The Roles of a Global pH Sensor Protein ChvG in Homologous Recombination and Mutation of Agrobacterium tumefaciens Li Xiaobo (B Sc.，Nanjing University) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF BIOLOGICAL SCIENCES NATIONAL UNIVERSITY OF SINGAPORE 2006 ACKNOWLEDGEMENTS First of all, my deepest gratitude goes to my supervisor, Associate Professor Pan Shen Quan, not only for giving me the opportunity to undertake this interesting project but also for his patience, encouragement, practical and professional guidance throughout my Ph D candidature Secondly, I would like to express my heartfelt gratitude to Professor Wong Sek Man, for his patient guidance on my research project I also appreciate A/P Hong Yunhan, A/P Ge Ruowen, Assistant Professor Low Boon Chuan and Assistant Professor Yu Hao for giving me instructions during my study I would also like to thank the following friends and members in my laboratory who have helped me in one way or another: Alan John Lowton, Chang Limei, Guo Minliang, Hou Qingming, Jia Yonghui, Li Luoping, Lin Su, Qian Zhuolei, Tan Lu Wee, Sun Deying, Tang Hock Chun, Tu Haitao, Wang Long, and Yang Kun Special thanks are given to Alan and Hock Chun for proofreading this thesis I want to thank the friends from other laboratories who have assisted me in many ways too Finally, I thank the National University of Singapore for awarding me a research scholarship to carry out this interesting project i TABLE OF CONTENTS Acknowledgements i Table of Contents ii Summary vii List of Tables ix List of Figures x List of Abbreviations Chapter Literature Review 1.1 Overview of homologous recombination xii 1.1.1 Biochemical models of homologous recombination: (i) DNA strand invasion mechanism 1.1.2 Biochemical models of homologous recombination: (ii) DNA strandannealing mechanism 1.2 Overview of premutagenic damage causes 12 1.2.1 Replication errors made during normal DNA synthesis 13 1.2.2 Spontaneous DNA lesion 16 1.3 Overview of adaptive mutation 20 1.3.1 The beginning of modern adaptive mutation study 20 1.3.2 Classical lac reversion model of adaptive mutation in E coli 22 1.3.3 Features of adaptive point mutation in the classical lac system in E 24 1.3.4 Adaptive point mutation requires homologous recombination proteins 24 1.3.5 Adaptive mutation in FC40 requires conjugal function but not actual conjugation 26 1.3.6 Adaptive mutation produces mostly −1 deletion in small nucleotide repeats 28 1.3.7 SOS response regulates adaptive mutation 30 1.3.8 Mismatch repair is limited transiently during adaptive mutation 32 coli ii 1.3.8.1 Overview of mismatch directed repair 32 1.3.8.2 MutL becomes limiting during stationary-phase mutation 33 1.3.8.3 Study of mismatch repair in stationary phase in other assay 36 system 1.3.9 Hypermutation sub-population 38 1.3.10 Features of adaptive amplification in classical lac system in E coli 41 1.3.10.1 Hypothesis that adaptive amplification is the intermediate of point mutation 43 1.3.10.2 Evidence showing that adaptive amplification is a separate strategy 44 1.4 Overview of two-component system 45 1.4.1 General overview of two-component systems in prokaryotic cells 46 1.4.2 Structure and activities of sensor histidine protein kinase (HPK) 51 1.4.2.1 The kinase core module 51 1.4.2.2 Sensing domain 53 1.4.3 Linker domain 53 1.4.4 Structure and activities of response regulator proteins (RRs) 54 1.4.5 Two-component systems identified in A tumefaciens 55 1.4.5.1 VirA/VirG is the first two-component system identified in A tumefaciens 56 1.4.5.2 ChvG/ChvI is the second two-component system detected in A tumefaciens 57 1.5 Objectives of this study Chapter General Materials and Methods 61 63 2.1 Bacterial strains, plasmids, media and antibiotics 63 2.2 DNA manipulations 69 iii 2.2.1 Plasmid DNA preparation 69 2.2.2 Genomic DNA preparation from Agrobacterium 69 2.2.3 DNA digestion 70 2.2.4 Polymerase chain reaction 70 2.2.5 DNA gel electrophoresis and purification 72 2.2.6 Preparation of competent E coli cells 73 2.2.7 Transformation of E coli 74 2.2.8 Sequencing 74 Chapter ChvG can affect homologous recombination 75 3.1 Introduction 75 3.2 Materials and methods 76 3.2.1 Tri-parental mating 76 3.2.2 Preparation of electrocompetent A tumefaciens cells 76 3.2.3 Transformation of electrocompetent A tumefaciens cells with plasmid DNA or total DNA by electroporation 77 3.3 Results 78 3.3.1 ChvG can affect of RecA-dependent homologous recombination 78 3.3.2 ChvG can also affect RecA-independent DNA recombination 83 3.3.3 ChvG does not affect recombination-independent conjugation process 84 3.4 Discussion Chapter ChvG can regulate mutation both in rapid growth phase and in starvation 4.1 Introduction 4.1.1 Overview about transposition 86 90 90 91 iv 4.1.2 Three classes of transposable elements 92 4.1.3 Regulation mechanisms of transposition in bacteria 93 4.1.4 Host factors that affect the transposition 98 4.2 Materials and methods 101 4.2.1 Mutation assay and calculation of mutation frequency 101 4.2.2 Calculation of mutation rate (µ) 101 4.2.3 Random mutagenesis of Agrobacterium tumefaciens with mini-Tn5 transposon 102 4.2.4 Selection of mini-Tn5-inserted mutants with changed mutation phenotype to tetracycline 103 4.2.5 Stationary-phase mutation assay 104 4.2.5.1 Stationary-phase mutation assay 104 4.2.5.2 Estimation of the viable cell number during stationary-phase mutation assay 105 4.2.6 Norfloxacin resistance mutation assay 106 4.2.7 Semi-quantitative RT-PCR 106 4.2.7.1 RNA fixation for Agrobacterium tumefaciens cells 106 4.2.7.2 RNA isolation from Agrobacterium tumefaciens cells 107 4.2.7.3 cDNA synthesis 108 4.2.7.4 PCR amplification using synthesized cDNA as the substrate and the comparison of the transcription level of target genes 108 4.2.8 Tetracycline accumulation assay 110 4.2.8.1 Standard absorbance curve of tetracycline solution 110 4.2.8.2 Determination of tetracycline internal accumulation 110 4.3 Results 4.3.1 Mutation at chvG locus severely lowers the tetracycline-resistance mutation frequency in MG/L rich media but not in AB minimal media 111 111 v 4.3.2 Calculation of the mutation rate of the chvG− strain and the wild type strain 117 4.3.3 Mutagenesis of A tumefaciens with mini-Tn5 transposon 119 4.3.4 chvG+ and chvG− strains show different mutation spectra 124 4.3.5 Sequence analysis of the tetracycline-resistant mutants of chvG+ and chvG− strains 132 4.3.6 No significant difference in the transcription level of Tc-resistant mutation-related genes between chvG+ and chvG− strains 135 4.3.7 No significant difference in the transcription level of two IS426 putative transposases between chvG+ and chvG− strains 138 4.3.8 Comparison of the capacity of point mutation using norfloxacin as the 142 selection force 4.3.9 ChvG can regulate stationary-phase mutation too 4.4 Discussion 147 155 4.4.1 The implication that a similar mutation level occurs at a specific locus via different mutation mechanisms in different strains 155 4.4.2 Tentative explanation for the difference in point mutation level 158 4.4.3 The potential coupling of hypermutation and transposition 162 4.4.4 Membrane permeability assay is the important control experiment in our mutation assay 165 Chapter General conclusions and future perspective 170 5.1 General conclusions 170 5.2 Future perspective 172 Reference 173 vi Summary The process of homologous recombination is essential to all organisms Yet despite the extreme importance of homologous recombination, relatively less is known about its biological regulation In the current research project, we studied the effect of ChvG, the sensor protein of ChvG-ChvI two-component system of Agrobacterium tumefaciens, on the regulation of homologous gene recombination Gene recombination efficiency was compared between chvG+ and chvG− strains, exploiting general recombination (RecA-dependent) and intramolecular recombinogenic recombination (IRR) (RecA-independent) as well chvG+ strain was found to possess a much higher DNA recombination capacity These results suggest that loss of a functional ChvG may interfere with one or more key steps of homologous recombination process Mutation is also a fundamental biological process and it drives the evolution forward However, mutation is also a complicated biological process In the current study, we took the advantage of tetR-tetA operon to explore the potential role played by ChvG protein in the regulation of mutation process occurring in A tumefaciens Our mutation assay system is superior to some conventional reverse mutation assay systems This is because that most of reversion mutation systems are not satisfactory for determining mutational spectra in that for a given mutation, there are a very limited sites and/or kinds of mutations that can produce a reversion Some important sources of mutation, such as insertion of transposable element, are usually thoroughly excluded from the study that employs the reversion system In our experiments, firstly, the mutation phenotype was compared between chvG+ strain A6007 and chvG− derivative strain A6340 It is found that if selection vii was conducted on a rich medium (MG/L), the wild type strain showed a much higher mutation frequency However on simple selective media (AB), a comparable mutation level was obtained This suggests that the fitness under selection makes the substantial contribution to the final mutation result In order to analyze the molecular basis of mutation, PCR and sequencing were utilized For wild type strain A6007, more than 90% mutants were point mutants; while for chvG− strain A6340, more than 90% mutants accorded to insertion of transposons This different mutation pattern implies that bacteria strains could have evolved to be capable to invoke to various mutation mechanisms to keep a constant mutation rate at a specific genome locus Mutation assay was further extended to the stationary-phase because there may be fundamental difference in terms of origin of mutation arising at these two growth phases To this, wild type strain and chvG− strain were starved on agar plates without readily-usable carbon source and the time course of mutation frequency and mutation spectra were tracked continuously Loss of functional ChvG was found to be able to render bacterial cells a hypermutation state during starvation In addition, at stationary phase, most of mutation occurring in chvG wild type strain was insertion-mediated, just like the situation observed in chvG− strain during exponential growth Our finding bears on the evolutionary significance because bacterial population usually spends most of its time in kinds of stress in its natural niches viii LIST OF TABLES Table 1.1 Recombination components Table 2.1 Bacterial strains and plasmids 64 Table 2.2 Media preparation 66 Table 2.3 Antibiotics and other stock solutions used in this study 68 Table 3.1 The efficiency or frequency of homologous recombination, IRR, conjugation and mutation 82 Table 4.1 Host factors involved in transposition 100 Table 4.2 Tetracycline-resistance mutation frequency and the effect of composition of the growth media or selection media on mutation frequency 116 Table 4.3 Fluctuation assay 118 Table 4.4 Mutation phenotypes derivative strains Table 4.5 Mutation spectra and the distribution of various mutations 131 Table 4.6 Mutation capacity of mini-Tn5-inserted derivative strains of A6007 146 Table 4.7 Time course of mutation under starvation 154 of mini-Tn5-containing A6007 123 ix Huisman O., Errada PR, Signon L and Kleckner N 1989 Mutational analysis of IS10's outside end EMBO J 8(7):2101-9 Ilves H., Horak R and Kivisaar M 2001 Involvement of sigma(S) in starvationinduced transposition of Pseudomonas putida transposon Tn4652 J Bacteriol 183:5445-8 Inoue M., Kamiya H., Fujikawa K., OotsuyamaY., Murata-Kamiya N et al 1998 Induction of chromosomal gene mutations in Escherichia coli by direct incorporation of oxidatively damaged nucleotides New evaluation method for mutagenesis by damaged DNA precursors in vivo J Biol Chem 273:11069–74 Inoue, H., Nojima, H., and Okayama, H 1990 High efficiency transformation of Escherichia coli with plasmids Gene 96: 23-26 Jaruga P and Dizdaroglu M 1996 Repair of products of oxidative DNA base damage in human cells Nucleic Acids Res 24:1389-94 Jia Y H., Li L P., Hou Q M and Shen Q Pan 2002 An Agrobacterium gene involved in tumorigenesis encodes an outer membrane protein exposed on the bacterial cell surface Gene 284: 113-124 Jiang ZY, Rushing BG, Bai Y., Gest H and Bauer CE 1998 Isolation of Rhodospirillum centenum mutants defective in phototactic colony motility by transposon mutagenesis J Bacteriol.180(5):1248-55 Jin S., Roitsch T., Ankenbauer RG, Gordon MP and Nester EW 1990a The VirA protein of Agrobacterium tumefaciens is autophosphorylated and is essential for vir gene regulation J Bacteriol 172: 525-530 Jin S., Prusti RK, Roitsch T., Ankenbauer RG and Nester EW 1990b Phospharylation of the VirG protein of Agrobacterium tumefaciens by the autophosphorylated VirA protein: essential role in biological activity of VirG J Bacteriol 172: 4945-4950 Jin S., Roitsch T., Christie PJ and Nester EW 1990c The regulatory VirG protein specifically binds to a cis-acting regulatory sequence involved in transcriptional activation of Agrobacterium tumefaciens virulence genes J Bacteriol 172: 531-537 Johnson RC and Reznikoff WS 1983 DNA sequences at the ends of transposon Tn5 required for transposition Nature 304:280-2 Joseph JW and Kolodner R 1983 Exonuclease VIII of Escherichia coli I Purification and physical properties J Biol Chem 258:10411-7 Jourlin C., Bengrine A., Chippaux M and Mejean V 1996 An unorthodox sensor protein (TorS) mediates the induction of the tor structural genes in response to trimethylamine N-oxide in Escherichia coli Mol Microbiol 20:1297-306 181 Joyce CM, Kelley WS and Grindley ND 1982 Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I J Biol Chem 257:1958-64 Kamiya H and Kasai H 1995 Formation of 2-hydroxydeoxyadenosine triphosphate, an oxidatively damaged nucleotide, and its incorporation by DNA polymerases Steady-state kinetics of the incorporation J Biol Chem 270:19446-50 Kamiya H and Kasai H 1997b Substitution and deletion mutations induced by 2hydroxyadenine in Escherichia coli: effects of sequence contexts in leading and lagging strands Nucleic Acids Res 25:304-11 Kamiya H and Kasai H 1997a Mutations induced by 2-hydroxyadenine on a shuttle vector during leading and lagging strand syntheses in mammalian cells Biochemistry 36:11125-30 Karem K and Foster JW 1993 The influence of DNA topology on the environmental regulation of a pH-regulated locus in Salmonella typhimurium Mol Microbiol 10:75-86 Karran P and Lindahl T 1980 Hypoxanthine in deoxyribonucleic acid: generation by heat-induced hydrolysis of adenine residues and release in free form by a deoxyribonucleic acid glycosylase from calf thymus Biochemistry19:6005-11 Kasai H and Nishimura S 1984 Hydroxylation of deoxyguanosine at the C-8 position by ascorbic acid and other reducing agents Nucleic Acids Res 12:2137-45 Keim P and Lark KG 1990 The RecE recombination pathway mediates recombination between partially homologous DNA sequences: structural analysis of recombination products J Struct Biol 104:97-106 Kittle JD, Simons RW, Lee J and Kleckner N 1989 Insertion sequence IS10 antisense pairing initiates by an interaction between the 5' end of the target RNA and a loop in the anti-sense RNA J Mol Biol 210:561-72 Kleckner N 1990 Regulation of transposition in bacteria Annu Rev Cell Biol 6:297-327 Koch AL 1971 The adaptive responses of Escherichia coli to a feast and famine existence Microb Physiol 6:147-217 Konforti BB and Davis RW 1987 3' homologous free ends are required for stable joint molecule formation by the RecA and single-stranded binding proteins of Escherichia coli Proc Natl Acad Sci U S A 84:690-4 Konforti BB and Davis RW 1990 The preference for a 3' homologous end is intrinsic to RecA-promoted strand exchange J Biol Chem 265:6916-20 Kolodner RD 1995 Mismatch repair: mechanisms and relationship to cancer susceptibility Trends Biochem Sci 20:397-401 182 Kornberg A and Baker TA 1992 DNA Replication (Freeman, New York), 2nd Ed Kornberg RD and Lorch Y 1995 Interplay between chromatin structure and transcription Curr Opin Cell Biol 7:371-5 Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD and Rehrauer WM 1994 Biochemistry of homologous recombination in Escherichia coli Microbiol Rev 58:401-65 Kramer W., Kramer B., Williamson MS and Fogel S 1989 Cloning and nucleotide sequence of DNA mismatch repair gene PMS1 from Saccharomyces cerevisiae: homology of PMS1 to procaryotic MutL and HexB J Bacteriol 171:5339-46 Kruklitis R and Nakai H Participation of the bacteriophage Mu A protein and host factors in the initiation of Mu DNA synthesis in vitro J Biol Chem 269(23):1646977 Kuan CT and Tessman I 1991 LexA protein of Escherichia coli represses expression of the Tn5 transposase gene J Bacteriol 173(20):6406-10 Kunkel TA 1993 Nucleotide repeats Slippery DNA and diseases Nature 365:207–8 Kunkel TA and Erie DA 2005 DNA mismatch repair Annu Rev Biochem 74:681710 Kunkel TA, Patel SS and Johnson KA 1994 Error-prone replication of repeated DNA sequences by T7 DNA polymerase in the absence of its processivity subunit Proc Natl Acad Sci USA 91:6830–34 Labes M., Puhler A and Simon R 1990 A new family of RSF1010-derived expression and lac-fusion broad-host-range vectors for gram-negative bacteria Gene 89(1):37-46 Lanka E and Wilkins BM 1995 DNA processing reactions in bacterial conjugation Annu Rev Biochem 64:141-69 Lauster R., Reynaud CA, Martensson IL, Peter A., Bucchini D., Jami J and Weill JC 1993 Promoter, enhancer and silencer elements regulate rearrangement of an immunoglobulin transgene EMBO J 12:4615-23 Lavoie BD and Chaconas G 1994 A second high affinity HU binding site in the phage Mu transpososome J Biol Chem 269:15571-6 Layton JC and Foster PL 2003 Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS, in Escherichia coli Mol Microbiol 50:549-61 Lea DE and Coulson CA 1949 The distribution of the numbers of mutants in bacterial populations J Genetics 49:264-285 183 Leroux B., Yanofsky MF, Winans SC, Ward JE, Ziegler SF and Nester EW 1987 Characterization of the virA locus of Agrobacterium tumefaciens: a transcriptional regulator and host range determinant EMBO J 6: 849-856 Levchenko I., Luo L., Baker TA 1995 Disassembly of the Mu transposase tetramer by the ClpX chaperone Genes Dev 9(19):2399-408 Li Luoping, PhD thesis National University of Singapore Singapore 2001 Li L., Jia Y., Hou Q., Charles TC, Nester EW and Pan SQ 2002 A global pH sensor: Agrobacterium sensor protein ChvG regulates acid-inducible genes on its two chromosomes and Ti plasmid Proc Natl Acad Sci U S A 99:12369-74 Lieb M and Rehmat S 1995 Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins J Bacteriol 177:660-6 Lindahl T 1967 Irreversible heat inactivation of transfer ribonucleic acids J Biol Chem 242:1970-3 Lindahl T and Nyberg B 1972 Rate of depurination of native deoxyribonucleic acid Biochemistry 11:3610-8 Lindahl T and Nyberg B 1974 Heat-induced deamination of cytosine residues in deoxyribonucleic acid Biochemistry 13:3405-10 Lindahl T 1993 Instability and decay of the primary structure of DNA Nature 362:709-15 Ljungman M and Hanawalt PC 1992 Efficient protection against oxidative DNA damage in chromatin Mol Carcinog 5:264-9 Lloyd RG and Sharples GJ 1993 Dissociation of synthetic Holliday junctions by E coli RecG protein EMBO J.12:17-22 Longerich S., Galloway AM, Harris RS, Wong C and Rosenberg SM 1995 Adaptive mutation sequences reproduced by mismatch repair-deficiency Proc Natl Acad Sci USA 92:12017–20 Loomis WF, Shaulsky G and Wang N 1997 Histidine kinases in signal transduction pathways of eukaryotes J Cell Sci 110:1141-5 Lovett ST, Luisi-DeLuca C and Kolodner RD 1988 The genetic dependence of recombination in recD mutants of Escherichia coli Genetics 120:37-45 Lavoie BD and Chaconas G 1994 A second high affinity HU binding site in the phage Mu transpososome J Biol Chem 269(22):15571-6 Lukat GS, Lee BH, Mottonen JM, Stock AM and Stock JB 1991 Roles of the highly conserved aspartate and lysine residues in the response regulator of bacterial chemotaxis J Biol Chem 266: 8348-8354 184 Luo ZQ and Farrand SK 1999 Cloning and characterization of a tetracycline resistance determinant present in Agrobacterium tumefaciens C58 J Bacteriol 181:618-26 Luria SE and Delbrück M 1943 Mutations of bacteria from virus sensitivity to virus resistance Genetics 28:491-511 Lyamichev V., Brow MA and Dahlberg JE 1993 Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases Science 260:778-83 Maas WK, Wang C., Lima T., Hach A and Lim D 1996 Multicopy single-stranded DNA of Escherichia coli enhances mutation and recombination frequencies by titrating MutS protein Mol Microbiol 19:505-9 MacPhee DG 1985 Indications that mutagenesis in Salmonella may be subject to catabolite repression Mutat Res 151(1):35-41 MacPhee DG 1993 Directed mutation: paradigm postponed Mutat Res 285:109-16 Maki H 2002 Origins of spontaneous mutations: specificity and directionality of base-substitution, frameshift, and sequence-substitution mutageneses Annu Rev Genet 36: 279-303 Makino K., Shinagawa H., Amemura M., Kimura S., Nakata A and Ishihama A 1988 Regulation of the phosphate regulon of Escherichia coli: activation of pstS transcription by PhoB protein in vitro J Mol Biol 203: 85-95 Makris JC, Nordmann PL and Reznikoff WS 1990 Integration host factor plays a role in IS50 and Tn5 transposition J Bacteriol 172(3):1368-73 Mantis NJ and Winans SC 1993 The chromosomal response regulatory gene chvI of Agrobacterium tumefaciens complements an Escherichia coli phoB mutation and is required for virulence J Bacteriol 175: 6626-6636 Marger MD and Saier MH Jr 1993 A major superfamily of transmembrane facilitators that catalyse uniport, symport and antiport Trends Biochem Sci 18:1320 Marsischky GT, Filosi N., Kane MF and Kolodner R 1996 Redundancy of Saccharomyces cerevisiae MSH3 and MSH6 in MSH2-dependent mismatch repair Genes Dev.10:407-20 Martinez JL and Baquero F 2000 Mutation frequencies and antibiotic resistance Antimicrob Agents Chemother 44:1771-7 Mayr E (1982) The Growth of Biological Thought, Diversity, Evolution, and inheritance (Cambridge, MA: Belknap) McClintock B 1952 Chromosome organization and genic expression Cold Spring Harb Symp Quant Biol 16:13-47 185 McCommas SA and Syvanen M 1988 Temporal control of transposition in Tn5 J Bacteriol 170:889-94 McKenzie GJ, Harris RS, Lee PL and Rosenberg SM 2000 The SOS response regulates adaptive mutation Proc Natl Acad Sci USA 97:6646-51 McKenzie GJ, Lombardo MJ and Rosenberg SM 1998 Recombination-dependent mutation in Escherichia coli occurs in stationary phase Genetics 149:1163-5 McPartland A., Green L and Echols H 1980 Control of recA gene RNA in E coli: regulatory and signal genes Cell 20:731-7 Melchers LS., Regensburg-Tuink TJG., Bourret RB, Sedee NJA, Schilperoort RA, and Hooykaas PJJ 1989 Membrane topology and functional analysis of the sensory protein virA of Agrobacterium tumefaciens EMBO J 8: 1919-1925 Mello JA, Acharya S., Fishel R and Essigmann JM 1996 The mismatch-repair protein hMSH2 binds selectively to DNA adducts of the anticancer drug cisplatin Chem Biol 3:579-89 Metzgar D and Wills C 2000 Evidence for the adaptive evolution of mutation rates Cell 101:581-4 Michaels ML and Miller JH 1992 The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8oxoguanine) J Bacteriol 174:6321-5 Miller JH 1996 Spontaneous mutators in bacteria: insights into pathways of mutagenesis and repair Annu Rev Microbiol 50:625-43 Mizuno T 1997 Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli DNA Res 4:161-8 Mizuuchi K and Baker TA 2002 In Mobile DNA II, edited by Craig NL (2002 ASM Press, Washington, D.C.) pp.12-23 Moat et al 2002 In Microbial Physiology (Moat AL, Foster JW and Spector MP, Eds.) Wiley-Liss, Inc., New York Modrich P 1991 Mechanisms and biological effects of mismatch repair Annu Rev Genet 25:229-53 Modrich P 1994 Mismatch repair, genetic stability, and cancer Science 266:1959-60 Modrich P 1995 Mismatch repair, genetic stability and tumour avoidance Philos Trans R Soc Lond B Biol Sci 347:89-95 Morey NJ, Greene CN and Jinks-Robertson S 2000 Genetic analysis of transcriptionassociated mutation in Saccharomyces cerevisiae Genetics 154(1):109-20 186 Mortimer PG and Piddock LJ 1993 The accumulation of five antibacterial agents in porin-deficient mutants of Escherichia coli J Antimicrob Chemother 32:195-213 Msadek T 1999 When the going gets tough: survival strategies and environmental signaling networks in Bacillus subtilis Trends Microbiol 7:201-7 Müller B., Burdett I and West SC 1992 Unusual stability of recombination intermediates made by Escherichia coli RecA protein EMBO J 11(7):2685-93 Müller-Hill B and Kania J 1974 Lac repressor can be fused to β-galactosidase Nature 249:561–62 Nakagawa T., Datta A and Kolodner RD 1999 Multiple functions of MutS- and MutL-related heterocomplexes Proc Natl Acad Sci U S A 96:14186-8 Nevo-Caspi Y and Kupiec M 1994 Transcriptional induction of Ty recombination in yeast Proc Natl Acad Sci U S A 91:12711-5 New L., Liu K and Crouse GF 1993 The yeast gene MSH3 defines a new class of eukaryotic MutS homologues Mol Gen Genet 239:97-108 Nikaido H and Thanassi DG 1993 Penetration of lipophilic agents with multiple protonation sites into bacterial cells: tetracyclines and fluoroquinolones as examples Antimicrob Agents Chemother 37:1393-9 Nickoloff JA 1992 Transcription enhances intrachromosomal homologous recombination in mammalian cells Mol Cell Biol 12:5311-8 Ninfa AJ and Magasanik B 1986 Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli Proc Natl Acad Sci USA 83: 5909-5913 Nixon BT, Ronson CW and Ausubel FM 1986 Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC Proc Natl Acad Sci USA 83: 7850-7854 Nohmi T., Battista JR, Dodson LA and Walker GC 1988 RecA mediated cleavage activates UmuD for mutagenesis: mechanistic relationship between transcriptional derepression and posttranslational activation Proc Natl Acad Sci USA 85: 18161820 Okada T and Keeney S 2005 Homologous recombination: needing to have my say Curr Biol 15:R200-2 Oltz EM, Alt FW, Lin WC, Chen J., Taccioli G., Desiderio S and Rathbun G 1993 A V(D)J recombinase-inducible B-cell line: role of transcriptional enhancer elements in directing V(D)J recombination Mol Cell Biol 13:6223-30 187 Panyutin IG and Hsieh P 1993 Formation of a single base mismatch impedes spontaneous DNA branch migration J Mol Biol 230:413-24 Pansegrau W., Lanka E., Barth PT, Figurski DH, Guiney DG, Haas D, Helinski DR, Schwab H., Stanisich VA and Thomas CM 1994 Complete nucleotide sequence of Birmingham IncP alpha plasmids Compilation and comparative analysis J Mol Biol 239:623-63 Pan SQ, Charles T, Jin S., Wu Z and Nester EW 1993 Preformed dimeric state of the sensor protein VirA is involved in Plant- Agrobacterium signal transduction Proc Natl Acad Sci USA 90: 9939-9943 Pao SS, Paulsen IT and Saier MH Jr 1998 Major facilitator superfamily Microbiol Mol Biol Rev 62:1-34 Park EM, Shigenaga MK, Degan P., Korn TS, Kitzler JW, et al 1992 Assay of excised oxidative DNA lesions: isolation of 8-oxoguanine and its nucleoside derivatives from biological fluids with a monoclonal antibody column Proc Natl Acad Sci USA 89:3375–79 Park H and Inouye M 1997 Mutational analysis of the linker region of EnvZ, an osmosensor in Escherichia coli J Bacteriol 179:4382-90 Parkinson JS and Kofoid EC 1992 Communication modules in bacterial signaling proteins Annu Rev Genet 26: 71-112 Parkinson JS, Parker SR, Talbert PB and Houtsm SE 1983 Interactions between chemotaxis genes and flagellar genes in Escherichia coli J Bacteriol 155: 265-274 Pedraza-Reyes M and Yasbin RE 2004 Contribution of the mismatch DNA repair system to the generation of stationary-phase-induced mutants of Bacillus subtilis J Bacteriol 186:6485-91 Pettersson ME, Andersson DI, Roth JR and Berg OG 2005 The amplification model for adaptive mutation: simulations and analysis Genetics 169:1105-15 Phadnis SH and Berg DE 1987 Identification of base pairs in the outside end of insertion sequence IS50 that are needed for IS50 and Tn5 transposition Proc Natl Acad Sci U S A 84(24):9118-22 Phadnis SH, Sasakawa C and Berg DE 1986 Localization of action of the IS50encoded transposase protein Genetics 112:421-7 Pham PT, Olson MW, McHenry CS and Schaaper RM 1999 Mismatch extension by Escherichia coli DNA polymerase III holoenzyme J Biol Chem 274:3705–10 Ponticelli AS, Schultz DW, Taylor AF and Smith GR 1985 Chi-dependent DNA strand cleavage by RecBC enzyme Cell 41:145-51 188 Powell BS and Kado CI 1990 Specific binding of VirG to the vir box requires a Cterminal domain and exhibits a minimum concentration threshold Mol Microbiol 12:2159-66 Prival MJ and Cebula T 1996 Adaptive mutation and slow-growing revertants of an Escherichia coli lacZ amber mutant Genetics 144:1337–41 Prolla TA, Christie DM and Liskay RM 1994 Dual requirement in yeast DNA mismatch repair for MLH1 and PMS1, two homologs of the bacterial mutL gene Mol Cell Biol 14:407-15 Pugsley AP and Schnaitman CA 1978 Identification of three genes controlling production of new outer membrane pore proteins in Escherichia coli K-12 J Bacteriol 135:1118-29 Purmal AA, Kow YW and Wallace SS 1994 Major oxidative products of cytosine, 5-hydroxycytosine and 5-hydroxyuracil, exhibit sequence context-dependent mispairing in vitro Nucleic Acids Res 22:72-8 Ryan FJ 1959 Bacterial mutation in stationary phase and the question of cell turnover J Gen Microbiol 21:530–49 Radicella JP, Park PU and Fox MS 1995 Adaptive mutation in Escherichia coli: a role for conjugation Science 268:418–20 Radman M and Wagner R 1988 The high fidelity of DNA duplication Sci Am 259:40-6 Raleigh EA and Kleckner N 1986 Quantitation of insertion sequence IS10 transposase gene expression by a method generally applicable to any rarely expressed gene Proc Natl Acad Sci U S A 83:1787-91 Reece RJ and Maxwell A 1991 The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein Nucleic Acids Res 19:1399-405 Reenan RA and Kolodner RD 1992 Isolation and characterization of two Saccharomyces cerevisiae genes encoding homologs of the bacterial HexA and MutS mismatch repair proteins Genetics 32:963-73 Register JC 3rd and Griffith J 1985 The direction of RecA protein assembly onto single strand DNA is the same as the direction of strand assimilation during strand exchange J Biol Chem 260:12308-12 Resnick MA 1976 The repair of double-strand breaks in DNA; a model involving recombination J Theor Biol 59(1):97-106 Reynolds AE, Felton J and Wright A 1981 Insertion of DNA activates the cryptic bgl operon in E coli K12 Nature 293:625-9 189 Ripley LS 1990 Frameshift mutation: determinants of specificity Annu Rev Genet 24:189–213 Roberts D., Hoopes BC, McClure WR and Kleckner N 1985 IS10 transposition is regulated by DNA adenine methylation Cell 43:117-30 Ronson CW, Nixon BT and Ausubel F 1987 Conserved domains in bacterial regulatory proteins that respond to environmental stimuli Cell 49: 579-581 Rosche WA and Foster PL 1999 The role of transient hypermutators in adaptive mutation in Escherichia coli Proc Natl Acad Sci U S A 96:6862-7 Rosche WA and Foster PL 2000 Determining mutation rates in bacterial populations Methods 20:4-17 Rosenberg SM 2001 Evolving responsively: adaptive mutation Nat Rev Genet 2:504-15 Rosenberg SM, Harris RS and Torkelson J 1995 Molecular handles on adaptive mutation Mol Microbiol 18:185-9 Ross-Macdonald P and Roeder GS 1994 Mutation of a meiosis-specific MutS homolog decreases crossing over but not mismatch correction Cell 79:1069-80 Roth JR, Benson N., Galitski T., Haack K., Lawrence JG and Meisel L (1996) Rearrangements of the bacterial chromosome: formation and applications In Escherichia coli and Salmonella Cellular and Molecular Biology, F.C Neidhardt, R Curtiss, J.L Ingraham, E.C.C Lin, K.B Low, B Magasanik, W.S Reznikoff, M Riley, M Schaechter and H E Umbarger, eds (Washington, DC: ASM Press), pp 2256–2276 Ryan FJ, Okada T, and Nagata T 1963 Spontaneous mutation in spheroplasts of Escherichia coli J Gen Microbiol 30:193–99 Sambrook, J F., Fritsch, E F., and Maniatis, T 1989 Molecular cloning: A laboratory Manual Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY Schaaper RM and Dunn RL 1991 Spontaneous mutation in the Escherichia coli lacI gene Genetics 129:317-26 Schaaper RM and Radman M 1989 The extreme mutator effect of Escherichia coli mutD5 results from saturation of mismatch repair by excessive DNA replication errors EMBO J 8(11):3511-6 Schaeffer L., Roy R., Humbert S., Moncollin V., Vermeulen W., Hoeijmakers JH, Chambon P and Egly JM DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor Science 260:58-63 190 Schardl, C L., Byrd, A D., Benzion, G., Altschuler, M A., Hildebrand, D F., and Hunt, A G 1987 Design and construction of a versatile system for the expression of foreign genes in plants Gene 61: 1-11 Schnappinger D and Hillen W 1996 Tetracyclines: antibiotic action, uptake, and resistance mechanisms Arch Microbiol 165:359-69 Schnetz K and Rak B 1992 IS5: a mobile enhancer of transcription in Escherichia coli Proc Natl Acad Sci U S A 89:1244-8 Selby CP and Sancar A 1993 Molecular mechanism of transcription-repair coupling Science 260:53-8 Shapiro R 1981 In Chromosome Damage and Repair (eds Seeberg E and Kleppe K.) New York: Plenum 3pp Shapiro JA 1984 Observations on the formation of clones containing araB-lacZ cistron fusions Mol Gen Genet 194:79–90 Shapiro JA 1997 Genome organization, natural genetic engineering and adaptive mutation Trends Genet 13:98-104 Shinagawa H., Iwasaki H., Kato T and Nakata A 1988 RecA protein dependent cleavage of UmuD protein and SOS mutagenesis Proc Natl Acad Sci USA 85: 1806-1810 Signon L and Kleckner N 1995 Negative and positive regulation of Tn10/IS10promoted recombination by IHF: two distinguishable processes inhibit transposition off of multicopy plasmid replicons and activate chromosomal events that favor evolution of new transposons Genes Dev 9:1123-36 Simons RW and Kleckner N 1983 Translational control of IS10 transposition Cell 34:683-91 Sloane DL, Goodman MF and Echols H 1988 The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzyme Nucleic Acids Res 6:6465–75 Sola-Landa A., Pizarro-Cerda J., Grillo MJ, Moreno E., Moriyon I., Blasco JM, Gorvel JP and Lopez-Goni I 1998 A two-component regulatory system playing a critical role in plant pathogens and endosymbionts is present in Brucella abortus and controls cell invasion and virulence Mol Microbiol 29:125-38 Spratt BG 1989 Resistance to β-lactam antibiotics mediated by alterations of penicillin-binding proteins In Microbial Resistance to Drugs (Bryan LC, Ed.), p 77 Springer, Berlin Stahl F W 1992 ibid 132:865 191 Stahl FW, Thomason LC, Siddiqi I and Stahl MM 1990 Further tests of a recombination model in which chi removes the RecD subunit from the RecBCD enzyme of Escherichia coli Genetics 126:519-33 Stark GR and Wahl GM 1984 Gene amplification Annu Rev Biochem.53:447-91 Stewart RC 1993 Activating and inhibitory mutations in the regulatory domain of CheB, the methylesterase in bacterial chemotaxis J Biol Chem 268: 1921-1930 Stock AM, Robinson VL and Goudreau PN 2000 Two-component signal transduction Annu Rev Biochem 69:183-215 Suarez, A., Guttler, A., Stratz, M., Staendner, L H., Timmis, K N., and Guzman, C A 1997 Green fluorescent protein-based reporter systems for genetic analysis of bacteria including monocopy applications Gene 196:69-74 Sung HM and Yasbin RE 2000 Transient growth requirement in Bacillus subtilis following the cessation of exponential growth Appl Environ Microbiol 66:1220-2 Sung HM and Yasbin RE 2002 Adaptive, or stationary-phase, mutagenesis, a component of bacterial differentiation in Bacillus subtilis J Bacteriol 184:5641-53 Symington LS 2002 Role of RAD52 epistasis group genes in homologous recombination and double-strand break repair Microbiol Mol Biol Rev 66(4):63070 Szostak JW, Orr-Weaver TL, Rothstein RJ and Stahl FW 1983 The double-strandbreak repair model for recombination Cell 33:25-35 Taddei F., Matic I and Radman M 1995 cAMP-dependent SOS induction and mutagenesis in resting bacterial populations Proc Natl Acad Sci USA 92:11736-40 Tajiri T, Maki H and Sekiguchi M 1995 Functional cooperation of MutT, MutM and MutY proteins in preventing mutations caused by spontaneous oxidation of guanine nucleotide in Escherichia coli Mutat Res 336:257–67 Tang M., Shen X., Frank EG., O’Donnell M., Woodgate R and Goodman MF 1999 UmuD'(2)C is an error-prone DNA polymerase, Escherichia coli pol V Proc Natl Acad Sci USA 96:8919–8924 Taylor A and Smith GR 1980 Unwinding and rewinding of DNA by the recBC enzyme Cell 22: 447-457 Thaler DS, Sampson E., Siddiqi I., Rosenberg SM, Thomason LC, Stahl FW and Stahl MM 1989 Recombination of bacteriophage lambda in recD mutants of Escherichia coli Genome 31:53-67 Thaler DS and Stahl FW 1988 DNA double-chain breaks in recombination of phage lambda and of yeast Annu Rev Genet 22:169-97 192 Thanassi DG, Suh GS and Nikaido H 1995 Role of outer membrane barrier in efflux-mediated tetracycline resistance of Escherichia coli J Bacteriol 177:998-1007 Tlsty TD, Albertini AM and Miller JH 1984 Gene amplification in the lac region of E coli Cell 37:217-24 Thomas BJ and Rothstein R 1989 Elevated recombination rates in transcriptionally active DNA Cell 56:619-30 Tlsty TD, Margolin BH and Lum K 1989 Differences in the rates of gene amplification in nontumorigenic and tumorigenic cell lines as measured by Luria– Delbrück fluctuation analysis Proc Natl Acad Sci USA 86:9441–9445 Tokishita S-I, and Mizuno T 1994 Transmembrane signal transduction by the Escherichia coli osmotic sensor, EnvZ: intermolecular complementation of transmembrane signaling Mol Microbiol 13: 435-444 Torkelson J., Harris RS, Lombardo MJ, Nagendran J., Thulin C and Rosenberg SM 1997 Genome-wide hypermutation in a subpopulation of stationary-phase cells underlies recombination-dependent adaptive mutation EMBO J.16:3303-11 Tsaneva IR, Muller B and West SC 1992 ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E coli Cell 69:117180 Twiss E., Coros AM, Tavakoli NP and Derbyshire KM 2005 Transposition is modulated by a diverse set of host factors in Escherichia coli and is stimulated by nutritional stress Mol Microbiol 57:1593-607 Umezu K., Nakayama K and Nakayama H 1990 Escherichia coli RecQ protein is a DNA helicase Proc Natl Acad Sci U S A 87:5363-7 Vanderleyden J., Desair J., De Meirsman C., Michiels K, Van Gool AP, Chilton MD and Jen GC 1986 Nucleotide sequence of an insertion sequence (IS) element identified in the T-DNA region of a spontaneous variant of the Ti-plasmid pTiT37 Nucleic Acids Res 14:6699-709 Volz K 1993 Structural conservation in the CheY superfamily Biochemistry 32:11741-53 Wagner J., Gruz P., Kim SR., Yamada M., Matsui K., Fuchs RP and Nohmi T 1999 The dinB gene encodes a novel E coli DNA polymerase, DNA polIV, involved in mutagenesis Mol Cell 4:281–286 Weinreich MD, Makris JC and Reznikoff WS 1991 Induction of the SOS response in Escherichia coli inhibits Tn5 and IS50 transposition J Bacteriol 173(21):6910-8 193 Weinreich MD and Reznikoff WS 1992 Fis plays a role in Tn5 and IS50 transposition J Bacteriol.174(14):4530-7 Weinstock GM, McEntee K and Lehman IR 1979 ATP-dependent renaturation of DNA catalyzed by the recA protein of Escherichia coli Proc Natl Acad Sci U S A 76:126-30 Weiss V and Magasanik B 1988 Phosphorylation of nitrogen regulator I (NRI) of Escherichia coli Proc Natl Acad Sci USA 85: 8919-8923 West AH and Stock AM 2001 Histidine kinases and response regulator proteins in two-component signaling systems Trends Biochem Sci 26:369-76 West SC, Cassuto E and Howard-Flanders P 1982 Postreplication repair in E coli: strand exchange reactions of gapped DNA by RecA protein Mol Gen Genet 187:209-17 Westerhoff HV, O'Dea MH, Maxwell A and Gellert M 1988 DNA supercoiling by DNA gyrase A static head analysis Cell Biophys 12:157-81 Whitby MC and Lloyd RG 1995 Branch migration of three-strand recombination intermediates by RecG, a possible pathway for securing exchanges initiated by 3'tailed duplex DNA EMBO J 14:3302-10 Whitby MC, Ryder L and Lloyd RG 1993 Reverse branch migration of Holliday junctions by RecG protein: a new mechanism for resolution of intermediates in recombination and DNA repair Cell 75:341-50 Wiater LA, Grindley ND 1990 Integration host factor increases the transpositional immunity conferred by gamma delta ends J Bacteriol.172(9):4951-8 Winans SC 1992 Two-way chemical signaling in Agrobacterium-pant interactions Microbiol Rev 56: 12-31 Winans SC, Ebert PR, Stachel SE, Gordon MP and Nester EW 1986 A gene essential for Agrobacterium virulence is homologous to a family of positive regulatory loci Proc Natl Acad Sci USA 83: 8278-8282 Winans SC, Kerstetter RA, Ward JE and Nester EW 1989 A protein required for transcriptional regulation of Agrobacterium virulence genes spans the cytoplasmic membrane J Bacteriol 171: 1616-1622 Winans SC, Mantis NJ, Chen CY, Chang CH and Han D-C 1994 Host recognition by the VirA, VirG two-component regulatory proteins of Agrobacterium tumefaciens Research in Microbiol 145: 461-473 Windle BE and Wahl GM 1992 Molecular dissection of mammalian gene amplification: new mechanistic insights revealed by analyses of very early events Mutat Res 276:199-224 194 Wood RD and Lindahl T 1990 Xeroderma pigmentosum A gene for tumour prevention Nature 348:13-4 Xu, X Q., and Pan, S Q 2000 An Agrobacterium catalase is a virulence factor involved in tumorigenesis Mol Microbiol 35: 407-414 Yamaguchi A., Iwasaki-Ohba Y., Ono N., Kaneko-Ohdera M and Sawai T 1991 Stoichiometry of metal-tetracycline/H+ antiport mediated by transposon Tn10encoded tetracycline resistance protein in Escherichia coli FEBS Lett 282:415-8 Yasuda T., Morimatsu K., Horii T., Nagata T and Ohmori H 1998 Inhibition of Escherichia coli RecA coprotease activities by DinI EMBO J 17:3207-16 Yin JC and Reznikoff WS 1988 p2 and inhibition of Tn5 transposition J Bacteriol 170:3008-15 Yoshida H., Bogaki M., Nakamura M and Nakamura S 1990 Quinolone resistancedetermining region in the DNA gyrase gyrA gene of Escherichia coli Antimicrob Agents Chemother 34:1271-2 Yoshida H., Nakamura M., Bogaki M., Ito H., Kojima T., Hattori H and Nakamura S 1993 Mechanism of action of quinolones against Escherichia coli DNA gyrase Antimicrob Agents Chemother 37:839-45 Yoshiyama K., Higuchi K., Matsumura H and Maki H 2001 Directionality of DNA replication fork movement strongly affects the generation of spontaneous mutations in Escherichia coli J Mol Biol 307:1195-206 Zahrt TC, Mora GC and Maloy S 1994 Inactivation of mismatch repair overcomes the barrier to transduction between Salmonella typhimurium and Salmonella typhi J Bacteriol 176:1527-9 Zerbib D., Polard P., Escoubas JM, Galas D and Chandler M 1990 The regulatory role of the IS1-encoded InsA protein in transposition Mol Microbiol 4:471-7 Zhao X., Xu C., Domagala J., Drlica K 1997 DNA topoisomerase targets of the fluoroquinolones: a strategy for avoiding bacterial resistance Proc Natl Acad Sci U S A 94:13991-6 195 ... Adenine is deaminated to hypoxanthine in DNA at only 2-3% of the rate of cytosine deamination and the deamination of guanine to xanthine is even smaller than that for adenine (Karran and Lindahl, 1980)... tetracycline and 143 x norfloxacin Fig 4.13 Starvation mutation assay 149 Fig 4.14 Mutation pattern at stationary phase 152 Fig 4.15 Growth curve of the chvG+ strain A6 007 and the chvG? ?? strain A6 340... description in 1991 (Cairns and Foster, 1991), FC40 has become the most popular strain in the study of adaptive mutation The reason is clear: the abundance of adaptive lac+ mutations that appear makes the