Fig. 8
From: Remarkably coherent population structure for a dominant Antarctic Chlorobium species
Ca. Chlorobium antarcticum cobalamin pathways. Steps common to the anaerobic and aerobic pathways, black connecting arrows; reactions specific to the anaerobic pathway, green arrows; cobinamide and pseudocobalamin salvaging, purple arrows; cobalt and cobalamin precursor transport, orange arrows; multi-step processes, dashed arrows connecting intermediate substrates; genes present in Ca. Chlorobium antarcticum, black font; genes not identified in Ca. Chlorobium antarcticum, grey font; genes in LCRs, red font. For additional details, see anaerobic and aerobic pathways genes in Additional file 1: Fig. S3; relative coverages for LCRs showing seasonal changes in abundance in Fig. 4, Additional file 1: Tables S4, S5, and S6; predicted bifunctional properties of genes in LCRs associated with anaerobic cobalamin production in Additional file 1: Table S6. Pathway information was derived from BioCyc online service [58, 59] and published data [60,61,62,63,64,65,66,67]. Cobalamin biosynthesis genes and enzymes listed in the order they function in the pathway: gltX, glutamyl-tRNA synthetase; hemA, glutamyl-tRNA reductase; hemL, glutamate-1-semialdehyde 2,1-aminomutase; hemB, porphobilinogen synthase; hemC, hydroxymethylbilane synthase; hemD, uroporphyrinogen-III synthase; cysG, uroporphyrin-III C-methyltransferase; sirC, precorrin-2 dehydrogenase; cbiK, sirohydrochlorin cobaltochelatase; cbiL, cobalt-precorrin-2 C20-methyltransferase; cbiH, cobalt-precorrin-3 C17-methyltransferase; cbiF, cobalt-precorrin-4 C11-methyltransferase; cbiG, cobalt-precorrin-5A hydrolase; cbiD, cobalt-precorrin-5B C1-methyltransferase; cbiJ, cobalt-precorrin-6A reductase; cbiT, cobalt-precorrin-6B C15-methyltransferase (decarboxylating); cbiE, cobalt-precorrin-7 C5-methyltransferase; cbiC, cobalt-precorrin-8 methylmutase; cbiA, cobyrinate A,C-diamide synthase; cobA, cobyrinate A,C-diamide adenosyltransferase; cobQ, adenosylcobyrate synthase; cobD, adenosylcobinamide-phosphate synthase; cobP/cobU, adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; cobS, adenosylcobalamin 5′-phosphate synthase; bzaAB, 5-hydroxybenzimidazole synthase subunits A and B; bzaC, 5-hydroxybenzimidazole O-methyltransferase; bzaD, 5-methoxybenzimidazole C-methyltransferase; bzaE, anaerobic 5,6-dimethylbenzimidazole synthase; cobT, nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase; cobC, adenosylcobalamine-5′-phosphate phosphatase. Cobinamide and pseudocobalamin salvaging gene: cbiZ, adenosylcobinamide amidohydrolase. Cobalamin transport genes: btuB, outer membrane TonB-dependent transporter; btuC, ABC transporter permease subunit; btuD, ABC-transporter ATP-binding subunit; btuF, cobalamin-binding periplasmic protein. Cobalt transport genes: cbiM, ECF-transporter cobalt-binding component; cbiN, ECF-transporter transmembrane component; cbiQ and cbiO, ECF-transporter ATP-binding components