Chromosomal periodicity and positional networks of genes in Escherichia coli
Abstract The structure of dynamic folds in microbial chromosomes is largely unknown. Here, we find that genes with a highly biased codon composition and characterizing a functional core in Escherichia coli K12 show to be periodically distributed along the arcs, suggesting an encoded three‐dimensiona...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2010-05-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/msb.2010.21 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849225802050174976 |
|---|---|
| author | Anthony Mathelier Alessandra Carbone |
| author_facet | Anthony Mathelier Alessandra Carbone |
| author_sort | Anthony Mathelier |
| collection | DOAJ |
| description | Abstract The structure of dynamic folds in microbial chromosomes is largely unknown. Here, we find that genes with a highly biased codon composition and characterizing a functional core in Escherichia coli K12 show to be periodically distributed along the arcs, suggesting an encoded three‐dimensional genomic organization helping functional activities among which are translation and, possibly, transcription. This extends to functional classes of genes that are shown to systematically organize into two independent positional gene networks, one driven by metabolic genes and the other by genes involved in cellular processing and signaling. We conclude that functional reasons justify periodic gene organization. This finding generates new questions on evolutionary pressures imposed on the chromosome. Our methodological approach is based on single genome analysis. Given either core genes or genes organized in functional classes, we analyze the detailed distribution of distances between pairs of genes through a parameterized model based on signal processing and find that these groups of genes tend to be separated by a regular integral distance. The methodology can be applied to any set of genes and can be taken as a footprint for large‐scale bacterial and archaeal analysis. |
| format | Article |
| id | doaj-art-de2ceff53feb4068b4a1711ec32d1bbd |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2010-05-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-de2ceff53feb4068b4a1711ec32d1bbd2025-08-24T12:00:36ZengSpringer NatureMolecular Systems Biology1744-42922010-05-016111210.1038/msb.2010.21Chromosomal periodicity and positional networks of genes in Escherichia coliAnthony Mathelier0Alessandra Carbone1UPMC Univ Paris 06, FRE3214, Génomique Analytique, 15 rue de l'École de MédecineUPMC Univ Paris 06, FRE3214, Génomique Analytique, 15 rue de l'École de MédecineAbstract The structure of dynamic folds in microbial chromosomes is largely unknown. Here, we find that genes with a highly biased codon composition and characterizing a functional core in Escherichia coli K12 show to be periodically distributed along the arcs, suggesting an encoded three‐dimensional genomic organization helping functional activities among which are translation and, possibly, transcription. This extends to functional classes of genes that are shown to systematically organize into two independent positional gene networks, one driven by metabolic genes and the other by genes involved in cellular processing and signaling. We conclude that functional reasons justify periodic gene organization. This finding generates new questions on evolutionary pressures imposed on the chromosome. Our methodological approach is based on single genome analysis. Given either core genes or genes organized in functional classes, we analyze the detailed distribution of distances between pairs of genes through a parameterized model based on signal processing and find that these groups of genes tend to be separated by a regular integral distance. The methodology can be applied to any set of genes and can be taken as a footprint for large‐scale bacterial and archaeal analysis.https://doi.org/10.1038/msb.2010.21chromosome structureCOGs classescore genesEscherichia coli K12essential genes |
| spellingShingle | Anthony Mathelier Alessandra Carbone Chromosomal periodicity and positional networks of genes in Escherichia coli Molecular Systems Biology chromosome structure COGs classes core genes Escherichia coli K12 essential genes |
| title | Chromosomal periodicity and positional networks of genes in Escherichia coli |
| title_full | Chromosomal periodicity and positional networks of genes in Escherichia coli |
| title_fullStr | Chromosomal periodicity and positional networks of genes in Escherichia coli |
| title_full_unstemmed | Chromosomal periodicity and positional networks of genes in Escherichia coli |
| title_short | Chromosomal periodicity and positional networks of genes in Escherichia coli |
| title_sort | chromosomal periodicity and positional networks of genes in escherichia coli |
| topic | chromosome structure COGs classes core genes Escherichia coli K12 essential genes |
| url | https://doi.org/10.1038/msb.2010.21 |
| work_keys_str_mv | AT anthonymathelier chromosomalperiodicityandpositionalnetworksofgenesinescherichiacoli AT alessandracarbone chromosomalperiodicityandpositionalnetworksofgenesinescherichiacoli |