Tryptophan is the only known substrate other than pyruvate that is used for fermentative cell growth in this organism . Two buy Staurosporine copies of the gene (Dhaf_1324 and Dhaf_2460) coding for tryptophanase which converts tryptophan to indole, pyruvate, and ammonia were identified in association with two permease genes (Dhaf_1325 and Dhaf_2459). These gene sets were also observed in Y51 (DSY4041-4042 and DSY1331-1332). Complete biosynthetic pathways are present for the formation of amino acids, nucleic acid precursors, as well as fatty acids and phospholipids.
The genome also encodes complete biosynthetic pathways for various enzyme cofactors and prosthetic groups including NAD(P), menaquinone, heme, thiamine pyrophosphate, pyridoxal phosphate, riboflavin, pantothenate, folate, and biotin. SIS3 clinical trial However, the genome of D. hafniense DCB-2 appears to lack a gene for dihydrofolate reductase, a ubiquitous enzyme that is
required for the synthesis of tetrahydrofolate (THF). THF is involved in one-carbon transfer reactions Bortezomib cost and in the synthesis of purine bases, glycine, and serine. The gene was neither found in the Y51 genome, nor in those of other members of the Peptococcaceae family listed in IMG (Integrated Microbial Genomes), suggesting that this group of organisms may have evolved an unconventional dihydrofolate reductase for the synthesis of THF. The tricarboxylic acid cycle (TCA) of D. hafniense DCB-2 and Y51 appears incomplete since they lack the gene coding for 2-oxoglutarate Chlormezanone dehydrogenase, and the cycle lacks the anaplerotic glyoxylate bypass (Figure 2). In most autotrophic bacteria and anaerobic Archaea, the TCA cycle operates in a reductive, biosynthetic direction . In line with this observation, DCB-2 and Y51 are apparently capable of performing the reductive TCA cycle due to the possession of additional enzymes such as fumarate reductase and citrate lyase to potentially bypass the unidirectional steps of the conventional oxidative TCA cycle  (Figure 2). However, the reconstruction of the TCA cycle based solely
on genome sequence should be carefully addressed, as observed in Clostridium acetobutylicum where both functional oxidative and reductive TCA cycles were confirmed experimentally in contrast to the previous genomic interpretation . Figure 2 Carbon metabolic pathways of D. hafniense DCB-2. The pathways were constructed based on the presence or absence of key metabolic genes in D. hafniense DCB-2. The acetyl-CoA degradation and related genes are shown in more detail (boxed). Enzymes for the numbered reactions in figure are listed below with their potential genes; 1. pyruvate kinase; Dhaf_2755. 2. phosphoenolpyruvate synthase; Dhaf_1117, Dhaf_1622, Dhaf_3294. 3. pyruvate, phosphate dikinase; Dhaf_1046, Dhaf_4240, Dhaf_4251. 4. D-lactate dehydrogenase (cytochrome); Dhaf_3228, Dhaf_4382. 5. L-lactate dehydrogenase; Dhaf_1965. 6. PEP carboxykinase; Dhaf_1134. 7. malate dehydrogenase (NADP+); Dhaf_0902, Dhaf_3085. 8.