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

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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/H2O 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.

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Acknowledgments

Work from the authors’ laboratory was supported by the Deutsche Forschungsgemeinschaft. We are grateful to Profs. U. Deppenmeier (Bonn), B. Ludwig (Frankfurt), J. R. Andreesen (Halle) and M. Rother (Frankfurt) for critical reading of the manuscript.

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Authors and Affiliations

  1. Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany

    Eva Biegel, Silke Schmidt & Volker Müller

  2. Department of Microbiology and Cell Biology, University of La Laguna, 38206, La Laguna, Tenerife, Spain

    José M. González

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  1. Eva Biegel
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Correspondence to Volker Müller.

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Fig. S1

Genomic organization of rnf genes. nth encodes for endonuclease III. Membrane-bound subunits are indicated by an asterisk. A rnf cluster ABCDGE, B rnf cluster CDGEAB, C rnf cluster BCDGEA, D rnf organization in archaea. x encodes for a hypothetical protein. R. capsulatus: Rhodobacter capsulatus, A. vinelandii: Azotobacter vinelandii, E. coli: Escherichia coli, V. cholerae: Vibrio cholerae, K. pneumoniae: Klebsiella pneumoniae, A. woodii: Acetobacterium woodii, C. tetani: Clostridium tetani, A. metalliredigens: Alkaliphilus metalliredigens, T. pseudethanolicus: Thermoanaerobacter pseudethanolicus, C. kluyveri: Clostridium kluyveri, R. torques: Ruminococcus torques, B. vulgatus: Bacteroides vulgatus, C. limicola: Chlorobium limicola, P. sp.: Parabacteroides sp., P. aestuarii: Prosthecochloris aestuarii, P. uenonsis: Porphyromonas uenonsis, M. acetivorans: Methanosarcina acetivorans, M. burtonii: Methanococcoides burtonii (TIFF 79 kb)

Fig. S2

Topology model of RnfD (based on SOSUI prediction, [132]). The N- and C-termini are indicated. Threonine 157 is highlighted in grey as potential FMN-binding site. Aspartate 250 and glutamate 300 are highlighted (black) as potential amino acids involved in Na+ binding (TIFF 124 kb)

Fig. S3

Topology model of RnfG (based on SOSUI prediction, [132]). The N- and C-termini are indicated. Threonine 185 is highlighted in grey as potential FMN-binding site (TIFF 97 kb)

Fig. S4

Topology model of RnfE (based on Sääf et al. 1999). The N- and C-termini are indicated. Aspartate 129 is highlighted (black) as potential Na+ binding site (TIFF 106 kb)

Fig. S5

Topology model of RnfA (based on Sääf et al. 1999). The N- and C-termini are indicated. Glutamate 88 is highlighted (black) as potential Na+ binding site (TIFF 105 kb)

Fig. S6

Topology model of RnfB (based on SOSUI prediction, [132]). The N- and C-termini are indicated. Conserved cysteines are highlighted in grey, that might form the FeS cluster binding sites (TIFF 132 kb)

Fig. S7

Alignment of RnfD and NqrB. Alignment was done using ClustalW (http://www.ebi.ac.uk/Tools/clustalw2/index.html [133]). An asterisk indicates complete amino acid conservation. The arrow shows the potential Na+-binding site. VC-Vibrio cholerae, AW-Acetobacterium woodii (TIFF 91 kb)

Fig. S8

Alignment of RnfE and NqrD. Alignment was done using ClustalW (http://www.ebi.ac.uk/Tools/clustalw2/index.html [133]). An asterisk indicates complete amino acid conservation. The arrow shows the potential Na+-binding site. VC-Vibrio cholerae, AW-Acetobacterium woodii (TIFF 62 kb)

Fig. S9

Alignment of RnfA and NqrE. Alignment was done using ClustalW (http://www.ebi.ac.uk/Tools/clustalw2/index.html [133]). An asterisk indicates complete amino acid conservation. The arrow shows the potential Na+-binding site. VC-Vibrio cholerae, AW-Acetobacterium woodii (TIFF 59 kb)

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Biegel, E., Schmidt, S., González, J.M. et al. Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes. Cell. Mol. Life Sci. 68, 613–634 (2011). https://doi.org/10.1007/s00018-010-0555-8

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