Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes.

Edgardo Galán-Vásquez,Agustino Martínez-Antonio,Ismael Sánchez-Osorio,Marc Robinson-Rechavi

doi:10.1371/journal.pone.0146901

Abstract

The description of transcriptional regulatory networks has been pivotal in the understanding of operating principles under which organisms respond and adapt to varying conditions. While the study of the topology and dynamics of these networks has been the subject of considerable work, the investigation of the evolution of their topology, as a result of the adaptation of organisms to different environmental conditions, has received little attention. In this work, we study the evolution of transcriptional regulatory networks in bacteria from a genome reduction perspective, which manifests itself as the loss of genes at different degrees. We used the transcriptional regulatory network of Escherichia coli as a reference to compare 113 smaller, phylogenetically-related γ-proteobacteria, including 19 genomes of symbionts. We found that the type of regulatory action exerted by transcription factors, as genomes get progressively smaller, correlates well with their degree of conservation, with dual regulators being more conserved than repressors and activators in conditions of extreme reduction. In addition, we found that the preponderant conservation of dual regulators might be due to their role as both global regulators and nucleoid-associated proteins. We summarize our results in a conceptual model of how each TF type is gradually lost as genomes become smaller and give a rationale for the order in which this phenomenon occurs.

Highlights

Transcription is an essential molecular process through which cells respond and adapt to changing environmental conditions, such as different kinds of stress and nutrient deficiencies [1]. The regulation of this dynamic process is usually carried-out by proteins called transcription factors (TFs), which bind to upstream regions of target genes (TGs) and promote or inhibit the synthesis of RNA molecules
We studied the evolution of transcriptional regulatory network (TRN) in bacteria taking as a reference the regulatory network of E. coli
Earlier studies of evolution in TRNs have primarily focused on network growth and the comparison of genomes from free-living organism as the underlying methodology

Summary

Introduction

Transcription is an essential molecular process through which cells respond and adapt to changing environmental conditions, such as different kinds of stress and nutrient deficiencies [1]. The regulation of this dynamic process is usually carried-out by proteins called transcription factors (TFs), which bind to upstream regions (called promoters) of target genes (TGs) and promote or inhibit the synthesis of RNA molecules (and the subsequent production of proteins). Other molecular regulatory mechanisms might be operating at other stages of the gene expression process, such as DNA-methylation, RNA interference, etc., transcriptional regulation mediated by TFs is the predominant type of control in gene expression [3]. According to the number of genes they regulate, TFs can be ranked and defined as global regulators, when they act as hubs (highly connected nodes) in a network; and local regulators, when they regulate few genes, usually an operon or genes represented as terminal nodes in a regulatory network [5]

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Conclusion