Sequence tolerance of the phage lambda PRM promoter: implications for evolution of gene regulatory circuitry

Noncanonical amino acids as prophage inducers for protein regulation in bacteria-based delivery systems

Genetically engineered bacteria represent a promising drug delivery tool for disease treatment. The development of new strategies for specific and independent protein regulation is necessary, especially for combination protein drug therapy. Using the well-studied Escherichia coli phage λ as a model system, we applied noncanonical amino acids (ncAAs) as novel inducers for protein regulation in a bacteria-based delivery system. Screening the permissive sites of the Cro protein revealed that incorporation of AlocK at the K8 site with the MbPylRS-349F/tRNAPyl system produced a functional Cro-K8AlocK variant. Using an engineered λ lysogen expressing the MbPylRS-349F/tRNAPyl pair, Cro-8X, and the reporter mNeonGreen, in vitro and in vivo experiments showed that AlocK led to bacterial lysis through prophage activation and the release of mNeonGreen. If mNeonGreen was integrated into the λ prophage genome, λ phages released due to AlocK induction delivered the reporter gene into the recipient E. coli strain, enabling mNeonGreen expression. Furthermore, insertion of pIF at the F14 site with the AfpIFRS/tRNATyr pair produced a functional Cro-F14pIF variant. Importantly, AfpIFRS/tRNATyr and MbPylRS-349F/tRNAPyl pairs were confirmed to be mutually orthogonal. In a mixture of two engineered λ lysogens expressing different aaRS/tRNAs, Cro-ncAAs, and reporter proteins, AlocK and pIF independently induced bacterial lysis and activated the expression of mNeonGreen and mCherry in the recipient E. coli strain. Collectively, the proposed bacteria-based delivery system provides two options for protein delivery and enables independent regulation of multiple proteins with ncAAs, offering a novel approach for in situ protein regulation and combination therapy.

IMPORTANCE

The use of genetically engineered bacteria as drug delivery vectors has attracted more and more attention in recent years. A key issue with bacteria-based delivery systems is how to regulate multiple protein drugs. Based on genetic code expansion technology, we developed a new strategy of using ncAAs as small molecular inducers for in situ protein regulation and engineered λ phage lysogen into a bacteria-based delivery system that can function in two delivery modes. Furthermore, this strategy enables independent regulation of multiple proteins by different ncAAs, offering important implications for combination therapy. This approach requires minimal genetic engineering efforts, and similar strategies can be applied to engineer other prophage-bacteria systems or study phage biology. This work expands the therapeutic applications of ncAAs and lysogenic phages.

The origin of genetic and metabolic systems: Evolutionary structuralinsights

DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.

Bacteriophage self-counting in the presence of viral replication

When host cells are in low abundance, temperate bacteriophages opt for dormant (lysogenic) infection. Phage lambda implements this strategy by increasing the frequency of lysogeny at higher multiplicity of infection (MOI). However, it remains unclear how the phage reliably counts infecting viral genomes even as their intracellular number increases because of replication. By combining theoretical modeling with single-cell measurements of viral copy number and gene expression, we find that instead of hindering lambda's decision, replication facilitates it. In a nonreplicating mutant, viral gene expression simply scales with MOI rather than diverging into lytic (virulent) and lysogenic trajectories. A similar pattern is followed during early infection by wild-type phage. However, later in the infection, the modulation of viral replication by the decision genes amplifies the initially modest gene expression differences into divergent trajectories. Replication thus ensures the optimal decision-lysis upon single-phage infection and lysogeny at higher MOI.

Transcription Initiation by Mix and Match Elements: Flexibility for Polymerase Binding to Bacterial Promoters

Bacterial RNA polymerase is composed of a core of subunits (β β′, α1, α2, ω), which have RNA synthesizing activity, and a specificity factor (σ), which identifies the start of transcription by recognizing and binding to sequence elements within promoter DNA. Four core promoter consensus sequences, the –10 element, the extended –10 (TGn) element, the –35 element, and the UP elements, have been known for many years; the importance of a nontemplate G at position -5 has been recognized more recently. However, the functions of these elements are not the same. The AT-rich UP elements, the –35 elements (–35TTGACA–30), and the extended –10 (15TGn–13) are recognized as double-stranded binding elements, whereas the –5 nontemplate G is recognized in the context of single-stranded DNA at the transcription bubble. Furthermore, the –10 element (–12TATAAT–7) is recognized as both double-stranded DNA for the T:A bp at position –12 and as nontemplate, single-stranded DNA from positions –11 to –7. The single-stranded sequences at positions –11 to –7 as well as the –5 contribute to later steps in transcription initiation that involve isomerization of polymerase and separation of the promoter DNA around the transcription start site. Recent work has demonstrated that the double-stranded elements may be used in various combinations to yield an effective promoter. Thus, while some minimal number of contacts is required for promoter function, polymerase allows the elements to be mixed and matched. Interestingly, which particular elements are used does not appear to fundamentally alter the transcription bubble generated in the stable complex. In this review, we discuss the multiple steps involved in forming a transcriptionally competent polymerase/promoter complex, and we examine what is known about polymerase recognition of core promoter elements. We suggest that considering promoter elements according to their involvement in early (polymerase binding) or later (polymerase isomerization) steps in transcription initiation rather than simply from their match to conventional promoter consensus sequences is a more instructive form of promoter classification.

Refactoring the λ phage lytic/lysogenic decision with a synthetic regulator

In this work, we explore the refactoring of the circuitry of λ phage by engineering a new-to-nature regulator that responds to an ad hoc input signal that behaves orthogonal with respect to the host cell. We tailored a chimeric regulator, termed Qλ, between the CI protein of the λ phage and the BzdR repressor from Azoarcus sp. strain CIB that responds to benzoyl-CoA. When the Qλ was expressed in the appropriate Escherichia coli cells, it was able to reprogram the lytic/lysogenic λ phage decision according to the intracellular production of benzoyl-CoA. Our results are also an example of how generating new artificial regulators that respond to effectors of choice may be useful to control different cellular processes.

Synthetic biology outside the cell: linking computational tools to cell-free systems

As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

High-yield, zero-leakage expression system with a translational switch using site-specific unnatural amino Acid incorporation

Synthetic biologists construct complex biological circuits by combinations of various genetic parts. Many genetic parts that are orthogonal to one another and are independent of existing cellular processes would be ideal for use in synthetic biology. However, our toolbox is still limited with respect to the bacterium Escherichia coli, which is important for both research and industrial use. The site-specific incorporation of unnatural amino acids is a technique that incorporates unnatural amino acids into proteins using a modified exogenous aminoacyl-tRNA synthetase/tRNA pair that is orthogonal to any native pairs in a host and is independent from other cellular functions. Focusing on the orthogonality and independency that are suitable for the genetic parts, we designed novel AND gate and translational switches using the unnatural amino acid 3-iodo-l-tyrosine incorporation system in E. coli. A translational switch was turned on after addition of 3-iodo-l-tyrosine in the culture medium within minutes and allowed tuning of switchability and translational efficiency. As an application, we also constructed a gene expression system that produced large amounts of proteins under induction conditions and exhibited zero-leakage expression under repression conditions. Similar translational switches are expected to be applicable also for eukaryotes such as yeasts, nematodes, insects, mammalian cells, and plants.

Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells

DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation. The "genetic switch" of bacteriophage λ determines whether a prophage stays incorporated in the E. coli chromosome or enters the lytic cycle of phage propagation and cell lysis. Past studies have shown that long-range DNA interactions between the operator sequences O(R) and O(L) (separated by 2.3 kb), mediated by the λ repressor CI (accession number P03034), play key roles in regulating the λ switch. In vitro, it was demonstrated that DNA segments harboring the operator sequences formed loops in the presence of CI, but CI-mediated DNA looping has not been directly visualized in vivo, hindering a deep understanding of the corresponding dynamics in realistic cellular environments. We report a high-resolution, single-molecule imaging method to probe CI-mediated DNA looping in live E. coli cells. We labeled two DNA loci with differently colored fluorescent fusion proteins and tracked their separations in real time with ∼40 nm accuracy, enabling the first direct analysis of transcription-factor-mediated DNA looping in live cells. Combining looping measurements with measurements of CI expression levels in different operator mutants, we show quantitatively that DNA looping activates transcription and enhances repression. Further, we estimated the upper bound of the rate of conformational change from the unlooped to the looped state, and discuss how chromosome compaction may impact looping kinetics. Our results provide insights into transcription-factor-mediated DNA looping in a variety of operator and CI mutant backgrounds in vivo, and our methodology can be applied to a broad range of questions regarding chromosome conformations in prokaryotes and higher organisms.

Role of cis-acting sites in stimulation of the phage λ P(RM) promoter by CI-mediated looping

The lysogenic state of phage λ is maintained by the CI repressor. CI binds to three operators each in the right operator (O(R)) and left operator (O(L)) regions, which lie 2.4 kb apart. At moderate CI levels, the predominant binding pattern is two dimers of CI bound cooperatively at each regulatory region. The resulting tetramers can then interact, forming an octamer and a loop of the intervening DNA. CI is expressed from the P(RM) promoter, which lies in the O(R) region and is subjected to multiple regulatory controls. Of these, the most recently discovered is stimulation by loop formation. In this work, we have investigated the mechanism by which looping stimulates P(RM). We find that two cis-acting sites lying in the O(L) region are involved. One site, an UP element, is required for stimulation. Based on the behavior of other promoters with UP elements located upstream of the -35 region, we suggest that a subunit of RNA polymerase (RNAP) bound at P(RM) binds to the UP element located in the O(L) region. In addition, adjacent to the UP element lies a binding site for integration host factor (IHF); this site plays a less critical role but is required for stimulation of the weak prm240 allele. A loop with CI at the O(L)2 and O(L)3 operators does not stimulate P(RM), while one with CI only at O(L)2 provides some stimulation. We discuss possible mechanisms for stimulation.

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.

Redefining Escherichia coli σ(70) promoter elements: -15 motif as a complement of the -10 motif

Classical elements of σ(70) bacterial promoters include the -35 element ((-35)TTGACA(-30)), the -10 element ((-12)TATAAT(-7)), and the extended -10 element ((-15)TG(-14)). Although the -35 element, the extended -10 element, and the upstream-most base in the -10 element ((-12)T) interact with σ(70) in double-stranded DNA (dsDNA) form, the downstream bases in the -10 motif ((-11)ATAAT(-7)) are responsible for σ(70)-single-stranded DNA (ssDNA) interactions. In order to directly reflect this correspondence, an extension of the extended -10 element to a so-called -15 element ((-15)TGnT(-12)) has been recently proposed. I investigated here the sequence specificity of the proposed -15 element and its relationship to other promoter elements. I found a previously undetected significant conservation of (-13)G and a high degeneracy at (-15)T. I therefore defined the -15 element as a degenerate motif, which, together with the conserved stretch of sequence between -15 and -12, allows treating this element analogously to -35 and -10 elements. Furthermore, the strength of the -15 element inversely correlates with the strengths of the -35 element and -10 element, whereas no such complementation between other promoter elements was found. Despite the direct involvement of -15 element in σ(70)-dsDNA interactions, I found a significantly stronger tendency of this element to complement weak -10 elements that are involved in σ(70)-ssDNA interactions. This finding is in contrast to the established view, according to which the -15 element provides a sufficient number of σ(70)-dsDNA interactions, and suggests that the main parameter determining a functional promoter is the overall promoter strength.

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.

Decision making at a subcellular level determines the outcome of bacteriophage infection

When the process of cell-fate determination is examined at single-cell resolution, it is often observed that individual cells undergo different fates even when subject to identical conditions. This "noisy" phenotype is usually attributed to the inherent stochasticity of chemical reactions in the cell. Here we demonstrate how the observed single-cell heterogeneity can be explained by a cascade of decisions occurring at the subcellular level. We follow the postinfection decision in bacteriophage lambda at single-virus resolution, and show that a choice between lysis and lysogeny is first made at the level of the individual virus. The decisions by all viruses infecting a single cell are then integrated in a precise (noise-free) way, such that only a unanimous vote by all viruses leads to the establishment of lysogeny. By detecting and integrating over the subcellular "hidden variables," we are able to predict the level of noise measured at the single-cell level.

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.

Tuning a genetic switch: experimental evolution and natural variation of prophage induction

Genetic switches allow organisms to modulate their phenotype in response to environmental changes. Understanding the evolutionary processes by which switches are tuned is central to understanding how phenotypic variation is realized. Prophage induction by phage lambda is the classic example of a genetic switch and allows lambda to move between two different modes of transmission: as a lysogen it reproduces vertically as a component of the host genome; as a free phage it reproduces horizontally by infectious epidemic spread. We show that the lambda switch can respond rapidly to selection for alteration in sensitivity and threshold. Sequencing of candidate genes in the genetic circuitry underlying the switch revealed mutations of likely adaptive significance in some, but not all candidates, suggesting that the core genetic circuitry plays a limited role in the fine-tuning of the switch in vivo. The relative ease with which the switch could be tuned by selection was further indicated by extensive variation in sensitivity and threshold of its response function among wild lambdoid phages. Together, our findings emphasize the adaptive significance of a finely tuned switch and draw attention to the selective factors shaping prophage induction in natural phage populations.

Binding cooperativity in phage lambda is not sufficient to produce an effective switch

In the wild-type phage lambda, binding of CI to O(R)2 helps polymerase bound to P(RM) transition from a closed to open complex. Activators on other promoters increase the polymerase-DNA binding energy, or affect both the binding energy and the closed-open transition probability. Using a validated mathematical model, we show that these two modes of upregulation have very different effects on the promoter function. We predict that if CI(2) bound to O(R)2 produced equal increase in RNAP-DNA binding constant (compared to wild-type increase in the closed-open transition probability), the lysogen would be significantly less stable.

DNA looping can enhance lysogenic CI transcription in phage lambda

The lysogenic state of bacteriophage lambda is maintained by CI repressor, which negatively regulates two promoters to block lytic gene expression. Expression of CI is itself controlled by positive and negative feedback as CI binds to O(R) to regulate the P(RM) promoter. In addition to direct interactions with operator DNA, CI tetramers bound at O(L) and O(R) can come together to form an octamer, looping the DNA that lies between them and allowing O(L) to assist with negative regulation of P(RM). We used a fluorescent reporter protein to measure the CI concentration for a set of constructs that differ in their ability to assume various forms of the looped structure. Based on the observed steady-state fluorescence for these constructs, the presence of O(L) increases P(RM) activation unless both operators can be fully occupied. By calculating the probabilities for the underlying operator configurations present in each construct, two different models for the mechanism of enhanced activation allow us to predict that when the DNA is looped, P(RM) activation can be 2- to 4-fold higher than is possible for unlooped DNA. Based on our results, transcriptional regulation for lambda's lysogenic/lytic switch includes both activation and repression due to DNA looping.

Cooperative DNA binding by CI repressor is dispensable in a phage lambda variant

Complex gene regulatory circuits contain many interacting components. In principle, all of these components and interactions may be essential to the function of the circuit. Alternatively, some of them may be refinements to a simpler version of the circuit that improve its fitness. In this work, we have tested whether a particular property of a critical regulatory protein, CI, is essential to the behavior of the phage lambda regulatory circuit. In the lysogenic state, CI represses the expression of the lytic genes, allowing a stable lysogenic state, by binding cooperatively to six operators. A mutant phage lacking cooperativity because of a change in cI could not form stable lysogens; however, this defect could be suppressed by the addition of mutations that altered two cis-acting sites but did not restore cooperativity. The resulting triple mutant was able to grow lytically, form stable single lysogens, and switch to lytic growth upon prophage induction, showing a threshold response in switching similar to that of wild-type lambda. We conclude that cooperative DNA binding by CI is not essential for these properties of the lambda circuitry, provided that suppressors increase the level of CI. Unlike wild-type lysogens, mutant lysogens were somewhat unstable under certain growth conditions. We surmise that cooperativity is a refinement to a more basic circuit, and that it affords increased stability to the lysogenic state in response to environmental variations.

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.

Conservation and diversity in the immunity regions of wild phages with the immunity specificity of phage lambda

The gene regulatory circuitry of phage lambda is among the best-understood circuits. Much of the circuitry centres around the immunity region, which includes genes for two repressors, CI and Cro, and their cis-acting sites. Related phages, termed lambdoid phages, have different immunity regions, but similar regulatory circuitry and genome organization to that of lambda, and show a mosaic organization, arising by recombination between lambdoid phages. We sequenced the immunity regions of several wild phages with the immunity specificity of lambda, both to determine whether natural variation exists in regulation, and to analyse conservation and variability in a region rich in well-studied regulatory elements. CI, Cro and their cis-acting sites are almost identical to those in lambda, implying that regulatory mechanisms controlled by the immunity region are conserved. A segment adjacent to one of the operator regions is also conserved, and may be a novel regulatory element. In most isolates, different alleles of two regulatory proteins (N and CII) flank the immunity region; possibly the lysis-lysogeny decision is more variable among isolates. Extensive mosaicism was observed for several elements flanking the immunity region. Very short sequence elements or microhomologies were also identified. Our findings suggest mechanisms by which fine-scale mosaicism arises.

Transcription initiation by mix and match elements: flexibility for polymerase binding to bacterial promoters

Bacterial RNA polymerase is composed of a core of subunits (beta, beta', alpha1, alpha2, omega), which have RNA synthesizing activity, and a specificity factor (sigma), which identifies the start of transcription by recognizing and binding to sequences elements within promoter DNA. Four core promoter consensus sequences, the -10 element, the extended -10 (TGn) element, the -35 element, and the UP elements, have been known for many years; the importance of a nontemplate G at position -5 has been recognized more recently. However, the functions of these elements are not the same. The AT-rich UP elements, the -35 elements ((-35)TTGACA(-30)), and the extended -10 ((-15)TGn(-13)) are recognized as double stranded binding elements, whereas the -5 nontemplate G is recognized in the context of single-stranded DNA at the transcription bubble. Furthermore, the -10 element ((-12)TATAAT(-7)) is recognized as both double strand DNA for the T:A bp at position -12 and as nontemplate, single-strand DNA from positions -11 to -7. The single-strand sequences at positions -11 to -7 as well as the -5 contribute to later steps in transcription initiation that involve isomerization of polymerase and separation of the promoter DNA around the transcription start site. Recent work has demonstrated that the double strand elements may be used in various combinations to yield an effective promoter. Thus, while some minimal number of contacts is required for promoter function, polymerase allows the elements to be mixed and matched. Interestingly, which particular elements are used does not appear to fundamentally alter the transcription bubble generated in the stable complex. In this review, we discuss the multiple steps involved in forming a transcriptionally competent polymerase/promoter complex, and we examine what is known about polymerase recognition of core promoter elements. We suggest that considering promoter elements according to their involvement in early (polymerase binding) or later (polymerase isomerization) steps in transcription initiation rather than simply from their match to conventional promoter consensus sequences is a more instructive form of promoter classification.

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.

Genetic parts to program bacteria

Genetic engineering is entering a new era, where microorganisms can be programmed using synthetic constructs of DNA encoding logic and operational commands. A toolbox of modular genetic parts is being developed, comprised of cell-based environmental sensors and genetic circuits. Systems have already been designed to be interconnected with each other and interfaced with the control of cellular processes. Engineering theory will provide a predictive framework to design operational multicomponent systems. On the basis of these developments, increasingly complex cellular machines are being constructed to build specialty chemicals, weave biomaterials, and to deliver therapeutics.

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

Using a module exchange approach, we have tested a long-standing model for the role of Cro repressor in lambda prophage induction. This epigenetic switch from lysogeny to the lytic state occurs on activation of the host SOS system, which leads to specific cleavage of CI repressor. It has been proposed that Cro repressor, which operates during lytic growth and which we shall term the lytic repressor, is crucial to prophage induction. In this view, Cro binds to the O(R)3 operator, thereby repressing the cI gene and making the switch irreversible. Here we tested this model by replacing lambda Cro with a dimeric form of Lac repressor and adding several lac operators. This approach allowed us to regulate the function of the lytic repressor at will and to prevent it from repressing cI, because lac repressor could not repress P(RM) in our constructs. Repression of cI by the lytic repressor was not required for prophage induction to occur. However, our evidence suggests that this binding can make induction more efficient, particularly at intermediate levels of DNA damage that otherwise cause induction of only a fraction of the population. These results indicate that this strategy of module exchange will have broad applications for analysis of gene regulatory circuits.

Switches in Bacteriophage Lambda Development

The lysis-lysogeny decision of bacteriophage lambda (lambda) is a paradigm for developmental genetic networks. There are three key features, which characterize the network. First, after infection of the host bacterium, a decision between lytic or lysogenic development is made that is dependent upon environmental signals and the number of infecting phages per cell. Second, the lysogenic prophage state is very stable. Third, the prophage enters lytic development in response to DNA-damaging agents. The CI and Cro regulators define the lysogenic and lytic states, respectively, as a bistable genetic switch. Whereas CI maintains a stable lysogenic state, recent studies indicate that Cro sets the lytic course not by directly blocking CI expression but indirectly by lowering levels of CII which activates cI transcription. We discuss how a relatively simple phage like lambda employs a complex genetic network in decision-making processes, providing a challenge for theoretical modeling.

Positive autoregulation of cI is a dispensable feature of the phage lambda gene regulatory circuitry

Complex gene regulatory circuits contain many features that are likely to contribute to their operation. It is unclear, however, whether all these features are necessary for proper circuit behavior or whether certain ones are refinements that make the circuit work better but are dispensable for qualitatively normal behavior. We have addressed this question using the phage lambda regulatory circuit, which can persist in two stable states, the lytic state and the lysogenic state. In the lysogenic state, the CI repressor positively regulates its own expression by stimulating transcription from the P(RM) promoter. We tested whether this feature is an essential part of the regulatory circuitry. Several phages with a cI mutation preventing positive autoregulation and an up mutation in the P(RM) promoter showed near-normal behavior. We conclude that positive autoregulation is not necessary for proper operation of the lambda circuitry and speculate that it serves a partially redundant function of stabilizing a bistable circuit, a form of redundancy we term "circuit-level redundancy." We discuss our findings in the context of a two-stage model for evolution and elaboration of regulatory circuits from simpler to more complex forms.

Revisited gene regulation in bacteriophage lambda

The contribution of bacteriophage lambda to gene control research is far from over. A revised model of the lambda genetic switch includes extra cooperativity through octamerization of the cI repressor protein, mediated by long-range DNA looping. Structural analysis reveals remarkably subtle transcriptional activation by cI. The action of cI, activation by cII, and aspects of antitermination by N and Q all confirm the utility and versatility of simple, weak adhesive interactions mediated by nucleic acid tethers. New genetic and quantitative analysis of the lambda gene network is challenging cherished ideas about how complex behaviours emerge from this regulatory system.

Regulatory circuit design and evolution using phage lambda

Bistable gene regulatory circuits can adopt more than one stable epigenetic state. To understand how natural circuits have this and other systems properties, several groups have designed regulatory circuits de novo. Here we describe an alternative approach. We have modified an existing bistable circuit, that of phage lambda. With this approach, we used powerful genetic selections to identify functional circuits and selected for variants with altered behavior. The lambda circuit involves two antagonistic repressors, CI and Cro. We replaced lambda Cro with a module that included Lac repressor and several lac operators. Using a combinatorial approach, we isolated variants with different types of regulatory behavior. Several resembled wild-type lambda--they could grow lytically, could form highly stable lysogens, and carried out prophage induction. Another variant could form stable lysogens in the presence of a ligand for Lac repressor but switched to the lytic state when the ligand was removed. Several isolates evolved toward a desired behavior under selective pressure. These results strongly support the idea that complex circuits can arise during the course of evolution by a combination of simpler regulatory modules. They also underscore the advantages of modifying a natural circuit as an approach to understanding circuit design, systems behavior, and circuit evolution.