In G. metallireducens, there is no full-length modE gene, but a gene encoding the C-terminal molybdopterin-binding (MopI) domain of ModE (Gmet_0511) is present in the same location (Figure 6). Phylogenetic analysis shows that the Gmet_0511 gene product is the closest known relative of G. sulfurreducens ModE, and that it has evolved out of the Geobacteraceae/LY2606368 datasheet Chlorobiaceae cluster of full-length ModE proteins by loss of the N-terminal ModE-specific domain https://www.selleckchem.com/products/i-bet151-gsk1210151a.html (data not shown). The ScanACE software detected only one of the ModE-binding sites of G. sulfurreducens at the corresponding location in the G. metallireducens genome, but some vestigial sites were
apparent when other syntenous locations were selleck inhibitor visually inspected (Additional file 3: Table S3), indicating that the ModE regulon once existed in G. metallireducens, but recent loss of the ModE N-terminal domain is allowing the regulatory sites to disappear gradually over the course of genome sequence evolution due to the absence of selective pressure for these sites to remain conserved. Thus, genes that may be controlled globally by ModE in G. sulfurreducens and other Geobacteraceae to optimize molybdenum cofactor-dependent
processes have recently acquired independence in G. metallireducens. Amino acid biosynthesis and its regulation The two genomes differ in several aspects of amino acid biosynthesis and its regulation. To make aspartate from oxaloacetate, a homolog of Bacillus circulans aspartate aminotransferase [44] is present in G. metallireducens (Gmet_2078; 65% identical), whereas a homolog of the Sinorhizobium meliloti enzyme [45] is found in G. sulfurreducens (GSU1242; 52% identical). Both species possess asparagine synthetase (Gmet_2172 = GSU1953 and Gmet_2024, 30% and 24% identical to asnB of B. subtilis [46]) and glutamine synthetase (Gmet_1352 = GSU1835, 61% identical to glnA of
Fremyella diplosiphon [47]), as well as an aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase operon (Gmet_0076, Gmet_0075, Gmet_0073 = GSU3383, GSU3381, GSU3380, 36–53% identical to the homologous subunits in B. subtilis [48]) that includes glutamine synthetase adenylyltransferase (glnE; Gmet_0071 = GSU3378). The G. sulfurreducens glnE gene may be inactive due to a deletion AZD9291 of ~ 45 codons in the C-terminal domain. For biosynthesis of lysine, threonine and methionine, G. metallireducens and other Geobacteraceae possess a linked pair of aspartate-4-semialdehyde dehydrogenase genes: Pseudomonas aeruginosa-type Gmet_0603 (69% identity) [49] and Mycobacterium bovis-type Gmet_0604 (47% identity) [50], but G. sulfurreducens has only the former (GSU2878). A haloacid dehalogenase family protein (Gmet_1630 = GSU1694) encoded between two genes of the threonine biosynthesis pathway could be the enzyme required to complete the pathway, a phosphoserine:homoserine phosphotransferase analogous to that of P.