Membrane topology and mutational analysis of CydDC, an ABC-type cysteine exporter required for cytochrome assembly Free

Abstract

Cytochrome is a respiratory quinol oxidase in . Besides the structural genes ( and ) encoding the oxidase complex, the and genes, encoding an ABC-type transporter, are required for assembly of this oxidase. Recently, cysteine has been identified as a substrate (allocrite) that is transported from the cytoplasm by CydDC, but the mechanism of cysteine export to the periplasm and its role there remain unknown. To initiate an understanding of structure–function relationships in CydDC, its membrane topography was analysed by generating protein fusions between random and selected residues in the two polypeptides with both alkaline phosphatase and -galactosidase. CydD and CydC are experimentally shown each to have six transmembrane segments, two major cytoplasmic loops and three minor periplasmic loops; both termini of each protein face the cytoplasm. The allele is shown to have two point mutations (G319D, G429E) within the ATP-binding domain of CydD; either mutation alone is sufficient to cause loss or severe reduction of cytochrome assembly. A comparative sequence analysis prompted the targeting of residues in CydD for site-directed mutational analysis, which identified (i) the ‘start’ methionine residue, (ii) essential residues in the ATP-binding site (Walker sequence A) and (iii) a duplicated positively charged heptameric motif, R-G/T-L/M-X-T/V-L-R, in CydD cytoplasmic loop II. The replacement of arginines in these motifs with glycines resulted in Cyd phenotypes; however, activity could be restored at these positions by replacing the glycine with lysine or histidine and hence returning the positive charge. The conservation of these charges in CydD-like proteins indicates functional importance. Evolutionary aspects of bacterial genes are discussed.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.27191-0
2004-10-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/micro/150/10/mic1503415.html?itemId=/content/journal/micro/10.1099/mic.0.27191-0&mimeType=html&fmt=ahah

References

  1. Altschul, S. F., Madden, T. L., Schäffer A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J.(1997). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef] [Google Scholar]
  2. Ames, G. F.-L. & Lecar, H.(1992). ATP-dependent bacterial transporters and cystic fibrosis: analogy between channels and transporters. FASEB J 6, 2660–2666. [Google Scholar]
  3. Andersson, H. & von Heijne, G.(1993). Position-specific Asp-Lys pairing can affect signal sequence function and membrane protein topology. J Biol Chem 268, 21389–21393. [Google Scholar]
  4. Bebbington, K. J. & Williams, H. D.(1993). Investigation of the role of the cydD gene product in production of a functional cytochrome d oxidase in Escherichia coli. FEMS Microbiol Lett 112, 19–24.[CrossRef] [Google Scholar]
  5. Borisov, V. B., Sedelnikova, S. E., Poole, R. K. & Konstantinov, A. A. J.(2001). Interaction of cytochrome bd with carbon monoxide at low and room temperatures: evidence that only a small fraction of heme b595 reacts with CO. J Biol Chem 276, 22095–22099.[CrossRef] [Google Scholar]
  6. Boyd, D. & Beckwith, J.(1989). Positively charged amino acid residues can act as topogenic determinants in membrane proteins. Proc Natl Acad Sci U S A 86, 9446–9450.[CrossRef] [Google Scholar]
  7. Brandl, C. J. & Deber, C. M.(1986). Hypothesis about the function of membrane-buried proline residues in transport proteins. Proc Natl Acad Sci U S A 83, 917–921.[CrossRef] [Google Scholar]
  8. Chang, G.(2003). Structure of MsbA from Vibrio cholera: a multidrug resistance ABC transporter homolog in a closed conformation. J Mol Biol 330, 419–430.[CrossRef] [Google Scholar]
  9. Chang, G. & Roth, C. B.(2001). Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters. Science 293, 1793–1800.[CrossRef] [Google Scholar]
  10. Cook, G. M. & Poole, R. K.(2000). Oxidase and periplasmic cytochrome assembly in Escherichia coli K-12: CydDC and CcmAB are not required for haem-membrane association. Microbiology 146, 527–536. [Google Scholar]
  11. Cook, G. M., Loder, C., Søballe, B., Stafford, G. P., Membrillo-Hernández, J. & Poole, R. K.(1998). A factor produced by Escherichia coli K-12 inhibits the growth of E. coli mutants defective in the cytochrome bd quinol oxidase complex: enterochelin rediscovered. Microbiology 144, 3297–3308.[CrossRef] [Google Scholar]
  12. Cook, G. M., Cruz-Ramos, H., Moir, A. J. & Poole, R. K.(2002). A novel haem compound accumulated in Escherichia coli overexpressing the cydDC operon, encoding an ABC-type transporter required for cytochrome assembly. Arch Microbiol 178, 358–369.[CrossRef] [Google Scholar]
  13. Cotter, P. A., Chepuri, V., Gennis, R. B. & Gunsalus, R. P.(1990). Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product. J Bacteriol 172, 6333–6338. [Google Scholar]
  14. Danchin, A., Guerdoux-Jamet, P., Moszer, I. & Nitschke, P.(2000). Mapping the bacterial cell architecture into the chromosome. Philos Trans R Soc Lond B Biol Sci 355, 179–190.[CrossRef] [Google Scholar]
  15. Dandekar, T., Snel, B., Huynen, M. & Bork, P.(1998). Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23, 324–328.[CrossRef] [Google Scholar]
  16. Delaney, J. M., Ang, D. & Georgopoulos, C.(1992). Isolation and characterization of the Escherichia coli htrD gene, whose product is required for growth at high temperatures. J Bacteriol 174, 1240–1247. [Google Scholar]
  17. Delaney, J. M., Wall, D. & Georgopoulos, C.(1993). Molecular characterization of the Escherichia coli htrD gene: cloning, sequence, regulation, and involvement with cytochrome d oxidase. J Bacteriol 175, 166–175. [Google Scholar]
  18. D'Mello, R., Hill, S. & Poole, R. K.(1996). The cytochrome bd quinol oxidase in Escherichia coli has an extremely high oxygen affinity and two oxygen-binding haems: implications for regulation of activity in vivo by oxygen inhibition. Microbiology 142, 755–763.[CrossRef] [Google Scholar]
  19. Edwards, S. E., Loder, C. S., Wu, G., Corker, H., Bainbridge, B. W., Hill, S. & Poole, R. K.(2000). Mutation of cytochrome bd quinol oxidase results in reduced stationary phase survival, iron deprivation, metal toxicity and oxidative stress in Azotobacter vinelandii. FEMS Microbiol Lett 185, 71–77.[CrossRef] [Google Scholar]
  20. Endley, S., McMurray, D. & Ficht, T. A.(2001). Interruption of the cydB locus in Brucella abortus attenuates intracellular survival and virulence in the mouse model of infection. J Bacteriol 183, 2454–2462.[CrossRef] [Google Scholar]
  21. Esposti, D. E., De Vries, S., Crimi, M., Ghelli, A., Patarnello, T. & Meyer, A.(1993). Mitochondrial cytochrome b: evolution and structure of the protein. Biochim Biophys Acta 1143, 243–271.[CrossRef] [Google Scholar]
  22. Ewart, G. D., Cannell, D., Cox, G. B. & Howells, A. J.(1994). Mutational analysis of the traffic ATPase (ABC) transporters involved in uptake of eye pigment precursors in Drosophila melanogaster. Implications for structure-function relationships. J Biol Chem 269, 10370–10377. [Google Scholar]
  23. Gennis, R. B. & Stewart, V.(1996). Respiration. In Escherichia coli and Salmonella. Cellular and Molecular Biology, pp. 217–261. Washington, DC: American Society for Microbiology.
  24. Georgiou, C. D., Fang, H. & Gennis, R. B.(1987). Identification of the cydC locus required for expression of the functional form of the cytochrome d terminal oxidase complex in Escherichia coli. J Bacteriol 169, 2107–2112. [Google Scholar]
  25. Giacomini, A., Corich, V., Ollero, F. J., Squartini, A. & Nuti, M. P.(1992). Experimental conditions may affect reproducibility of the beta-galactosidase assay. FEMS Microbiol Lett 79, 87–90. [Google Scholar]
  26. Goldman, B. S., Gabbert, K. K. & Kranz, R. G.(1996a). Use of heme reporters for studies of cytochrome biosynthesis and heme transport. J Bacteriol 178, 6338–6347. [Google Scholar]
  27. Goldman, B. S., Gabbert, K. K. & Kranz, R. G.(1996b). The temperature-sensitive growth and survival phenotypes of Escherichia coli cydDC and cydAB strains are due to deficiencies in cytochrome bd and are corrected by exogenous catalase and reducing agents. J Bacteriol 178, 6348–6351. [Google Scholar]
  28. Gort, A. S., Ferber, D. M. & Imlay, J. A.(1999). The regulation and role of the periplasmic copper, zinc superoxide dismutase of Escherichia coli. Mol Microbiol 32, 179–191.[CrossRef] [Google Scholar]
  29. Holland, I. B. & Blight, M. A.(1999). ABC-ATPases, adaptable energy generators fuelling transmembrane movement of a variety of molecules in organisms from bacteria to humans. J Mol Biol 293, 381–399.[CrossRef] [Google Scholar]
  30. Itoh, T., Takemoto, K., Mori, H. & Gojobori, T.(1999). Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol 16, 332–346.[CrossRef] [Google Scholar]
  31. Jünemann, S.(1997). Cytochrome bd terminal oxidase. Biochim Biophys Acta 1321, 107–127.[CrossRef] [Google Scholar]
  32. Juty, N. S., Moshiri, F., Merrick, M., Anthony, C. & Hill, S.(1997). The Klebsiella pneumoniae cytochrome bd′ terminal oxidase complex and its role in microaerobic nitrogen fixation. Microbiology 143, 2673–2683.[CrossRef] [Google Scholar]
  33. Kalnenieks, U., Galinina, N., Bringer-Meyer, S. & Poole, R. K.(1998). Membrane d-lactate oxidase in Zymomonas mobilis: evidence for a branched respiratory chain. FEMS Microbiol Lett 168, 91–97. [Google Scholar]
  34. Kelley, L. A., MacCallum, R. M. & Sternberg, M. J. E.(2000). Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 299, 499–520. [Google Scholar]
  35. Kelly, M. J., Poole, R. K., Yates, M. G. & Kennedy, C.(1990). Cloning and mutagenesis of genes encoding the cytochrome bd terminal oxidase complex in Azotobacter vinelandii: mutants deficient in the cytochrome d complex are unable to fix nitrogen in air. J Bacteriol 172, 6010–6019. [Google Scholar]
  36. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. L.(2001). Predicting transmembrane protein topology with a hidden Markov Model: application to complete genomes. J Mol Biol 305, 567–580.[CrossRef] [Google Scholar]
  37. Lawrence, J. G. & Roth, J. R.(1996). Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143, 1843–1860. [Google Scholar]
  38. Lee, C., Li, P., Inouye, H., Brickman, E. R. & Beckwith, J.(1989). Genetic studies on the inability of β-galactosidase to be translocated across the Escherichia coli cytoplasmic membrane. J Bacteriol 171, 4609–4616. [Google Scholar]
  39. Lindqvist, A., Membrillo-Hernández, J., Poole, R. K. & Cook, G. M.(2000). Role of respiratory oxidases in protecting Escherichia coli K12 from oxidative stress. Antonie van Leeuwenhoek 78, 23–31.[CrossRef] [Google Scholar]
  40. Linton, K. J. & Higgins, C. F.(1998). The Escherichia coli ATP-binding cassette (ABC) proteins. Mol Microbiol 28, 5–13. [Google Scholar]
  41. Mackenzie, S. M., Brooker, M. R., Gill, T. R., Cox, G. B., Howells, A. J. & Ewart, G. D.(1999). Mutations in the white gene of Drosophila melanogaster affecting ABC transporters that determine eye colouration. Biochim Biophys Acta 1419, 173–185.[CrossRef] [Google Scholar]
  42. Maloy, S. R., Stewart, V. J. & Taylor, R. K.(1996).Genetic Analysis of Pathogenic Bacteria. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  43. Manoil, C.(1990). Analysis of protein localization by use of gene fusions with complementary properties. J Bacteriol 172, 1035–1042. [Google Scholar]
  44. Manoil, C. & Bailey, J.(1997). A simple screen for permissive sites in proteins: analysis of Escherichia coli lac permease. J Mol Biol 267, 250–263.[CrossRef] [Google Scholar]
  45. Manoil, C. & Beckwith, J.(1985). TnphoA: a transposon probe for protein export signals. Proc Natl Acad Sci U S A 82, 8129–8133.[CrossRef] [Google Scholar]
  46. Markwell, M. A., Hass, S. M., Bieber, L. L. & Tolbert, N. E.(1978). A modification of the Lowry procedure to simplify protein determination in membrane and lipoprotein samples. Anal Biochem 87, 206–210.[CrossRef] [Google Scholar]
  47. Michaelis, S., Inouye, H., Oliver, D. & Beckwith, J.(1983). Mutations that alter the signal sequence of alkaline phosphatase in Escherichia coli. J Bacteriol 154, 366–374. [Google Scholar]
  48. Miller, J. H.(1972).Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  49. Moller, S., Croning, M. D. R. & Apweiler, R.(2001). Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17, 646–653.[CrossRef] [Google Scholar]
  50. Nakashima, H. & Nishikawa, K.(1992). The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins. FEBS Lett 303, 141–146.[CrossRef] [Google Scholar]
  51. Ninfa, E. G., Atkinson, M. R., Kamberov, E. S. & Ninfa, A. J.(1993). Mechanisms of autophosphorylation of Escherichia coli nitrogen regulator II (NRII or NtrB): trans-phosphorylation between subunits. J Bacteriol 175, 7024–7032. [Google Scholar]
  52. Olsen, D. B., Sayers, J. R. & Eckstein, F.(1993). Site-directed mutagenesis of single-stranded and double-stranded DNA by phosphorothionate approach. Methods Enzymol 217, 189–217. [Google Scholar]
  53. Osborne, J. P. & Gennis, R. B.(1999). Sequence analysis of cytochrome bd oxidase suggests a revised topology for subunit I. Biochim Biophys Acta 1410, 32–50.[CrossRef] [Google Scholar]
  54. Parsonage, D., Wilke-Mounts, S. & Senior, A. E.(1987). Directed mutagenesis of the β-subunit of F1-ATPase from Escherichia coli. J Biol Chem 262, 8022–8026. [Google Scholar]
  55. Pi, J., Dogovski, C. & Pittard, A. J.(1998). Functional consequences of changing proline residues in the phenylalanine-specific permease of Escherichia coli. J Bacteriol 180, 5515–5519. [Google Scholar]
  56. Pittman, M. S., Corker, H., Wu, G., Binet, M. B., Moir, A. J. G. & Poole, R. K.(2002). Cysteine is exported from the Escherichia coli cytoplasm by CydDC, an ABC-type transporter required for cytochrome assembly. J Biol Chem 277, 49841–49849.[CrossRef] [Google Scholar]
  57. Poole, R. K. & Cook, G. M.(2000). Redundancy of aerobic respiratory chains in bacteria? Routes, reasons and regulation. Adv Microb Physiol 43, 165–224. [Google Scholar]
  58. Poole, R. K. & Haddock, B. A.(1974). Energy-linked reduction of nicotinamide-adenine dinucleotide in membranes derived from normal and various respiratory-deficient mutant strains of Escherichia coli K12. Biochem J 144, 77–85. [Google Scholar]
  59. Poole, R. K., Williams, H. D., Downie, J. A. & Gibson, F.(1989). Mutations affecting the cytochrome d-containing oxidase complex of Escherichia coli K12: identification and mapping of a fourth locus, cydD. J Gen Microbiol 135, 1865–1874. [Google Scholar]
  60. Poole, R. K., Hatch, L., Cleeter, M. W., Gibson, F., Cox, G. B. & Wu, G.(1993). Cytochrome bd biosynthesis in Escherichia coli: the sequences of the cydC and cydD genes suggest that they encode the components of an ABC membrane transporter. Mol Microbiol 10, 421–430.[CrossRef] [Google Scholar]
  61. Poole, R. K., Gibson, F. & Wu, G.(1994). The cydD gene product, component of a heterodimeric ABC transporter, is required for assembly of periplasmic cytochrome c and of cytochrome bd in Escherichia coli. FEMS Microbiol Lett 117, 217–223.[CrossRef] [Google Scholar]
  62. Roussel, A. & Cambillau, C.(1991). ‘TurboFrodo’, Silicon Graphics Geometry Partners Directory, p. 86. Mountain View, CA: Silicon Graphics.
  63. Sato, M. & Mueckler, M.(1999). A conserved amino acid motif (R-X-G-R-R) in the Glut1 glucose transporter is an important determinant of membrane topology. J Biol Chem 274, 24721–24725.[CrossRef] [Google Scholar]
  64. Schmitt, L. & Tampe, R.(2002). Structure and mechanism of ABC transporters. Curr Opin Struct Biol 12, 754–760.[CrossRef] [Google Scholar]
  65. Siegele, D. A., Imlay, K. R. & Imlay, J. A.(1996). The stationary-phase-exit defect of cydC (surB) mutants is due to the lack of a functional terminal cytochrome oxidase. J Bacteriol 178, 6091–6096. [Google Scholar]
  66. Simons, R. W., Houman, F. & Kleckner, N.(1987). Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 53, 85–96.[CrossRef] [Google Scholar]
  67. Sonnhammer, E. L. L., von Heijne, G. & Krogh, A.(1998). A hidden Markov model for predicting transmembrane helices in protein sequences. In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, vol. 5, pp. 175–182. Edited by J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff & C. Sensen. Menlo Park, CA: AAAI/MIT Press.
  68. Tamames, J.(2001). Evolution of gene order conservation in prokaryotes. Genome Biol 2, 1–11. [Google Scholar]
  69. Tearle, R. G., Belote, J. M., McKeown, M., Baker, B. S. & Howells, A. J.(1989). Cloning and characterisation of the scarlet gene of Drosophila melanogaster. Genetics 122, 595–606. [Google Scholar]
  70. Urbatsch, I. L., Sankaran, B., Weber, J. & Senior, A. E.(1995). P-glycoprotein is stably inhibited by vanadate-induced trapping of nucleotide at a single catalytic site. J Biol Chem 270, 19383–19390.[CrossRef] [Google Scholar]
  71. Vieira, J. & Messing, J.(1987). Production of single-stranded plasmid DNA. Methods Enzymol 153, 3–11. [Google Scholar]
  72. von Heijne, G.(1992). Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 225, 487–494.[CrossRef] [Google Scholar]
  73. Way, S. S., Sallustio, S., Magliozzo, R. S. & Goldberg, M. B.(1999). Impact of either elevated or decreased levels of cytochrome bd expression on Shigella flexneri virulence. J Bacteriol 181, 1229–1237. [Google Scholar]
  74. Winstedt, L., Yoshida, K., Fujita, Y. & von Wachenfeldt, C.(1998). Cytochrome bd biosynthesis in Bacillus subtilis: characterization of the cydABCD operon. J Bacteriol 180, 6571–6580. [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.27191-0
Loading
/content/journal/micro/10.1099/mic.0.27191-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed