an understanding of the mutagenesis mechanism. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Haining Xu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Chunhua Dai
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Institute of Food Physical Processing, Jiangsu University, Zhenjiang, China
| | - Yingxiu Tang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Xueting Xu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Ekene Christopher Umego
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Department of Food Science and Technology, University of Nigeria, Nsukka, Nigeria
| | - Ronghai He
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Institute of Food Physical Processing, Jiangsu University, Zhenjiang, China
| | - Haile Ma
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Institute of Food Physical Processing, Jiangsu University, Zhenjiang, China
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96
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Menuhin-Gruman I, Arbel M, Amitay N, Sionov K, Naki D, Katzir I, Edgar O, Bergman S, Tuller T. Evolutionary Stability Optimizer (ESO): A Novel Approach to Identify and Avoid Mutational Hotspots in DNA Sequences While Maintaining High Expression Levels. ACS Synth Biol 2022; 11:1142-1151. [PMID: 34928133 PMCID: PMC8938948 DOI: 10.1021/acssynbio.1c00426] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Modern
synthetic biology procedures rely on the ability to generate
stable genetic constructs that keep their functionality over long
periods of time. However, maintenance of these constructs requires
energy from the cell and thus reduces the host’s fitness. Natural
selection results in loss-of-functionality mutations that negate the
expression of the construct in the population. Current approaches
for the prevention of this phenomenon focus on either small-scale,
manual design of evolutionary stable constructs or the detection of
mutational sites with unstable tendencies. We designed the Evolutionary
Stability Optimizer (ESO), a software tool that enables the large-scale
automatic design of evolutionarily stable constructs with respect
to both mutational and epigenetic hotspots and allows users to define
custom hotspots to avoid. Furthermore, our tool takes the expression
of the input constructs into account by considering the guanine-cytosine
(GC) content and codon usage of the host organism, balancing the trade-off
between stability and gene expression, allowing to increase evolutionary
stability while maintaining the high expression. In this study, we
present the many features of the ESO and show that it accurately predicts
the evolutionary stability of endogenous genes. The ESO was created
as an easy-to-use, flexible platform based on the notion that directed
genetic stability research will continue to evolve and revolutionize
current applications of synthetic biology. The ESO is available at
the following link: https://www.cs.tau.ac.il/~tamirtul/ESO/.
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Affiliation(s)
- Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Matan Arbel
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Niv Amitay
- School of Electrical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Karin Sionov
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Itai Katzir
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Omer Edgar
- School of Medicine, The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel 6997801
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97
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Allen C, Finkel SE. Vibrio harveyi Exhibits the Growth Advantage in Stationary Phase Phenotype during Long-Term Incubation. Microbiol Spectr 2022; 10:e0214421. [PMID: 35080444 PMCID: PMC8791185 DOI: 10.1128/spectrum.02144-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/26/2021] [Indexed: 11/20/2022] Open
Abstract
The bioluminescent marine bacterium Vibrio harveyi can exist within a host, acting as a mutualist or a parasitic microbe, and as planktonic cells in open seawater. This study demonstrates the ability of V. harveyi populations to survive and adapt under nutrient stress conditions in the laboratory, starting in an initially rich medium. V. harveyi populations remain viable into long-term stationary phase, for at least 1 month, without the addition of nutrients. To determine whether these communities are dynamic, populations were sampled after 10, 20, and 30 days of incubation and examined for their competitive ability when cocultured with an unaged, parental population. While populations incubated for 10 or 20 days showed some fitness advantage over parental populations, only after 30 days of incubation did all populations examined outcompete parental populations in coculture, fully expressing the growth advantage in stationary phase (GASP) phenotype. The ability to express GASP, in the absence of additional nutrients after inoculation, verifies the dynamism of long-term stationary-phase V. harveyi populations, implies the ability to generate genetic diversity, and demonstrates the plasticity of the V. harveyi genome, allowing for rapid adaptation for survival in changing culture environments. Despite the dynamism, the adaptation to the changing culture environment occurs less rapidly than in Escherichia coli, possibly due to Vibrio harveyi's lower mutation frequency. IMPORTANCE Vibrio harveyi populations exist in many different niches within the ocean environment, as free-living cells, symbionts with particular squid and fish species, and parasites to other marine organisms. It is important to understand V. harveyi's ability to survive and evolve within each of these niches. This study focuses on V. harveyi's lifestyle outside the host environment, demonstrating this microbe's ability to survive long-term culturing after inoculation in an initially rich medium and revealing increased competitive fitness correlated with incubation time when aged V. harveyi populations are cocultured with unaged, parental cultures. Thus, this study highlights the development of the growth advantage in stationary phase (GASP) phenotype in V. harveyi populations suggesting a dynamic population with fluctuating genotype frequencies throughout long-term, host-independent incubation.
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Affiliation(s)
- Calista Allen
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States
| | - Steven E. Finkel
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States
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98
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Abstract
How do mutational biases influence the process of adaptation? A common assumption is that selection alone determines the course of adaptation from abundant preexisting variation. Yet, theoretical work shows broad conditions under which the mutation rate to a given type of variant strongly influences its probability of contributing to adaptation. Here we introduce a statistical approach to analyzing how mutation shapes protein sequence adaptation. Using large datasets from three different species, we show that the mutation spectrum has a proportional influence on the types of changes fixed in adaptation. We also show via computer simulations that a variety of factors can influence how closely the spectrum of adaptive substitutions reflects the spectrum of variants introduced by mutation. Evolutionary adaptation often occurs by the fixation of beneficial mutations. This mode of adaptation can be characterized quantitatively by a spectrum of adaptive substitutions, i.e., a distribution for types of changes fixed in adaptation. Recent work establishes that the changes involved in adaptation reflect common types of mutations, raising the question of how strongly the mutation spectrum shapes the spectrum of adaptive substitutions. We address this question with a codon-based model for the spectrum of adaptive amino acid substitutions, applied to three large datasets covering thousands of amino acid changes identified in natural and experimental adaptation in Saccharomyces cerevisiae, Escherichia coli, and Mycobacterium tuberculosis. Using species-specific mutation spectra based on prior knowledge, we find that the mutation spectrum has a proportional influence on the spectrum of adaptive substitutions in all three species. Indeed, we find that by inferring the mutation rates that best explain the spectrum of adaptive substitutions, we can accurately recover the species-specific mutation spectra. However, we also find that the predictive power of the model differs substantially between the three species. To better understand these differences, we use population simulations to explore the factors that influence how closely the spectrum of adaptive substitutions mirrors the mutation spectrum. The results show that the influence of the mutation spectrum decreases with increasing mutational supply (Nμ) and that predictive power is strongly affected by the number and diversity of beneficial mutations.
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99
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Chen Z, Wang X, Song Y, Zeng Q, Zhang Y, Luo H. Prochlorococcus have low global mutation rate and small effective population size. Nat Ecol Evol 2022; 6:183-194. [PMID: 34949817 DOI: 10.1038/s41559-021-01591-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/14/2021] [Indexed: 12/27/2022]
Abstract
Prochlorococcus are the most abundant free-living photosynthetic carbon-fixing organisms in the ocean. Prochlorococcus show small genome sizes, low genomic G+C content, reduced DNA repair gene pool and fast evolutionary rates, which are typical features of endosymbiotic bacteria. Nevertheless, their evolutionary mechanisms are believed to be different. Evolution of endosymbiotic bacteria is dominated by genetic drift owing to repeated population bottlenecks, whereas Prochlorococcus are postulated to have extremely large effective population sizes (Ne) and thus drift has rarely been considered. However, accurately extrapolating Ne requires measuring an unbiased global mutation rate through mutation accumulation, which is challenging for Prochlorococcus. Here, we managed this experiment over 1,065 days using Prochlorococcus marinus AS9601, sequenced genomes of 141 mutant lines and determined its mutation rate to be 3.50 × 10-10 per site per generation. Extrapolating Ne additionally requires identifying population boundaries, which we defined using PopCOGenT and over 400 genomes related to AS9601. Accordingly, we calculated its Ne to be 1.68 × 107, which is only reasonably greater than that of endosymbiotic bacteria but surprisingly smaller than that of many free-living bacteria extrapolated using the same approach. Our results therefore suggest that genetic drift is a key driver of Prochlorococcus evolution.
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Affiliation(s)
- Zhuoyu Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaojun Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yu Song
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Clear Water Bay, Hong Kong SAR
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China. .,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Clear Water Bay, Hong Kong SAR.
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100
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Monroe JG, Srikant T, Carbonell-Bejerano P, Becker C, Lensink M, Exposito-Alonso M, Klein M, Hildebrandt J, Neumann M, Kliebenstein D, Weng ML, Imbert E, Ågren J, Rutter MT, Fenster CB, Weigel D. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature 2022; 602:101-105. [PMID: 35022609 PMCID: PMC8810380 DOI: 10.1038/s41586-021-04269-6] [Citation(s) in RCA: 152] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/17/2021] [Indexed: 12/24/2022]
Abstract
Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome-mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.
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Affiliation(s)
- J Grey Monroe
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
- Department of Plant Sciences, University of California Davis, Davis, CA, USA.
| | - Thanvi Srikant
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | | | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Faculty of Biology, Ludwig Maximilian University, Martinsried, Germany
| | - Mariele Lensink
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Marie Klein
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Julia Hildebrandt
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Daniel Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Mao-Lun Weng
- Department of Biology, Westfield State University, Westfield, MA, USA
| | - Eric Imbert
- ISEM, University of Montpellier, Montpellier, France
| | - Jon Ågren
- Department of Ecology and Genetics, EBC, Uppsala University, Uppsala, Sweden
| | - Matthew T Rutter
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - Charles B Fenster
- Oak Lake Field Station, South Dakota State University, Brookings, SD, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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