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Ultraviolet Mutagenesis and Inducible DNA Repair in Escherichia Coli EVELYN M

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Ultraviolet Mutagenesis and Inducible DNA Repair in Escherichia Coli EVELYN M BAcERIOLOGICAL REVIEWS, Dec. 1976, p. 869-907 Vol. 40, No. 4 Copyright © 1976 American Society for Microbiology Printed in U.S.A. Ultraviolet Mutagenesis and Inducible DNA Repair in Escherichia coli EVELYN M. WITKIN Department ofBiological Sciences, Douglass College, Rutgers University, New Brunswick, New Jersey 08903 INTRODUCTION .............................................................. 869 Enzymatic Repair of UV Damage in E. coli ......... .......................... 869 Error-Proof and Error-Prone Pathways of DNA Repair ....... ................. 871 The "SOS" Hypothesis: the Regulatory Role of DNA Damage ...... ............ 874 EVIDENCE FOR THE INDUCIBILITY OF ERROR-PRONE REPAIR ("SOS REPAIR") ACTIVITY ..................................................... 875 SOS Repair of Bacteriophage DNA ............ ............................... 875 SOS Repair of Bacterial DNA ................ ................................ 876 Evidence from studies of repair-deficient mutants ....... .................... 876 Evidence from studies of postreplication repair ........ ...................... 879 MANIFESTATIONS OF SOS REPAIR AND THEIR SIGNIFICANCE ..... ...... 879 Mutation Frequency Response to Increasing Fluence of UV Radiation ..... ..... 879 The UV Lesion Responsible for Induction of SOS Functions .................... 880 Kinetics of Induction and Decay of SOS Repair Activity ....... ................ 882 Time of Action of SOS Repair in UV Mutagenesis ...... ........................ 882 Cryptic Premutational Lesions Susceptible to SOS Repair ...................... 884 Mutator Effect of SOS Repair on Undamaged DNA ....... ..................... 885 PLASMIDS AND SOS REPAIR ................................................ 886 MECHANISM OF SOS REPAIR ............................................... 886 Mechanism of SOS Repair in Bacteriophage ......... .......................... 886 Mechanism of SOS Repair in Bacteria ........... ............................. 887 IMPLICATIONS OF SOS REPAIR FOR CARCINOGENESIS ................... 888 REGULATION OF SOS REPAIR AND OTHER UV-INDUCIBLE FUNCTIONS . 889 PROTEASES AND THE EXPRESSION OF SOS FUNCTIONS .................. 894 CONCLUSIONS ............................................................... 895 APPENDIX................................................................... 896 LITERATURE CITED .......................................................... 898 INTRODUCTION of UV radiation are described in detail else- Mutagens change the genetic script by pro- where (88, 91, 93, 102). The brief summary moting errors in replication or in repair of de- given here is intended only to provide sufficient oxyribonucleic acid (DNA). Ultraviolet (UV) background for discussion of UV mutagenesis. light owes its powerful mutagenic effect in UV radiation produces a variety of photo- Escherichia coli primarily to misrepair of ra- products in DNA (169, 197, 202), among which damage the intrastrand cyclobutane-type dimer of adja- diation to the bacterial chromosome cent pyrimidines (8) has been identified as a (26, 125, 230). Recent developments indicate major cause of lethal, mutagenic and tumoro- that the error-prone repair activity responsible genic effects in a wide spectrum of organisms for UV mutagenesis in E. coli and some of its (92, 95, 216, 225). Wild-type strains of E. coli phages is repressed in undamaged wild-type effectively neutralize the potentially lethal ef- cells, but is expressed, as one of a metabolically fects of as many as a thousand pyrimidine di- diverse but coordinately regulated group of in- mers by utilizing one or more of three types of ducible functions, in response to UV radiation enzymatic DNA repair, which are represented or other agents that damage DNA or interrupt in Fig. 1. Photoreactivation (120) is accom- its replication (53, 77, 174, 240). This article plished by "photoreactivating enzyme" (PRE), summarizes current evidence for the inducibil- which binds pyrimidine dimers in the dark but ity ofmutagenic DNA repair and explores some requires "photoreactivating light" (PRL) in the of its implications. Other aspects of UV muta- range of wavelengths mainly between 310 and genesis in microorganisms have recently been 400 nm to "split" or monomerize them in situ reviewed (3, 62, 66, 67, 130). (183, 184). Since PRE acts specifically on pyrim- idine dimers (193), photoreversibility by this Enzymatic Repair of UV Damage in E. coli enzyme indicates that a UV-initiated biological Enzymatic repair mechanisms operating in phenomenon requires the more or less persist- bacteria which minimize the damaging effects ent presence of at least one pyrimidine dimer. 869 870 WITKIN BACTERIOL. REV. A B C PHOTOREACTIVATION EXCISION REPAIR POSTREPLICATION REPAIR ("short patch" pathway) (recombinational) UV pyrimidine UV UV A climer A'A n A ~~~~~~~~~~3'. photoreativoting incision by replication enzyme bindsI dimer correndonucleose II 5- -3: 3 5 5' : 3' 3 V excision and repair (discontinuous daughter strands) photoreactivating light replication by DNA polymerose I recombinational exchanges I by recombination enzymes _D _ dimer _ split 3' 5 5 3: 3'- V 5 enzyme sealing by polynu- repair replication r released cleotide ligase and ligase sealing rv I 5, A ntact repaired DNA DNAlIA (continuous daughter strands) replication replication replication (dimers split) (dimers removed) (dimers still present) FIG. 1. Major pathways ofenzymatic repair ofdamage to DNA caused by UV radiation in E. coli. All three of these repair mechanisms are error-proof in principle. Symbols: -A... or -v, pyrimidine dimer or other noninstructive UV photoproduct; heavy lines, daughter strands produced in first postirradiation DNA replication; light lines, parental (UV-irradiated) strands of DNA; wavy lines, DNA polymerized during repair replication. Adapted from Hanawalt (91). See text for additional references. In the dark, pyrimidine dimers are not chem- of the sugar-phosphate linkage by polynucleo- ically reversed, but may be removed from the tide ligase. Alternate pathways of excision re- DNA by a multienzymatic mechanism, excision pair, utilizing DNA polymerase III (244) or repair (20, 195). The distortion of the double DNA polymerase II (144), have been demon- helix caused by a pyrimidine dimer (or by some strated in mutants lacking activity of DNA other kinds of DNA lesions) is recognized by polymerase I. In addition to the "short-patch" correndonuclease II, the product of the uvrA type of excision repair shown in Fig. 1B, a and uvrB genes ofE. coli (22), which makes a "long-patch" pathway has been identified single-strand nick, or incision, on the 5' side of which requires the products of the recA+ and the dimer. An exonucleolytic excision releases lexA + gene products, among others, and occurs the oligonucleotide bearing the pyrimidine di- only in growth-supporting media (49, 245, 248). mer plus some bases on either side ofit, and the Pyrimidine dimers, that are neither photoen- "excision gap" is patched by repair replication zymatically split nor removed from the DNA by (170), the intact region of the strand opposite excision repair (as in excision-deficient Uvr- the gap serving as template for accurate re- mutants kept in the dark) block the continuous placement of the missing nucleotides. In wild- progress of the DNA replication complex, but type E. coli, the excision and resynthesis steps do not prevent subsequent reinitiation of DNA are probably effected simultaneously by DNA synthesis at a point beyond the dimer (185). polymerase I (50, 78, 119), although efficient When pyrimidine dimers or other noninstruc- excision requires additional gene products, in- tive lesions are present in the template strand, cluding those ofuvrC (103), uvrE (200, 201, 213) daughter strands are detected initially as seg- and mfd (73, 74) genes. The final step is sealing ments ofrelatively low molecular weight, their VOL. 40, 1976 UV MUTAGENESIS AND DNA REPAIR IN E. COLI 871 continuity interrupted by gaps about 1,000 nu- some pathways of postreplication repair will be cleotides long (114) which correspond approxi- considered below, as they may relate to UV mately in number and position to the dimers in mutagenesis. the parental strand (7, 105). These "daughter- strand gaps" are secondary UV lesions, caused Error-Proof and Error-Prone Pathways of by the replication of DNA containing primary DNA Repair UV photoproducts that prevent base pairing. The possibility that UV-induced mutations The third major type of enzymatic DNA repair, originate as errors in the repair of radiation postreplication repair (Fig. 1C), operates to damage (223) has been substantiated by the connect the daughter-strand segments, thereby finding that UV mutability is eliminated by endowing them with the continuity required for mutations in either the recA (124, 151, 229) or further replication (185). The formation and lexA (159, 227) genes of E. coli, which also joining of daughter-strand segments synthe- cause extreme UV sensitivity and abolish some sized on UV-irradiated templates should not be pathways of DNA repair. Although they are confused with the discontinuous synthesis and UV-nonmutable, recA- and lexA- strains are much more rapid joining of Okazaki fragments spontaneously mutable and are also mutable by at normal DNA replication forks (128). Al- agents believed to cause only replication errors though first demonstrated in Uvr- strains, (125, 241). Since recA- and lexA- mutants per- postreplication repair occurs also in Uvr+ form some kinds ofDNA repair efficiently
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