Team:NYC Wetware/Deinococcus/Candidate Genes

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D. rad Genes for Cloning

Name	Other Name	Number	Function	Cnnxn to Radioresistance	Recommended By	Citations
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)

E. coli Genes for Cloning

AhpC	Other Name	Organism of Origin	Function	Cnnxn to Radioresistance	Recommended By	Citations
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
Dps		E. coli	DNA-binding protein from starved cells – protect DNA by binding to form condensed co-crystal and by preventing oxidative damage - induced by oxyR	Upregulate for Fe (II) sequestration that helps with oxidative damage	Jim Imlay
SodA	Mn-SOD	E. coli	‘Catalyzes dismutation of superoxide into oxygen and HOOH – fixes iron		Frederik Domann
SodB	Fe-SOD	E. coli	Catalyzes dismutation of superoxide into oxygen and HOOH		Frederik Domann
Fur		E. coli	Transcriptional activator of bacterial sodB	Upregulate…	Frederik Domann
RecA		E. coli		Repair of DNA Double Strand Breaks		http://www.photobiology.info/Smith_DSB.html
RecN		E. coli		Repair of DNA Double Strand Breaks		http://www.photobiology.info/Smith_DSB.html
KatE		E. coli
KatG		E. coli
AhpC		E. coli
Tpx		E. coli
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