Novel polyhydroxyalkanoate beads for use as a vaccine against tuberculosis : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Microbiology at Massey University, Manawatū, New Zealand

Tuberculosis was in 1993 declared as a re-emerging disease by the World Health Organization. The only vaccine currently available, BCG, an attenuated strain of Mycobacterium bovis, does not protect adults against the pulmonary disease, which is the form of transmission. New vaccine candidates are being developed to provide protection against tuberculosis. Subunit vaccines offer a safer alternative than whole cell preparations and provide the possibility of utilizing only the components that mediate protective immune responses. This thesis describes the production of bacterially derived polyhydroxyalkanoate (PHA) beads for use as a delivery system for Mycobacterium tuberculosis reverse vaccinology antigens and immune modulators. In the first study, the immunogenicity of beads derived from an endotoxin-free host, Clear coli, displaying M. tuberculosis antigens Rv1626, Rv2032 and Rv1789 was evaluated in mice. Beads displaying Rv1626 were selected for further studies based on the magnitude and specificity of the immune response elicited. In a final study, the immune modulators Cpe30, CS.T3378-395 and Flagellin were co-displayed with Rv1626 antigen on beads and the immunogenicity of these functionalised beads evaluated in mice. Vaccinations with Rv1626 beads and the immune modulators Cpe30 and CS. T3378-395 induced a Th1/Th17 skewed immune response. These beads were then assessed for their ability to protect mice against aerosol challenge with Mycobacterium bovis. Rv1626 beads reduced the bacterial loads in 0.48 log10 compared with the negative control group but the inclusion of immune modulators did not enhance the immunogenicity or protection induced by Rv1626 beads. This study has demonstrated the potential of PHA beads delivering a single reverse vaccinology antigen for protection against tuberculosis infection in mice. While the co-display of immune modulators did not improve the protection induced by the antigen, further studies are needed to determine optimal doses for delivery of immune modulators to enhance protective immunity

Novel particulate vaccine candidates recombinantly produced by pathogenic and nonpathogenic bacterial hosts : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology at Massey University, Manawatu, New Zealand.

Polyhydroxyalkanoates (PHAs) are biopolyesters synthesized as small spherical cytoplasmic inclusion bodies by a range of bacteria. Recently, PHA beads have been investigated for use as a vaccine delivery platform by using engineered heterologous production hosts that allowed the efficient display of vaccine candidate antigens on the beads surface and were found to greatly improve immunogenicity of the displayed antigens. However, like other subunit vaccines, these antigen-displaying (vaccine) PHA beads only provide a limited repertoire of antigens. In this thesis we investigate the idea of directly utilizing the disease causative pathogen or model organism to produce vaccine PHA beads with a large antigenic repertoire. These beads are hypothesized to have the potential to induce greater protective immunity compared to production of the same PHA bead in a heterologous production host. This concept was exemplified with Pseudomonas aeruginosa and Mycobacterium tuberculosis as model human pathogens. For P. aeruginosa we describe the engineering of this bacterium to promote PHA and Psl (polysaccharide) production. This represents a new mode of functional display for the engineering, production, and validation of a novel OprI/F-AlgE fusion antigen-displayed on PHA beads. For the disease tuberculosis we investigated the use of nonpathogenic M. smegmatis as a model organism for M. tuberculosis. We described the bioengineering, production, and validation of Ag85AESAT- 6 displayed on PHA beads produced in M. smegmatis. Here we showed that both organisms were harnessed to produce custom-made PHA beads for use as particulate subunit vaccines that carried copurifying pathogen-derived proteins as a large antigenic repertoire and the ability of these vaccine PHA beads to generate a protective immune response. This novel bioengineering concept of particulate subunit vaccine production could be applied to a range of pathogens naturally producing PHA inclusions for developing efficacious subunit vaccines for infectious diseases

Polyhydroxyalkanoate beads as a particulate vaccine against Streptococcus pneumoniae and Neisseria meningitidis : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Microbiology at Massey University, Manawatu, New Zealand

Listed in 2018 Dean's List of Exceptional ThesesStreptococcus pneumoniae and Neisseria meningitidis are the major causes of pneumonia and meningitis, respectively, worldwide. Capsular polysaccharide-protein vaccines (conjugate vaccines) provide protection against these diseases but not protection against infections caused by serotypes and serogroups not included in these vaccines. Proteins have been increasingly considered as antigens for vaccine development due to their more structurally conserved composition when compared to capsular polysaccharides. Proteins subunit vaccines are safe and protective; however, they have limitations such as serotype-dependent immunity, and low immunogenicity of the proteins, requiring adjuvant to be included in these formulations or delivery systems that enhance the desired immune response. In addition, complex production procedures are required, increasing production costs and therefore market prices making these vaccines inaccessible for many people affected by these diseases. Recently, bacterial storage polymer inclusions have been developed as protein antigen carriers. Polyhydroxyalkanoate, in particular 3-polyhydroxybutyrate (PHB) inclusions have been successfully bioengineered to display antigens from pathogens like Mycobacterium tuberculosis and Hepatitis C virus. These particulate vaccine candidates elicited both a Th1 and Th2 immunity patterns combined with a protective immune response against Mycobacterium bovis in mice. This thesis focuses on the study of polyhydroxybutyrate (PHB) beads properties as a carrier/delivery system engineered to display antigens from extracellular bacteria. The antigens Pneumococcal adhesin A, Pneumolysin (proteins) and 19F capsular polysaccharide (CPS) from Streptococcus pneumoniae, and Neisserial adhesin A, factor H binding protein (proteins) and serogroup C CPS from Neisseria meningitidis were displayed on the PHB bead surface. These antigenic proteins were produced as fusion proteins on the PHB bead surface, while the CPS was covalently attached by chemical conjugation. Mice vaccinated with these PHB beads produced strong and antigen-specific antibody levels. In addition, splenocytes from the same mice generated both IL-17A and IFN-ɣ production. The antibodies elicited against antigenic pneumococcal proteins were able to recognise the same protein in the context of an Streptococcus pneumoniae whole cell lysate from more than six different strains, while antibodies produced after vaccination with 19F CPS conjugate to PHB showed high opsonophagocytic titers against the homologous strain. In the case of Neisseria meningitidis, bactericidal antibodies were elicited in mice vaccinated with PHB beads displaying proteinaceous and CPS antigens. Overall, this thesis shows that PHB as particulate vaccine candidate holds the promise of a broadly protective vaccine that can be produced cost-effectively for widespread application to prevent diseases caused by Neisseria meningitidis and Streptococcus pneumoniae

Engineering Bacillus megaterium for production of functional intracellular materials

Background: Over the last 10-15 years, a technology has been developed to engineer bacterial polyhydroxybutyrate (PHB) inclusions as functionalized beads, for applications such as vaccines, diagnostics and enzyme immobilization. This has been achieved by translational fusion of foreign proteins to the PHB synthase (PhaC). The respective fusion protein mediates self-assembly of PHB inclusions displaying the desired protein function. So far, beads have mainly been produced in recombinant Escherichia coli which is problematic for some applications as the lipopolysaccharides (LPS) co-purified with such inclusions are toxic to humans and animals. Results: In this study, we have engineered the formation of functional PHB inclusions in the Gram-positive bacterium Bacillus megaterium, an LPS-free and established industrial production host. As B. megaterium is a natural PHB producer, the PHB-negative strain PHA05 was used to avoid any background PHB production. Plasmid-mediated T7 promoter-driven expression of the genes encoding β-ketothiolase (phaA), acetoacetyl-CoA-reductase (phaB) and PHB synthase (phaC) enabled/effected PHB production by B. megaterium PHA05. To produce functionalized PHB inclusions, the N- and C-terminus of PhaC was fused to four and two IgG binding Z-domains from Staphylococcus aureus, respectively. The ZZ-domain PhaC fusion protein was strongly overproduced at the surface of the PHB inclusions and the corresponding isolated ZZ-domain displaying PHB beads were found to purify IgG with a binding capacity of 40-50 mg IgG/g beads. As B. megaterium has the ability to sporulate and respective endospores could co-purify with cellular inclusions, a sporulation negative production strain was generated by disrupting the spoIIE gene in PHA05. This strain did not produce spores when tested under sporulation inducing conditions and it was still able to synthesize ZZ-domain displaying PHB beads. Conclusions: This study provides proof of concept for the successful genetic engineering of B. megaterium as a host for the production of functionalized PHB beads. Disruption of the spoIIE gene rendered B. megaterium incapable of sporulation but particularly suitable for production of functionalized PHB beads. This sporulation-negative mutant represents an improved industrial production strain for biotechnological processes otherwise impaired by the possibility of endospore formation.fals

Potential of Diverse Prokaryotic Organisms for Glycerol-based Polyhydroxyalkanoate Production

The potential and performance of various Gram-negative, Gram-positive and archaeal wild type microorganisms, and bacterial mixed cultures, as well as the application of genetically engineered strains as whole-cell biocatalysts for glycerol-based polyhydroxyalkanoate production are analyzed and assessed. This encompasses the comparison of growth and polyhydroxyalkanoate accumulation kinetics, thermo-mechanical properties of isolated glycerol-based polyhydroxyalkanoate of different composition on the monomeric level, and the presentation of mathematical models developed to describe glycerol-based polyhydroxyalkanoate production processes. For all these aspects, the article provides a detailed compilation of the contemporary state of knowledge, and gives an outlook to expected future developments

The effect of temperature during culture enrichment on methanotrophic polyhydroxyalkanoate production

Producción CientíficaClimate change and plastic pollution are likely the most relevant environmental problems of the 21st Century. Thus, one of the most promising solutions to remedy both environmental problems simultaneously is the bioconversion of greenhouse gases, such as methane (CH4), into bioplastics (PHAs). However, the optimization of this bioconversion platform is still required to turn CH4 biotransformation into a cost-effective and cost-competitive process. In this context, the research presented here aimed at elucidating the best temperature culture conditions to enhance both PHA accumulation and methane degradation. Six different enrichments were carried out at 25, 30 and 37 °C using different inocula and methane as the only energy and carbon source. CH4 biodegradation rates, specific growth rates, PHA accumulations and the community structure were characterized. Higher temperatures (30 and 37 °C) increased the PHAs accumulation up to 30% regardless of the inoculum. Moreover, Methylocystis became the dominant genus (∼30% of the total population) regardless of the temperature and inoculum used. This research demonstrated for the first time the fundamental role of temperature in increasing both the accumulation of PHAs and methane abatement during the enrichment of PHA cell-factories from methane, thus enhancing the cost-effectiveness of the process.Ministerio de Economía, Industria y Competitividad, TheEuropean FEDER program and the European Commission (CTM2015-73228-JIN, H2020-MSCA-IF-2016: CH4BioVal-GA:750126 and Red NOVEDAR)

Controlled biotechnological production of polyhydroxyalkanoates

Předložená diplomová práce se zabývá produkcí polyhydroxyalkanoátů (PHA) bakterií Cupriavidus necator H16. Cílem práce byla příprava, selekce a charakterizace mutantních kmenů schopných vyšší produkce PHA. V teoretické části byla zpracována literární rešerše zabývající se nejdůležitějšími typy PHA, bakterií Cupriavidus necator a způsoby indukce mutageneze. V experimentální části byly připraveny mutantní kmeny pomocí fyzikální a chemické mutageneze. Mutantní kmeny schopné nadprodukce PHA byly selektovány pomocí kultivace na minerálním médium s olejem. Pro další studium byly vybrány 4 mutantní kmeny schopné nadprodukce PHA. Tyto mutantní kmeny byly dále podrobeny biochemické charakterizaci. Byly naměřeny specifické aktivity vybraných intracelulárních enzymů včetně enzymů podílejících se na biosyntéze PHA. Také byla naměřena resistence mutantů vůči oxidačnímu stresu. Bylo zjištěno, že mutantní kmeny schopné nadprodukce PHA mají vyšší aktivity enzymů produkujících NADPH. NADPH je jeden z klíčových substrátů ovlivňujících směr toku acetyl-CoA metabolizmem. Vyšší intracelulární koncentrace NADPH parciálně inhibuje Krebsův cyklus a aktivuje akumulaci PHA. Aktivity acetoacetyl-CoA reduktázy a PHA syntázy, enzymů zapojených do syntézy PHA, těchto mutantů proto byly také vyšší stejně jako molekulová hmotnost připravených polymerů. Aplikace fyzikálních a chemických mutagenů je způsob, kterým lze připravit biotechnologicky perspektivní mutantní kmeny schopné nadprodukce PHA.This diploma thesis deals with production of polyhydroxyalkanoates (PHA) by bacterial strain Cupriavidus necator H16. Goal of this work was preparation, selection and characterization of mutant strains overproducing PHA. Theoretical focuses on the most important PHA, bacteria Cupriavidus necator and mutagenesis techniques. In practical part mutant strains were prepared through physical and chemical mutagenesis. Mutant strains overproducing PHA were selected by cultivation in mineral medium with oil. For further study, 4 mutant strains overproducing PHA were selected. These mutants were biochemically characterized. Specific activities of several intracellular enzymes including enzymes involved in PHA biosynthesis were measured. Resistance of mutants against oxidative stress was measured as well. Mutant strains overproducing PHA revealed higher enzymatic activities of NADPH producing enzymes. Generally, NADPH is one of the substrates influencing flux of acetyl-CoA throughout the metabolism; higher intracellular concentration of NADPH partially inhibits TCA cycle and activates accumulation of PHA. Therefore, activities of acetoacetyl-CoA reductase and PHB synthase, enzymes directly involved in PHA synthesis were higher as compared to wild strain as well as molecular weight of produced materials. It can be concluded that biotechnologically perspective mutagens capable of PHA overproduction can be prepared by application of chemical and physical mutagens.

A novel programmable lysozyme-based lysis system in Pseudomonas putida for biopolymer production

Indexación: Scopus; Web of Science.Cell lysis is crucial for the microbial production of industrial fatty acids, proteins, biofuels, and biopolymers. In this work, we developed a novel programmable lysis system based on the heterologous expression of lysozyme. The inducible lytic system was tested in two Gram-negative bacterial strains, namely Escherichia coli and Pseudomonas putida KT2440. Before induction, the lytic system did not significantly arrest essential physiological parameters in the recombinant E. coli (ECPi) and P. putida (JBOi) strain such as specific growth rate and biomass yield under standard growth conditions. A different scenario was observed in the recombinant JBOi strain when subjected to PHA-producing conditions, where biomass production was reduced by 25% but the mcl-PHA content was maintained at about 30% of the cell dry weight. Importantly, the genetic construct worked well under PHA-producing conditions (nitrogen-limiting phase), where more than 95% of the cell population presented membrane disruption 16 h post induction, with 75% of the total synthesized biopolymer recovered at the end of the fermentation period. In conclusion, this new lysis system circumvents traditional, costly mechanical and enzymatic cell-disrupting procedures.https://www.nature.com/articles/s41598-017-04741-2.pd

Controlled Production and Degradation of Selected Biomaterials

Předložená disertační práce se zabývá studiem produkce a degradace polymerních materiálů s využitím mikroorganismů. Hlavní pozornost je upřena ke studiu produkce polyesterů bakteriálního původu - polyhydroxyalkanoátů. Tyto materiály jsou akumulovány celou řadou bakterií jako zásobní zdroj uhlíku, energie a redukční síly. Díky svým mechanickým vlastnostem, kterými silně připomínají tradiční syntetické polymery jako jsou polyetylén nebo polypropylén, a také díky své snadné odbouratelnosti v přírodním prostředí, jsou polyhydroxyalkanoáty považovány za ekologickou alternativu k tradičním plastům vyráběným z ropy. Polyhydroxyalkanoáty mají potenciál najít řadu aplikací v průmyslu, zemědělství ale také v medicíně. Významná část předložené práce je zaměřena na produkci polyhydroxyalkanoátů z odpadních substrátů pocházejících především z potravinářských výrob. Testována byla odpadní syrovátka nebo odpadní oleje z různých zdrojů. Právě využití levných odpadních substrátů je strategií, která by mohla přispět ke snížení ceny polyhydroxyalkanoátů a tím usnadnit jejich masové rozšíření. Podle výsledků dosažených v této práci jsou právě odpadní olejové substráty velice perspektivní cestou k ekonomicky rentabilní biotechnologické produkci polyhydroxyalkanoátů. Další část předložené práce se zabývá studiu spojení metabolické role polyhydroxyalkanoátů a stresové odpovědi bakterií. V této práci bylo zjištěno, že expozice bakteriální kultury řízené dávce etanolu nebo peroxidu vodíku významně navýší dosažené výtěžky a to o přibližně 30 %. Po aplikaci výše zmíněných stresových faktorů došlo k aktivaci metabolických drah vedoucí k odbourání stresového faktoru z média. Výsledkem bylo navýšení poměru NAD(P)H/NAD(P)+, což vedlo k částečné inhibici Krebsova cyklu a naopak aktivaci biosyntetické dráhy polyhydroxyalkanoátů. Mimoto došlo k významnému navýšení molekulové hmotnosti výsledných materiálů. Podle těchto výsledků se regulovaná aplikace vhodně zvolených stresových podmínek zdá být zajímavou strategií, která vede nejen k navýšení celkových výtěžků, ale také významnému zlepšení vlastností polymeru. Poslední část disertační práce se zabývala studiem procesu biodegradace polyuretanových materiálů. Polyuretanové eleastomery byly modifikovány rozličnými biopolymery za účelem navýšení jejich biodegradability. Tyto materiály byly posléze vystaveny působení směsné termofilní kultury jako modelového systému, který simuluje přirozené konsorcium bakterií. Přítomnost testovaných materiálů v kultivačním médiu vedla k neobvyklým růstovým charakteristikám bakteriální kultury. V průběhu prvních několika dní byl růst kultury silně inhibován, nicméně po překonání této neobvykle dlouhé lag-fáze došlo k intenzivnímu nárůstu kultury. Hlavní podíl na hmotnostním úbytku testovaných materiálů během experimentů měl samovolný rozpad materiálů, nicméně byl pozorován i vliv bakteriální kultury, kdy míra biotické degradace závisela na použitém modifikačním činidle. Nejvyšší míra biotické degradace byla pozorována u polyuretanového materiálu modifikovaného acetylovanou celulózou. Lag-fáze byla způsobena uvolněním nezreagovaného katalyzátoru (dibutylcínlaurát) a polyolu do kultivačního média. Bakteriální kultura se však po čase dokázala na přítomnost toxických látek v médiu adaptovat nebo je dokázala eliminovat.Proposed dissertation thesis is aimed at the study of production and degradation of polymeric materials using microorganisms. The main attention is given to polyesters of bacterial origin - polyhydroxyalkanoates. These materials are accumulated by a wide variety of bacterial strains which use polyhydroxyalkanoates as a storage of carbon, energy and reducing power. Thanks to their mechanical properties, that are similar to those of traditional synthetic plastics such as polyethelene or polypropylene, and thanks to their biodegradability, polyhydroxyalkanoates are considered to be environmental-friendly alternative to traditional plastics of petrochemical origin. Thus, polyhydroxyalkanoates have many potential applications in industry, agriculture as well as in medicine. Important part of this thesis is focused on production of polyhydroxyalknotes from waste substrates coming from food industry. Among tested substrates was waste cheese whey or waste plant edible oils of different origin. Utilization of cheap waste substrates for polyhydroxyalkanoates production could facilitate economically feasible process of large scale production of polyhydroxyalkanoates. According to the results presented in this thesis, waste oils are very promising substrates for biotechnological production of polyhydroxyalkanoates. Next part of the thesis deals with involvement of polyhydroxyalkanoates into stress response of bacteria. It was observed, that exposition of bacterial culture to controlled dose of ethanol or hydrogen peroxide resulted in significantly enhanced yields (abut 30 %). After stress factors application, particular metabolic pathways involved in stress response were activated in order to endure stress conditions. Subsequently, NAD(P)H/NAD(P)+ ratio increased and, thus, Krebs cycle was partially inhibited whereas polyhydroxyalkanoates synthetic pathway was activated. Moreover, application of stress factors increased molecular weights of polymers. Therefore, strategy based on application of controlled dose of stress not only enhanced polymer yields, but, moreover, improved properties of materials. The last part of thesis describes the investigation of biodegradation of polyurethane elastomeric films modified by various biopolymers in presence of mixed thermophillic culture as a model of natural bacterial consortium. The presence of materials in cultivation medium resulted in delayed but intensive growth of bacterial culture. The unusually long lag-phase was caused by release of un-reacted polyether polyol and tin catalyst from materials. The main part of material degradation was caused by abiotic degradation of elastomeric films, nevertheless, also bacterial culture slightly contributed to material decomposition. The measure of biotic degradation strongly depended on type of used modification agent. The highest tendency to undergo biotic degradation was observed for elastomeric film modified by acetylated cellulose.

A Feasibility Analysis for the Development of a Facility Utilizing Olive Oil Mill Production Waste as a Carbon Substrate in Polyhydroxyalkanoate Production in Morocco

This thesis presents a market study and economic feasibility analysis on developing a facility utilizing olive oil production waste as a carbon substrate in polyhydroxyalkanoate production. Three underlying questions will be explored within this thesis: (1) Can olive oil mill effluents be utilized to produce an environmentally friendly polyhydroxyalkanoate bio-plastic?;, (2) Is there potential for the bio-plastic polyhydroxyalkanoate to enter Morocco\u27s plastic market?;, (3) Is it likely that a bio-plastic facility utilizing olive oil mill production waste to create polyhydroxyalkanoate would have long term profitability? This research provides a pathway toward a new solution to a pervasive environmental concern facing Morocco as well as provides options for better and more sustainable business actions, decisions, products, or strategies