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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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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 |
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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 |
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