Physical genome map of the unicellular cyanobacterium Synechococcus sp. strain PCC 7002 (original) (raw)

Abstract

A physical restriction map of the genome of the cyanobacterium Synechococcus sp. strain PCC 7002 was assembled from AscI, NotI, SalI, and SfiI digests of intact genomic DNA separated on a contour-clamped homogeneous electric field pulsed-field gel electrophoresis system. An average genome size of 2.7 x 10(6) bp was calculated from 21 NotI, 37 SalI, or 27 SfiI fragments obtained by the digestions. The genomic map was assembled by using three different strategies: linking clone analysis, pulsed-field fragment hybridization, and individual clone hybridization to singly and doubly restriction-digested large DNA fragments. The relative positions of 21 genes or operons were determined, and these data suggest that the gene order is not highly conserved between Synechococcus sp. strain PCC 7002 and Anabaena sp. strain PCC 7120.

5106

Images in this article

Selected References

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

  1. Bancroft I., Wolk C. P., Oren E. V. Physical and genetic maps of the genome of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol. 1989 Nov;171(11):5940–5948. doi: 10.1128/jb.171.11.5940-5948.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Binder B. J., Chisholm S. W. Relationship between DNA cycle and growth rate in Synechococcus sp. strain PCC 6301. J Bacteriol. 1990 May;172(5):2313–2319. doi: 10.1128/jb.172.5.2313-2319.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Borthakur D., Haselkorn R. Nucleotide sequence of the gene encoding the 33 kDa water oxidizing polypeptide in Anabaena sp. strain PCC 7120 and its expression in Escherichia coli. Plant Mol Biol. 1989 Oct;13(4):427–439. doi: 10.1007/BF00015555. [DOI] [PubMed] [Google Scholar]
  4. Brand S. N., Tan X., Widger W. R. Cloning and sequencing of the petBD operon from the cyanobacterium Synechococcus sp. PCC 7002. Plant Mol Biol. 1992 Nov;20(3):481–491. doi: 10.1007/BF00040607. [DOI] [PubMed] [Google Scholar]
  5. Bryant D. A., de Lorimier R., Guglielmi G., Stevens S. E., Jr Structural and compositional analyses of the phycobilisomes of Synechococcus sp. PCC 7002. Analyses of the wild-type strain and a phycocyanin-less mutant constructed by interposon mutagenesis. Arch Microbiol. 1990;153(6):550–560. doi: 10.1007/BF00245264. [DOI] [PubMed] [Google Scholar]
  6. Burnap R. L., Sherman L. A. Deletion mutagenesis in Synechocystis sp. PCC6803 indicates that the Mn-stabilizing protein of photosystem II is not essential for O2 evolution. Biochemistry. 1991 Jan 15;30(2):440–446. doi: 10.1021/bi00216a020. [DOI] [PubMed] [Google Scholar]
  7. Buzby J. S., Porter R. D., Stevens S. E., Jr Plasmid transformation in Agmenellum quadruplicatum PR-6: construction of biphasic plasmids and characterization of their transformation properties. J Bacteriol. 1983 Jun;154(3):1446–1450. doi: 10.1128/jb.154.3.1446-1450.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chu G., Vollrath D., Davis R. W. Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science. 1986 Dec 19;234(4783):1582–1585. doi: 10.1126/science.3538420. [DOI] [PubMed] [Google Scholar]
  9. Essich E., Stevens S. E., Jr, Porter R. D. Chromosomal transformation in the cyanobacterium Agmenellum quadruplicatum. J Bacteriol. 1990 Apr;172(4):1916–1922. doi: 10.1128/jb.172.4.1916-1922.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Giovannoni S. J., Turner S., Olsen G. J., Barns S., Lane D. J., Pace N. R. Evolutionary relationships among cyanobacteria and green chloroplasts. J Bacteriol. 1988 Aug;170(8):3584–3592. doi: 10.1128/jb.170.8.3584-3592.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Golden S. S., Brusslan J., Haselkorn R. Expression of a family of psbA genes encoding a photosystem II polypeptide in the cyanobacterium Anacystis nidulans R2. EMBO J. 1986 Nov;5(11):2789–2798. doi: 10.1002/j.1460-2075.1986.tb04569.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Golden S. S., Sherman L. A. Optimal conditions for genetic transformation of the cyanobacterium Anacystis nidulans R2. J Bacteriol. 1984 Apr;158(1):36–42. doi: 10.1128/jb.158.1.36-42.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Golden S. S., Stearns G. W. Nucleotide sequence and transcript analysis of three photosystem II genes from the cyanobacterium Synechococcus sp. PCC7942. Gene. 1988 Jul 15;67(1):85–96. doi: 10.1016/0378-1119(88)90011-x. [DOI] [PubMed] [Google Scholar]
  14. Johnson C. H., Kruft V., Subramanian A. R. Identification of a plastid-specific ribosomal protein in the 30 S subunit of chloroplast ribosomes and isolation of the cDNA clone encoding its cytoplasmic precursor. J Biol Chem. 1990 Aug 5;265(22):12790–12795. [PubMed] [Google Scholar]
  15. Karreman C., de Waard A. Agmenellum quadruplicatum M.AquI, a novel modification methylase. J Bacteriol. 1990 Jan;172(1):266–272. doi: 10.1128/jb.172.1.266-272.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  17. Mazel D., Houmard J., Castets A. M., Tandeau de Marsac N. Highly repetitive DNA sequences in cyanobacterial genomes. J Bacteriol. 1990 May;172(5):2755–2761. doi: 10.1128/jb.172.5.2755-2761.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Murphy R. C., Bryant D. A., Porter R. D., de Marsac N. T. Molecular cloning and characterization of the recA gene from the cyanobacterium Synechococcus sp. strain PCC 7002. J Bacteriol. 1987 Jun;169(6):2739–2747. doi: 10.1128/jb.169.6.2739-2747.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Pakrasi H. B., Williams J. G., Arntzen C. J. Targeted mutagenesis of the psbE and psbF genes blocks photosynthetic electron transport: evidence for a functional role of cytochrome b559 in photosystem II. EMBO J. 1988 Feb;7(2):325–332. doi: 10.1002/j.1460-2075.1988.tb02816.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Palmer J. D., Thompson W. F. Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell. 1982 Jun;29(2):537–550. doi: 10.1016/0092-8674(82)90170-2. [DOI] [PubMed] [Google Scholar]
  21. Rhiel E., Stirewalt V. L., Gasparich G. E., Bryant D. A. The psaC genes of Synechococcus sp. PCC7002 and Cyanophora paradoxa: cloning and sequence analysis. Gene. 1992 Mar 1;112(1):123–128. doi: 10.1016/0378-1119(92)90313-e. [DOI] [PubMed] [Google Scholar]
  22. Roberts T. M., Koths K. E. The blue-green alga agmenellum quadruplicatum contains covalently closed DNA circles. Cell. 1976 Dec;9(4 Pt 1):551–557. doi: 10.1016/0092-8674(76)90037-4. [DOI] [PubMed] [Google Scholar]
  23. Rosenberg S. M., Stahl M. M., Kobayashi I., Stahl F. W. Improved in vitro packaging of coliphage lambda DNA: a one-strain system free from endogenous phage. Gene. 1985;38(1-3):165–175. doi: 10.1016/0378-1119(85)90215-x. [DOI] [PubMed] [Google Scholar]
  24. Schaefer M. R., Golden S. S. Differential expression of members of a cyanobacterial psbA gene family in response to light. J Bacteriol. 1989 Jul;171(7):3973–3981. doi: 10.1128/jb.171.7.3973-3981.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Schluchter W. M., Bryant D. A. Molecular characterization of ferredoxin-NADP+ oxidoreductase in cyanobacteria: cloning and sequence of the petH gene of Synechococcus sp. PCC 7002 and studies on the gene product. Biochemistry. 1992 Mar 31;31(12):3092–3102. doi: 10.1021/bi00127a009. [DOI] [PubMed] [Google Scholar]
  26. Shinozaki K., Ohme M., Tanaka M., Wakasugi T., Hayashida N., Matsubayashi T., Zaita N., Chunwongse J., Obokata J., Yamaguchi-Shinozaki K. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986 Sep;5(9):2043–2049. doi: 10.1002/j.1460-2075.1986.tb04464.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Smith C. L., Cantor C. R. Purification, specific fragmentation, and separation of large DNA molecules. Methods Enzymol. 1987;155:449–467. doi: 10.1016/0076-6879(87)55030-3. [DOI] [PubMed] [Google Scholar]
  28. Smith C. L., Econome J. G., Schutt A., Klco S., Cantor C. R. A physical map of the Escherichia coli K12 genome. Science. 1987 Jun 12;236(4807):1448–1453. doi: 10.1126/science.3296194. [DOI] [PubMed] [Google Scholar]
  29. Vermaas W. F., Williams J. G., Rutherford A. W., Mathis P., Arntzen C. J. Genetically engineered mutant of the cyanobacterium Synechocystis 6803 lacks the photosystem II chlorophyll-binding protein CP-47. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9474–9477. doi: 10.1073/pnas.83.24.9474. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Waterbury P. G., Lane M. J. Generation of lambda phage concatemers for use as pulsed field electrophoresis size markers. Nucleic Acids Res. 1987 May 11;15(9):3930–3930. doi: 10.1093/nar/15.9.3930. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Webb R., Reddy K. J., Sherman L. A. Regulation and sequence of the Synechococcus sp. strain PCC 7942 groESL operon, encoding a cyanobacterial chaperonin. J Bacteriol. 1990 Sep;172(9):5079–5088. doi: 10.1128/jb.172.9.5079-5088.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Zhou D. X., Mache R. Presence in the stroma of chloroplasts of a large pool of a ribosomal protein not structurally related to any Escherichia coli ribosomal protein. Mol Gen Genet. 1989 Oct;219(1-2):204–208. doi: 10.1007/BF00261178. [DOI] [PubMed] [Google Scholar]
  33. de Lorimier R., Bryant D. A., Porter R. D., Liu W. Y., Jay E., Stevens S. E., Jr Genes for the alpha and beta subunits of phycocyanin. Proc Natl Acad Sci U S A. 1984 Dec;81(24):7946–7950. doi: 10.1073/pnas.81.24.7946. [DOI] [PMC free article] [PubMed] [Google Scholar]