Team:NYC Wetware/Deinococcus/Candidate Genes

| MntH||NRAMP transporter||DR_1709||Mn (II) transporter||Upregulate in order to establish Mn:Fe ratio similar to that of D. rad [other members of oxyR regulon?]||Jim Imlay||

| Dps||||||DNA-binding protein from starved cells – protect DNA by binding to form condensed co-crystal and by preventing oxidative damage - induced by oxyR||||Jim Imlay||

| PprI||IrrE||DR_0167||Positive regulator of recA and other gamma irradiation-induced genes||Important effect||Blasius||

| PprA||||DR_A0346||DNA binding and tethering of termini, stimulation of DNA ligases and catalase||Strongly induced upon ionizing radiation - Important effect||Battista||

| RecA||||DR_2340||Double strand break repair||Inverse DNA strand exchange pathway - Important effect||Battista||

| RecO||||DR_0819||DNA annealing during homologous recombination||Strong defect in growth and increased radiosensitivity of strain devoid of RecO - Important effect||Blasius||

| SodB ||Fe-SOD||||Catalyzes dismutation of superoxide into oxygen and HOOH – fixes iron||||Frederik Domann||

| SodA||Mn-SOD||DR_1279?||‘’ – fixes manganese||Increases resistance to UV and HOOH damage in E. coli – But why? Without catalase/peroxidase?||Frederik Domann||

| Fur||||||Transcriptional activator of bacterial sodB||Upregulate…||Frederik Domann||

| SOD?||predicted SODs||DR_1546, DR_A0202||superoxide dismutation||||||Omelchenko et al., 2005

| Catalases||predicted catalses||DR_1998, DR_A0259, DR_A 0146||Hydrogen peroxide to water and oxygen||Catalase is important next enzyme after SOD. If not present, H2O2 accumulate and have deleterious effect||||Omelchenko et al., 2005

| Thioredoxin||||DR_0994||reverses oxidized sulfur species||Important for defense against oxidative stress||||Obiero et al., 2010  :Journal of Bacteriology, January 2010, p. 494-501, Vol. 192, No. 2

| Thioredoxin reductase||||||maintains reduced Thioredoxin enzyme levels||Important for defense against oxidative stress||||

| DdrB||||DR_0070||Single strand binding protein||Strongly induced upon ionizing radiation - Important effect||Battista||

| DdrA||||DR_0423||End-capping||Strongly induced upon ionizing radiation, homolog of Rad52 - Important effect||Battista||

| DdrC||||DR_0003||Unknown||Strongly induced upon ionizing radiation - Modest effect||Battista||

| DdrD||||DR_0326||Protection of 3\' ends of single strand DNA||Strongly induced upon ionizing radiation - Modest effect||Battista||

| RecN||||DR_1477||DNA Repair Protein||Mutant shows general repair deficiency||Blasius||

| RecF||||||||||||

| PolA||||DR_1707||DNA polymerase, probably involved in translesion synthesis||important role in ESDSA DSB repair pathway, modulated by Mn(II) - Important effect||Blasius||

| PolX||||DR_0467||DNA polymerase/ 3\'-5\' exonuclease||Nuclease is structure modulated, uses Mn(I) - Modest effect||Blasius||

| SbcD||||DR_1921||Homolog of Mre11, DNA end processing||Additive effect of SbcCD and PolX deficiencies||Blasius||

| SbcC||||DR_1922||Homolog of Rad50, DNA end processing||Homolog of Mre11, DNA end processing||Blasius Paper||

| RuvB||||DR_0576||Resolution of Hollyday junctions||||Blasius||

| RadA||||DR_1105||RecA-like function||||Blasius||

| ClpP||||DR_1972||Proteolytic subunit of ATP-dependent Clp protease||||Blasius||

| ClpX||||DR_1973||ATP-binding subunit of ATP-dependent Clp protease||||Blasius||

| CrtB||||DR_0862||Phytoene synthase||Carotenoids have antioxidant properties, are located at the cell\'s 1st line of defense- the cell wall/membrane. Also they may be able to \"take the hit\" of ionizing radiation, thus protecting cytosolic components||Blasius||Zhang et al., 2007 (Arch Microbilogy)

| CrtI||||DR_0861||Phytoene desaturase||KO of carotenoid synthesis genes DR0861 and DR0862 resulted in increased sensitivity to oxidants, ionizing radiation and UV||Blasius||Zhang et al., 2007 (Arch Microbilogy)

| Crtlm||||DR_0801||Carotenoid synthesis||||These genes boxed off are in the biosynthesis pathway for deinoxathin, the major carotenoid pigment in D. rad. It also has antioxidant properties||Tian & Hua., 2010

| CrtO||||DR_0093||Carotenoid synthesis||||||

| CruF||||DR_0091||Carotenoid synthesis||||||

| CrtD||||DR_2250||Carotenoid synthesis||||||

| OxyR||||DR_0615||Oxidative stress resistance||little connection to IR resistance. MntH expresison is also downregulated by this regulon (which is contrary to what we would like to see)||||Nevermind. This protein was expressed in E. coli before and was not able to complement an E coli OxyR KO. It presumably does not bind the E coli polymerase  

| OxyR2||||DR_A0336||Oxidative stress resistance||Novel OxyR enzyme- this means D. rad has multiple OxyRs!!!||||Yin et al., 2010 (Jornal of Microbiology)

| deiNOS||deinococcus nitric oxide synthase||DR_2597||Nitirc oxide production||KO causes increase in susceptibility to UV irradiation.  Slower recover following insult||||Patel et al., 2009., Adak et al, 2002

| ObgE||||?||GTPase that regulates cel growth/proliferation||decreased ObgE afte NOS KO implicated as an important mediator of growth recovery following UV insult||||Patel et al., 2009.,

| Hypothetical protein||||DR_A0282||nucleotide binding protein??- perhaps DNA repair||mutant had 10X less survival to 14Gy gamma. Enzyme also is manganese dependent!!!||||Das & Misra., 2011

| predicted ATP-dependent ABC-type transporter (Mn (II))||||DR_2284 DR_2523||Mn (II) transport||possibly maintain intracellular Mn(II) ratio.||||Daly et al., 2004 (Science mag, supporting information)

|}

 

{| {{table}}

| align="center" style="background:#f0f0f0;"|'''Cnnxn to Radioresistance'''

| MntH||||E. coli||Mn (II) transporter||Upregulate in order to establish Mn:Fe ratio similar to that of D. rad [other members of oxyR regulon?]||Jim Imlay||

| BtuE||||E. coli||||||||

|-

| OsmC||||E. coli||||||||

| phrA||||E. coli||photolyase activities||remove UV-induced DNA lesions from the genome||||

| phrB||||E. coli||photolyase activities||remove UV-induced DNA lesions from the genome||||

| recB||||E. coli||exonuclease V subunit, recBCD enzyme subunit, nuclease, helicase||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html

| recC||||E. coli||exonuclease V subunit, recBCD enzyme subunit, nuclease, helicase||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html

| recF||||E. coli||RecFOR complex stabilizes the RecA filament-DNA complex||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html

| recJ||||E. coli||5\'-3\' exonuclease||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html

| lexA||||E. coli||repressor of the SOS regulon||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html

| uvrD||||E. coli||helicase II||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html

| radA||||E. coli||sms, recombination intermediate stabilization||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html

| ruvA||||E. coli||recombination intermediate stabilization||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html

| ruvB||||E. coli||recombination intermediate stabilization||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html

| ruvC||||E. coli||recombination intermediate stabilization||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html

| recG||||E. coli||radC, recombination intermediate stabilization||Repair of DNA Double Strand Breaks||||http://www.photobiology.info/Smith_DSB.html