ArticleNucleic acids research2004
Where does bacterial replication start? Rules for predicting the oriC region.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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Who cites it
105 citing papers in PubMed.
- Article
- Complete Genome Sequence and Comparative Genomics ofMicroorganisms · 2026Article
- Computational prediction of replication origins: a comparative review of methods, benchmarks, and trends from heuristics to deep learning.Briefings in bioinformatics · 2026Review
- Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome.Nature communications · 2026Article
- PolyP inhibits CobB deacetylase triggering a regulatory coupling to prevent DNA replication initiation.Nucleic acids research · 2026Article
- Genomics, transcriptomics, and laboratory experiments link bioconvection to nitrogen fixation.Frontiers in microbiology · 2026Article
- UV induces codirectional replication-transcription conflicts and an alternative DnaA-dependent replication origin in the rnhAB mutants of Escherichiacoli.Nucleic acids research · 2025Article
- Article
- MCM2-7 loading-dependent ORC release ensures genome-wide origin licensing.Nature communications · 2024Article
- Complete genome sequence ofMicrobiology resource announcements · 2024Article
- The bacterial replication origin BUS promotes nucleobase capture.Nature communications · 2023Article
- Identification of herpesvirus transcripts from genomic regions around the replication origins.Scientific reports · 2023Article
- De novo genome assembly resolving repetitive structures enables genomic analysis of 35 European Mycoplasmopsis bovis strains.BMC genomics · 2023Article
- Inhibition of Replication Fork Formation and Progression: Targeting the Replication Initiation and Primosomal Proteins.International journal of molecular sciences · 2023Review
- Article
- Evolutionary conservation ofFrontiers in microbiology · 2023Article
- Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins.Genomics, proteomics & bioinformatics · 2022Article
- B-assembler: a circular bacterial genome assembler.BMC genomics · 2022Article
- Computational characterization and analysis of molecular sequence data of Elizabethkingia meningoseptica.BMC research notes · 2022Article
- Mobile origin-licensing factors confer resistance to conflicts with RNA polymerase.Cell reports · 2022Article
45 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Three methods, based on DNA asymmetry, the distribution of DnaA boxes and dnaA gene location, were applied to identify the putative replication origins in 120 chromosomes. The chromosomes were classified according to the agreement of these methods and the applicability of these methods was evaluated. DNA asymmetry is the most universal method of putative oriC identification in bacterial chromosomes, but it should be applied together with other methods to achieve better prediction. The three methods identify the same region as a putative origin in all Bacilli and Clostridia, many Actinobacteria and gamma Proteobacteria. The organization of clusters of DnaA boxes was analysed in detail. For 76 chromosomes, a DNA fragment containing multiple DnaA boxes was identified as a putative origin region. Most bacterial chromosomes exhibit an overrepresentation of DnaA boxes; many of them contain at least two clusters of DnaA boxes in the vicinity of the oriC region. The additional clusters of DnaA boxes are probably involved in controlling replication initiation. Surprisingly, the characteristic features of the initiation of replication, i.e. a cluster of DnaA boxes, a dnaA gene and a switch in asymmetry, were not found in some of the analysed chromosomes, particularly those of obligatory intracellular parasites or endosymbionts. This is presumably connected with many mechanisms disturbing DNA asymmetry, translocation or disappearance of the dnaA gene and decay of the Escherichia coli perfect DnaA box pattern.
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