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Drugs 34 Suppl 2:64-88

149. MacLean, R. C., G. Bell, and P. B. Rainey. 2004. The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proc Natl Acad Sci U S A 101:8072-7.

150. Macvanin, M., J. Bjorkman, S. Eriksson, M. Rhen, D. I. Andersson, and D.

Hughes. 2003. Fusidic acid-resistant mutants of Salmonella enterica serovar Typhimurium with low fitness in vivo are defective in RpoS induction. Antimicrob Agents Chemother 47:3743-9.

151. Maisnier-Patin, S., and D. I. Andersson. 2004. Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution. Res Microbiol 155:360-9.

152. Maisnier-Patin, S., O. G. Berg, L. Liljas, and D. I. Andersson. 2002.

Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium. Mol Microbiol 46:355-66.

153. Mao, E. F., L. Lane, J. Lee, and J. H. Miller. 1997. Proliferation of mutators in A cell population. J Bacteriol 179:417-22.

154. Margolis, P., C. Hackbarth, S. Lopez, M. Maniar, W. Wang, Z. Yuan, R.

White, and J. Trias. 2001. Resistance of Streptococcus pneumoniae to deformylase inhibitors is due to mutations in defB. Antimicrob Agents Chemother 45:2432-5.

155. Margolis, P. S., C. J. Hackbarth, D. C. Young, W. Wang, D. Chen, Z. Yuan, R. White, and J. Trias. 2000. Peptide deformylase in Staphylococcus aureus: resistance to inhibition is mediated by mutations in the formyltransferase gene. Antimicrob Agents Chemother 44:1825-31.

156. Mastroeni, P., and M. Sheppard. 2004. Salmonella infections in the mouse model:

host resistance factors and in vivo dynamics of bacterial spread and distribution in the tissues. Microbes Infect 6:398-405.

157. Matic, I., M. Radman, F. Taddei, B. Picard, C. Doit, E. Bingen, E. Denamur, and J. Elion. 1997. Highly variable mutation rates in commensal and pathogenic Escherichia coli. Science 277:1833-4.

158. Matic, I., F. Taddei, and M. Radman. 2004. Survival versus maintenance of genetic stability: a conflict of priorities during stress. Res Microbiol 155:337-41.

159. Matthews, R. G. 1996. One-Carbon Metabolism, p. 600-611. In F. V. e. a.

Neidhardt (ed.), Escherichia coli and Salmonella Cellular and Molecular Biology, 2 ed, vol. 1. ASM Press, Washington, DC.

160. Maynard-Smith, J., and J. Haigh. 1974. Hitchhiking effect of a favourable gene.

Genet Res 23:23-25.

161. Mazodier, P., and J. Davies. 1991. Gene transfer between distantly related bacteria. Annu Rev Genet 25:147-71.

162. McClelland, M., K. E. Sanderson, J. Spieth, S. W. Clifton, P. Latreille, L.

Courtney, S. Porwollik, J. Ali, M. Dante, F. Du, S. Hou, D. Layman, S.

Leonard, C. Nguyen, K. Scott, A. Holmes, N. Grewal, E. Mulvaney, E. Ryan, H. Sun, L. Florea, W. Miller, T. Stoneking, M. Nhan, R. Waterston, and R. K.

Wilson. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852-6.

163. McKenzie, G. J., and S. M. Rosenberg. 2001. Adaptive mutations, mutator DNA polymerases and genetic change strategies of pathogens. Curr Opin Microbiol 4:586-164. Merkel, T. J., J. L. Dahl, R. H. Ebright, and R. J. Kadner. 1995. Transcription 94.

activation at the Escherichia coli uhpT promoter by the catabolite gene activator protein. J Bacteriol 177:1712-8.

165. Miesel, L., D. A. Rozwarski, J. C. Sacchettini, and W. R. Jacobs, Jr. 1998.

Mechanisms for isoniazid action and resistance. Novartis Found Symp 217:209-20;

166. Miller, J. H. 1996. Spontaneous mutators in bacteria: insights into pathways of mutagenesis and repair. Annu Rev Microbiol 50:625-43.

167. Miller, J. H., A. Suthar, J. Tai, A. Yeung, C. Truong, and J. L. Stewart. 1999.

Direct selection for mutators in Escherichia coli. J Bacteriol 181:1576-84.

168. Minassian, M. A., D. A. Lewis, D. Chattopadhyay, B. Bovill, G. J.

Duckworth, and J. D. Williams. 1998. A comparison between single-dose fosfomycin trometamol (Monuril) and a 5-day course of trimethoprim in the treatment of uncomplicated lower urinary tract infection in women. Int J Antimicrob Agents 10:39-47.

169. Mira, A., and N. A. Moran. 2002. Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria. Microb Ecol 44:137-170. Mira, A., H. Ochman, and N. A. Moran. 2001. Deletional bias and the evolution 43.

of bacterial genomes. Trends Genet 17:589-96.

171. Modrich, P. 1991. Mechanisms and biological effects of mismatch repair. Annu Rev Genet 25:229-53.

172. Modrich, P. 1989. Methyl-directed DNA mismatch correction. J Biol Chem 264:6597-600.

173. Moran, N. A. 1996. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A 93:2873-8.

174. Moran, N. A. 2002. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108:583-6.

175. Moran, N. A. 2003. Tracing the evolution of gene loss in obligate bacterial symbionts. Curr Opin Microbiol 6:512-8.

176. Moran, N. A., and A. Mira. 2001. The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol 2:RESEARCH0054.

177. Moran, N. A., G. R. Plague, J. P. Sandstrom, and J. L. Wilcox. 2003. A genomic perspective on nutrient provisioning by bacterial symbionts of insects. Proc Natl Acad Sci U S A 100 Suppl 2:14543-8.

178. Moran, N. A., and J. J. Wernegreen. 2000. Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends in Ecology and Evolution 15:321-326.

179. Muller, H. J. 1964. The Relation of Recombination to Mutational Advance. Mutat Res 106:2-9.

180. Mushegian, A. R., and E. V. Koonin. 1996. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 93:10268-73.

181. Nagaev, I., J. Bjorkman, D. I. Andersson, and D. Hughes. 2001. Biological cost and compensatory evolution in fusidic acid-resistant Staphylococcus aureus. Mol Microbiol 40:433-9.

182. Napolitano, R., R. Janel-Bintz, J. Wagner, and R. P. Fuchs. 2000. All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis. Embo J 19:6259-65.

183. Newton, D. T., C. Creuzenet, and D. Mangroo. 1999. Formylation is not essential for initiation of protein synthesis in all eubacteria. J Biol Chem 274:22143-184. Notley-McRobb, L., and T. Ferenci. 2000. Experimental analysis of molecular 6.

events during mutational periodic selections in bacterial evolution. Genetics 156:1493-501.

185. Notley-McRobb, L., S. Seeto, and T. Ferenci. 2002. Enrichment and elimination of mutY mutators in Escherichia coli populations. Genetics 162:1055-62.

186. Ohl, M. E., and S. I. Miller. 2001. Salmonella: a model for bacterial pathogenesis.

Annu Rev Med 52:259-74.

187. Olekhnovich, I. N., J. L. Dahl, and R. J. Kadner. 1999. Separate contributions of UhpA and CAP to activation of transcription of the uhpT promoter of Escherichia coli.

J Mol Biol 292:973-86.

188. Oliver, A., R. Canton, P. Campo, F. Baquero, and J. Blazquez. 2000. High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection.

Science 288:1251-4.

189. Oosterom, J. 1991. Epidemiological studies and proposed preventive measures in the fight against human salmonellosis. Int J Food Microbiol 12:41-51.

190. Orr, H. A. 2003. The distribution of fitness effects among beneficial mutations.

Genetics 163:1519-26.

191. Palmer, B. R., and M. G. Marinus. 1994. The dam and dcm strains of Escherichia coli--a review. Gene 143:1-12.

192. Parkhill, J., G. Dougan, K. D. James, N. R. Thomson, D. Pickard, J. Wain, C.

Churcher, K. L. Mungall, S. D. Bentley, M. T. Holden, M. Sebaihia, S. Baker, D. Basham, K. Brooks, T. Chillingworth, P. Connerton, A. Cronin, P. Davis, R. M. Davies, L. Dowd, N. White, J. Farrar, T. Feltwell, N. Hamlin, A.

Haque, T. T. Hien, S. Holroyd, K. Jagels, A. Krogh, T. S. Larsen, S. Leather, S. Moule, P. O'Gaora, C. Parry, M. Quail, K. Rutherford, M. Simmonds, J.

Skelton, K. Stevens, S. Whitehead, and B. G. Barrell. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413:848-52.

193. Parry, C. M., T. T. Hien, G. Dougan, N. J. White, and J. J. Farrar. 2002.

Typhoid fever. N Engl J Med 347:1770-82.

194. Pfennig, K. S. 2001. Evolution of pathogen virulence: the role of variation in host phenotype. Proc R Soc Lond B Biol Sci 268:755-60.

195. Pham, P., J. G. Bertram, M. O'Donnell, R. Woodgate, and M. F. Goodman.

2001. A model for SOS-lesion-targeted mutations in Escherichia coli. Nature 409:366-196. Pham, P., S. Rangarajan, R. Woodgate, and M. F. Goodman. 2001. Roles of 70.

DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli. Proc Natl Acad Sci U S A 98:8350-4.

197. Poole, K. 2004. Resistance to beta-lactam antibiotics. Cell Mol Life Sci 61:2200-23.

198. Poon, A., and S. P. Otto. 2000. Compensating for our load of mutations: freezing the meltdown of small populations. Evolution Int J Org Evolution 54:1467-79.

199. Postma, P. W., J. W. Lengeler, and G. R. Jacobson. 1993.

Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria.

Microbiol Rev 57:543-94.

200. Radman, M., I. Matic, and F. Taddei. 1999. Evolution of evolvability. Ann N Y Acad Sci 870:146-55.

201. Radman, M., F. Taddei, and I. Matic. 2000. DNA repair systems and bacterial evolution. Cold Spring Harb Symp Quant Biol 65:11-9.

202. Radman, M., F. Taddei, and I. Matic. 2000. Evolution-driving genes. Res Microbiol 151:91-5.

203. Rangarajan, S., R. Woodgate, and M. F. Goodman. 2002. Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins. Mol Microbiol 43:617-28.

204. Rayssiguier, C., D. S. Thaler, and M. Radman. 1989. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342:396-401.

205. Reid, S. D., C. J. Herbelin, A. C. Bumbaugh, R. K. Selander, and T. S.

Whittam. 2000. Parallel evolution of virulence in pathogenic Escherichia coli. Nature 406:64-7.

206. Reynolds, M. G. 2000. Compensatory evolution in rifampin-resistant Escherichia coli.

Genetics 156:1471-81.

207. Roth, J. R., and D. I. Andersson. 2004. Amplification-mutagenesis--how growth under selection contributes to the origin of genetic diversity and explains the phenomenon of adaptive mutation. Res Microbiol 155:342-51.

208. Rozen, D. E., J. A. de Visser, and P. J. Gerrish. 2002. Fitness effects of fixed beneficial mutations in microbial populations. Curr Biol 12:1040-5.

209. Rupp, W. D. 1996. DNA Repair Mechanisms. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella Cellular and Molecular Biology. ASM Press, Washington, D. C.

210. Said-Salim, B., B. Mathema, and B. N. Kreiswirth. 2003. Community-acquired methicillin-resistant Staphylococcus aureus: an emerging pathogen. Infect Control Hosp

211. Sander, P., B. Springer, T. Prammananan, A. Sturmfels, M. Kappler, M.

Pletschette, and E. C. Bottger. 2002. Fitness cost of chromosomal drug resistance-conferring mutations. Antimicrob Agents Chemother 46:1204-11.

212. Schaaper, R. M. 1998. Antimutator mutants in bacteriophage T4 and Escherichia coli. Genetics 148:1579-85.

213. Schaaper, R. M. 1993. Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J Biol Chem 268:23762-5.

214. Schaaper, R. M. 1989. Escherichia coli mutator mutD5 is defective in the mutHLS pathway of DNA mismatch repair. Genetics 121:205-12.

215. Schaaper, R. M., and R. L. Dunn. 1991. Spontaneous mutation in the Escherichia coli lacI gene. Genetics 129:317-26.

216. Schaaper, R. M., and M. Radman. 1989. The extreme mutator effect of Escherichia coli mutD5 results from saturation of mismatch repair by excessive DNA replication errors. Embo J 8:3511-6.

217. Schaechter, M. 2001. Escherichia coli and Salmonella 2000: the view from here.

Microbiol Mol Biol Rev 65:119-30.

218. Schofield, M. J., and P. Hsieh. 2003. DNA mismatch repair: molecular mechanisms and biological function. Annu Rev Microbiol 57:579-608.

219. Schofield, M. J., S. Nayak, T. H. Scott, C. Du, and P. Hsieh. 2001. Interaction of Escherichia coli MutS and MutL at a DNA mismatch. J Biol Chem 276:28291-9.

220. Schrag, S. J., V. Perrot, and B. R. Levin. 1997. Adaptation to the fitness costs of antibiotic resistance in Escherichia coli. Proc R Soc Lond B Biol Sci 264:1287-91.

221. Schumacher, G., and K. Bussmann. 1978. Cell-free synthesis of proteins related to sn-glycerol-3-phosphate transport in Escherichia coli. J Bacteriol 135:239-50.

222. Shen, P., and H. V. Huang. 1986. Homologous recombination in Escherichia coli:

dependence on substrate length and homology. Genetics 112:441-57.

223. Sherman, D. R., K. Mdluli, M. J. Hickey, T. M. Arain, S. L. Morris, C. E.

Barry, 3rd, and C. K. Stover. 1996. Compensatory ahpC gene expression in isoniazid-resistant Mycobacterium tuberculosis. Science 272:1641-3.

224. Shigenobu, S., H. Watanabe, M. Hattori, Y. Sakaki, and H. Ishikawa. 2000.

Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS.

Nature 407:81-6.

225. Silva, F. J., A. Latorre, and A. Moya. 2001. Genome size reduction through multiple events of gene disintegration in Buchnera APS. Trends Genet 17:615-8.

226. Silva, F. J., A. Latorre, and A. Moya. 2003. Why are the genomes of endosymbiotic bacteria so stable? Trends Genet 19:176-80.

227. Smith, K. C., L. Armitige, and A. Wanger. 2003. A review of tuberculosis:

reflections on the past, present and future of a global epidemic disease. Expert Rev Anti Infect Ther 1:483-91.

228. Sniegowski, P. D., P. J. Gerrish, T. Johnson, and A. Shaver. 2000. The evolution of mutation rates: separating causes from consequences. Bioessays 22:1057-66.

229. Sniegowski, P. D., P. J. Gerrish, and R. E. Lenski. 1997. Evolution of high mutation rates in experimental populations of E. coli. Nature 387:703-5.

230. Snyder, J. A., B. J. Haugen, E. L. Buckles, C. V. Lockatell, D. E. Johnson, M.

S. Donnenberg, R. A. Welch, and H. L. Mobley. 2004. Transcriptome of uropathogenic Escherichia coli during urinary tract infection. Infect Immun 72:6373-231. Sonti, R. V., and J. R. Roth. 1989. Role of gene duplications in the adaptation of 81.

Salmonella typhimurium to growth on limiting carbon sources. Genetics 123:19-28.

232. Stambuk, S., and M. Radman. 1998. Mechanism and control of interspecies recombination in Escherichia coli. I. Mismatch repair, methylation, recombination and replication functions. Genetics 150:533-42.

233. Sutton, M. D., B. T. Smith, V. G. Godoy, and G. C. Walker. 2000. The SOS response: recent insights into umuDC-dependent mutagenesis and DNA damage tolerance. Annu Rev Genet 34:479-497.

234. Svanborg, C., and G. Godaly. 1997. Bacterial virulence in urinary tract infection.

Infect Dis Clin North Am 11:513-29.

235. Taddei, F., M. Radman, J. Maynard-Smith, B. Toupance, P. H. Gouyon, and B. Godelle. 1997. Role of mutator alleles in adaptive evolution. Nature 387:700-2.

236. Tamas, I., L. Klasson, B. Canback, A. K. Naslund, A. S. Eriksson, J. J.

Wernegreen, J. P. Sandstrom, N. A. Moran, and S. G. Andersson. 2002. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296:2376-9.

237. Tamas, I., L. M. Klasson, J. P. Sandstrom, and S. G. Andersson. 2001.

Mutualists and parasites: how to paint yourself into a (metabolic) corner. FEBS Lett 498:135-9.

238. Tang, M., P. Pham, X. Shen, J. S. Taylor, M. O'Donnell, R. Woodgate, and M. F. Goodman. 2000. Roles of E. coli DNA polymerases IV and V in lesion-targeted and unlesion-targeted SOS mutagenesis. Nature 404:1014-8.

239. Tang, M., X. Shen, E. G. Frank, M. O'Donnell, R. Woodgate, and M. F.

Goodman. 1999. UmuD'(2)C is an error-prone DNA polymerase, Escherichia coli pol V. Proc Natl Acad Sci U S A 96:8919-24.

240. Taylor, J. S., and J. Raes. 2004. Duplication and Divergence: The Evolution of New Genes and Old Ideas. Annu Rev Genet.

241. Tenaillon, O., E. Denamur, and I. Matic. 2004. Evolutionary significance of stress-induced mutagenesis in bacteria. Trends Microbiol 12:264-70.

242. Tenaillon, O., H. Le Nagard, B. Godelle, and F. Taddei. 2000. Mutators and sex in bacteria: conflict between adaptive strategies. Proc Natl Acad Sci U S A 97:10465-70.

243. Tenaillon, O., F. Taddei, M. Radmian, and I. Matic. 2001. Second-order selection in bacterial evolution: selection acting on mutation and recombination rates in the course of adaptation. Res Microbiol 152:11-6.

244. Tenaillon, O., B. Toupance, H. Le Nagard, F. Taddei, and B. Godelle. 1999.

Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria. Genetics 152:485-93.

245. Travisano, M., J. A. Mongold, A. F. Bennett, and R. E. Lenski. 1995.

Experimental tests of the roles of adaptation, chance, and history in evolution.

Science 267:87-90.

246. Trobner, W., and R. Piechocki. 1984. Competition between isogenic mutS and mut+ populations of Escherichia coli K12 in continuously growing cultures. Mol Gen Genet 198:175-6.

247. Trobner, W., and R. Piechocki. 1981. Competition growth between Escherichia coli mutL and mut+ in continuously growing cultures. Z Allg Mikrobiol 21:347-9.

248. Trobner, W., and R. Piechocki. 1984. Selection against hypermutability in Escherichia coli during long term evolution. Mol Gen Genet 198:177-8.

249. Wagner, J., P. Gruz, S. R. Kim, M. Yamada, K. Matsui, R. P. Fuchs, and T.

Nohmi. 1999. The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV, involved in mutagenesis. Mol Cell 4:281-6.

250. Walker, G. C. 1996. The SOS Response of Escherichia coli. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella Cellular and Molecular Biology. ASM Press, Washington, D. C.

251. Wallace, D. C., and H. J. Morowitz. 1973. Genome size and evolution.

Chromosoma 40:121-6.

252. Wernegreen, J. J. 2002. Genome evolution in bacterial endosymbionts of insects.

Nat Rev Genet 3:850-61.

253. Wernegreen, J. J., and N. A. Moran. 1999. Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes. Mol Biol Evol 16:83-97.

254. Whitlock, M. C. 2000. Fixation of new alleles and the extinction of small populations: drift load, beneficial alleles, and sexual selection. Evolution Int J Org Evolution 54:1855-61.

255. Winfield, M. D., and E. A. Groisman. 2003. Role of nonhost environments in the lifestyles of Salmonella and Escherichia coli. Appl Environ Microbiol 69:3687-94.

256. Worth, L., Jr., T. Bader, J. Yang, and S. Clark. 1998. Role of MutS ATPase activity in MutS,L-dependent block of in vitro strand transfer. J Biol Chem 273:23176-82.

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