3.D.15.  Organohalide Respiration-driven PMF Generation (OP-PMF) Family

Dehalococcoides strains grow obligately by respiration with hydrogen as an electron donor and halogenated compounds as terminal electron acceptors, catalysed by a single membrane-integrated protein supercomplex. Many insights have been gained into the respiratory complex based on physiological experiments, biochemical analyses, genome sequencing, and proteomics. The mode of energy conservation involves a respiratory complex. The proton required for periplasmic dehalogenation originates from inside the cell, suggesting an electrogenic protonation of the electron acceptor, while two protons are released into the periplasm by hydrogen oxidation. This simple mechanism of pmf generation aligns with the subunit composition of the respiratory complex, the orientation of the subunits in the membrane, the absence of quinones as electron mediators, the rigidity of the cell membrane, as evidenced by its phospholipid fatty acid composition, and with proton channels formed by protonatable amino acid residues identified in the AlphaFold2-predicted structure of one of the membrane-spanning subunits. The respiration model is characterised by: (i) electrogenic protonation of the electron acceptor; (ii) reliance on a single protein complex for pmf generation without quinones; (iii) lack of transmembrane cytochromes; (iv) presence of both redox-active centres on the same side of the membrane, both facing the periplasm; and (v) restriction of the electron flow to periplasmic subunits of the respiratory complex. This type of respiration may represent an ancestral, quinone-free mechanism, offering inspiring new biotechnological applications.

There may be 7 protein constituents of the complex:

1.  HupL  Ni-Fe H2 uptake hydrogenase, large subunit of 526 aas

2.  HupS  Ni-Fe H2 uptake hydropenase, small subunit of 354 aas

3.  HupX  4Fe-4 S cluster binding protein of 267 aas

4.  OmcA  Organohalide resperation molybdoenzyme A

5.  OmcB  Organohalide resperation molybdoenzyme B

6.  RdhA  Reductive dehalogenase anchoring protein of 554 aas

7.  RdhB  Reductive dehalogenase anchoring protein of 99 aas.

Proteins 1 - 3 and 6 and 7 werre listed in NCBI, but 4 and 5 were not.

Bioremediation of toxic organohalogens resulted in the identification of organohalide-respiring bacteria harbouring reductive dehalogenases (RDases). RDases consist of the catalytic subunit (RdhA, encoded by rdhA) that has a single N-terminal TMS, and a small putative membrane anchor (RdhB, encoded by rdhB with 3 TMSs) that locates the A subunit to the outside of the cytoplasmic membrane. An rdhA gene has been found in an uncultured δ-proteobacterial genome that was not accompanied by an rdhB gene, but it contained TMSs at its N-terminus. It is likely a hybrid of RdhA and RdhB, directly connected to the membrane with TMSs. Hybrid putative rdh genes are present in the genomes of pure cultures and uncultured members of Bacteriodetes and Delta-proteobacteria, but also in the genomes of the candidate divisions. The encoded hybrid putative RDases have the cytoplasmic or exoplasmic C-terminal localization and cluster phylogenetically separately from the existing RDase groups (Atashgahi 2019).