Conserved nucleotide sequences (possible promoters and riboswitches) were identified on the 5′ sides of several biosynthetic operons (Table 2). The lysine biosynthesis operon in G. sulfurreducens Protein Tyrosine Kinase inhibitor and other
Geobacteraceae begins with a P. aeruginosa-type meso-diaminopimelate decarboxylase (GSU0158; 51% identity) [52], whereas G. metallireducens has two isoenzymes in other locations (Gmet_0219, 30% identical to the E. coli enzyme [53], with homologs in a few Geobacteraceae; Gmet_2019, 31% identical to the P. aeruginosa enzyme [52], unique to G. metallireducens). The recently identified L,L-diaminopimelate aminotransferase (dapL; Gmet_0213 = GSU0162) [54] is co-transcribed with the dapAB genes encoding the two preceding enzymes of lysine biosynthesis,
but separated from them by a predicted short RNA element (Gmet_R1005 = GSU0160.1), also found in 23 other locations on the G. metallireducens chromosome (Additional file 4: Figure S1, Additional file 5: Table S4). Table 2 Conserved nucleotide sequences 5′ of biosynthetic operons. Operon Locus tag and sequence coordinates G. metallireducens G. sulfurreducens aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase (gatCAB-mtnA-glnE-nth) Gmet_P0076 93465..93502 GSU3383.1 3719308..3719345 lysine (dapA) Gmet_P0211 244588..244640 GSU0157.1 176066..176117 aromatic amino acids (aroG-2) Gmet_R0069 384337..384528 GSUR082 3450692..3450963 cobalamin (cobUTSCB-thiC-2; cbiM-1-cbiQ-1-cbiO-1-cbiX-cobH-cbiD-cobLIM-cbiG-cobQ-cbiB-cobD) Gmet_R0070 513498..513761 no match GSU3011.1
3302884..3303201 GSU3004.1 3296929..3297108 Selleckchem eFT508 methionine (metC-1-metC-2; metX)1 Gmet_R0073 765279..765444 Gmet_R0129 3145553..3145656 GSUR063 1014004..1014271 GSU2461.2 2700118..2700220 leucine (leuA)2 Gmet_P1265 1425160..1425452 GSU1906.1 2085440..2085740 leucine/isoleucine Depsipeptide ic50 (leuCD) Gmet_P1268 1428650..1428793 GSU1903.1 2082057..2082203 coenzyme A (panBC) Gmet_P1642 1843163..1843275 GSU1704.1 1868745..1868863 pyrimidines (pyrRBC-carAB) Gmet_P1768 1983157..1983191 GSU1269.1 1384886..1384920 tryptophan (iorAB-paaK) Gmet_P1827 2042198..2042288 GSU1739.1 1905464..1905561 purines, pyrimidines (purMN, rimI-pyrKD) Gmet_P1844 2056600..2056732 GSU1757.1 1920275..1920400 guanine (guaBA) Gmet_P2293 2600787..2600857 GSU2195.1 2408782..2408854 serine (serA) Gmet_P2378 2689446..2689518 GSU1197.1 1301091..1301163 thiamin (thiE/D-thiC-1; thiS-1-thiG-tenI)3 Gmet_R0131 3292750…3292897 Gmet_R0134 3319520..3319741 GSUR060 640780..640988 GSU0589.1 622533..622801 arginine (argBDFG) Gmet_P0203 3719308..3719345 GSU0149.1 167623..167663 1The sequence 5′ of metC-1, metC-2, and metX is a SAM-responsive riboswitch. 2The sequence 5′ of leuA is a T-box, an RNA structure that LY333531 recognizes the aminoacylation state of tRNA. 3The sequence 5′ of thiamin biosynthesis operons is a thiamin diphosphate-responsive riboswitch.