Adaptive Mutations In RNA-Based Regulatory Mechanisms: Computational and Experimental Investigations

References

• Barash, D. 2003. Deleterious mutation prediction in the secondary structure of RNAs. Nucleic Acids Res. 31(22): 6578-6584.
   Google Scholar
• Cairns, J., Overbaugh, J., Miller, S. 1988. The origin of mutants. Nature 335: 142-145.
   Google Scholar
• Churkin, A., Barash, D. 2006. RNAMute: RNA secondary structure mutation analysis tool. BMC Bioinformatics 7: 221.
   Google Scholar
• Cowperthwaite, M.C., Bull, J.J., Meyers, L.A. 2005. Distributions of beneficial fitness effects in RNA. Genetics 170(4): 1449-1457.
   Google Scholar
• Cohan, F.M., Roberts, M.S., King, E.C. 1991. The potential for genetic exchange by Transformation within a natural population of Bacillus subtilis. Evolution 45: 1393-1421.
   Google Scholar
• Darwin, C. 1859. The origin of species by means of natural selection. John Murray, London.
   Google Scholar
• Derhavets, E., Korol, A., Pavlicek, T., Nevo, E. 1997. Adaptation to stressful environment and mutation rate: a case study in Drosophila melanogaster. Drosophila Information Service 80: 53.
   Google Scholar
• Fidalgo, M., Barrales, R.R., Ibeas, J.I., Jimenez, J. 2006. Adaptive evolution by mutations in FLO11 gene. Proc. Natl. Acad. Sci. USA 103(30): 11228-11233.
   Google Scholar
• Gelfand, M.S., Mironov, A.A., Jomantas, J., Kozlov, Y.I., Perumov, D.A. 1999. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet. 15 (11): 439-442.
   Google Scholar
• Grishkan, I., Beharav, A., Nevo, E. 2007. Adaptive biodiversity of soil microfungi in extreme Negev Desert, Israel. Biol. J. Linn. Soc., in press.
   Google Scholar
• Grundy, F.J., Henkin, T.M. 1998. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram-positive bacteria. Mol. Microbiol. 30: 737-749.
   Google Scholar
• Hall, B.G. 1990. Spontaneous point mutations that occur more often when advantageous than when neutral. Genetics 126: 5-16.
   Google Scholar
• Hendrickson, H., Slechta, E.S., Bergthorsson, U., Andersson, D.I., Roth, J.R. 2002. Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification. Proc. Natl. Acad. Sci. USA 99(4): 2164-9.
   Google Scholar
• Higgs, P.G. 2000. RNA secondary structure: physical and computational aspects. Q. Rev. Biophys. 33: 199-253.
   Google Scholar
• Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M., Schuster, P. 1994. Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125: 167-188.
   Google Scholar
• Lamb, B.C., Saleem, M., Scott, W., Thapa, N., Nevo, E. 1998. Inherited and environmentally-induced differences in mutation frequencies between wild strains of Sordaria fimicola from "Evolution Canyon". Genetics 149: 87-99.
   Google Scholar
• Mathews, D.H., Sabina, J., Zuker, M., Turner, D.H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288(5): 911-940.
   Google Scholar
• Miranda-Rios, J., Navarro, M., Soberon, M. 2001. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc. Natl. Acad. Sci. USA 98: 9736-9741.
   Google Scholar
• Mironov, A.S., Gusarov, I., Rafikov, R., Lopez, L.E., Shatalin, K., Kreneva, R.A., Perumov, D.A., Nudler, E. 2002. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111: 747-756.
   Google Scholar
• Nevo, E. 2001. Evolution of genome-phenome diversity under environmental stress. Proc. Natl. Acad. Sci. USA 98: 6233-6240.
   Google Scholar
• Nevo, E., Oren, A., Wasser, S. 2003. Fungal life in the Dead Sea. Koeltz Scientific Books, Konigstein, Germany.
   Google Scholar
• Nudler, E., Mironov, A.S. 2004. The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29(1): 11-17.
   Google Scholar
• Rodionov, D.A., Vitreschak, A.G., Mironov, A.A., Gelfand, M.S. 2002. Comparative genomics of thiamin biosynthesis in procaryotes. J. Biol. Chem. 277: 48949-48959.
   Google Scholar
• Rosenberg, S.M. 2001. Evolving responsively: adaptive mutation. Nat. Rev. Genet. 2: 504-14.
   Google Scholar
• Roth, J.R., Kugelberg, E., Reams, A.B., Kofoid, E., Andersson, D.I. 2006. Origins of mutations under selection: the adaptive mutation controversy. Annu. Rev. Microbiol. 60: 477-501.
   Google Scholar
• Sabeti, P.C., Schaffner, S.F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., Palma, A., Mikkelsen, T.S., Altshuler, D., Lander, E.S. 2006. Positive natural selection in the human lineage. Science 312 (5780): 1614-1620.
   Google Scholar
• Schuster, P., Fontana, W., Stadler, P.F., Hofacker, I.L. 1994. From sequences to shapes and back: a case study in RNA secondary structures. Proc. Biol. Sci. 255(1344): 279-284.
   Google Scholar
• Shapiro, J.A. 1984. Observations on the formation of clones containing araB-lacZ fusions. Mol. Gen. Genet. 194: 79-90.
   Google Scholar
• Sikorski, J., Nevo, E. 2005. Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at "Evolution Canyons" I and II, Israel. Proc. Natl. Acad. Sci. USA 102(44): 15924-9.
   Google Scholar
• Sikorski, J., Jahr, H., Wackernagel, W. 2001a. The structure of a local population of phytopathogenic Pseudomonas brassicacearum from agricultural soil indicates development under purifying selection pressure. Environ. Microbiol. 3(3): 176-186.
   Google Scholar
• Sikorski, J., Stackebrandt, E., Wackernagel, W. 2001b. Pseudomonas kilonensis sp. nov., a bacterium isolated from agricultural soil. Int. J. Syst. Evol. Microbiol. 51: 1549-1555.
   Google Scholar
• Slechta, E.S., Bunny, K.L., Kugelberg, E., Kofoid, E., Andersson, D.I., Roth, J.R. 2003. Adaptive mutation: general mutagenesis is not a programmed response to stress but results from rare coamplification of dinB with lac. Proc. Natl. Acad. Sci. USA 100(22): 12847-52.
   Google Scholar
• Winkler, W.C., Nahvi, A., Breaker, R.R. 2002. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419(6910): 952-956.
   Google Scholar
• Winkler, W.C., Breaker, R.R. 2003. Genetic control by metabolite-binding riboswitches. Chem. Bio. Chem. 4: 1024-1032.
   Google Scholar
• Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucl. Acids Res. 31: 3406-3415.
   Google Scholar
• Zuker, M., Sankoff, D. 1984. RNA secondary structures and their prediction. Bull. Math. Biol. 46(4): 591-621.
   Google Scholar