ArticleBMC genomics2011
Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Complete Genome Sequence and Comparative Genomics ofMicroorganisms · 2026Article
- Interplay between the Xer recombination system and the dissemination of antibioresistance in Acinetobacter baumannii.Nucleic acids research · 2025Article
- Enrichment of horizontally transferred gene clusters in bacterial extracellular vesicles via non lytic mechanisms.The ISME journal · 2025Article
- Article
- Determination of the chromosomal position effects for plug-and-play application in theSynthetic and systems biotechnology · 2024Article
- The effect of site-specific recombinases XerCD on the removal of over-replicated chromosomal DNA through outer membrane vesicles in bacteria.Microbiology spectrum · 2024Article
- Reekeekee- and roodoodooviruses, two differentVirus evolution · 2023Article
- The Xer activation factor of TLCΦ expands the possibilities for Xer recombination.Nucleic acids research · 2022Article
- Chromosome choreography during the non-binary cell cycle of a predatory bacterium.Current biology : CB · 2021Article
- A Fork Trap in the Chromosomal Termination Area Is Highly Conserved across AllInternational journal of molecular sciences · 2021Article
- Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes.Molecular systems biology · 2021Article
- Article
- Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution SitemSystems · 2021Article
- Selection for ancient periodic motifs that do not impart DNA bending.PLoS genetics · 2020Article
- Spatial Patterns of Gene Expression in Bacterial Genomes.Journal of molecular evolution · 2020Article
- Article
- Characterization of the Chromosome Dimer Resolution Site in Caulobacter crescentus.Journal of bacteriology · 2019Article
- Article
- The TLCΦ satellite phage harbors a Xer recombination activation factor.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Genome and proteome of the chlorophyll f-producing cyanobacterium Halomicronema hongdechloris: adaptative proteomic shifts under different light conditions.BMC genomics · 2019Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDuring the replication process of bacteria with circular chromosomes, an odd number of homologous recombination events results in concatenated dimer chromosomes that cannot be partitioned into daughter cells. However, many bacteria harbor a conserved dimer resolution machinery consisting of one or two tyrosine recombinases, XerC and XerD, and their 28-bp target site, dif.
resultsTo study the evolution of the dif/XerCD system and its relationship with replication termination, we report the comprehensive prediction of dif sequences in silico using a phylogenetic prediction approach based on iterated hidden Markov modeling. Using this method, dif sites were identified in 641 organisms among 16 phyla, with a 97.64% identification rate for single-chromosome strains. The dif sequence positions were shown to be strongly correlated with the GC skew shift-point that is induced by replicational mutation/selection pressures, but the difference in the positions of the predicted dif sites and the GC skew shift-points did not correlate with the degree of replicational mutation/selection pressures.
conclusionsThe sequence of dif sites is widely conserved among many bacterial phyla, and they can be computationally identified using our method. The lack of correlation between dif position and the degree of GC skew suggests that replication termination does not occur strictly at dif sites.
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