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Kordium VA. Defining life and evolution: Essay on the origin, expansion, and evolution of living matter. Biosystems 2021; 209:104500. [PMID: 34352326 DOI: 10.1016/j.biosystems.2021.104500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022]
Abstract
This essay aims to define the origin, expansion, and evolution of living matter. The first formations, identified as remains, fossils, traces etc. of life are almost as old as the Earth itself. During four billion years, life on the Earth has continuously existed and been implemented in the range of conditions, ensuring the liquid state of water. During the entire period of life existence, its evolution was proceeding with the tendency of multidirectionality, after each catastrophe tending to the diversity and vastness of distribution, and all the currently living species, regardless of their complexity, have the same evolutionary age. The property of reproductive surplus (multiplication) is inherent in all the living matter. The reproduction of all the living matter is implemented via the "development" - a process of continuous occurrence of something new that did not exist in the previous moment in the reproduced individual at each specific moment of time with the tendency towards the reproduction of a "copy". In its fundamental basis, Life is based on a programme, its material support is implemented and exists not in the field of causative-consecutive events, but in the field of programmed-causative-consecutive events. This predetermines the "biology laws", the behaviour of the material constituent of Life at each time period, and the future of the material constituent of life.
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Affiliation(s)
- Vitaly A Kordium
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kyiv, 03143, Ukraine.
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2
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Boege Y, Malehmir M, Healy ME, Bettermann K, Lorentzen A, Vucur M, Ahuja AK, Böhm F, Mertens JC, Shimizu Y, Frick L, Remouchamps C, Mutreja K, Kähne T, Sundaravinayagam D, Wolf MJ, Rehrauer H, Koppe C, Speicher T, Padrissa-Altés S, Maire R, Schattenberg JM, Jeong JS, Liu L, Zwirner S, Boger R, Hüser N, Davis RJ, Müllhaupt B, Moch H, Schulze-Bergkamen H, Clavien PA, Werner S, Borsig L, Luther SA, Jost PJ, Weinlich R, Unger K, Behrens A, Hillert L, Dillon C, Di Virgilio M, Wallach D, Dejardin E, Zender L, Naumann M, Walczak H, Green DR, Lopes M, Lavrik I, Luedde T, Heikenwalder M, Weber A. A Dual Role of Caspase-8 in Triggering and Sensing Proliferation-Associated DNA Damage, a Key Determinant of Liver Cancer Development. Cancer Cell 2017; 32:342-359.e10. [PMID: 28898696 PMCID: PMC5598544 DOI: 10.1016/j.ccell.2017.08.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 06/30/2017] [Accepted: 08/16/2017] [Indexed: 12/11/2022]
Abstract
Concomitant hepatocyte apoptosis and regeneration is a hallmark of chronic liver diseases (CLDs) predisposing to hepatocellular carcinoma (HCC). Here, we mechanistically link caspase-8-dependent apoptosis to HCC development via proliferation- and replication-associated DNA damage. Proliferation-associated replication stress, DNA damage, and genetic instability are detectable in CLDs before any neoplastic changes occur. Accumulated levels of hepatocyte apoptosis determine and predict subsequent hepatocarcinogenesis. Proliferation-associated DNA damage is sensed by a complex comprising caspase-8, FADD, c-FLIP, and a kinase-dependent function of RIPK1. This platform requires a non-apoptotic function of caspase-8, but no caspase-3 or caspase-8 cleavage. It may represent a DNA damage-sensing mechanism in hepatocytes that can act via JNK and subsequent phosphorylation of the histone variant H2AX.
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Affiliation(s)
- Yannick Boege
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Mohsen Malehmir
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Marc E Healy
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Kira Bettermann
- Department of Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Anna Lorentzen
- Institute of Virology, Technische Universität München, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Mihael Vucur
- Department of Medicine III, Division of GI and Hepatobiliary Oncology, University Hospital RWTH Aachen, 52056 Aachen, Germany
| | - Akshay K Ahuja
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Friederike Böhm
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Joachim C Mertens
- Gastroenterology and Hepatology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Yutaka Shimizu
- Centre for Cell Death, Cancer, and Inflammation, Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Lukas Frick
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Caroline Remouchamps
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-R, University of Liège, 4000 Liège, Belgium
| | - Karun Mutreja
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Devakumar Sundaravinayagam
- DNA Repair and Maintenance of Genome Stability, Max-Delbruck Center for Molecular Medicine (MDC) Berlin, 13125 Berlin, Germany
| | - Monika J Wolf
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH and University Zurich, 8057 Zurich, Switzerland
| | - Christiane Koppe
- Department of Medicine III, Division of GI and Hepatobiliary Oncology, University Hospital RWTH Aachen, 52056 Aachen, Germany
| | - Tobias Speicher
- Department of Biology, Institute of Molecular Health Sciences, ETH, Zurich, Switzerland
| | | | - Renaud Maire
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Jörn M Schattenberg
- I. Department of Medicine, University Medical Center, Johannes Gutenberg-University, 55122 Mainz, Germany
| | - Ju-Seong Jeong
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lei Liu
- Department of Surgery, Technische Universität München, 80333 Munich, Germany
| | - Stefan Zwirner
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; Translational Gastrointestinal Oncology Group, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Regina Boger
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Norbert Hüser
- Department of Surgery, Technische Universität München, 80333 Munich, Germany
| | - Roger J Davis
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Beat Müllhaupt
- Gastroenterology and Hepatology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | | | - Pierre-Alain Clavien
- Clinic of Visceral and Transplantation Surgery, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Sabine Werner
- Department of Biology, Institute of Molecular Health Sciences, ETH, Zurich, Switzerland
| | - Lubor Borsig
- Institute of Physiology, University of Zurich, 8057 Zurich, Switzerland
| | - Sanjiv A Luther
- Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland
| | - Philipp J Jost
- III. Medizinische Klinik, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Ricardo Weinlich
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Laura Hillert
- Department of Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Christopher Dillon
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michela Di Virgilio
- DNA Repair and Maintenance of Genome Stability, Max-Delbruck Center for Molecular Medicine (MDC) Berlin, 13125 Berlin, Germany
| | - David Wallach
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Emmanuel Dejardin
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-R, University of Liège, 4000 Liège, Belgium
| | - Lars Zender
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; Translational Gastrointestinal Oncology Group, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Henning Walczak
- Centre for Cell Death, Cancer, and Inflammation, Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Inna Lavrik
- Department of Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Tom Luedde
- Department of Medicine III, Division of GI and Hepatobiliary Oncology, University Hospital RWTH Aachen, 52056 Aachen, Germany
| | - Mathias Heikenwalder
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, 8091 Zurich, Switzerland; Institute of Virology, Technische Universität München, Helmholtz Zentrum München, 85764 Munich, Germany; Institute of Chronic Inflammation and Cancer, Deutsches Krebs-Forschungszentrum (DKFZ), 69120 Heidelberg, Germany.
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, 8091 Zurich, Switzerland.
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Thorvaldsen S. A Mutation Model from First Principles of the Genetic Code. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:878-886. [PMID: 26485722 DOI: 10.1109/tcbb.2015.2489641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The paper presents a neutral Codons Probability Mutations (CPM) model of molecular evolution and genetic decay of an organism. The CPM model uses a Markov process with a 20-dimensional state space of probability distributions over amino acids. The transition matrix of the Markov process includes the mutation rate and those single point mutations compatible with the genetic code. This is an alternative to the standard Point Accepted Mutation (PAM) and BLOcks of amino acid SUbstitution Matrix (BLOSUM). Genetic decay is quantified as a similarity between the amino acid distribution of proteins from a (group of) species on one hand, and the equilibrium distribution of the Markov chain on the other. Amino acid data for the eukaryote, bacterium, and archaea families are used to illustrate how both the CPM and PAM models predict their genetic decay towards the equilibrium value of 1. A family of bacteria is studied in more detail. It is found that warm environment organisms on average have a higher degree of genetic decay compared to those species that live in cold environments. The paper addresses a new codon-based approach to quantify genetic decay due to single point mutations compatible with the genetic code. The present work may be seen as a first approach to use codon-based Markov models to study how genetic entropy increases with time in an effectively neutral biological regime. Various extensions of the model are also discussed.
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Abstract
All living organisms are continually exposed to agents that damage their DNA, which threatens the integrity of their genome. As a consequence, cells are equipped with a plethora of DNA repair enzymes to remove the damaged DNA. Unfortunately, situations nevertheless arise where lesions persist, and these lesions block the progression of the cell's replicase. In these situations, cells are forced to choose between recombination-mediated "damage avoidance" pathways or a specialized DNA polymerase (pol) to traverse the blocking lesion. The latter process is referred to as Translesion DNA Synthesis (TLS). As inferred by its name, TLS not only results in bases being (mis)incorporated opposite DNA lesions but also bases being (mis)incorporated downstream of the replicase-blocking lesion, so as to ensure continued genome duplication and cell survival. Escherichia coli and Salmonella typhimurium possess five DNA polymerases, and while all have been shown to facilitate TLS under certain experimental conditions, it is clear that the LexA-regulated and damage-inducible pols II, IV, and V perform the vast majority of TLS under physiological conditions. Pol V can traverse a wide range of DNA lesions and performs the bulk of mutagenic TLS, whereas pol II and pol IV appear to be more specialized TLS polymerases.
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Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks. Adv Microb Physiol 2013; 61:1-36. [PMID: 23046950 DOI: 10.1016/b978-0-12-394423-8.00001-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Transcriptional regulation plays a significant role in the biological response of bacteria to changing environmental conditions. Therefore, mapping transcriptional regulatory networks is an important step not only in understanding how bacteria sense and interpret their environment but also to identify the functions involved in biological responses to specific conditions. Recent experimental and computational developments have facilitated the characterization of regulatory networks on a genome-wide scale in model organisms. In addition, the multiplication of complete genome sequences has encouraged comparative analyses to detect conserved regulatory elements and infer regulatory networks in other less well-studied organisms. However, transcription regulation appears to evolve rapidly, thus, creating challenges for the transfer of knowledge to nonmodel organisms. Nevertheless, the mechanisms and constraints driving the evolution of regulatory networks have been the subjects of numerous analyses, and several models have been proposed. Overall, the contributions of mutations, recombination, and horizontal gene transfer are complex. Finally, the rapid evolution of regulatory networks plays a significant role in the remarkable capacity of bacteria to adapt to new or changing environments. Conversely, the characteristics of environmental niches determine the selective pressures and can shape the structure of regulatory network accordingly.
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Mozhayskiy V, Tagkopoulos I. Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution. BMC Bioinformatics 2012; 13 Suppl 10:S13. [PMID: 22759418 PMCID: PMC3382434 DOI: 10.1186/1471-2105-13-s10-s13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Horizontal gene transfer (HGT) is a process that facilitates the transfer of genetic material between organisms that are not directly related, and thus can affect both the rate of evolution and emergence of traits. Recent phylogenetic studies reveal HGT events are likely ubiquitous in the Tree of Life. However, our knowledge of HGT's role in evolution and biological organization is very limited, mainly due to the lack of ancestral evolutionary signatures and the difficulty to observe complex evolutionary dynamics in a laboratory setting. Here, we utilize a multi-scale microbial evolution model to comprehensively study the effect of HGT on the evolution of complex traits and organization of gene regulatory networks. Results Large-scale simulations reveal a distinct signature of the Distribution of Fitness Effect (DFE) for HGT events: during evolution, while mutation fitness effects become more negative and neutral, HGT events result in a balanced effect distribution. In either case, lethal events are significantly decreased during evolution (33.0% to 3.2%), a clear indication of mutational robustness. Interestingly, evolution was accelerated when populations were exposed to correlated environments of increasing complexity, especially in the presence of HGT, a phenomenon that warrants further investigation. High HGT rates were found to be disruptive, while the average transferred fragment size was linked to functional module size in the underlying biological network. Network analysis reveals that HGT results in larger regulatory networks, but with the same sparsity level as those evolved in its absence. Observed phenotypic variability and co-existing solutions were traced to individual gain/loss of function events, while subsequent re-wiring after fragment integration was necessary for complex traits to emerge.
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Affiliation(s)
- Vadim Mozhayskiy
- Department of Computer Science and UC Davis Genome Center, University of California Davis, Davis, California 95616, USA
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Cliff JB, Kreuzer HW, Ehrhardt CJ, Wunschel DS. The Microbe: The Basics of Structure, Morphology, and Physiology as They Relate to Microbial Characterization and Attribution. CHEMICAL AND PHYSICAL SIGNATURES FOR MICROBIAL FORENSICS 2012. [PMCID: PMC7123343 DOI: 10.1007/978-1-60327-219-3_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This chapter is meant to (1) review classical methods used to characterize and classify microbes and (2) introduce new molecular methods used in microbial characterization. The fundamental composition of microbes is discussed as well as their importance in classification of microbes into genus and species. Classical microbiological methods in general seek to define the common features of specific bacterial groups as a means of classification and identification of microbes. Thus, the focus was to describe the common features which discriminated closely related groups of organisms. In contrast, the newer molecular methods often seek to expand the classification of microbes not only as a means to organize microbial phylogeny but also to differentiate signatures between microbes identified within a species in greater detail. Molecular biology tools are used both as an adjunct to established methods and as replacement for classical methods for detection, discrimination, or identification of bacterial and viral species.
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Affiliation(s)
- John B. Cliff
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Crawley, 6009 West Australia Australia
| | - Helen W. Kreuzer
- Chemical and Biological Signature Scienc, Pacific Northwest National Laboratory, PO Box 999, MS P7-50, Richland, 99352 Washington USA
| | - Christopher J. Ehrhardt
- Department of Forensic Science, Virginia Commonwealth University, 1020 W. Main Street, Richmond, 23284 Virginia USA
| | - David S. Wunschel
- Chemical and Biological Signature Scienc, Pacific Northwest National Laboratory, PO Box 999, MS P7-50, Richland, 99352 Washington USA
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Sidorenko J, Jatsenko T, Saumaa S, Teras R, Tark-Dame M, Hõrak R, Kivisaar M. Involvement of specialized DNA polymerases Pol II, Pol IV and DnaE2 in DNA replication in the absence of Pol I in Pseudomonas putida. Mutat Res 2011; 714:63-77. [PMID: 21763330 DOI: 10.1016/j.mrfmmm.2011.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 06/15/2011] [Accepted: 06/28/2011] [Indexed: 05/31/2023]
Abstract
The majority of bacteria possess a different set of specialized DNA polymerases than those identified in the most common model organism Escherichia coli. Here, we have studied the ability of specialized DNA polymerases to substitute Pol I in DNA replication in Pseudomonas putida. Our results revealed that P. putida Pol I-deficient cells have severe growth defects in LB medium, which is accompanied by filamentous cell morphology. However, growth of Pol I-deficient bacteria on solid rich medium can be restored by reduction of reactive oxygen species in cells. Also, mutants with improved growth emerge rapidly. Similarly to the initial Pol I-deficient P. putida, its adapted derivatives express a moderate mutator phenotype, which indicates that DNA replication carried out in the absence of Pol I is erroneous both in the original Pol I-deficient bacteria and the adapted derivatives. Analysis of the spectra of spontaneous Rif(r) mutations in P. putida strains lacking different DNA polymerases revealed that the presence of specialized DNA polymerases Pol II and Pol IV influences the frequency of certain base substitutions in Pol I-proficient and Pol I-deficient backgrounds in opposite ways. Involvement of another specialized DNA polymerase DnaE2 in DNA replication in Pol I-deficient bacteria is stimulated by UV irradiation of bacteria, implying that DnaE2-provided translesion synthesis partially substitutes the absence of Pol I in cells containing heavily damaged DNA.
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Affiliation(s)
- Julia Sidorenko
- Department of Genetics, Tartu University and Estonian Biocentre, Tartu, Estonia
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García-Ortíz MV, Marsin S, Arana ME, Gasparutto D, Guérois R, Kunkel TA, Radicella JP. Unexpected role for Helicobacter pylori DNA polymerase I as a source of genetic variability. PLoS Genet 2011; 7:e1002152. [PMID: 21731507 PMCID: PMC3121766 DOI: 10.1371/journal.pgen.1002152] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 05/09/2011] [Indexed: 01/28/2023] Open
Abstract
Helicobacter pylori, a human pathogen infecting about half of the world population, is characterised by its large intraspecies variability. Its genome plasticity has been invoked as the basis for its high adaptation capacity. Consistent with its small genome, H. pylori possesses only two bona fide DNA polymerases, Pol I and the replicative Pol III, lacking homologues of translesion synthesis DNA polymerases. Bacterial DNA polymerases I are implicated both in normal DNA replication and in DNA repair. We report that H. pylori DNA Pol I 5′- 3′ exonuclease domain is essential for viability, probably through its involvement in DNA replication. We show here that, despite the fact that it also plays crucial roles in DNA repair, Pol I contributes to genomic instability. Indeed, strains defective in the DNA polymerase activity of the protein, although sensitive to genotoxic agents, display reduced mutation frequencies. Conversely, overexpression of Pol I leads to a hypermutator phenotype. Although the purified protein displays an intrinsic fidelity during replication of undamaged DNA, it lacks a proofreading activity, allowing it to efficiently elongate mismatched primers and perform mutagenic translesion synthesis. In agreement with this finding, we show that the spontaneous mutator phenotype of a strain deficient in the removal of oxidised pyrimidines from the genome is in part dependent on the presence of an active DNA Pol I. This study provides evidence for an unexpected role of DNA polymerase I in generating genomic plasticity. Helicobacter pylori is the main cause of ulcers and gastric cancers. One the characteristics of this bacterial species is that it displays an amazing capacity to change its genetic information. This genetic variability provides H. pylori with an adaptation potential that allows it to successfully colonise the stomach of about half the human population. Here we identified a surprising source of genomic plasticity in an enzyme also involved in the maintenance of DNA integrity. Indeed, we show that DNA polymerase I, one of the only two DNA polymerases that are found in H. pylori, although essential for DNA replication and repair, contributes to mutagenesis due to its biochemical characteristics.
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Affiliation(s)
| | - Stéphanie Marsin
- CEA, Institut de Radiobiologie Cellulaire et Moléculaire, UMR 217 CNRS/CEA, Fontenay aux Roses, France
| | - Mercedes E. Arana
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | | | - Raphaël Guérois
- CEA, iBiTecS, Gif sur Yvette, France
- CNRS, URA 2096, Gif sur Yvette, France
| | - Thomas A. Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - J. Pablo Radicella
- CEA, Institut de Radiobiologie Cellulaire et Moléculaire, UMR 217 CNRS/CEA, Fontenay aux Roses, France
- * E-mail:
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Proofreading deficiency of Pol I increases the levels of spontaneous rpoB mutations in E. coli. Mutat Res 2011; 712:28-32. [PMID: 21459099 DOI: 10.1016/j.mrfmmm.2011.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 03/07/2011] [Accepted: 03/24/2011] [Indexed: 11/23/2022]
Abstract
The fidelity role of DNA polymerase I in chromosomal DNA replication in E. coli was investigated using the rpoB forward target. These experiments indicated that in a strain carrying a proofreading-exonuclease-defective form of Pol I (polAexo mutant) the frequency of rpoB mutations increased by about 2-fold, consistent with a model that the fidelity of DNA polymerase I is important in controlling the overall fidelity of chromosomal DNA replication. DNA sequencing of rpoB mutants revealed that the Pol I exonuclease deficiency lead to an increase in a variety of base-substitution mutations. A polAexo mutator effect was also observed in strains defective in DNA mismatch repair and carrying the dnaE915 antimutator allele. Overall, the data are consistent with a proposed role of Pol I in the faithful completion of Okazaki fragment gaps at the replication fork.
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Effect of translesion DNA polymerases, endonucleases and RpoS on mutation rates in Salmonella typhimurium. Genetics 2010; 185:783-95. [PMID: 20421601 DOI: 10.1534/genetics.110.116376] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been suggested that bacteria have evolved mechanisms to increase their mutation rate in response to various stresses and that the translesion DNA polymerase Pol IV under control of the LexA regulon and the alternative sigma factor RpoS are involved in regulating this mutagenesis. Here we examined in Salmonella enterica serovar Typhimurium LT2 the rates for four different types of mutations (rifampicin, nalidixic acid, and chlorate resistance and Lac(+) reversion) during various growth conditions and with different levels of four translesion DNA polymerases (Pol II, Pol IV, Pol V, and SamAB) and RpoS. Constitutive derepression of the LexA regulon by a lexA(def) mutation had no effect on Lac(+) reversion rates but increased the other three mutation rates up to 11-fold, and the contribution of the translesion DNA polymerases to this mutagenesis varied with the type of mutation examined. The increase in mutation rates in the lexA(def) mutant required the presence of the LexA-controlled UvrB protein and endonucleases UvrC and Cho. With regard to the potential involvement of RpoS in mutagenesis, neither an increase in RpoS levels conferred by artificial overexpression from a plasmid nor long-term stationary phase incubation or slow growth caused an increase in any of the four mutation rates measured, alone or in combination with overexpression of the translesion DNA polymerases. In conclusion, mutation rates are remarkably robust and no combination of growth conditions, induction of translesion DNA polymerases by inactivation of LexA, or increased RpoS expression could confer an increase in mutation rates higher than the moderate increase caused by derepression of the LexA regulon alone.
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Sammarco PW, Strychar KB. Effects of Climate Change/Global Warming on Coral Reefs: Adaptation/Exaptation in Corals, Evolution in Zooxanthellae, and Biogeographic Shifts. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/15555270902905377] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Curti E, McDonald JP, Mead S, Woodgate R. DNA polymerase switching: effects on spontaneous mutagenesis in Escherichia coli. Mol Microbiol 2008; 71:315-31. [PMID: 19019142 PMCID: PMC2680738 DOI: 10.1111/j.1365-2958.2008.06526.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Escherichia coli possesses five known DNA polymerases (pols). Pol III holoenzyme is the cell's main replicase, while pol I is responsible for the maturation of Okazaki fragments and filling gaps generated during nucleotide excision repair. Pols II, IV and V are significantly upregulated as part of the cell's global SOS response to DNA damage and under these conditions, may alter the fidelity of DNA replication by potentially interfering with the ability of pols I and III to complete their cellular functions. To test this hypothesis, we determined the spectrum of rpoB mutations arising in an isogenic set of mutL strains differentially expressing the chromosomally encoded pols. Interestingly, mutagenic hot spots in rpoB were identified that are susceptible to the actions of pols I–V. For example, in a recA730 lexA(Def) mutL background most transversions were dependent upon pols IV and V. In contrast, transitions were largely dependent upon pol I and to a lesser extent, pol III. Furthermore, the extent of pol I-dependent mutagenesis at one particular site was modulated by pols II and IV. Our observations suggest that there is considerable interplay among all five E. coli polymerases that either reduces or enhances the mutagenic load on the E. coli chromosome.
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Affiliation(s)
- Elena Curti
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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14
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Acharya N, Abu-Nasr NF, Kawaguchi G, Imai M, Yamamoto K. Frameshift mutations produced by 9-aminoacridine in wild-type, uvrA and recA strains of Escherichia coli; specificity within a hotspot. JOURNAL OF RADIATION RESEARCH 2007; 48:361-8. [PMID: 17611351 DOI: 10.1269/jrr.07036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The endogenous tonB gene of Escherichia coli was used as a target for 9-aminoacridine-induced mutations that were identified in recA(-) and uvrA(-) cells. The cytotoxicity of 9-aminoacridine was enhanced in the uvrA and recA strains compared to the wild-type strain, and the mutagenicity of 9-aminoacridine in the uvrA and recA strains was similar to that in the wild type. For all three strains, the most common mutations were minus frameshifts in repetitive G:C base-pairs followed by minus frameshifts in nonrepetitive G:C base-pairs. 9-aminoacridine-induced minus frameshifts in the wild-type strain were distributed with several hot and warm spots. These sites were also hot and warm spots for minus frameshifts in the recA and uvrA stains. Furthermore, they were hot and warm sites in a 9-aminoacridine-treated strain carrying the target tonB gene oriented in the opposite direction. 9-Aminoacridine is known to interact with DNA to form intercalations which are involved in minus frameshift mutagenesis. In this study, we therefore argue that 1) 9-aminoacridine can induce bulky DNA lesions which are excised by nucleotide excision repair and not involved in mutagenesis, 2) the presence or absence of a recA-dependent repair pathway does not influence the mutagenic effect of 9-aminoacridine, and 3) both leading strand and lagging strand replication equally produce minus frameshifts, therefore gene orientation is not an important determinant of the formation of hot and warm spots by 9-aminoacridine.
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Affiliation(s)
- Niranjan Acharya
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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15
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Moyano AJ, Luján AM, Argaraña CE, Smania AM. MutS deficiency and activity of the error-prone DNA polymerase IV are crucial for determining mucA as the main target for mucoid conversion in Pseudomonas aeruginosa. Mol Microbiol 2007; 64:547-59. [PMID: 17493134 DOI: 10.1111/j.1365-2958.2007.05675.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Pseudomonas aeruginosa colonizes the respiratory tract of cystic fibrosis (CF) patients, where mutators along with mucoid variants emerge leading to chronic infection. Mucoid conversion generally involves mutations inactivating the mucA gene. This study correlates the frequency and nature of mucA mutations with the activity of factors determining the mutation rate, such as MutS and polymerase IV (Pol IV). Results show that: (i) the emergence frequency of mucoid variants was higher in isolates arising from mutS populations compared with the wild-type strain; (ii) in both strains mucoid conversion occurred mainly by mucA mutations; (iii) however, the mutator strain harboured mostly mucA22 (a common allele in CF isolates), while the wild type showed a wider spectrum of mucA mutations with low incidence of mucA22; (iv) disruption of dinB in the wild-type and mutS strains decreased drastically the emergence frequency of mucoid variants; (v) furthermore, the incidence of mucA mutations diminished in the mutS dinB double mutant strain which consisted only in mucA22; (vi) finally, the mucoid isolates obtained from the dinB strain showed an unexpected absence of mucA mutations. Taken together results demonstrate the implication of both MutS and Pol IV in determining mucA as the main target for conversion to mucoidy.
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Affiliation(s)
- Alejandro J Moyano
- Centro de Investigaciones en Química Biológica de Córdoba, CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, Argentina
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16
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Imai M, Tago YI, Ihara M, Kawata M, Yamamoto K. Role of the 5´ → 3´ exonuclease and Klenow fragment of Escherichia coli DNA polymerase I in base mismatch repair. Mol Genet Genomics 2007; 278:211-20. [PMID: 17457612 DOI: 10.1007/s00438-007-0239-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 04/02/2007] [Indexed: 10/23/2022]
Abstract
We have previously demonstrated that the Escherichia coli strain mutS DeltapolA had a higher rate of transition and minus frameshift mutations than mutS or DeltapolA strains. We argued that DNA polymerase I (PolI) corrects transition mismatches. PolI, encoded by the polA gene, possesses Klenow and 5' --> 3' exonuclease domains. In the present study, rates of mutation were found to be higher in Klenow-defective mutS strains and 5' --> 3' exonuclease-defective mutS strains than mutS or polA strains. The Klenow-defective or 5' --> 3' exonuclease-defective mutS strains showed a marked increase in transition mutations. Sites of transition mutations in mutS, Klenow-defective mutS and 5' --> 3' exonuclease-defective mutS strains are different. Thus, it is suggested that, in addition to mutS function, both the Klenow and 5' --> 3' exonuclease domains are involved in the decrease of transition mutations. Transition hot and warm spots in mutS+ polA+ strains were found to differ from those in mutS and mutS DeltapolA strains. We thus argue that all the spontaneous transition mutations in the wild-type strain do not arise from transition mismatches left unrepaired by the MutS system or MutS PolI system.
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Affiliation(s)
- Masaru Imai
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
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17
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Hardin A, Villalta CF, Doan M, Jabri M, Chockalingham V, White SJ, Fowler RG. A molecular characterization of spontaneous frameshift mutagenesis within the trpA gene of Escherichia coli. DNA Repair (Amst) 2007; 6:177-89. [PMID: 17084112 PMCID: PMC1804121 DOI: 10.1016/j.dnarep.2006.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 09/05/2006] [Accepted: 09/25/2006] [Indexed: 10/24/2022]
Abstract
Spontaneous frameshift mutations are an important source of genetic variation in all species and cause a large number of genetic disorders in humans. To enhance our understanding of the molecular mechanisms of frameshift mutagenesis, 583 spontaneous Trp+ revertants of two trpA frameshift alleles in Escherichia coli were isolated and DNA sequenced. In order to measure the contribution of methyl-directed mismatch repair to frameshift production, mutational spectra were constructed for both mismatch repair-proficient and repair-defective strains. The molecular origins of practically all of the frameshifts analyzed could be explained by one of six simple models based upon misalignment of the template or nascent DNA strands with or without misincorporation of primer nucleotides during DNA replication. Most frameshifts occurred within mononucleotide runs as has been shown often in previous studies but the location of the 76 frameshift sites was usually outside of runs. Mismatch repair generally was most effective in preventing the occurrence of frameshifts within runs but there was much variation from site to site. Most frameshift sites outside of runs appear to be refractory to mismatch repair although the small number of occurrences at most of these sites make firm conclusions impossible. There was a dense pattern of reversion sites within the trpA DNA region where reversion events could occur, suggesting that, in general, most DNA sequences are capable of undergoing spontaneous mutational events during replication that can lead to small deletions and insertions. Many of these errors are likely to occur at low frequencies and be tolerated as events too costly to prevent or repair. These studies also revealed an unpredicted flexibility in the primary amino acid sequence of the trpA product, the alpha subunit of tryptophan synthase.
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Affiliation(s)
- Aaron Hardin
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192, USA
| | | | - Michael Doan
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192, USA
| | - Mouna Jabri
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192, USA
| | | | - Steven J. White
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192, USA
| | - Robert G. Fowler
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192, USA
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18
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Comai L, Henikoff S. TILLING: practical single-nucleotide mutation discovery. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 45:684-94. [PMID: 16441355 DOI: 10.1111/j.1365-313x.2006.02670.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In the post-genomic sequencing era, an expanding portfolio of genomic technologies has been applied to the study of gene function. Reverse genetics approaches that provide targeted inactivation of genes identified by sequence analysis include TILLING (for Targeting Local Lesions IN Genomes). TILLING searches the genomes of mutagenized organisms for mutations in a chosen gene, typically single base-pair substitutions. This review covers practical aspects of the technology, ranging from building the mutagenized population to mutation discovery, and discusses possible improvements to current protocols and the impact of new genomic methods for mutation discovery in relation to the future of the TILLING approach.
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Affiliation(s)
- Luca Comai
- Department of Biology, Box 355325, University of Washington, Seattle, WA 98195, USA.
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19
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Imai M, Tago YI, Endo K, Ohnishi G, Nagata Y, Nunoshiba T, Yamamoto K. Spontaneous Mutagenesis in Escherichia coli and Saccharomyces cerevisiae. Genes Environ 2006. [DOI: 10.3123/jemsge.28.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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