Table 1.

Basic metabolic pathways in D. radiodurans

PathwayGenes in the pathwayaGenes missingbComments
Glycolysis glk, pgi, pfkA, fba/dhnA, tpi, gapA, pgk, pgm/yibO, eno, pykA Complete pathway
Gluconeogenesis ppsA, eno, pgm, pgk, gapA, tpi, fba/dhnA, fbp, pgi fbp(CE--)Likely functional pathway
Pentose phosphate shunt and pentose biosynthesis zwf, gnd, tktA, talA, yhfD, rpiA, deoC Complete pathway
Entner-Doudoroff pathway zwf, edd, eda, gnd eda(CEB-)Likely functional pathway
TCA cycle gltA, acnA, icd, sucA, sucB, sucC, sucD, frdA, frdB, fumA, fumC, mdh fumA (-E--)Likely functional pathway
Glyoxalate bypass glcB, AceA Rare pathway present in E. coli, M. tuberculosis, and few other bacteria
Purine biosynthesis prsA, purF, purD, purN/purT, purL, purM, purK, purE, purC, purB, purH2, purH1, purA, guaB, guaA Complete pathway
Purine salvage purU, deoD, xapA, apt, xpt, hpt xapA (CEBR) D. radiodurans has two apt genes of archaeal type
Pyrimidine biosynthesis curA, carB, pyrB, pyrC/ygeZ, pyrD, pyrE, pyrF, pyrH, ndk, pyrG Complete pathway
Pyrimidine salvage cdd, upp, udk, deoD, deoA, nrdF, nrdE, pfs/amn, tdk Complete pathway with two nrdE (one is of archaeal type with intein)
Thimidylate biosynthesis dcd, dut, thyA, tmk, ndk dcd (CE-R), dut(CEBR)Pathway could be functional if unknown analogs ofdcd and dut are present
Histidine biosynthesis prsA, hisG, hisI2, hisI, hisA, hisH, hisF, hisB2, hisC, hisB1, hisD Complete pathway
Branched-chain amino acid biosynthesis ilvA, ilvB, ilvN, ilvC, ilvD, leuA, leuC, leuD, leuB, ilvE Complete pathway
Glutamate and glutamine biosynthesis gltB, gdhA, glnA Complete pathway; D. radiodurans has two glnA genes, One is for the rare class III glutamine synthase; in R1 strain this gene has a frameshift
Aspartate and asparagine biosynthesis aspC, asnB, asnA, ansA asnB(-EBR), asnA (-E--)Pathway could be functional if unknown analogs of asnB and asnA are present
Aromatic amino acid biosynthesis aroG/kdsA, aroB, aroD, aroE, aroK, aroA, aroC, pheA1, pheA2, tyrA2, tyrB, trpD1, trpE, trpD2, trpC2, trpC1, trpA, trpB tyrB (-E--) D. radiodurans has both aroG and kdsA; D. radiodurans and B. subtilis have rare bifunctional protein: chorismate mutase (tyrA1) and 2-dehydro-3-deoxyphosphoheptonate aldolase (aroG); D. radiodurans has two trpE genes, one of which is fused to trpG; same fusion is also found inAsospirillum and Rhizobium; reverse fusion is inStreptomyces
Serine and glycine metabolism serA, serC, serB, glyA, gcvP, gsvT, gsvH, lpd serC (-EB-), serB (-E-R)Pathway could be functional if unknown analogs of serB andserC are present
Threonine biosynthesis thrA, asd, thrB, thrC Complete pathway
Methionine biosynthesis metL1/thrA1, asd, metL2/thrA2, metA, metB, metC, metE/metH metA (-EB-)Incomplete and unlikely to be a functional pathway
Cysteine biosynthesis cysD/cysH, cysC, cysN, cysI, cysJ, cysK/cysM, cysE cysD/cysN, cysM, cysE (CEBR), cysJ (CEB-)Unlikely to be a functional pathway
Arginine biosynthesis argJ, argB, argC, argD, argE, argF, argG, argH, argI Likely functional pathway; circular type as in gram-positive bacteria; some genes were acquired from archaea (see Table 11)
Proline metabolism argB, argE, proB, proA, proC, putA Complete pathway
Lysine biosynthesis dapA, dapB, dapD, dapC, dapE, dapF, lysA dapA, dapB, dapF (CEBR), dapD(-EB-)Unlikely to be a functional pathway; dapC may be substituted by other aminotransferase; the closest gene todapE is more likely to be an ortholog of B. subtilis rocB and therefore is probably involved in degradation of amino acids rather than in lysine biosynthesis
Fatty acid biosynthesis accB, accC, accA, accD, acpP, fabB/fabF, fabH, fabD, fabG, fabI, fadA, BS_mmgB, caiD Complete pathway;D. radiodurans encodes four accA, fouraccD, four BS_mmgB, and five caiD
NAD biosynthesis nadB, nadA, nadC, nadD, nadE, pncB nadB, nadA, nadC, nadD (CEBR)Unlikely to be a functional pathway
Riboflavin and FAD biosynthesis ribA, ribD, ribB, ribE, ribC, ribG Complete pathway
Siroheme biosynthesis hemA, hemL, hemB, hemC, hemD, cysG2, cysG1 D. radioduranshas two other genes related to this pathway; hemF andhemY
Cobalamin biosynthesis cysG2, cbiL, cbiH, cbiF, cbiJ, cbiE, cbiT, cbiC, cbiA, cobN, cobA, cbiP, cobD, cbiB, cobT, cobS, cobU cbiL, cbiH, cbiJ, cbiE, cbiT, cbiC, cobN (C--R)Possible partly functional pathway
Biotin biosynthesis bioW, bioF, bioA, bioD, bioB, birA, bioH bioW (--B-), bioA, bioD, bioB(CEBR)Pathway could be functional if unknown analogs ofbioD and bioW are present; bioAaminotransferase can be substituted by paralogous enzyme, and any biotin synthase-related enzyme may replace bioB
Pyridoxal phosphate biosynthesis yaeM, ldh, serC, pdxA, pdxJ, BS_yaad, pdxH, pdxK pdxA, pdxJ, (CE--) D. radiodurans has an ortholog of BS_yaad which is found so far only in archaea and eukaryotes
Thiamine biosynthesis thiC, thiD, thiK, thiE, thiL thiK (-EB-), thiL (CEBR)Pathway could be functional if unknown analogs of thiK andthiL are present
Ubiquinone and menaquinone biosynthesis menF, menD, menC, menE, menB, menA, menG, ubiA, ubiX, ubiB, ubiH, ubiE, ubiG menF, menD, menC, menE, menB, menA, (CEBR), menG (CE-R)Unlikely functional pathway of menaquinone biosynthesis; there are some paralogs ofmenC, but they are unlikely to be related to this pathway; synthesis of ubiquinone is likely to be present; only ubiGis missed, but it exists only in E. coli, Rickettsia and yeast
NAHD-ubiquinone oxidoreducataseAll 14 subunits in one operonComplete pathway
H+-ATPase8 subunits in one operonComplete pathway; vacuolar-type H+-ATPase like in archaea, Thermus, spirochetes, and Chlamydia
Cytochrome c andb-dependent electron transport cccA/cccB, qcrB, ctaA, ctaE, ctaF, ctaD, ctaB, ctaC, ccdA, sdhC, ccmG, ccmF, ccmE, ccmD, ccmC, ccmB, ccmA, ccmH, cydB, cydA ctaF, ccmA, ccmD(-E--), cydA, cydB (CEBR)Probably functional pathway; component of heme exporter (such proteins are definitely present and some of them can perform this function)
  • a The gene names and pathway classification follow the biochemical data and nomenclature described for E. coli and S. enterica serovarTyphimurium (152).

  • b The presence or absence in bacteria with large genomes is indicated in parentheses after the names of genes that are missing in D. radiodurans. Abbreviations are as follows: C, Synechocystis sp.; E, E. coli; B, B. subtilis; R, M. tuberculosis.