Tailoring the Host Range of Ackermannviridae Bacteriophages through Chimeric Tailspike Proteins.

Host range is a major determinant in the industrial utility of a bacteriophage. A model host range permits broad recognition across serovars of a target bacterium while avoiding cross-reactivity with commensal microbiota. Searching for a naturally occurring bacteriophage with ideal host ranges is challenging, time-consuming, and restrictive. To address this, SPTD1.NL, a previously published luciferase reporter bacteriophage for Salmonella, was used to investigate manipulation of host range through receptor-binding protein engineering. Similar to related members of the Ackermannviridae bacteriophage family, SPTD1.NL possessed a receptor-binding protein gene cluster encoding four tailspike proteins, TSP1-4. Investigation of the native gene cluster through chimeric proteins identified TSP3 as the tailspike protein responsible for Salmonella detection. Further analysis of chimeric phages revealed that TSP2 contributed off-target Citrobacter recognition, whereas TSP1 and TSP4 were not essential for activity against any known host. To improve the host range of SPTD1.NL, TSP1 and TSP2 were sequentially replaced with chimeric receptor-binding proteins targeting Salmonella. This engineered construct, called RBP-SPTD1-3, was a superior diagnostic reporter, sensitively detecting additional Salmonella serovars while also demonstrating improved specificity. For industrial applications, bacteriophages of the Ackermannviridae family are thus uniquely versatile and may be engineered with multiple chimeric receptor-binding proteins to achieve a custom-tailored host range.

Development of a Replication-Deficient Bacteriophage Reporter Lacking an Essential Baseplate Wedge Subunit.

Engineered bacteriophages (phages) can be effective diagnostic reporters for detecting a variety of bacterial pathogens. Although a promising biotechnology, the large-scale use of these reporters may result in the unintentional release of genetically modified viruses. In order to limit the potential environmental impact, the ability of these phages to propagate outside the laboratory was targeted. The phage SEA1 has been previously engineered to facilitate food safety as an accurate and sensitive reporter for Salmonella contamination. In this study, homologous recombination was used to replace the expression of an essential baseplate wedge subunit (gp141) in SEA1 with a luciferase, NanoLuc®. This reporter, referred to as SEA1Δgp141.NL, demonstrated a loss of plaque formation and a failure to increase in titer following infection of Salmonella. SEA1Δgp141.NL was thus incapable of producing infectious progeny in the absence of gp141. In contrast, production of high titer stocks was possible when gp141 was artificially supplied in trans during infection. As a reporter, SEA1Δgp141.NL facilitated rapid, sensitive, and robust detection of Salmonella despite an inability to replicate. These results suggest that replication-deficient reporter phages are an effective method to obtain improved containment without sacrificing significant performance or the ease of production associated with many phage-based diagnostic methods.

Validation of PhageDx™ Cronobacter Assay for the Identification of Cronobacter Spp. in Powdered Infant Formula: AOAC Performance Tested MethodSM 051803.

BACKGROUND: The PhageDx™Cronobacter Assay is based on the infection of Cronobacter spp. by specific bacteriophages and expression of a luciferase reporter gene. Results are generated in as little as 18.5 h for powdered infant formula (PIF). OBJECTIVE: An AOAC Performance Tested MethodsSM (PTM) study was conducted to validate the PhageDx Cronobacter Assay for the detection of Cronobacter in 10, 100, and 300 g milk- and soy-based PIF test portions. METHOD: The performance of the PhageDx method was compared to the ISO 22964:2006/2017 Microbiology of the Food Chain-Horizontal Method for the Detection of Cronobacter spp. and the U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) Chapter 29 Cronobacter: 2012. Inclusivity/exclusivity, product consistency and stability, and robustness testing also were conducted. RESULTS: There was no significant difference between the 10, 100, or 300 g test portions for the milk and soy PIF matrixes between the PhageDx Cronobacter Assay, the ISO 22964:2006/2017, and the FDA BAM Chapter 29 Cronobacter: 2012 methods. The reporter bacteriophages were specific for Cronobacter and infected 75 strains in inclusivity testing. They did not infect 35 non-Cronobacter bacteria in exclusivity testing. Robustness testing showed that the method performed well with specific deviations from the standard protocol. Consistency and stability testing demonstrated that the recombinant phage gave consistent results across three production lots and was stable when stored under appropriate conditions for at least 3 months. CONCLUSIONS: Work in the submitting and independent laboratories demonstrated that the PhageDx Cronobacter Assay meets the qualifications for PTM status. HIGHLIGHTS: The PhageDx Cronobacter Assay is a rapid, simple, and specific test that has shown equivalence to both the FDA BAM and ISO reference methods for detecting Cronobacter spp. in PIF.

Validation of PhageDx™Salmonella Assay in Raw Ground Turkey and Powdered Infant Formula: AOAC Performance Tested MethodSM 121904.

BACKGROUND: The PhageDx™Salmonella Assay is based on the infection of Salmonella spp. by specific bacteriophages and expression of a luciferase reporter gene. Results are generated in as little as 9.5 h for raw ground turkey and 18.5 h for milk-based powdered infant formula (PIF). OBJECTIVE: An AOAC Performance Tested MethodsSM (PTM) study was conducted to validate the PhageDx Salmonella Assay for the detection of Salmonella in 25 g raw ground turkey and 100 g PIF test portions. METHOD: The performance of the PhageDx Salmonella Assay was compared to that of the U.S. Department of Agriculture (USDA), Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook (MLG) 4.10 for raw ground turkey and the U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) Chapter 5 for PIF. Inclusivity/exclusivity, product consistency and stability, and robustness testing were conducted. RESULTS: There was no significant difference between the 25 g raw ground turkey and 100 g PIF PhageDx Salmonella Assay and the USDA/FSIS MLG 4.10 and FDA/BAM Chapter 5, respectively. The reporter bacteriophages were specific for Salmonella and infected 108 strains in inclusivity testing. They did not infect 30 non-Salmonella bacteria in exclusivity testing. Robustness testing showed that the method performed well with specific deviations from the standard protocol. Consistency and stability testing demonstrated that the recombinant phage gave consistent results across three production lots and was stable when stored under appropriate conditions for at least eight months. CONCLUSIONS: The data collected in the validation study demonstrate that the PhageDx Salmonella Assay meets the qualifications for PTM status. HIGHLIGHTS: The PhageDx Salmonella Assay is a rapid, specific, sensitive assay capable of detecting a wide range of Salmonella spp. with a significantly shorter turn around time than the USDA/FSIS and FDA reference methods.

Validation of the PhageDx™ Listeria Assay for Detection of Listeria Spp. on Stainless Steel and Ceramic Environmental Surfaces AOAC Performance Tested MethodSM 102005.

BACKGROUND: The PhageDx™ Listeria Assay is a simple, specific, and sensitive assay based on the infection of Listeria spp. by selected bacteriophages and the resultant expression of a luciferase reporter gene. Results are generated in as little as 24.5 h for stainless steel and ceramic environmental surfaces. OBJECTIVE: An AOAC Performance Tested MethodsSM (PTM) study was conducted to validate the PhageDx Listeria Assay for the detection of Listeria on stainless steel and ceramic surfaces. METHOD: The performance of the PhageDx method was compared to that of the U.S. Food and Drug Administration (FDA) Bacterial Analytical Manual (BAM) Ch. 10. Inclusivity/exclusivity, product consistency and stability, and robustness testing also were conducted. RESULTS: Inclusivity testing demonstrated that the reporter bacteriophages were specific for Listeria ssp. and detected 58/61 Listeria strains tested, including all 34 L. monocytogenes strains. The reporter bacteriophage also was shown to not detect 46/47 non-Listeria bacteria in exclusivity testing. Robustness testing showed that the method performed well with specific deviations from the standard protocol. Consistency and stability testing demonstrated that the recombinant phage gave consistent results across three production lots and was stable when stored under appropriate conditions for at least 6 months. Matrix studies on stainless steel and ceramic surfaces showed that there was no significant difference between the PhageDx Listeria Assay and the FDA/BAM Chapter 10 reference method. CONCLUSIONS AND HIGHLIGHTS: The validation study demonstrates that the PhageDx Listeria Assay is an effective method for the detection of Listeria spp. on stainless steel and ceramic environmental surfaces and meets the qualifications for AOAC PTM status.

Isolation and engineering of a Listeria grayi bacteriophage.

The lack of bacteriophages capable of infecting the Listeria species, Listeria grayi, is academically intriguing and presents an obstacle to the development of bacteriophage-based technologies for Listeria. We describe the isolation and engineering of a novel L. grayi bacteriophage, LPJP1, isolated from farm silage. With a genome over 200,000 base pairs, LPJP1 is the first and only reported jumbo bacteriophage infecting the Listeria genus. Similar to other Gram-positive jumbo phages, LPJP1 appeared to contain modified base pairs, which complicated initial attempts to obtain genomic sequence using standard methods. Following successful sequencing with a modified approach, a recombinant of LPJP1 encoding the NanoLuc luciferase was engineered using homologous recombination. This luciferase reporter bacteriophage successfully detected 100 stationary phase colony forming units of both subspecies of L. grayi in four hours. A single log phase colony forming unit was also sufficient for positive detection in the same time period. The recombinant demonstrated complete specificity for this particular Listeria species and did not infect 150 non-L. grayi Listeria strains nor any other bacterial genus. LPJP1 is believed to be the first reported lytic bacteriophage of L. grayi as well as the only jumbo bacteriophage to be successfully engineered into a luciferase reporter.

Suppressive roles of calreticulin in prostate cancer growth and metastasis.

Calreticulin is an essential, multifunctional Ca(2+)-binding protein that participates in the regulation of intracellular Ca(2+) homeostasis, cell adhesion, and chaperoning. Calreticulin is abundantly expressed and regulated by androgens in prostate epithelial cells. Given the importance of both calreticulin in multiple essential cellular activities and androgens in prostate cancer, we investigated the possibility of a role for calreticulin in prostate cancer progression. Immunohistochemistry revealed the down-regulation of calreticulin in a subset of human prostate cancer specimens. Prostate cancer cells overexpressing exogenous calreticulin produced fewer colonies in both monolayer culture and soft agar. Furthermore, calreticulin overexpression also inhibited tumor growth in the orthotopic PC3 xenograft tumor model and macroscopic lung metastasis in the rat Dunning AT3.1 prostate tumor model. To address the potential mechanism of calreticulin suppression of prostate cancer, we generated calreticulin mutants with different functional domains deleted. The calreticulin mutants containing the P-domain, which binds to other endoplasmic reticulum chaperone proteins, were sufficient for the suppression of PC3 growth in colony formation assays. Overall, our data support the hypothesis that calreticulin inhibits growth and/or metastasis of prostate cancer cells and that this suppression requires the P-domain.

Accurate and sensitive detection of Salmonella in foods by engineered bacteriophages.

Salmonella is a major causative agent of foodborne illness and rapid identification of this pathogen is essential to prevent disease. Currently most assays require high bacterial burdens or prolonged enrichment to achieve acceptable performance. A reduction in testing time without loss of sensitivity is critical to allow food processors to safely decrease product holding time. To meet this need, a method was developed to detect Salmonella using luciferase reporter bacteriophages. Bacteriophages were engineered to express NanoLuc, a novel optimized luciferase originating from the deep-sea shrimp Oplophorus gracilirostris. NanoLuc-expressing bacteriophages had a limit of detection of 10-100 CFU per mL in culture without enrichment. Luciferase reporters demonstrated a broad host range covering all Salmonella species with one reporter detecting 99.3% of 269 inclusivity strains. Cross-reactivity was limited and only observed with other members of the Enterobacteriaceae family. In food matrix studies, a cocktail of engineered bacteriophages accurately detected 1 CFU in either 25 g of ground turkey with a 7 h enrichment or 100 g of powdered infant formula with a 16 h enrichment. Use of the NanoLuc reporter assay described herein resulted in a considerable reduction in enrichment time without a loss of sensitivity.

Cytoplasmic localization of the androgen receptor is independent of calreticulin.

Identification and characterization of factors regulating intracellular localization of the androgen receptor (AR) are fundamentally important because nucleocytoplasmic trafficking of AR is a critical step in AR regulation by androgen manipulation. Normally, AR is localized to the cytoplasm in the absence of androgen. Upon ligand binding, AR translocates to the nucleus, where it can modulate transcription of AR-responsive genes. The withdrawal of androgen results in the export of unliganded AR from the nucleus to the cytoplasm, where it is transcriptionally inactive. Calreticulin has been implicated as a possible nuclear export factor for AR because the two proteins form a complex. In this study, we assessed whether the cytoplasmic localization of AR requires binding to calreticulin. To test this we substituted the calreticulin binding sequence (CBS) KVFFKR (residues 579-584) with the amino acids RLAARK in AR and monitored the cellular localization of a GFP-AR fusion protein in the absence of androgen. We also determined if knockdown or knockout of calreticulin expression affected the cytoplasmic localization of the AR. We found that a mutated CBS did not affect the localization of AR and that in the absence of androgen, AR is localized to the cytoplasm regardless of its ability to interact with calreticulin. Also, a reduction in the levels or loss of calreticulin did not affect the localization of AR. These data argue that calreticulin is not required for the cytoplasmic localization of AR.

Requirement of PDZ-containing proteins for cell cycle regulation and differentiation in the mouse lens epithelium.

The roles of PDZ domain-containing proteins such as Dlg and Scrib have been well described for Drosophila; however, their requirement for mammalian development is poorly understood. Here we show that Dlg, Scrib, MAGI1, MAGI3, and MPDZ are expressed in the mouse ocular lens. We demonstrate that the increase in proliferation and defects in cellular adhesion and differentiation observed in epithelia of lenses that express E6, a viral oncoprotein that can bind to several PDZ proteins, including the human homologs of Dlg and Scrib, is dependent on E6's ability to bind these proteins via their PDZ domains. Analyses of lenses from mice carrying an insertional mutation in Dlg (dlg(gt)) show increased proliferation and proliferation in spatially inappropriate regions of the lens, a phenotype similar to that of lenses expressing E6. The results from this study indicate that multiple PDZ domain-containing proteins, including Dlg and Scrib, may be required for maintaining the normal pattern of growth and differentiation in the lens. Furthermore, the phenotypic similarities among the Drosophila dlg mutant, the lenses of dlg(gt) mice, and the lenses of E6 transgenic mice suggest that Dlg may have a conserved function in regulating epithelial cell growth and differentiation across species.

Development and Implementation of a High-Throughput High-Content Screening Assay to Identify Inhibitors of Androgen Receptor Nuclear Localization in Castration-Resistant Prostate Cancer Cells.

Patients with castration-resistant prostate cancer (CRPC) can be treated with abiraterone, a potent inhibitor of androgen synthesis, or enzalutamide, a second-generation androgen receptor (AR) antagonist, both targeting AR signaling. However, most patients relapse after several months of therapy and a majority of patients with relapsed CRPC tumors express the AR target gene prostate-specific antigen (PSA), suggesting that AR signaling is reactivated and can be targeted again to inhibit the relapsed tumors. Novel small molecules capable of inhibiting AR function may lead to urgently needed therapies for patients resistant to abiraterone, enzalutamide, and/or other previously approved antiandrogen therapies. Here, we describe a high-throughput high-content screening (HCS) campaign to identify small-molecule inhibitors of AR nuclear localization in the C4-2 CRPC cell line stably transfected with GFP-AR-GFP (2GFP-AR). The implementation of this HCS assay to screen a National Institutes of Health library of 219,055 compounds led to the discovery of 3 small molecules capable of inhibiting AR nuclear localization and function in C4-2 cells, demonstrating the feasibility of using this cell-based phenotypic assay to identify small molecules targeting the subcellular localization of AR. Furthermore, the three hit compounds provide opportunities to develop novel AR drugs with potential for therapeutic intervention in CRPC patients who have relapsed after treatment with antiandrogens, such as abiraterone and/or enzalutamide.

Deregulated cell cycle control in lens epithelial cells by expression of inhibitors of tumor suppressor function.

Previous studies have shown that cell cycle proteins such as retinoblastoma protein (pRB) are essential for cell cycle withdrawal in differentiating lens cells. However, little is known about which factors are critical for cell cycle control in the lens epithelial cells. Here we use the K14 promoter to direct expression of E6 and E7, oncogenes from human papillomavirus type 16, which are known to bind and inactivate p53 and pRB, as molecular tools to study cell cycle regulation in the lens epithelium of transgenic mice. Expression of either gene resulted in increased proliferation and apoptosis, and in the case of E6, a unique epithelial phenotype characterized by multilayering and intercellular vacuoles was observed. Lenses from mice expressing E7 mutants, which are defective in inactivating pRB proteins, were normal and the lens phenotype in the E6 mice was p53-independent. Thus, cell proliferation in the lens epithelium is controlled by multiple factors including, but not necessarily limited to, the pRB family.

Localization of PDZ domain containing proteins Discs Large-1 and Scribble in the mouse eye.

PURPOSE: In invertebrates such as Drosophila melanogaster and Caenorhabditis elegans, the PDZ domain containing proteins, Discs large (Dlg) and Scribble (Scrib), are found localized to specific junctional complexes and have been shown to be required for establishing and maintaining epithelial cell adhesion, polarity, and proliferation during development. In addition, they are known to be critical for neural development. However, the mechanisms and pathways through which they act in mammalian systems, especially in vivo, are poorly understood. The purpose of this study was to characterize the distribution of Dlg-1 and Scrib in various structures of the mouse eye and the regions where these proteins overlap with known adhesion proteins. METHODS: Embryos or mouse eyes were embedded, sectioned, subjected to immunofluorescence with antibodies to Dlg-1, Scrib, and E-cadherin, N-cadherin, or ZO-1, and stained sections viewed under confocal microscopy. RESULTS: Dlg-1 and Scrib were found widely distributed throughout the eye. In the lens, overlap was observed with E- and N-cadherin and ZO-1 in regions where adherens junctions are found, as well as in the complexes that attach lens cells to the underlying capsule. Overlap of Dlg-1 and Scrib with E-cadherin and ZO-1 was observed in the portions of the cornea and in the retinal pigment epithelium. However, in the neural retina, there appeared to be little, if any, overlap of Dlg-1 or Scrib with adhesion proteins, consistent with a role in synapse biology in the neural retina rather than adhesion. CONCLUSIONS: The observed localization of Dlg-1 and Scrib with cadherins suggests that these proteins may play roles in cell adhesion, polarity and proliferation, as they do in invertebrates, suggesting cross-species conservation of function for these PDZ proteins. However, the broader distribution of these PDZ proteins within the eye suggests they may play more diverse roles in cell adhesion and differentiation.

Splicing Factor Prp8 Interacts With NES(AR) and Regulates Androgen Receptor in Prostate Cancer Cells.

Androgen receptor (AR) plays a pivotal role in the development of primary as well as advanced castration-resistant prostate cancer. Previous work in our lab identified a novel nuclear export signal (NES) (NES(AR)) in AR ligand-binding domain essential for AR nucleocytoplasmic trafficking. By characterizing the localization of green fluorescence protein (GFP)-tagged NES(AR), we designed and executed a yeast mutagenesis screen and isolated 7 yeast mutants that failed to display the NES(AR) export function. One of those mutants was identified as the splicing factor pre-mRNA processing factor 8 (Prp8). We further showed that Prp8 could regulate NES(AR) function using short hairpin RNA knockdown of Prp8 coupled with a rapamycin export assay in mammalian cells and knockdown of Prp8 could induce nuclear accumulation of GFP-tagged AR in PC3 cells. Prp8 expression was decreased in castration-resistant LuCaP35 xenograft tumors as compared with androgen-sensitive xenografts. Laser capture microdissection and quantitative PCR showed Prp8 mRNA levels were decreased in human prostate cancer specimens with high Gleason scores. In prostate cancer cells, coimmunoprecipitation and deletion mutagenesis revealed a physical interaction between Prp8 and AR mainly mediated by NES(AR). Luciferase assay with prostate specific antigen promoter-driven reporter demonstrated that Prp8 regulated AR transcription activity in prostate cancer cells. Interestingly, Prp8 knockdown also increased polyubiquitination of endogenous AR. This may be 1 possible mechanism by which it modulates AR activity. These results show that Prp8 is a novel AR cofactor that interacts with NES(AR) and regulates AR function in prostate cancer cells.

Characterization of karyopherins in androgen receptor intracellular trafficking in the yeast model.

BACKGROUND: Mechanisms regulating androgen receptor (AR) subcellular localization represent an essential component of AR signaling. Karyopherins are a family of nucleocytoplasmic trafficking factors. In this paper, we used the yeast model to study the effects of karyopherins on the subcellular localization of the AR. METHODS: Yeast mutants deficient in different nuclear transport factors were transformed with various AR based, GFP tagged constructs and their localization was monitored using microscopy. RESULTS: We showed that yeast can mediate androgen-induced AR nuclear localization and that in addition to the import factor, Importinα/ß, this process required the import karyopherin Sxm1. We also showed that a previously identified nuclear export sequence (NES(AR)) in the ligand binding domain of AR does not appear to rely on karyopherins for cytoplasmic localization. CONCLUSIONS: These results suggest that while AR nuclear import relies on karyopherin activity, AR nuclear export and/or cytoplasmic localization may require other undefined mechanisms.

Requirement for Dlgh-1 in planar cell polarity and skeletogenesis during vertebrate development.

The development of specialized organs is tightly linked to the regulation of cell growth, orientation, migration and adhesion during embryogenesis. In addition, the directed movements of cells and their orientation within the plane of a tissue, termed planar cell polarity (PCP), appear to be crucial for the proper formation of the body plan. In Drosophila embryogenesis, Discs large (dlg) plays a critical role in apical-basal cell polarity, cell adhesion and cell proliferation. Craniofacial defects in mice carrying an insertional mutation in Dlgh-1 suggest that Dlgh-1 is required for vertebrate development. To determine what roles Dlgh-1 plays in vertebrate development, we generated mice carrying a null mutation in Dlgh-1. We found that deletion of Dlgh-1 caused open eyelids, open neural tube, and misorientation of cochlear hair cell stereociliary bundles, indicative of defects in planar cell polarity (PCP). Deletion of Dlgh-1 also caused skeletal defects throughout the embryo. These findings identify novel roles for Dlgh-1 in vertebrates that differ from its well-characterized roles in invertebrates and suggest that the Dlgh-1 null mouse may be a useful animal model to study certain human congenital birth defects.

The PDZ ligand domain of the human papillomavirus type 16 E6 protein is required for E6's induction of epithelial hyperplasia in vivo.

Human papillomaviruses (HPVs) are the causative agent of warts. Infections with high-risk HPVs are associated with anogenital and head and neck cancers. One of the viral genes responsible for HPV's oncogenic activity is E6. Mice expressing the HPV-16 E6 protein in their epidermis (K14E6(WT)) develop epithelial hyperplasia and squamous carcinomas. Numerous cellular proteins interact with E6, some of which can be grouped based on common amino acid motifs in their E6-binding domains. One such group, the PDZ partners, including hDLG, hSCRIBBLE, MUPP1, and MAGI, bind to the carboxy-terminal four amino acids of E6 through their PDZ domains. E6's interaction with the PDZ partners leads to their degradation. Additionally, E6's binding to PDZ proteins has been correlated with its ability to transform baby rat kidney cells in tissue culture and to confer tumorigenicity onto cells in xenograft experiments. To address whether the ability of E6 to bind PDZ domain partners is necessary for E6 to confer epithelial hyperproliferation in vivo, we generated transgenic mice that express in stratified squamous epithelia a mutant of E6 lacking the last six amino acids at its carboxyl terminus, E6(Delta 146-151), from the human keratin 14 (K14) promoter. The K14E6(Delta 146-151) mice exhibit a radiation response similar to that of the K14E6(WT) mice, demonstrating that this protein, as predicted, retains an ability to inactivate p53. However, the K14E6(Delta 146-151) mice fail to display epithelial hyperplasia. These results indicate that an interaction of E6 with PDZ partners is necessary for its induction of epithelial hyperplasia.