Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli

Evolution of transcriptional regulation in closely related bacteria

BACKGROUND

The exponential growth of the number of fully sequenced genomes at varying taxonomic closeness allows one to characterize transcriptional regulation using comparative-genomics analysis instead of time-consuming experimental methods. A transcriptional regulatory unit consists of a transcription factor, its binding site and a regulated gene. These units constitute a graph which contains so-called "network motifs", subgraphs of a given structure. Here we consider genomes of closely related Enterobacteriales and estimate the fraction of conserved network motifs and sites as well as positions under selection in various types of non-coding regions.

RESULTS

Using a newly developed technique, we found that the highest fraction of positions under selection, approximately 50%, was observed in synvergon spacers (between consecutive genes from the same strand), followed by ~45% in divergon spacers (common 5'-regions), and ~10% in convergon spacers (common 3'-regions). The fraction of selected positions in functional regions was higher, 60% in transcription factor-binding sites and ~45% in terminators and promoters. Small, but significant differences were observed between Escherichia coli and Salmonella enterica. This fraction is similar to the one observed in eukaryotes.The conservation of binding sites demonstrated some differences between types of regulatory units. In E. coli, strains the interactions of the type "local transcriptional factor gene" turned out to be more conserved in feed-forward loops (FFLs) compared to non-motif interactions. The coherent FFLs tend to be less conserved than the incoherent FFLs. A natural explanation is that the former imply functional redundancy.

CONCLUSIONS

A naïve hypothesis that FFL would be highly conserved turned out to be not entirely true: its conservation depends on its status in the transcriptional network and also from its usage. The fraction of positions under selection in intergenic regions of bacterial genomes is roughly similar to that of eukaryotes. Known regulatory sites explain 20±5% of selected positions.

Gene network homology in prokaryotes using a similarity search approach: queries of quorum sensing signal transduction

Bacterial cell-cell communication is mediated by small signaling molecules known as autoinducers. Importantly, autoinducer-2 (AI-2) is synthesized via the enzyme LuxS in over 80 species, some of which mediate their pathogenicity by recognizing and transducing this signal in a cell density dependent manner. AI-2 mediated phenotypes are not well understood however, as the means for signal transduction appears varied among species, while AI-2 synthesis processes appear conserved. Approaches to reveal the recognition pathways of AI-2 will shed light on pathogenicity as we believe recognition of the signal is likely as important, if not more, than the signal synthesis. LMNAST (Local Modular Network Alignment Similarity Tool) uses a local similarity search heuristic to study gene order, generating homology hits for the genomic arrangement of a query gene sequence. We develop and apply this tool for the E. coli lac and LuxS regulated (Lsr) systems. Lsr is of great interest as it mediates AI-2 uptake and processing. Both test searches generated results that were subsequently analyzed through a number of different lenses, each with its own level of granularity, from a binary phylogenetic representation down to trackback plots that preserve genomic organizational information. Through a survey of these results, we demonstrate the identification of orthologs, paralogs, hitchhiking genes, gene loss, gene rearrangement within an operon context, and also horizontal gene transfer (HGT). We found a variety of operon structures that are consistent with our hypothesis that the signal can be perceived and transduced by homologous protein complexes, while their regulation may be key to defining subsequent phenotypic behavior.

Bacteria communicate with each other through a network of small molecules that are secreted and perceived by nearest neighbors. In a process known as quorum sensing, bacteria communicate their cell density and certain behaviors emerge wherein the population of cells acts as a coordinated community. One small signaling molecule, AI-2, is synthesized by many bacteria so that in a natural ecosystem comprised of many secreting cells of different species, the molecule may be present in an appreciable concentration. The perception of the signal may be key to unlocking its importance, as some cells may recognize it at lower concentrations than others, etc. We have created a searching algorithm that finds similar gene sets among various bacteria. Here, we looked for signal transduction pathways similar to the one studied in E. coli. We found exact replicas to that of E. coli, but also found pathways with missing genes, added genes of unknown function, as well as different patterns by which the genes may be regulated. We suspect these attributes may play a significant role in determining quorum sensing behaviors. This, in turn, may lead to new discoveries for controlling groups of bacteria and possibly reducing the prevalence of infectious disease.

The ecology of bacterial genes and the survival of the new

Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.

Evolution of two-component signal transduction systems

To exist in a wide range of environmental niches, bacteria must sense and respond to a variety of external signals. A primary means by which this occurs is through two-component signal transduction pathways, typically composed of a sensor histidine kinase that receives the input stimuli and then phosphorylates a response regulator that effects an appropriate change in cellular physiology. Histidine kinases and response regulators have an intrinsic modularity that separates signal input, phosphotransfer, and output response; this modularity has allowed bacteria to dramatically expand and diversify their signaling capabilities. Recent work has begun to reveal the molecular basis by which two-component proteins evolve. How and why do orthologous signaling proteins diverge? How do cells gain new pathways and recognize new signals? What changes are needed to insulate a new pathway from existing pathways? What constraints are there on gene duplication and lateral gene transfer? Here, we review progress made in answering these questions, highlighting how the integration of genome sequence data with experimental studies is providing major new insights.

The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective

Using profiles of phylogenetic profiles (P-cubic) we compared the evolutionary dynamics of different kinds of functional associations. Ordered from most to least evolutionarily stable, these associations were genes in the same operons, genes whose products participate in the same biochemical pathway, genes coding for physically interacting proteins and genes in the same regulons. Regulons showed the most plastic functional interactions with evolutionary stabilities barely better than those of unrelated genes. Further regulon analyses showed that global regulators contain less evolutionarily stable associations than local regulators. Genes co-repressed by global regulators had a higher evolutionary conservation than genes co-activated by global regulators. However, the reverse was true for genes co-repressed and co-activated by local regulators. Of all the regulon-related associations, the relationship between regulators and their target genes showed the most evolutionary stability. Different negative data sets built to contrast against each of the analysed kinds of modules also differed in evolutionary conservation revealing further underlying genome organization. Applying P-cubic analyses to other genomes might help visualize genome organization, understand the evolutionary importance and plasticity of functional associations and compare the quality of data sets expected to reflect functional interactions, such as those coming from high-throughput experiments.

High-density transcriptional initiation signals underline genomic islands in bacteria

Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of "alien" elements which probably undergo special temporal-spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these "exotic" regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs) in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased "non-optimal" codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for "alien" regions, but also provide hints to the special evolutionary course and transcriptional regulation of GI regions.

Evolutionary origin of the Rhodobacter sphaeroides specialized RpoN sigma factors

Gene duplication and horizontal gene transfer (HGT) are two events that enable the generation of new genes. Rhodobacter sphaeroides (WS8 and 2.4.1 strains) has four copies of the rpoN gene that are not functionally interchangeable. Until now, this is the only example of specialization of this sigma factor. In this work, we aimed to determine whether the multiple copies of this gene originated from HGT or through gene duplication. Our results suggest a multiplication origin of the different rpoN copies that occurred after the Rhodobacter clade separated. Functional tests indicate that the specialization of the rpoN genes is not restricted to R. sphaeroides. We propose that the rpoN copy involved in nitrogen fixation is the ancestral gene and that the other rpoN genes have acquired new specificities.

Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella

BACKGROUND

Changes in transcriptional regulation underlie many of the phenotypic differences observed within and between species of bacteria. Lateral genetic transfer (LGT) can significantly impact the transcription factor (TF) genes which drive these transcriptional changes. Although much emphasis has been placed on LGT of intact genes, the units of transfer and recombination do not necessarily correspond to regions delineated by exact gene boundaries. Here we apply phylogenetic and network-based methods to investigate the relationship between units of lateral transfer and recombination within the Escherichia coli - Shigella clade and the topological properties of genes in the E. coli transcriptional regulatory network (TRN).

RESULTS

We carried out a systematic phylogenetic study of genetic transfer among 5282 sets of putatively orthologous genes from 27 strains belonging to the E. coli - Shigella clade. We then used these results to examine the evolutionary histories of TF genes, as well as the transcriptional regulation of lateral genes. We found evidence of LGT in 2655 (50.3%) gene sets: 678 (12.8%) show evidence of recombination breakpoints within the gene boundaries. Thus, within- and whole- gene lateral transfer is widespread among strains of E. coli and Shigella. We found that unlike global regulators, which have mostly evolved vertically, neighbour regulators (genes which regulate adjacent genes on the chromosome) have frequently been subject to transfer within the E. coli - Shigella clade. At least 56 (62%) of the 90 neighbour regulator gene sets examined show evidence of LGT, 19 (34%) of which have internal recombination breakpoints. Neighbour regulators show no evidence of co-transfer with their nearby target genes. Rather, the frequency of recombination breakpoints, and conflicting evolutionary histories among neighbour regulators and their target genes, suggest that the genomic regions encoding these genes have been constructed through successive layering of LGT events within the clade. We find no difference in the relative complexity of regulation (i.e. the number of regulators) of lateral versus vertical genes.

CONCLUSIONS

Neighbour regulators show higher frequencies of transfer than other types of regulatory genes. This implicates the topological properties of regulatory genes in the TRN, and their physical proximity to targets on the chromosome, as contributing to successful LGT. The prevalence of recombination breakpoints within regulatory and target gene sets indicates that within-gene transfer has had a significant cumulative effect on the evolution of regulatory interactions in E. coli and Shigella.

Hydrogen peroxide-dependent DNA release and transfer of antibiotic resistance genes in Streptococcus gordonii

Certain oral streptococci produce H(2)O(2) under aerobic growth conditions to inhibit competing species like Streptococcus mutans. Additionally, H(2)O(2) production causes the release of extracellular DNA (eDNA). eDNA can participate in several important functions: biofilm formation and cell-cell aggregation are supported by eDNA, while eDNA can serve as a nutrient and as an antimicrobial agent by chelating essential cations. eDNA contains DNA fragments of a size that has the potential to transfer genomic information. By using Streptococcus gordonii as a model organism for streptococcal H(2)O(2) production, H(2)O(2)-dependent eDNA release was further investigated. Under defined growth conditions, the eDNA release process was shown to be entirely dependent on H(2)O(2). Chromosomal DNA damage seems to be the intrinsic signal for the release, although only actively growing cells were proficient eDNA donors. Interestingly, the process of eDNA production was found to be coupled with the induction of the S. gordonii natural competence system. Consequently, the production of H(2)O(2) triggered the transfer of antibiotic resistance genes. These results suggest that H(2)O(2) is potentially much more than a simple toxic metabolic by-product; rather, its production could serve as an important environmental signal that facilitates species evolution by transfer of genetic information and an increase in the mutation rate.

The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold

Background

Bacterial populations are highly successful at colonizing new habitats and adapting to changing environmental conditions, partly due to their capacity to evolve novel virulence and metabolic pathways in response to stress conditions and to shuffle them by horizontal gene transfer (HGT). A common theme in the evolution of new functions consists of gene duplication followed by functional divergence. UlaG, a unique manganese-dependent metallo-β-lactamase (MBL) enzyme involved in L-ascorbate metabolism by commensal and symbiotic enterobacteria, provides a model for the study of the emergence of new catalytic activities from the modification of an ancient fold. Furthermore, UlaG is the founding member of the so-called UlaG-like (UlaGL) protein family, a recently established and poorly characterized family comprising divalent (and perhaps trivalent) metal-binding MBLs that catalyze transformations on phosphorylated sugars and nucleotides.

Results

Here we combined protein structure-guided and sequence-only molecular phylogenetic analyses to dissect the molecular evolution of UlaG and to study its phylogenomic distribution, its relatedness with present-day UlaGL protein sequences and functional conservation. Phylogenetic analyses indicate that UlaGL sequences are present in Bacteria and Archaea, with bona fide orthologs found mainly in mammalian and plant-associated Gram-negative and Gram-positive bacteria. The incongruence between the UlaGL tree and known species trees indicates exchange by HGT and suggests that the UlaGL-encoding genes provided a growth advantage under changing conditions. Our search for more distantly related protein sequences aided by structural homology has uncovered that UlaGL sequences have a common evolutionary origin with present-day RNA processing and metabolizing MBL enzymes widespread in Bacteria, Archaea, and Eukarya. This observation suggests an ancient origin for the UlaGL family within the broader trunk of the MBL superfamily by duplication, neofunctionalization and fixation.

Conclusions

Our results suggest that the forerunner of UlaG was present as an RNA metabolizing enzyme in the last common ancestor, and that the modern descendants of that ancestral gene have a wide phylogenetic distribution and functional roles. We propose that the UlaGL family evolved new metabolic roles among bacterial and possibly archeal phyla in the setting of a close association with metazoans, such as in the mammalian gastrointestinal tract or in animal and plant pathogens, as well as in environmental settings. Accordingly, the major evolutionary forces shaping the UlaGL family include vertical inheritance and lineage-specific duplication and acquisition of novel metabolic functions, followed by HGT and numerous lineage-specific gene loss events.

Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches

Horizontal genetic transfer (HGT) has played an important role in bacterial evolution at least since the origins of the bacterial divisions, and HGT still facilitates the origins of bacterial diversity, including diversity based on antibiotic resistance. Adaptive HGT is aided by unique features of genetic exchange in bacteria such as the promiscuity of genetic exchange and the shortness of segments transferred. Genetic exchange rates are limited by the genetic and ecological similarity of organisms. Adaptive transfer of genes is limited to those that can be transferred as a functional unit, provide a niche-transcending adaptation, and are compatible with the architecture and physiology of other organisms. Horizontally transferred adaptations may bring about fitness costs, and natural selection may ameliorate these costs. The origins of ecological diversity can be analyzed by comparing the genomes of recently divergent, ecologically distinct populations, which can be discovered as sequence clusters. Such genome comparisons demonstrate the importance of HGT in ecological diversification. Newly divergent populations cannot be discovered as sequence clusters when their ecological differences are coded by plasmids, as is often the case for antibiotic resistance; the discovery of such populations requires a screen for plasmid-coded functions. This paper reviews the features of bacterial genetics that allow HGT, the similarities between organisms that foster HGT between them, the limits to the kinds of adaptations that can be transferred, and amelioration of fitness costs associated with HGT; the paper also reviews approaches to discover the origins of new, ecologically distinct bacterial populations and the role that HGT plays in their founding.

Linking fold, function and phylogeny: a comparative genomics view on protein (domain) evolution

Domains are the building blocks of all globular proteins and present one of the most useful levels at which protein function can be understood. Through recombination and duplication of a limited set of domains, proteomes evolved and the collection of protein superfamilies in an organism formed. As such, the presence of a shared domain can be regarded as an indicator of similar function and evolutionary history, but it does not necessarily imply it since convergent evolution may give rise to similar gene functions as well as architectures.Through the wealth of sequences and annotation data brought about by genomics, evolutionary links can be sought for via homology relationships and comparative genomics, structural modeling and phylogenetics. The goal hereby is not only to predict the function of newly discovered proteins, but also to spell out their pathway of evolution and, possibly, identify their most likely origin. This can ultimately help to understand protein function and functional relationships of protein families. Additionally, through comparison with transcriptional data, evolutionary data can be linked to gene (and genome) activity and thus allow for the identification of common principles behind fast evolving proteins and relatively stable ones.In this review, we describe the basic principles of studying protein (domain) evolution and illustrate recent developments in molecular evolution and give valuable new insights in the field of comparative genomics. As an example, we include here molecular models of the multiple PDZ domain protein MUPP-1 and present a simple comparative genomic view on its structural course of evolution.

Genome-wide transcriptome and proteome analysis of Escherichia coli expressing IrrE, a global regulator of Deinococcus radiodurans

Gram-negative bacterium Escherichia coli and the Gram-positive Deinococcus radiodurans fundamentally differ in their cell structures and gene regulations. We have previously reported that IrrE, a Deinococcus genus-specific global regulator, confers significantly enhanced tolerance to various abiotic stresses. To better understand the global effects of IrrE on the regulatory networks, we carried out combined transcriptome and proteome analysis of E. coli expressing the IrrE protein. Our analysis showed that 216 (4.8%) of all E. coli genes were induced and 149 (3.3%) genes were repressed, including those for trehalose biosynthesis, nucleotides biosynthesis, carbon source utilization, amino acid utilization, acid resistance, a hydrogenase and an oxidase. Also regulated were the EvgSA two-component system, the GadE, GadX and PurR master regulators, and 10 transcription factors (AppY, GadW, YhiF, AsnC, BetI, CynR, MhpR, PrpR, TdcA and KdgR). These results demonstrated that IrrE acts as global regulator and consequently improves abiotic stress tolerances in the heterologous host E. coli. The implication of our findings is discussed in relation to the evolutionary role of horizontal gene transfer in bacterial regulatory networks and environmental adaptation.

The emergence of modularity in biological systems

In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may spontaneously organize to a structured form. That is, we seek to explain how biology nucleated from among the many possibilities in chemistry. The emergence of modular organization of biological structure will be described as a symmetry-breaking phase transition, with modularity as the order parameter. Experimental support for this description will be reviewed. Examples will be presented from pathogen structure, metabolic networks, gene networks, and protein-protein interaction networks. Additional examples will be presented from ecological food networks, developmental pathways, physiology, and social networks.

Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes

Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus), average-sized genomes (Bacillus, Enterobacteriaceae), and large genomes (Pseudomonas, Bradyrhizobiaceae) to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes--xenologs--persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes--paralogs--are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein-protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life's biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families.

Phylogenetic evidence of noteworthy microflora from the subsurface of the former Homestake gold mine, Lead, South Dakota

Molecular characterization of subsurface microbial communities in the former Homestake gold mine, South Dakota, was carried out by 16S rDNA sequence analysis using a water sample and a weathered soil-like sample. Geochemical analyses indicated that both samples were high in sulphur, rich in nitrogen and salt, but with significantly different metal concentrations. Microbial diversity comparisons unexpectedly revealed three distinct operational taxonomic units (OTUs) belonging to the archaeal phylum Thaumarchaeota, typically identified from marine environments, and one OTU belonging to a potentially novel phylum that fell sister to Thaumarchaeota. To our knowledge this is only the second report of Thaumarchaeota in a terrestrial environment. The majority of the clones from Archaea sequence libraries fell into two closely related OTUs and were grouped most closely to an ammonia-oxidizing, carbon-fixing and halophilic thaumarchaeote genus, Nitrosopumilus. The two samples showed neither Euryarchaeota nor Crenarchaeota members that have often been identified from other subsurface terrestrial ecosystems. Bacteria OTUs containing the highest percentage of sequences were related to sulphur-oxidizing bacteria of the orders Chromatiales and Thiotrichales. Community members of Bacteria from individual Homestake ecosystems were heterogeneous and distinctive to each community, with unique phylotypes identified within each sample.

Conditions for the evolution of gene clusters in bacterial genomes

Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been proposed to account for the evolution of these structures. For instance, natural selection may directly favour gene clusters through a variety of mechanisms, such as increased efficiency of coregulation. An alternative and controversial hypothesis is the selfish operon model, which asserts that clustered arrangements of genes are more easily transferred to other species, thus improving the prospects for survival of the cluster. According to another hypothesis (the persistence model), genes that are in close proximity are less likely to be disrupted by deletions. Here we develop computational models to study the conditions under which gene clusters can evolve and persist. First, we examine the selfish operon model by re-implementing the simulation and running it under a wide range of conditions. Second, we introduce and study a Moran process in which there is natural selection for gene clustering and rearrangement occurs by genome inversion events. Finally, we develop and study a model that includes selection and inversion, which tracks the occurrence and fixation of rearrangements. Surprisingly, gene clusters fail to evolve under a wide range of conditions. Factors that promote the evolution of gene clusters include a low number of genes in the pathway, a high population size, and in the case of the selfish operon model, a high horizontal transfer rate. The computational analysis here has shown that the evolution of gene clusters can occur under both direct and indirect selection as long as certain conditions hold. Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters.

Genes involved in a common pathway or function are frequently found near each other on bacterial chromosomes. A number of hypotheses have been previously presented to explain this observation. A particularly influential theory is the selfish operon model, which posits that horizontal transfer could promote gene clustering by favouring transfer of arrangements of genes that are close together. Subsequent theoretical development and analysis of genomic data have contributed to the debate about the plausibility of this model. Here, by re-examining the evolutionary dynamics of gene clusters, we provide and discuss conditions under which gene clusters can evolve. We find that first, some form of bias for clustering is required for clusters to evolve. This bias can be in the form of bias in horizontal transfer towards genes that are close together, or direct natural selection for gene proximity. Our computational work does not present a theoretical obstacle to the selfish operon model as a possible explanation for the evolution of gene clusters.

Asymmetric cross-regulation between the nitrate-responsive NarX-NarL and NarQ-NarP two-component regulatory systems from Escherichia coli K-12

The NarX-NarL and NarQ-NarP sensor-response regulator pairs control Escherichia coli gene expression in response to nitrate and nitrite. Previous analysis suggests that the Nar two-component systems form a cross-regulation network in vivo. Here we report on the kinetics of phosphoryl transfer between different sensor-regulator combinations in vitro. NarX exhibited a noticeable kinetic preference for NarL over NarP, whereas NarQ exhibited a relatively slight kinetic preference for NarL. These findings were substantiated in reactions containing one sensor and both response regulators, or with two sensors and a single response regulator. We isolated 21 NarX mutants with missense substitutions in the cytoplasmic central and transmitter modules. These confer phenotypes that reflect defects in phospho-NarL dephosphorylation. Five of these mutants, all with substitutions in the transmitter DHp domain, also exhibited NarP-blind phenotypes. Phosphoryl transfer assays in vitro confirmed that these NarX mutants have defects in catalysing NarP phosphorylation. By contrast, the corresponding NarQ mutants conferred phenotypes indicating comparable interactions with both NarP and NarL. Our overall results reveal asymmetry in the Nar cross-regulation network, such that NarQ interacts similarly with both response regulators, whereas NarX interacts preferentially with NarL.

Evolution, ecology and the engineered organism: lessons for synthetic biology

An understanding of evolution and ecology will be critical to the success of synthetic biology.

As the scope and complexity of synthetic biology grows, an understanding of evolution and ecology will be critical to its success.

Horizontal gene transfer in evolution: facts and challenges

The contribution of horizontal gene transfer to evolution has been controversial since it was suggested to be a force driving evolution in the microbial world. In this paper, I review the current standpoint on horizontal gene transfer in evolutionary thinking and discuss how important horizontal gene transfer is in evolution in the broad sense, and particularly in prokaryotic evolution. I review recent literature, asking, first, which processes are involved in the evolutionary success of transferred genes and, secondly, about the extent of horizontal gene transfer towards different evolutionary times. Moreover, I discuss the feasibility of reconstructing ancient phylogenetic relationships in the face of horizontal gene transfer. Finally, I discuss how horizontal gene transfer fits in the current neo-Darwinian evolutionary paradigm and conclude there is a need for a new evolutionary paradigm that includes horizontal gene transfer as well as other mechanisms in the explanation of evolution.

Lateral genetic transfer: open issues

Lateral genetic transfer (LGT) is an important adaptive force in evolution, contributing to metabolic, physiological and ecological innovation in most prokaryotes and some eukaryotes. Genomic sequences and other data have begun to illuminate the processes, mechanisms, quantitative extent and impact of LGT in diverse organisms, populations, taxa and environments; deep questions are being posed, and the provisional answers sometimes challenge existing paradigms. At the same time, there is an enhanced appreciation of the imperfections, biases and blind spots in the data and in analytical approaches. Here we identify and consider significant open questions concerning the role of LGT in genome evolution.

Evolution of transcriptional regulatory circuits in bacteria

Related organisms typically respond to a given cue by altering the level or activity of orthologous transcription factors, which, paradoxically, often regulate expression of distinct gene sets. Although promoter rewiring of shared genes is primarily responsible for regulatory differences among related eukaryotic species, in bacteria, species-specific genes are often controlled by ancestral transcription factors, and regulatory circuit evolution has been further shaped by horizontal gene transfer. Modifications in transcription factors and in promoter structure also contribute to divergence in bacterial regulatory circuits.

Toolbox model of evolution of prokaryotic metabolic networks and their regulation

It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a simple model in which metabolic and regulatory networks of prokaryotes are shaped by horizontal gene transfer of coregulated metabolic pathways. Adapting to a new environmental condition monitored by a new transcription factor (e.g., learning to use another nutrient) involves both acquiring new enzymes and reusing some of the enzymes already encoded in the genome. As the repertoire of enzymes of an organism (its toolbox) grows larger, it can reuse its enzyme tools more often and thus needs to get fewer new ones to master each new task. From this observation, it logically follows that the number of functional tasks and their regulators increases faster than linearly with the total number of genes encoding enzymes. Genomes can also shrink, e.g., because of a loss of a nutrient from the environment, followed by deletion of its regulator and all enzymes that become redundant. We propose several simple models of network evolution elaborating on this toolbox argument and reproducing the empirically observed quadratic scaling. The distribution of lengths of pathway branches in our model agrees with that of the real-life metabolic network of Escherichia coli. Thus, our model provides a qualitative explanation for broad distributions of regulon sizes in prokaryotes.

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

BACKGROUND

A myriad of methods to reverse-engineer transcriptional regulatory networks have been developed in recent years. Direct methods directly reconstruct a network of pairwise regulatory interactions while module-based methods predict a set of regulators for modules of coexpressed genes treated as a single unit. To date, there has been no systematic comparison of the relative strengths and weaknesses of both types of methods.

RESULTS

We have compared a recently developed module-based algorithm, LeMoNe (Learning Module Networks), to a mutual information based direct algorithm, CLR (Context Likelihood of Relatedness), using benchmark expression data and databases of known transcriptional regulatory interactions for Escherichia coli and Saccharomyces cerevisiae. A global comparison using recall versus precision curves hides the topologically distinct nature of the inferred networks and is not informative about the specific subtasks for which each method is most suited. Analysis of the degree distributions and a regulator specific comparison show that CLR is 'regulator-centric', making true predictions for a higher number of regulators, while LeMoNe is 'target-centric', recovering a higher number of known targets for fewer regulators, with limited overlap in the predicted interactions between both methods. Detailed biological examples in E. coli and S. cerevisiae are used to illustrate these differences and to prove that each method is able to infer parts of the network where the other fails. Biological validation of the inferred networks cautions against over-interpreting recall and precision values computed using incomplete reference networks.

CONCLUSION

Our results indicate that module-based and direct methods retrieve largely distinct parts of the underlying transcriptional regulatory networks. The choice of algorithm should therefore be based on the particular biological problem of interest and not on global metrics which cannot be transferred between organisms. The development of sound statistical methods for integrating the predictions of different reverse-engineering strategies emerges as an important challenge for future research.

Engineering transcription factors with novel DNA-binding specificity using comparative genomics

The transcriptional program for a gene consists of the promoter necessary for recruiting RNA polymerase along with neighboring operator sites that bind different activators and repressors. From a synthetic biology perspective, if the DNA-binding specificity of these proteins can be changed, then they can be used to reprogram gene expression in cells. While many experimental methods exist for generating such specificity-altering mutations, few computational approaches are available, particularly in the case of bacterial transcription factors. In a previously published computational study of nitrogen oxide metabolism in bacteria, a small number of amino-acid residues were found to determine the specificity within the CRP (cAMP receptor protein)/FNR (fumarate and nitrate reductase regulatory protein) family of transcription factors. By analyzing how these amino acids vary in different regulators, a simple relationship between the identity of these residues and their target DNA-binding sequence was constructed. In this article, we experimentally tested whether this relationship could be used to engineer novel DNA–protein interactions. Using Escherichia coli CRP as a template, we tested eight designs based on this relationship and found that four worked as predicted. Collectively, these results in this work demonstrate that comparative genomics can inform the design of bacterial transcription factors.

Regulation by transcription factors in bacteria: beyond description

Transcription is an essential step in gene expression and its understanding has been one of the major interests in molecular and cellular biology. By precisely tuning gene expression, transcriptional regulation determines the molecular machinery for developmental plasticity, homeostasis and adaptation. In this review, we transmit the main ideas or concepts behind regulation by transcription factors and give just enough examples to sustain these main ideas, thus avoiding a classical ennumeration of facts. We review recent concepts and developments: cis elements and trans regulatory factors, chromosome organization and structure, transcriptional regulatory networks (TRNs) and transcriptomics. We also summarize new important discoveries that will probably affect the direction of research in gene regulation: epigenetics and stochasticity in transcriptional regulation, synthetic circuits and plasticity and evolution of TRNs. Many of the new discoveries in gene regulation are not extensively tested with wetlab approaches. Consequently, we review this broad area in Inference of TRNs and Dynamical Models of TRNs. Finally, we have stepped backwards to trace the origins of these modern concepts, synthesizing their history in a timeline schema.

Functional models for large-scale gene regulation networks: realism and fiction

High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different conditions, times, environments. We now possess a certain amount of information about these two levels of description, stored in libraries, databases and ontologies. A current challenge is to bridge the gap between topology and function, i.e. developing quantitative models aimed at characterizing the expression patterns of large sets of genes. However, approaches that work well for small networks become impossible to master at large scales, mainly because parameters proliferate. In this review we discuss the state of the art of large-scale functional network models, addressing the issue of what can be considered as "realistic" and what the main limitations may be. We also show some directions for future work, trying to set the goals that future models should try to achieve. Finally, we will emphasize the possible benefits in the understanding of biological mechanisms underlying complex multifactorial diseases, and in the development of novel strategies for the description and the treatment of such pathologies.

Differential replication dynamics for large and small Vibrio chromosomes affect gene dosage, expression and location

Background

Replication of bacterial chromosomes increases copy numbers of genes located near origins of replication relative to genes located near termini. Such differential gene dosage depends on replication rate, doubling time and chromosome size. Although little explored, differential gene dosage may influence both gene expression and location. For vibrios, a diverse family of fast growing gammaproteobacteria, gene dosage may be particularly important as they harbor two chromosomes of different size.

Results

Here we examined replication dynamics and gene dosage effects for the separate chromosomes of three Vibrio species. We also investigated locations for specific gene types within the genome. The results showed consistently larger gene dosage differences for the large chromosome which also initiated replication long before the small. Accordingly, large chromosome gene expression levels were generally higher and showed an influence from gene dosage. This was reflected by a higher abundance of growth essential and growth contributing genes of which many locate near the origin of replication. In contrast, small chromosome gene expression levels were low and appeared independent of gene dosage. Also, species specific genes are highly abundant and an over-representation of genes involved in transcription could explain its gene dosage independent expression.

Conclusion

Here we establish a link between replication dynamics and differential gene dosage on one hand and gene expression levels and the location of specific gene types on the other. For vibrios, this relationship appears connected to a polarisation of genetic content between its chromosomes, which may both contribute to and be enhanced by an improved adaptive capacity.

The fate of new bacterial genes

Bacteria experience a continual influx of novel genetic material from a wide range of sources and yet their genomes remain relatively small. This aspect of bacterial evolution indicates that most newly arriving sequences are rapidly eliminated; however, numerous new genes persist, as evident from the presence of unique genes in almost all bacterial genomes. This review summarizes the methods for identifying new genes in bacterial genomes and examines the features that promote the retention and elimination of these evolutionary novelties.

What determines the assembly of transcriptional network motifs in Escherichia coli?

Transcriptional networks are constituted by a collection of building blocks known as network motifs. Why do motifs appear? An adaptive model of motif emergence was recently questioned in favor of neutralist scenarios. Here, we provide a new picture of motif assembly in Escherichia coli which partially clarifies these contrasting explanations. This is based on characterizing the linkage between motifs and sensing or response specificity of their constituent transcriptional factors (TFs). We find that sensing specificity influences the distribution of autoregulation, while the tendency of a TF to establish feed-forward loops (FFLs) depends on response specificity, i.e., regulon size. Analysis of the latter pattern reveals that coregulation between large regulon-size TFs is common under a network neutral model, leading to the assembly of a great number of FFLs and bifans. In addition, neutral exclusive regulation also leads to a collection of single input modules -the fourth basic motif. On the whole, and even under the conservative neutralist scenario considered, a substantial group of regulatory structures revealed adaptive. These structures visibly function as fully-fledged working units.

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution.

Evidence of horizontal gene transfer between human and animal commensal Escherichia coli strains identified by microarray

Bacteria exchange genetic material by horizontal gene transfer (HGT). To evaluate the impact of HGT on Escherichia coli genome plasticity, 19 commensal strains collected from the intestinal floras of humans and animals were analyzed by microarrays. Strains were hybridized against an oligoarray containing 2700 E. coli K12 chromosomal genes. A core (genes shared among compared genomes) and a flexible gene pool (genes unique for each genome) have been identified. Analysis of hybridization signals evidenced 1015 divergent genes among the 19 strains and each strain showed a specific genomic variability pattern. Four hundred and fifty-eight genes were characterized by higher rates of interstrain variation and were considered hyperdivergent. These genes are not randomly distributed onto the chromosome but are clustered in precise regions. Hyperdivergent genes belong to the flexible gene pool and show a specific GC content, differing from that of the chromosome, indicating acquisition by HGT. Among these genes, those involved in defense mechanisms and cell motility as well as intracellular trafficking and secretion were far more represented than others. The observed genome plasticity contributes to the maintenance of genetic diversity and may therefore be a source of evolutionary adaptation and survival.

Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio

Background

Bacterial genome sequences are being determined rapidly, but few species are physiologically well characterized. Predicting regulation from genome sequences usually involves extrapolation from better-studied bacteria, using the hypothesis that a conserved regulator, conserved target gene, and predicted regulator-binding site in the target promoter imply conserved regulation between the two species. However many compared organisms are ecologically and physiologically diverse, and the limits of extrapolation have not been well tested. In E. coli K-12 the leucine-responsive regulatory protein (Lrp) affects expression of ~400 genes. Proteus mirabilis and Vibrio cholerae have highly-conserved lrp orthologs (98% and 92% identity to E. coli lrp). The functional equivalence of Lrp from these related species was assessed.

Results

Heterologous Lrp regulated gltB, livK and lrp transcriptional fusions in an E. coli background in the same general way as the native Lrp, though with significant differences in extent. Microarray analysis of these strains revealed that the heterologous Lrp proteins significantly influence only about half of the genes affected by native Lrp. In P. mirabilis, heterologous Lrp restored swarming, though with some pattern differences. P. mirabilis produced substantially more Lrp than E. coli or V. cholerae under some conditions. Lrp regulation of target gene orthologs differed among the three native hosts. Strikingly, while Lrp negatively regulates its own gene in E. coli, and was shown to do so even more strongly in P. mirabilis, Lrp appears to activate its own gene in V. cholerae.

Conclusion

The overall similarity of regulatory effects of the Lrp orthologs supports the use of extrapolation between related strains for general purposes. However this study also revealed intrinsic differences even between orthologous regulators sharing >90% overall identity, and 100% identity for the DNA-binding helix-turn-helix motif, as well as differences in the amounts of those regulators. These results suggest that predicting regulation of specific target genes based on genome sequence comparisons alone should be done on a conservative basis.

The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment

BACKGROUND

Despite the prevalence of horizontal gene transfer (HGT) in bacteria, to this date there were few studies on HGT in the context of gene expression, operons and protein-protein interactions. Using the recently available data set on the E. coli protein-protein interaction network, we sought to explore the impact of HGT on genome structure and protein networks.

RESULTS

We classified the E. coli genes into three categories based on their evolutionary conservation: a set of 2158 Core genes that are shared by all E. coli strains, a set of 1044 Non-core genes that are strain-specific, and a set of 1053 genes that were putatively acquired by horizontal transfer. We observed a clear correlation between gene expressivity (measured by Codon Adaptation Index), evolutionary rates, and node connectivity between these categories of genes. Specifically, we found the Core genes are the most highly expressed and the most slowly evolving, while the HGT genes are expressed at the lowest level and evolve at the highest rate. Core genes are the most likely and HGT genes are the least likely to be member of the operons. In addition, we found the Core genes on average are more highly connected than Non-core and HGT genes in the protein interaction network, however the HGT genes displayed a significantly higher mean node degree than the Core and Non-core genes in the defence COG functional category. Interestingly, HGT genes are more likely to be connected to Core genes than expected by chance, which suggest a model of differential attachment in the expansion of cellular networks.

CONCLUSION

Results from our analysis shed light on the mode and mechanism of the integration of horizontally transferred genes into operons and protein interaction networks.