Conventional Metabolic Pathways of D. radiodurans and Systems that Generate and Defend Against Free Radicals
The pathways are color coded as follows: Black, catabolism of fructose, lactate and acetate; pyruvate oxidative decarboxylation; TCA cycle (tricarboxylic acid cycle). Brown, reactions of the glyoxylate bypass. Blue, methionine, serine biosynthesis, and electron transfer coupled to ATP synthesis. Purple, cysteine biosynthesis and sulfate reduction. Green, basic ammonia metabolism. For each reaction, the gene name and/or D.radiodurans' gene number is shown. Red crosses show the location of predicted disruptions (missing genes) of biosynthetic pathways. Red arrows and boxes show the dominant reactions leading to the generation of free radicals. Typically during irradiation, ~80% of DNA damage is caused indirectly by irradiation-induced short-lived free radicals, the remaining ~20% by direct interaction between gamma-photons and DNA [Brim et al., 2000; Schulte-Frohlindeet et al., 1986; Von Sonntag et al., 1987; Zaider et al., 1994]. Black boxes include defense systems against free radical damage. Blue boxes outside the cell show proteases and substrates: Blue substrates in these boxes have predicted specified transporters, orange substrates do not have predicted specified transporters, but some are believed to be transported based on experimental evidence. Long dashed blue lines show conventional pathways leading to degradation of amino acids. Long solid blue lines indicate transport based on experimental evidence. Inside the cell, blue boxes indicate substrates that support growth, orange ovals indicate substrates which do not support growth. Abbreviations: APS, adenylylsulfate; PAPS, phosphoadenylylsulfate; NAD, nicotinamide adenine dinucleotide (oxidized form); NADH, nicotinamide adenine dinucleotide (reduced form); NADP, nicotinamide adenine dinucleotide phosphate (oxidized form); NMN, nicotinamide mononucleotide; FMN, flavin mononucleotide; FAD, flavin adenine dinucleotide (oxidized form); FADH, flavin adenine dinucleotide (reduced form); ATP, adenosine triphosphate; ADP, adenosine diphosphate; PEP, phosphoenolpyruvate; nicotinate-AD, nicotinic acid adenine dinucleotide; nicotinate-NM, nicotinic acid mononucleotide; E1, subunit of phosphotransferase system; Pi, orthophosphate; PPi, pyrophosphate; Q, ubiquinone; SOD, superoxide dismutase; O2.-, superoxide radical; O2-, peroxide ion; OH., hydroxyl radical; e-aq, hydrated electrons.
All TCA cycle genes in D. radiodurans (including genes for its glyoxylate bypass) are functionally expressed based on our annotation [Makarova et al., 2001], proteome analysis [Lipton et al., 2002], and whole genome expression analysis during recovery from irradiation [Liu et al., 2003] However, it is unable to use succinate, fumarate, malate, and alpha-ketoglutarate as sole carbon/energy sources for growth in defined minimal medium (DMM). We find that four genes (nadABCD) required for NAD biosynthesis are absent, and consistent with this prediction, D. radiodurans is dependent on exogenous nicotinic acid.