Team:NYC Wetware/Deinococcus/Candidate Genes

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Name Other Name Number Function Cnnxn to Radioresistance Recommended By Citations Team Member Choice ' ' ' ' ' ' ' ' ' ' '
MntHNRAMP transporterDR_1709Mn (II) transporterUpregulate in order to establish Mn:Fe ratio similar to that of D. rad [other members of oxyR regulon?]Jim ImlayDavid
DpsDNA-binding protein from starved cells – protect DNA by binding to form condensed co-crystal and by preventing oxidative damage - induced by oxyRJim ImlayDavid
PprIIrrEDR_0167Positive regulator of recA and other gamma irradiation-induced genesImportant effectBlasiusDavid
PprADR_A0346DNA binding and tethering of termini, stimulation of DNA ligases and catalaseStrongly induced upon ionizing radiation - Important effectBattistaJake
RecADR_2340Double strand break repairInverse DNA strand exchange pathway - Important effectBattistaJake
RecODR_0819DNA annealing during homologous recombinationStrong defect in growth and increased radiosensitivity of strain devoid of RecO - Important effectBlasiusJake
SodB Fe-SODCatalyzes dismutation of superoxide into oxygen and HOOH – fixes ironFrederik Domann
SodAMn-SODDR_1279?‘’ – fixes manganeseIncreases resistance to UV and HOOH damage in E. coli – But why? Without catalase/peroxidase?Frederik Domann
FurTranscriptional activator of bacterial sodBUpregulate…Frederik Domann
SOD?predicted SODsDR_1546, DR_A0202superoxide dismutationOmelchenko et al., 2005
Catalasespredicted catalsesDR_1998, DR_A0259, DR_A 0146Hydrogen peroxide to water and oxygenCatalase is important next enzyme after SOD. If not present, H2O2 accumulate and have deleterious effectOmelchenko et al., 2005
ThioredoxinDR_0994reverses oxidized sulfur speciesImportant for defense against oxidative stressObiero et al., 2010  :Journal of Bacteriology, January 2010, p. 494-501, Vol. 192, No. 2
Thioredoxin reductasemaintains reduced Thioredoxin enzyme levelsImportant for defense against oxidative stress
DdrBDR_0070Single strand binding proteinStrongly induced upon ionizing radiation - Important effectBattista
DdrADR_0423End-cappingStrongly induced upon ionizing radiation, homolog of Rad52 - Important effectBattista
DdrCDR_0003UnknownStrongly induced upon ionizing radiation - Modest effectBattista
DdrDDR_0326Protection of 3\' ends of single strand DNAStrongly induced upon ionizing radiation - Modest effectBattista
RecNDR_1477DNA Repair ProteinMutant shows general repair deficiencyBlasius
RecF
PolADR_1707DNA polymerase, probably involved in translesion synthesisimportant role in ESDSA DSB repair pathway, modulated by Mn(II) - Important effectBlasius
PolXDR_0467DNA polymerase/ 3\'-5\' exonucleaseNuclease is structure modulated, uses Mn(I) - Modest effectBlasius
SbcDDR_1921Homolog of Mre11, DNA end processingAdditive effect of SbcCD and PolX deficienciesBlasius
SbcCDR_1922Homolog of Rad50, DNA end processingHomolog of Mre11, DNA end processingBlasius Paper
RuvBDR_0576Resolution of Hollyday junctionsBlasius
RadADR_1105RecA-like functionBlasius
ClpPDR_1972Proteolytic subunit of ATP-dependent Clp proteaseBlasius
ClpXDR_1973ATP-binding subunit of ATP-dependent Clp proteaseBlasius
CrtBDR_0862Phytoene synthaseCarotenoids 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 componentsBlasiusZhang et al., 2007 (Arch Microbilogy)
CrtIDR_0861Phytoene desaturaseKO of carotenoid synthesis genes DR0861 and DR0862 resulted in increased sensitivity to oxidants, ionizing radiation and UVBlasiusZhang et al., 2007 (Arch Microbilogy)
CrtlmDR_0801Carotenoid synthesisThese genes boxed off are in the biosynthesis pathway for deinoxathin, the major carotenoid pigment in D. rad. It also has antioxidant propertiesTian & Hua., 2010
CrtODR_0093Carotenoid synthesis
CruFDR_0091Carotenoid synthesis
CrtDDR_2250Carotenoid synthesis
OxyRDR_0615Oxidative stress resistancelittle 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
OxyR2DR_A0336Oxidative stress resistanceNovel OxyR enzyme- this means D. rad has multiple OxyRs!!!Yin et al., 2010 (Jornal of Microbiology)
deiNOSdeinococcus nitric oxide synthaseDR_2597Nitirc oxide productionKO causes increase in susceptibility to UV irradiation. Slower recover following insultPatel et al., 2009., Adak et al, 2002
ObgE?GTPase that regulates cel growth/proliferationdecreased ObgE afte NOS KO implicated as an important mediator of growth recovery following UV insultPatel et al., 2009.,Already present in D. rad as well
Hypothetical proteinDR_A0282nucleotide binding protein??- perhaps DNA repairmutant 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_2523Mn (II) transportpossibly maintain intracellular Mn(II) ratio.Daly et al., 2004 (Science mag, supporting information)DR2283 was also discussed, but has homology to permeases and therefore probably would allow Mn to exit the cell
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