Multiple copies of the amo and hao gene clusters. Repeat regions of amo and hao clusters with near 100% identity are shown on the same background color. Selected putative promoters and terminators are shown. Gene clusters include amo operon copies 1 and 2 duplicate regions containing amoCAB, orf4, orf5, copC, and copD; amo/hao ammonia catabolic supercluster; and Nmul_A0177 (amoC) identical copy and Nmul_A2467 amoC divergent copy. Nmul_A0805, Nmul_A1082, and Nmul_A2622 encode hydroxylamine oxidoreductase. Nmul_A0804, Nmul_A1083, and Nmul_A2661 encode the Orf2 protein. Nmul_A0803, Nmul_A1084, and Nmul_A2660 (cycA) encode cytochrome C-554. Nmul_A0802, Nmul_A1085, and Nmul_A2659 (cycB) encode tetraheme cytochrome Cm552. Nmul_A2663 (focA) encodes a formate nitrite transporter. See text for additional discussion and reference 2 for more details of gene nomenclature.

Unique hydrogenase and urease gene clusters of N. multiformis. (A) The hydrogenase-encoding gene cluster from Nmul_A1662 to Nmul_A1677 (Nmul_A1662-1677; genes are abbreviated by their last four numbers) and its putative products and functions are as follows: Nmul_A1662, exonuclease metallo-beta-lactamase RNA processing enzyme; Nmul_A1663, response regulator GAF:metal-dependent phosphohydrolase HD domain (sigma-54 related); Nmul_A1664 (hypC), chaperone; Nmul_A1665 (hypA), hydrogenase expression and synthesis; Nmul_A1666 (hypB), hydrogenase accessory protein; Nmul_A1667 (hypD), hydrogenase formation; Nmul_A1668 (hypF), [NiFe] hydrogenase maturation protein; Nmul_A1669 (hypE), hydrogenase expression/formation protein; Nmul_A1670 to Nmul_A1673, four subunits of hydrogen dehydrogenase (EC 1.12.1.2) (Nmul_A1670 [hoxF], NAD-reducing hydrogenase [diaphorase] and 51-kDa alpha subunit; Nmul_A1671 [hoxU] ferredoxin gamma subunit Nmul_A1672 [hoxY], coenzyme F420-reducing delta 20-kDa small-subunit; Nmul_A1673 [hoxH], large-subunit); Nmul_A1674, unknown with N-terminal signal sequence and C-terminal PEP motif; Nmul_A1675 (hoxW), hydrogenase maturation peptidase; Nmul_A1676, GCN5-related acetyltransferase coenzyme A-binding transcriptional activation; Nmul_A1677, unknown function with N-terminal signal sequence and C-terminal PEP motif. (B) Urease-encoding cluster and regulatory regions, including the genes from Nmul_A1233 to Nmul_A1246 (Nmul_A1233-1246; genes are abbreviated by their last four numbers), and their products or functions are as follows: Nmul_A1233, TonB-dependent receptor; Nmul_A1234, putative transcriptional regulator and CopG family of nickel-responsive regulators; Nmul_A1235, two-component transcriptional regulator LuxR (regulatory protein, response regulator receiver containing a CheY-like receiver domain and a helix-turn-helix DNA-binding domain); Nmul_A1236, periplasmic sensor signal transduction histidine kinase; Nmul_A1237, FmdC precursor and urea-responsive OM porin; Nmul_A1238, accessory protein UreD; Nmul_A1239 to Nmul_A1241, structural subunits UreA, UreB, and UreC, respectively; Nmul_A1242 to Nmul_A1244, accessory proteins UreE, UreF, and UreG, respectively; Nmul_A1245, urea transporter; Nmul_A1246, transcriptional regulator, putative ATPase, winged helix family.

EPS, LPS, and capsule clusters in N. multiformis. (A) Nmul_A0238 to Nmul_A0262 (Nmul_A0238-0262). EPS cluster with similarity to cluster in Methylobacillus sp. strain 12S (AB062506). Gene designations for orthologs in Methylobacillus sp. strain 12S are given, and genes essential for the production of the EPS methanolan in Methylobacillus sp. strain 12S are highlighted. (B) Putative EPS and LPS cluster including Nmul_A2530 to Nmul_A2515 (Nmul_A2530-2515) and their putative products and functions are as follows: Nmul_A2529, polysaccharide export to OM protein; Nmul_A2528, EPS biosynthesis chain length determinant similar to Wzz; Nmul_A2527, capsular polysaccharide biosynthesis protein; Nmul_A2526, signal peptide motif for secreted protein of unknown function; Nmul_A2525, type II transport ATPase; Nmul_A2524, polysaccharide deacetylase; Nmul_A2523, conserved hypothetical protein; Nmul_A2522, glycosyltransferase; Nmul_A2521 (epsH), EpsH (EPS locus protein H) involved in processing proteins to OM locations; Nmul_A2520, glycosyltransferase group 1, similar to wapH in P. putida (PP_4943); Nmul_A2519, asparagine synthase; Nmul_A2516, methyltransferase; Nmul_A2515, FkbH domain membrane protein involved in bacterial cell division. (C) Nmul_A0264-0292 putative EPS and LPS gene clusters. Nmul_A0264 to Nmul_A0292 (Nmul_A0264-0292) putative EPS and LPS gene clusters encoding proteins are shown as follows: Nmul_A0264 to Nmul_A0267, synthesis of dTDP-l-rhamnose (rfbBDAC); Nmul_A0268, fatty acid desaturase; Nmul_A0270, UDP-glucose/GDP-mannose dehydrogenase; Nmul_A0271, polysaccharide biosynthesis CapD; Nmul_A0277, dolichyl-P-beta-d-mannosyl transferase; Nmul_A0278 to Nmul_A0292, several glycosyltransferases, capK gene, and a polysaccharide biosynthesis protein often implicated in polysaccharide capsule biosynthesis.