Evolution of transcriptional regulatory circuits in bacteria

Early Career Research Award Lecture. Structure, evolution and dynamics of transcriptional regulatory networks

The availability of entire genome sequences and the wealth of literature on gene regulation have enabled researchers to model an organism's transcriptional regulation system in the form of a network. In such a network, TFs (transcription factors) and TGs (target genes) are represented as nodes and regulatory interactions between TFs and TGs are represented as directed links. In the present review, I address the following topics pertaining to transcriptional regulatory networks. (i) Structure and organization: first, I introduce the concept of networks and discuss our understanding of the structure and organization of transcriptional networks. (ii) Evolution: I then describe the different mechanisms and forces that influence network evolution and shape network structure. (iii) Dynamics: I discuss studies that have integrated information on dynamics such as mRNA abundance or half-life, with data on transcriptional network in order to elucidate general principles of regulatory network dynamics. In particular, I discuss how cell-to-cell variability in the expression level of TFs could permit differential utilization of the same underlying network by distinct members of a genetically identical cell population. Finally, I conclude by discussing open questions for future research and highlighting the implications for evolution, development, disease and applications such as genetic engineering.

COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms

Increasingly large-scale expression compendia for different species are becoming available. By exploiting the modularity of the coexpression network, these compendia can be used to identify biological processes for which the expression behavior is conserved over different species. However, comparing module networks across species is not trivial. The definition of a biologically meaningful module is not a fixed one and changing the distance threshold that defines the degree of coexpression gives rise to different modules. As a result when comparing modules across species, many different partially overlapping conserved module pairs across species exist and deciding which pair is most relevant is hard. Therefore, we developed a method referred to as conserved modules across organisms (COMODO) that uses an objective selection criterium to identify conserved expression modules between two species. The method uses as input microarray data and a gene homology map and provides as output pairs of conserved modules and searches for the pair of modules for which the number of sharing homologs is statistically most significant relative to the size of the linked modules. To demonstrate its principle, we applied COMODO to study coexpression conservation between the two well-studied bacteria Escherichia coli and Bacillus subtilis. COMODO is available at: http://homes.esat.kuleuven.be/∼kmarchal/Supplementary_Information_Zarrineh_2010/comodo/index.html.

Characterization of combinatorial patterns generated by multiple two-component sensors in E. coli that respond to many stimuli

Two-component systems enable bacteria to sense changes in their environment and adjust gene expression in response. Multiple two-component systems could function as a combinatorial sensor to discriminate environmental conditions. A combinatorial sensor is composed of a set of sensors that are non-specifically activated to different magnitudes by many stimuli, such that their collective activity pattern defines the signal. Using promoter reporters and flow cytometry, we measured the response of three two-component systems in Escherichia coli that have been previously reported to respond to many environmental stimuli (EnvZ/OmpR, CpxA/CpxR, and RcsC/RcsD/RcsB). A chemical library was screened for the ability to activate the sensors and 13 inducers were identified that produce different patterns of sensor activity. The activities of the three systems are uncorrelated with each other and the osmolarity of the inducing media. Five of the seven possible non-trivial patterns generated by three sensors are observed. This data demonstrate one mechanism by which bacteria are able to use a limited set of sensors to identify a diverse set of compounds and environmental conditions.

Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?

The molecular evolution of cis-regulatory sequences is not well understood. Comparisons of closely related species show that cis-regulatory sequences contain a large number of sites constrained by purifying selection. In contrast, there are a number of examples from distantly related species where cis-regulatory sequences retain little to no sequence similarity but drive similar patterns of gene expression. Binding site turnover, whereby the gain of a redundant binding site enables loss of a previously functional site, is one model by which cis-regulatory sequences can diverge without a concurrent change in function. To determine whether cis-regulatory sequence divergence is consistent with binding site turnover, we examined binding site evolution within orthologous intergenic sequences from 14 yeast species defined by their syntenic relationships with adjacent coding sequences. Both local and global alignments show that nearly all distantly related orthologous cis-regulatory sequences have no significant level of sequence similarity but are enriched for experimentally identified binding sites. Yet, a significant proportion of experimentally identified binding sites that are conserved in closely related species are absent in distantly related species and so cannot be explained by binding site turnover. Depletion of binding sites depends on the transcription factor but is detectable for a quarter of all transcription factors examined. Our results imply that binding site turnover is not a sufficient explanation for cis-regulatory sequence evolution.

Comparative genomic analysis of fruiting body formation in Myxococcales

Genetic programs underlying multicellular morphogenesis and cellular differentiation are most often associated with eukaryotic organisms, but examples also exist in bacteria such as the formation of multicellular, spore-filled fruiting bodies in the order Myxococcales. Most members of the Myxococcales undergo a multicellular developmental program culminating in the formation of spore-filled fruiting bodies in response to starvation. To gain insight into the evolutionary history of fruiting body formation in Myxococcales, we performed a comparative analysis of the genomes and transcriptomes of five Myxococcales species, four of these undergo fruiting body formation (Myxococcus xanthus, Stigmatella aurantiaca, Sorangium cellulosum, and Haliangium ochraceum) and one does not (Anaeromyxobacter dehalogenans). Our analyses show that a set of 95 known M. xanthus development-specific genes--although suffering from a sampling bias--are overrepresented and occur more frequently than an average M. xanthus gene in S. aurantiaca, whereas they occur at the same frequency as an average M. xanthus gene in S. cellulosum and in H. ochraceum and are underrepresented in A. dehalogenans. Moreover, genes for entire signal transduction pathways important for fruiting body formation in M. xanthus are conserved in S. aurantiaca, whereas only a minority of these genes are conserved in A. dehalogenans, S. cellulosum, and H. ochraceum. Likewise, global gene expression profiling of developmentally regulated genes showed that genes that upregulated during development in M. xanthus are overrepresented in S. aurantiaca and slightly underrepresented in A. dehalogenans, S. cellulosum, and H. ochraceum. These comparative analyses strongly indicate that the genetic programs for fruiting body formation in M. xanthus and S. aurantiaca are highly similar and significantly different from the genetic program directing fruiting body formation in S. cellulosum and H. ochraceum. Thus, our analyses reveal an unexpected level of plasticity in the genetic programs for fruiting body formation in the Myxococcales and strongly suggest that the genetic program underlying fruiting body formation in different Myxococcales is not conserved. The evolutionary implications of this finding are discussed.

Target transcription binding sites differentiate two groups of MerR-monovalent metal ion sensors

The evolution of bacterial regulatory circuits often involves duplication of genes encoding transcription factors that may suffer both modifications in their detected signals, as well as, rewiring of their target operators. This, and subsequent horizontal gene transfer events contribute to generate a diverse array of regulatory pathways. In Salmonella, two homologous transcription factors CueR and GolS are responsible for Cu and Au sensing and resistance respectively. They share similarities not only in their sequence but also in their target binding sites, although they cluster separately among MerR-monovalent metal sensors. Here, we demonstrate that CueR and GolS can selectively distinguish their target binding sites by recognizing bases at positions 3' and 3 of their cognate operators. Swap of these bases results in switching regulator dependency. The differences in promoter architecture plus the environmentally controlled regulator's cytoplasmic availability warrant intra-regulon regulator-operator selectivity, and the proper response to metal injury. Furthermore, the presence of the distinctive operators' bases is widely extended among the two groups of MerR-monovalent metal sensors, providing evidence of the co-evolution of these factors and their target operators. This approach allows the prediction of regulator's dependency and the identification of transcription modules among groups of homologous transcription factors.

A proteomic analysis reveals differential regulation of the σ(S)-dependent yciGFE(katN) locus by YncC and H-NS in Salmonella and Escherichia coli K-12

The stationary phase sigma factor σ(S) (RpoS) controls a regulon required for general stress resistance of the closely related enterobacteria Salmonella and Escherichia coli. The σ(S)-dependent yncC gene encodes a putative DNA binding regulatory protein. Application of the surface-enhanced laser desorption/ionization-time of flight (SELDI-TOF) ProteinChip technology for proteome profiling of wild-type and mutant strains of Salmonella enterica serovar Typhimurium revealed potential protein targets for YncC regulation, which were identified by mass spectrometry, and subsequently validated. These proteins are encoded by the σ(S)-dependent operon yciGFEkatN and regulation of their expression by YncC operates at the transcriptional level, as demonstrated by gene fusion analyses and by in vitro transcription and DNase I footprinting experiments with purified YncC. The yciGFE genes are present (without katN) in E. coli K-12 but are poorly expressed, compared with the situation in Salmonella. We report that the yciGFE(katN) locus is silenced by the histone-like protein H-NS in both species, but that σ(S) efficiently relieves silencing in Salmonella but not in E. coli K-12. In Salmonella, YncC acts in concert with σ(S) to activate transcription at the yciG promoter (pyciG). When overproduced, YncC also activated σ(S)-dependent transcription at pyciG in E. coli K-12, but solely by countering the negative effect of H-NS. Our results indicate that differences between Salmonella and E. coli K-12, in the architecture of cis-acting regulatory sequences upstream of pyciG, contribute to the differential regulation of the yciGFE(katN) genes by H-NS and YncC in these two enterobacteria. In E. coli, this locus is subject to gene rearrangements and also likely to horizontal gene transfer, consistent with its repression by the xenogeneic silencer H-NS.

DNA damage triggers genetic exchange in Helicobacter pylori

Many organisms respond to DNA damage by inducing expression of DNA repair genes. We find that the human stomach pathogen Helicobacter pylori instead induces transcription and translation of natural competence genes, thus increasing transformation frequency. Transcription of a lysozyme-like protein that promotes DNA donation from intact cells is also induced. Exogenous DNA modulates the DNA damage response, as both recA and the ability to take up DNA are required for full induction of the response. This feedback loop is active during stomach colonization, indicating a role in the pathogenesis of the bacterium. As patients can be infected with multiple genetically distinct clones of H. pylori, DNA damage induced genetic exchange may facilitate spread of antibiotic resistance and selection of fitter variants through re-assortment of preexisting alleles in this important human pathogen.

All organisms have genetic programs to respond to stressful conditions. The human stomach pathogen, Helicobacter pylori, survives on the surface of the stomach lining for the lifetime of its host and causes a chronic inflammatory response. In this niche, H. pylori is likely exposed to constant DNA damage and requires DNA repair systems to survive in the host. Many bacteria encode a genetic program for a coordinated response to DNA damage called the SOS response, which typically includes transcriptional induction of DNA repair systems and mutagenic DNA polymerases and a temporary halt to cell division. This study demonstrates that H. pylori has a distinct DNA damage response: instead of activating DNA repair systems, it induces both DNA uptake machinery and an enzyme that liberates DNA from neighboring cells. This capacity for genetic exchange enhances recombination of exogenous DNA into the genome, thus contributing to both the high genetic diversity observed between H. pylori clinical isolates and the spread of antibiotic resistance.

Reconstruction of the core and extended regulons of global transcription factors

The processes underlying the evolution of regulatory networks are unclear. To address this question, we used a comparative genomics approach that takes advantage of the large number of sequenced bacterial genomes to predict conserved and variable members of transcriptional regulatory networks across phylogenetically related organisms. Specifically, we developed a computational method to predict the conserved regulons of transcription factors across α-proteobacteria. We focused on the CRP/FNR super-family of transcription factors because it contains several well-characterized members, such as FNR, FixK, and DNR. While FNR, FixK, and DNR are each proposed to regulate different aspects of anaerobic metabolism, they are predicted to recognize very similar DNA target sequences, and they occur in various combinations among individual α-proteobacterial species. In this study, the composition of the respective FNR, FixK, or DNR conserved regulons across 87 α-proteobacterial species was predicted by comparing the phylogenetic profiles of the regulators with the profiles of putative target genes. The utility of our predictions was evaluated by experimentally characterizing the FnrL regulon (a FNR-type regulator) in the α-proteobacterium Rhodobacter sphaeroides. Our results show that this approach correctly predicted many regulon members, provided new insights into the biological functions of the respective regulons for these regulators, and suggested models for the evolution of the corresponding transcriptional networks. Our findings also predict that, at least for the FNR-type regulators, there is a core set of target genes conserved across many species. In addition, the members of the so-called extended regulons for the FNR-type regulators vary even among closely related species, possibly reflecting species-specific adaptation to environmental and other factors. The comparative genomics approach we developed is readily applicable to other regulatory networks.

An important property of living systems is the use of regulatory networks to appropriately program gene expression. Central to the function of regulatory networks are transcription factors that regulate gene expression by binding to specific DNA sequences. Despite the central role of these regulatory networks, the processes driving their organization and evolution across organisms are poorly understood. This paper describes the use of comparative genomics and high-throughput approaches to predict the organization and evolution of transcriptional regulatory networks across a large group of species. We focused on regulatory networks controlling cellular responses to changes in O₂ levels because this signal has major consequences on many biological systems. Our analysis predicts that related regulatory networks share a core set of target genes across diverse species while other target genes vary according to the organism's specific lifestyle. Our approach of defining transcriptional regulatory networks across a wide range of organisms should be of general utility to studying similar questions in other systems.

Positive autoregulation shapes response timing and intensity in two-component signal transduction systems

Positive feedback loops are regulatory elements that can modulate expression output, kinetics and noise in genetic circuits. Transcriptional regulators participating in such loops are often expressed from two promoters, one constitutive and one autoregulated. Here, we investigate the interplay of promoter strengths and the intensity of the stimulus activating the transcriptional regulator in defining the output of a positively autoregulated genetic circuit. Using a mathematical model of two-component regulatory systems, which are present in all domains of life, we establish that positive feedback strongly affects the steady-state output levels at both low and high levels of stimulus if the constitutive promoter of the regulator is weak. By contrast, the effect of positive feedback is negligible when the constitutive promoter is sufficiently strong, unless the stimulus intensity is very high. Furthermore, we determine that positive feedback can affect both transient and steady state output levels even in the simplest genetic regulatory systems. We tested our modeling predictions by abolishing the positive feedback loop in the two-component regulatory system PhoP/PhoQ of Salmonella enterica, which resulted in diminished induction of PhoP-activated genes.

The promise of evolutionary systems biology: lessons from bacterial chemotaxis

Bacterial chemotaxis and the signaling networks underlying it provide us with a model system for studying the molecular basis of behavior and information processing. Although chemotaxis is well characterized at both the phenotype and genotype levels in the model organism Escherichia coli, it is not yet possible to predict chemotaxis behavior in diverse bacteria on the basis of their environment or genome sequence. Moreover, we still cannot propose a plausible evolutionary trajectory from minimal systems to present-day chemotaxis networks. The analysis of all sequenced bacterial genomes provides a prediction of their chemotaxis networks and reveals substantial structural diversity. Additionally, it uncovers a set of previously unknown proteins that could be the "missing" link between complex present-day chemotaxis networks and simpler, ancestral systems composed of a few proteins. Further evaluation of these findings with experimental and modeling studies will allow us to distill evolutionary design principles in chemotaxis signaling networks.

microRNA evolution in a human transcription factor and microRNA regulatory network

BACKGROUND

microRNAs (miRNAs) are important cellular components. The understanding of their evolution is of critical importance for the understanding of their function. Although some specific evolutionary rules of miRNAs have been revealed, the rules of miRNA evolution in cellular networks remain largely unexplored. According to knowledge from protein-coding genes, the investigations of gene evolution in the context of biological networks often generate valuable observations that cannot be obtained by traditional approaches.

RESULTS

Here, we conducted the first systems-level analysis of miRNA evolution in a human transcription factor (TF)-miRNA regulatory network that describes the regulatory relations among TFs, miRNAs, and target genes. We found that the architectural structure of the network provides constraints and functional innovations for miRNA evolution and that miRNAs showed different and even opposite evolutionary patterns from TFs and other protein-coding genes. For example, miRNAs preferentially coevolved with their activators but not with their inhibitors. During transcription, rapidly evolving TFs frequently activated but rarely repressed miRNAs. In addition, conserved miRNAs tended to regulate rapidly evolving targets, and upstream miRNAs evolved more rapidly than downstream miRNAs.

CONCLUSIONS

In this study, we performed the first systems level analysis of miRNA evolution. The findings suggest that miRNAs have a unique evolution process and thus may have unique functions and roles in various biological processes and diseases. Additionally, the network presented here is the first TF-miRNA regulatory network, which will be a valuable platform of systems biology.

Evolution of the RpoS regulon: origin of RpoS and the conservation of RpoS-dependent regulation in bacteria

The RpoS sigma factor in proteobacteria regulates genes in stationary phase and in response to stress. Although of conserved function, the RpoS regulon may have different gene composition across species due to high genomic diversity and to known environmental conditions that select for RpoS mutants. In this study, the distribution of RpoS homologs in prokaryotes and the differential dependence of regulon members on RpoS for expression in two gamma-proteobacteria (Escherichia coli and Pseudomonas aeruginosa) were examined. Using a maximum-likelihood phylogeny and reciprocal best hits analysis, we show that the RpoS sigma factor is conserved within gamma-, beta-, and delta-proteobacteria. Annotated RpoS of Borrelia and the enteric RpoS are postulated to have separate evolutionary origins. To determine the conservation of RpoS-dependent gene expression across species, reciprocal best hits analysis was used to identify orthologs of the E. coli RpoS regulon in the RpoS regulon of P. aeruginosa. Of the 186 RpoS-dependent genes of E. coli, 50 proteins have an ortholog within the P. aeruginosa genome. Twelve genes of the 50 orthologs are RpoS-dependent in both species, and at least four genes are regulated by RpoS in other gamma-proteobacteria. Despite RpoS conservation in gamma-, beta-, and delta-proteobacteria, RpoS regulon composition is subject to modification between species. Environmental selection for RpoS mutants likely contributes to the evolutionary divergence and specialization of the RpoS regulon within different bacterial genomes.

Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12

The bacterial SeqA protein binds to hemi-methylated GATC sequences that arise in newly synthesized DNA upon passage of the replication machinery. In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. This sequesters oriC, thereby preventing reinitiation of replication. However, the genome-wide DNA binding properties of SeqA are unknown, and hence, here, we describe a study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays. Our data show that SeqA binding correlates with the frequency and spacing of GATC sequences across the entire genome. Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain. Using synchronized cultures, we show that SeqA distribution differs with the cell cycle. SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.

The BatR/BatS two-component regulatory system controls the adaptive response of Bartonella henselae during human endothelial cell infection

Here, we report the first comprehensive study of Bartonella henselae gene expression during infection of human endothelial cells. Expression of the main cluster of upregulated genes, comprising the VirB type IV secretion system and its secreted protein substrates, is shown to be under the positive control of the transcriptional regulator BatR. We demonstrate binding of BatR to the promoters of the virB operon and a substrate-encoding gene and provide biochemical evidence that BatR and BatS constitute a functional two-component regulatory system. Moreover, in contrast to the acid-inducible (pH 5.5) homologs ChvG/ChvI of Agrobacterium tumefaciens, BatR/BatS are optimally activated at the physiological pH of blood (pH 7.4). By conservation analysis of the BatR regulon, we show that BatR/BatS are uniquely adapted to upregulate a genus-specific virulence regulon during hemotropic infection in mammals. Thus, we propose that BatR/BatS two-component system homologs represent vertically inherited pH sensors that control the expression of horizontally transmitted gene sets critical for the diverse host-associated life styles of the alphaproteobacteria.

The effect of mobile element IS10 on experimental regulatory evolution in Escherichia coli

Mobile genetic elements are widespread in bacteria, where they cause several kinds of mutations. Although their effects are on the whole negative, rare beneficial mutations caused by insertion sequence elements are frequently selected in some experimental evolution systems. For example, in earlier work, we found that strains of Escherichia coli that lack the sigma factor RpoS adapt to a high-osmolarity environment by the insertion of element IS10 into the promoter of the otsBA operon, rewiring expression from RpoS dependent to RpoS independent. We wished to determine how the presence of IS10 in the genome of this strain shaped the evolutionary outcome. IS10 could influence the outcome by causing mutations that confer adaptive phenotypes that cannot be achieved by strains without the element. Alternatively, IS10 could influence evolution by increasing the rate of appearance of certain classes of beneficial mutations even if they are no better than those that could be achieved by a strain without the element. We found that populations evolved from an IS10-free strain did not upregulate otsBA. An otsBA-lacZY fusion facilitated the recovery of a number of mutations that upregulate otsB without involving IS10 and found that two caused greater fitness increases than IS10 insertion, implying that evolution could have upregulated otsBA in the IS10-free strain. Finally, we demonstrate that there is epistasis between the IS10 insertion into the otsBA promoter and the other adaptive mutations, implying that introduction of IS10 into the otsBA promoter may alter the trajectory of adaptive evolution. We conclude that IS10 exerts its effect not by creating adaptive phenotypes that could not otherwise occur but by increasing the rate of appearance of certain adaptive mutations.

Tissue tropisms in group A streptococcal infections

Group A Streptococcus (GAS) is a human-specific pathogen that is highly prevalent throughout the world. The vast majority of GAS infections lead to a mild disease involving the epithelial surfaces of either the throat or skin. The concept of distinct sets of 'throat' and 'skin' strains of GAS has long been conceived. From an ecological standpoint, the epithelium of the throat and skin are important because it is where the organism is most successful in reproducing and transmitting to new hosts. This article examines key features of the epidemiology, population biology and molecular pathogenesis that underlie the tissue site preferences for infection exhibited by GAS, with an emphasis on work from our laboratory on skin tropisms. Recombinational replacement with orthologous gene forms, following interspecies transfer, appears to be an important genetic step leading up to the exploitation of new niches by GAS.

ArcS, the cognate sensor kinase in an atypical Arc system of Shewanella oneidensis MR-1

The availability of oxygen is a major environmental factor for many microbes, in particular for bacteria such as Shewanella species, which thrive in redox-stratified environments. One of the best-studied systems involved in mediating the response to changes in environmental oxygen levels is the Arc two-component system of Escherichia coli, consisting of the sensor kinase ArcB and the cognate response regulator ArcA. An ArcA ortholog was previously identified in Shewanella, and as in Escherichia coli, Shewanella ArcA is involved in regulating the response to shifts in oxygen levels. Here, we identified the hybrid sensor kinase SO_0577, now designated ArcS, as the previously elusive cognate sensor kinase of the Arc system in Shewanella oneidensis MR-1. Phenotypic mutant characterization, transcriptomic analysis, protein-protein interaction, and phosphotransfer studies revealed that the Shewanella Arc system consists of the sensor kinase ArcS, the single phosphotransfer domain protein HptA, and the response regulator ArcA. Phylogenetic analyses suggest that HptA might be a relict of ArcB. Conversely, ArcS is substantially different with respect to overall sequence homologies and domain organizations. Thus, we speculate that ArcS might have adopted the role of ArcB after a loss of the original sensor kinase, perhaps as a consequence of regulatory adaptation to a redox-stratified environment.

Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system

Sequence data from the past decade has laid bare the significance of horizontal gene transfer in creating genetic diversity in the bacterial world. Regulatory evolution, in which non-coding DNA is mutated to create new regulatory nodes, also contributes to this diversity to allow niche adaptation and the evolution of pathogenesis. To survive in the host environment, Salmonella enterica uses a type III secretion system and effector proteins, which are activated by the SsrA-SsrB two-component system in response to the host environment. To better understand the phenomenon of regulatory evolution in S. enterica, we defined the SsrB regulon and asked how this transcription factor interacts with the cis-regulatory region of target genes. Using ChIP-on-chip, cDNA hybridization, and comparative genomics analyses, we describe the SsrB-dependent regulon of ancestral and horizontally acquired genes. Further, we used a genetic screen and computational analyses integrating experimental data from S. enterica and sequence data from an orthologous regulatory system in the insect endosymbiont, Sodalis glossinidius, to identify the conserved yet flexible palindrome sequence that defines DNA recognition by SsrB. Mutational analysis of a representative promoter validated this palindrome as the minimal architecture needed for regulatory input by SsrB. These data provide a high-resolution map of a regulatory network and the underlying logic enabling pathogen adaptation to a host.

All organisms have a means to control gene expression ensuring correct spatiotemporal deployment of gene products. In bacteria, gene control presents a challenge because one species can reside in multiple niches, requiring them to coordinate gene expression with environmental sensing. Also, widespread acquisition of DNA by horizontal gene transfer demands a mechanism to integrate new genes into existing regulatory circuitry. The environmental awareness issue can be controlled using two-component regulatory systems that connect environmental cues to transcription factor activation, whereas the integration problem can be resolved using DNA regulatory evolution to create new regulatory connections between genes. The evolutionary significance of regulatory evolution for host adaptation is not fully known. We studied the convergence of environmental sensing and genetic networks by examining how the Salmonella enterica SsrA-SsrB two-component system, activated in response to host cues, has integrated ancestral and acquired genes into a common regulon. We identified a palindrome as the major element apportioning SsrB on the chromosome. SsrB binding sites have been selected to co-regulate a gene program involved in pathogenic adaptation of Salmonella to its host. In addition, our results indicate that promoter architecture emerging from SsrB-dependent regulatory evolution may support both mutualistic and parasitic bacteria-host relationships.

Evolutionary tinkering with conserved components of a transcriptional regulatory network

A surprising level of evolutionary plasticity is revealed by analysis of differences between related yeasts in the mechanisms regulating the essential cellular process of ribosomal gene expression.

Gene expression variation between species is a major contributor to phenotypic diversity, yet the underlying flexibility of transcriptional regulatory networks remains largely unexplored. Transcription of the ribosomal regulon is a critical task for all cells; in S. cerevisiae the transcription factors Rap1, Fhl1, Ifh1, and Hmo1 form a multi-subunit complex that controls ribosomal gene expression, while in C. albicans this regulation is under the control of Tbf1 and Cbf1. Here, we analyzed, using full-genome transcription factor mapping, the roles, in both S. cerevisiae and C. albicans, of each orthologous component of this complete set of regulators. We observe dramatic changes in the binding profiles of the generalist regulators Cbf1, Hmo1, Rap1, and Tbf1, while the Fhl1-Ifh1 dimer is the only component involved in ribosomal regulation in both fungi: it activates ribosomal protein genes and rDNA expression in a Tbf1-dependent manner in C. albicans and a Rap1-dependent manner in S. cerevisiae. We show that the transcriptional regulatory network governing the ribosomal expression program of two related yeast species has been massively reshaped in cis and trans. Changes occurred in transcription factor wiring with cellular functions, movements in transcription factor hierarchies, DNA-binding specificity, and regulatory complexes assembly to promote global changes in the architecture of the fungal transcriptional regulatory network.

Conserved metabolic machineries direct energy production and investment in most life forms. However, variation in the transcriptional regulation of the genes that encode this machinery has been observed and shown to contribute to phenotypic differences between species. Here, we show that the regulatory circuits governing the expression of central metabolic components (in this case the ribosomes) in different yeast species have an unexpected level of evolutionary plasticity. Most transcription factors involved in the regulation of expression of ribosomal genes have in fact been reused in new ways during the evolutionary time separating S. cerevisiae and C. albicans to generate global changes in transcriptional network structures and new ribosomal regulatory complexes.

Common patterns - unique features: nitrogen metabolism and regulation in Gram-positive bacteria

Gram-positive bacteria have developed elaborate mechanisms to control ammonium assimilation, at the levels of both transcription and enzyme activity. In this review, the common and specific mechanisms of nitrogen assimilation and regulation in Gram-positive bacteria are summarized and compared for the genera Bacillus, Clostridium, Streptomyces, Mycobacterium and Corynebacterium, with emphasis on the high G+C genera. Furthermore, the importance of nitrogen metabolism and control for the pathogenic lifestyle and virulence is discussed. In summary, the regulation of nitrogen metabolism in prokaryotes shows an impressive diversity. Virtually every phylum of bacteria evolved its own strategy to react to the changing conditions of nitrogen supply. Not only do the transcription factors differ between the phyla and sometimes even between families, but the genetic targets of a given regulon can also differ between closely related species.

The effect of orthology and coregulation on detecting regulatory motifs

BACKGROUND

Computational de novo discovery of transcription factor binding sites is still a challenging problem. The growing number of sequenced genomes allows integrating orthology evidence with coregulation information when searching for motifs. Moreover, the more advanced motif detection algorithms explicitly model the phylogenetic relatedness between the orthologous input sequences and thus should be well adapted towards using orthologous information. In this study, we evaluated the conditions under which complementing coregulation with orthologous information improves motif detection for the class of probabilistic motif detection algorithms with an explicit evolutionary model.

METHODOLOGY

We designed datasets (real and synthetic) covering different degrees of coregulation and orthologous information to test how well Phylogibbs and Phylogenetic sampler, as representatives of the motif detection algorithms with evolutionary model performed as compared to MEME, a more classical motif detection algorithm that treats orthologs independently.

RESULTS AND CONCLUSIONS

Under certain conditions detecting motifs in the combined coregulation-orthology space is indeed more efficient than using each space separately, but this is not always the case. Moreover, the difference in success rate between the advanced algorithms and MEME is still marginal. The success rate of motif detection depends on the complex interplay between the added information and the specificities of the applied algorithms. Insights in this relation provide information useful to both developers and users. All benchmark datasets are available at http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Storms_Valerie_PlosONE.

Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin

Archaea, which represent a large fraction of the phylogenetic diversity of organisms, are prokaryotes with eukaryote-like basal transcriptional machinery. This organization makes the study of their DNA-binding transcription factors (TFs) and their transcriptional regulatory networks particularly interesting. In addition, there are limited experimental data regarding their TFs. In this work, 3,918 TFs were identified and exhaustively analyzed in 52 archaeal genomes. TFs represented less than 5% of the gene products in all the studied species comparable with the number of TFs identified in parasites or intracellular pathogenic bacteria, suggesting a deficit in this class of proteins. A total of 75 families were identified, of which HTH_3, AsnC, TrmB, and ArsR families were universally and abundantly identified in all the archaeal genomes. We found that archaeal TFs are significantly small compared with other protein-coding genes in archaea as well as bacterial TFs, suggesting that a large fraction of these small-sized TFs could supply the probable deficit of TFs in archaea, by possibly forming different combinations of monomers similar to that observed in eukaryotic transcriptional machinery. Our results show that although the DNA-binding domains of archaeal TFs are similar to bacteria, there is an underrepresentation of ligand-binding domains in smaller TFs, which suggests that protein–protein interactions may act as mediators of regulatory feedback, indicating a chimera of bacterial and eukaryotic TFs’ functionality. The analysis presented here contributes to the understanding of the details of transcriptional apparatus in archaea and provides a framework for the analysis of regulatory networks in these organisms.