Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.
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.
Department of Biology, University of Florence, Florence, Italy.
Marco
M
Galardini
Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.
Matteo
M
Brilli
Dipartimento di Biotecnologie Agrarie, Sezione di Microbiologia, University of Florence, Florence, Italy.
Giulia
G
Spini
Department of Biology, University of Florence, Florence, Italy.
Matteo
M
Rossi
Department of Biology, University of Florence, Florence, Italy.
Bianca
B
Roncaglia
Department of Biology, University of Florence, Florence, Italy.
Alessia
A
Bani
Department of Biology, University of Florence, Florence, Italy.
Manuela
M
Chiancianesi
Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.
Marco
M
Moretto
Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.
Kristof
K
Engelen
Department of Biology, University of Florence, Florence, Italy; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CRA-RPS), Rome, Italy.
Giovanni
G
Bacci
Interdisciplinary Research Institute USR3078, CNRS-Universit Lille Nord de France, Villeneuve d'Ascq, France.
Francesco
F
Pini
Interdisciplinary Research Institute USR3078, CNRS-Universit Lille Nord de France, Villeneuve d'Ascq, France.
Emanuele G
EG
Biondi
Department of Biology, University of Florence, Florence, Italy.
Marco
M
Bazzicalupo
Department of Biology, University of Florence, Florence, Italy.
Alessio
A
Mengoni
D019295:Computational Biology; D019143:Evolution, Molecular; D053263:Gene Regulatory Networks / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D008957:Models, Genetic; D016962:Sinorhizobium meliloti / Q000235:genetics