The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces

Mao, Xizeng; Zhang, Han; Yin, Yanbin; Xu, Ying

doi:10.1093/nar/gks605

Cited by 45 publications

(47 citation statements)

References 37 publications

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“…Intriguingly, certain categories of weakly expressed or even silent genes, such as prophages and other horizontally transferred genes, are highly abundant in the leading strand (Campbell 2002;Hao and Golding 2009). On the other hand, regulatory functions are more frequent in the lagging strand than expected (Mao et al 2012). A number of models have been proposed to explain why selection against head-on collisions causes gene strand bias.…”

Section: Replication Recombination and Segregationmentioning

confidence: 99%

Coevolution of the Organization and Structure of Prokaryotic Genomes

Touchon

Rocha

2016

Cold Spring Harb Perspect Biol

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The cytoplasm of prokaryotes contains many molecular machines interacting directly with the chromosome. These vital interactions depend on the chromosome structure, as a molecule, and on the genome organization, as a unit of genetic information. Strong selection for the organization of the genetic elements implicated in these interactions drives replicon ploidy, gene distribution, operon conservation, and the formation of replication-associated traits. The genomes of prokaryotes are also very plastic with high rates of horizontal gene transfer and gene loss. The evolutionary conflicts between plasticity and organization lead to the formation of regions with high genetic diversity whose impact on chromosome structure is poorly understood. Prokaryotic genomes are remarkable documents of natural history because they carry the imprint of all of these selective and mutational forces. Their study allows a better understanding of molecular mechanisms, their impact on microbial evolution, and how they can be tinkered in synthetic biology.

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Section: Replication Recombination and Segregationmentioning

confidence: 99%

Coevolution of the Organization and Structure of Prokaryotic Genomes

Touchon

Rocha

2016

Cold Spring Harb Perspect Biol

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“…Because of continuous updates, our database has been widely used in the comparative genomics analysis. For example, as a source of data, DoriC has been used in the study of the relationship between the functionality of essential genes and gene strand bias in bacterial genomes (13), in the analysis of nucleotide compositional asymmetry between the leading and lagging strands of bacterial genomes (14), in the investigation of the association between growth-related traits and minimal generation times (15), in an algorithm for prediction of putative essential and core-essential genes in Mycoplasma genomes (16), in the research on coordination of spatiotemporal gene expression during the bacterial growth cycle (17) and in the study of the variation in terms of the percentage of leading strand genes across different bacteria (18), etc. It is expected that the new release of the database, DoriC 5.0, will promote the study of oriCs in both bacteria and archaea.…”

Section: Introductionmentioning

confidence: 99%

DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes

Gao

Luo

Zhang

2012

Nucleic Acids Research

121

111

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Replication of chromosomes is one of the central events in the cell cycle. Chromosome replication begins at specific sites, called origins of replication (oriCs), for all three domains of life. However, the origins of replication still remain unknown in a considerably large number of bacterial and archaeal genomes completely sequenced so far. The availability of increasing complete bacterial and archaeal genomes has created challenges and opportunities for identification of their oriCs in silico, as well as in vivo. Based on the Z-curve theory, we have developed a web-based system Ori-Finder to predict oriCs in bacterial genomes with high accuracy and reliability by taking advantage of comparative genomics, and the predicted oriC regions have been organized into an online database DoriC, which is publicly available at http://tubic.tju.edu.cn/doric/ since 2007. Five years after we constructed DoriC, the database has significant advances over the number of bacterial genomes, increasing about 4-fold. Additionally, oriC regions in archaeal genomes identified by in vivo experiments, as well as in silico analyses, have also been added to the database. Consequently, the latest release of DoriC contains oriCs for >1500 bacterial genomes and 81 archaeal genomes, respectively.

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“…The numbers of coding regions in two strands of replication were calculated for each genome and the strand with higher frequency of coding regions were taken as the LeS, following the usual convention [3, 52]. …”

Section: Methodsmentioning

confidence: 99%

Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: a new appraisal

2014

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BackgroundThe Firmicutes often possess three conspicuous genome features: marked Purine Asymmetry (PAS) across two strands of replication, Strand-biased Gene Distribution (SGD) and presence of two isoforms of DNA polymerase III alpha subunit, PolC and DnaE. Despite considerable research efforts, it is not clear whether the co-existence of PAS, PolC and/or SGD is an essential and exclusive characteristic of the Firmicutes. The nature of correlations, if any, between these three features within and beyond the lineages of Firmicutes has also remained elusive. The present study has been designed to address these issues.ResultsA large-scale analysis of diverse bacterial genomes indicates that PAS, PolC and SGD are neither essential nor exclusive features of the Firmicutes. PolC prevails in four bacterial phyla: Firmicutes, Fusobacteria, Tenericutes and Thermotogae, while PAS occurs only in subsets of Firmicutes, Fusobacteria and Tenericutes. There are five major compositional trends in Firmicutes: (I) an explicit PAS or G + A-dominance along the entire leading strand (II) only G-dominance in the leading strand, (III) alternate stretches of purine-rich and pyrimidine-rich sequences, (IV) G + T dominance along the leading strand, and (V) no identifiable patterns in base usage. Presence of strong SGD has been observed not only in genomes having PAS, but also in genomes with G-dominance along their leading strands – an observation that defies the notion of co-occurrence of PAS and SGD in Firmicutes. The PolC-containing non-Firmicutes organisms often have alternate stretches of R-dominant and Y-dominant sequences along their genomes and most of them show relatively weak, but significant SGD. Firmicutes having G + A-dominance or G-dominance along LeS usually show distinct base usage patterns in three codon sites of genes. Probable molecular mechanisms that might have incurred such usage patterns have been proposed.ConclusionCo-occurrence of PAS, strong SGD and PolC should not be regarded as a genome signature of the Firmicutes. Presence of PAS in a species may warrant PolC and strong SGD, but PolC and/or SGD not necessarily implies PAS.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-430) contains supplementary material, which is available to authorized users.

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The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces

Cited by 45 publications

References 37 publications

Coevolution of the Organization and Structure of Prokaryotic Genomes

Coevolution of the Organization and Structure of Prokaryotic Genomes

DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes

Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: a new appraisal

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