Table 1 Phyletic distribution and components of prominent gene neighborhoods of prokaryotic beta-grasp proteins
Row | Gene neighborhood type | Phyletic pattern | Protein coded by conserved genes neighborhoods/comments |
|---|---|---|---|
1 | Thiamine biosynthesis | All known bacterial lineages | ThiS, ThiG, ThiF, ThiC, ThiD, ThiE, ThiH and ThiO Comment: In many proteobacteria and the actinobacterium Rubrobacter xylanophilus, the ThiS is fused to a ThiG. In a subset of δ/ε proteobacteria and low GC Gram-positive bacteria, the ThiS is fused to a ThiF and these operons also encode a second solo ThiS-like protein |
2 | Molybdenum cofactor biosynthesis | All known bacterial and most archaeal lineages | MoaE, MoaC and MoaA Comment: In some rare instances, MoeB is present in the same operon as MoaD |
3 | Tungsten cofactor biosynthesis | Euryarchaea: Mace, Mmaz, Paby, Pfur, Pfur, Phor, and Tkod α, β, γ, δ/ε proteobacteria: Aehr, Asp., Dace, Ddes, Dpsy, Dvul, Gmet, Gsul, Mmag, Pcar, Pnap, Ppro, Rfer, Rgel, Sfum, and Wsuc Low GC Gram positive: Chyd, Moth, Swol, Teth, and The Actinobacteria: Sthe Other bacteria: Tth | MoaD, aldehyde-ferredoxin oxidoreductase, MoeB, MoaE, MoeA, pyridine disulfide oxidoreductase, and 4Fe-S ferredoxin Comment: In Azoarcus, the MoaD is fused carboxyl-terminal to the aldehyde ferredoxin oxidoreductase (Figure 3) |
4a | Siderophore biosynthesis | β and γ proteobacteria: Neur, Nmul, Rsol, Pflu, Hche, Pstu, and Pput | ThiS/MoaD-like Ub (PdtH), E1-like enzyme fused to a Rhodanese domain (PdtF), JAB (PdtG), CaiB-like CoA transferase (PdtI), and AMP-acid ligase (PdtJ) Comment: Experimentally characterized siderophores encoded by this pathway include PDTC and quinolobactin |
4b | Uncharacterized operon encoding a ThiS/MoaD, a JAB peptidase, and E1-like enzyme | γ, δ/ε proteobacteria: Adeha, Aehra, and Noce Cyanobacteria: Ana, Avar, Gvioa, Npun, Pmar Syn, and Telo | E1 fused to a Rhodanese domain and JAB Comment: aThese species also possess a ThiS/MoaD-like Ub |
4c | Uncharacterized operon with a ThiS/MoaD, E1-like enzyme, a JAB, and a cysteine synthase | α, γ proteobacteria: Paer and Rpal Acidobacteria: Susi Actinobacteria: Rxyl Bacteroidetes/Chlorobi: Srub Chloroflexus: Caur | E1 is fused to a Rhodanese domain |
4d | Uncharacterized operon with a ThiS/MoaD, JAB, cysteine synthase, and ClpS | Actinobacteria: Fsp., Mtub, Nfar, Nsp., Save, Scoe, and Tfus | Comment: Additionally the operon encodes an uncharacterized conserved protein with an α-helical domain (Figure 3) |
4e | Operons with genes for sulfur metabolism proteins | δ/ε proteobacteria: Gmet and Wsuc Low GC Gram positive: Amet, Bcer, Chyd, Csac, Cthe, and Dhaf Bacteroidetes/Chlorobi: Cpha Actinobacteria: Nsp. and Acel Crenarchaea: Pyae | ThiS/MoaD-like protein, JAB, E1-like protein, SirA, sulfite/sulfate ABC transporters, PAPS reductase, ATP sulfurylase, sulfite reductase, O-acetylhomoserine sulfhydrylase, and adenylylsulfate kinase Comment: The ThiS/MoaD domain in Nsp and Acel are fused to a sulfite reductase |
5 | Phage tail assembly associated Ub | Lambdoid and T1 phages | Ub-like TAPI, TAPK protein with a JAB and NlpC domains, and TAPJ Comment: The TAPI proteins additionally have a carboxyl-terminal domain that is separated from the Ub domain by a glycine rich region. In some prophages, TAPI is fused to the TAPJ protein. In one particular prophage of Ecol (Figure 3) the TAPI is fused to the JAB. The NlpC domains of these versions almost always lack the JAB domain. These latter operons also encode a β-strand rich domain containing protein (labeled 'Z' in Figure 4) |
6a | Uncharacterized operon with a triple module protein containing an E2-like, E1-like, and JAB domains | α, β, γ, δ/ε proteobacteria: gKT 71, Goxy, Maqu, Msp, Nwin, Obat, Pnap, Rmet, Rsph, Saci, Sdeg, and Xaxo Low GC Gram positive: Cper | Triple module protein with E2 (UBC), E1-like domain and JAB, lined in a single polypeptide in that order. Comment: In most operons, these are almost always next to a metallo-β-lactamase |
6b | Uncharacterized operon encoding a multidomain protein with E2 and E1 domains | α, β, γ, δ/ε proteobacteria: Ecol, Elit, Gura, Obat, Parc, Pber, Retl, RhNGR234a, Rosp., Rusp., Shsp., and Vcho Actinobacteria: Asp. Low GC Gram positive: Cper | Multidomain protein with E2 and E1 domains, JAB, and polβ superfamily nucleotidyl transferase Comment: Both the E2 + E1 protein and the JAB are closely related to the corresponding sequences of the operons in the previous row of the table. Most of these operons are in ICE-like mobile elements and plasmids |
6c | Uncharacterized operon encoding a distinctive multidomain protein with E2 and E1 related domains | α proteobacteria: Mlot, Mmag, Retl, RhNGR234, and Rpal | Multidomain E2 + E1 protein, JAB, and predicted metal binding protein Comment: In Mmag and Rpal, the E1 domain is fused to a distinct domain instead of E2. The E2-like domain has a conserved cysteine in place of the conserved histidine of the classical E2s |
6d | Uncharacterized operon coding a Ub-like protein, a JAB, an E1-like protein, and an E2-like protein | β, δ/ε proteobacteria: Asp., Bvie, Cnec, Daro, Pnap, Ppro, Posp., Rfer, Rmet, and Rsol Low GC Gram positive: Bcer and Bthu Cyanobacteria: Ana and Avar Bacteroides: Bthe | Ub-like protein, JAB, E1-like, E2-like, and novel α-helical protein Comment: The E2-like protein lacks the conserved histidine of the classical E2-fold. However, they have an absolutely conserved histidine carboxyl-terminal to the conserved cysteine. The rapidly diverging α-helical protein has several absolutely conserved charged residues, suggesting that it may function as an enzyme. The JAB domains of this family additionally have an amino-terminal α + β domain characterized by a conserved arginine and tryptophan residue |
6e | Uncharacterized operons coding a protein with tandem repeats of a ubiquitin-like domain (polyUbl) | α, β, γ, δ/ε proteobacteria: Amac, Bviec, Mlotb, Nhamc, Pnapc, Rmetb, Rpalb, Shsp.b, and Vparb Actinobacteria: Fsp.b Cyanobacteria: Ana and Syn | PolyUbl, inactive E2-/RWD like UBC fold domain, multidomain protein with a JAB fused to an E1 domain, and a metal-binding protein (labeled Y in Figure 3) Comment: The polyUbls contain between two and three Ub-like domains (Figure 3). bSome versions of the E1 domain have a distinct domain in place of the JAB domain (domain X in Figure 3). cIn some species the polyUbl is fused to an inactive E2-like domain. Amac has a solo Ub-like domain |
7 | Ubl fused to Mut7-C | Wide range of β proteobacteria and Avin Actinobacteria: Mtub, Scoe, Save, Mavi, Nfar, and Tfus Acidobacteria: Susi Cyanobacteria: Npun Tmar | No conserved genome context |
8 | Uncharacterized operon encoding a RnfH family protein | A wide range of β and γ proteobacteria and Mmag | Ub-like RnfH, a START domain containing protein, SmpA, and SmpB |
9 | Mobile RnfH operon | α, β, γ proteobacteria: Asp., Daro, Pstu, Rcap, and Zmob | Ub-like RnfH, RnfB, RnfC, RnfD, RnfG, and RnfE Comment: These components are part of an electron transport chain involved in reductive reactions such as nitrogen fixation |
10 | Toluene-O-xylene mono-oxygenase hydroxylase | α, β, and γ proteobacteria: Bcep, Bsp., Daro, Paer, Pmen, Psp. Reut, Rmet, Rpic, and Xaut Actinobacteria: Rsp. and Fsp. | Ub-like TmoB, toluene-4-mono-oxygenase hydroxylase (TmoA), hydroxylase/mono-oxygenase regulatory protein (TmoD), toluene-4-mono-oxygenase hydroxylase (TmoE), Rieske 2Fe-S protein (TmoC), NADH-ferredoxin oxidoreductase (TmoF), 4-oxalocrotonate decarboxylase (4OCDC), and 4-oxalocrotonate tautomerase (4OCTT) |
11 | YukD-like ubiquitin | Low GC Gram positive: Bcer, Bcla, Bhal, Blic, Bsub, Bthu, Cace, Cthe, Linn, Lmon, Oihe, Saga, Saur, and Saur Actinobacteria: Cjei, Jsp., Mavi, Mbov, Mfla, Mlep, Msp., Mtub, Mvan, Nfar, Nsp., Save, and Scoe | Ub-like YukD, FtsK-like ATPase, S/T kinase, YueB-like membrane protein, subtilisin-like protease, ESAT-6 like virulence factor, PE domain, and PPE domain Comment: The Ub-like YukD in actinobacteria is fused to a multipass integral membrane domain with 12 transmembrane helices |