Cargando…

The structural code of cyanobacterial genomes

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 pack...

Descripción completa

Detalles Bibliográficos
Autores principales: Lehmann, Robert, Machné, Rainer, Herzel, Hanspeter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132750/
https://www.ncbi.nlm.nih.gov/pubmed/25056315
http://dx.doi.org/10.1093/nar/gku641
_version_ 1782330673338515456
author Lehmann, Robert
Machné, Rainer
Herzel, Hanspeter
author_facet Lehmann, Robert
Machné, Rainer
Herzel, Hanspeter
author_sort Lehmann, Robert
collection PubMed
description 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.
format Online
Article
Text
id pubmed-4132750
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-41327502014-12-01 The structural code of cyanobacterial genomes Lehmann, Robert Machné, Rainer Herzel, Hanspeter Nucleic Acids Res Computational Biology 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. Oxford University Press 2014-08-18 2014-07-23 /pmc/articles/PMC4132750/ /pubmed/25056315 http://dx.doi.org/10.1093/nar/gku641 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Computational Biology
Lehmann, Robert
Machné, Rainer
Herzel, Hanspeter
The structural code of cyanobacterial genomes
title The structural code of cyanobacterial genomes
title_full The structural code of cyanobacterial genomes
title_fullStr The structural code of cyanobacterial genomes
title_full_unstemmed The structural code of cyanobacterial genomes
title_short The structural code of cyanobacterial genomes
title_sort structural code of cyanobacterial genomes
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132750/
https://www.ncbi.nlm.nih.gov/pubmed/25056315
http://dx.doi.org/10.1093/nar/gku641
work_keys_str_mv AT lehmannrobert thestructuralcodeofcyanobacterialgenomes
AT machnerainer thestructuralcodeofcyanobacterialgenomes
AT herzelhanspeter thestructuralcodeofcyanobacterialgenomes
AT lehmannrobert structuralcodeofcyanobacterialgenomes
AT machnerainer structuralcodeofcyanobacterialgenomes
AT herzelhanspeter structuralcodeofcyanobacterialgenomes