ArticleBMC genomics2020
Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 21 citations in OpenAlex.
- Comparative pathogenomics and in silico analysis of energy metabolism in Acinetobacter baumannii ST195 and novel Turkish isolates encoding blaOXA-23, blaOXA-66, and blaOXA-852.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome.Nature communications · 2026Article
- Evolutionary constraints on RNA polymerase gene positioning in the genome of fast-growing bacteria.Nucleic acids research · 2026Article
- Interpretable learning algorithms enable pathogenic potential assessment and virulence-associated gene discovery ofFrontiers in microbiology · 2026Article
- TheMicrobiology and molecular biology reviews : MMBR · 2025Review
- Comparative Genomic Analysis of TwoMicroorganisms · 2025Article
- Genome Analysis of a Newly Sequenced B. subtilis SRCM117797 and Multiple Public B. subtilis Genomes Unveils Insights into Strain Diversification and Biased Core Gene Distribution.Current microbiology · 2024Article
- Pan-Genome Plasticity and Virulence Factors: A Natural Treasure Trove forAntibiotics (Basel, Switzerland) · 2024Review
- Chromosomal gene order defines several structural classes of Staphylococcus epidermidis genomes.PloS one · 2024Article
- Cell cycle-coordinated maintenance of theEcoSal Plus · 2023Review
- Comparative genomics of symbioticMicrobial genomics · 2023Article
- Ploidy inGenes · 2023Review
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- Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria.Microbial genomics · 2023Article
- Chromosomal Position of Ribosomal Protein Genes Affects Long-Term Evolution of Vibrio cholerae.mBio · 2023Article
- Bipartite Genomes inInternational journal of molecular sciences · 2023Article
- The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid.G3 (Bethesda, Md.) · 2021Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories.
resultsWe calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression.
conclusionThe pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement.
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