Cyclo-diphenylalanine production in Aspergillus nidulans through stepwise metabolic engineering.

Cyclo-diphenylalanine (cFF) is a symmetrical aromatic diketopiperazine (DKP) found wide-spread in microbes, plants, and resulting food products. As different bioactivities continue being discovered and relevant food and pharmaceutical applications gradually emerge for cFF, there is a growing need for establishing convenient and efficient methods to access this type of compound. Here, we present a robust cFF production system which entailed stepwise engineering of the filamentous fungal strain Aspergillus nidulans A1145 as a heterologous expression host. We first established a preliminary cFF producing strain by introducing the heterologous nonribosomal peptide synthetase (NRPS) gene penP1 to A. nidulans A1145. Key metabolic pathways involving shikimate and aromatic amino acid biosynthetic support were then engineered through a combination of gene deletions of competitive pathway steps, over-expressing feedback-insensitive enzymes in phenylalanine biosynthesis, and introducing a phosphoketolase-based pathway, which diverted glycolytic flux toward the formation of erythrose 4-phosphate (E4P). Through the stepwise engineering of A. nidulans A1145 outlined above, involving both heterologous pathway addition and native pathway metabolic engineering, we were able to produce cFF with titers reaching 611 mg/L in shake flask culture and 2.5 g/L in bench-scale fed-batch bioreactor culture. Our study establishes a production platform for cFF biosynthesis and successfully demonstrates engineering of phenylalanine derived diketopiperazines in a filamentous fungal host.

Harnessing synthetic biology for advancing RNA therapeutics and vaccine design.

Recent global events have drawn into focus the diversity of options for combatting disease across a spectrum of prophylactic and therapeutic approaches. The recent success of the mRNA-based COVID-19 vaccines has paved the way for RNA-based treatments to revolutionize the pharmaceutical industry. However, historical treatment options are continuously updated and reimagined in the context of novel technical developments, such as those facilitated through the application of synthetic biology. When it comes to the development of genetic forms of therapies and vaccines, synthetic biology offers diverse tools and approaches to influence the content, dosage, and breadth of treatment with the prospect of economic advantage provided in time and cost benefits. This can be achieved by utilizing the broad tools within this discipline to enhance the functionality and efficacy of pharmaceutical agent sequences. This review will describe how synthetic biology principles can augment RNA-based treatments through optimizing not only the vaccine antigen, therapeutic construct, therapeutic activity, and delivery vector. The enhancement of RNA vaccine technology through implementing synthetic biology has the potential to shape the next generation of vaccines and therapeutics.

Microbial Dimerization and Chlorination of Isoflavones by a Takla Makan Desert-Derived Streptomyces sp. HDN154127.

Sixteen new biisoflavones, bisoflavolins A-N (1-16), were discovered from cultures of the Takla Makan desert-derived strain Streptomyces sp. HDN154127. The chemical structures, including axial chirality, were elucidated by NMR, MS, and ECD analyses. Antibacterial activity of dimerized compounds was tested against seven different bacteria. The dimerized compounds showed better activity (MIC from 0.8 to 50.0 µM) than the corresponding monomers (daidzein and genistein, MIC > 50.0 µM). The rare dimeric and chlorinated structures in 1-16 were proved to be biotransformation products obtained from soy isoflavones and sodium chloride, which constituted the culture medium. This is the first report of an actinomycete that promotes both dimerization and chlorination utilizing natural isoflavones as skeletons sources.

Intranasal Vaccine Delivery Technology for Respiratory Tract Disease Application with a Special Emphasis on Pneumococcal Disease.

This mini-review will cover recent trends in intranasal (IN) vaccine delivery as it relates to applications for respiratory tract diseases. The logic and rationale for IN vaccine delivery will be compared to methods and applications accompanying this particular administration route. In addition, we will focus extended discussion on the potential role of IN vaccination in the context of respiratory tract diseases, with a special emphasis on pneumococcal disease. Here, elements of this disease, including its prevalence and impact upon the elderly population, will be viewed from the standpoint of improving health outcomes through vaccine design and delivery technology and how IN administration can play a role in such efforts.

Influenza Virus Infects and Depletes Activated Adaptive Immune Responders.

Influenza infections cause several million cases of severe respiratory illness, hospitalizations, and hundreds of thousands of deaths globally. Secondary infections are a leading cause of influenza's high morbidity and mortality, and significantly factored into the severity of the 1918, 1968, and 2009 pandemics. Furthermore, there is an increased incidence of other respiratory infections even in vaccinated individuals during influenza season. Putative mechanisms responsible for vaccine failures against influenza as well as other respiratory infections during influenza season are investigated. Peripheral blood mononuclear cells (PBMCs) are used from influenza vaccinated individuals to assess antigen-specific responses to influenza, measles, and varicella. The observations made in humans to a mouse model to unravel the mechanism is confirmed and extended. Infection with influenza virus suppresses an ongoing adaptive response to vaccination against influenza as well as other respiratory pathogens, i.e., Adenovirus and Streptococcus pneumoniae by preferentially infecting and killing activated lymphocytes which express elevated levels of sialic acid receptors. These findings propose a new mechanism for the high incidence of secondary respiratory infections due to bacteria and other viruses as well as vaccine failures to influenza and other respiratory pathogens even in immune individuals due to influenza viral infections.

Antibacterial p-Terphenyl with a Rare 2,2'-Bithiazole Substructure and Related Compounds Isolated from the Marine-Derived Actinomycete Nocardiopsis sp. HDN154086.

Assisted by MS/MS-based molecular networking and X-ray diffraction analysis, five new p-terphenyl derivatives, namely, nocarterphenyls D-H (1-5), were obtained and characterized from the cultures of the marine sediment-derived actinomycete Nocardiopsis sp. HDN154086. The skeleton of nocarterphenyl D (1) was defined to possess a rare 2,2'-bithiazole scaffold, naturally occurring for the first time, and nocarterphenyls E-H (2-5) are p-terphenylquinones with unusual thioether linked fatty acid methyl ester substitutions. Compound 1 showed promising activity against multiple bacteria with MIC values ranging from 1.5 to 6.2 µM, and 2 exhibited notable antibacterial activity against MRSA which surpassed the positive control ciprofloxacin.

Siderophore natural products as pharmaceutical agents.

Siderophore natural products are characterized by an ability to tightly chelate metals. The origins of such compounds are often pathogenic microbes utilizing siderophores as virulence factors during host infection. The mechanism for siderophore formation typically involves the activity of nonribosomal peptide synthetases producing compounds across functional group classifications that include catecholate, phenolate, hydroxamate, and mixed categories. Though siderophore production has been a hallmark of pathogenicity, the evolutionarily-optimized binding abilities of siderophores suggest the possibility of re-directing the compounds towards alternative beneficial applications. In this mini-review, we will first describe siderophore formation origins before discussing alternative applications as pharmaceutical products. In so doing, we will cover examples and applications that include reducing metal overload, targeted antibiotic delivery, cancer treatment, vaccine development, and diagnostics. Included in this analysis will be a discussion on the native production hosts of siderophores and prospects for improvement in compound access through the adoption of heterologous biosynthesis.

Complex natural product production methods and options.

Natural products have had a major impact upon quality of life, with antibiotics as a classic example of having a transformative impact upon human health. In this contribution, we will highlight both historic and emerging methods of natural product bio-manufacturing. Traditional methods of natural product production relied upon native cellular host systems. In this context, pragmatic and effective methodologies were established to enable widespread access to natural products. In reviewing such strategies, we will also highlight the development of heterologous natural product biosynthesis, which relies instead on a surrogate host system theoretically capable of advanced production potential. In comparing native and heterologous systems, we will comment on the base organisms used for natural product biosynthesis and how the properties of such cellular hosts dictate scaled engineering practices to facilitate compound distribution. In concluding the article, we will examine novel efforts in production practices that entirely eliminate the constraints of cellular production hosts. That is, cell free production efforts will be introduced and reviewed for the purpose of complex natural product biosynthesis. Included in this final analysis will be research efforts made on our part to test the cell free biosynthesis of the complex polyketide antibiotic natural product erythromycin.

Improving E. coli Bactofection by Expression of Bacteriophage ΦX174 Gene E.

Bactofection, a bacterial-mediated form of genetic transfer, is highlighted as an alternative mechanism for gene therapy. A key advantage of this system for immune-reactivity purposes stems from the nature of the bacterial host capable of initiating an immune response by attracting recognition and cellular uptake by antigen-presenting cells (APCs). The approach is also a suitable technique to deliver larger genetic constructs more efficiently as it can transfer plasmids of varying sizes into target mammalian cells. Given these advantages, bacterial vectors are being studied as potential carriers for the delivery of plasmid DNA into target cells to enable expression of heterologous proteins. The bacteria used for bactofection are generally nonpathogenic; however, concerns arise due to the use of a biological agent. To overcome such concerns, enhanced bacterial degradation has been engineered as an attenuation and safety feature for bactofection vectors. In particular, the ΦX174 lysis E (LyE) gene can be repurposed to both minimize bacterial survival within mammalian hosts while also improving overall gene delivery. More specifically, an engineered bacterial vector carrying the LyE gene showed improved gene delivery and safety profiles when tested with murine RAW264.7 macrophage APCs. This chapter outlines steps taken to engineer E. coli for LyE expression as a safer and more effective genetic antigen delivery bactofection vehicle in the context of vaccine utility.

Vaccine Delivery and Immune Response Basics.

In this opening chapter, we outline the basics of vaccine delivery and subsequent immune reactivity. Vaccine delivery is an augmentation to immunization more generally in that a delivery reagent is harnessed to improve administration of the key ingredient (i.e., the antigen) needed to provoke an immune response. In this chapter, we discuss the evolution of vaccine design and how such efforts evolved into targeted administration/delivery of key antigens. We then provide overview descriptions of vaccine immune responses and methods for assessment. More generally, the chapter sets the tone for the remainder of this book, which will focus upon each step of the vaccine process with a special emphasis on how vaccine delivery contributes to overall health outcomes.

A Hybrid Biological-Biomaterial Vector for Antigen Delivery.

A hybrid biological-biomaterial vector composed of a biocompatible polymeric biomaterial coating and an Escherichia coli core was designed and developed for antigen delivery. It provides a unique and efficient mechanism to transport antigens (protein or genetic) via different mechanisms of vector design that include antigen cellular localization (cytoplasm, periplasm, cellular surface) and nonnative functionalities that assist in antigen delivery. Based on a variety of E. coli strain development and polymer chemistry tools, the hybrid vector can be constructed into a number of formats for the purpose of optimized uptake and processing by antigen presenting cells, serving as the basis for a potent subsequent immune response. This chapter serves to outline a protocol for assembling a hybrid biological-biomaterial vector for use as a vaccine delivery system.

Liposomal Dual Delivery of Both Polysaccharide and Protein Antigens.

Pneumococcal disease is caused by Streptococcus pneumoniae, a colonizing microorganism characterized by transitioning from a benign commensal to a virulent pathogen in the presence of suitable circumstances, which then poses a serious infectious disease threat afflicting millions of people. Especially affected are the young and elderly through outcomes that include pneumonia, bacteremia, meningitis, and otitis media. Current prevention vaccine options on the market contain capsular polysaccharides conjugated to the Diphtheria CRM197 protein (Pfizer) or are composed of only pneumococcal polysaccharides (Merck), and in both cases, limitations prevent the generation of comprehensive disease protection. Through the use of a liposomal carrier, we present an alternative methodology for producing a vaccine product via noncovalent colocalization of both polysaccharide and protein classes of complementary pneumococcal disease immunogens.

Liposomal Encapsulation of Polysaccharides (LEPS) as an Effective Vaccine Strategy to Protect Aged Hosts Against S. pneumoniae Infection.

Despite the availability of licensed vaccines, pneumococcal disease caused by the bacteria Streptococcus pneumoniae (pneumococcus), remains a serious infectious disease threat globally. Disease manifestations include pneumonia, bacteremia, and meningitis, resulting in over a million deaths annually. Pneumococcal disease disproportionally impacts older adults aged ≥65 years. Interventions are complicated through a combination of complex disease progression and 100 different bacterial capsular polysaccharide serotypes. This has made it challenging to develop a broad vaccine against S. pneumoniae, with current options utilizing capsular polysaccharides as the primary antigenic content. However, current vaccines are substantially less effective in protecting the elderly. We previously developed a Liposomal Encapsulation of Polysaccharides (LEPS) vaccine platform, designed around limitations of current pneumococcal vaccines, that allowed the noncovalent coupling of polysaccharide and protein antigen content and protected young hosts against pneumococcal infection in murine models. In this study, we modified the formulation to make it more economical and tested the novel LEPS vaccine in aged hosts. We found that in young mice (2-3 months), LEPS elicited comparable responses to the pneumococcal conjugate vaccine Prevnar-13. Further, LEPS immunization of old mice (18-22 months) induced comparable antibody levels and improved antibody function compared to Prevnar-13. Importantly, LEPS protected old mice against both invasive and lung localized pneumococcal infections. In summary, LEPS is an alternative and effective vaccine strategy that protects aged hosts against different manifestations of pneumococcal disease.

Consolidated plasmid Design for Stabilized Heterologous Production of the complex natural product Siderophore Yersiniabactin.

Yersiniabactin (Ybt) is a hybrid polyketide-nonribosomal complex natural product also known as a siderophore for its iron chelation properties. The native producer of Ybt, Yersinia pestis, is a priority pathogen responsible for the plague in which the siderophore properties of Ybt are used to sequester iron and other metal species upon host infection. Alternatively, the high metal binding properties of Ybt enable a plethora of potentially valuable applications benefiting from metal remediation and/or recovery. For these applications, a surrogate production source is highly preferred relative to the pathogenic native host. In this work, we present a modification to the heterologous Escherichia coli production system established for Ybt biosynthesis. In particular, the multiple plasmids originally used to express the genetic pathway required for Ybt biosynthesis were consolidated to a single, copy-amplifiable plasmid. In so doing, plasmid stability was improved from ~30% to ≥80% while production values maintained at 20-30% of the original system, which resulted in titers of 0.5-3 mg/L from shake flask vessels.

Grafting Activated Graphene Oxide Nanosheets onto Ultrafiltration Membranes Using Polydopamine to Enhance Antifouling Properties.

Graphene oxide (GO) nanosheets are negatively charged and exhibit excellent antifouling properties. However, their hydrophilicity makes it challenging for their grafting onto membrane surfaces to improve antifouling properties for long-term underwater operation. Herein, we demonstrate a versatile approach to covalently graft GO onto ultrafiltration membrane surfaces in aqueous solutions at ≈22 °C. The membrane surface is first primed using dopamine and then reacted with activated GO (aGO) containing amine-reactive esters. The aGO grafting improves the membrane surface hydrophilicity without decreasing water permeance. When the membranes are challenged with 1.0 g/L sodium alginate in a constant-flux crossflow system, the aGO grafting increases the critical flux by 20% and reduces the fouling rate by 63% compared with the pristine membrane. The modified membranes demonstrate stability for 48 h operation and interval cleanings using NaOH solutions.

Monacycliones G-K and ent-Gephyromycin A, Angucycline Derivatives from the Marine-Derived Streptomyces sp. HDN15129.

Six new angucycline derivatives, named monacycliones G-K (1-5) and ent-gephyromycin A (6), as well as three known ones (7-9) were discovered from the marine sediment-derived actinomycete Streptomyces sp. HDN15129 guided by Global Natural Products Social (GNPS) molecular networking. Structures including absolute configurations were elucidated by extensive NMR, MS, and ECD analyses. Among them, monacyclione G (1) possesses a unique scaffold featuring a xanthone core linked to the aminodeoxysugar ossamine, and monacycliones H-J (2-4) are rare examples of natural angucyclines with an S-methyl group. Monacycliones I and J (3 and 4) showed cytotoxic activity against multiple human cancer cell lines, with IC50 values ranging from 3.5 to 10 µM.

Heterologous biosynthesis as a platform for producing new generation natural products.

Natural products have demonstrated value across numerous application areas, with antibiotics a notable historical example. Native cellular hosts provide an initial option in efforts to harness natural product production. However, various complexities associated with native hosts, including fastidious growth traits and limited molecular biology tools, have prompted an alternative approach termed heterologous biosynthesis that relies upon a surrogate biological system to reconstitute the biosynthetic sequence stemming from transplanted genetic blueprint. In turn, heterologous biosynthesis offers the benefit of enzymatically driven complex natural product formation combined with the prospect of improved compound access via scalable cellular production. In this review, we conduct a literature meta-analysis of heterologous natural product biosynthesis over the period of 2011-2020 with the goal of identifying trends in heterologous natural product host selection, target natural products, and compound-host selection tendencies, with associated commentary on the research directions of heterologous biosynthesis based upon this analysis.

Extended Polysaccharide Analysis within the Liposomal Encapsulation of Polysaccharides System.

The Liposomal Encapsulation of Polysaccharides (LEPS) dual antigen vaccine carrier system was assessed across two distinct polysaccharides for encapsulation efficiency, subsequent liposomal surface adornment with protein, adjuvant addition, and size and charge metrics. The polysaccharides derive from two different serotypes of Streptococcus pneumoniae and have traditionally served as the active ingredients of vaccines against pneumococcal disease. The LEPS system was designed to mimic glycoconjugate vaccines that covalently couple polysaccharides to protein carriers; however, the LEPS system uses a noncovalent co-localization mechanism through protein liposomal surface attachment. In an effort to more thoroughly characterize the LEPS system across individual vaccine components and thus support broader future utility, polysaccharides from S. pneumoniae serotypes 3 and 4 were systematically compared within the LEPS framework both pre- and post-surface protein attachment. For both polysaccharides, ≥85% encapsulation efficiency was achieved prior to protein surface attachment. Upon protein attachment with either a model protein (GFP) or a pneumococcal disease antigen (PncO), polysaccharide encapsulation was maintained at ≥61% encapsulation efficiency. Final LEPS carriers were also evaluated with and without alum as an included adjuvant, with encapsulation efficiency maintained at ≥30%, while protein surface attachment efficiency was maintained at ≥~50%. Finally, similar trends and distributions were observed across the different polysaccharides when assessed for liposomal zeta potential and size.