Role of the lytic repressor in prophage induction of phage lambda as analyzed by a module-replacement approach

Strategies for developing phages into novel antimicrobial tailocins

Tailocins are high-molecular-weight bacteriocins produced by bacteria to kill related environmental competitors by binding and puncturing their target. Tailocins are promising alternative antimicrobials, yet the diversity of naturally occurring tailocins is limited. The structural similarities between phage tails and tailocins advocate using phages as scaffolds for developing new tailocins. This article reviews three strategies for producing tailocins: disrupting the capsid-tail junction of phage particles, blocking capsid assembly during phage propagation, and creating headless phage particles synthetically. Particularly appealing is the production of tailocins through synthetic biology using phages with contractile tails as scaffolds to unlock the antimicrobial potential of tailocins.

Liver X Receptor-Inducible Host E3 Ligase IDOL Targets a Human Cytomegalovirus Reactivation Determinant

Liver X receptor (LXR) signaling broadly restricts virus replication; however, the mechanisms of restriction are poorly defined. Here, we demonstrate that the cellular E3 ligase LXR-inducible degrader of low-density lipoprotein receptor (IDOL) targets the human cytomegalovirus (HMCV) UL136p33 protein for turnover. UL136 encodes multiple proteins that differentially impact latency and reactivation. UL136p33 is a determinant of reactivation. UL136p33 is targeted for rapid turnover by the proteasome, and its stabilization by mutation of lysine residues to arginine results in a failure to quiet replication for latency. We show that IDOL targets UL136p33 for turnover but not the stabilized variant. IDOL is highly expressed in undifferentiated hematopoietic cells where HCMV establishes latency but is sharply downregulated upon differentiation, a stimulus for reactivation. We hypothesize that IDOL maintains low levels of UL136p33 for the establishment of latency. Consistent with this hypothesis, knockdown of IDOL impacts viral gene expression in wild-type (WT) HCMV infection but not in infection where UL136p33 has been stabilized. Furthermore, the induction of LXR signaling restricts WT HCMV reactivation from latency but does not affect the replication of a recombinant virus expressing a stabilized variant of UL136p33. This work establishes the UL136p33-IDOL interaction as a key regulator of the bistable switch between latency and reactivation. It further suggests a model whereby a key viral determinant of HCMV reactivation is regulated by a host E3 ligase and acts as a sensor at the tipping point between the decision to maintain the latent state or exit latency for reactivation. IMPORTANCE Herpesviruses establish lifelong latent infections, which pose an important risk for disease particularly in the immunocompromised. Our work is focused on the betaherpesvirus human cytomegalovirus (HCMV) that latently infects the majority of the population worldwide. Defining the mechanisms by which HCMV establishes latency or reactivates from latency is important for controlling viral disease. Here, we demonstrate that the cellular inducible degrader of low-density lipoprotein receptor (IDOL) targets a HCMV determinant of reactivation for degradation. The instability of this determinant is important for the establishment of latency. This work defines a pivotal virus-host interaction that allows HCMV to sense changes in host biology to navigate decisions to establish latency or to replicate.

Control of λ Lysogenic Escherichia coli Cells by Synthetic λ Phage Carrying cIantisense

Enterobacterial phage λ is a temperate phage that infects Escherichia coli and has a lytic-lysogenic life cycle. CI, a λ repressor, regulates the expression of lytic transcripts and acts as a major genetic switch that determines the lysogenic state. To manipulate the genome of phage λ, the CRISPR-Cas9 genome editing system was constructed in lysogenic E. coli MG1655 cells. For instance, we successfully changed cI857 to cIWT in the phage genome through Cas9-mediated single-nucleotide editing. A lytic phage was prepared by introducing an amber mutation in the middle of the cI gene, but it could not lyse lysogenic MG1655 cells. We prepared a phage expressing cI antisense mRNA by reverse substitution of the cI gene. Lysis of λ cI857 lysogenic cells occurred by the infection of the λ cIantisense. These results suggest an effective lysogenic cell control method by a synthetic phage expressing antisense mRNA of the genetic switch gene. It is expected to be applied as a tool to control harmful lysogenic microorganisms.

RNA polymerase efficiently transcribes DNA-scaffolded, cooperative bacteriophage repressor complexes

DNA can act as a scaffold for the cooperative binding of protein oligomers. For example, the phage 186 CI repressor forms a wheel of seven dimers wrapped in DNA with specific binding sites, while phage λ CI repressor dimers bind to two well-separated sets of operators, forming a DNA loop. Atomic force microscopy was used to measure transcription elongation by E. coli RNA polymerase through these protein complexes. 186 CI, or λ CI, bound along unlooped DNA negligibly interfered with transcription by RNAP. Wrapped and looped topologies induced by these scaffolded, cooperatively bound repressor oligomers did not form significantly better roadblocks to transcription. Thus, despite binding with high affinity, these repressors are not effective roadblocks to transcription.

Gradients in gene essentiality reshape antibacterial research

Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.

Characterization of a T4-like Bacteriophage vB_EcoM-Sa45lw as a Potential Biocontrol Agent for Shiga Toxin-Producing Escherichia coli O45 Contaminated on Mung Bean Seeds

Application of lytic bacteriophages is a promising and alternative intervention technology to relieve antibiotic resistance pressure and control bacterial pathogens in the food industry. Despite the increase of produce-associated outbreaks caused by non-O157 Shiga toxin-producing E. coli (STEC) serogroups, the information of phage application on sprouts to mitigate these pathogens is lacking. Therefore, the objective of this study was to characterize a T4-like Escherichia phage vB_EcoM-Sa45lw (or Sa45lw) for the biocontrol potential of STEC O45 on mung bean seeds. Phage Sa45lw belongs to the Tequatrovirus genus under the Myoviridae family and displays a close evolutionary relationship with a STEC O157-infecting phage AR1. Sa45lw contains a long-tail fiber gene (gp37), sharing high genetic similarity with the counterpart of Escherichia phage KIT03, and a unique tail lysozyme (gp5) to distinguish its host range (STEC O157, O45, ATCC 13706, and Salmonella Montevideo and Thompson) from phage KIT03 (O157 and Salmonella enterica). No stx, antibiotic resistance, and lysogenic genes were found in the Sa45lw genome. The phage has a latent period of 27 min with an estimated burst size of 80 PFU/CFU and is stable at a wide range of pH (pH 3 to pH 10.5) and temperatures (-80°C to 50°C). Phage Sa45lw is particularly effective in reducing E. coli O45:H16 both in vitro (MOI = 10) by 5 log and upon application (MOI = 1,000) on the contaminated mung bean seeds for 15 min by 2 log at 25°C. These findings highlight the potential of phage application against non-O157 STEC on sprout seeds. IMPORTANCE Seeds contaminated with foodborne pathogens, such as Shiga toxin-producing E. coli, are the primary sources of contamination in produce and have contributed to numerous foodborne outbreaks. Antibiotic resistance has been a long-lasting issue that poses a threat to human health and the food industry. Therefore, developing novel antimicrobial interventions, such as bacteriophage application, is pivotal to combat these pathogens. This study characterized a lytic bacteriophage Sa45lw as an alternative antimicrobial agent to control pathogenic E. coli on the contaminated mung bean seeds. The phage exhibited antimicrobial effects against both pathogenic E. coli and Salmonella without containing virulent or lysogenic genes that could compromise the safety of phage application. In addition, after 15 min of phage treatment, Sa45lw mitigated E. coli O45:H16 on the contaminated mung bean seeds by a 2-log reduction at room temperature, demonstrating the biocontrol potential of non-O157 Shiga toxin-producing E. coli on sprout seeds.

Characterization of the genetic switch from phage ɸ13 important for Staphylococcus aureus colonization in humans

Temperate phages are bacterial viruses that after infection either reside integrated into a bacterial genome as prophages forming lysogens or multiply in a lytic lifecycle. The decision between lifestyles is determined by a switch involving a phage-encoded repressor, CI, and a promoter region from which lytic and lysogenic genes are divergently transcribed. Here, we investigate the switch of phage ɸ13 from the human pathogen Staphylococcus aureus. ɸ13 encodes several virulence factors and is prevalent in S. aureus strains colonizing humans. We show that the ɸ13 switch harbors a cI gene, a predicted mor (modulator of repression) gene, and three high-affinity operator sites binding CI. To quantify the decision between lytic and lysogenic lifestyle, we introduced reporter plasmids that carry the 1.3 kb switch region from ɸ13 with the lytic promoter fused to lacZ into S. aureus and Bacillus subtilis. Analysis of β-galactosidase expression indicated that decision frequency is independent of host factors. The white "lysogenic" phenotype, which relies on the expression of cI, could be switched to a stable blue "lytic" phenotype by DNA damaging agents. We have characterized lifestyle decisions of phage ɸ13, and our approach may be applied to other temperate phages encoding virulence factors in S. aureus.

Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities

Emerging data indicate that gut dysbiosis contributes to many human diseases, including several comorbidities that develop after traumatic spinal cord injury (SCI). To date, all analyses of SCI-induced gut dysbiosis have used 16S rRNA amplicon sequencing. This technique has several limitations, including being susceptible to taxonomic "blind spots," primer bias, and an inability to profile microbiota functions or identify viruses. Here, SCI-induced gut dysbiosis was assessed by applying genome- and gene-resolved metagenomic analysis of murine stool samples collected 21 days after an experimental SCI at the 4th thoracic spine (T4) or 10th thoracic spine (T10) spinal level. These distinct injuries partially (T10) or completely (T4) abolish sympathetic tone in the gut. Among bacteria, 105 medium- to high-quality metagenome-assembled genomes (MAGs) were recovered, with most (n = 96) representing new bacterial species. Read mapping revealed that after SCI, the relative abundance of beneficial commensals (Lactobacillus johnsonii and CAG-1031 spp.) decreased, while potentially pathogenic bacteria (Weissella cibaria, Lactococcus lactis _A, Bacteroides thetaiotaomicron) increased. Functionally, microbial genes encoding proteins for tryptophan, vitamin B6, and folate biosynthesis, essential pathways for central nervous system function, were reduced after SCI. Among viruses, 1,028 mostly novel viral populations were recovered, expanding known murine gut viral species sequence space ∼3-fold compared to that of public databases. Phages of beneficial commensal hosts (CAG-1031, Lactobacillus, and Turicibacter) decreased, while phages of pathogenic hosts (Weissella, Lactococcus, and class Clostridia) increased after SCI. Although the microbiomes and viromes were changed in all SCI mice, some of these changes varied as a function of spinal injury level, implicating loss of sympathetic tone as a mechanism underlying gut dysbiosis.IMPORTANCE To our knowledge, this is the first article to apply metagenomics to characterize changes in gut microbial population dynamics caused by a clinically relevant model of central nervous system (CNS) trauma. It also utilizes the most current approaches in genome-resolved metagenomics and viromics to maximize the biological inferences that can be made from these data. Overall, this article highlights the importance of autonomic nervous system regulation of a distal organ (gut) and its microbiome inhabitants after traumatic spinal cord injury (SCI). By providing information on taxonomy, function, and viruses, metagenomic data may better predict how SCI-induced gut dysbiosis influences systemic and neurological outcomes after SCI.

Prophage LambdaSo uses replication interference to suppress reproduction of coexisting temperate phage MuSo2 in Shewanella oneidensis MR-1

Many bacterial genomes carry multiple prophages that compete with each other, potentially affecting the physiology, fitness, and pathogenicity of their hosts. However, molecular mechanisms of such prophage-prophage conflicts remain poorly understood. The genome of Shewanella oneidensis MR-1, a Gammaproteobacterium residing in aquatic environments and notable for its ability to reduce metal ions, harbours four prophages, two of which (LambdaSo and MuSo2) form infectious virions during biofilm formation. Here, we constructed indicator strains of LambdaSo and MuSo2 by deleting the corresponding prophages from the MR-1 chromosome and investigated their reproduction. Interestingly, the fitness of MuSo2 increased in the absence of LambdaSo, suggesting that prophage LambdaSo repressed MuSo2 reproduction. Partial deletion of LambdaSo from the MR-1 chromosome revealed that gene cluster R of LambdaSo, which was responsible for the switch to the lytic cycle and LambdaSo genome replication initiation, was necessary and sufficient to repress MuSo2. Furthermore, activation of cluster R genes facilitated replication of cluster R-encoding DNA and inhibited host and MuSo2 DNA replication. These findings suggest that LambdaSo represses MuSo2 propagation by inhibiting DNA replication during simultaneous induction. We predict that such a mechanism of inter-prophage interference is more widespread in bacteria than currently appreciated.

Occurrence, integrity and functionality of AcaML1-like viruses infecting extreme acidophiles of the Acidithiobacillus species complex

General knowledge on the diversity and biology of microbial viruses infecting bacterial hosts from extreme acidic environments lags behind most other econiches. In this study, we analyse the AcaML1 virus occurrence in the taxon, its genetic composition and infective behaviour under standard acidic and SOS-inducing conditions to assess its integrity and functionality. Occurrence analysis in sequenced acidithiobacilli showed that AcaML1-like proviruses are confined to the mesothermophiles Acidithiobacillus caldus and Thermithiobacillus tepidarius. Among A. caldus strains and isolates this provirus had a modest prevalence (30%). Comparative genomic analysis revealed a significant conservation with the T. tepidarius AcaML1-like provirus, excepting the tail genes, and a high conservation of the virus across strains of the A. caldus species. Such conservation extends from the modules architecture to the gene level, suggesting that organization and composition of these viruses are preserved for functional reasons. Accordingly, the AcaML1 proviruses were demonstrated to excise from their host genomes under DNA-damaging conditions triggering the SOS-response and to produce DNA-containing VLPs. Despite this fact, under the conditions evaluated (acidic) the VLPs obtained from A. caldus ATCC 51756 could not produce productive infections of a candidate sensitive strain (#6) nor trigger it lysis.

YMC-2011, a Temperate Phage of Streptococcus salivarius 57.I

Streptococcus salivarius is an abundant isolate of the oral cavity. The genome of S. salivarius 57.I consists of a 2-Mb chromosome and a 40,758-bp circular molecule, designated YMC-2011. Annotation of YMC-2011 revealed 55 open reading frames, most of them associated with phage production, although plaque formation is not observed in S. salivarius 57.I after lytic induction using mitomycin C. Results from Southern hybridization and quantitative real-time PCR confirmed that YMC-2011 exists extrachromosomally, with an estimated copy number of 3 to 4. Phage particles were isolated from the supernatant of mitomycin C-treated S. salivarius 57.I cultures, and transmission electron microscopic examination indicated that YMC-2011 belongs to the Siphoviridae family. Phylogenetic analysis suggests that phage YMC-2011 and the cos-type phages of Streptococcus thermophilus originated from a common ancestor. An extended -10 element (p _L ) and a σ⁷⁰-like promoter (p _R ) were mapped 5' to Ssal_phage00013 (encoding a CI-like repressor) and Ssal_phage00014 (encoding a hypothetical protein), respectively, using 5' rapid amplification of cDNA ends, indicating that YMC-2011 transcribes at least two mRNAs in opposite orientations. Studies using promoter-chloramphenicol acetyltransferase reporter gene fusions revealed that p _R , but not p _L , was sensitive to mitomycin C induction, suggesting that the switch from lysogenic growth to lytic growth was controlled mainly by the activity of these two promoters. In conclusion, a lysogenic state is maintained in S. salivarius 57.I, presumably by the repression of genes encoding proteins for lytic growth.IMPORTANCE The movement of mobile genetic elements such as bacteriophages and the establishment of lysogens may have profound effects on the balance of microbial ecology where lysogenic bacteria reside. The discovery of phage YMC-2011 from Streptococcus salivarius 57.I suggests that YMC-2011 and Streptococcus thermophilus-infecting phages share an ancestor. Although S. salivarius and S. thermophilus are close phylogenetically, S. salivarius is a natural inhabitant of the human mouth, whereas S. thermophilus is commonly found in the mammary mucosa of bovine species. Thus, the identification of YMC-2011 suggests that horizontal gene transfer via phage infection could take place between species from different ecological niches.

Evolution of genetic switch complexity

The circuitry of the phage λ genetic switch determining the outcome of lytic or lysogenic growth is well-integrated and complex, raising the question as to how it evolved. It is plausible that it arose from a simpler ancestral switch with fewer components that underwent various additions and refinements, as it adapted to vast numbers of different hosts and conditions. We have recently identified a new class of genetic switches found in mycobacteriophages and other prophages, in which immunity is dependent on integration. These switches contain only three genes (integrase, repressor and cro) and represent a major departure from the λ-like circuitry, lacking many features such as xis, cII and cIII. These small self-contained switches represent an unrealized, elegant circuitry for controlling infection outcome. In this addendum, we propose a model of possible events in the evolution of a complex λ-like switch from a simpler integration-dependent switch.

The effect of nonspecific binding of lambda repressor on DNA looping dynamics

The λ repressor (CI) protein-induced DNA loop maintains stable lysogeny, yet allows efficient switching to lysis. Herein, the kinetics of loop formation and breakdown has been characterized at various concentrations of protein using tethered particle microscopy and a novel, to our knowledge, method of analysis. Our results show that a broad distribution of rate constants and complex kinetics underlie loop formation and breakdown. In addition, comparison of the kinetics of looping in wild-type DNA and DNA with mutated o3 operators showed that these sites may trigger nucleation of nonspecific binding at the closure of the loop. The average activation energy calculated from the rate constant distribution is consistent with a model in which nonspecific binding of CI between the operators shortens their effective separation, thereby lowering the energy barrier for loop formation and broadening the rate constant distribution for looping. Similarly, nonspecific binding affects the kinetics of loop breakdown by increasing the number of loop-securing protein interactions, and broadens the rate constant distribution for this reaction. Therefore, simultaneous increase of the rate constant for loop formation and reduction of that for loop breakdown stabilizes lysogeny. Given these simultaneous changes, the frequency of transitions between the looped and the unlooped state remains nearly constant. Although the loop becomes more stable thermodynamically with increasing CI concentration, it still opens periodically, conferring sensitivity to environmental changes, which may require switching to lytic conditions.

Effects of macromolecular crowding on genetic networks

The intracellular environment is crowded with proteins, DNA, and other macromolecules. Under physiological conditions, macromolecular crowding can alter both molecular diffusion and the equilibria of bimolecular reactions and therefore is likely to have a significant effect on the function of biochemical networks. We propose a simple way to model the effects of macromolecular crowding on biochemical networks via an appropriate scaling of bimolecular association and dissociation rates. We use this approach, in combination with kinetic Monte Carlo simulations, to analyze the effects of crowding on a constitutively expressed gene, a repressed gene, and a model for the bacteriophage λ genetic switch, in the presence and absence of nonspecific binding of transcription factors to genomic DNA. Our results show that the effects of crowding are mainly caused by the shift of association-dissociation equilibria rather than the slowing down of protein diffusion, and that macromolecular crowding can have relevant and counterintuitive effects on biochemical network performance.

Decision making in living cells: lessons from a simple system

The life cycle of bacteriophage lambda serves as a simplified paradigm for cell-fate decisions. The ongoing quantitative, high-resolution experimental investigation of this life cycle has produced some important insights in recent years. These insights have to do with the way cells choose among alternative fates, how they maintain long-term memory of their gene-expression state, and how they switch from one stable state to another. The recent studies have highlighted the role of spatiotemporal effects in cellular processes and the importance of distinguishing chemical stochasticity from possible hidden variables in cellular decision making.

Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene

Bacterial lysogeny serves as a simple paradigm for cell differentiation.

We characterize the activity of the fate-determining genes, cI and cro, with single-molecule resolution.

Stability of the lysogenic state is found to depend in a simple manner on the frequency of activity bursts from cI.

The ability of living cells to maintain an inheritable memory of their gene-expression state is key to cellular differentiation. Bacterial lysogeny serves as a simple paradigm for long-term cellular memory. In this study, we address the following question: in the absence of external perturbation, how long will a cell stay in the lysogenic state before spontaneously switching away from that state? We show by direct measurement that lysogen stability exhibits a simple exponential dependence on the frequency of activity bursts from the fate-determining gene, cI. We quantify these gene-activity bursts using single-molecule-resolution mRNA measurements in individual cells, analyzed using a stochastic mathematical model of the gene-network kinetics. The quantitative relation between stability and gene activity is independent of the fine details of gene regulation, suggesting that a quantitative prediction of cell-state stability may also be possible in more complex systems.

Evolution of complex gene regulatory circuits by addition of refinements

How do complex gene regulatory circuits evolve? These circuits involve many interacting components, which work together to specify patterns of gene expression. They typically include many subtle mechanistic features, but in most cases it is unclear whether these features are essential for the circuit to work at all, or if instead they make a functional circuit work better. In the latter case, such a feature is here termed 'dispensable', and it is plausible that the feature has been added at a late stage in the evolution of the circuit. This review describes experimental tests of this question, using the phage λ gene regulatory circuit. Several features of this circuit are found to be dispensable, in the sense that the circuitry works without these features, though not as well as the wild type. In some cases, second-site suppressor mutations are needed to confer near-normal behavior in the absence of such a feature. These findings are discussed here in the context of a two-stage model for evolution of gene regulatory circuits. In this model, a circuit evolves by assembly of a primitive or basic form, followed by adjustment of parameters and addition of qualitatively new features. Pathways are suggested for the addition of such features to a more basic form. Selected examples in other systems are described. Some of the dispensable features of phage λ may be evolutionary refinements. Finding that a feature is dispensable, however, does not prove that it is a late addition - it is possible that it was essential early in evolution, and became dispensable as the circuit evolved. Conversely, a late addition might have become essential. As ongoing work provides additional examples of dispensable features, it may become clearer how often they represent refinements.

Stability and instability in the lysogenic state of phage lambda

Complex gene regulatory circuits exhibit emergent properties that are difficult to predict from the behavior of the components. One such property is the stability of regulatory states. Here we analyze the stability of the lysogenic state of phage λ. In this state, the virus maintains a stable association with the host, and the lytic functions of the virus are repressed by the viral CI repressor. This state readily switches to the lytic pathway when the host SOS system is induced. A low level of SOS-dependent switching occurs without an overt stimulus. We found that the intrinsic rate of switching to the lytic pathway, measured in a host lacking the SOS response, was almost undetectably low, probably less than 10(-8)/generation. We surmise that this low rate has not been selected directly during evolution but results from optimizing the rate of switching in a wild-type host over the natural range of SOS-inducing conditions. We also analyzed a mutant, λprm240, in which the promoter controlling CI expression was weakened, rendering lysogens unstable. Strikingly, the intrinsic stability of λprm240 lysogens depended markedly on the growth conditions; lysogens grown in minimal medium were nearly stable but switched at high rates when grown in rich medium. These effects on stability likely reflect corresponding effects on the strength of the prm240 promoter, measured in an uncoupled assay system. Several derivatives of λprm240 with altered stabilities were characterized. This mutant and its derivatives afford a model system for further analysis of stability.

Predicting gene-regulation functions: lessons from temperate bacteriophages

Gene-regulation functions (GRF) provide a unique characteristic of a cis-regulatory module (CRM), relating the concentrations of transcription factors (input) to the promoter activities (output). The challenge is to predict GRFs from the sequence. Here we systematically consider the lysogeny-lysis CRMs of different temperate bacteriophages such as the Lactobacillus casei phage A2, Escherichia coli phages lambda, and 186 and Lactococcal phage TP901-1. This study allowed explaining a recent experimental puzzle on the role of Cro protein in the lambda switch. Several general conclusions have been drawn: 1), long-range interactions, multilayer assembly and DNA looping may lead to complex GRFs that cannot be described by linear functions of binding site occupancies; 2), in general, GRFs cannot be described by the Boolean logic, whereas a three-state non-Boolean logic suffices for the studied examples; 3), studied CRMs of the intact phages seemed to have a similar GRF topology (the number of plateaus and peaks corresponding to different expression regimes); we hypothesize that functionally equivalent CRMs might have topologically equivalent GRFs for a larger class of genetic systems; and 4) within a given GRF class, a set of mechanistic-to-mathematical transformations has been identified, which allows shaping the GRF before carrying out a system-level analysis.

Qualitatively distinct phenotypes in the design space of biochemical systems

Although characterization of the genotype has undergone revolutionary advances as a result of the successful genome projects, the chasm between our understanding of a fully characterized gene sequence and the phenotypic repertoire of the organism is as broad and deep as it was in the pre-genomic era. There are two fundamental unsolved problems that provide the context for the challenges in relating genotype to phenotype. We address one of these and describe a generic method for constructing a system design space in which qualitatively distinct phenotypes can be identified and counted, their relative fitness analyzed and compared, and their tolerance to change measured.

A computational study of lambda-lac mutants

We present a comprehensive, computational study of the properties of bacteriophage lambda mutants designed by Atsumi and Little (2006 Proc. Natl. Acad. Sci. 103 4558-63). These phages underwent a genetic reconstruction where Cro was replaced by a dimeric form of the Lac repressor. To clarify the theoretical characteristics of these mutants, we built a detailed thermodynamic model. The mutants all have a different genetic wiring than the wild-type lambda. One group lacks regulation of P(RM) by the lytic protein. These mutants only exhibit the lysogenic equilibrium, with no transiently active P(R). The other group lacks the negative feedback from CI. In this group, we identify a handful of bi-stable mutants, although the majority only exhibit the lysogenic equilibrium. The experimental identification of functional phages differs from our predictions. From a theoretical perspective, there is no reason why only 4 out of 900 mutants should be functional. The differences between theory and experiment can be explained in two ways. Either, the view of the lambda phage as a bi-stable system needs to be revised, or the mutants have in fact not undergone a modular replacement, as intended by Atsumi and Little, but constitute instead a wider systemic change.

Lambda-prophage induction modeled as a cooperative failure mode of lytic repression

We analyze a system-level model for lytic repression of lambda phage in E. coli using reliability theory, showing that the repressor circuit comprises four redundant components whose failure mode is prophage induction. Our model reflects the specific biochemical mechanisms involved in regulation, including long-range cooperative binding, and its detailed predictions for prophage induction in E. coli under ultraviolet radiation are in good agreement with experimental data.

Guidance for data collection and computational modelling of regulatory networks

Many model regulatory networks are approaching the depth of characterisation of bacteriophage lambda, wherein the vast majority of individual components and interactions are identified, and research can focus on understanding whole network function and the role of interactions within that broader context. In recent years, the study of the system-wide behaviour of phage lambda's genetic regulatory network has been greatly assisted by the combination of quantitative measurements with theoretical and computational analyses. Such research has demonstrated the value of a number of general principles and guidelines for making use of the interplay between experiments and modelling. In this chapter we discuss these guidelines and provide illustration through reference to case studies from phage lambda biology.In our experience, computational modelling is best facilitated with a large and diverse set of quantitative, in vivo data, preferably obtained from standardised measurements and expressed as absolute units rather than relative units. Isolation of subsets of regulatory networks may render a system amenable to 'bottom-up' modelling, providing a valuable tool to the experimental molecular biologist. Decoupling key components and rendering their concentration or activity an independent experimental variable provide excellent information for model building, though conclusions drawn from isolated and/or decoupled systems should be checked against studies in the full physiological context; discrepancies are informative. The construction of a model makes possible in silico experiments, which are valuable tools for both the data analysis and the design of wet experiments.

The bacteriophage lambda CI protein finds an asymmetric solution

The CI protein of bacteriophage lambda (lambdaCI) is both a repressor and activator of transcription that has served as a model for understanding how gene regulatory proteins work. A dimeric DNA-binding protein, lambdaCI also forms higher-order oligomers that allow it to bind cooperatively to both adjacent and nonadjacent operator sites within the phage genome. The ability of phage lambda to transition efficiently from one program of gene expression to another depends upon the formation of these higher-order protein-DNA complexes. A recently determined crystal structure of a DNA-bound lambdaCI dimer reveals that the two subunits of the dimer adopt different conformations. This unexpected asymmetry helps explain how these higher-order complexes are assembled.

Cro's role in the CI Cro bistable switch is critical for {lambda}'s transition from lysogeny to lytic development

CI represses cro; Cro represses cI. This double negative feedback loop is the core of the classical CI-Cro epigenetic switch of bacteriophage lambda. Despite the classical status of this switch, the role in lambda development of Cro repression of the P(RM) promoter for CI has remained unclear. To address this, we created binding site mutations that strongly impaired Cro repression of P(RM) with only minimal effects on CI regulation of P(RM). These mutations had little impact on lambda development after infection but strongly inhibited the transition from lysogeny to the lytic pathway. We demonstrate that following inactivation of CI by ultraviolet treatment of lysogens, repression of P(RM) by Cro is needed to prevent synthesis of new CI that would otherwise significantly impede lytic development. Thus a bistable CI-Cro circuit reinforces the commitment to a developmental transition.

Single independent operator sites are involved in the genetic switch of the Lactobacillus delbrueckii bacteriophage mv4

The lysogeny region of the Lactobacillus delbrueckii bacteriophage mv4 contains two divergently oriented ORFs coding for the Rep (221 aa) and Tec (64 aa) proteins. The transcription of these two genes was analysed by primer extension and Northern blot experiments on lysogenic strains. The location of the transcription initiation sites of rep and tec in the intergenic region allowed the identification of the divergently oriented non overlapping promoters P(rep) and P(tec). Transcriptional fusions analysis showed that Rep negatively regulates the P(tec) promoter and activates its own transcription, and that Tec is a negative regulator of the two promoters. As demonstrated by gel mobility shift assays, the repressor Rep binds to a single specific 17 bp site located between the P(tec) -10 and -35 regions whereas Tec binds to a single specific 40 bp long complex operator site located between the two promoters. The presence of a single specific operator site for each repressor in the intergenic region is an unusual feature.

Modelling transcriptional interference and DNA looping in gene regulation

We describe a hybrid statistical mechanical and dynamical approach for modelling the formation of closed, open and elongating complexes of RNA polymerase, the interactions of these polymerases to produce transcriptional interference, and the regulation of these processes by a DNA-binding and DNA-looping regulatory protein. As a model system, we have used bacteriophage 186, for which genetic, biochemical and structural studies have suggested that the CI repressor binds as a 14-mer to form alternative DNA-looped complexes, and activates lysogenic transcription indirectly by relieving transcriptional interference caused by the convergent lytic promoter. The modelling showed that the original mechanisms proposed to explain this relief of transcriptional interference are not consistent with the available in vivo reporter data. However, a good fit to the reporter data was given by a revised model that incorporates a novel predicted regulatory mechanism: that RNA polymerase bound at the lysogenic promoter protects itself from transcriptional interference by recruiting CI to the lytic promoter. This mechanism and various estimates of in vivo biochemical parameters for the 186 CI system should be testable. Our results demonstrate the power of mathematical modelling for the extraction of detailed biochemical information from in vivo data.

Noise in timing and precision of gene activities in a genetic cascade

The timing of events along the induction cascade of bacteriophage lambda is independent of UV dose and displays increased relative temporal precision with cascade progression.

This behavior is reproduced by a model of a cascade consisting of independent steps that shows that higher temporal precision can be attained by a cascade consisting of a large number of fast steps.

The observed cell-cell variability in cascade timing is not due to differences in uniform dilation of intervals between events among cells, but rather to the independent distribution of interval durations within the cascade, consistently with the modular architecture of the lambda genome.

The single-cell time lapse study reveals a bistable regime at low UV doses in which some cells are induced while others are not, evidence for a commitment point beyond which lysis will occur, and an unexpected shutoff of the lambda pR promoter.

Stochasticity or noise, an inherent property of all biological networks, is often manifested by different phenotypic behaviors in clonal populations of cells (Raser and O'Shea, 2005). Noise can arise, for instance, from sources such as cell–cell variations in small numbers of regulatory molecules or from the stochastic nature of molecular interactions (Paulsson, 2005). Besides affecting the number of molecules in a cell, noise may also lead to variability in timing of particular events along a given pathway. In this work, we studied temporal noise in the induction cascade of phage lambda.

Infection of a bacterial cell by bacteriophage lambda can lead to two different fates (Ptashne, 2004; Dodd et al, 2005; Oppenheim et al, 2005): the phage can either multiply inside the host leading to its eventual lysis and the generation of progeny virions (the lytic pathway) or, alternatively, it can integrate its genome into the host's genome (prophage state), replicating passively with the latter (the lysogenic pathway). The prophage state is highly stable, being maintained by a phage-encoded repressor, which shuts off phage genes leading to lytic growth. However, the lytic pathway can be induced in a lysogenic cell, through the activation of the bacterial SOS response to DNA damage (Little, 1996), for example by UV irradiation. Once activated, the SOS response results in cleavage of the lambda repressor, leading to expression of the phage early and late genes, and culminating in the lysis of the host cell.

The lambda induction cascade has been extensively characterized over the years. We built upon this knowledge to tap the cascade at different points and quantitatively analyze the progressive loss of temporal coherence between cells, as different stages along the cascade are executed, following synchronous induction. Using time-lapse microscopy, we monitored the time of activation of early and late genes in individual cells using lambda pR and pR′-tR′ promoter-GFP fusions, respectively, by means of reporter plasmids, and finally the time of lysis. Sample results are shown in Figure 2.

At low UV levels (5 J/m²), the network exhibits bistability: only approximately 40% of the bacteria lyse, whereas the others continue to divide, following a lag period. At high UV levels (20 J/m²), almost all bacteria lyse. We found that the timing of events in cells that lyse is independent of UV dose. This is in contrast to the known behavior of the SOS network (Friedman et al, 2005), indicating that these two networks proceed independently. Following induction, a surprising shutoff in the activity of the pR promoter is observed in all cells (see Figure 2). Furthermore, the data show that whereas early genes are expressed in all cells irrespective of cell fate, late genes are expressed only in the lysing cells, indicating that similar to infection, a specific commitment checkpoint is operating.

To characterize the temporal variability in a cell population, we used the coefficient of variation, defined as the non-dimensional ratio of the standard deviation and the mean time of occurrence of a particular event. We studied the changes in both standard deviation and coefficient of variation in timing of various events along the lambda induction cascade, from the expression of the early genes to the ultimate lysis of the cells. As shown in Figure 6, the absolute noise as measured by the standard deviation increases as the cascade progresses. In contrast, the coefficient of variation, which measures variability relative to the time of occurrence, decreases. Simple theoretical considerations described in the text yield a necessary and sufficient condition for a monotonic decrease in the coefficient of variation. Higher temporal precision can be achieved when the cascade is composed of a large number of fast steps.

Further support for the independence of network modules is furnished by a correlation analysis of the times of occurrence of different steps along the lytic cascade. This analysis also indicates that the variability in lysis time is not due to differences in the global rate of cascade progression, but probably to random fluctuations in the execution time of the various cascade stages. Indeed, phage lambda gene expression architecture is well known to have evolved from a number of independent regulatory modules (Hendrix, 2003).

Biological developmental pathways require proper timing of gene expression. We investigated timing variations of defined steps along the lytic cascade of bacteriophage λ. Gene expression was followed in individual lysogenic cells, after induction with a pulse of UV irradiation. At low UV doses, some cells undergo partial induction and eventually divide, whereas others follow the lytic pathway. The timing of events in cells committed to lysis is independent of the level of activation of the SOS response, suggesting that the lambda network proceeds autonomously after induction. An increased loss of temporal coherence of specific events from prophage induction to lysis is observed, even though the coefficient of variation of timing fluctuations decreases. The observed temporal variations are not due to cell factors uniformly dilating the timing of execution of the cascade. This behavior is reproduced by a simple model composed of independent stages, which for a given mean duration predicts higher temporal precision, when a cascade consists of a large number of steps. Evidence for the independence of regulatory modules in the network is presented.

A synthetic phage lambda regulatory circuit

Analysis of synthetic gene regulatory circuits can provide insight into circuit behavior and evolution. An alternative approach is to modify a naturally occurring circuit, by using genetic methods to select functional circuits and evolve their properties. We have applied this approach to the circuitry of phage lambda. This phage grows lytically, forms stable lysogens, and can switch from this regulatory state to lytic growth. Genetic selections are available for each behavior. We previously replaced lambda Cro in the intact phage with a module including Lac repressor, whose function is tunable with small molecules, and several cis-acting sites. Here, we have in addition replaced lambda CI repressor with another tunable module, Tet repressor and several cis-acting sites. Tet repressor lacks several important properties of CI, including positive autoregulation and cooperative DNA binding. Using a combinatorial approach, we isolated phage variants with behavior similar to that of WT lambda. These variants grew lytically and formed stable lysogens. Lysogens underwent prophage induction upon addition of a ligand that weakens binding by the Tet repressor. Strikingly, however, addition of a ligand that weakens binding by Lac repressor also induced lysogens. This finding indicates that Lac repressor was present in the lysogens and was necessary for stable lysogeny. Therefore, these isolates had an altered wiring diagram from that of lambda. We speculate that this complexity is needed to compensate for the missing features. Our method is generally useful for making customized gene regulatory circuits whose activity is regulated by small molecules or protein cofactors.

Rewiring the severe acute respiratory syndrome coronavirus (SARS-CoV) transcription circuit: engineering a recombination-resistant genome

Live virus vaccines provide significant protection against many detrimental human and animal diseases, but reversion to virulence by mutation and recombination has reduced appeal. Using severe acute respiratory syndrome coronavirus as a model, we engineered a different transcription regulatory circuit and isolated recombinant viruses. The transcription network allowed for efficient expression of the viral transcripts and proteins, and the recombinant viruses replicated to WT levels. Recombinant genomes were then constructed that contained mixtures of the WT and mutant regulatory circuits, reflecting recombinant viruses that might occur in nature. Although viable viruses could readily be isolated from WT and recombinant genomes containing homogeneous transcription circuits, chimeras that contained mixed regulatory networks were invariantly lethal, because viable chimeric viruses were not isolated. Mechanistically, mixed regulatory circuits promoted inefficient subgenomic transcription from inappropriate start sites, resulting in truncated ORFs and effectively minimize viral structural protein expression. Engineering regulatory transcription circuits of intercommunicating alleles successfully introduces genetic traps into a viral genome that are lethal in RNA recombinant progeny viruses.

Lambda's Switch: Lessons from a Module Swap

A recent experiment has replaced Cro, a crucial component of lambda's genetic switch, with the lac repressor (plus two lac operators). The resulting hybrid phage is viable, but a subtle phenotypic defect explains a puzzle concerning the workings of the switch.