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DNA Repair and Mutagenesis Main sites of modification of DNA bases by methylating agents. The arrow sizes reflect the relative yields of the different methylated products. Atoms or groups involved in Watson–Crick hydrogen bonding are shown in red. Bases methylated at positions indicated by the black arrows are processed primarily by AlkA; those methylated at sites marked with blue arrows are addressed by O6-methylguanine DNA methyltransferase, and those methylated at positions marked with the green arrows are processed by AlkB AlkB-mediated demethylation of N3-methyladenine and N1-methylcytosine. The methyl groups are converted to hydroxymethyl moieties, which are spontaneously lost in the form of formaldehyde to regenerate the unmodified bases (the aberrant methyl groups and their oxidation products are shown in red). Note that the cofactors (blue) are consumed during the reaction in stoichiometric amount WT recF 80 10 40 20 40 20 60 uvrA 0 100 0 10 20 30 40 50 60 WT 80 Percent 6-4 repair WT WT recF recF uvrA uvrA w+ recF uvrA 0 60 recF 60 Time Percent CPD repair 100 Time recF removes UV-induced lesions from the DNA 0 10 40 20 20 40 60 0 uvrA 0 10 20 30 40 50 60 Minutes following irradiation WT WT recF recF uvrA uvrA w+ recF uvrA E. coli that are unable to remove DNA lesions are sensitive to UV irradiation UV dose J/m2 0 5 10 20 40 80 120 WT uvrA uvrB uvrC People that are unable to remove DNA lesions are also sensitive to UV irradiation Photo taken from Friedberg, EC., Walker GC., Siede, W (1995) in DNA Repair and Mutagenesis (ASM Press, Washington DC) LexA normally binds to the promoter regions and represses more than 40 genes lexA DNA replication bubble OFF =RecA umuC uvrA recA OFF OFF OFF However, following UVinduced DNA damage or other replication arresting events... lexA OFF umuC uvrA recA OFF OFF OFF OFF umuC uvrA recA OFF OFF OFF lexA ON umuC uvrA recA ON ON ON lexA OFF OFF =UV-induced DNA damage ...RecA binds to the single strand regions that are generated when replication forks are arrested lexA umuC =LexA uvrA recA OFF OFF The bound RecA serves to protect the replication fork DNA from degradation and also promotes the autocatalyic cleavage and subsequent degradation of the LexA protein, leading to the derepression of the SOS genes. Once the arresting lesions have been repaired and replication has been restored, the single strand substrate for RecA binding is no longer present, LexA is no longer cleaved and its cellular concentration accumulates. Then, once again, LexA binds to the promoters and represses the expression of the SOS genes, including that of lexA and recA. 0.1 0.1 0.1 10 0.1 yceO solA yceP dinI pyrC yceB grxB yceL rimJ yceH mviM mviN flgN flgM flgA flgB flgC flgD flgE flgF flgG flgH flgI flgJ flgK flgL rne b1085 rluC yceF yceD rpmF plsX fabH fabD fabG acpP fabF pabC yceG tmk holB ycfH ptsG fhuE ycfF ycfL ycfM ycfN nagZ ycfP ndh ycfJ ycfJ ycfQ ycfR ycfS mfd ycfT ycfU ycfV ycfW ycfX cobB ycfZ ymfA potD potC potB potA pepT ycfD phoQ phoP purB ycfC trmU ymfB ymfC icd ymfD ymfE lit intE ymfG ymfH ymfI ymfJ ymfK b1146 ymfL ymfM ymfN ymfR ymfO ymfP ymfQ ycfK ymfS ymfS 0.1 tfaE stfE pinE mcrA icdC elbA ycgX ycgE ycgF ycgZ ymgA ymgB ymgC ycgG ymgF ycgH b1170 ymgD b1172 ycgI minE minD minC ycgJ ycgK ycgL ycgM ycgN hlyE umuD umuC dsbB nhaB fadR ycgB dadA dadX ycgO ldcA emtA ycgR ymgE ymgE ycgY ycgY treA ycgC ycgS ycgT ycgT ycgU ycgV ychF pth ychH ychM prs ychB lolB hemA prfA hemK ychQ ychA kdsA chaA chaB chaC ychN ychO narL narX narK narG narH narJ narI b1228 tpr tyrV tyrT purU ychJ rssA rssB galU hns tdk ychG ISZ adhE ychE oppA oppB oppC oppD oppF yciU cls kch yccT yccU yccV yccW yccX yccK yccA serT hyaA hyaB hyaC hyaD hyaE hyaF appC appB yccB appA yccC yccY yccZ ymcA ymcA ymcB ymcC ymcD ymcD IS1D cspH cspG sfa yccL yccM torS torT torR torC torA torD yccD cbpA yccE yccE agp yccJ yccJ wrbA ymdF ycdG ycdH ycdI ycdJ ycdK ycdL ycdM ycdC putA putP ycdN b1017 ycdO ycdB phoH ycdP ycdQ ycdR ycdS ycdT ISD3 ISD3 ymdE ycdU b1030 ycdV serX ycdW ycdX ycdY ycdZ csgG csgF csgE csgD csgB csgA csgC ymdA ymdB ymdC mdoC mdoG mdoH yceK msyB b1052 yceE htrB yceA yceI yceJ 0.1 10 yciI tonB yciA yciB yciC ompW yciE yciE yciF yciF yciG trpA trpB trpC trpD trpE trpL trpL trpH yciO yciQ yciL btuR yciK sohB yciN topA cysB yciX acnA ribA pgpB yciS yciM pyrF yciH osmB yciT yciR rnb yciW fabI ycjD sapF sapD sapC sapB sapA ymjA ycjJ ycjK ycjL ycjC aldH ordL goaG pspF pspA pspB pspC pspD pspE ycjM ycjN ycjO ycjP ycjQ ycjR ycjS ycjT ycjU ycjV ompG ycjW ycjX ycjX ycjF tyrR tpx ycjG ycjI ycjY ycjZ mppA ynaI IS5F ynaJ ydaA fnr ogt abgT abgB abgA abgR ydaL ydaL ydaM ydaN dbpA ydaO ybjP ybjQ ybjR ybjS ybjT ltaE poxB ybjV ybjW ybjE aqpZ ybjD ybjX ybjY ybjZ cspD yljA clpA serW infA aat cydC cydD trxB lrp ftsK ftsK lolA ycaJ serS dmsA dmsB dmsC ycaC ycaD ycaM ycaN ycaK pflA pflB focA ycaO ycaP serC aroA ycaL cmk rpsA ihfB ycaI msbA lpxK ycaQ ycaR kdsB ycbJ ycbC smtA mukF mukE mukB ycbB ycbK ycbL aspC ompF asnS pncB pepN ssuB ssuC ssuD ssuA ssuE ycbQ ycbR ycbS ycbT ycbU ycbV ycbF pyrD ycbW ycbX ycbY uup pqiA pqiB ymbA rmf fabA ycbZ ycbG ompA sulA yccR yccS yccF helD mgsA 0.1 intR ydaQ ydaC lar recT recE racC racC ydaE kil sieB ydaF ydaG racR ydaS ydaT ydaU ydaV ydaW rzpR trkG rzoR ynaK ydaY b1367 ynaA lomR IS5Y IS5Y stfR tfaR pinR ynaE ynaF ompN ydbK ydbJ hslJ ldhA ydbH ynbE ydbL feaR feaB tynA maoC paaA paaB paaC paaD paaE paaF paaG paaH paaI paaJ paaK paaX paaY ydbA IS2D IS2D IS2D IS30C IS30A ydbC ydbD ynbA ynbB ynbC ynbD acpD hrpA ydcF aldA gapC gapC cybB hokB ydcA mokB sokB trg ydcI ydcJ ydcG b1425 ydcH rimL ydcK tehA tehB ydcL yncK ydcM ydcO ydcN ydcP yncJ b1437 ybhI ybhJ ybhC ybhB bioA bioB bioF bioC bioD uvrB ybhK moaA moaB moaC moaD moaE ybhL ybhM ybhN ybhO ybhP ybhP ybhQ ybhQ ybhR ybhS ybhF ybhG ybiH rhlE ybiA dinG ybiB ybiC ybiJ ybiI ybiX fiu ybiM ybiN ybiO glnQ glnP glnH dps ybiF ybiF ompX ybiP b0816 ybiQ ybiR ybiS ybiT ybiU ybiV ybiW ybiY mipB moeB moeA ybiK yliA yliA yliB yliC yliD yliE yliF yliG yliH yliI yliJ dacC deoR ybjG cmr ybjH ybjI ybjJ ybjK ybjL ybjM ybjM grxA ybjC nfsA rimK ybjN potF potG potH potI ybjO ybjF artJ artM artQ artI artP 0.1 10 ydcQ ydcR ydcS ydcT ydcU ydcV ydcW ydcX ydcY ydcZ yncA yncB yncC yncD yncE ansP yncG yncH yncH rhsE ydcD yncI b1459 ydcC ydcE yddH nhoA yddE narV narW narY narZ narZ narU yddJ yddK yddL yddG fdnG fdnH fdnI yddM adhP sfcA rpsV bdm osmC ddpF ddpD ddpC ddpB ddpA ddpX yddU yddV yddW xasA gadB pqqL yddB yddA ydeM ydeN ydeO b1500 ydeP ydeQ ydeR ydeS ydeT yneL hipA hipB hipB ydeU ydeK ydeV ydeW ego ydeY ydeZ yneA yneB yneC tam yneE uxaB yneF yneG yneH yneI yneJ yneK ydeA marC marR marA marB marB ydeD 10 810 910 1120 10 1510 820 920 1030 1210 1310 1410 1520 830 930 1040 1130 1140 1220 1320 1330 1420 1430 1530 1540 840 940 1050 1230 850 950 1060 1150 1240 1250 1340 1350 1440 1550 860 960 970 1070 1160 1360 1450 1560 1570 870 980 1080 1170 1260 1370 1460 1470 1580 880 990 1090 1180 1270 1380 1480 1590 1600 890 1000 1190 1280 900 1 1010 1020 1 10 1100 1110 1 1200 1 1290 1300 1 10 1390 1400 1 10 1490 1500 1 1610 1 2820 kb 10 wild type lexA1 +UV 1 -UV oraA recA 0.1 0 20 40 minutes 60 0 20 40 60 minutes lexA -77
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