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. 1993 Aug 15;294(Pt 1):239–251. doi: 10.1042/bj2940239

Organization and sequences of genes for the subunits of ATP synthase in the thermophilic cyanobacterium Synechococcus 6716.

H S Van Walraven 1, R Lutter 1, J E Walker 1
PMCID: PMC1134591  PMID: 8363578

Abstract

The sequences of the genes for the nine subunits of ATP synthase in the thermophilic cyanobacterium Synechococcus 6716 have been determined. The genes were identified by comparison of the encoded proteins with sequences of ATP synthase subunits in other species, and confirmed for subunits alpha, beta, delta and epsilon, by determining their N-terminal sequences. They are arranged at three separate loci. Six of them are in one cluster in the order a: c: b': b: delta: alpha, and those for the beta and epsilon subunits form a second and separate cluster. The gene for the gamma-subunit is at a third site. As in other bacteria, the gene for subunit a is immediately preceded by a gene coding for a small hydrophobic protein of unknown function, known as uncI in Escherichia coli. The gene orders in Synechococcus 6716 are related to the orders of ATP synthase genes in the plastid genomes of higher plants, and particularly of a red alga and a diatom. The sequences of the subunits are similar to those of chloroplast ATP synthase, the alpha, beta and c subunits being particularly well conserved. Differences in the primary structures of the Synechococcus 6716 and chloroplast gamma subunits probably underlie different mechanisms of activation of ATP synthase. The nucleotide sequences that are presented also contain 12 other open reading frames. One of them encodes a protein sequence related to the E. coli DNA repair enzyme, photolyase, and another codes for a protein that contains internal repeats related to sequences in the myosin heavy chain.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Berzborn R. J., Klein-Hitpass L., Otto J., Schünemann S., Oworah-Nkruma R., Meyer H. E. The "additional subunit" CF0II of the photosynthetic ATP-synthase and the thylakoid polypeptide, binding ferredoxin NADP reductase: are they different? Z Naturforsch C. 1990 Jul-Aug;45(7-8):772–784. [PubMed] [Google Scholar]
  2. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bird C. R., Koller B., Auffret A. D., Huttly A. K., Howe C. J., Dyer T. A., Gray J. C. The wheat chloroplast gene for CF(0) subunit I of ATP synthase contains a large intron. EMBO J. 1985 Jun;4(6):1381–1388. doi: 10.1002/j.1460-2075.1985.tb03790.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Boer P. H., Gray M. W. The URF 5 gene of Chlamydomonas reinhardtii mitochondria: DNA sequence and mode of transcription. EMBO J. 1986 Jan;5(1):21–28. doi: 10.1002/j.1460-2075.1986.tb04172.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
  6. Brusilow W. S., Scarpetta M. A., Hawthorne C. A., Clark W. P. Organization and sequence of the genes coding for the proton-translocating ATPase of Bacillus megaterium. J Biol Chem. 1989 Jan 25;264(3):1528–1533. [PubMed] [Google Scholar]
  7. Collins J., Hohn B. Cosmids: a type of plasmid gene-cloning vector that is packageable in vitro in bacteriophage lambda heads. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4242–4246. doi: 10.1073/pnas.75.9.4242. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cozens A. L., Walker J. E. The organization and sequence of the genes for ATP synthase subunits in the cyanobacterium Synechococcus 6301. Support for an endosymbiotic origin of chloroplasts. J Mol Biol. 1987 Apr 5;194(3):359–383. doi: 10.1016/0022-2836(87)90667-x. [DOI] [PubMed] [Google Scholar]
  9. Curtis S. E. Genes encoding the beta and epsilon subunits of the proton-translocating ATPase from Anabaena sp. strain PCC 7120. J Bacteriol. 1987 Jan;169(1):80–86. doi: 10.1128/jb.169.1.80-86.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dunn S. D. The polar domain of the b subunit of Escherichia coli F1F0-ATPase forms an elongated dimer that interacts with the F1 sector. J Biol Chem. 1992 Apr 15;267(11):7630–7636. [PubMed] [Google Scholar]
  11. Falk G., Hampe A., Walker J. E. Nucleotide sequence of the Rhodospirillum rubrum atp operon. Biochem J. 1985 Jun 1;228(2):391–407. doi: 10.1042/bj2280391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Falk G., Walker J. E. DNA sequence of a gene cluster coding for subunits of the F0 membrane sector of ATP synthase in Rhodospirillum rubrum. Support for modular evolution of the F1 and F0 sectors. Biochem J. 1988 Aug 15;254(1):109–122. doi: 10.1042/bj2540109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Falk G., Walker J. E. Transcription of Rhodospirillum rubrum atp operon. Biochem J. 1985 Aug 1;229(3):663–668. doi: 10.1042/bj2290663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Farrell P. J., Deininger P. L., Bankier A., Barrell B. Homologous upstream sequences near Epstein-Barr virus promoters. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1565–1569. doi: 10.1073/pnas.80.6.1565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Foster D. L., Fillingame R. H. Stoichiometry of subunits in the H+-ATPase complex of Escherichia coli. J Biol Chem. 1982 Feb 25;257(4):2009–2015. [PubMed] [Google Scholar]
  16. Gay N. J., Walker J. E. The atp operon: nucleotide sequence of the promoter and the genes for the membrane proteins, and the delta subunit of Escherichia coli ATP-synthase. Nucleic Acids Res. 1981 Aug 25;9(16):3919–3926. doi: 10.1093/nar/9.16.3919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Howe C. J., Auffret A. D., Doherty A., Bowman C. M., Dyer T. A., Gray J. C. Location and nucleotide sequence of the gene for the proton-translocating subunit of wheat chloroplast ATP synthase. Proc Natl Acad Sci U S A. 1982 Nov;79(22):6903–6907. doi: 10.1073/pnas.79.22.6903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ivey D. M., Krulwich T. A. Organization and nucleotide sequence of the atp genes encoding the ATP synthase from alkaliphilic Bacillus firmus OF4. Mol Gen Genet. 1991 Oct;229(2):292–300. doi: 10.1007/BF00272169. [DOI] [PubMed] [Google Scholar]
  19. Ketcham S. R., Davenport J. W., Warncke K., McCarty R. E. Role of the gamma subunit of chloroplast coupling factor 1 in the light-dependent activation of photophosphorylation and ATPase activity by dithiothreitol. J Biol Chem. 1984 Jun 10;259(11):7286–7293. [PubMed] [Google Scholar]
  20. Kostrzewa M., Zetsche K. Large ATP synthase operon of the red alga Antithamnion sp. resembles the corresponding operon in cyanobacteria. J Mol Biol. 1992 Oct 5;227(3):961–970. doi: 10.1016/0022-2836(92)90238-f. [DOI] [PubMed] [Google Scholar]
  21. Krumholz L. R., Esser U., Simoni R. D. Nucleotide sequence of the unc operon of Vibrio alginolyticus. Nucleic Acids Res. 1989 Oct 11;17(19):7993–7994. doi: 10.1093/nar/17.19.7993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  23. Lightowlers R. N., Howitt S. M., Hatch L., Gibson F., Cox G. The proton pore in the Escherichia coli F0F1-ATPase: substitution of glutamate by glutamine at position 219 of the alpha-subunit prevents F0-mediated proton permeability. Biochim Biophys Acta. 1988 Apr 22;933(2):241–248. doi: 10.1016/0005-2728(88)90031-x. [DOI] [PubMed] [Google Scholar]
  24. Lill H., Nelson N. The atp1 and atp2 operons of the cyanobacterium Synechocystis sp. PCC 6803. Plant Mol Biol. 1991 Oct;17(4):641–652. doi: 10.1007/BF00037050. [DOI] [PubMed] [Google Scholar]
  25. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  26. Lubberding H. J., Zimmer G., van Walraven H. S., Schrickx J., Kraayenhof R. Isolation, purification and characterization of the ATPase complex from the thermophilic cyanobacterium Synechococcus 6716. Eur J Biochem. 1983 Dec 1;137(1-2):95–99. doi: 10.1111/j.1432-1033.1983.tb07800.x. [DOI] [PubMed] [Google Scholar]
  27. Matsudaira P. Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J Biol Chem. 1987 Jul 25;262(21):10035–10038. [PubMed] [Google Scholar]
  28. McCarn D. F., Whitaker R. A., Alam J., Vrba J. M., Curtis S. E. Genes encoding the alpha, gamma, delta, and four F0 subunits of ATP synthase constitute an operon in the cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol. 1988 Aug;170(8):3448–3458. doi: 10.1128/jb.170.8.3448-3458.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Miki J., Maeda M., Mukohata Y., Futai M. The gamma-subunit of ATP synthase from spinach chloroplasts. Primary structure deduced from the cloned cDNA sequence. FEBS Lett. 1988 May 9;232(1):221–226. doi: 10.1016/0014-5793(88)80421-6. [DOI] [PubMed] [Google Scholar]
  30. Mills D. R., Kramer F. R. Structure-independent nucleotide sequence analysis. Proc Natl Acad Sci U S A. 1979 May;76(5):2232–2235. doi: 10.1073/pnas.76.5.2232. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Morrissey J. H. Silver stain for proteins in polyacrylamide gels: a modified procedure with enhanced uniform sensitivity. Anal Biochem. 1981 Nov 1;117(2):307–310. doi: 10.1016/0003-2697(81)90783-1. [DOI] [PubMed] [Google Scholar]
  32. Nalin C. M., McCarty R. E. Role of a disulfide bond in the gamma subunit in activation of the ATPase of chloroplast coupling factor 1. J Biol Chem. 1984 Jun 10;259(11):7275–7280. [PubMed] [Google Scholar]
  33. Ohta S., Yohda M., Ishizuka M., Hirata H., Hamamoto T., Otawara-Hamamoto Y., Matsuda K., Kagawa Y. Sequence and over-expression of subunits of adenosine triphosphate synthase in thermophilic bacterium PS3. Biochim Biophys Acta. 1988 Mar 30;933(1):141–155. doi: 10.1016/0005-2728(88)90064-3. [DOI] [PubMed] [Google Scholar]
  34. Pancic P. G., Strotmann H., Kowallik K. V. Chloroplast ATPase genes in the diatom Odontella sinensis reflect cyanobacterial characters in structure and arrangement. J Mol Biol. 1992 Mar 20;224(2):529–536. doi: 10.1016/0022-2836(92)91017-j. [DOI] [PubMed] [Google Scholar]
  35. Pick U., Racker E. Purification and reconstitution of the N,N'-dicyclohexylcarbodiimide-sensitive ATPase complex from spinach chloroplasts. J Biol Chem. 1979 Apr 25;254(8):2793–2799. [PubMed] [Google Scholar]
  36. Sancar G. B., Smith F. W., Lorence M. C., Rupert C. S., Sancar A. Sequences of the Escherichia coli photolyase gene and protein. J Biol Chem. 1984 May 10;259(9):6033–6038. [PubMed] [Google Scholar]
  37. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Schmidt G., Rodgers A. J., Howitt S. M., Munn A. L., Hudson G. S., Holten T. A., Whitfeld P. R., Bottomley W., Gibson F., Cox G. B. The chloroplast CF0I subunit can replace the b-subunit of the F0F1-ATPase in a mutant strain of Escherichia coli K12. Biochim Biophys Acta. 1990 Feb 2;1015(2):195–199. doi: 10.1016/0005-2728(90)90020-5. [DOI] [PubMed] [Google Scholar]
  39. Schneppe B., Deckers-Hebestreit G., Altendorf K. Overproduction and purification of the uncI gene product of the ATP synthase of Escherichia coli. J Biol Chem. 1990 Jan 5;265(1):389–395. [PubMed] [Google Scholar]
  40. Schumann J., Richter M. L., McCarty R. E. Partial proteolysis as a probe of the conformation of the gamma subunit in activated soluble and membrane-bound chloroplast coupling factor 1. J Biol Chem. 1985 Sep 25;260(21):11817–11823. [PubMed] [Google Scholar]
  41. Senior A. E. ATP synthesis by oxidative phosphorylation. Physiol Rev. 1988 Jan;68(1):177–231. doi: 10.1152/physrev.1988.68.1.177. [DOI] [PubMed] [Google Scholar]
  42. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  43. Staden R. Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res. 1982 Aug 11;10(15):4731–4751. doi: 10.1093/nar/10.15.4731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Stutterheim E., Henneke M. A., Berden J. A. Studies on the structure and conformation of yeast mitochondrial ATPase using aurovertin and methanol as probes. Biochim Biophys Acta. 1980 Oct 3;592(3):415–430. doi: 10.1016/0005-2728(80)90089-4. [DOI] [PubMed] [Google Scholar]
  45. Tybulewicz V. L., Falk G., Walker J. E. Rhodopseudomonas blastica atp operon. Nucleotide sequence and transcription. J Mol Biol. 1984 Oct 25;179(2):185–214. doi: 10.1016/0022-2836(84)90465-0. [DOI] [PubMed] [Google Scholar]
  46. Walker J. E., Fearnley I. M., Lutter R., Todd R. J., Runswick M. J. Structural aspects of proton-pumping ATPases. Philos Trans R Soc Lond B Biol Sci. 1990 Jan 30;326(1236):367–378. doi: 10.1098/rstb.1990.0018. [DOI] [PubMed] [Google Scholar]
  47. Walker J. E., Lutter R., Dupuis A., Runswick M. J. Identification of the subunits of F1F0-ATPase from bovine heart mitochondria. Biochemistry. 1991 Jun 4;30(22):5369–5378. doi: 10.1021/bi00236a007. [DOI] [PubMed] [Google Scholar]
  48. Walker J. E., Saraste M., Gay N. J. E. coli F1-ATPase interacts with a membrane protein component of a proton channel. Nature. 1982 Aug 26;298(5877):867–869. doi: 10.1038/298867a0. [DOI] [PubMed] [Google Scholar]
  49. Walker J. E., Saraste M., Gay N. J. The unc operon. Nucleotide sequence, regulation and structure of ATP-synthase. Biochim Biophys Acta. 1984 Sep 6;768(2):164–200. doi: 10.1016/0304-4173(84)90003-x. [DOI] [PubMed] [Google Scholar]
  50. Walker J. E. The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains. Q Rev Biophys. 1992 Aug;25(3):253–324. doi: 10.1017/s003358350000425x. [DOI] [PubMed] [Google Scholar]
  51. Werner S., Schumann J., Strotmann H. The primary structure of the gamma-subunit of the ATPase from Synechocystis 6803. FEBS Lett. 1990 Feb 12;261(1):204–208. doi: 10.1016/0014-5793(90)80671-5. [DOI] [PubMed] [Google Scholar]
  52. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  53. van Walraven H. S., Lubberding H. J., Marvin H. J., Kraayenhof R. Characterization of reconstituted ATPase complex proteoliposomes prepared from the thermophilic cyanobacterium Synechococcus 6716. Eur J Biochem. 1983 Dec 1;137(1-2):101–106. doi: 10.1111/j.1432-1033.1983.tb07801.x. [DOI] [PubMed] [Google Scholar]

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