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Academic Appointments


Research & Scholarship

Current Research and Scholarly Interests


The photochemistry and radiation chemistry of DNA, the genetic control and biochemical bases of the multiple pathways of DNA repair, and the roles of DNA repair processes in radiation and spontaneous mutagenesis. Over 190 papers have been published on these and related topics.

Publications

Journal Articles


  • Recombinational DNA repair: the ignored repair systems BIOESSAYS Smith, K. C. 2004; 26 (12): 1322-1326

    Abstract

    The recent finding of a role for the recA gene in DNA replication restart does not negate previous data showing the existence of recA-dependent recombinational DNA repair, which occurs when there are two DNA duplexes present, as in the case for recA-dependent excision repair, for postreplication repair (i.e., the repair of DNA daughter-strand gaps), and for the repair of DNA double-strand breaks. Recombinational DNA repair is critical for the survival of damaged cells.

    View details for DOI 10.1002/bies.20109

    View details for Web of Science ID 000225523600008

    View details for PubMedID 15551273

  • SPONTANEOUS MUTAGENESIS - EXPERIMENTAL, GENETIC AND OTHER FACTORS MUTATION RESEARCH Smith, K. C. 1992; 277 (2): 139-162

    Abstract

    Spontaneous mutations are "the net result of all that can go wrong with DNA during the life cycle of an organism" (Glickman et al., 1986). Thus, the types and amounts of spontaneous mutations produced are the resultant of all the cellular processes that are mutagenic and those that are antimutagenic. It is not widely appreciated that the types and frequencies of spontaneous mutations change markedly with subtle changes in experimental conditions. All types of mutations are produced spontaneously, i.e., base substitutions, frameshifts, insertions and deletions. However, very few papers have appeared that are devoted exclusively to the study of the mechanisms of spontaneous mutagenesis, and of the subtle experimental factors that affect the types and frequencies of spontaneous mutations. This is unfortunate because spontaneous mutagenesis appears to play a major role in evolution, aging, and carcinogenesis. This review emphasizes subtle experimental variables that markedly affect the results of a spontaneous mutation experiment. A thorough understanding of these variables eliminates the need for a theory of "directed" mutagenesis. The intrinsic instability of DNA, and the types of normal metabolic lesions that are produced in DNA that lead to mutations via errors made in replication, repair, and recombination are reviewed, as is the genetic control of spontaneous mutagenesis. As with spontaneous mutagenesis, spontaneous carcinogenesis can also be considered to be the net result of all that can go wrong with DNA during the life of an organism.

    View details for Web of Science ID A1992JD16900002

    View details for PubMedID 1378531

  • INVOLVEMENT OF RECB-MEDIATED (BUT NOT RECF-MEDIATED) REPAIR OF DNA DOUBLE-STRAND BREAKS IN THE GAMMA-RADIATION PRODUCTION OF LONG DELETIONS IN ESCHERICHIA-COLI MUTATION RESEARCH SARGENTINI, N. J., Smith, K. C. 1992; 265 (1): 83-101

    Abstract

    Experiments were designed to determine the association between the repair of gamma-radiation-induced DNA double-strand breaks (DSB) and the induction of 700-1000 bp long deletions (Lac(-)----Lac+), base substitutions (leuB19----Leu+), and frameshifts (trpE9777----Trp+) in Escherichia coli K-12. Over the range of 2.5-20 krad, deletions were induced with linear kinetics, as has been shown for the induction of DSB, while the induction kinetics of base substitutions and frameshifts were curvilinear. Like the repair of DSB, deletion induction showed an absolute requirement for an intact recB gene as well as a dependency on the type of preirradiation growth medium; these requirements were not seen for base substitutions or frameshifts. In addition, about 80% of the spontaneous deletions were absent in the recB21 strain. A recC1001 mutation, which confers a 'hyper-Rec' phenotype, increased the rate of gamma-radiation-induced deletions as well as the low-dose production of base substitutions and frameshifts. A recF143 mutation increased the yield of gamma-radiation-induced deletions without increasing base substitutions or frameshifts. A mutS mutation markedly enhanced the gamma-radiation induction of frameshifts, and had a slight effect on base substitutions, but did not affect the induction of deletions. Resistance to gamma-irradiation and the capacity to repair DSB (albeit at about half the normal rate) were restored to the radiosensitive recB21 strain by the addition of the sbcB21 and sbcC201 mutations. However, the radioresistant recB sbcBC strain, which is recombination proficient via the RecF pathway, was still grossly deficient in the ability to produce deletions. A model for deletion induction as a by-product of the recB-dependent (Chi-dependent) repair of gamma-radiation-induced DSB is discussed, as is the inability to detect deletions in cells that use only the recF-dependent (Chi-independent) mechanism to repair DSB.

    View details for Web of Science ID A1992GY36900008

    View details for PubMedID 1370245

  • ROLE OF RUVAB GENES IN UV-RADIATION AND GAMMA-RADIATION AND CHEMICAL MUTAGENESIS IN ESCHERICHIA-COLI MUTATION RESEARCH SARGENTINI, N. J., Smith, K. C. 1989; 215 (1): 115-129

    Abstract

    Escherichia coli umuC122::Tn 5 was mutagenized with N-methyl-N'-nitro-N-nitrosoguanidine to isolate mutations that block the residual gamma-radiation mutagenesis observed in umuC strains. Two of these mutations were shown by transductional mapping and plasmid complementation to map in the ruvA and ruvB genes (i.e., ruvA200 and ruvB201). Whereas ruvA200 was complemented by ruvA+ plasmids, the only other known ruvA mutation, ruvA59::Tn10 required both the ruvA+ and ruvB+ genes to show complementation. The ruvA200, ruvB201, ruvA59::Tn10 and ruvB60::Tn10 mutations all reduced gamma-radiation-induced ochre reversion [argE3(Oc)----Arg+] to about 30% of the wild-type level, and they all reduced UV-radiation-induced ochre reversion to about 15% of the wild-type level. The ruvA200 and ruvB201 mutants also showed reduced gamma- and UV-radiation mutagenesis with two other assays [hisG4(Oc)----His+ and Rifs----Rifr]. Streptozotocin mutagenesis (Rifr) was reduced to about half of the wild-type level in ruv strains, but ethyl methanesulfonate mutagenesis was normal. While the umuC strain did not show the oxygen enhancement of gamma-radiation mutagenesis, the ruvA200 strain showed an oxygen effect that was similar to that shown by the wild-type strain. When the ruvA200 mutation was combined with the umuC mutation, gamma-radiation mutagenesis was further reduced to 5% of the wild-type level and cells showed a synergistic sensitization to UV- and gamma-radiation-induced killing. A mutational spectrum analysis indicates a general depression of both umuC-dependent and umuC-independent gamma-radiation mutagenesis in the ruvA strain, which is in contrast with the site-specific reduction in gamma-radiation mutagenesis that is observed in the umuC mutant. The reduced radiation mutagenesis in the ruvA strain could not be correlated with a reduction in transcription of the recA or umuC genes.

    View details for Web of Science ID A1989AZ13100013

    View details for PubMedID 2554134

  • MUTATIONAL SPECTRUM ANALYSIS OF UMUC-INDEPENDENT AND UMUC-DEPENDENT GAMMA-RADIATION MUTAGENESIS IN ESCHERICHIA-COLI MUTATION RESEARCH SARGENTINI, N. J., Smith, K. C. 1989; 211 (2): 193-203

    Abstract

    gamma-Radiation mutagenesis (oxic versus anoxic) was examined in wild-type, umuC and recA strains of Escherichia coli K-12. Mutagenesis [argE3(Oc)----Arg+] was blocked in a delta (recA-srlR)306 strain at the same doses that induced mutations in umuC122::Tn5 and wild-type strains, indicating that both umuC-independent and umuC-dependent mechanisms function within recA-dependent misrepair. Analyses of various suppressor and back mutations that result in argE3 and hisG4 ochre reversion and an analysis of trpE9777 (+1 frameshift) reversion were performed on umuC and wild-type cells irradiated in the presence and absence of oxygen. While the umuC strain showed the gamma-radiation induction of base substitution and frameshifts when irradiated in the absence of oxygen, the umuC mutation blocked all oxygen-dependent base-substitution mutagenesis, but not all oxygen-dependent frameshift mutagenesis. For anoxically irradiated cells, the yields of GC----AT [i.e., at the supB and supE (Oc) loci] and AT----GC transitions (i.e., at the argE3 and hisG4 loci) were essentially umuC independent, while the yields of (AT or GC)----TA transversions (i.e., at the supC, supL, supM, supN and supX loci) were heavily umuC dependent. These data suggest new concepts about the nature of the DNA lesions and the mutagenic mechanisms that lead to gamma-radiation mutagenesis.

    View details for Web of Science ID A1989T937200002

    View details for PubMedID 2538729

  • THE ROLES OF RECBCD, SSB AND RECA PROTEINS IN THE FORMATION OF HETERODUPLEXES FROM LINEAR-DUPLEX DNA INVITRO MOLECULAR AND GENERAL GENETICS Wang, T. C., Smith, K. C. 1989; 216 (2-3): 315-320

    Abstract

    The formation of heteroduplexes from linear duplex DNA, where one molecule possesses a DNA double-strand break, was assayed by agarose gel electrophoresis. Using unlabeled whole-length linear duplex DNA and 3H-labeled half-length linear duplex DNA (obtained from plasmid pACYC184), the appearance of 3H-labeled DNA that migrated as whole-length linear DNA was taken as evidence for formation of heteroduplex DNA. When the DNA mixtures were incubated with RecA, RecBCD, or Ssb proteins, or any double or triple combination of these proteins under a variety of reaction conditions, no heteroduplex DNA was detected. However, heteroduplex DNA was detected when the DNA mixtures were first incubated briefly with the RecBCD and Ssb proteins under reaction conditions that allow unwinding to proceed, and then the MgCl2 concentration was raised such that renaturation could proceed. The inclusion of the RecBCD and Ssb proteins was sufficient to catalyze the slow formation of heteroduplex DNA, but the presence of RecA protein greatly increased the kinetics. The roles of the RecBCD, Ssb and RecA proteins in heteroduplex formation in vitro are discussed.

    View details for Web of Science ID A1989U365500017

    View details for PubMedID 2747619

  • DIFFERENT EFFECTS OF RECJ AND RECN MUTATIONS ON THE POSTREPLICATION REPAIR OF UV-DAMAGED DNA IN ESCHERICHIA-COLI-K-12 JOURNAL OF BACTERIOLOGY Wang, T. C., Smith, K. C. 1988; 170 (6): 2555-2559

    Abstract

    Two mutations known to affect recombination in a recB recC sbsBC strain, recJ284::Tn10 and recN262, were examined for their effects on the postreplication repair of UV-damaged DNA. The recJ mutation did not affect the UV radiation sensitivity of uvrB and uvrB recF cells, but it increased the sensitivity of uvrB recN (approximately 3-fold) and uvrB recB (approximately 8-fold) cells. On the other hand, the recN mutation did not affect the UV sensitivity of uvrB recB cells, but it increased the sensitivity of uvrB (approximately 1.5-fold) and uvrB recF (approximately 4-fold) cells. DNA repair studies indicated that the recN mutation produced a partial deficiency in the postreplication repair of DNA double-strand breaks that arise from unrepaired daughter strand gaps, while the recJ mutation produced a deficiency in the repair of daughter strand gaps in uvrB recB cells (but not in uvrB cells) and a deficiency in the repair of both daughter strand gaps and double-strand breaks in uvrA recB recC shcBC cells. Together, these results indicate that the recJ and recN genes are involved in different aspects of postreplication repair.

    View details for Web of Science ID A1988N699900022

    View details for PubMedID 3286613

  • GENETIC AND PHENOTYPIC ANALYSES INDICATING OCCURRENCE OF THE RECN262 AND RADB101 MUTATIONS AT THE SAME LOCUS IN ESCHERICHIA-COLI JOURNAL OF BACTERIOLOGY SARGENTINI, N. J., Smith, K. C. 1988; 170 (5): 2392-2394

    Abstract

    The radB101 and recN262 mutations showed essentially identical phenotypes when compared in isogenic Escherichia coli strains for their effects on gamma and UV radiation survival and on conjugal recombination in a uvrA recB recC sbcB sbcC strain. Complementation tests involving attempts to reconstitute a radB+ recN+ strain by transductions between radB101 and recN262 donors and recipients, and tests involving plasmids carrying recN+ and recN::Tn1000 inserts, indicated that the radB and recN genes are identical. We suggest that the radB101 mutation now be referred to as recN2001.

    View details for Web of Science ID A1988N190500060

    View details for PubMedID 3283110

  • ROLE OF DNA-POLYMERASE-I IN POSTREPLICATION REPAIR - A REEXAMINATION WITH ESCHERICHIA-COLI DELTA-POLA JOURNAL OF BACTERIOLOGY Sharma, R. C., Smith, K. C. 1987; 169 (10): 4559-4564

    Abstract

    Using strains of Escherichia coli K-12 that are deleted for the polA gene, we have reexamined the role of DNA polymerase I (encoded by polA) in postreplication repair after UV irradiation. The polA deletion (in contrast to the polA1 mutation) made uvrA cells very sensitive to UV radiation; the UV radiation sensitivity of a uvrA delta polA strain was about the same as that of a uvrA recF strain, a strain known to be grossly deficient in postreplication repair. The delta polA mutation interacted synergistically with a recF mutation in UV radiation sensitization, suggesting that the polA gene functions in pathways of postreplication repair that are largely independent of the recF gene. When compared to a uvrA strain, a uvrA delta polA strain was deficient in the repair of DNA daughter strand gaps, but not as deficient as a uvrA recF strain. Introduction of the delta polA mutation into uvrA recF cells made them deficient in the repair of DNA double-strand breaks after UV irradiation. The UV radiation sensitivity of a uvrA polA546(Ts) strain (defective in the 5'----3' exonuclease of DNA polymerase I) determined at the restrictive temperature was very close to that of a uvrA delta polA strain. These results suggest a major role for the 5'----3' exonuclease activity of DNA polymerase I in postreplication repair, in the repair of both DNA daughter strand gaps and double-strand breaks.

    View details for Web of Science ID A1987K219800020

    View details for PubMedID 3308845

  • RECA-DEPENDENT DNA-REPAIR IN UV-IRRADIATED ESCHERICHIA-COLI JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY Smith, K. C., Wang, T. C., Sharma, R. C. 1987; 1 (1): 1-11

    Abstract

    UV-radiation-induced lesions in DNA result in the formation of excision gaps, daughter-strand gaps (DSG) and double-strand breaks (DSB), which are repaired by several different mechanisms. Postreplication repair. The recA gene is a master gene that controls all of the pathways of postreplication repair. The repair of DSG proceeds by one pathway that is also recF dependent, and one pathway that is constitutive and independent of the recF and recBC genes. A small fraction of the recF recB-independent repair of DSG is dependent upon the umuC gene, and may define an error-prone pathway of postreplication repair. Unrepaired DSG can be converted to DSB, which are normally repaired by the RecBCD pathway. However, in the recBC sbcB background, these DSB are repaired by a recF-dependent process. The RecF pathways of postreplication repair appear to utilize DNA containing a single-stranded region (either a gap or a DSB with a single-stranded end), while the RecBCD pathway appears to utilize the blunt ends of duplex DNA to promote the recombinational repair of DSB. The polA gene (especially the 5'----3' exonuclease activity of DNA polymerase I) functions in pathways of postreplication repair (both for the repair of DSG and DSB) that are largely independent of the recF gene. Nucleotide excision repair. The repair of excision gaps is independent of the recA gene in cells with unreplicated chromosomes, but is recA dependent in cells with partially replicated chromosomes at the time of UV irradiation. This recA-dependent repair of excision gaps appears to be analogous to the recF- and recB-dependent pathways of postreplication repair, i.e. the RecF pathway repairs DNA gaps, and the RecBCD pathway repairs the DSB that arise at unrepaired gaps.

    View details for Web of Science ID A1987K162800001

    View details for PubMedID 3149975

  • SCIENCE OF PHOTOBIOLOGY BIOSCIENCE Smith, K. C. 1974; 24 (1): 45-48

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