ArticlePLoS computational biology2015
Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 47 citations in OpenAlex.
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- Scent of a Symbiont: The Personalized Genetic Relationships of Rhizobium-Plant Interaction.International journal of molecular sciences · 2022Review
- Why are rhizobial symbiosis genes mobile?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Determination of the two-component systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages.Nucleic acids research · 2021Article
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- Destabilization of the Tumor-Inducing Plasmid from an Octopine-TypeG3 (Bethesda, Md.) · 2019Article
- Identification of Modules With Similar Gene Regulation and Metabolic Functions Based on Co-expression Data.Frontiers in molecular biosciences · 2019Article
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- Inter-replicon Gene Flow Contributes to Transcriptional Integration in theG3 (Bethesda, Md.) · 2018Article
- Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii.PLoS genetics · 2018Article
- Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti.PLoS genetics · 2018Article
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Authors and funding
14 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. Recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. The evolution of such networks within and outside the species boundary is however still obscure. Sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a significant knowledge of its transcription factors (TF). Each replicon has a specific functional and evolutionary mark; which might also emerge from the analysis of their regulatory signatures. Here we have studied the plasticity of the regulatory network within and outside the S. meliloti species, looking for the presence of 41 TFs binding motifs in 51 strains and 5 related rhizobial species. We have detected a preference of several TFs for one of the three replicons, and the function of regulated genes was found to be in accordance with the overall replicon functional signature: house-keeping functions for the chromosome, metabolism for the chromid, symbiosis for the megaplasmid. This therefore suggests a replicon-specific wiring of the regulatory network in the S. meliloti species. At the same time a significant part of the predicted regulatory network is shared between the chromosome and the chromid, thus adding an additional layer by which the chromid integrates itself in the core genome. Furthermore, the regulatory network distance was found to be correlated with both promoter regions and accessory genome evolution inside the species, indicating that both pangenome compartments are involved in the regulatory network evolution. We also observed that genes which are not included in the species regulatory network are more likely to belong to the accessory genome, indicating that regulatory interactions should also be considered to predict gene conservation in bacterial pangenomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.