Table 4.

Some unusual predicted operons in D. radiodurans

Gene clusteraProtein descriptionBest hit: species and GI numberComment
DR0298Deoxypurine kinase subunit, YAAF Bacillus subtilis (586859)Clear case of gene exchange with gram-positive bacteria; essential enzymes for biosynthesis of deoxyribonucleotides
DR0299Deoxypurine kinase subunit, YAAG Bacillus subtilis(586860)
DR0398Alkaline-shock-like protein Bacillus subtilis (2337812)Clear case of gene exchange with gram-positive bacteria; possibly stress related; conserved operon in B. subtilis and T. maritima; all three bacteria encode an additional copy of alkaline-shock-like protein
DR0390Uncharacterized protein, YloV ortholog Bacillus subtilis(2337813)
DR0544Highly conserved membrane transporter Pyrococcus horikoshii (3256923)Likely gene exchange with archaea; possibly related to the multidrug resistance system
DR0545Small conserved membrane protein, possibly involved in multidrug resistance Methanobacterium thermoautotrophicum(2621904)
DR0674Argininosuccinate synthase, ArgG Thermotoga maritima (4982360)Acetyltransferase cluster disrupts ArgG/ArgH operon present in some other bacteria
DR0675Amino acetyltransferase Synechocystis(1651699)
DR0676Amino acetyltransferase, related to phosphinothricin acetyltransferase Escherichia coli(1742360)
DR0677Amino acetyltransferase Salmonella enterica serovar Typhimurium (586786)
DR0678Argininosuccinate lyase (ArgH) Bacillus subtilis (2293243)DR0681 and DR0683 may have evolved by internal duplication; DR0679 and DR0680 together may comprise a mobile element; this pair of genes is present twice more in the D. radiodurans genome
DR0679Small nucleotidyltransferase Synechocystis(1653122)
DR0680Uncharacterized protein next to small nucleotidyltransferases Synechocystis(1652090)
DR0681Amino acetyltransferase Aquifex aeolicus (2983780)
DR0682Amino acetyltransferase Salmonella enterica serovar Typhimurium (586786)
DR0683Amino acetyltransferase Aquifex aeolicus (2983780)
DR0689Uracil-DNA glycosylase (Ung)Human (137031)Likely horizontal transfer from a eukaryote or a eukaryotic virus
DR0690Topoisomerase IBOrf virus (521138)
DR0796Amino acetyltransferase Bacillus subtilis(1881232)Acetyltransferase cluster; DR0796 and DR0797 are possible products of internal duplication
DR0797Amino acetyltransferase Synechocystis(1651699)
DR0798Amino acetyltransferase Bacillus subtilis (1881232)
DR0853Rab/Ras family small GTPase Myxococcus xanthus (94524)Potential operon conserved also in Thermus, Myxococcus and archaea; involved in gliding motility in Myxococcus
DR0854Protein associated with a GTPase Myxococcus xanthus(94525)
DR0861Phytoene dehydrogenase, CRTI Flavobacterium (1842244)Carotenoid biosynthesis genes; Possibly involved in pigment biosynthesis inDeinococcus
DR0862Phytoene synthase, CRTB Thermus thermophilus(585011)
DR0993Uncharacterized protein associated with GTPase Methanococcus jannaschii (1591982)Cluster of genes that are expanded in Deinococcus and encode uncharacterized small proteins often associated with Ras/Rab family GTPase (see also DR0853–DR0854 and DR2180–DR2181)
DR0994Uncharacterized protein associated with GTPaseDistantly related to the family of GTPase-associated proteins
DR0995Uncharacterized protein associated with GTPase Aquifex aeolicus(2984135)
DR1175N-terminal CheY family domain +C-terminal histidine kinase Mycobacterium tuberculosis(2960188)Signal transduction system; proteins with modified domain architectures compared to M. tuberculosis andSynechocystis
DR1174Histidine kinase with 3 PAS +3 PAC + GAF domains Synechocystis(1652132)
DR1232Pilin IV-like secreted protein Psedomonas putida (544344)Pilin IV cluster also including a GTPase with a possible regulatory role; probably responsible for DNA transformation
DR1233Pilin IV-like secreted protein Legionella pneumophila(3002996)
DR1234Pilin IV-like secreted protein Klebsiella oxytoca(131598)
DR1235Dynamin-like GTPase Arabidopsis thaliana (4587579)
DR1596Glucose-6-phosphate 1-dehydrogenase Synechocystis (2494656)Clear case of gene exchange with cyanobacteria
DR1597OPCA, OxPPCycle gene, involved in assembly of glucose-6-phosphate 1-dehydrogenase Synechocystis(2498703)
DR1641DinB/YfiT superfamily proteinBoth distantly similar to Bacillus subtilis(2633163)See main text
DR1642DinB/YfiT superfamily protein
DR1928Glycerol kinase (GlpK) Borrelia burgdorferi (2688136)Clear case of gene exchange with spirochetes
DR1929Glycerol uptake facilitator (GlpK) Borrelia burgdorferi(2688137)
DR2180Uncharacterized protein associated with GTPase Aquifex aeolicus (2984135)Clear case of gene exchange with thermophiles (See above)
DR2181RAB/RAS-like small bacterial GTPase, inactivated Aquifex aeolicus(2984130)
DR2220Tellurium resistance protein (TerB)Plasmid R478 (950680)Tellurium resistance gene cluster; probable acquisition of a plasmid fragment; stress response-related genes; operon is probably disrupted by a transposon
DR2221Tellurium resistance, member ofDictyostelium-type cAMP-binding protein family Alcaligenes sp. (135597)
DR2222TransposaseNo significant similarity
DR2223Tellurium resistance, member ofDictyostelium-type cAMP-binding protein family Alcaligenes sp. (78205)
DR2224Tellurium resistance, member of Dictyostelium-type cAMP-binding protein familyPlasmid R478 (1181183)
DR2225Tellurium resistance, member of Dictyostelium-type cAMP-binding protein familyPlasmid R478 (950682)
DR2226Tellurium resistance, membrane protein (TerC) Mycobacterium tuberculosis(2105065)
DR2254Amino-acetyltransferase Streptomyces coelicolor (5531439)Acetyltransferase cluster; these proteins are likely to be a product of internal duplication
DR2255Amino-acetyltransferase Streptomyces coelicolor (5531439)
DR2311Uncharacterized protein, YeiN ortholog Escherichia coli (465602)Among bacteria, YeiN orthologs are present only in Deinococcus and gamma proteobacteria; in eukaryotes, their counterparts are fused with the kinase gene; probable gene exchange with proteobacteria
DR2312RBSK family ribokinase, YeiI ortholog fused to HTH domain Escherichia coli (2507177)
DRA0231Oxidoreductase Escherichia coli (2495497)Highly conserved paralogous gene cluster is located next to this one in the chromosome (DRA0235–37), but in the opposite orientation
DRA0232Flavoprotein dehydrogenase Escherichia coli(2495498)
DRA0233Dehydrogenase, iron sulfur protein Escherichia coli(2495499)
DRA0331Von Willebrand factor A domain, Mg2+ binding Synechocystis sp. (2496792)Serine/threonine protein kinase-based regulatory system
DRA0332PKN2 family serine threonine kinase Anabaena sp. (1709645)
DRA0333Zn-finger and FHA domain-containing protein, ortholog of cyanobacterial FraH Anabaena sp. (556608)
DRA0334Inactive kinase +PP2C phosphoprotein phosphatase Mycobacterium tuberculosis (1552573)
DRB0143AAA superfamily NTPase related to 5-methylcytosine-specific restriction enzyme subunit McrB Escherichia coli (1790805)Mcr operon is present only in E. coli and D. radiodurans; a clear case of horizontal gene exchange
DRB0144Homolog of the McrC subunit of the McrBC restriction-modification system Escherichia coli (1790804)
  • a A gene cluster was considered a likely operon if the genes were localized on the same DNA strand and the distance between them was less than 100 bp.