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Ghasemi F, Tirandaz A. Environment assisted quantum model for studying RNA-DNA-error correlation created due to the base tautomery. Sci Rep 2023; 13:10788. [PMID: 37402822 PMCID: PMC10319750 DOI: 10.1038/s41598-023-38019-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/30/2023] [Indexed: 07/06/2023] Open
Abstract
The adaptive mutation phenomenon has been drawing the attention of biologists for several decades in evolutionist community. In this study, we propose a quantum mechanical model of adaptive mutation based on the implications of the theory of open quantum systems. We survey a new framework that explain how random point mutations can be stabilized and directed to be adapted with the stresses introduced by the environments according to the microscopic rules dictated by constraints of quantum mechanics. We consider a pair of entangled qubits consist of DNA and mRNA pair, each coupled to a distinct reservoir for analyzing the spreed of entanglement using time-dependent perturbation theory. The reservoirs are physical demonstrations of the cytoplasm and nucleoplasm and surrounding environments of mRNA and DNA, respectively. Our predictions confirm the role of the environmental-assisted quantum progression of adaptive mutations. Computing the concurrence as a measure that determines to what extent the bipartite DNA-mRNA can be correlated through entanglement, is given. Preventing the entanglement loss is crucial for controlling unfavorable point mutations under environmental influences. We explore which physical parameters may affect the preservation of entanglement between DNA and mRNA pair systems, despite the destructive role of interaction with the environments.
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Affiliation(s)
- Fatemeh Ghasemi
- Department of Energy Engineering, Sharif University of Technology, P.O. Box 11365-9516, Tehran, Iran.
| | - Arash Tirandaz
- Department of Chemistry, Bu-Ali Sina University, Hamedan, Iran.
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Deng S. The origin of genetic and metabolic systems: Evolutionary structuralinsights. Heliyon 2023; 9:e14466. [PMID: 36967965 PMCID: PMC10036676 DOI: 10.1016/j.heliyon.2023.e14466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.
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Santiago-Alarcon D, Tapia-McClung H, Lerma-Hernández S, Venegas-Andraca SE. Quantum aspects of evolution: a contribution towards evolutionary explorations of genotype networks via quantum walks. J R Soc Interface 2020; 17:20200567. [PMID: 33171071 PMCID: PMC7729038 DOI: 10.1098/rsif.2020.0567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022] Open
Abstract
Quantum biology seeks to explain biological phenomena via quantum mechanisms, such as enzyme reaction rates via tunnelling and photosynthesis energy efficiency via coherent superposition of states. However, less effort has been devoted to study the role of quantum mechanisms in biological evolution. In this paper, we used transcription factor networks with two and four different phenotypes, and used classical random walks (CRW) and quantum walks (QW) to compare network search behaviour and efficiency at finding novel phenotypes between CRW and QW. In the network with two phenotypes, at temporal scales comparable to decoherence time TD, QW are as efficient as CRW at finding new phenotypes. In the case of the network with four phenotypes, the QW had a higher probability of mutating to a novel phenotype than the CRW, regardless of the number of mutational steps (i.e. 1, 2 or 3) away from the new phenotype. Before quantum decoherence, the QW probabilities become higher turning the QW effectively more efficient than CRW at finding novel phenotypes under different starting conditions. Thus, our results warrant further exploration of the QW under more realistic network scenarios (i.e. larger genotype networks) in both closed and open systems (e.g. by considering Lindblad terms).
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Affiliation(s)
- Diego Santiago-Alarcon
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología, A.C. Carr. Antigua a Coatepec 351, Col. El Haya, C.P. 91070, Xalapa, Veracruz, Mexico
| | - Horacio Tapia-McClung
- Centro de Investigación en Inteligencia Artificial, Universidad Veracruzana, Sebastián Camacho 5, Centro, Xalapa-Enríquez, Veracruz, Mexico
| | - Sergio Lerma-Hernández
- Facultad de Física, Universidad Veracruzana, Circuito Aguirre Beltrán s/n, Xalapa, Veracruz 91000, Mexico
| | - Salvador E. Venegas-Andraca
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Avenue Eugenio Garza Sada 2501, Monterrey 64849, Nuevo Leon, Mexico
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Abstract
Populations adapt physiologically using regulatory mechanisms and genetically by means of mutations that improve growth. During growth under selection, genetic adaptation can be rapid. In several genetic systems, the speed of adaptation has been attributed to cellular mechanisms that increase mutation rates in response to growth limitation. An alternative possibility is that growth limitation serves only as a selective agent but acts on small-effect mutations that are common under all growth conditions. The genetic systems that initially suggested stress-induced mutagenesis have been analyzed without regard for multistep adaptation and some include features that make such analysis difficult. To test the selection-only model, a simpler system is examined, whose behavior was originally attributed to stress-induced mutagenesis (Yang et al. 2001, 2006). A population with a silent chromosomal lac operon gives rise to Lac+ revertant colonies that accumulate over 6 days under selection. Each colony contains a mixture of singly and doubly mutant cells. Evidence is provided that the colonies are initiated by pre-existing single mutants with a weak Lac+ phenotype. Under selection, these cells initiate slow-growing clones, in which a second mutation arises and improves growth of the resulting double mutant. The system shows no evidence of general mutagenesis during selection. Selection alone may explain rapid adaptation in this and other systems that give the appearance of mutagenesis.
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Ivancić-Bacće I, Vlasić I, Cogelja-Cajo G, Brcić-Kostić K, Salaj-Smic E. Roles of PriA protein and double-strand DNA break repair functions in UV-induced restriction alleviation in Escherichia coli. Genetics 2006; 174:2137-49. [PMID: 17028321 PMCID: PMC1698619 DOI: 10.1534/genetics.106.063750] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been widely considered that DNA modification protects the chromosome of bacteria E. coli K-12 against their own restriction-modification systems. Chromosomal DNA is protected from degradation by methylation of target sequences. However, when unmethylated target sequences are generated in the host chromosome, the endonuclease activity of the EcoKI restriction-modification enzyme is inactivated by the ClpXP protease and DNA is protected. This process is known as restriction alleviation (RA) and it can be induced by UV irradiation (UV-induced RA). It has been proposed that chromosomal unmethylated target sequences, a signal for the cell to protect its own DNA, can be generated by homologous recombination during the repair of damaged DNA. In this study, we wanted to further investigate the genetic requirements for recombination proteins involved in the generation of unmethylated target sequences. For this purpose, we monitored the alleviation of EcoKI restriction by measuring the survival of unmodified lambda in UV-irradiated cells. Our genetic analysis showed that UV-induced RA is dependent on the excision repair protein UvrA, the RecA-loading activity of the RecBCD enzyme, and the primosome assembly activity of the PriA helicase and is partially dependent on RecFOR proteins. On the basis of our results, we propose that unmethylated target sequences are generated at the D-loop by the strand exchange of two hemi-methylated duplex DNAs and subsequent initiation of DNA replication.
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Affiliation(s)
- Ivana Ivancić-Bacće
- Department of Molecular Biology, Faculty of Science, University of Zagreb, Croatia.
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7
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Babynin EV. The effect of extracellular metabolites on the frequency of thy+ revertants in Salmonella typhimurium populations. Microbiology (Reading) 2006. [DOI: 10.1134/s0026261706040138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Shu J, Schellhorn HE, Murphy TM. Stationary phase-induction of G-->T mutations in Escherichia coli. Mutat Res 2006; 596:106-12. [PMID: 16490219 DOI: 10.1016/j.mrfmmm.2005.12.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Revised: 11/16/2005] [Accepted: 12/22/2005] [Indexed: 11/25/2022]
Abstract
A series of Escherichia coli mutants, constructed originally by Cupples and Miller [C.G. Cupples, J.H. Miller, A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions, Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 5345-5349], provides a unique system for quantifying base-change mutations, and the repair processes that limit their establishment, in bacteria under selective and non-selective conditions. We focussed on one strain in which a T-->G replacement inactivates the lacZ gene. Reversions of this strain can occur through oxidation of G, leading to G-->T transversions. We show that spontaneous reversions occurred both in lactose (selective) and glucose (non-selective) medium. The number of revertants per viable cell was much greater in medium containing lactose or both sugars than glucose alone. In glucose medium, the rate of reversion was highest below 0.6% glucose and strongly inhibited at and above that level. Evidence that reversions occurred through G-->T transversions in both lactose and glucose media came from two observations: by sequence analysis of a series of revertants and by comparing the reversion rates in strains possessing and lacking the mutM gene (encoding formamidopyrimidine DNA glycosylase, FPG). However, the rate of reversion was stimulated by reducing O2 to 1% and inhibited or delayed by increasing O2 to 90%. In mutM- cells grown on glucose medium, the proportion of revertants increased over a 5-day period. In contrast, in mutM+ cells, revertants appeared primarily during the first 2-3 days after plating; few new revertants appeared in the following days. These data imply that base excision repair initiated by FPG was less effective in the first 2 days and more effective later in stationary phase.
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Affiliation(s)
- Joline Shu
- Section of Plant Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
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Arber W. Dual Nature of the Genome: Genes for the Individual Life and Genes for the Evolutionary Progress of the Population. IUBMB Life 2005; 57:263-6. [PMID: 16036608 DOI: 10.1080/15216540500092625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Biological evolution is here postulated to be driven coordinately by the products of specific evolution genes and by non-genetic elements such as the intrinsic properties of matter and random encounter with environmental factors. Evolution genes are supposed to have their own evolutionary history in which second-order selection was exerted at the population level. The products of evolution genes can act as generators of genetic variations and/or as modulators of the frequency of genetic variation. Three major natural strategies, each with a number of specific mechanisms contribute to the overall spontaneous production of genetic variants. Each of these three strategies contributes its own specific quality to genetic variation. The difficulties of experimentally investigating these strategies and a wider discussion of some of the postulates within the scientific community are outlined. Finally, the general relevance of the postulated duality of the genome for our world view is briefly mentioned.
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Affiliation(s)
- Werner Arber
- Biozentrum, University of Basel, Basel, Switzerland.
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Saumaa S, Tover A, Kasak L, Kivisaar M. Different spectra of stationary-phase mutations in early-arising versus late-arising mutants of Pseudomonas putida: involvement of the DNA repair enzyme MutY and the stationary-phase sigma factor RpoS. J Bacteriol 2002; 184:6957-65. [PMID: 12446646 PMCID: PMC135458 DOI: 10.1128/jb.184.24.6957-6965.2002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2002] [Accepted: 09/17/2002] [Indexed: 11/20/2022] Open
Abstract
Stationary-phase mutations occur in populations of stressed, nongrowing, and slowly growing cells and allow mutant bacteria to overcome growth barriers. Mutational processes in starving cells are different from those occurring in growing bacteria. Here, we present evidence that changes in mutational processes also take place during starvation of bacteria. Our test system for selection of mutants based on creation of functional promoters for the transcriptional activation of the phenol degradation genes pheBA in starving Pseudomonas putida enables us to study base substitutions (C-to-A or G-to-T transversions), deletions, and insertions. We observed changes in the spectrum of promoter-creating mutations during prolonged starvation of Pseudomonas putida on phenol minimal plates. One particular C-to-A transversion was the prevailing mutation in starving cells. However, with increasing time of starvation, the importance of this mutation decreased but the percentage of other types of mutations, such as 2- to 3-bp deletions, increased. The rate of transversions was markedly elevated in the P. putida MutY-defective strain. The occurrence of 2- to 3-bp deletions required the stationary-phase sigma factor RpoS, which indicates that some mutagenic pathway is positively controlled by RpoS in P. putida.
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Affiliation(s)
- Signe Saumaa
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Estonia
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11
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Cefalì E, Patanè S, Arena A, Saitta G, Guglielmino S, Cappello S, Nicolò M, Allegrini M. Morphologic variations in bacteria under stress conditions: near-field optical studies. SCANNING 2002; 24:274-283. [PMID: 12507381 DOI: 10.1002/sca.4950240601] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The morphologic and structural variations suffered by cells of a population of Pseudomonas aeruginosa ATCC 27853 under stress conditions were investigated by using scanning near-field optical microscopy. The analysis of the images, supported by microbiological data, showed that the bacteria evolved from the initial distribution of rod-shaped cells of standard size to a population with structural and morphologic modifications. The detection of variations in the optical reflectivity over a subwavelength scale (< or = 100 nm), combined with the concurrently acquired topographical signal, allowed the visualisation of rod-shaped bacteria going towards a lytic process and entire "U"-shaped cells. In the latter cells, which derived from a morphology refolding of rod bacteria, cellular matter seemed to rearrange itself to attain a coccoid stress resistant form, responsible for the residual viability of the population.
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Affiliation(s)
- E Cefalì
- INFM and Department of Physics, University of Messina, Messina, Italy
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12
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Sung HM, Yasbin RE. Adaptive, or stationary-phase, mutagenesis, a component of bacterial differentiation in Bacillus subtilis. J Bacteriol 2002; 184:5641-53. [PMID: 12270822 PMCID: PMC139596 DOI: 10.1128/jb.184.20.5641-5653.2002] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptive (stationary-phase) mutagenesis occurs in the gram-positive bacterium Bacillus subtilis. Furthermore, taking advantage of B. subtilis as a paradigm for the study of prokaryotic differentiation and development, we have shown that this type of mutagenesis is subject to regulation involving at least two of the genes that are involved in the regulation of post-exponential phase prokaryotic differentiation, i.e., comA and comK. On the other hand, a functional RecA protein was not required for this type of mutagenesis. The results seem to suggest that a small subpopulation(s) of the culture is involved in adaptive mutagenesis and that this subpopulation(s) is hypermutable. The existence of such a hypermutable subpopulation(s) raises important considerations with respect to evolution, the development of specific mutations, the nature of bacterial populations, and the level of communication among bacteria in an ecological niche.
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Affiliation(s)
- Huang-Mo Sung
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75080, USA
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13
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Andaluz E, Ciudad T, Larriba G. An evaluation of the role ofLIG4in genomic instability and adaptive mutagenesis inCandida albicans. FEMS Yeast Res 2002. [DOI: 10.1111/j.1567-1364.2002.tb00103.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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14
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Abstract
Organisms control the specificity and frequency with which they mutate via their complement of proteins. The mismatch repair (MMR) proteins correct errors after they are made. The DNA polymerases of the cell determine the response to damaged DNA which has not been repaired by excision. Polymerase action can be considered as consisting of three main steps: addition of a base, proofreading of the added nucleotide and elongation. Each of these steps is kinetically complex and can be modulated. The modulation accounts for different behaviors of organisms in response to stress. The recent findings of DNA polymerases with properties appropriate for dealing with damaged DNA may help to account for the phenomenon of spontaneous mutation and for the hypermutability associated with immunoglobulin maturation and carcinogenesis.
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Affiliation(s)
- Bernard S Strauss
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
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15
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Abstract
Deletions in the plasmid pMC874 join the promoter of the km(r) (kanamycin resistance) gene coding for the enzyme aminoglycoside 3'-phosphotransferase to a promoterless lac operon downstream giving a phenotypic change from Lac(-)-->Lac(+). They differ from most deletions studied in Escherichia coli, which occur in actively dividing cells, in several important respects, as follows. (1) They occur in "resting" cells incubating on McConkey's or minimal lactose agar and increase in number gradually over a period of 1-2 weeks. Thus, like "adaptive" mutations, they are time rather than generation dependent. (2) They are extremely rare events (frequency 1x10(-11)-5x10(-11)) in wild type cells, but their frequency is increased between 1 and 2 orders of magnitude by null recC(-) mutations. In these respects they differ from "adaptive" mutations which are equally frequent in recC(+) and recC(-) cells. (3) Their frequency is not increased by mutations which stimulate log phase deletions. (4) Based on a computer search for homologies and sequencing of one deletion, it appears that they differ from log phase deletions in that they can occur in the absence of major terminal homologies (direct repeats) or intervening homologies (inverted repeats) which could stabilize a transient secondary structure and determine the deletion endpoints. Thus, they are not explained by the misaligned mutagenesis model. In conclusion, resting phase deletions occur through a totally different pathway from deletions in actively dividing cells and probably originate from unrepaired double strand breaks.
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Affiliation(s)
- E Balbinder
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, 4200 East Ninth Avenue, Denver, CO 80262, USA
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Powell SC, Wartell RM. Different characteristics distinguish early versus late arising adaptive mutations in Escherichia coli FC40. Mutat Res 2001; 473:219-28. [PMID: 11166039 DOI: 10.1016/s0027-5107(00)00149-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Escherichia coli strain FC40 has frequently been employed to investigate the mechanism of adaptive mutations. The strain cannot utilize lactose due to a +1 frameshift mutation that reduces beta-galactosidase to about 1% of normal levels. Cells undergo a high rate of mutation from Lac- to Lac+ when cells are grown with lactose as the sole energy source. Almost all Lac+ colonies arising 3-6 days after plating result from a base pair deletion in runs of iterated base pairs within a 130-bp target region. In this study we characterized Lac+ colonies arising 3-10 days after plating. Temperature gradient gel electrophoresis (TGGE) was used to detect mutations in the target region as a function of the day a colony appears. TGGE results confirmed the occurrence of mutations within the target region in 36 of 37 FC40 Lac+ colonies arising on days 3-7. However, mutations in this region were not detected in 23 of 37 Lac+ colonies arising from days 8-10. Sequencing data verified the TGGE results. Half of the Lac+ mutants arising on days 8-10 with no base pair change in the target region were unstable and exhibited a Lac- phenotype after successive growth cycles in rich medium. The results suggest that amplification of the lac operon region is a common factor in late arising colonies, and that different characteristics distinguish early and late arising Lac+ colonies.
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Affiliation(s)
- S C Powell
- Georgia Institute of Technology, School of Biology, Atlanta, GA 30332, USA
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Bhamre S, Gadea BB, Koyama CA, White SJ, Fowler RG. An aerobic recA-, umuC-dependent pathway of spontaneous base-pair substitution mutagenesis in Escherichia coli. Mutat Res 2001; 473:229-47. [PMID: 11166040 DOI: 10.1016/s0027-5107(00)00155-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antimutator alleles indentify genes whose normal products are involved in spontaneous mutagenesis pathways. Mutant alleles of the recA and umuC genes of Escherichia coli, whose wild-type alleles are components of the inducible SOS response, were shown to cause a decrease in the level of spontaneous mutagenesis. Using a series of chromosomal mutant trp alleles, which detect point mutations, as a reversion assay, it was shown that the reduction in mutagenesis is limited to base-pair substitutions. Within the limited number of sites than could be examined, transversions at AT sites were the favored substitutions. Frameshift mutagenesis was slightly enhanced by a mutant recA allele and unchanged by a mutant umuC allele. The wild-type recA and umuC genes are involved in the same mutagenic base-pair substitution pathway, designated "SOS-dependent spontaneous mutagenesis" (SDSM), since a recAumuC strain showed the same degree and specificity of antimutator activity as either single mutant strain. The SDSM pathway is active only in the presence of oxygen, since wild-type, recA, and umuC strains all show the same levels of reduced spontaneous mutagenesis anaerobically. The SDSM pathway can function in starving/stationary cells and may, or may not, be operative in actively dividing cultures. We suggest that, in wild-type cells, SDSM results from basal levels of SOS activity during DNA synthesis. Mutations may result from synthesis past cryptic DNA lesions (targeted mutagenesis) and/or from mispairings during synthesis with a normal DNA template (untargeted mutagenesis). Since it occurs in chromosomal genes of wild-type cells, SDSM may be biologically significant for isolates of natural enteric bacterial populations where extended starvation is often a common mode of existence.
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Affiliation(s)
- S Bhamre
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192, USA
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18
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Abstract
The appearance over many days of Lac(+) frameshift mutations in Escherichia coli strain FC40 incubated on lactose selection plates is a classic example of apparent "adaptive" mutation in an episomal gene. We show that endogenously overproduced carotenoids reduce adaptive mutation under selective conditions by a factor of around two. Carotenoids are known to scavenge singlet oxygen suggesting that the accumulation of oxidative base damage may be an integral part of the adaptive mutation phenomenon. If so, the lesion cannot be 7,8-dihydro-8-oxoguanine since adaptive mutation in FC40 is unaffected by mutM and mutY mutations. If active oxygen species such as singlet oxygen are involved in adaptive mutation then they should also induce frameshift mutations in FC40 under non-selective conditions. We show that such mutations can be induced under non-selective conditions by protoporphyrin photosensitisation and that this photodynamic induction is reduced by a factor of just over two when endogenous carotenoids are present. We argue that the involvement of oxidative damage would in no way be inconsistent with current understanding of the mechanism of adaptive mutation and the role of DNA polymerases.
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Affiliation(s)
- B A Bridges
- MRC Cell Mutation Unit, University of Sussex, Falmer, BN1 9RR, Brighton, UK.
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19
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Chevalier S, Burini JF, Freulet-Marriere MA, Regeard C, Schoofs G, Guespin-Michel J, De Mot R, Orange N. Characterization of an OprF-deficient mutant suggests that OprF is an essential protein for Pseudomonas fluorescens strain MF0. Res Microbiol 2000; 151:619-27. [PMID: 11081577 DOI: 10.1016/s0923-2508(00)90128-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A stable OprF-deficient mutant for Pseudomonas fluorescens strain MF0 was constructed using reverse genetics. This mutant, called MF372, showed a rounded morphology and grew more slowly in minimal medium, but not in rich medium. Contrary to other Pseudomonas strains, the loss of OprF for strain MF0 was accompanied by an altered outer membrane composition. At least three outer membrane proteins were overexpressed, apparently as a consequence of adaptive mutations. The N-terminal sequence of two of them revealed strong similarities with porins of the OprD family from P. aeruginosa. The data presented here shows that OprF may be an essential protein for this P. fluorescens strain.
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Affiliation(s)
- S Chevalier
- Laboratoire de microbiologie du froid, université de Rouen, IFRSI 61CNRS-Inserm, Evreux, France.
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21
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Ren L, Al Mamun AA, Humayun MZ. Requirement for homologous recombination functions for expression of the mutA mistranslator tRNA-induced mutator phenotype in Escherichia coli. J Bacteriol 2000; 182:1427-31. [PMID: 10671469 PMCID: PMC94434 DOI: 10.1128/jb.182.5.1427-1431.2000] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of the Escherichia coli mutA mutator phenotype requires recA, recB, recC, ruvA, and ruvC gene, but not recD, recF, recO, or recR genes. Thus, the recBCD-dependent homologous recombination system is a component of the signal pathway that activates an error-prone DNA polymerase in mutA cells.
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Affiliation(s)
- L Ren
- Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey-New Jersey Medical School, Newark, New Jersey 07103-2714, USA
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22
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Foster PL. Adaptive mutation in Escherichia coli. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2000; 65:21-9. [PMID: 12760017 PMCID: PMC2929248 DOI: 10.1101/sqb.2000.65.21] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- P L Foster
- Department of Biology, Jordan Hall 142, Indiana University, Bloomington, Indiana 47405-6801, USA
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Godoy VG, Gizatullin FS, Fox MS. Some features of the mutability of bacteria during nonlethal selection. Genetics 2000; 154:49-59. [PMID: 10628968 PMCID: PMC1460914 DOI: 10.1093/genetics/154.1.49] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe the mutability of the Trp(-) chromosomal +1 frameshift mutation trpE7999 during nonlethal selection, finding that the appearance of Trp(+) revertants behaves similarly to that of episomal Lac(+) revertants. In addition, we show that a feature of the Lac(+) and Trp(+) mutability is the accumulation of Trp(+) and Lac(+) revertants with additional unselected mutations, most of which are not due to heritable mutators. The cells undergoing nonlethal selection apparently experience an epigenetic change resulting in a subset of bacteria with elevated mutability that often remain hypermutable for the duration of selection. The epigenetic change provoked by nonlethal selection appears to be mediated by a unique function provided by the F'128 episome.
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Affiliation(s)
- V G Godoy
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Storchová Z, Vondrejs V. Starvation-associated mutagenesis in yeast Saccharomyces cerevisiae is affected by Ras2/cAMP signaling pathway. Mutat Res 1999; 431:59-67. [PMID: 10656486 DOI: 10.1016/s0027-5107(99)00157-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The number of revertants with restored ability to form colony increases in a time-dependent manner during long-term selective starvation of dense mutant microbial cultures. This is due to starvation-associated (also called adaptive) mutations that arise in a replication independent manner. Here we report that in Saccharomyces cerevisiae the frequency of starvation-associated reversions of mutant genes whose products are necessary for amino acids biosynthesis are influenced by Ras2/cAMP signaling pathway. This signaling pathway is a yeast general regulatory pathway involved in nutritional sensing, UV response, sporulation control and life span control and its changes are manifested in both, cell cycle and life cycle. Inactivation of the RAS2 gene causes an increase in number of starvation-associated revertants in comparison to an isogenic wild type strain and a strain with constitutively activated Ras2/cAMP signaling pathway. Therefore, we suggest that starvation-associated mutagenesis is different from spontaneous mutagenesis and is related to the cellular capacity to adopt distinct physiological states in response to environmental signals.
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Affiliation(s)
- Z Storchová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic.
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Ogi T, Kato T, Kato T, Ohmori H. Mutation enhancement by DINB1, a mammalian homologue of the Escherichia coli mutagenesis protein dinB. Genes Cells 1999; 4:607-18. [PMID: 10620008 DOI: 10.1046/j.1365-2443.1999.00289.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The Escherichia coli dinB gene is an SOS gene known to be required for lambda phage untargeted mutagenesis. When over-expressed, it exhibits a potent mutagenic activity without any exogenous treatment to damage DNA. Frameshift mutations at a run of identical bases are most enhanced. The product DinB is structurally related to the E. coli UmuC protein and the Saccharomyces cerevisiae Rev1 and Rad30 proteins, all of which are shown to be involved in bypass synthesis at a DNA lesion. RESULTS We have cloned and sequenced human and mouse cDNAs encoding a DinB homologue. Their products are highly similar to DinB and less similar to UmuC, Rev1 or Rad30, and hence the genes were named DINB1 for human and Dinb1 for mouse. Both genes were expressed most abundantly in testis. Transient expression of the mouse cDNA in cultured mouse cells resulted in a nearly 10-fold increase in the incidence of point mutations, among which about 30% were frameshift mutations. CONCLUSIONS The above results suggest that a mutagenic mechanism, a so-called untargeted type, also operates in mammalian cells. Taken together with recent findings that human cells have multiple DNA polymerases for translesion synthesis which are homologous to the S. cerevisiae Rev3 and Rad30 proteins, our results imply that multiple mutagenic pathways are conserved from bacteria to higher eukaryotes.
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Affiliation(s)
- T Ogi
- Institute for Virus Research, Kyoto University, Kawahara-machi, Sakyo-ku, Kyoto 606-8507, Japan
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26
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Abstract
The structure of eukaryotic DNA, with its repeated sequences, makes base addition and loss a major obstacle to the maintenance of genetic stability. As compared to the bacteria, much of the mismatch repair capacity of the eukaryotic cell must be devoted to the surveillance of frameshift changes. Any alteration in the activity of proteins which recognize frameshifts or which hold the DNA in place during replication is likely to result in genomic instability.
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Affiliation(s)
- B S Strauss
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
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Janbon G, Sherman F, Rustchenko E. Appearance and properties of L-sorbose-utilizing mutants of Candida albicans obtained on a selective plate. Genetics 1999; 153:653-64. [PMID: 10511546 PMCID: PMC1460764 DOI: 10.1093/genetics/153.2.653] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This is the first report that adaptive mutagenesis can arise by chromosomal nondisjunction, a phenomenon previously associated exclusively with DNA alterations. We previously uncovered a novel regulatory mechanism in Candida albicans in which the assimilation of an alternative sugar, l-sorbose, was determined by copy number of chromosome 5, such that monosomic strains utilized l-sorbose, whereas disomic strains did not. We present evidence that this formation of monosomy of chromosome 5, which is apparently a result of nondisjunction, appeared with increased frequencies after a selective condition was applied, i.e., by adaptive mutagenesis. The rate of formation of l-sorbose-utilizing mutants per viable cell per day ranged from 10(-6) at the initial time of detection to 10(-2) after 4 days of incubation on the selective plate.
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Affiliation(s)
- G Janbon
- Department of Biochemistry, University of Rochester Medical School, Rochester, New York 14642, USA
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Abstract
Evolution and development are both lineage processes but are often conceptualized as occurring by different and mutually exclusive mechanisms. It is conventionally asserted that evolution occurs via the random generation of diversity and the subsequent survival of those that pass selection. On the other hand, development is too often presented as proceeding via the unfolding of a deterministic program encoded in the DNA sequence. In biology, universal generalizations are rare and dogmas are often wrong for particular cases. Deterministic mechanisms contribute some of the new DNA sequences that subsequently become substrates for natural selection. Conversely, stochastic and selective mechanisms are intrinsic to development, and also to maintenance of the immune, and possibly, nervous systems. Cancer appears to be another process that straddles distinctions between evolutionary and developmental modes of hereditary change and stabilization. DNA sequence changes are an essential feature of many cancers, but there are also aspects of the disease similar to developmental lineage gone awry. The literature suggests that the cellular changes that give rise to cancer occur by mechanisms commonly associated with both evolutionary and developmental lineage pathways.
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Affiliation(s)
- D S Thaler
- Sackler Laboratory of Molecular Genetics and Informatics, Rockefeller University, Box 174, 1230 York Ave., New York, NY 10021-6399, USA.
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Foster PL, Rosche WA. Mechanisms of mutation in nondividing cells. Insights from the study of adaptive mutation in Escherichia coli. Ann N Y Acad Sci 1999; 870:133-45. [PMID: 10415479 PMCID: PMC2928472 DOI: 10.1111/j.1749-6632.1999.tb08873.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
When populations of cells are subjected to nonlethal selection, mutations arise in the absence of cell division, a phenomenon that has been called "adaptive mutation." In a strain of Escherichia coli that cannot metabolize lactose (Lac-) but that reverts to lactose utilization (Lac+) when lactose is its sole energy and carbon source, the mutational process consists of two components. (1) A highly efficient, recombination-dependent mechanism giving rise to mutations on the F' episome that carries the Lac- allele; and (2) a less efficient, unknown mechanism giving rise to mutations elsewhere in the genome. Both selected and nonselected mutations arise in the Lac- population, but nonselected mutations are enriched in Lac+ mutants, suggesting that some Lac+ cells have passed though a transient period of increased mutation. These results have several evolutionary implications. (1) DNA synthesis initiated by recombination could be an important source of spontaneous mutation, particularly in cells that are not undergoing genomic replication. (2) The highly active mutational mechanism on the episome could be important in the horizontal transfer of variant alleles among species that carry and exchange conjugal plasmids. (3) A sub-population of cells in a state of transient mutation could be a source of multiple variant alleles and could provide a mechanism for rapid adaptive evolution under adverse conditions.
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Affiliation(s)
- P L Foster
- Department of Environmental Health, Boston University School of Public Health, Massachusetts 02118-2394, USA.
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THALER DAVID. Introduction to the Poster Presentations: Developmental Themes and Evolution. Ann N Y Acad Sci 1999. [DOI: 10.1111/j.1749-6632.1999.tb08899.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Foster PL, Rosche WA. Increased episomal replication accounts for the high rate of adaptive mutation in recD mutants of Escherichia coli. Genetics 1999; 152:15-30. [PMID: 10224241 PMCID: PMC1460594 DOI: 10.1093/genetics/152.1.15] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adaptive mutation has been studied extensively in FC40, a strain of Escherichia coli that cannot metabolize lactose (Lac-) because of a frameshift mutation affecting the lacZ gene on its episome. recD mutants of FC40, in which the exonuclease activity of RecBCD (ExoV) is abolished but its helicase activity is retained, have an increased rate of adaptive mutation. The results presented here show that, in several respects, adaptive mutation to Lac+ involves different mechanisms in recD mutant cells than in wild-type cells. About half of the apparent increase in the adaptive mutation rate of recD mutant cells is due to a RecA-dependent increase in episomal copy number and to growth of the Lac- cells on the lactose plates. The remaining increase appears to be due to continued replication of the episome, with the extra copies being degraded or passed to recD+ recipients. In addition, the increase in adaptive mutation rate in recD mutant cells is (i) dependent on activities of the single-stranded exonucleases, RecJ and ExoI, which are not required for (in fact, slightly inhibit) adaptive mutation in wild-type cells, and (ii) enhanced by RecG, which opposes adaptive mutation in wild-type cells.
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Affiliation(s)
- P L Foster
- Department of Environmental Health, Boston University School of Public Health, Boston, Massachusetts 02118, USA.
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34
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Vasi FK, Lenski RE. Ecological strategies and fitness tradeoffs inEscherichia coli mutants adapted to prolonged starvation. J Genet 1999. [DOI: 10.1007/bf02994702] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Jayaraman R. Emergence of a mutagenic ochre suppressor mutation under lactose selection in appm mutant ofEscherichia coli harbouring the F′lacZU118 episome. J Genet 1999. [DOI: 10.1007/bf02994701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Abstract
A decade of research on adaptive mutation has revealed a plethora of mutagenic mechanisms that may be important in evolution. The DNA synthesis associated with recombination could be an important source of spontaneous mutation in cells that are not proliferating. The movement of insertion elements can be responsive to environmental conditions. Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements. Some conjugative plasmids can recombine with their host's chromosome, and may acquire chromosomal genes that could then spread through the population and even to other species. Finally, a subpopulation of transient hypermutators could be a source of multiple variant alleles, providing a mechanism for rapid evolution under adverse conditions.
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Affiliation(s)
- P L Foster
- Department of Biology, Indiana University, Bloomington 47405, USA.
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37
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Abstract
Environmental and physiological stress conditions can transiently alter the fidelity of DNA replication. The DNA damage-mediated SOS response in Escherichia coli is the best-known example of such an 'inducible mutagenesis' or 'transient mutator' pathway. Emerging evidence suggests the existence of a number of other stress-inducible pathways that also affect the fidelity of replication. Among the more provocative recent findings are UVM, an SOS-independent damage-inducible mutagenic pathway, and a new recA-dependent but umuD/C-independent pathway that appears to be provoked by translational stress. These findings alter our view of inducible mutagenesis, and anticipate the existence of previously unrecognized links between protein synthesis and DNA replication.
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Affiliation(s)
- M Z Humayun
- Department of Microbiology and Molecular Genetics, UMDNJ - New Jersey Medical School, Newark 07103-2714, USA.
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38
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Andersson DI, Slechta ES, Roth JR. Evidence that gene amplification underlies adaptive mutability of the bacterial lac operon. Science 1998; 282:1133-5. [PMID: 9804552 DOI: 10.1126/science.282.5391.1133] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Adaptive mutability is the apparent alteration in specificity or rate of mutability seen in bacteria during stress. A model is proposed by which gene amplification during selective growth can give the appearance of adaptive mutability without requiring any change in mutability. The model is based on two assumptions, that a mutant lac locus with residual function allows growth if its copy number is increased, and that true reversion events are made more likely by replication of chromosomes with many copies of the locus. Apparent directed mutability, its recombination requirement, and its apparent independence of cell growth are all accounted for by the model. Evidence is provided for the required residual function and gene amplification.
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Affiliation(s)
- D I Andersson
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
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Stambuk S, Radman M. Mechanism and control of interspecies recombination in Escherichia coli. I. Mismatch repair, methylation, recombination and replication functions. Genetics 1998; 150:533-42. [PMID: 9755187 PMCID: PMC1460348 DOI: 10.1093/genetics/150.2.533] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A genetic analysis of interspecies recombination in Escherichia coli between the linear Hfr DNA from Salmonella typhimurium and the circular recipient chromosome reveals some fundamental aspects of recombination between related DNA sequences. The MutS and MutL mismatch binding proteins edit (prevent) homeologous recombination between these 16% diverged genomes by at least two distinct mechanisms. One is MutH independent and presumably acts by aborting the initiated recombination through the UvrD helicase activity. The RecBCD nuclease might contribute to this editing step, presumably by preventing reiterated initiations of recombination at a given locus. The other editing mechanism is MutH dependent, requires unmethylated GATC sequences, and probably corresponds to an incomplete long-patch mismatch repair process that does not depend on UvrD helicase activity. Insignificant effects of the Dam methylation of parental DNAs suggest that unmethylated GATC sequences involved in the MutH-dependent editing are newly synthesized in the course of recombination. This hypothetical, recombination-associated DNA synthesis involves PriA and RecF functions, which, therefore, determine the extent of MutH effect on interspecies recombination. Sequence divergence of recombining DNAs appears to limit the frequency, length, and stability of early heteroduplex intermediates, which can be stabilized, and the recombinants mature via the initiation of DNA replication.
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Affiliation(s)
- S Stambuk
- Laboratoire de Mutagénèse, Institut Jacques Monod, 75251-Paris Cedex 05, France.
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40
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The possible involvement of CHI sequences in adaptive mutagenesis: Evidence from sequence analysis. J Genet 1998. [DOI: 10.1007/bf02966596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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41
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Strauss BS. Our contribution to the public fear of cancer. ENVIRONMENTAL HEALTH PERSPECTIVES 1998; 106:A312-A313. [PMID: 9734996 PMCID: PMC1533126 DOI: 10.1289/ehp.98106a312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Affiliation(s)
- B A Bridges
- MRC Cell Mutation Unit, University of Sussex, Falmer, Brighton, UK.
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43
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von Borstel RC, Savage EA, Wang Q, Hennig UG, Ritzel RG, Lee GS, Hamilton MD, Chrenek MA, Tomaszewski RW, Higgins JA, Tenove CJ, Liviero L, Hastings PJ, Korch CT, Steinberg CM. Topical reversion at the HIS1 locus of Saccharomyces cerevisiae. A tale of three mutants. Genetics 1998; 148:1647-54. [PMID: 9560384 PMCID: PMC1460089 DOI: 10.1093/genetics/148.4.1647] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mutants of the HIS1 locus of the yeast Saccharomyces cerevisiae are suitable reporters for spontaneous reversion events because most reversions are topical, that is, within the locus itself. Thirteen mutations of his1-1 now have been identified with respect to base sequence. Revertants of three mutants and their spontaneous reversion rates are presented: (1) a chain termination mutation (his1-208, née his1-1) that does not revert by mutations of tRNA loci and reverts only by intracodonic suppression; (2) a missense mutation (his1-798, née his1-7) that can revert by intragenic suppression by base substitutions of any sort, including a back mutation as well as one three-base deletion; and (3) a -1 frameshift mutation (his1-434, née his1-19) that only reverts topically by +1 back mutation, +1 intragenic suppression, or a -2 deletion. Often the +1 insertion is accompanied by base substitution events at one or both ends of a run of A's. Missense suppressors of his1-798 are either feeders or nonfeeders, and at four different locations within the locus, a single base substitution encoding an amino acid alteration will suffice to turn the nonfeeder phenotype into a feeder phenotype. Late-appearing revertants of his1-798 were found to be slowly growing leaky mutants rather than a manifestation of adaptive mutagenesis. Spontaneous revertants of his1-208 and his1-434 produced no late-arising colonies.
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Affiliation(s)
- R C von Borstel
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.
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