Nucleic Acids Research, 1995, Vol. 23, No. 5 729-735
© 1995
MOLECULAR BIOLOGY |
Singular over-representation of an octameric palindrome, HIP1, in DNA from many cyanobacteria
Department of Biochemistry and Genetics, The Medical School, University of Newcastle Newcastle NE2 4HH, UK 1Daresbury Laboratory Daresbury, Warrington WA4 4AD, UK 2Department of Biological Sciences, University of Durham Durham DH1 3LE, UK
*To whom correspondence should be addressed
Received December 19, 1994. Revised January 26, 1995. Accepted January 26, 1995.
An octameric palindrome (5'-GCGATCGC-3') is abundant In cyanobacterial sequences within databases (GenBank/EMBL)and was designated HIP1 (highly iterated palindrome). The frequency of occurrence of all 256 octameric palindromes has nowbeen determined in sub-databases revealing large and unique over-representation of HIP1 in cyanobacterial entries. DNA sequences from other bacteria were searched for any over-represented octameric palindromes analogous to HIP1. Only two sequences were identified, in the genomes of a thermophile and halophillc archaebac-teria, although these were less abundant than HIP1 in cyanobacteria and relate to codon usage. To test the proposed widespread distribution of HIP1 in DNA from the cyanobacterlum Synechococcus PCC 6301, randomly selected genomic clones were partly sequenced. HIP1 constituted 2.5% of the novel sequences, equivalent to a site on average once every 320 nucleotides. An oligonucleotide including HIP1 was also tested in PCR. Multiple products were obtained using template DNA from cyanobacterial strains in which HIP1 is abundant in known sequences, and some strains generated characteristic HIP-PCR banding patterns. However, analysis of DNA from one strain (not previously represented In databases) by random sequencing, HIP-PCR and Pvul digestion, confirms that not all cyanobacterial genomes are rich in HIP1
+Present address: School of Biological Sciences, University of Birmingham, Birmingham B15 2TT, UK
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. R. de Figueiredo, A. Alves, M. J. Pereira, and A. Correia Molecular characterization of bloom-forming Aphanizomenon strains isolated from Vela Lake (Western Central Portugal) J. Plankton Res., November 23, 2009; (2009) fbp111v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Elhai, M. Kato, S. Cousins, P. Lindblad, and J. L. Costa Very small mobile repeated elements in cyanobacterial genomes Genome Res., September 1, 2008; 18(9): 1484 - 1499. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. K. Ashby and J. Houmard Cyanobacterial Two-Component Proteins: Structure, Diversity, Distribution, and Evolution Microbiol. Mol. Biol. Rev., June 1, 2006; 70(2): 472 - 509. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. E. Wilson, O. Sarnelle, B. A. Neilan, T. P. Salmon, M. M. Gehringer, and M. E. Hay Genetic Variation of the Bloom-Forming Cyanobacterium Microcystis aeruginosa within and among Lakes: Implications for Harmful Algal Blooms Appl. Envir. Microbiol., October 1, 2005; 71(10): 6126 - 6133. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Karlin Colloquium Perspective: Statistical signals in bioinformatics PNAS, September 20, 2005; 102(38): 13355 - 13362. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Pomati, B. P. Burns, and B. A. Neilan Identification of an Na+-Dependent Transporter Associated with Saxitoxin-Producing Strains of the Cyanobacterium Anabaena circinalis Appl. Envir. Microbiol., August 1, 2004; 70(8): 4711 - 4719. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Mrazek, L. H. Gaynon, and S. Karlin Frequent oligonucleotide motifs in genomes of three streptococci Nucleic Acids Res., October 1, 2002; 30(19): 4216 - 4221. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. M. Orcutt, U. Rasmussen, E. A. Webb, J. B. Waterbury, K. Gundersen, and B. Bergman Characterization of Trichodesmium spp. by Genetic Techniques Appl. Envir. Microbiol., May 1, 2002; 68(5): 2236 - 2245. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Matsuoka, K. Takahama, and T. Ogawa Gene replacement in cyanobacteria mediated by a dominant streptomycin-sensitive rps12 gene that allows selection of mutants free from drug resistance markers Microbiology, August 1, 2001; 147(8): 2077 - 2087. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. V. Matveyev, K. T. Young, A. Meng, and J. Elhai DNA methyltransferases of the cyanobacterium Anabaena PCC 7120 Nucleic Acids Res., April 1, 2001; 29(7): 1491 - 1506. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Mrazek, D. Bhaya, A. R. Grossman, and S. Karlin Highly expressed and alien genes of the Synechocystis genome Nucleic Acids Res., April 1, 2001; 29(7): 1590 - 1601. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Bhaya, D. Vaulot, P. Amin, A. W. Takahashi, and A. R. Grossman Isolation of Regulated Genes of the Cyanobacterium Synechocystis sp. Strain PCC 6803 by Differential Display J. Bacteriol., October 15, 2000; 182(20): 5692 - 5699. [Abstract] [Full Text]
|
|
|
|
|
|
M. D. LeBlanc, G. Aspeslagh, N. P. Buggia, and B. D. Dyer An Annotated Catalog of Inverted Repeats of Caenorhabditis elegans Chromosomes III and X, with Observations Concerning Odd/Even Biases and Conserved Motifs Genome Res., September 1, 2000; 10(9): 1381 - 1392. [Abstract] [Full Text]
|
|
|
|
|
|
F. Engelbrecht, K. Marin, and M. Hagemann Expression of the ggpS Gene, Involved in Osmolyte Synthesis in the Marine Cyanobacterium Synechococcus sp. Strain PCC 7002, Revealed Regulatory Differences between This Strain and the Freshwater Strain Synechocystis sp. Strain PCC 6803 Appl. Envir. Microbiol., November 1, 1999; 65(11): 4822 - 4829. [Abstract] [Full Text]
|
|
|
|
|
|
M. Scharnagl, S. Richter, and M. Hagemann The Cyanobacterium Synechocystis sp. Strain PCC 6803 Expresses a DNA Methyltransferase Specific for the Recognition Sequence of the Restriction Endonuclease PvuI J. Bacteriol., August 15, 1998; 180(16): 4116 - 4122. [Abstract] [Full Text]
|
|