The Heme/Copper(Iron)-Superfamily


The following distinct topics have in the past been addressed by our group:
Composite Phylogeny of the Superfamily
Genomic Survey of cbb3-Type Oxidases
Characterisation of the cbb3-Type Oxidase from Rubrivivax gelatinosus
Characterisation of qNOR from Sulfurihydrogenibium azorenze
Binding of NO to HCOs
aa3:c552-Interaction in Paracoccus denitrificans



Composite Phylogeny of the Superfamily


HCO_phylo The figure to the left shows the composite phylogeny of the catalytic subunits of all hitherto known classes of O2- and NO-reductases. As discussed in the corresponding article (Ducluzeau et al. 2009), we interpret the tree topology as indicating qNO-reductase (i.e. quinol-oxidising NO reductase) to represent the ancestral enzyme present prior to the divergence of Archaea and Bacteria. In our scenario, several duplicate versions of this enzyme existed in the common ancestor of Archaea and Bacteria, some of which evolved independently into oxygen reductases after photosynthetic O2-production has set in by positioning electron-donating tyrosine residues in appropriate positions close to the binuclear centre (Figure to the right). For details and underpinnings of this scenario, please see Ducluzeau et al. 2009. HCO_Tyrs


These results imply that the enzyme NO-reductase in fact was the ancestor of all extant O2-reductases. In order to be energetically sensible, an ancestral NO-reductase requires sufficient amounts of its substrate, nitric oxide, to be present in the Archaean environment. Our colleague Michael J. Russell made us aware of a possible paleogeochemical source for the mass production of nitrogen oxides, via the reaction of atmospheric CO2 and N2 to NO. The detailed chemical reaction schemes are described in Ducluzeau et al. 2009. According to our scenario, the denitrification pathway or segments thereof would have been producing energy via Mitchellian chemiosmosis in the early Archaean (see Figure to the right). One enzyme from this chain, i.e. NO-reductase, would then have (several times independently) evolved into the extant forms of O2 reductases.

The conclusions drawn in this work are the result of an extensive interdisciplinary interaction of bioenergetics (BIP9) and palaeogeochemistry (Michael J. Russell, JPL).
HCO_Tyrs



Genomic Survey of cbb3-Type Oxidases

The distribution of gene clusters related to cbb3-type oxidases within published genomes was analysed. Members of this class of HCO were found in almost all phyla of the Bacteria (A in figure to the right). No archaeal representatives were detected. The gene cluster turned out to be strongly heterogeneous and only the diade of genes coding for the catalytic subunit, ccoN and the monoheme cytochrome subunit, ccoO, were found to be ubiquitous and in a conserved gene order. This suggests the CcoO and CcoN subunits as the functional core of the enzyme to which additional subunits have been added in different phyla of the bacterial tree (see figure to the right, B), very much like the situation observed for the Rieske/cytb complexes. For details of the obtained results and conclusions, please see Ducluzeau et al. 2008.
An Excel-file detailing the list of entry numbers for all proteins analysed in this study can be downloaded here
HCO_Tyrs



Characterisation of the cbb3-Type Oxidase from Rubrivivax gelatinosus

We have studied the cbb3 oxidase from the beta-proteobacterium Rubrivivax gelatinosus in membranes and detergent-solubilised samples as well as isolated subunits and site-directed mutants thereof. This work is part of an extensive collaboration with the Centre de Génétique Moléculaire (CNRS/UPR 2167) in Gif-sur-Yvette and is steered in Gif by our colleague Soufian Ouchane.
  • A publication describing the obtained results and conclusions will be submitted in early 2009 (Ouchane, van Lis, Ducluzeau,Agalidis, Kalfaoui Hassani, Liebl, Astier, Nitschke and Schoepp-Cothenet, in preparation).





    Characterisation of qNOR from S. azorense

    The menaquinol-oxidising nitric oxide reductase (qNOR) from the Aquificalis Sulfurihydrogenibium (S.) azorense was expressed in E. coli, purified and characterised with respect to its biochemical and biophysical properties. A publication describing these results is in preparation.
  • This projet is financially supported by ANR (06-BLAN-0384) and is carried out by R. van Lis .


    Binding of NO to HCOs

    In preparation


    aa3:c552-Interaction in Paracoccus denitrificans

    In preparation



    aa3_c552
    References:

    Ducluzeau, A.-L., van Lis, R., Duval, S., Schoepp-Cothenet, B., Russell, M.J. and Nitschke, W. (2009)
    Trends in Biochemical Sciences 34, 9-15
    [pdf-file]
    Was nitric oxide the first deep electron sink?

    Ducluzeau, A.-L., Ouchane, S. and Nitschke, W. (2008)
    Mol. Biol. Evol. 25, 1158-1166
    [pdf-file]
    cbb3 oxidases are an ancient innovation of the domain Bacteria

    Pilet, E., Nitschke, W., Liebl, U. and Vos, M.H. (2007)
    Biochim.Biophys.Acta Bioenergetics 1767, 387-392
    [pdf-file]
    Accommodation of NO in the active site of mammalian and bacterial cytochrome c oxidase aa3

    Lipowski, G., Liebl, U., Guigliarelli, B., Nitschke, W. and Schoepp-Cothenet, B. (2006)
    FEBS Lett. 580, 5988-5992
    [pdf-file]
    Conformation of the c552 : aa3 electron transfer complex in Paracoccus denitrificans studied by EPR on oriented samples

    Pilet, E., Nitschke, W., Rappaport, F., Soulimane, T., Lambry, J.-C., Liebl, U. and Vos, M. (2004)
    Biochemistry 43, 14118-14127
    [pdf-file]
    NO binding and dynamics in reduced heme-copper oxidases aa3 from Paracoccus denitrificans and ba3 from Thermus thermophilus


    Last update: December 23, 2008
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