Chapter 12 : Stationary-Phase-Induced Mutagenesis: Is Directed Mutagenesis Alive and Well within Neo-Darwinian Theory?

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Stationary-Phase-Induced Mutagenesis: Is Directed Mutagenesis Alive and Well within Neo-Darwinian Theory?, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817749/9781555812713_Chap12-1.gif /docserver/preview/fulltext/10.1128/9781555817749/9781555812713_Chap12-2.gif


This chapter attempts to raise questions about mutagenesis and how these processes enhance evolution. The focus of the chapter is on the controversial process that has been termed "adaptive" mutagenesis. Although the work described in the chapter concentrates on prokaryotic model systems, it is clear that all organisms under stress appear to have genetic mechanisms that permit increase in allelic diversity. The chapter adds to the renewed interest in directed mutagenesis, retromutagenesis, transpositional mutagenesis, stationary-phase-induced mutagenesis, and the influences that these processes have had on the evolution of species. In 1988, an article by John Cairns and his collaborators forced a rethinking about how spontaneous mutants might arise, and challenged the very tenets of neo-Darwinian theory. It explores some of the possibilities that might exist for departures from the classic mode of thinking associated with the generation of mutations. Adaptive or stationary-phase-induced mutagenesis may be under genetic control and part of eubacterial development. Mismatch repair (MMR) was first suggested to be involved in "adaptive" or stationary-phase-induced mutagenesis in the study of the lac system in . There is an ancient superfamily of DNA polymerases that are error prone (they make mistakes during the replication process). These polymerases must play an important role in the survival of species otherwise they would not have been conserved during the evolutionary process. The phenomenon called adaptive or stationary-phase-induced mutagenesis presents a model for investigating the mechanisms associated with the evolutionary process.

Citation: Yashin R, Pedraza-Reyes M. 2004. Stationary-Phase-Induced Mutagenesis: Is Directed Mutagenesis Alive and Well within Neo-Darwinian Theory?, p 181-191. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch12

Key Concept Ranking

DNA Synthesis
DNA Damage and Repair
DNA Polymerase III
DNA Polymerase IV
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


1. Bridges, B. 2000. DNA polymerases and SOS mutagenesis: can one reconcile the biochemical and genetic data? BioEssays 22:933937.
2. Bridges, B. A. 1995. mutY 'directs' mutation? Nature 375:741.
3. Bridges, B. A. 1998. The role of DNA damage in stationary phase ('adaptive') mutation. Mutat. Res. 408:19.
4. Bull, H. J.,, G. J. McKenzie,, P. J. Hastings,, and S. M. Rosenberg. 2000. Response to John Cairns: the contribution of transiently hypermutable cells to mutation in stationary phase. Genetics 156:925926.
5. Cairns, J. 2000. The contribution of bacterial hyper-mutators to mutation in stationary phase. Genetics 156:923.
6. Cairns, J.,, J. Overbaugh,, and S. Miller. 1988. The origin of mutants. Nature 335:142145.
7. Dubnau, D. 1991. Genetic competence in Bacillus subtilis. Microbiol. Rev. 55:395424.
8. Dubnau, D.,, and C. M. J. Lovett,. 2002. Transformation and recombination, p. 473482. In A. L. Sonenshein,, J. A. Hoch,, and R. Losick (ed.), Bacillus subtilis and Its Closest Relative. American Society for Microbiology, Washington, D.C.
9. Foster, P. L.,, and J. M. Trimarchi. 1994. Adaptive reversion of a frameshift mutation in Escherichia coli by simple base deletions in homo-polymeric runs. Science 265:407409.
10. Friedberg, E. C.,, R. Wagner,, and M. Radman. 2002. Specialized DNA Polymerases, cellular survival, and the genesis of mutations. Science 296: 16271630.
11. Galitski, T.,, and J. R. Roth. 1995. Evidence that F plasmid transfer replication underlies apparent adaptive mutation. Science 268:421423.
12. Gómez-Gómez, J.,, J. Blazquez,, F. Baquero,, and J. Martinez. 1997. H-NS and RpoS regulate emergence of Lac Ara+ mutants of Escherichia coli MCS2.J. Bacteriol. 179:46204622.
13. Graham, J. B.,, and C. A. Istock. 1978. Genetic exchange in Bacillus subtilis in soil. Mol. Gen. Genet. 166:287290.
14. Halas, A.,, H. Baranowska,, and Z. Policinska. 2002. The influence of the mismatch-repair system on stationary-phase mutagenesis in the yeast Saccharomyces cerevisiae. Curr. Genet. 42:140146.
15. Harris, R. S.,, H. J. Bull,, and S. M. Rosenberg. 1997. A direct role for DNA polymerase III in adaptive reversion of a frameshift mutation in Escherichia coli. Mutat. Res. 375:1924.
16. Holmquist, G. P. 2002. Cell-selfish modes of evolution and mutation directed after transcriptional bypass. Mutat. Res. 510:141152.
17. Kasak, L.,, R. Horak,, and M. Kivisaar. 1997. Promoter-creating mutations in Pseudomonas putida: a model system for the study of mutation in starving bacteria. Proc. Natl. Acad. Sci. USA 94: 31343139.
18. Kim, S. R.,, G. Maenhaut-Michel,, M. Yamada,, Y. Yamamoto,, K. Matsui,, T. Sofuni,, T. Nohmi,, and H. Ohmori. 1997. Multiple pathways for SOS-induced mutagenesis in Escherichia coli: an overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA. Proc. Natl. Acad. Sci. USA 94:1379213797.
19. Makinoshima, H.,, A. Nishimura,, and A. Ishihama. 2002. Fractionation of Escherichia coli cell populations at different stages during growth transition to stationary phase. Mol. Microbiol. 43: 269279.
20. McKenzie, G. J.,, and S. M. Rosenberg. 2001. Adaptive mutations, mutator DNA polymerases and genetic change strategies of pathogens. Curr. Opin. Microbiol. 4:586594.
21. Msadek, T. 1999. When the going gets tough: survival strategies and environmental signaling networks in Bacillus subtilis. Trends Microbiol. 7:201207.
22. Reuven, N. B.,, G. Arad,, A. Maor-Shoshani,, and Z. Livneh. 1999. The mutagenesis protein UmuC is a DNA polymerase activated by UmuD', RecA, and SSB and is specialized for translesion replication. J. Biol. Chem. 274:3176331766.
23. Rosenberg, S. M.,, C. Thulin,, and R. S. Harris. 1998. Transient and heritable mutators in adaptive evolution in the lab and in nature. Genetics 148: 15591566.
24. Rudner, R.,, A. Murray,, and N. Huda. 1999. Is there a link between mutation rates and the stringent response in Bacillus subtilis? Ann. N. Y. Acad. Sci. 870:418422.
25. Selby, C. P.,, and A. Sancar. 1993. Molecular mechanism of transcription-repair coupling. Science 260:5358.
26. Slechta, E. S.,, J. Harold,, D. I. Andersson,, and J. R. Roth. 2002. The effect of genomic position on reversion of a lac frameshift mutation (lacIZ33) during non-lethal selection (adaptive mutation). Mol. Microbiol. 44:10171032.
27. Sung, H.-M.,, and R. E. Yasbin. 2002. Adaptive, or stationary-phase, mutagenesis, a component of bacterial differentiation in Bacillus subtilis. J. Bacteriol. 184:56415653.
28. 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. USA 96:89198924.
29. Torkelson, J.,, R. S. Harris,, M. J. Lombardo,, J. Nagendran,, C. Thulin,, and S. M. Rosenberg. 1997. Genome-wide hypermutation in a subpopulation of stationary-phase cells underlies recombination-dependent adaptive mutation. EMBO J. 16: 33033311.
30. 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 4:281286.
31. Wright, B. E. 2000. A biochemical mechanism for nonrandom mutations and evolution. J. Bacteriol. 182:29933001.
32. Zalieckas, J. M.,, L. V. Wray, Jr.,, A. E. Ferson,, and S. H. Fisher. 1998. Transcription-repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons. Mol. Microbiol. 27:10311038.
33. Cairns, J.,, J. Overbaugh,, and S. Miller. 1988. The origin of mutants. Nature 335:142145.
34. Dobzhansky, T. 1950. The genetic basis of evolution. Sci. Am. 182:3241.
35. Grossman, A. D. 1995. Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis. Annu. Rev. Genet. 29:477508.
36. Luria, S. E.,, and M. Delbruck. 1943. Mutations of bacteria from virus sensitive to virus resistance. Genetics 28:491511.
37. Modrich, P.,, and R. Lahue. 1996. Mismatch repair in replication fidelity, genetic recombination and cancer. Annu. Rev. Biochem. 65:101133.
38. Newcomb, H. B. 1949. Origin of bacterial variants. Nature 164:150.
39. Shapiro, J. A. 1998. Thinking about bacterial populations as multicellular organisms. Annu. Rev. Microbiol. 52:81104.
40. 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. 34:479399.
41. Walker, G. C., 1987. The SOS response of E. coli, p. 13461357. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella typhimurium. American Society for Microbiology, Washington, D.C.
42. Witkin, E. M. 1976. Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli. Bacteriol. Rev. 40:869907.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error