Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

PLoS Computational Biology
Marco GalardiniAlessio Mengoni

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 regul...Continue Reading

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Citations

Nov 21, 2015·Nucleic Acids Research·Marco MorettoKristof Engelen
Nov 25, 2017·Frontiers in Microbiology·Alice CheccucciAlessio Mengoni
Aug 11, 2017·Microbiology and Molecular Biology Reviews : MMBR·George C diCenzo, Turlough M Finan
Mar 23, 2018·G3 : Genes - Genomes - Genetics·George C diCenzoTurlough M Finan
Nov 30, 2019·Environmental Microbiology·Ludovic Vial, Florence Hommais
Nov 11, 2018·Genes·Camilla FagorziAlessio Mengoni
Apr 20, 2018·Frontiers in Microbiology·Nicolás ToroRafael Nisa-Martínez
Jan 11, 2020·Frontiers in Molecular Biosciences·Edgardo Galán-Vásquez, Ernesto Perez-Rueda
Nov 30, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Grace E WardellEllie Harrison

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Methods Mentioned

BETA
PCR
PCA
electrophoresis

Software Mentioned

GHMM
NumPy
hmmbuild
Phylo
DendroPy package
Biopython library
DuctApe suite
CONTIGuator
Gephi
SciPy library

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