Santos-Zavaleta et al. BMC Genomics (2019) 20:299 https://doi.org/10.1186/s12864-019-5619-z RESEARCH ARTICLE Open Access Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes A. Santos-Zavaleta1* , E. Pérez-Rueda2,3*, M. Sánchez-Pérez1, D. A. Velázquez-Ramírez1 and J. Collado-Vides1 Abstract Background: Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms. Results: In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σS regulon in this bacterium. Based on an analysis of orthologs in 18 archaeal and 69 bacterial taxonomical divisions and using E. coli K- 12 as a framework, we suggest three main events that resulted in this regulon’s actual form: (i) in a first step, rpoS,a gene widely distributed in bacteria and archaea cellular domains, was recruited to regulate genes involved in ancient metabolic processes, such as those associated with glycolysis and the tricarboxylic acid cycle; (ii) in a second step, the regulon recruited those genes involved in metabolic processes, which are mainly taxonomically constrained to Proteobacteria, with some secondary losses, such as those genes involved in responses to stress or starvation and cell adhesion, among others; and (iii) in a posterior step, Crl might have been recruited in Enterobacteriaceae; because its taxonomical pattern constrained to this bacterial order, however further analysis are necessary. Conclusions: Therefore, we suggest that the regulon Crl is highly flexible for phenotypic adaptation, probably as consequence of the diverse growth environments associated with all organisms in which members of this regulatory network are present. Keywords: Crl regulon, Stress response, Transcription factors, Comparative genomics, Bacteria, Archaea Background bacterium Escherichia coli K-12, seven sigma factors Gene expression in bacteria is coordinated through the have been experimentally identified, together with DNA-binding transcription factors (TFs), blocking or around 300 different TFs responsible for recognizing allowing the access of the RNA polymerase (RNAP)-- and activating almost all of their genes [1]. Among these, sigma factor to the promoter and providing bacteria with RpoD, or σ70, regulates around 40% of the total gene the ability to activate or repress multiple genes under repertoire, whereas alternative sigma factors such as different metabolic stimuli or growth conditions. In the RpoS (σS), the master regulator of the stationary-phase response [2], regulate between 5 and 10% of the total * Correspondence: [email protected]; [email protected] genes in E. coli K-12 [3]. 1Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Morelos, Sigma factors and TFs regulate a large diversity of Mexico genes, hierarchically organized in regulons [4]. Previous 2Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Sede comparative genomics studies have suggested that regu- Mérida, Universidad Nacional Autónoma de México, Unidad Académica de Ciencias y Tecnología, 97302 Mérida, Yucatán, Mexico lons exhibit considerable plasticity across the evolution Full list of author information is available at the end of the article of bacterial species [5]. In this regard, comparison of the © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Santos-Zavaleta et al. BMC Genomics (2019) 20:299 Page 2 of 13 gene composition of the PhoPQ regulon in E. coli and microarray analysis), and inferences made from a mutant Salmonella enterica serovar Typhimurium revealed a phenotype (mutation of a TF with a visible cell pheno- very small overlap in both species, suggesting a low simi- type), among other analyses. Therefore, 86 genes were larity in composition between the target genes that are included in this work as members of the σS sigmulon, of regulated by PhoP in S. Typhimurium strains and in E. which 37 had already been reported in both RegulonDB coli K-12 [6]. Incidentally, this plasticity in bacterial reg- and EcoCyc database; whereas, 49 genes identified by ulons is evidence of lineage-specific modifications [7]. microarray data and crl rpoS double mutants [8–16], in We conducted an exhaustive analysis concerning the previous works were also added (see Additional file 1). conservation of the Crl regulon in Bacteria and Archaea From the 86 genes identified as members of this regulon cellular domains, using as a reference the currently (see Table 1 and Fig. 1), 34 have a σS-type promoter ex- known system in E. coli K-12. Contrary to the most perimentally determined and 8 genes have 13 σS-type common regulatory mechanisms that involve the direct promoters predicted by computational approaches [17]. binding to operators or activators, Crl is an RNAP holo- These 86 genes are organized in 77 transcription units enzyme assembly factor that was originally identified in (TUs), where 52% are TUs with only one gene. curli production. It is expressed at low temperatures Previously, genes under the control of Crl were classi- (30 °C) [8] during the transition phase between the ex- fied in four main categories depending on their role(s) in ponential and stationary phases, under low osmolarity, the cell: DNA metabolism, central metabolism, response as well as in stationary phase [9]. In E. coli,Crlhasa to environmental modifications, and miscellaneous [11]. global regulatory effect in stationary phase, through σS, Based on Gene Ontology (GO) annotations, multifunc- as it reorganizes the transcriptional machinery [10], tional classification, and KEGG pathway maps to stimulating the association of σS with the RNAP core, categorize functions, Crl-regulated genes appear to be tilting the competition between σS and σ70 during the involved in metabolic processes such as energy metabol- stationary phase in response to different stress condi- ism, amino acid, carbohydrate, and lipid metabolism, tions [11, 12][8, 13]; its production is concomitant and biosynthetic processes such as glycan biosynthesis with the accumulation of σS [8]. and biosynthesis of other secondary metabolites, among Assembling the different pieces of the Crl regulon and other metabolic processes. These functions correlate its regulatory network into one global picture is one of with results of the enrichment analysis using PANTHER, our objectives in this work. The evaluation of this regu- which showed that catabolic processes, metabolic pro- lon in Bacteria and Archaea will provide clues about cesses, and cellular responses to xenobiotic stimuli were how the regulation of genes by Crl has been recruited in overrepresented among the functions associated with all the organisms, i.e., if the regulated genes were re- genes under the control of Crl (See Fig. 2). cruited similar to Crl or if they followed different path- In general, genes under Crl control are involved in ways. To this end, 86 genes under the control of Crl in regulating many aspects of cellular metabolism through E. coli K-12 were compiled from exhaustive literature Crl’s interaction with a subset of genes of the σS regulon searches. To our knowledge, this is the first attempt to [8] in addition to quorum sensing playing a major role describe the genes regulated by Crl in E. coli K-12; in in cell-to-cell communication during stationary phase addition, few Crl homologs were identified among bac- and in different processes such as biofilm formation or terial and archaeal genomes, constrained to Enterobacte- virulence, transporters [11] and genes involved in the riaceae species. Finally, members of the regulon were uptake and utilization of β-glucosides [16]. identified as widely distributed beyond enterobacteria, suggesting that Crl was recruited in a secondary evolu- Composition of the Crl regulon tionary event to regulate a specific subset of genes, most In order to determine whether additional TFs also likely genes involved in a functional response in entero- regulate the genes under the control of Crl, RegulonDB bacteria to contend against starvation. was used to evaluate how genes associated with Crl are also regulated by alternative TFs or sigma factors. A Results total of 24 genes were identified as exclusively con- 86 genes belong to the Crl regulon trolled by Crl, whereas 62 are regulated by additional