Next Article in Journal
Combining Protein and Strain Engineering for the Production of Glyco-Engineered Horseradish Peroxidase C1A in Pichia pastoris
Next Article in Special Issue
Identification of Specific Variations in a Non-Motile Strain of Cyanobacterium Synechocystis sp. PCC 6803 Originated from ATCC 27184 by Whole Genome Resequencing
Previous Article in Journal
Rational Protein Engineering Guided by Deep Mutational Scanning
Previous Article in Special Issue
Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map
Article Menu
Issue 9 (September) cover image

Export Article

Open AccessArticle
Int. J. Mol. Sci. 2015, 16(9), 23111-23126; doi:10.3390/ijms160923111

Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes

1,2,†
,
1,2,†
,
1,2
,
1,2,* and 1,2,*
1
Center of Bioinformatics, Key Laboratory for NeuroInformation of the Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
2
Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Patrick C. Y. Woo
Received: 27 July 2015 / Revised: 18 August 2015 / Accepted: 18 September 2015 / Published: 23 September 2015
(This article belongs to the Special Issue Microbial Genomics and Metabolomics)
View Full-Text   |   Download PDF [1075 KB, uploaded 23 September 2015]   |  

Abstract

Composition bias from Chargaff’s second parity rule (PR2) has long been found in sequenced genomes, and is believed to relate strongly with the replication process in microbial genomes. However, some disagreement on the underlying reason for strand composition bias remains. We performed an integrative analysis of various genomic features that might influence composition bias using a large-scale dataset of 1111 genomes. Our results indicate (1) the bias was stronger in obligate intracellular bacteria than in other free-living species (p-value = 0.0305); (2) Fusobacteria and Firmicutes had the highest average bias among the 24 microbial phyla analyzed; (3) the strength of selected codon usage bias and generation times were not observably related to strand composition bias (p-value = 0.3247); (4) significant negative relationships were found between GC content, genome size, rearrangement frequency, Clusters of Orthologous Groups (COG) functional subcategories A, C, I, Q, and composition bias (p-values < 1.0 × 10−8); (5) gene density and COG functional subcategories D, F, J, L, and V were positively related with composition bias (p-value < 2.2 × 10−16); and (6) gene density made the most important contribution to composition bias, indicating transcriptional bias was associated strongly with strand composition bias. Therefore, strand composition bias was found to be influenced by multiple factors with varying weights. View Full-Text
Keywords: strand composition bias; multiple factors; gene density; genomic features; COG functional category; obligate intracellular bacteria strand composition bias; multiple factors; gene density; genomic features; COG functional category; obligate intracellular bacteria
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Zhao, H.-L.; Xia, Z.-K.; Zhang, F.-Z.; Ye, Y.-N.; Guo, F.-B. Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes. Int. J. Mol. Sci. 2015, 16, 23111-23126.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top