Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes

Abstract

Microbes have a fascinating repertoire of bioenergetic enzymes and a huge variety of electron transport chains to cope with very different environmental conditions, such as different oxygen concentrations, different electron acceptors, pH and salinity. However, all these electron transport chains cover the redox span from NADH + H(+) as the most negative donor to oxygen/H(2)O as the most positive acceptor or increments thereof. The redox range more negative than -320 mV has been largely ignored. Here, we have summarized the recent data that unraveled a novel ion-motive electron transport chain, the Rnf complex, that energetically couples the cellular ferredoxin to the pyridine nucleotide pool. The energetics of the complex and its biochemistry, as well as its evolution and cellular function in different microbes, is discussed.

Fig. 1

Model of caffeate respiration in A. woodii, showing the flow of electrons from electron donors (fructose or hydrogen) to the acceptor caffeate. Fno/Rnf couples the flow of electrons from reduced ferredoxin (Fd_red) to NAD⁺ thereby generating a sodium ion gradient across the cytoplasmic membrane. For explanations, see text. ox oxidized, red reduced

Fig. 2

Topology model of Rnf subunits. Rnf subunits are indicated. N- and C-termini are as indicated. Fd ferredoxin, red reduced, ox oxidized. For explanations, see text

Fig. 3

Model of Ech and Rnf complexes. The potential difference between electron donor and acceptor is used to build up a transmembrane ion potential that is then used by ATP synthase to synthesize ATP. Fd ferredoxin, ox oxidized, red reduced

Fig. 4

The redox span used for energy conserving reactions in biology and the enzymes used. Rnf and Ech cover the most reduced range from −500 to −320 mV, complex I and Nqr the range from −320 to +90 mV, complex III from +90 to +240 mV, complex IV from +240 to +816 mV. For the sake of clarity, the region from −320 to +816 mV is shown by only four respiratory enzyme complexes. Please note that there are a couple of enzymes that work in this region. Fd ferredoxin, red reduced, UQ ubiquinone

Fig. 5

Maximum likelihood tree of the RnfD homologs. The tree contains representative sequences from the phyla where RnfD is found (Proteobacteria, Firmicutes, Methanosarcinaceae, Fusobacteria, Dictyoglomi, Spirochaetes, Bacteroidetes/Chlorobi, Synergistales, Thermotogales). The sequence of the NqrB homolog of Pseudomonas aeruginosa (accession number NP_251688) served as the outgroup. Number between parentheses is the Genbank accession number. Scale bar represents the number of substitutions per site

Fig. 6

Maximum likelihood tree of the RnfC homologs from representative sequences. The sequence of Desulfatibacillum alkenivorans AK-01 (accession number YP_002433501) served as the outgroup. Number between parentheses is the Genbank accession number. Scale bar represents the number of substitutions per site

Fig. 7

Model of proposed electron flow in E. coli. Electrons deriving from NADH are channeled through the complex to keep SoxR in its reduced state. When oxidized SoxR activates target genes against oxidative stress. For explanation, see text. red reduced, ox oxidized

Fig. 8

Model of proposed electron flow in C. tetani. For explanation, see text. Fd ferredoxin, red reduced, ox oxidized. C. tetani is a peptolytic Clostridium that preferentialy ferments amino acids and the degradation of many amino acids results in the formation of pyruvate

Fig. 9

Metabolism of C. kluyveri. For the sake of simplicity, only the formation of butyrate and H₂ is shown. Reactions involved in caproate formation are analogous (butyryl-CoA condenses with acetyl-CoA). Ten mol NADH are consumed by the butyryl-CoA-DH complex. They are bifurcated to produce 5 mol butyryl-CoA and 5 mol Fd_red. Fd_red is either used by hydrogenase to produce H₂ or by Rnf to produce NADH and thereby generating an ion gradient. For further explanation, see text. [H] reducing equivalents, Fd ferredoxin, red reduced, ox oxidized

Fig. 10

Model of involvement of Rnf in metabolism of M. acetivorans. A possible way of electron transport is shown. Note that other ways of electron transport are possible (see “Physiological roles of Rnf in different bacteria”). For explanation, see text. MP methanophenazine, Cdh CO-dehydrogenase/acetyl-CoA synthase, Hdr heterodisulfide reductase, Cyt c cytochrome c, CoM coenzyme M, CoB coenzyme B, H ₄ SPT tetrahydrosarcinapterin. Fd ferredoxin, ox oxidized, red reduced