title: The structural code of cyanobacterial genomes.
abstract: A periodic bias in nucleotide frequency with a period of about 11 bp is characteristic for bacterial genomes. This signal is commonly interpreted to relate to the helical pitch of negatively supercoiled DNA. Functions in supercoiling-dependent RNA transcription or as a 'structural code' for DNA packaging have been suggested. Cyanobacterial genomes showed especially strong periodic signals and, on the other hand, DNA supercoiling and supercoiling-dependent transcription are highly dynamic and underlie circadian rhythms of these phototrophic bacteria. Focusing on this phylum and dinucleotides, we find that a minimal motif of AT-tracts (AT2) yields the strongest signal. Strong genome-wide periodicity is ancestral to a clade of unicellular and polyploid species but lost upon morphological transitions into two baeocyte-forming and a symbiotic species. The signal is intermediate in heterocystous species and weak in monoploid picocyanobacteria. A pronounced 'structural code' may support efficient nucleoid condensation and segregation in polyploid cells. The major source of the AT2 signal are protein-coding regions, where it is encoded preferentially in the first and third codon positions. The signal shows only few relations to supercoiling-dependent and diurnal RNA transcription in Synechocystis sp. PCC 6803. Strong and specific signals in two distinct transposons suggest roles in transposase transcription and transpososome formation.
authors: Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstraße 43, D-10115, Berlin, Germany.
authors: Robert
authors: R
authors: Lehmann
authors: Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstraße 43, D-10115, Berlin, Germany Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17, A-1090, Vienna, Austria raim@tbi.univie.ac.at.
authors: Rainer
authors: R
authors: Machné
authors: Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstraße 43, D-10115, Berlin, Germany.
authors: Hanspeter
authors: H
authors: Herzel
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D000458:Cyanobacteria / Q000235:genetics*; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000737:chemistry*; D004278:DNA, Superhelical / Q000737:chemistry; D016680:Genome, Bacterial
chemical_list: D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D004278:DNA, Superhelical