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Höfler T, Nascimento MM, Zeitlow M, Kim JY, Trimpert J. Evolutionary Dynamics of Accelerated Antiviral Resistance Development in Hypermutator Herpesvirus. Mol Biol Evol 2024; 41:msae119. [PMID: 38879872 PMCID: PMC11226790 DOI: 10.1093/molbev/msae119] [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: 02/04/2024] [Revised: 05/09/2024] [Accepted: 06/12/2024] [Indexed: 07/07/2024] Open
Abstract
Antiviral therapy is constantly challenged by the emergence of resistant pathogens. At the same time, experimental approaches to understand and predict resistance are limited by long periods required for evolutionary processes. Here, we present a herpes simplex virus 1 mutant with impaired proofreading capacity and consequently elevated mutation rates. Comparing this hypermutator to parental wild type virus, we study the evolution of antiviral drug resistance in vitro. We model resistance development and elucidate underlying genetic changes against three antiviral substances. Our analyzes reveal no principle difference in the evolutionary behavior of both viruses, adaptive processes are overall similar, however significantly accelerated for the hypermutator. We conclude that hypermutator viruses are useful for modeling adaptation to antiviral therapy. They offer the benefit of expedited adaptation without introducing apparent bias and can therefore serve as an accelerator to predict natural evolution.
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Affiliation(s)
- Thomas Höfler
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany
| | - Mariana Mara Nascimento
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany
| | - Michaela Zeitlow
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany
| | - Ji Yoon Kim
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
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Gumustop I, Ortakci F. Analyzing the genetic diversity and biotechnological potential of Leuconostoc pseudomesenteroides by comparative genomics. Front Microbiol 2023; 13:1074366. [PMID: 36713205 PMCID: PMC9875049 DOI: 10.3389/fmicb.2022.1074366] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
Leuconostoc pseudomesenteroides is a lactic acid bacteria species widely exist in fermented dairy foods, cane juice, sourdough, kimchi, apple dumpster, caecum, and human adenoid. In the dairy industry, Ln. pseudomesenteroides strains are usually found in mesophilic starter cultures with lactococci. This species plays a crucial role in the production of aroma compounds such as acetoin, acetaldehyde, and diacetyl, thus beneficially affecting dairy technology. We performed genomic characterization of 38 Ln. pseudomesenteroides from diverse ecological niches to evaluate this species' genetic diversity and biotechnological potential. A mere ~12% of genes conserved across 38 Ln. pseudomesenteroides genomes indicate that accessory genes are the driving force for genotypic distinction in this species. Seven main clades were formed with variable content surrounding mobile genetic elements, namely plasmids, transposable elements, IS elements, prophages, and CRISPR-Cas. All but three genomes carried CRISPR-Cas system. Furthermore, a type IIA CRISPR-Cas system was found in 80% of the CRISPR-Cas positive strains. AMBR10, CBA3630, and MGBC116435 were predicted to encode bacteriocins. Genes responsible for citrate metabolism were found in all but five strains belonging to cane juice, sourdough, and unknown origin. On the contrary, arabinose metabolism genes were only available in nine strains isolated from plant-related systems. We found that Ln. pseudomesenteroides genomes show evolutionary adaptation to their ecological environment due to niche-specific carbon metabolism and forming closely related phylogenetic clades based on their isolation source. This species was found to be a reservoir of type IIA CRISPR-Cas system. The outcomes of this study provide a framework for uncovering the biotechnological potential of Ln. pseudomesenteroides and its future development as starter or adjunct culture for dairy industry.
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Qin X, Wang H, Miao C, Yang X, Zhang Y, Feng J, Forsythe SJ, Man C, Jiang Y. Comparative genomics reveals environmental adaptation differences between Cronobacter species. Food Res Int 2021; 147:110541. [PMID: 34399518 DOI: 10.1016/j.foodres.2021.110541] [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: 12/10/2020] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
The genus Cronobacter is an opportunistic food-borne pathogen which is able to adapt to diverse environments and shows considerable genetic diversity. Genomic analysis can be used to reveal the variation across the genus with respect to virulence, drug resistance and factors involved in horizontal gene transfer mechanisms, such as integrons, conjugative plasmids, and recombinases. In this study, whole-genome comparative analysis of 27 Cronobacter genomes (12 existing and 15 newly assembled genomes) was performed. A total of 110,010 protein-coding genes were grouped into 11,262 clusters, including 2637 core genes, 4814 strain-specific genes and 3811 dispensable genes. Clusters of Orthologous Groups (COG) analysis indicated that 97.35% of the core genes were for substrate transport and metabolism, and the antibiotic resistance genetic determinants were classified into 136 antibiotic resistance ontologies (AROs). A total of 80 genomic islands (GIs) were identified which contained several type VI secretion system gene clusters, and these were likely to have been acquired by horizontal gene transfer. This study has generated a comprehensive characterization of the genus Cronobacter, leading to a better understanding of the mechanisms and ecological functions among the genome features, speciation, and environmental adaptation strategies.
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Affiliation(s)
- Xue Qin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Engineering, Northeast Agricultural University, Harbin 150030, China
| | - Hao Wang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Chao Miao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Engineering, Northeast Agricultural University, Harbin 150030, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Engineering, Northeast Agricultural University, Harbin 150030, China
| | - Yanming Zhang
- SinoGenoMax Co., Ltd./Chinese National Human Genome Center, Beijing 100176, China
| | - Jing Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Engineering, Northeast Agricultural University, Harbin 150030, China
| | | | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Engineering, Northeast Agricultural University, Harbin 150030, China.
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Engineering, Northeast Agricultural University, Harbin 150030, China.
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Li Z, Song Q, Wang M, Ren J, Liu S, Zhao S. Comparative genomics analysis of Pediococcus acidilactici species. J Microbiol 2021; 59:573-583. [PMID: 33990913 DOI: 10.1007/s12275-021-0618-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/05/2021] [Accepted: 02/23/2021] [Indexed: 01/24/2023]
Abstract
Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.
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Affiliation(s)
- Zhenzhen Li
- BGI College, Zhengzhou University, Zhengzhou, 450052, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Qi Song
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- Key Laboratory of Genomics, Ministry of Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mingming Wang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Junli Ren
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Songling Liu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- Key Laboratory of Genomics, Ministry of Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China.
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Korona R, Levin BR. PHAGE-MEDIATED SELECTION AND THE EVOLUTION AND MAINTENANCE OF RESTRICTION-MODIFICATION. Evolution 2017; 47:556-575. [PMID: 28568719 DOI: 10.1111/j.1558-5646.1993.tb02113.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/1992] [Accepted: 08/08/1992] [Indexed: 11/28/2022]
Abstract
Restriction-modification (R-M) was discovered because it provides bacteria with immunity to phage infection. But, is phage-mediated selection the sole mechanism responsible for the evolution and maintenance of these ubiquitous and multiply evolved systems? In an effort to answer this question, we have performed experiments with laboratory populations of E. coli and phage and computer simulations. We consider two ecological situations whereby phage-mediated selection could favor R-M immunity; i) when bacteria with a novel R-M system invade communities of phage-sensitive bacteria in which there are one or more species of phage, and ii) when bacteria colonize bacterial-free habitats in which phage are present. The results of our experiments indicate that in established communities of bacteria and phage, the advantage R-M provides an invading population of bacteria is ephemeral. Within short order, mutants resistant (refractory) to the phage evolve in the dominant population and subsequently in the invading population. The outcome of competition then depends on the relative fitness of the resistant states of these bacterial clones, rather than R-M. As a consequence of sequential selection for independent mutants, this rapid evolution of resistance occurs even when two and three species of phage are present. While in our experiments resistance also evolved when bacteria colonized new habitats in which phage were present, a novel R-M system greatly augmented the likelihood of their becoming established. We interpret the results of this study as support for the hypothesis that the latter, colonization selection, may play an important role in the evolution and maintenance of restriction-modification. However, we also see these results and other observations we discuss as questioning whether protection against phage is the unique biological role of restriction-modification.
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Affiliation(s)
- Ryszard Korona
- Department of Zoology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Bruce R Levin
- Department of Zoology, University of Massachusetts, Amherst, MA, 01003, USA
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Gutiérrez-Barranquero JA, Cazorla FM, de Vicente A, Sundin GW. Complete sequence and comparative genomic analysis of eight native Pseudomonas syringae plasmids belonging to the pPT23A family. BMC Genomics 2017; 18:365. [PMID: 28486968 PMCID: PMC5424326 DOI: 10.1186/s12864-017-3763-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pPT23A family of plasmids appears to be indigenous to the plant pathogen Pseudomonas syringae and these plasmids are widely distributed and widely transferred among pathovars of P. syringae and related species. pPT23A-family plasmids (PFPs) are sources of accessory genes for their hosts that can include genes important for virulence and epiphytic colonization of plant leaf surfaces. The occurrence of repeated sequences including duplicated insertion sequences on PFPs has made obtaining closed plasmid genome sequences difficult. Therefore, our objective was to obtain complete genome sequences from PFPs from divergent P. syringae pathovars and also from strains of P. syringae pv. syringae isolated from different hosts. RESULTS The eight plasmids sequenced ranged in length from 61.6 to 73.8 kb and encoded from 65 to 83 annotated orfs. Virulence genes including type III secretion system effectors were encoded on two plasmids, and one of these, pPt0893-29 from P. syringae pv. tabaci, encoded a wide variety of putative virulence determinants. The PFPs from P. syringae pv. syringae mostly encoded genes of importance to ecological fitness including the rulAB determinant conferring tolerance to ultraviolet radiation. Heavy metal resistance genes encoding resistance to copper and arsenic were also present in a few plasmids. The discovery of part of the chromosomal genomic island GI6 from P. syringae pv. syringae B728a in two PFPs from two P. syringae pv. syringae hosts is further evidence of past intergenetic transfers between plasmid and chromosomal DNA. Phylogenetic analyses also revealed new subgroups of the pPT23A plasmid family and confirmed that plasmid phylogeny is incongruent with P. syringae pathovar or host of isolation. In addition, conserved genes among seven sequenced plasmids within the same phylogenetic group were limited to plasmid-specific functions including maintenance and transfer functions. CONCLUSIONS Our sequence analysis further revealed that PFPs from P. syringae encode suites of accessory genes that are selected at species (universal distribution), pathovar (interpathovar distribution), and population levels (intrapathovar distribution). The conservation of type IV secretion systems encoding conjugation functions also presumably contributes to the distribution of these plasmids within P. syringae populations.
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Affiliation(s)
- José A. Gutiérrez-Barranquero
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Francisco M. Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - George W. Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
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Zelenin AV, Rodionov AV, Bolsheva NL, Badaeva ED, Muravenko OV. Genome: Origins and evolution of the term. Mol Biol 2016. [DOI: 10.1134/s0026893316040178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Arber W. Horizontal Gene Transfer among Bacteria and Its Role in Biological Evolution. Life (Basel) 2014; 4:217-24. [PMID: 25370194 PMCID: PMC4187160 DOI: 10.3390/life4020217] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022] Open
Abstract
This is a contribution to the history of scientific advance in the past 70 years concerning the identification of genetic information, its molecular structure, the identification of its functions and the molecular mechanisms of its evolution. Particular attention is thereby given to horizontal gene transfer among microorganisms, as well as to biosafety considerations with regard to beneficial applications of acquired scientific knowledge.
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Affiliation(s)
- Werner Arber
- Biozentrum, University of Basel, Klingelbergstr. 50/70, CH-4056 Basel, Switzerland.
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9
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Norris V, Merieau A. Plasmids as scribbling pads for operon formation and propagation. Res Microbiol 2013; 164:779-87. [PMID: 23587635 DOI: 10.1016/j.resmic.2013.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 04/01/2013] [Indexed: 12/31/2022]
Abstract
Many bacterial genes are in operons and the process whereby operons are formed is therefore fundamental. To help elucidate this process, we propose in the Scribbling Pad hypothesis that bacteria have been constantly using plasmids for genetic experimentation and, in particular, for the construction of operons. This hypothesis simultaneously solves the problems of the creation of operons and the way operons are propagated. We cite results in the literature to support the hypothesis and make experimental predictions to test it.
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Affiliation(s)
- Vic Norris
- Theoretical Biology Unit, Department of Biology, University of Rouen, 76821 Mont Saint Aignan cedex, France.
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10
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Vasu K, Nagaraja V. Diverse functions of restriction-modification systems in addition to cellular defense. Microbiol Mol Biol Rev 2013; 77:53-72. [PMID: 23471617 PMCID: PMC3591985 DOI: 10.1128/mmbr.00044-12] [Citation(s) in RCA: 386] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Restriction-modification (R-M) systems are ubiquitous and are often considered primitive immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are an indication of their success as a defense mechanism against invading genomes. However, their cellular defense function does not adequately explain the basis for their immaculate specificity in sequence recognition and nonuniform distribution, ranging from none to too many, in diverse species. The present review deals with new developments which provide insights into the roles of these enzymes in other aspects of cellular function. In this review, emphasis is placed on novel hypotheses and various findings that have not yet been dealt with in a critical review. Emerging studies indicate their role in various cellular processes other than host defense, virulence, and even controlling the rate of evolution of the organism. We also discuss how R-M systems could have successfully evolved and be involved in additional cellular portfolios, thereby increasing the relative fitness of their hosts in the population.
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Affiliation(s)
- Kommireddy Vasu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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11
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Arber W. Genetic engineering compared to natural genetic variations. N Biotechnol 2010; 27:517-21. [DOI: 10.1016/j.nbt.2010.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 05/08/2010] [Indexed: 11/16/2022]
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12
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Rivera-Vega L, Mittapalli O. Molecular characterization of mariner-like elements in emerald ash borer, Agrilus planipennis (Coleoptera, Polyphaga). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2010; 74:205-216. [PMID: 20602451 DOI: 10.1002/arch.20357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Emerald ash borer (EAB, Agrilus planipennis), an exotic invasive pest, has killed millions of ash trees (Fraxinus spp.) in North America and continues to threaten the very survival of the entire Fraxinus genus. Despite its high-impact status, to date very little knowledge exists for this devastating insect pest at the molecular level. Mariner-like elements (MLEs) are transposable elements, which are ubiquitous in occurrence in insects and other invertebrates. Because of their low specificity and broad host range, they can be used for epitope-tagging, gene mapping, and in vitro mutagenesis. The majority of the known MLEs are inactive due to in-frame shifts and stop codons within the open reading frame (ORF). We report on the cloning and characterization of two MLEs in A. planipennis genome (Apmar1 and Apmar2). Southern analysis indicated a very high copy number for Apmar1 and a moderate copy number for Apmar2. Phylogenetic analysis revealed that both elements belong to the irritans subfamily. Based on the high copy number for Apmar1, the full-length sequence was obtained using degenerate primers designed to the inverted terminal repeat (ITR) sequences of irritans MLEs. The recovered nucleotide sequence for Apmar1 consisted of 1,292 bases with perfect ITRs, and an ORF of 1,050 bases encoding a putative transposase of 349 amino acids. The deduced amino acid sequence of Apmar1 contained the conserved regions of mariner transposases including WVPHEL and YSPDLAP, and the D,D(34)D motif. Both Apmar1 and Apmar2 could represent useful genetic tools and provide insights on EAB adaptation.
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Affiliation(s)
- L Rivera-Vega
- Department of Entomology, The Ohio State University/Ohio Agricultural and Research Development Center, Wooster, Ohio 44691, USA
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13
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Arber W. Systemic aspects of biological evolution. J Biotechnol 2009; 144:242-4. [PMID: 19497339 DOI: 10.1016/j.jbiotec.2009.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Accepted: 05/26/2009] [Indexed: 10/20/2022]
Abstract
In recent years molecular mechanisms and natural strategies have been explored that spontaneously generate genetic variations at low rates without seriously affecting genetic stability at the level of populations. Thereby acquired knowledge suggests systemic aspects of evolutionary interdependences both in the past and in future evolutionary developments. The natural strategy of DNA acquisition by horizontal gene transfer interconnects different branches of the tree of evolution at random times. This makes in principle the entire global gene pool of the biosphere available to any kinds of living beings for their further evolutionary development. The relevance of this knowledge for risk assessments of genetically engineered organisms is discussed.
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Affiliation(s)
- Werner Arber
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
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14
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Chatterjee R, Yuan L. Directed evolution of metabolic pathways. Trends Biotechnol 2006; 24:28-38. [PMID: 16298446 DOI: 10.1016/j.tibtech.2005.11.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Revised: 09/08/2005] [Accepted: 11/07/2005] [Indexed: 10/25/2022]
Abstract
The modification of cellular metabolism is of biotechnological and commercial significance because naturally occurring metabolic pathways are the source of diverse compounds used in fields ranging from medicine to bioremediation. Directed evolution is the experimental improvement of biocatalysts or cellular properties through iterative genetic diversification and selection procedures. The creation of novel metabolic functions without disrupting the balanced intracellular pool of metabolites is the primary challenge of pathway manipulation. The introduction of coordinated changes across multiple genetic elements, in conjunction with functional selection, presents an integrated approach for the modification of metabolism with benign physiological consequences. Directed evolution formats take advantage of the dynamic structures of genomes and genomic sub-structures and their ability to evolve in multiple directions in response to external stimuli. The elucidation, design and application of genome-restructuring mechanisms are key elements in the directed evolution of cellular metabolic pathways.
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15
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Delamarre SC, Chang HJ, Batt CA. Identification and characterization of two polyhydroxyalkanoate biosynthesis loci in Pseudomonas sp. strain 3Y2. Appl Microbiol Biotechnol 2005; 69:293-303. [PMID: 16175367 DOI: 10.1007/s00253-005-0020-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 05/19/2005] [Accepted: 05/20/2005] [Indexed: 11/28/2022]
Abstract
A Pseudomonas strain, 3Y2, that produced polyhydroxyalkanoate (PHA) polymers consisting of 3-hydroxybutyric acid (3HB) and medium-chain-length 3-hydroxyalkanoate (mcl-HA) units, with up to 30% 3HB, was isolated. Two PHA biosynthesis loci (pha ( Ps-1) and pha ( Ps-2)) from 3Y2 were cloned by polymerase chain reaction amplification techniques. The pha ( Ps-2) locus was similar to the PHA biosynthesis loci of other PHA-producing Pseudomonas strains, with five tandem open reading frames (ORFs) located in the order ORF1( Ps-2)-phaC1 ( Ps-2)-phaZ ( Ps-2)-phaC2 ( Ps-2)-phaD ( Ps-2). The pha ( Ps-1) locus that contains phaC1 ( Ps-1)-phaZ ( Ps-1) appears to have arisen by a duplication event that placed it downstream of a gene (ORF1( Ps-1)), encoding a putative glucose-methanol-choline flavoprotein oxidoreductase. The PHA synthases 1 encoded by phaC1 ( Ps-1) and phaC1 ( Ps-2) were investigated by heterologous expression in Wautersia eutropha PHB(-)4. Both synthases displayed similar substrate specificities for incorporating 3HB and mcl-HA units into PHA. The ability of PhaC1( Ps-1) to confer PHA synthesis, however, appeared reduced compared to that of PhaC1( Ps-2), since cells harboring PhaC1( Ps-1) accumulated 2.5 to 4.6 times less PHA than cells expressing PhaC1( Ps-2). Primary sequence analysis revealed that PhaC1( Ps-1) had markedly diverged from the other PHA synthases with a relatively high substitution rate (14.9 vs 2% within PhaC1( Ps-2)). The mutations affected a highly conserved C-terminal region and the surroundings of the essential active site cysteine (Cys296) with a loss of hydrophobicity. This led us to predict that if phaC1 ( Ps-1) produces a protein product in the native strain, it is likely that PhaC1( Ps-1) may be destined for elimination by the accumulation of inactivating mutations, although its specialization to accommodate different substrates cannot be eliminated.
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Affiliation(s)
- Soazig C Delamarre
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA
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16
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Abstract
It is often tacitly assumed that all gene products serve the needs of life functions of the individual carrying the genome. However, a close look at the formation of genetic variations, which are the drivers of biological evolution, reveals a different view. While a majority of the products of genes, such as housekeeping genes and genes essential for each individual, when exposed to particular life conditions respond to the definition given above, other gene products clearly carry out evolutionary functions at the level of populations. Products of these evolution genes act as generators of genetic variations and/or as modulators of the frequency of genetic variation. This is most readily seen with bacterial populations. Many different mechanisms contribute to the occasional, overall formation of genetic variations. These mechanisms can be grouped into three mechanistically and qualitatively different strategies of generating genetic variations. In addition to the activities of evolution genes, specific properties of matter such as tautomery also contribute to the formation of genetic variations. The views that nature cares actively for biological evolution are documented by evidence taken mainly from microbial genetics. Essential elements of the theory of molecular evolution are discussed, as well as the relevance of this theory for higher organisms and its impact on our worldview.
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Affiliation(s)
- Werner Arber
- Biozentrum, University of Basel, Basel, Switzerland.
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17
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Kleisner K, Markoŝ A. Semetic rings: towards the new concept of mimetic resemblances. Theory Biosci 2005; 123:209-22. [PMID: 18202864 DOI: 10.1016/j.thbio.2004.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Accepted: 09/20/2004] [Indexed: 11/28/2022]
Abstract
In order to better understand mimicry and similar phenomena, we introduce the concept of seme as means of horizontal (i.e. trans-lineage) transfer of images. Together with horizontal exchange of genes and epigenetic signals, semes complete the triad of powerful channels enabling synchronous communication across the biosphere.
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Affiliation(s)
- Karel Kleisner
- Department of Philosophy and History of Science, Faculty of Sciences, Charles University Prague, Viniĉná 7, 128 44, Praha 2, Czech Republic,
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Łobocka MB, Rose DJ, Plunkett G, Rusin M, Samojedny A, Lehnherr H, Yarmolinsky MB, Blattner FR. Genome of bacteriophage P1. J Bacteriol 2004; 186:7032-68. [PMID: 15489417 PMCID: PMC523184 DOI: 10.1128/jb.186.21.7032-7068.2004] [Citation(s) in RCA: 200] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Accepted: 07/09/2004] [Indexed: 11/20/2022] Open
Abstract
P1 is a bacteriophage of Escherichia coli and other enteric bacteria. It lysogenizes its hosts as a circular, low-copy-number plasmid. We have determined the complete nucleotide sequences of two strains of a P1 thermoinducible mutant, P1 c1-100. The P1 genome (93,601 bp) contains at least 117 genes, of which almost two-thirds had not been sequenced previously and 49 have no homologs in other organisms. Protein-coding genes occupy 92% of the genome and are organized in 45 operons, of which four are decisive for the choice between lysis and lysogeny. Four others ensure plasmid maintenance. The majority of the remaining 37 operons are involved in lytic development. Seventeen operons are transcribed from sigma(70) promoters directly controlled by the master phage repressor C1. Late operons are transcribed from promoters recognized by the E. coli RNA polymerase holoenzyme in the presence of the Lpa protein, the product of a C1-controlled P1 gene. Three species of P1-encoded tRNAs provide differential controls of translation, and a P1-encoded DNA methyltransferase with putative bifunctionality influences transcription, replication, and DNA packaging. The genome is particularly rich in Chi recombinogenic sites. The base content and distribution in P1 DNA indicate that replication of P1 from its plasmid origin had more impact on the base compositional asymmetries of the P1 genome than replication from the lytic origin of replication.
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Affiliation(s)
- Małgorzata B Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Ul. Pawinskiego 5A, 02-106 Warsaw, Poland.
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19
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Arber W. Biological evolution: Lessons to be learned from microbial population biology and genetics. Res Microbiol 2004; 155:297-300. [PMID: 15207860 DOI: 10.1016/j.resmic.2004.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Accepted: 01/27/2004] [Indexed: 11/25/2022]
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Abstract
Biological evolution is known to be driven by the availability of genetic variants. Spontaneous genetic variation can be the result of a number of specific molecular mechanisms. These can be grouped into three qualitatively different natural strategies of generating genetic variations, namely local sequence changes, DNA rearrangement within the genome and horizontal gene transfer, which is referred to here as DNA acquisition. All of these strategies bring about alterations in the DNA sequences of the genome, thus corresponding to the molecular genetic definition of the term mutation. A detailed inspection of specific mechanisms of mutagenesis reveals on the one hand the impact of non-genetic internal and environmental factors, and on the other hand the specific involvement of gene products. The underlying so-called evolution genes can be classified into generators of genetic variations and into modulators of the frequency of genetic variation. These evolution genes are postulated to have themselves undergone biological evolution under the pressure of second-order selection. On the basis of a few selected examples of mutagenesis, elements for a theory of molecular evolution are collected without a claim for completeness. Philosophical dimensions as well as practical aspects of the advanced knowledge on specific molecular mechanisms involved in molecular evolution are also briefly discussed.
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Affiliation(s)
- Werner Arber
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
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21
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Berndt C, Meier P, Wackernagel W. DNA restriction is a barrier to natural transformation in Pseudomonas stutzeri JM300. MICROBIOLOGY (READING, ENGLAND) 2003; 149:895-901. [PMID: 12686632 DOI: 10.1099/mic.0.26033-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Natural transformation is a mechanism for intra- and interspecific transfer of chromosomal DNA in Pseudomonas stutzeri. During this process a single strand derived from duplex DNA is transported into the cytoplasm and recombined with resident DNA. By electroporation, which introduces duplex DNA into cells, 100-fold lower transformation frequencies of P. stutzeri JM300 were observed with shuttle vector or broad-host-range plasmid DNA when the plasmids had replicated in Escherichia coli and not in P. stutzeri JM300. Moreover, the natural transformation with cloned chromosomal P. stutzeri JM300 DNA was reduced about 40-fold when the DNA had not been propagated in P. stutzeri JM300 but in E. coli. Restriction was also active during natural transformation by single-stranded DNA. Restriction during natural transformation and electroporation was abolished in mutants isolated from mutagenized JM300 cells after applying a multiple plasmid electroporation strategy for the enrichment of restriction-defective strains. The mutants had retained the ability for DNA modification. The P. stutzeri strain ATCC 17587 was found to have no restriction-modification system as seen in JM300. It is discussed whether restriction during natural transformation acts at presynaptic or postsynaptic stages of transforming DNA. Restriction as a barrier to transformation apparently contributes to sexual isolation and therefore may promote speciation in the highly diverse species P. stutzeri.
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Affiliation(s)
- Cecilia Berndt
- Genetik, Fachbereich Biologie, Geo- und Umweltwissenschaften, Carl von Ossietzky Universität Oldenburg, POB 2503, D-26111 Oldenburg, Germany
| | - Petra Meier
- Genetik, Fachbereich Biologie, Geo- und Umweltwissenschaften, Carl von Ossietzky Universität Oldenburg, POB 2503, D-26111 Oldenburg, Germany
| | - Wilfried Wackernagel
- Genetik, Fachbereich Biologie, Geo- und Umweltwissenschaften, Carl von Ossietzky Universität Oldenburg, POB 2503, D-26111 Oldenburg, Germany
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22
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23
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Evolution of Prokaryotic Genomes. Curr Top Microbiol Immunol 2002. [DOI: 10.1007/978-3-662-09217-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Fang Z, Kenna DT, Doig C, Smittipat DN, Palittapongarnpim P, Watt B, Forbes KJ. Molecular evidence for independent occurrence of IS6110 insertions at the same sites of the genome of Mycobacterium tuberculosis in different clinical isolates. J Bacteriol 2001; 183:5279-84. [PMID: 11514510 PMCID: PMC95409 DOI: 10.1128/jb.183.18.5279-5284.2001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several characteristics of Mycobacterium tuberculosis (e.g., conserved genome and low growth rate) have severely restricted the study of the microorganism. The discovery of IS6110 raised hopes of overcoming these obstacles. However, our knowledge of this IS element is relatively limited; even its two basic characteristics (transposition mechanism and target site selection) are far from well understood. In this study, IS6110 insertions in ipl loci (iplA and iplB) in two collections of clinical isolates of M. tuberculosis from different geographic locations, one from Scotland and the other from Thailand, were investigated. Five different IS6110 insertions in the loci were identified: ipl-4::IS6110, ipl-5::IS6110, ipl-11::IS6110, ipl-12::IS6110, and ipl-13::IS6110. An attempt to establish the phylogenetic relationship of the isolates containing these insertions was unsuccessful, suggesting that some of these insertions may have arisen from more than one event. This possibility is further supported by the observation that IS6110 copies existed in the same site but with different orientations in different isolates, and the insertion site of ipl-1::IS6110 harbored IS6110 copies in both iplA and iplB in different strains. All these suggest the independent occurrence of IS6110 insertions at the same sites of the genome of M. tuberculosis in different clinical isolates. The implications of this finding are discussed.
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Affiliation(s)
- Z Fang
- Public Health Laboratory Services Mycobacteria Reference Unit and Department of Infection, Guy's, King's and St. Thomas' School of Medicine, London, United Kingdom.
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25
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Rocha EP, Danchin A, Viari A. Evolutionary Role of Restriction/Modification Systems as Revealed by Comparative Genome Analysis. Genome Res 2001. [DOI: 10.1101/gr.153101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Type II restriction modification systems (RMSs) have been regarded either as defense tools or as molecular parasites of bacteria. We extensively analyzed their evolutionary role from the study of their impact in the complete genomes of 26 bacteria and 35 phages in terms of palindrome avoidance. This analysis reveals that palindrome avoidance is not universally spread among bacterial species and that it does not correlate with taxonomic proximity. Palindrome avoidance is also not universal among bacteriophage, even when their hosts code for RMSs, and depends strongly on the genetic material of the phage. Interestingly, palindrome avoidance is intimately correlated with the infective behavior of the phage. We observe that the degree of palindrome and restriction site avoidance is significantly and consistently less important in phages than in their bacterial hosts. This result brings to the fore a larger selective load for palindrome and restriction site avoidance on the bacterial hosts than on their infecting phages. It is then consistent with a view where type II RMSs are considered as parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial third player in the host–parasite relationship between bacteria and phages.
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Wernegreen JJ, Moran NA. Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera). J Bacteriol 2001; 183:785-90. [PMID: 11133977 PMCID: PMC94939 DOI: 10.1128/jb.183.2.785-790.2001] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2000] [Accepted: 10/16/2000] [Indexed: 11/20/2022] Open
Abstract
This study tested for horizontal transfer of plasmids among Buchnera aphidicola strains associated with ecologically and phylogenetically related aphid hosts (Uroleucon species). Phylogenetic congruence of Buchnera plasmid (trpEG and leuABC) and chromosomal (dnaN and trpB) genes supports strictly vertical long-term transmission of plasmids, which persist due to their contributions to host nutrition rather than capacity for infectious transfer. Synonymous divergences indicate elevated mutation on plasmids relative to chromosomal genes.
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Affiliation(s)
- J J Wernegreen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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28
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Abstract
The nature of the role played by mobile elements in host genome evolution is reassessed considering numerous recent developments in many areas of biology. It is argued that easy popular appellations such as "selfish DNA" and "junk DNA" may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism. Transposable elements are potent, broad spectrum, endogenous mutators that are subject to the influence of chance as well as selection at several levels of biological organization. Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions.
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Affiliation(s)
- M G Kidwell
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson 85721, USA.
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29
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Bouchard JD, Moineau S. Homologous recombination between a lactococcal bacteriophage and the chromosome of its host strain. Virology 2000; 270:65-75. [PMID: 10772980 DOI: 10.1006/viro.2000.0226] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic exchanges constitute a significant means by which bacteriophages acquire novel characteristics. Phages of Lactococcus lactis occupy a particular niche, the dairy factory environment, where their populations are subjected to constant changes. Little is known about the mechanisms of evolution that lead to the genetic diversity of lactococcal phages. In this study, we described two DNA exchanges involving the lytic phage ul36, a member of the P335 species, and its L. lactis host. They occurred by homologous recombination with phage-related sequences present in the host chromosome. Both mutants generated by these recombination events are insensitive to the phage resistance mechanism AbiK and one has a reduced burst size as well as a new origin of replication. We propose that this type of DNA exchange with prophages or remnants of prophages occurs frequently within the P335 species as supported by DNA-DNA comparisons between P335-like phages.
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Affiliation(s)
- J D Bouchard
- Department of Biochemistry and Microbiology, Faculté des Sciences et de Génie, Québec, G1K 7P4, Canada
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31
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Abstract
On the basis of established knowledge of microbial genetics one can distinguish three major natural strategies in the spontaneous generation of genetic variations in bacteria. These strategies are: (1) small local changes in the nucleotide sequence of the genome, (2) intragenomic reshuffling of segments of genomic sequences and (3) the acquisition of DNA sequences from another organism. The three general strategies differ in the quality of their contribution to microbial evolution. Besides a number of non-genetic factors, various specific gene products are involved in the generation of genetic variation and in the modulation of the frequency of genetic variation. The underlying genes are called evolution genes. They act for the benefit of the biological evolution of populations as opposed to the action of housekeeping genes and accessory genes which are for the benefit of individuals. Examples of evolution genes acting as variation generators are found in the transposition of mobile genetic elements and in so-called site-specific recombination systems. DNA repair systems and restriction-modification systems are examples of modulators of the frequency of genetic variation. The involvement of bacterial viruses and of plasmids in DNA reshuffling and in horizontal gene transfer is a hint for their evolutionary functions. Evolution genes are thought to undergo biological evolution themselves, but natural selection for their functions is indirect, at the level of populations, and is called second-order selection. In spite of an involvement of gene products in the generation of genetic variations, evolution genes do not programmatically direct evolution towards a specific goal. Rather, a steady interplay between natural selection and mixed populations of genetic variants gives microbial evolution its direction.
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Affiliation(s)
- W Arber
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056, Basel, Switzerland.
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32
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Abstract
Three strategies of different quality contribute in parallel to the natural formation of genetic variants in bacteria: (1) small local alterations of DNA sequences; (2) recombinational reshuffling of segments of the genome; and (3) acquisition of DNA sequences by horizontal gene transfer. Key enzymes involved in these processes often act as variation generators by making use of structural flexibilities of biological macromolecules and of the effect of random encounter. In the theory of molecular evolution, genetic determinants of variation generators as well as of modulators of the frequency of genetic variation are defined as evolutionary genes. This postulate is consistent with the notion that spontaneous mutagenesis is in general not adaptive and that the direction of evolution depends on natural selection exerted on populations of genetic variants.
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Affiliation(s)
- W Arber
- Biozentrum, University of Basel, Switzerland
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33
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De Vos D, Bouton C, Sarniguet A, De Vos P, Vauterin M, Cornelis P. Sequence diversity of the oprI gene, coding for major outer membrane lipoprotein I, among rRNA group I pseudomonads. J Bacteriol 1998; 180:6551-6. [PMID: 9851998 PMCID: PMC107757 DOI: 10.1128/jb.180.24.6551-6556.1998] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/1998] [Accepted: 09/17/1998] [Indexed: 11/20/2022] Open
Abstract
The sequence of oprI, the gene coding for the major outer membrane lipoprotein I, was determined by PCR sequencing for representatives of 17 species of rRNA group I pseudomonads, with a special emphasis on Pseudomonas aeruginosa and Pseudomonas fluorescens. Within the P. aeruginosa species, oprI sequences for 25 independent isolates were found to be identical, except for one silent substitution at position 96. The oprI sequences diverged more for the other rRNA group I pseudomonads (85 to 91% similarity with P. aeruginosa oprI). An accumulation of silent and also (but to a much lesser extent) nonsilent substitutions in the different sequences was found. A clustering according to the respective presence and/or positions of the HaeIII, PvuII, and SphI sites could also be obtained. A sequence cluster analysis showed a rather widespread distribution of P. fluorescens isolates. All other rRNA group I pseudomonads clustered in a manner that was in agreement with other studies, showing that the oprI gene can be useful as a complementary phylogenetic marker for classification of rRNA group I pseudomonads.
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Affiliation(s)
- D De Vos
- Laboratory of Microbial Interactions, Department of Immunology, Parasitology, and Ultrastructure, Flanders Interuniversity Institute of Biotechnology, Vrije Universiteit Brussel, B-1640 Sint Genesius Rode, Belgium
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34
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Nakatsu CH, Korona R, Lenski RE, de Bruijn FJ, Marsh TL, Forney LJ. Parallel and divergent genotypic evolution in experimental populations of Ralstonia sp. J Bacteriol 1998; 180:4325-31. [PMID: 9721265 PMCID: PMC107437 DOI: 10.1128/jb.180.17.4325-4331.1998] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetic rearrangements within a population of bacteria were analyzed to understand the degree of divergence occurring after experimental evolution. We used 18 replicate populations founded from Ralstonia sp. strain TFD41 that had been propagated for 1,000 generations with 2,4-dichlorophenoxyacetic acid (2,4-D) as the carbon source. Genetic divergence was examined by restriction fragment length polymorphism analysis of the incumbent plasmid that carries the 2,4-D catabolic genes and by amplification of random regions of the genome via PCR. In 18 evolved clones examined, we observed duplication within the plasmid, including the tfdA gene, which encodes a 2,4-D dioxygenase that catalyzes the first step in the 2,4-D catabolic pathway. In 71 of 72 evolved clones, a common 2.4-kb PCR product was lost when genomic fingerprints produced by PCR amplification using degenerate primers based on repetitive extragenic palindromic (REP) sequences (REP-PCR) were compared. The nucleotide sequence of the 2.4-kb PCR product has homology to the TRAP (tripartite ATP-independent periplasmic) solute transporter gene family. Hybridization of the 2. 4-kb REP-PCR product from the ancestor to genomic DNA from the evolved populations showed that the loss of the PCR product resulted from deletions in the genome. Deletions in the plasmid and presence and/or absence of other REP-PCR products were also found in these clones but at much lower frequencies. The common and uncommon genetic changes observed show that both parallel and divergent genotypic evolution occurred in replicate populations of this bacterium.
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Affiliation(s)
- C H Nakatsu
- NSF Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA.
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35
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Kunz BA, Ramachandran K, Vonarx EJ. DNA sequence analysis of spontaneous mutagenesis in Saccharomyces cerevisiae. Genetics 1998; 148:1491-505. [PMID: 9560369 PMCID: PMC1460101 DOI: 10.1093/genetics/148.4.1491] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
To help elucidate the mechanisms involved in spontaneous mutagenesis, DNA sequencing has been applied to characterize the types of mutation whose rates are increased or decreased in mutator or antimutator strains, respectively. Increased spontaneous mutation rates point to malfunctions in genes that normally act to reduce spontaneous mutation, whereas decreased rates are associated with defects in genes whose products are necessary for spontaneous mutagenesis. In this article, we survey and discuss the mutational specificities conferred by mutator and antimutator genes in the budding yeast Saccharomyces cerevisiae. The implications of selected aspects of the data are considered with respect to the mechanisms of spontaneous mutagenesis.
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Affiliation(s)
- B A Kunz
- School of Biological and Chemical Sciences, Deakin University, Geelong, Victoria, Australia.
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36
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Stibitz S, Yang MS. Genomic fluidity of Bordetella pertussis assessed by a new method for chromosomal mapping. J Bacteriol 1997; 179:5820-6. [PMID: 9294440 PMCID: PMC179472 DOI: 10.1128/jb.179.18.5820-5826.1997] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The genomic organization of Bordetella pertussis strains has been examined by using a new method. This method does not depend on the prior determination of a restriction map of the bacterial chromosome but is based on the ability to measure directly the distance between two genes. This is accomplished through the integration at each gene of a suicide vector containing a cleavage site for the intron-encoded endonuclease I-SceI, which is not otherwise found in the chromosome. Integration is mediated by homologous recombination between the chromosomal and cloned plasmid copies of a gene of interest. Digestion with I-SceI gives rise to a fragment the size of which represents the distance between the two genes. Multiple pairwise determinations within a set of genes provide sufficient information to derive a map of the relative gene positions. Mapping a set of 11 to 13 genes for five strains of B. pertussis and one strain of B. parapertussis revealed extensive divergence of gene order between B. pertussis Tohama I, B. pertussis 18-323, and B. parapertussis ATCC 15311. Less extensive divergence of gene order was observed between B. pertussis Tohama I and B. pertussis Tohama III, BP165, and Wellcome 28, with most of the observed differences explainable by large inversions.
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Affiliation(s)
- S Stibitz
- Division of Bacterial Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA.
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37
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Osborn AM, Bruce KD, Strike P, Ritchie DA. Distribution, diversity and evolution of the bacterial mercury resistance (mer) operon. FEMS Microbiol Rev 1997; 19:239-62. [PMID: 9167257 DOI: 10.1111/j.1574-6976.1997.tb00300.x] [Citation(s) in RCA: 174] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mercury and its compounds are distributed widely across the earth. Many of the chemical forms of mercury are toxic to all living organisms. However, bacteria have evolved mechanisms of resistance to several of these different chemical forms, and play a major role in the global cycling of mercury in the natural environment. Five mechanisms of resistance to mercury compounds have been identified, of which resistance to inorganic mercury (HgR) is the best understood, both in terms of the mechanisms of resistance to mercury and of resistance to heavy metals in general. Resistance to inorganic mercury is encoded by the genes of the mer operon, and can be located on transposons, plasmids and the bacterial chromosome. Such systems have a worldwide geographical distribution, and furthermore, are found across a wide range of both Gram-negative and Gram-positive bacteria from both natural and clinical environments. The presence of mer genes in bacteria from sediment cores suggest that mer is an ancient system. Analysis of DNA sequences from mer operons and genes has revealed genetic variation both in operon structure and between individual genes from different mer operons, whilst analysis of bacteria which are sensitive to inorganic mercury has identified a number of vestigial non-functional operons. It is hypothesised that mer, due to its ubiquity with respect to geographical location, environment and species range, is an ancient system, and that ancient bacteria carried genes conferring resistance to mercury in response to increased levels of mercury in natural environments, perhaps resulting from volcanic activity. Models for the evolution of both a basic mer operon and for the Tn21-related family of mer operons and transposons are suggested. The study of evolution in bacteria has recently become dominated by the generation of phylogenies based on 16S rRNA genes. However, it is important not to underestimate the roles of horizontal gene transfer and recombinational events in evolution. In this respect mer is a suitable system for evaluating phylogenetic methods which incorporate the effects of horizontal gene transfer. In addition, the mer operon provides a model system in the study of environmental microbiology which is useful both as an example of a genotype which is responsive to environmental pressures and as a generic tool for the development of new methodology for the analysis of bacterial communities in natural environments.
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Affiliation(s)
- A M Osborn
- School of Biological Sciences, Donnan Laboratories, University of Liverpool, UK
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38
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Rozsa FW, Meyer TF, Fussenegger M. Inversion of Moraxella lacunata type 4 pilin gene sequences by a Neisseria gonorrhoeae site-specific recombinase. J Bacteriol 1997; 179:2382-8. [PMID: 9079926 PMCID: PMC178977 DOI: 10.1128/jb.179.7.2382-2388.1997] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A plasmid library of Neisseria gonorrhoeae sequences was screened for the ability to mediate recombinations on a sequence containing the Moraxella lacunata type 4 pilin gene invertible region in Escherichia coli. A plasmid containing the N. gonorrhoeae sequence encoding the putative recombinase (gcr) was identified and sequenced. Plasmids containing gcr were able to mediate site-specific recombinations despite a weak amino acid homology to Piv, the native M. lacunata pilin gene invertase. The gcr gene is present only in pathogenic strains of Neisseria tested; however, in our assays gene knockouts of gcr did not alter the variation of surface features that play a role in the pathogenesis of N. gonorrhoeae.
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Affiliation(s)
- F W Rozsa
- Department of Microbiology, Biozentrum, University of Basel, Switzerland.
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Schiaffino A, Beuzón CR, Uzzau S, Leori G, Cappuccinelli P, Casadesús J, Rubino S. Strain typing with IS200 fingerprints in Salmonella abortusovis. Appl Environ Microbiol 1996; 62:2375-80. [PMID: 8779575 PMCID: PMC168018 DOI: 10.1128/aem.62.7.2375-2380.1996] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A collection of Salmonella abortusovis isolates was examined for the presence of insertion element IS200. All proved to contain three or four copies of the element. One IS200 hybridization band of approximately 9 kb was found in all isolates, indicating that all S. abortusovis strains carry an IS200 element in similar or identical locations; this band can be potentially useful for serovar identification. S. abortusovis collection isolates from distinct geographic areas were highly polymorphic, suggesting that IS200 fingerprints might provide information on the geographic origin of S. abortusovis strains. Isolates obtained from the same geographic area (the island of Sardinia, Italy) were less polymorphic: all shared three constant IS200 hybridization bands, indicating that they derive from a single ancestor. Most strains analyzed contained an additional copy of IS200 in the variable region of the virulence plasmid. Certain Sardinian flocks proved to be infected by only one S. abortusovis strain, while others harbored two strains. Strain typing with IS200 fingerprints proved to be more reliable than plasmid analysis, because the latter yielded a high degree of polymorphism, even among isolates from the same flock.
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Affiliation(s)
- A Schiaffino
- Instituto di Microbiologia e Virologia, Facoltà di Medicina, Università degli Studi di Sassari, Italy
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Cameron RK, Ulycznyj PI, DuBow MS. Mu transposase-stimulated illegitimate recombination of Tn3kan- and IS101-containing plasmids. Res Microbiol 1995; 146:601-16. [PMID: 8584785 DOI: 10.1016/0923-2508(96)81059-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The transposable bacteriophage Mu and the mobile genetic elements Tn3 and IS101 replicatively transpose to random target sites, produce 5 bp target site duplications, and contain the sequence 5'-PuCGAAAPu-3' starting at bp 21 from their ends. The presence of these shared characteristics, plus the fact that Mu transposase can specifically bind to the termini of Tn3 and IS101 in vitro, suggests that the elements may be evolutionarily conserved and retain some functional capacity to transpose each other's DNA. To examine this proposition, in vivo transposition-mating assays were performed and demonstrated that Mu transposase stimulated the formation of recA-independent recombination products between Tn3kan- or IS101-containing plasmids and a target plasmid (pOX38cam) up to 200-fold. However, when transferred to recA+ hosts, these recA-independent products yielded resolution products suggestive of illegitimate recombination, as similar recombination and resolution products were generated, at reduced frequencies, in the absence of Mu transposase. Thus, Mu transposase may stimulate a host-mediated, recA-independent illegitimate recombination reaction. As adjacent pSC101 sequences, including a formerly unknown but functional IHF site (bp 2238-2251), were required for Mu transposase-stimulated IS101 illegitimate recombination, IHF may be one of the putative host factors involved in these recombination reactions.
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Affiliation(s)
- R K Cameron
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
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Rozsa FW, Viollier P, Fussenegger M, Hiestand-Nauer R, Arber W. Cin-mediated recombination at secondary crossover sites on the Escherichia coli chromosome. J Bacteriol 1995; 177:1159-68. [PMID: 7868587 PMCID: PMC176719 DOI: 10.1128/jb.177.5.1159-1168.1995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The Cin recombinase is known to mediate DNA inversion between two wild-type cix sites flanking genetic determinants for the host range of bacteriophage P1. Cin can also act with low frequency at secondary (or quasi) sites (designated cixQ) that have lower homology to either wild-type site. An inversion tester sequence able to reveal novel operon fusions was integrated into the Escherichia coli chromosome, and the Cin recombinase was provided in trans. Among a total of 13 Cin-mediated inversions studied, three different cixQ sites had been used. In two rearranged chromosomes, the breakpoints of the inversions were mapped to cixQ sites in supB and ompA, representing inversions of 109 and 210 kb, respectively. In the third case, a 2.1-kb inversion was identified at a cixQ site within the integrated sequences. This derivative itself was a substrate for a second inversion of 1.5 kb between the remaining wild-type cix and still another cixQ site, thus resembling a reversion. In analogy to that which is known from DNA inversion on plasmids, homology of secondary cix sites to wild-type recombination sites is not a strict requirement for inversion to occur on the chromosome. The chromosomal rearrangements which resulted from these Cin-mediated inversions were quite stable and suffered no growth disadvantage compared with the noninverted parental strain. The mechanistic implications and evolutionary relevance of these findings are discussed.
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Affiliation(s)
- F W Rozsa
- Department of Microbiology, University of Basel, Switzerland
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Osborn A, Bruce K, Strike P, Ritchie D. Sequence Conservation between Regulatory Mercury Resistance Genes in Bacteria from Mercury Polluted and Pristine Environments. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80441-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Recchia GD, Hall RM. Plasmid evolution by acquisition of mobile gene cassettes: plasmid pIE723 contains the aadB gene cassette precisely inserted at a secondary site in the incQ plasmid RSF1010. Mol Microbiol 1995; 15:179-87. [PMID: 7752893 DOI: 10.1111/j.1365-2958.1995.tb02232.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Gene cassettes are mobile DNA elements which contain a specific recombination site, a 59-base element, recognized by the site-specific recombination system of integrons. Gene cassettes are normally found inserted at a unique site in an integron, downstream of a promoter which directs transcription of the cassette-associated genes. However, insertion of a gene cassette into a secondary site in a plasmid which does not contain an integron is also formally possible. Sequence analysis of the aadB gene in pIE723, a plasmid closely related to the IncQ plasmid RSF1010, revealed the presence of the complete aadB cassette inserted at a secondary site downstream of a known RSF1010 promoter. The site of insertion of the aadB cassette in RSF1010 conformed to the consensus for secondary sites recognized by the integron integrase (Int), and it is likely that the cassette was inserted via a single Int-mediated recombination event between the 59-base element of a free, circular aadB cassette and a secondary site in RSF1010. The cassette-associated recombination site was inactivated by the insertion, and Int-mediated excision of the aadB cassette from this non-specific location was not detectable, indicating that the cassette is stably inserted. The movement of gene cassettes to secondary sites is likely to play an important role in the acquisition of new genes by bacterial and plasmid genomes.
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Affiliation(s)
- G D Recchia
- CSIRO Division of Biomolecular Engineering, Sydney Laboratory, North Ryde, New South Wales, Australia
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Arber W, Naas T, Blot M. Generation of genetic diversity by DNA rearrangements in resting bacteria. FEMS Microbiol Ecol 1994. [DOI: 10.1111/j.1574-6941.1994.tb00224.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Gallori E, Bazzicalupo M, Dal Canto L, Fani R, Nannipieri P, Vettori C, Stotzky G. Transformation of Bacillus subtilis by DNA bound on clay in non-sterile soil. FEMS Microbiol Ecol 1994. [DOI: 10.1111/j.1574-6941.1994.tb00236.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Sandmeier H. Acquisition and rearrangement of sequence motifs in the evolution of bacteriophage tail fibres. Mol Microbiol 1994; 12:343-50. [PMID: 8065255 DOI: 10.1111/j.1365-2958.1994.tb01023.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular analysis reveals a surprising sharing of short gene segments among a variety of large double-stranded DNA bacteriophages of enteric bacteria. Ancestral genomes from otherwise unrelated phages, including lambda, Mu, P1, P2 and T4, must have exchanged parts of their tail-fibre genes. Individual genes appear as mosaics with parts derived from a common gene pool. Therefore, horizontal gene transfer emerges as a major factor in the evolution of a specific part of phage genomes. Current concepts of homologous recombination cannot account for the formation of such chimeric genes and the recombinational mechanisms responsible are not known. However, recombination sites for DNA invertases and recombination site-like sequences are present at the boundaries of gene segments conferring the specificity for the host receptor. This, together with the properties of the DNA inversion mechanism, suggests that these site-specific recombination enzymes could be responsible for the exchange of host-range determinants.
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Affiliation(s)
- H Sandmeier
- Department of Preventive Dentistry and Oral Microbiology, University of Basel, Switzerland
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Abstract
Recently, the well-preserved corpse of a prehistoric man with an age of approximately 5300 years bp was discovered in the Central European Alps. Analysis of materials associated with the individual has revealed the presence of microorganisms which are believed to have survived since the time of death. So far, two fungi have been isolated and identified as species of the genera Chaetomium and Absidia, respectively. In addition, we have obtained one bacterial isolate which we have identified as a Streptomyces species. Our findings demonstrate that microorganisms can remain viable under appropriate circumstances for thousands of years. The isolates may enable us to study evolutionary trends within microorganisms.
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Affiliation(s)
- K Haselwandter
- Department of Microbiology, University of Innsbruck, Austria
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49
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Abstract
A transposable element (TE) is a mobile sequence present in the genome of an organism. TEs can cause lethal mutations by inserting into essential genes, promoting deletions or leaving short sequences upon excision. They therefore may be gradually eliminated from mixed populations of haploid micro-organisms such as Escherichia coli if they cannot balance this mutation load. Horizontal transmission between cells is known to occur and promote the transfer of TEs, but at rates often too low to compensate for the burden to their hosts. Therefore, alternative mechanisms should be found by these elements to earn their keep in the cells. Several theories have been suggested to explain their long-term maintenance in prokaryotic genomes, but little molecular evidence has been experimentally obtained. In this paper, the permanence of transposable elements in bacterial populations is discussed in terms of costs or benefits for the element and for the host. It is observed that, in all studies yet reported, the elements do not behave in their host as selfish DNA but as a co-operative component for the evolution of the couple.
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Affiliation(s)
- M Blot
- Department of Microbiology, University of Basel, Switzerland
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Abstract
Molecular genetics, which has its roots mainly in the development of microbial genetics in the middle of this century, not only greatly facilitates investigations of essential cellular functions, but also offers a means to better understand evolutionary progress. Spontaneous mutagenesis, the driving force of biological evolution, depends on a multitude of mechanistically distinct processes, many of which are already quite well understood. Often, enzymes act as variation generators, and natural gene vectors help to spread functional domains, entire genes and groups of genes across natural isolation barriers. In this overview, particular attention is given to comparing three selected natural strategies for the generation of genetic diversity: nucleotide substitution, DNA rearrangements, and gene acquisition. All of these mechanisms, as well as many others, appear to fulfill their specific roles in microbial evolution. Rather than being the result of an accumulation of errors, biological evolution may depend on a multitude of specific biological functions, as well as on a certain degree of intrinsic structural flexibility of biological molecules.
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Affiliation(s)
- W Arber
- Department of Microbiology, Biozentrum, University of Basel, Switzerland
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