title: Identification of the contiguous Paracoccus denitrificans ccmF and ccmH genes: disruption of ccmF, encoding a putative transporter, results in formation of an unstable apocytochrome c and deficiency in siderophore production.
abstract: Apocytochrome C550 was detected in the periplasm of a new mutant of Paracoccus denitrificans, HN48, that is pleiotropically lacking c-type cytochromes, produces reduced levels of siderophores and carries a Tn5 insertion in the ccmF gene for which sequence data, along with that for the contiguous ccmH, are reported. A counterpart to the ccmF gene was found in an archaebacterium but could not be located in the yeast genome, whereas mitochondrial haem lyases in the latter were not present in an archaeobacterial or in eubacterial genomes. A topological analysis for CcmF is presented which indicates at least eleven transmembrane helices, suggesting a role as a transporter; evidence against the substrate being haem is presented but sequence similarity with Escherichia coli gamma-aminobutyric acid transporter was identified. Analysis by pulse-chase methodology has shown that, in this and another cytochrome-c-deficient mutant, the apo form of P. denitrificans cytochrome C550 is much less stable than the holo form, directly demonstrating the presence of a periplasmic degradation system in P. denitrificans that removes non-functional proteins. A variety of phenotypes are observed for P. denitrificans mutated in different ccm genes, thus indicating that the stability of the ccm gene products does not require assembly of a complex of all the Ccm proteins.
authors.affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: David A
authors.initials: DA
authors.lastname: Pearce
authors.affiliation: The Oxford Centre for Molecular Sciences, New Chemistry Building, South Parks Road, Oxford, OX1 3QT, UK.|Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: M Dudley
authors.initials: MD
authors.lastname: Page
authors.affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: Hilary A C
authors.initials: HAC
authors.lastname: Norris
authors.affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: Esther J
authors.initials: EJ
authors.lastname: Tomlinson
authors.affiliation: The Oxford Centre for Molecular Sciences, New Chemistry Building, South Parks Road, Oxford, OX1 3QT, UK.|Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Ferguson
mesh_terms: D000595:Amino Acid Sequence; D001059:Apoproteins / Q000378:metabolism*; D001105:Archaea / Q000235:genetics; D001426:Bacterial Proteins / Q000032:analysis / Q000235:genetics* / Q000378:metabolism*; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D003001:Cloning, Molecular; D003574:Cytochrome c Group / Q000378:metabolism*; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D005294:Ferrochelatase / Q000032:analysis / Q000378:metabolism; D016680:Genome, Bacterial; D016681:Genome, Fungal; D006418:Heme / Q000378:metabolism; D008565:Membrane Proteins / Q000032:analysis / Q000235:genetics* / Q000378:metabolism*; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010231:Paracoccus denitrificans / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D019897:Periplasm / Q000201:enzymology / Q000378:metabolism; D010957:Plasmids; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017262:Siderophores / Q000378:metabolism*; D015003:Yeasts / Q000235:genetics; D005680:gamma-Aminobutyric Acid / Q000378:metabolism
chemical_list: D001059:Apoproteins; D001426:Bacterial Proteins; D002352:Carrier Proteins; D003574:Cytochrome c Group; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D008565:Membrane Proteins; D017262:Siderophores; C066265:apocytochrome c550, Paracoccus denitrificans; D006418:Heme; D005680:gamma-Aminobutyric Acid; D005294:Ferrochelatase