Figure 1.
Development of dissimilatory sulfite reductase-like protein (Dsr-LP), F420H2-dependent sulfite reductase (Fsr) and dissimilatory sulfite reductase (Dsr).
Fsr-N and Fsr-C: N-terminal and C-terminal halves of Fsr, respectively. FGltS(I)-α and FGltS(I)-β: F420H2 dehydrogenase and glutamate synthase subunit of a putative F420H2-dependent glutamate synthase of methanogens; FpoF/FqoF: F420H2 dehydrogenase subunit of a membrane-bound proton pumping F420H2 dehydrogenase complexes of late evolving euryarchaea [36]; aFsr-α and aFsr-β: aSir and F420H2 dehydrogenase subunits of a putative F420H2-dependent assimilatory type siroheme sulfite reductase found in haloarchaea. * and ** are peripheral and additional iron sulfur cluster [Fe4-S4], respectively. Filled and unfilled boxed arrows show the path for the development of Fsr-N and Fsr-C, respectively. Dashed oval or circle, unidentified protein. X and Y1–3, unknown electron acceptors and donor, respectively.
Figure 2.
Distribution of Dsr-LP, Fsr, FGltS(I/II)-α and FpoF in methanogenic archaea.
The information has been presented on a 16S rRNA sequence based phylogenetic tree of methanogens for which whole genome sequences are available. Desulfurococcus fermentans was used as an outgroup. The confidence values presented at the branches of the tree were estimated from 1000 bootstrap repetitions; the scale bar underneath the tree indicates the number of base substitutions per site. (1 or 2), number of each type of sulfite reductase homolog in a methanogen. Dsr-LP: dissimilatory sulfite reductase-like proteins; Fsr, FGltS(I/II)-α, and FpoF: same as in the legend of Fig. 1. The Dsr-LP group numbers (Ia-d and IIIa-d) are according to Fig. 3. Color representation of Fsr-containing methanogens (color, characteristic); red, hyperthermophilic vent methanogen (except M. okinawensis is a thermophile); lavender, thermophile; blue, mesophile and psycrophile. Classification of FGltS according to Fig. 6 is shown in square brackets.
Figure 3.
The Dsr-LP classification (groups Ia-d and IIIa-d) is based on the presence and absence of the following functionally important sequence signatures: [Fe4-S4]-coupled siroheme binding site; iron sulfur cluster sites (*, peripheral; ** additional); and sulfite binding amino acid residues (Arg or Lys). Numbers 1–4 indicates the positions (1st, 2nd, 3rd and 4th) of sulfite binding amino acid residues. The amino acid sequences representing these characteristics are shown in Fig. S1. Groups IIa-d, represented by dotted-line box are hypothetical and yet to be detected.
Figure 4.
Phylogenetic tree of Dsr-LP and Dsr based on Maximum Likelihood method.
Dsr-LP (Groups Ia-d and IIIa-d) and Dsr, defined in Fig. 3 and its legend. Dsr and Fsr-C, defined in the legend of Fig. 1. Dv-DsrA/B and Af-DsrA/B, Dsr subunits A and B of Desulfovibrio vulgaris strain Hildenborough (ORFs DVU0402 and DVU0403) and Archaeoglobus fulgidus DSM 4304 (ORFs AF0423 and AF0424), respectively [64], [65]; Dv-alSir and CPE1438, anaerobic small sulfite reductase of Desulfovibrio vulgaris strain Hildenborough (ORF DVU_1597) and Clostridium perfringens strain 13, respectively [66]; The ORF numbers followed by “-C”, Fsr-C homologs. Abbreviation for organism names preceding the listed ORF numbers: MTBMA, Methanothermobacter marburgensis strain Marburg; MTH, Methanothermobacter thermautotrophicus ΔH; Metbo, Mehanobacterium sp. AL-21; RMTH, Methanothermococcus thermolithotrophicus (sequence obtained from Dr. William B. Whitman, University of Georgia); Mfer, Methanothermus fervidus DSM 2088; Maeo, Methanococcus aeolicus Nankai-3; Msp, Methanosphaera stadtmanae DSM 3091; MMP, Methanococcus maripaludis S2; Mpal, Methanosphaerula palustris E1-9c; Mpet, Methanoplanus petrolearius DSM 11571; Memar, Methanoculleus marisnigri JR1; MM, Methanosarcina mazei Gö1; MA, Methanosarcina acetivorans C2A; Mbar, Methanosarcina barkeri strain Fusaro; Mbur, Methanococcoides burtonii DSM 6242; Mmah, Methanohalophilus mahii DSM 5219; Metev, Methanohalobium evestigatum Z-7303; Mthe, Methanosaeta thermophila PT; MCON, Methanosaeta concilii GP-6; MCP, Methanocella paludicola SANAE; Mboo, Candidiatus Methanoregula boonei 6A8; Mlab, Methanocorpusculum labreanum Z; Mhun, Methanospirillum hungatei JF-1; Metbo, Methanobacterium sp. Al-21; Metok, Methanothermococcus okinawensis IH1; Metin, Methanocaldococcus infernus ME; MFS40622, Methanocaldococcus sp. FS406-22; MJ, Methanocaldococcus jannaschii DSM 2661; Mefer, Methanocaldococcus fervens AG86; Metvu, Methanocaldococcus vulcanius M7; MK, Methanopyrus kandleri AV19; GZ27A8_52, uncultured archaeon related to Methanosarcina and a member of an anaerobic methane oxidizing consortium; RCIX2692 and RCIX2197, uncultured methanogenic archaeon RC-1 and primary methane producer in rice rhizosphere. The bootstrap value shown at each branch is from 1000 replicates. Scale bar, number of amino acid substitutions per site. *, shows outliers. A and B, sub-clades of group IIId.
Figure 5.
Phylogenetic tree of Dsr-LP homologs based on Bayesian Markov chain Monte Carlo (MCMC) analysis.
ORF numbers and all abbreviations used are described in the legend of Fig. 4. For each branch a posterior probability value (0–1) is shown. Scale bar, number of amino acid substitutions per site.
Figure 6.
The sketches are based on respective amino acid sequence characteristics shown in Fig. S4. FGltS(I)-α and aFsr-β: F420H2-dehydrogenase subunit of a putative F420H2-dependent glutamate synthase of methanogens and a putative F420H2-dependent assimilatory type siroheme sulfite reductase found in haloarchaea; FpoF/FqoF: F420H2 dehydrogenase subunit of a membrane-bound proton pumping F420H2 dehydrogenase complex of late evolving euryarchaea [36]. Note: FGltS(II)-α departs significantly from Fsr-N in primary sequence and it is not included in Fig. S4. F420-interacting or β subunits of F420H2 reducing hydrogenase (FrhB) and formate dehydrogenase (FdhB) [67], [68] are shown for comparison.