New applications for phage integrases

Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line.

•

Phage integrases are site-specific recombinases that mediate controlled and precise DNA integration and excision.

•

The serine integrases, such as ϕC31 integrase, can be used for efficient recombination in heterologous hosts as they use short recombination substrates, they are directional and they do not require host factors.

•

Both serine and tyrosine integrases, such as λ integrase, are versatile tools for DNA cloning and assembly in vivo and in vitro.

•

Controlled expression of orthologous serine integrases and their cognate recombination directionality factors can be used to generate living biocomputers.

•

Serine integrases are increasingly being exploited for synthetic biology applications.

Comparative genomics of Shiga toxin encoding bacteriophages

Background

Stx bacteriophages are responsible for driving the dissemination of Stx toxin genes (stx) across their bacterial host range. Lysogens carrying Stx phages can cause severe, life-threatening disease and Stx toxin is an integral virulence factor. The Stx-bacteriophage vB_EcoP-24_B, commonly referred to as Ф24_B, is capable of multiply infecting a single bacterial host cell at a high frequency, with secondary infection increasing the rate at which subsequent bacteriophage infections can occur. This is biologically unusual, therefore determining the genomic content and context of Ф24_B compared to other lambdoid Stx phages is important to understanding the factors controlling this phenomenon and determining whether they occur in other Stx phages.

Results

The genome of the Stx2 encoding phage, Ф24_B was sequenced and annotated. The genomic organisation and general features are similar to other sequenced Stx bacteriophages induced from Enterohaemorrhagic Escherichia coli (EHEC), however Ф24_B possesses significant regions of heterogeneity, with implications for phage biology and behaviour. The Ф24_B genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system.

Conclusions

The data support the hypothesis that Stx phages are mosaic, and recombination events between the host, phages and their remnants within the same infected bacterial cell will continue to drive the evolution of Stx phage variants and the subsequent dissemination of shigatoxigenic potential.

Pesticide degradation in a 'biobed' composting substrate

Pesticides play an important role in the success of modern farming and food production. However, the release of pesticides to the environment arising from non-approved use, poor practice, illegal operations or misuse is increasingly recognised as contributing to water contamination. Biobeds appear to offer a cost-effective method for treating pesticide-contaminated waste. This study was performed to determine whether biobeds can degrade relatively complex pesticide mixtures when applied repeatedly. A pesticide mixture containing isoproturon, pendimethalin, chlorpyrifos, chlorothalonil, epoxiconazole and dimethoate was incubated in biomix and topsoil at concentrations to simulate pesticide disposal. Although the data suggest that interactions between pesticides are possible, the effects were of less significance in biomix than in topsoil. The same mixture was applied on three occasions at 30-day intervals. Degradation was significantly quicker in biomix than in topsoil. The rate of degradation, however, decreased with each additional treatment, possibly due to the toxicity of the pesticide mixture to the microbial community. Incubations with chlorothalonil and pendimethalin carried out in sterile and non-sterile biomix indicated that degradation, rather than irreversible adsorption to the matrix, was the main mechanism responsible for the reduction in recovered residues. Results from these experiments suggest that biobeds offer a viable means of treating pesticide waste.

One for all or all for one: heterogeneous expression and host cell lysis are key to gene transfer agent activity in Rhodobacter capsulatus

The gene transfer agent (RcGTA) of Rhodobacter capsulatus is the model for a family of novel bacteriophage-related genetic elements that carry out lateral transfer of essentially random host DNA. Genuine and putative gene transfer agents have been discovered in diverse genera and are becoming recognized as potentially an important source of genetic exchange and microbial evolution in the oceans. Despite being discovered over 30 years ago, little is known about many essential aspects of RcGTA biology. Here, we validate the use of direct fluorescence reporter constructs, which express the red fluorescent protein mCherry in R. capsulatus. A construct containing the RcGTA promoter fused to mCherry was used to examine the single-cell expression profiles of wild type and RcGTA overproducer R. capsulatus populations, under different growth conditions and growth phases. The majority of RcGTA production clearly arises from a small, distinct sub-set of the population in the wild type strain and a larger sub-set in the overproducer. The most likely RcGTA release mechanism concomitant with this expression pattern is host cell lysis and we present direct evidence for the release of an intracellular enzyme accompanying RcGTA release. RcGTA ORF s is annotated as a ‘cell wall peptidase’ but we rule out a role in host lysis and propose an alternative function as a key contributor to RcGTA invasion of a target cell during infection.

Degradation of pesticides in biobeds: the effect of concentration and pesticide mixtures

Biobeds aim to create an environment whereby any pesticide spills are retained and then degraded, thus reducing the potential for surface or groundwater contamination. Biobeds may receive high concentrations of relatively complex mixtures of pesticides. The effects of concentration and pesticide interaction on degradation rate were therefore investigated. At concentrations up to 20 times the maximum recommended application rate for isoproturon and chlorothalonil, the rate of degradation in topsoil and biomix decreased with increasing concentration. With the exception of isoproturon at concentrations above 11 mg kg(-1), degradation was quicker in biomix (a composted mixture of topsoil, compost, and wheat straw) than in topsoil. One possible explanation for faster isoproturon degradation in topsoil as compared to biomix may be that previous treatments of isoproturon applied to the field soil as part of normal agricultural practices had resulted in proliferation of microbial communities specifically adapted to use isoproturon as an energy source. Such microbial adaptation could enhance the performance of a biobed. Studies with a mixture of isoproturon and chlorothalonil showed that interactions between pesticides are possible. In biomix, the degradation of either isoproturon or chlorothalonil was unaffected by the presence of the other pesticide, whereas in topsoil, isoproturon DT(50) values increased from 18.5 to 71.5 days in the presence of chlorothalonil. These studies suggest that biobeds appear capable of treating high concentrations of more than one pesticide.

Identification and characterization of a direct activator of a gene transfer agent

Gene transfer agents (GTAs) are thought to be ancient bacteriophages that have been co-opted into serving their host and can now transfer any gene between bacteria. Production of GTAs is controlled by several global regulators through unclear mechanisms. In Rhodobacter capsulatus, gene rcc01865 encodes a putative regulatory protein that is essential for GTA production. Here, I show that rcc01865 (hereafter gafA) encodes a transcriptional regulator that binds to the GTA promoter to initiate production of structural and DNA packaging components. Expression of gafA is in turn controlled by the pleiotropic regulator protein CtrA and the quorum-sensing regulator GtaR. GafA and CtrA work together to promote GTA maturation and eventual release through cell lysis. Identification of GafA as a direct GTA regulator allows the first integrated regulatory model to be proposed and paves the way for discovery of GTAs in other species that possess gafA homologues.

Class IIa histone deacetylases are conserved regulators of circadian function

Class IIa histone deacetylases (HDACs) regulate the activity of many transcription factors to influence liver gluconeogenesis and the development of specialized cells, including muscle, neurons, and lymphocytes. Here, we describe a conserved role for class IIa HDACs in sustaining robust circadian behavioral rhythms in Drosophila and cellular rhythms in mammalian cells. In mouse fibroblasts, overexpression of HDAC5 severely disrupts transcriptional rhythms of core clock genes. HDAC5 overexpression decreases BMAL1 acetylation on Lys-537 and pharmacological inhibition of class IIa HDACs increases BMAL1 acetylation. Furthermore, we observe cyclical nucleocytoplasmic shuttling of HDAC5 in mouse fibroblasts that is characteristically circadian. Mutation of the Drosophila homolog HDAC4 impairs locomotor activity rhythms of flies and decreases period mRNA levels. RNAi-mediated knockdown of HDAC4 in Drosophila clock cells also dampens circadian function. Given that the localization of class IIa HDACs is signal-regulated and influenced by Ca(2+) and cAMP signals, our findings offer a mechanism by which extracellular stimuli that generate these signals can feed into the molecular clock machinery.

Cumulative effect of prophage burden on Shiga toxin production in Escherichia coli

Shigatoxigenic Escherichia coli (STEC) such as E. coli O157 are significant human pathogens, capable of producing severe, systemic disease outcomes. The more serious symptoms associated with STEC infection are primarily the result of Shiga toxin (Stx) production, directed by converting Stx bacteriophages. During phage-mediated replication and host cell lysis, the toxins are released en masse from the bacterial cells, and the severity of disease is linked inexorably to toxin load. It is common for a single bacterial host to harbour more than one heterogeneous Stx prophage, and it has also been recently proven that multiple isogenic prophage copies can exist in a single cell, contrary to the lambda immunity model. It is possible that in these multiple lysogens there is an increased potential for production of Stx. This study investigated the expression profiles of single and double isogenic lysogens of Stx phage 24(B) using quantitative PCR to examine transcription levels, and a reporter gene construct as a proxy for the translation levels of stx transcripts. Toxin gene expression in double lysogens was in excess of the single lysogen counterpart, both in the prophage state and after induction of the lytic life cycle. In addition, double lysogens were found to be more sensitive to an increased induction stimulus than single lysogens, suggesting that maintenance of a stable prophage is less likely when multiple phage genome copies are present. Overall, these data demonstrate that the phenomenon of multiple lysogeny in STEC has the potential to impact upon disease pathology through increased toxin load.

Degradation and leaching potential of pesticides in biobed systems

Biobeds provide a potential solution to pesticide contamination of surface waters arising from the farmyard. Previous work has shown that biobeds can effectively treat spills and splashes of pesticide. This study investigated the potential for biobeds to treat much larger volumes and amounts of pesticide waste not only arising from spills but also from washing processes. Two systems were assessed using a range of pesticides at the semi-field scale, ie a lined biobed system and an unlined system. Studies using the lined biobeds demonstrated that water management was crucial, with biobeds needing to be covered to exclude rain-water. Once covered, the top of the biobed became hydrophobic, restricting moisture loss and resulting in saturated conditions at depth. The drying out of the top layer coincided with a measured decrease in microbial biomass in the treated biobeds. Applied pesticides were effectively retained within the 0-5 cm layer. Whilst all pesticides tested degraded, low moisture content and microbial activity meant degradation rates were low. Studies using unlined biobeds showed that only the most mobile pesticides leached, and for these > 99% was removed by the system, with a significant proportion degraded within 9 months. Peak concentrations of the two most mobile pesticides did however exceeded the limits that are likely to be required by regulatory bodies. However, it is thought that these limits could be reached by optimisation of the system.

Leaching of pesticides from biobeds: effect of biobed depth and water loading

Pesticides may be released to farmyard surfaces as a result of spillages, leakages, and the decontamination of tractors and sprayers. Biobeds can be used to intercept and treat contaminated runoff, thus minimizing losses to the environment. Previous studies using lined and unlined biobeds showed that water management was the limiting factor for both systems. While lined biobeds effectively retained pesticides, the system rapidly became water logged and degradation was slow. Studies using unlined biobeds showed that >99% of the applied pesticides were removed by the system, with a significant proportion degraded within 9 months. However, peak concentrations of certain pesticides (Koc < 125) were unacceptable to the regulatory authorities. These experiments were designed to optimize the design and management of unlined biobeds. Experiments performed to investigate the relationship between biobed depth and water loading showed that biobeds need to have a minimum depth of 1-1.5 m. The surface area dimension of the biobed depends on the water loading, which is controlled by the nature and frequency of pesticide handling activities on the farm. Leaching losses of all but the most mobile (Koc < 15) pesticides were <0.32% of the applied dose from 1.5 m deep biobeds subject to a water loading of 1175 L m(-2). These were reduced to <0.06% when a water loading of 688 L m(-2) was applied and down to <0.0001% for a water loading of 202 L m(-2). On the basis of these data, a 1.5 m deep biobed, subject to a maximum water loading of 1121 L m(-2) and with a surface area of 40 m(2) should be able to treat < or =44000 L of pesticide waste and washings such that the average concentration of all pesticides, other than those classified as very mobile, does not exceed 5 microg L(-1). This level of treatment can be improved by further reduction in the hydraulic loading.

Effect of different soil textures on leaching potential and degradation of pesticides in biobeds

Biobeds can be used to intercept pesticide-contaminated runoff from the mixing/washdown area, creating optimum conditions for sorption and biodegradation such that the amount of pesticide reaching adjacent water bodies is significantly reduced. The biobed is built on the farm using locally available materials, which include, straw, compost, and topsoil. The topsoil acts as the inoculum for the system and is likely to vary in terms of its physical, chemical, and microbiological characteristics from one farm to another. This study therefore investigated the effects of using different soil types on the degradation and leaching potential from biobeds. Three contrasting topsoils were investigated. Leaching studies were performed using isoproturon, dimethoate, and mecoprop-P, which were applied at simulated disposal rates to 1.5 m deep biobeds. Annual average concentrations were similar for each soil type with leaching losses of even the most mobile (Koc = 12-25) pesticide <1.64% of the applied dose. Greater than 98% of the retained pesticides were degraded in all matrices. Degradation studies investigated the persistence of individual pesticides and pesticide mixtures in the different matrices. DT50 values for isoproturon, chlorothalonil, mecoprop-P, and metsulfuron-methyl applied at 4 times the maximum approved rate were similar across the biomix types and were all less than or equal to reported DT50 values for soil treated at approved rates. When applied as a mixture, DT50 values in each biomix increased, indicating that interactions between pesticides are possible. However, DT90 values of <167 days were obtained in all circumstances, indicating a negligible risk of accumulation. Studies therefore indicate that substrate will have little impact on biobed performance so it should be possible to use local soils in the construction process.

Recombination directionality factor gp3 binds ϕC31 integrase via the zinc domain, potentially affecting the trajectory of the coiled-coil motif

To establish a prophage state, the genomic DNA of temperate bacteriophages normally becomes integrated into the genome of their host bacterium by integrase-mediated, site-specific DNA recombination. Serine integrases catalyse a single crossover between an attachment site in the host (attB) and a phage attachment site (attP) on the circularized phage genome to generate the integrated prophage DNA flanked by recombinant attachment sites, attL and attR. Exiting the prophage state and entry into the lytic growth cycle requires an additional phage-encoded protein, the recombination directionality factor or RDF, to mediate recombination between attL and attR and excision of the phage genome. The RDF is known to bind integrase and switch its activity from integration (attP x attB) to excision (attL x attR) but its precise mechanism is unclear. Here, we identify amino acid residues in the RDF, gp3, encoded by the Streptomyces phage ϕC31 and within the ϕC31 integrase itself that affect the gp3:Int interaction. We show that residue substitutions in integrase that reduce gp3 binding adversely affect both excision and integration reactions. The mutant integrase phenotypes are consistent with a model in which the RDF binds to a hinge region at the base of the coiled-coil motif in ϕC31 integrase.

Exposure to sulfosulfuron in agricultural drainage ditches: field monitoring and scenario-based modelling

Field monitoring and scenario-based modelling were used to assess exposure of small ditches in the UK to the herbicide sulfosulfuron following transport via field drains. A site in central England on a high pH, clay soil was treated with sulfosulfuron, and concentrations were monitored in the single drain outfall and in the receiving ditch 1 km downstream. Drainflow in the nine months following application totalled 283 mm. Pesticide lost in the first 12.5 mm of flow was 99% of the total loading to drains (0.5% of applied). Significant dilution was observed in the receiving ditch and quantifiable residues were only detected in one sample (0.06 microg litre(-1)). The MACRO model was evaluated against the field data with minimal calibration. The parameterisation over-estimated the importance of macropore flow at the site. As a consequence, the maximum concentration in drainflow (2.3 microg litre(-1)) and the total loading to drains (0.76 g) were over-estimated by factors of 2.4 and 5, respectively. MACRO was then used to simulate long-term fate of the herbicide for each of 20 environmental scenarios. Resulting estimates for concentrations of sulfosulfuron in a receiving ditch were weighted according to the prevalence of each scenario to produce a probability distribution of daily exposure.

Application of serine integrases for secondary metabolite pathway assembly in Streptomyces

Serine integrases have been shown to be efficient tools for metabolic pathway assembly. To further improve the flexibility and efficiency of pathway engineering via serine integrases, we explored how multiple orthogonally active serine integrases can be applied for use in vitro for the heterologous expression of complex biosynthesis pathways in Streptomyces spp., the major producers of useful bioactive natural products. The results show that multiple orthogonal serine integrases efficiently assemble the genes from a complex biosynthesis pathway in a single in vitro recombination reaction, potentially permitting a versatile combinatorial assembly approach. Furthermore, the assembly strategy also permitted the incorporation of a well-characterised promoter upstream of each gene for expression in a heterologous host. The results demonstrate how site-specific recombination based on orthogonal serine integrases can be applied in Streptomyces spp.

Investigations into the causes of residue variability on carrots in the UK

A pilot study was established to determine whether the preferential flow of water and thus insecticide in carrot beds might be responsible for the high residues of organophosphorus insecticides detected in individual carrot roots grown in the UK. A field site typical of UK carrot growing conditions was selected on a sandy soil with a low organic carbon content. Brilliant blue dye was applied in water to a small number of field plots located in the carrot beds to trace water movement through the bed and not to simulate insecticide application or irrigation. The plots were excavated following sufficient time for infiltration and drainage. Horizontal and vertical cross-sections through the soil profile were cut and descriptions of the dye presence in relation to soil features and the position of the carrot roots were made. Dye tracing and soil analyses showed there was a clear mechanical cultivation effect which generated a preferential movement of dye and water within the bed. The subsequent growth of carrots also created additional pathways of preferential movement due to stem-flow or canopy drip. A second study which increased replication of samples and allowed analysis of triazophos and chlorfenvinphos residues in the carrots could not identify any single factor which was conclusively responsible for initiating high residues in individual roots.

The archetypal gene transfer agent RcGTA is regulated via direct interaction with the enigmatic RNA polymerase omega subunit

Gene transfer agents (GTAs) are small virus-like particles that indiscriminately package and transfer any DNA present in their host cell, with clear implications for bacterial evolution. The first transcriptional regulator that directly controls GTA expression, GafA, was recently discovered, but its mechanism of action has remained elusive. Here, we demonstrate that GafA controls GTA gene expression via direct interaction with the RNA polymerase omega subunit (Rpo-ω) and also positively autoregulates its own expression by an Rpo-ω-independent mechanism. We show that GafA is a modular protein with distinct DNA and protein binding domains. The functional domains we observe in Rhodobacter GafA also correspond to two-gene operons in Hyphomicrobiales pathogens. These data allow us to produce the most complete regulatory model for a GTA and point toward an atypical mechanism for RNA polymerase recruitment and specific transcriptional activation in the Alphaproteobacteria.

Evidence of traffic-related pollutant control in soil-based sustainable urban drainage systems (SUDS)

SUDS are being increasingly employed to control highway runoff and have the potential to protect groundwater and surface water quality by minimising the risks of both point and diffuse sources of pollution. While these systems are effective at retaining polluted solids by filtration and sedimentation processes, less is known of the detail of pollutant behaviour within SUDS structures. This paper reports on investigations carried out as part of a co-ordinated programme of controlled studies and field measurements at soft-engineered SUDS undertaken in the UK, observing the accumulation and behaviour of traffic-related heavy metals, oil and PAHs. The field data presented were collected from two extended detention basins serving the M74 motorway in the south-west of Scotland. Additional data were supplied from an experimental lysimeter soil core leaching study. Results show that basin design influences pollutant accumulation and behaviour in the basins. Management and/or control strategies are discussed for reducing the impact of traffic-related pollutants on the aqueous environment.

Medium-term performance and maintenance of SUDS: a case-study of Hopwood Park Motorway Service Area, UK

One of the main barriers to implementing SUDS is concern about performance and maintenance costs since there are few well-documented case-studies. This paper summarizes studies conducted between 2000 and 2008 of the performance and maintenance of four SUDS management trains constructed in 1999 at the Hopwood Park Motorway Service Area, central England. Assessments were made of the wildlife value and sedimentation in the SUDS ponds, the hydraulic performance of the coach park management train, water quality in all management trains, and soil/sediment composition in the grass filter strip, interceptor and ponds. Maintenance procedures and costs were also reviewed. Results demonstrate the benefits of a management train approach over individual SUDS units for flow attenuation, water treatment, spillage containment and maintenance. Peak flows, pond sediment depth and contaminant concentrations in sediment and water decreased through the coach park management train. Of the 2007 annual landscape budget of pounds 15,000 for the whole site, the maintenance costs for SUDS only accounted for pounds 2,500 compared to pounds 4,000 for conventional drainage structures. Furthermore, since sediment has been attenuated in the management trains, the cost of sediment removal after the recommended period of three years was only pounds 554 and, if the design is not compromised, less frequent removal will be required in future.

Penton blooming, a conserved mechanism of genome delivery used by disparate microviruses

Microviruses are single-stranded DNA viruses infecting bacteria, characterized by T = 1 shells made of single jelly-roll capsid proteins. To understand how microviruses infect their host cells, we have isolated and studied an unusually large microvirus, Ebor. Ebor belongs to the proposed "Tainavirinae" subfamily of Microviridae and infects the model Alphaproteobacterium Rhodobacter capsulatus. Using cryogenic electron microscopy, we show that the enlarged capsid of Ebor is the result of an extended C-terminus of the major capsid protein. The extra packaging space accommodates genes encoding a lytic enzyme and putative methylase, both absent in microviruses with shorter genomes. The capsid is decorated with protrusions at its 3-fold axes, which we show to recognize lipopolysaccharides on the host surface. Cryogenic electron tomography shows that during infection, Ebor attaches to the host cell via five such protrusions. This attachment brings a single pentameric capsomer into close contact with the cell membrane, creating a special vertex through which the genome is ejected. Both subtomogram averaging and single particle analysis identified two intermediates of capsid opening, showing that the interacting penton opens from its center via the separation of individual capsomer subunits. Structural comparison with the model Bullavirinae phage phiX174 suggests that this genome delivery mechanism may be widely present across Microviridae.

IMPORTANCE

Tailless Microviridae bacteriophages are major components of the global virosphere. Notably, microviruses are prominent members of the mammalian gut virome, and certain compositions have been linked to serious health disorders; however, a molecular understanding of how they initiate infection of their host remains poorly characterized. We demonstrate that trimeric protrusions located at the corners of a single microvirus capsomer mediate host cell attachment. This interaction triggers opening of the capsomer, driven by separation of subunits from its center, much like flower petals open during blooming. This extensive opening explains how the genome translocation apparatus, along with the genome itself, is able to exit the capsid. "Penton blooming" likely represents a conserved mechanism shared by diverse viruses possessing similar capsid architectures.

Selfless viruses - the biology and regulation of gene transfer agents

Gene transfer agents (GTAs) are genetic elements that have the potential to carry out high frequency horizontal gene transfer. GTAs are similar to small bacteriophages in many ways but, instead of prioritizing the spread of their own genes, they package and disseminate the entire genome of their bacterial host. Indiscriminate transfer of bacterial genes could clearly have a major impact on bacterial evolution, fitness and antimicrobial resistance. Over the past decade, numerous pleiotropic systems have been shown to influence GTA production (e.g. nutrient stress, quorum sensing, SOS response etc.) but all act indirectly and so the mechanism of activation has remained elusive. I will present recent work that identified the missing link that couples GTA production to host regulatory pathways. I will also offer insights into the mechanism of random DNA packaging, the evolutionary role of GTAs in the environment and their potential ecological niche.

Gene transfer agents: structural and functional properties of domesticated viruses

Horizontal exchange of DNA between bacteria and archaea is prevalent and has major potential implications for genome evolution, plasticity, and population fitness. Several transfer mechanisms have been identified, including gene transfer agents (GTAs). GTAs are intricately regulated domesticated viruses that package host DNA into virus-like capsids and transfer this DNA throughout the bacterial community. Several important advances have recently been made in our understanding of these unusual particles. In this review, we highlight some of these findings, primarily for the model GTA produced by Rhodobacter capsulatus but also for newly identified GTA producers. We provide key insights into these important genetic elements, including the differences between GTAs from their ancestral bacteriophages, their regulation and control, and their elusive evolutionary function.

The influence of coiled-coil motif of serine recombinase toward the directionality regulation

Serine integrases promote the recombination of two complementary DNA sequences, attP and attB, to create hybrid sequences, attL and attR. The reaction is unidirectional in the absence of an accessory protein called recombination directionality factor. We utilized tethered particle motion (TPM) experiments to investigate the reaction behaviors of two model serine integrases from Listeria innocua phage LI and Streptomyces coelicolor phage C31. Detailed kinetic analyses of wild-type and mutant proteins were carried out to verify the mechanisms of recombination directionality. In particular, we assessed the influence of a coiled-coil motif (CC) that is conserved in the C-terminal domain of serine integrases and is an important prerequisite for efficient recombination. Compared to wild type, we found that CC deletions in both serine integrases reduced the overall abundance of integrase (Int) att-site complexes and favored the formation of nonproductive complexes over recombination-competent complexes. Furthermore, the rate at which CC mutants formed productive synaptic complexes and disassembled aberrant nonproductive complexes was significantly reduced. It is notable that while the φC31 Int CC is essential for recombination, the LI Int CC plays an auxiliary role for recombination to stabilize protein-protein interactions and to control the directionality of the reaction.