Biodegradation of polyhydroxyalkanoic acids

Understanding the role of poly(3-hydroxybutyrate) depolymerases in waste management

Since conventional plastics are poorly degradable and harmful to living organisms, there is a need to look for alternative options such as poly(3-hydroxybutyrate) - PHB. This polymer is biodegradable via PHB depolymerases (PHBDs). Literature survey reveals that there are no comprehensive updates on PHBDs and in the current review, details regarding extracellular and intracellular forms of the enzyme are presented. Phylogenetically diverse PHBD-producing microorganisms are prevalent in a variety of natural and man-made habitats. These enzymes have been purified from different organisms and are seen to be active over a wide range of pH and temperatures. In general, extracellular PHBDs are made up of four constituents - signal peptide, catalytic domain [with a signature triad (serine, aspartate and histidine) and an oxyanion histidine], linker domain and substrate binding domain that enable degradation of PHB. Intracellular PHBDs have been mainly studied in bacterial genera such as Rhodobacter, Rhodospirillum, Ralstonia, Zoogloea, Pseudomonas, Sinorhizobium and Bacillus. Genes encoding them have been identified, characterized and cloned in other organisms. PHBD producers are envisioned to play a significant role in developing ecofriendly methods for removing PHB wastes thereby highlighting their practical relevance. Development of appropriate consortia including diverse PHBD producers and their introduction in waste disposal sites would enable treatment of PHB containing wastes. By using bioinformatics and synthetic biology-based approaches, further investigations on PHBDs from unexplored microorganisms can be undertaken and their role in the bioplastic waste management can be unraveled.

Production, isolation, optimization, and characterization of microbial PHA from Bacillus australimaris

Population explosion in recent years has driven the environment to overuse nondegradable substances. Microbial polyesters known as polyhydroxyalkanoates (PHAs) are generated and retained as cytoplasmic granules in microorganisms with restricted nutritional availability and can be used to manufacture bioplastics. The current study attempts to screen soil isolates for PHA production and optimize their media parameters. Among all the isolates, 17 were identified and confirmed by Sudan black staining, as they are screening for PHA production and are identified by their colony characteristics. The isolation of the most promising strain, GS-14, was achieved through the sodium hypochlorite method, and subsequent quantification involved establishing a standard curve of crotonic acid. Notably, isolate GS-14 presented the highest yield, which was determined by extrapolating its data onto the standard curve. Characterization of the PHA polymer was subsequently performed, and the results were used to discern its properties. FTIR confirmed characteristic PHA absorption bands, with a prominent C = O stretching peak at 1732 cm⁻¹. LC-MS detected a molecular mass of 641.6 g/mol, indicative of an oligomeric species, while the actual polymer molecular weight is estimated between 5,000 and 20,000 Da. DSC revealed an exothermic peak at 174 °C, allowing the calculation of crystallinity, a key determinant of mechanical properties. Furthermore, the PHA-producing organism was identified as Bacillus australimaris through the sequencing of 16 S ribosomal RNA. The media optimization was performed via Minitab software, with statistical analyses employed to interpret the resulting data comprehensively.

The biochemical mechanisms of plastic biodegradation

Since the invention of the first synthetic plastic, an estimated 12 billion metric tons of plastics have been manufactured, 70% of which was produced in the last 20 years. Plastic waste is placing new selective pressures on humans and the organisms we depend on, yet it also places new pressures on microorganisms as they compete to exploit this new and growing source of carbon. The limited efficacy of traditional recycling methods on plastic waste, which can leach into the environment at low purity and concentration, indicates the utility of this evolving metabolic activity. This review will categorize and discuss the probable metabolic routes for each industrially relevant plastic, rank the most effective biodegraders for each plastic by harmonizing and reinterpreting prior literature, and explain the experimental techniques most often used in plastic biodegradation research, thus providing a comprehensive resource for researchers investigating and engineering plastic biodegradation.

Bioplastic degradation and assimilation processes by a novel bacterium isolated from the marine plastisphere

Biosourced and biodegradable plastics offer a promising solution to reduce environmental impacts of plastics for specific applications. Here, we report a novel bacterium named Alteromonas plasticoclasticus MED1 isolated from the marine plastisphere that forms biofilms on foils of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). Experiments of degradation halo, plastic matrix weight loss, bacterial oxygen consumption and heterotrophic biosynthetic activity showed that the bacterial isolate MED1 is able to degrade PHBV and to use it as carbon and energy source. The likely entire metabolic pathway specifically expressed by this bacterium grown on PHBV matrices was shown by further genomic and transcriptomic analysis. In addition to a gene coding for a probable secreted depolymerase, a gene cluster was located that encodes characteristic enzymes involved in the complete depolymerization of PHBV, the transport of oligomers, and in the conversion of the monomers into intermediates of central carbon metabolism. The transcriptomic experiments showed the activation of the glyoxylate shunt during PHBV degradation, setting the isocitrate dehydrogenase activity as regulated branching point of the carbon flow entering the tricarboxylic acid cycle. Our study also shows the potential of exploring the natural plastisphere to discover new bacteria with promising metabolic capabilities.

Microbial PolyHydroxyAlkanoate (PHA) Biopolymers-Intrinsically Natural

Global pollution from fossil plastics is one of the top environmental threats of our time. At their end-of-life phase, fossil plastics, through recycling, incineration, and disposal result in microplastic formation, elevated atmospheric CO₂ levels, and the pollution of terrestrial and aquatic environments. Current regional, national, and global regulations are centered around banning plastic production and use and/or increasing recycling while ignoring efforts to rapidly replace fossil plastics through the use of alternatives, including those that occur in nature. In particular, this review demonstrates how microbial polyhydroxyalkanoates (PHAs), a class of intrinsically natural polymers, can successfully remedy the fossil and persistent plastic dilemma. PHAs are bio-based, biosynthesized, biocompatible, and biodegradable, and thus, domestically and industrially compostable. Therefore, they are an ideal replacement for the fossil plastics pollution dilemma, providing us with the benefits of fossil plastics and meeting all the requirements of a truly circular economy. PHA biopolyesters are natural and green materials in all stages of their life cycle. This review elaborates how the production, consumption, and end-of-life profile of PHAs are embedded in the current and topical, 12 Principles of Green Chemistry, which constitute the basis for sustainable product manufacturing. The time is right for a paradigm shift in plastic manufacturing, use, and disposal. Humankind needs alternatives to fossil plastics, which, as recalcitrant xenobiotics, contribute to the increasing deterioration of our planet. Natural PHA biopolyesters represent that paradigm shift.

Large-scale omics dataset of polymer degradation provides robust interpretation for microbial niche and succession on different plastisphere

While biodegradable polymers have received increased attention due to the recent marine plastic problem, few studies have compared microbiomes and their degradation processes among biodegradable polymers. In this study, we set up prompt evaluation systems for polymer degradation, allowing us to collect 418 microbiome and 125 metabolome samples to clarify the microbiome and metabolome differences according to degradation progress and polymer material (polycaprolactone [PCL], polybutylene succinate-co-adipate [PBSA], polybutylene succinate [PBS], polybutylene adipate-co-terephthalate [PBAT], and poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) [PHBH]). The microbial community compositions were converged to each polymer material, and the largest differences were observed between PHBH and other polymers. Such gaps were probably formed primarily by the presence of specific hydrolase genes (i.e., 3HB depolymerase, lipase, and cutinase) in the microorganisms. Time-series sampling suggested several steps for microbial succession: (1) initial microbes decrease abruptly after incubation starts; (2) microbes, including polymer degraders, increase soon after the start of incubation and show an intermediate peak; (3) microbes, including biofilm constructers, increase their abundance gradually. Metagenome prediction showed functional changes, where free-swimming microbes with flagella adhered stochastically onto the polymer, and certain microbes started to construct a biofilm. Our large-dataset-based results provide robust interpretations for biodegradable polymer degradation.

Influence of PHA Substrate Surface Characteristics on the Functional State of Endothelial Cells

The needs of modern regenerative medicine for biodegradable polymers are wide and varied. Restoration of the viability of the vascular tree is one of the most important components of the preservation of the usefulness of organs and tissues. The creation of vascular implants compatible with blood is an important task of vascular bioengineering. The function of the endothelial layer of the vessel, being largely responsible for the development of thrombotic complications, is of great importance for hemocompatibility. The development of surfaces with specific characteristics of biomaterials that are used in vascular technologies is one of the solutions for their correct endothelialization. Linear polyhydroxyalkanoates (PHAs) are biodegradable structural polymeric materials suitable for obtaining various types of implants and tissue engineering, having a wide range of structural and physicomechanical properties. The use of PHA of various monomeric compositions in endothelial cultivation makes it possible to evaluate the influence of material properties, especially surface characteristics, on the functional state of cells. It has been established that PHA samples with the inclusion of 3-hydroxyhexanoate have optimal characteristics for the formation of a human umbilical vein endothelial cell, HUVEC, monolayer in terms of cell morphology as well as the levels of expression of vinculin and VE-cadherin. The obtained results provide a rationale for the use of PHA copolymers as materials for direct contact with the endothelium in vascular implants.

Degradable Poly(3-hydroxybutyrate)-The Basis of Slow-Release Fungicide Formulations for Suppressing Potato Pathogens

Three-component slow-release fungicide formulations with different modes of action of the active ingredients for suppressing potato pathogens were constructed for the first time. The difenoconazole, mefenoxam, prothioconazole, and azoxystrobin fungicides were embedded in the degradable polymer P(3HB)/birch wood flour blend and examined using SEM, IR spectroscopy, X-ray analysis, DTA, and DSC. Results showed that no chemical bonds were established between the components and that they were physical mixtures that had a lower degree of crystallinity compared to the initial P(3HB), which suggested different crystallization kinetics in the mixtures. The degradation behavior of the experimental formulations was investigated in laboratory micro-ecosystems with pre-characterized field soil. The slow-release fungicide formulations were prolonged-action forms with a half-life of at least 50-60 d, enabling gradual and sustained delivery of the active ingredients to plants. All slow-release fungicide formulations had a strong inhibitory effect on the most common and harmful potato pathogens (Phytophthorainfestans, Alternarialongipes, Rhizoctoniasolani, and Fusariumsolani).

Biodegradation of polymers in managing plastic waste - A review

The modern economy that is fast-moving and convenience centric has led to excessive consumption of plastic. This has unwittingly led to egregious accumulation of plastic waste polluting the environment. Unfortunately, present means of plastic waste management have all been proven as less than adequate; namely recycling, landfill and incineration. Recent focus on plastic waste management has seen the confluence of the developments in biodegradable polymers and microbial engineering strategy for more expedient decomposition of plastic waste at composting facilities. This review paper is an assimilation of current developments in the areas of biodegradable polymer as well as microbial strategy towards management of polymer waste. Advents in biodegradable polymers have been promising, especially with aliphatic polyesters and starch in blends or co-polymers of these. Microbial strategies have been pursued for the identification of microbial strains and understanding of their enzymatic degradation process on polymers. New insights in these two areas have been focused in improving the rate of degradation of plastic waste at composting facilities. Recent alignment of testing and certification standards is outlined to give intimate insights into the mechanisms and factors influencing biodegradation. Despite recent milestones, economic viability of composting plastic waste in mainstream waste facilities is still a distance away. As it remains that a polymer that is biodegradable is functionally inferior to conventional polymers. Rather, it requires a shift in consumer behaviour to accept less durable biodegradable plastic products, this will then lower the threshold for biodegradable polymers to become a commercial reality.

Novel Polyhydroxybutyrate-Degrading Activity of the Microbulbifer Genus as Confirmed by Microbulbifer sp. SOL03 from the Marine Environment

Ever since bioplastics were globally introduced to a wide range of industries, the disposal of used products made with bioplastics has become an issue inseparable from their application. Unlike petroleum-based plastics, bioplastics can be completely decomposed into water and carbon dioxide by microorganisms in a relatively short time, which is an advantage. However, there is little information on the specific degraders and accelerating factors for biodegradation. To elucidate a new strain for biodegrading poly-3-hydroxybutyrate (PHB), we screened out one PHB-degrading bacterium, Microbulbifer sp. SOL03, which is the first reported strain from the Microbulbifer genus to show PHB degradation activity, although Microbulbifer species are known to be complex carbohydrate degraders found in high-salt environments. In this study, we evaluated its biodegradability using solid- and liquid-based methods in addition to examining the changes in physical properties throughout the biodegradation process. Furthermore, we established the optimal conditions for biodegradation with respect to temperature, salt concentration, and additional carbon and nitrogen sources; accordingly, a temperature of 37°C with the addition of 3% NaCl without additional carbon sources, was determined to be optimal. In summary, we found that Microbulbifer sp. SOL03 showed a PHB degradation yield of almost 97% after 10 days. To the best of our knowledge, this is the first study to investigate the potent bioplastic degradation activity of Microbulbifer sp., and we believe that it can contribute to the development of bioplastics from application to disposal.

Poly-β-Hydroxybutyrate Production by Rhodopseudomonas sp. Grown in Semi-Continuous Mode in a 4 L Photobioreactor

The synthesis of polyhydroxybutyrate (PHB) by photosynthetic non-sulfur bacteria is a potential approach for producing biodegradable plastics. In this work, acetate was used as a single carbon source to study the effect on PHB formation in Rhodopseudomonas sp. cultured in a cylindrical four-liter photobioreactor under semi-continuous mode. The cultivation process is divided into a symmetrical growth phase and a PHB accumulation phase separated temporally. The symmetrical growth phase (nutrient sufficient conditions) was followed by a sulfur-limited phase to promote PHB accumulation. The main novelty is the progressive lowering of the sulfur concentration into Rhodopseudomonas culture, which was obtained by two concomitant conditions: (1) sulfur consumption during the bacterial growth and (2) semi-continuous growth strategy. This caused a progressive lowering of the sulfur concentration into Rhodopseudomonas culturedue to the sulfur-free medium used to replace 2 L of culture (50% of the total) that was withdrawn from the photobioreactor at each dilution. The PHB content ranged from 9.26% to 15.24% of cell dry weight. At the steady state phase, the average cumulative PHB was >210 mg/L. Sulfur deficiency proved to be one of the most suitable conditions to obtain high cumulative PHB in Rhodopseudomonas culture.

Inspired by nature: Microbial production, degradation and valorization of biodegradable bioplastics for life-cycle-engineered products

The global environmental pollution by micro- and macro-plastics reveals the consequences of an extensive use of recalcitrant plastic products together with inappropriate waste management practices that fail to sufficiently recycle the broad types of conventional plastic waste. Biobased and biodegradable plastics are experiencing an uprising as their properties offer alternative waste management solutions for a more circular material economy. However, although the production of such bioplastics has advanced on scale, the end-of-life (EOL) (bio)technologies to promote circularity are lacking behind. While composting and biogas plants are the only managed EOL options today, advanced biotechnological recycling technologies for biodegradable bioplastics are still in an embryonic stage. Thus, developing efficient biotechnologies capable of transforming bioplastic waste into high-value chemical building blocks or into the constituents of the original polymer offers promising routes towards life-cycle-engineered products. This review aims at providing a comprehensive state-of-the-art overview of microbial-based processes involved in the complete lifecycle of bioplastics. The current trends in the bioplastic market, the beginning and EOL scenarios of bioplastics, and a critical discussion on the key factors and mechanisms governing microbial degradation are systematically presented. Also, a critical evaluation of terminology and international standards to quantify polymer biodegradability is provided together with the latest biotechnological recycling strategies, including the use of different pre-treatments for (bio)plastic waste. Finally, the challenges and future perspectives for the development of life-cycle-engineered biobased and biodegradable plastic products are discussed.

Improvement of polyhydroxybutyrate (PHB) plate-based screening method for PHB degrading bacteria using cell-grown amorphous PHB and recovered by sodium dodecyl sulfate (SDS)

Poly(3-hydroxybutyrate) (PHB) is a biobased and biodegradable plastic. Considering the environmental issues of petroleum-based plastics, PHB is promising as it can be degraded in a relatively short time by bacteria to water and carbon dioxide. Substantial efforts have been made to identify PHB-degrading bacteria. To identify PHB-degrading bacteria, solid-based growth or clear zone assays using PHB as the sole carbon source are the easiest methods; however, PHB is difficult to dissolve and distribute evenly, and bacteria grow slowly on PHB plates. Here, we suggest an improved PHB plate assay using cell-grown PHB produced by Halomonas sp. and recovered by sodium dodecyl sulfate (SDS). Preparation using SDS resulted in evenly distributed PHB plates that could be used for sensitive depolymerase activity screening in less time compared with solvent-melted pellet or cell-grown PHB. With this method, we identified 15 new strains. One strain, Cutibacterium sp. SOL05 (98.4% 16S rRNA similarity to Cutibacterium acne), showed high PHB depolymerase activity in solid and liquid conditions. PHB degradation was confirmed by clear zone size, liquid culture, scanning electron microscopy, and Fourier-transform infrared spectroscopy. The results indicate this method can be used to easily identify PHB-degrading bacteria from various sources to strengthen the benefits of bioplastics.

Biodegradability of poly(3-hydroxyalkanoate) and poly(ε-caprolactone) via biological carbon cycles in marine environments

Approximately 4.8–12.7 million tons of plastic waste has been estimated to be discharged into marine environments annually by wind and river currents. The Ellen MacArthur Foundation warns that the total weight of plastic waste in the oceans will exceed the total weight of fish in 2050 if the environmental runoff of plastic continues at the current rate. Hence, biodegradable plastics are attracting attention as a solution to the problems caused by plastic waste. Among biodegradable plastics, polyhydroxyalkanoates (PHAs) and poly(ε-caprolactone) (PCL) are particularly noteworthy because of their excellent marine biodegradability. In this review, the biosynthesis of PHA and cutin, a natural analog of PCL, and the biodegradation of PHA and PCL in carbon cycles in marine ecosystems are discussed. PHA is biosynthesized and biodegraded by various marine microbes in a wide range of marine environments, including coastal, shallow-water, and deep-sea environments. Marine cutin is biosynthesized by marine plants or obtained from terrestrial environments, and PCL and cutin are biodegraded by cutin hydrolytic enzyme-producing microbes in broad marine environments. Thus, biological carbon cycles for PHA and PCL exist in the marine environment, which would allow materials made of PHA and PCL to be quickly mineralized in marine environments.

Synergistic Mechanisms Underlie the Peroxide and Coagent Improvement of Natural-Rubber-Toughened Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) Mechanical Performance

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a promising bio-based and biodegradable thermoplastic with restricted industrial applications due to its brittleness and poor processability. Natural rubber (NR) has been used as a toughening agent, but further physical improvements are desired. In this study, rubber toughening efficiency was significantly improved through the synergistic use of a trifunctional acrylic coagent and an organic peroxide during reactive extrusion of PHBV and NR. The rheological, crystallization, thermal, morphological, and mechanical properties of PHBV/NR blends with 15% rubber loading were characterized. The peroxide and coagent synergistically crosslinked the rubber phase and grafted PHBV onto rubber backbones, leading to enhanced rubber modulus and cohesive strength as well as improved PHBV⁻rubber compatibility and blend homogeneity. Simultaneously, the peroxide⁻coagent treatment decreased PHBV crystallinity and crystal size and depressed peroxy-radical-caused PHBV degradation. The new PHBV/NR blends had a broader processing window, 75% better toughness (based on the notched impact strength data), and 100% better ductility (based on the tensile elongation data) than pristine PHBV. This new rubber-toughened PHBV material has balanced mechanical performance comparable to that of conventional thermoplastics and is suitable for a wide range of plastic applications.

Purification and characterization of new bio-plastic degrading enzyme from Burkholderia cepacia DP1

Depolymerase is an enzyme that plays an important role in the hydrolysis of polyhydroxyalkanoates [PHAs]. In the current study, Burkholderia cepacia DP1 was obtained from Penang, Malaysia in which the enzyme was purified using ion exchange and gel filtration (Superdex-75) column chromatography. The molecular mass of the enzyme was estimated to be 53.3 kDa using SDS-PAGE. The enzyme activity was increased to 36.8 folds with the recovery of 16.3% after purification. The enzyme activity was detected between pH 6.0-10 and at 35-55 °C with pH 6.0 and 45 °C facilitating the maximum activity. Depolymerase was inactivated by Tween-20, Tween-80, SDS and PMSF, but insensitive to metal ions (Mg²⁺, Ca²⁺, K⁺, Na²⁺, Fe³⁺) and organic solvents (methanol, ethanol, and acetone). The apparent K_m values of the purified P(3HB) depolymerase enzyme for P(3HB) and P(3HB-co-14%3HV) were 0.7 mg/ml and 0.8 mg/ml, respectively. The V_max values of the purified enzyme were 10 mg/min and 8.89 mg/min for P(3HB) and P(3HB-co-14%3HV), respectively. The current study discovered a new extracellular poly(3-hydroxybutyrate) [P(3HB)] depolymerase enzyme from Burkholderia cepacia DP1 isolated and purified to homogeneity from the culture supernatant. To the best of our knowledge, this is the first report demonstrating the purification and biochemical characterization of P(3HB) depolymerase enzyme from genus Burkholderia.

Microbial biosynthesis and in vivo depolymerization of intracellular medium-chain-length poly-3-hydroxyalkanoates as potential route to platform chemicals

Biosynthesis and in vivo depolymerization of intracellular medium-chain-length poly-3-hydroxyalkanoates (mcl-PHA) in Pseudomonas putida Bet001 grown on lauric acid were studied. Highest mcl-PHA fraction (>50 % of total biomass) and cell concentration (8 g L^-1 ) were obtained at carbon-to-nitrogen (C/N) ratio 20, starting cell concentration 1 g L^-1 , and 48 H fermentation. The mcl-PHA comprised of 3-hydroxyhexanoate (C₆ ), 3-hydroxyoctanote (C₈ ), 3-hydroxydecanoate (C₁₀ ), and 3-hydroxydodecanoate (C₁₂ ) monomers. In vivo action was studied in a mineral liquid medium without carbon source, and in different buffer solutions with varied pH, molarity, ionic strength, and temperature. The monomer liberation rate reflected the mol percentage distribution of the initial polymer subunit composition. Rate and percentage of in vivo depolymerization were highest in 0.2 M Tris-HCl buffer (pH 9, strength = 0.2 M, 30 °C) at 0.21 g L^-1  H^-1 and 98.6 ± 1.3 wt%, respectively. There is a congruity vis-à-vis to specific buffer type, molarity, pH, ionic strength, and temperature values for superior in vivo depolymerization activities. Direct products from in vivo depolymerization matched the individual monomeric composition of native mcl-PHA. It points to exo-type reaction for the in vivo process, and potential biological route to chiral molecules.

Crystal Structure and Substrate Specificity Modification of Acetyl Xylan Esterase from Aspergillus luchuensis

Acetyl xylan esterase (AXE) catalyzes the hydrolysis of the acetyl bonds present in plant cell wall polysaccharides. Here, we determined the crystal structure of AXE from Aspergillus luchuensis (AlAXEA), providing the three-dimensional structure of an enzyme in the Esterase_phb family. AlAXEA shares its core α/β-hydrolase fold structure with esterases in other families, but it has an extended central β-sheet at both its ends and an extra loop. Structural comparison with a ferulic acid esterase (FAE) from Aspergillus niger indicated that AlAXEA has a conserved catalytic machinery: a catalytic triad (Ser119, His259, and Asp202) and an oxyanion hole (Cys40 and Ser120). Near the catalytic triad of AlAXEA, two aromatic residues (Tyr39 and Trp160) form small pockets at both sides. Homology models of fungal FAEs in the same Esterase_phb family have wide pockets at the corresponding sites because they have residues with smaller side chains (Pro, Ser, and Gly). Mutants with site-directed mutations at Tyr39 showed a substrate specificity similar to that of the wild-type enzyme, whereas those with mutations at Trp160 acquired an expanded substrate specificity. Interestingly, the Trp160 mutants acquired weak but significant type B-like FAE activity. Moreover, the engineered enzymes exhibited ferulic acid-releasing activity from wheat arabinoxylan.IMPORTANCE Hemicelluloses in the plant cell wall are often decorated by acetyl and ferulic acid groups. Therefore, complete and efficient degradation of plant polysaccharides requires the enzymes for cleaving the side chains of the polymer. Since the Esterase_phb family contains a wide array of fungal FAEs and AXEs from fungi and bacteria, our study will provide a structural basis for the molecular mechanism of these industrially relevant enzymes in biopolymer degradation. The structure of the Esterase_phb family also provides information for bacterial polyhydroxyalkanoate depolymerases that are involved in biodegradation of thermoplastic polymers.

Enhancement of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) accumulation in Arxula adeninivorans by stabilization of production

Background

In recent years the production of biobased biodegradable plastics has been of interest of researchers partly due to the accumulation of non-biodegradable plastics in the environment and to the opportunity for new applications. Commonly investigated are the polyhydroxyalkanoates (PHAs) poly(hydroxybutyrate) and poly(hydroxybutyrate-co-hydroxyvalerate) (PHB-V). The latter has the advantage of being tougher and less brittle. The production of these polymers in bacteria is well established but production in yeast may have some advantages, e.g. the ability to use a broad spectrum of industrial by-products as a carbon sources.

Results

In this study we increased the synthesis of PHB-V in the non-conventional yeast Arxula adeninivorans by stabilization of polymer accumulation via genetic modification and optimization of culture conditions. An A. adeninivorans strain with overexpressed PHA pathway genes for β-ketothiolase, acetoacetyl-CoA reductase, PHAs synthase and the phasin gene was able to accumulate an unexpectedly high level of polymer. It was found that an optimized strain cultivated in a shaking incubator is able to produce up to 52.1% of the DCW of PHB-V (10.8 g L⁻¹) with 12.3%mol of PHV fraction. Although further optimization of cultivation conditions in a fed-batch bioreactor led to lower polymer content (15.3% of the DCW of PHB-V), the PHV fraction and total polymer level increased to 23.1%mol and 11.6 g L⁻¹ respectively. Additionally, analysis of the product revealed that the polymer has a very low average molecular mass and unexpected melting and glass transition temperatures.

Conclusions

This study indicates a potential of use for the non-conventional yeast, A. adeninivorans, as an efficient producer of polyhydroxyalkanoates.

Mechanical and biological effects of infiltration with biopolymers on 3D printed tricalciumphosphate scaffolds

The aim of this study was to evaluate the influence of infiltrating 3D printed (TCP) scaffolds with different biodegradable polymers on their mechanical and biological properties. 3D printed TCP scaffolds with interconnecting channels measuring 450±50 µm were infiltrated with four different biodegradable copolymers. To determine the average compressive strength, a uniaxial testing system was used. Additionally, scaffolds were seeded with MC3T3 cells and cell viability was assessed by live/dead-assay. Uninfiltrated TCP had an average compression strength of 1.92±0.38 MPa. Mechanical stability was considerably increased in all infiltrated scaffolds up to a maximum of 7.36±0.57 MPa. All scaffolds demonstrated high cell survival rates with a maximum of 94±10 % living cells. In conclusion, infiltration of 3D printed tricalcium phosphate scaffolds with biodegradable polymers significantly improved mechanical properties and biological properties were comparable to those of uninfiltrated TCP scaffolds.

Absence of ppGpp Leads to Increased Mobilization of Intermediately Accumulated Poly(3-Hydroxybutyrate) in Ralstonia eutropha H16

In this study, we constructed a set of Ralstonia eutropha H16 strains with single, double, or triple deletions of the (p)ppGpp synthase/hydrolase (spoT1), (p)ppGpp synthase (spoT2), and/or polyhydroxybutyrate (PHB) depolymerase (phaZa1 or phaZa3) gene, and we determined the impact on the levels of (p)ppGpp and on accumulated PHB. Mutants with deletions of both the spoT1 and spoT2 genes were unable to synthesize detectable amounts of (p)ppGpp and accumulated only minor amounts of PHB, due to PhaZa1-mediated depolymerization of PHB. In contrast, unusually high levels of PHB were found in strains in which the (p)ppGpp concentration was increased by the overexpression of (p)ppGpp synthase (SpoT2) and the absence of (p)ppGpp hydrolase. Determination of (p)ppGpp levels in wild-type R. eutropha under different growth conditions and induction of the stringent response by amino acid analogs showed that the concentrations of (p)ppGpp during the growth phase determine the amount of PHB remaining in later growth phases by influencing the efficiency of the PHB mobilization system in stationary growth. The data reported for a previously constructed ΔspoT2 strain (C. J. Brigham, D. R. Speth, C. Rha, and A. J. Sinskey, Appl Environ Microbiol 78:8033-8044, 2012, https://doi.org/10.1128/AEM.01693-12) were identified as due to an experimental error in strain construction, and our results are in contrast to the previous indication that the spoT2 gene product is essential for PHB accumulation in R. eutrophaIMPORTANCE Polyhydroxybutyrate (PHB) is an important intracellular carbon and energy storage compound in many prokaryotes and helps cells survive periods of starvation and other stress conditions. Research activities in several laboratories over the past 3 decades have shown that both PHB synthase and PHB depolymerase are constitutively expressed in most PHB-accumulating bacteria, such as Ralstonia eutropha This implies that PHB synthase and depolymerase activities must be well regulated in order to avoid a futile cycle of simultaneous PHB synthesis and PHB degradation (mobilization). Previous reports suggested that the stringent response in Rhizobium etli and R. eutropha is involved in the regulation of PHB metabolism. However, the levels of (p)ppGpp and the influence of those levels on PHB accumulation and PHB mobilization have not yet been determined for any PHB-accumulating species. In this study, we optimized a (p)ppGpp extraction procedure and a high-performance liquid chromatography-mass spectrometry (HPLC-MS)-based detection method for the quantification of (p)ppGpp in R. eutropha This enabled us to study the relationship between the concentrations of (p)ppGpp and the accumulated levels of PHB in the wild type and in several constructed mutant strains. We show that overproduction of the alarmone (p)ppGpp correlated with reduced growth and massive overproduction of PHB. In contrast, in the absence of (p)ppGpp, mobilization of PHB was dramatically enhanced.

Enhanced degradation of polyhydroxyalkanoates (PHAs) by newly isolated Burkholderia cepacia DP1 with high depolymerase activity

The contribution of microbial depolymerase has received much attention because of its potential in biopolymer degradation. In this study, the P(3HB) depolymerase enzyme of a newly isolated Burkholderia cepacia DP1 from soil in Penang, Malaysia, was optimized using response surface methodology (RSM). The factors affecting P(3HB) depolymerase enzyme production were studied using one-variable-at-a-time approach prior to optimization. Preliminary experiments revealed that the concentration of nitrogen source, concentration of carbon source, initial pH and incubation time were among the main factors influencing the enzyme productivity. An increase of 9.4 folds in enzyme production with an activity of 5.66 U/mL was obtained using optimal medium containing 0.028% N of di-ammonium hydrogen phosphate and 0.31% P(3HB-co-21%4HB) as carbon source at the initial pH of 6.8 for 38 h of incubation. Moreover, the RSM model showed great similarity between predicted and actual enzyme production indicating a successful model validation. This study warrants the ability of P(3HB) degradation by B. cepacia DP1 in producing higher enzyme activity as compared to other P(3HB) degraders being reported. Interestingly, the production of P(3HB) depolymerase was rarely reported within genus Burkholderia. Therefore, this is considered to be a new discovery in the field of P(3HB) depolymerase production.

In vitro synthesis of polyhydroxyalkanoates using thermostable acetyl-CoA synthetase, CoA transferase, and PHA synthase from thermotorelant bacteria

Thermostable enzymes are required for the rapid and sustainable production of polyhydroxyalkanoate (PHA) in vitro. The in vitro synthesis of PHA using the engineered thermostable synthase PhaC1_SG(STQK) has been reported; however, the non-thermostable enzymes acetyl-CoA synthetase (ACS) and CoA transferase (CT) from mesophilic strains were used as monomer-supplying enzymes in this system. In the present study, acs and ct were cloned from the thermophilic bacteria Pelotomaculum thermopropionicum JCM10971 and Thermus thermophilus JCM10941 to construct an in vitro PHA synthesis system using only thermostable enzymes. ACS from P. thermopropionicum (ACS_Pt) and CT from T. thermophilus (CT_Tt) were confirmed to have high thermostability, and their optimal temperatures were around 60°C and 75°C, respectively. The in vitro PHA synthesis was successfully performed by ACS_Pt, CT_Tt, PhaC1_SG(STQK), and poly(3-hydroxybutyrate) [P(3HB)] was synthesized at 45°C. Furthermore, the yields of P(3HB) and P(lactate-co-3HB) at 37°C were 1.4-fold higher than those of the in vitro synthesis system with non-thermostable ACS and CT from mesophilic strains. Overall, the thermostable ACS and CT were demonstrated to be useful for the efficient in vitro PHA synthesis at relatively high temperatures.

Coupled reactions on bioparticles: Stereoselective reduction with cofactor regeneration on PhaC inclusion bodies

Chiral alcohols are important building blocks for specialty chemicals and pharmaceuticals. The production of chiral alcohols from ketones can be carried out stereo selectively with alcohol dehydrogenases (ADHs). To establish a process for cost-effective enzyme immobilization on solid phase for application in ketone reduction, we used an established enzyme pair consisting of ADH from Rhodococcus erythropolis and formate dehydrogenase (FDH) from Candida boidinii for NADH cofactor regeneration and co-immobilized them on modified poly-p-hydroxybutyrate synthase (PhaC)-inclusion bodies that were recombinantly produced in Escherichia coli cells. After separate production of genetically engineered and recombinantly produced enzymes and particles, cell lysates were combined and enzymes endowed with a Kcoil were captured on the surface of the Ecoil presenting particles due to coiled-coil interaction. Enzyme-loaded particles could be easily purified by centrifugation. Total conversion of 4'-chloroacetophenone to (S)-4-chloro-α-methylbenzyl alcohol could be accomplished using enzyme-loaded particles, catalytic amounts of NAD(+) and formate as substrates for FDH. Chiral GC-MS analysis revealed that immobilized ADH retained enantioselectivity with 99 % enantiomeric excess. In conclusion, this strategy may become a cost-effective alternative to coupled reactions using purified enzymes.

Extracellular Polyhydroxyalkanoate Depolymerase by Acidovorax sp. DP5

Bacteria capable of degrading polyhydroxyalkanoates (PHA) by secreting extracellular depolymerase enzymes were isolated from water and soil samples collected from various environments in Malaysia. A total of 8 potential degraders exhibited clear zones on poly(3-hydroxybutyrate) [P(3HB)] based agar, indicating the presence of extracellular PHA depolymerase. Among the isolates, DP5 exhibited the largest clearing zone with a degradation index of 6.0. The highest degradation activity of P(3HB) was also observed with depolymerase enzyme of DP5 in mineral salt medium containing P(3HB). Based on biochemical characterization and 16S rRNA cloning and sequencing, isolate DP5 was found to belong to the genus Acidovorax and subsequently named as Acidovorax sp. DP5. The highest extracellular depolymerase enzyme activity was achieved when 0.25% (w/v) of P(3HB) and 1 g/L of urea were used as carbon and nitrogen source, respectively, in the culture media. The most suitable assay condition of the depolymerase enzyme in response to pH and temperature was tested. The depolymerase produced by strain Acidovorax sp. DP5 showed high percentage of degradation with P(3HB) films in an alkaline condition with pH 9 and at a temperature of 40°C.

The metabolism of (R)-3-hydroxybutyrate is regulated by the enhancer-binding protein PA2005 and the alternative sigma factor RpoN in Pseudomonas aeruginosa PAO1

A variety of soil-dwelling bacteria produce polyhydroxybutyrate (PHB), which serves as a source of energy and carbon under nutrient deprivation. Bacteria belonging to the genus Pseudomonas do not generally produce PHB but are capable of using the PHB degradation product (R)-3-hydroxybutyrate [(R)-3-HB] as a growth substrate. Essential to this utilization is the NAD+-dependent dehydrogenase BdhA that converts (R)-3-HB into acetoacetate, a molecule that readily enters central metabolism. Apart from the numerous studies that had focused on the biochemical characterization of BdhA, there was nothing known about the assimilation of (R)-3-HB in Pseudomonas, including the genetic regulation of bdhA expression. This study aimed to define the regulatory factors that govern or dictate the expression of the bdhA gene and (R)-3-HB assimilation in Pseudomonas aeruginosa PAO1. Importantly, expression of the bdhA gene was found to be specifically induced by (R)-3-HB in a manner dependent on the alternative sigma factor RpoN and the enhancer-binding protein PA2005.This mode of regulation was essential for the utilization of (R)-3-HB as a sole source of energy and carbon. However, non-induced levels of bdhA expression were sufficient for P. aeruginosa PAO1 to grow on ( ± )-1,3-butanediol, which is catabolized through an (R)-3-HB intermediate. Because this is, we believe, the first report of an enhancer-binding protein that responds to (R)-3-HB, PA2005 was named HbcR for (R)-3-hydroxybutyrate catabolism regulator.

Novel extracellular medium-chain-length polyhydroxyalkanoate depolymerase from Streptomyces exfoliatus K10 DSMZ 41693: a promising biocatalyst for the efficient degradation of natural and functionalized mcl-PHAs

Cloning and biochemical characterization of a novel extracellular medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase from Streptomyces exfoliatus K10 DSMZ 41693 are described. The primary structure of the depolymerase (PhaZSex2) includes the lipase consensus sequence (serine-histidine-aspartic acid) which is known for serine hydrolases. Secondary structure analysis shows 7.9 % α-helix, 43.9 % β-sheet, 19.4 % β-turns, and 31.2 % random coil, suggesting that this enzyme belongs to the α/β hydrolase fold family, in agreement with other PHA depolymerases and lipases. The enzyme was efficiently produced as an extracellular active form in Rhodococcus and purified by two consecutive hydrophobic chromatographic steps. Matrix-assisted laser desorption-time-of-flight (MALDI-TOF) analysis of the purified enzyme revealed a monomer of 27.6 kDa with a midpoint transition temperature of 44.2 °C. Remarkably, the activity is significantly enhanced by low concentrations of nonionic and anionic detergents and thermal stability is improved by the presence of 10 % glycerol. PhaZSex2 is an endo-exohydrolase that cleaves both large and small PHA molecules, producing (R)-3-hydroxyoctanoic acid monomers as the main reaction product. Markedly, PhaZSex2 is able to degrade functionalized polymers containing thioester groups in the side chain (PHACOS), releasing functional thioester-based monomers and oligomers demonstrating the potentiality of this novel biocatalyst for the industrial production of enantiopure (R)-3-hydroxyalkanoic acids.

A Simple Route for Purifying Extracellular Poly(3-hydroxybutyrate)-depolymerase from Penicillium pinophilum

This work proposes the purification of an active and efficient enzyme, extracellular poly(3-hydroxybutyrate) (PHB)-depolymerase, suitable for industrial applications. This is achieved by the application of an easy, fast, and cheap route, skipping the chromatography step. Chromatography with one or two columns is a common step in the purification procedure, which however renders the isolation of the enzyme a time consuming and an expensive process. A strain of the fungus Penicillium pinophilum (ATCC 9644) is used for the isolation of extracellular PHB-depolymerase. The molecular weight of the purified enzyme is about 35 kDa and is estimated by gel electrophoresis (SDS-PAGE, 12% polyacrylamide). The enzymatic activity of the isolated enzyme is determined to be 3.56-fold similar to that found by other researchers that have used chromatography for the isolation. The as-isolated enzyme disintegrates the poly(3-hydroxybutyrate) (PHB) films successfully, as it is demonstrated by the biodegradation test results provided here.

New insights in the formation of polyhydroxyalkanoate granules (carbonosomes) and novel functions of poly(3-hydroxybutyrate)

The metabolism of polyhydroxybutyrate (PHB) and related polyhydroxyalkanoates (PHAs) has been investigated by many groups for about three decades, and good progress was obtained in understanding the mechanisms of biosynthesis and biodegradation of this class of storage molecules. However, the molecular events that happen at the onset of PHB synthesis and the details of the initiation of PHB/PHA granule formation, as well as the complex composition of the proteinaceous surface layer of PHB/PHA granules, have only recently come into the focus of research and were not reviewed yet. In this contribution, we summarize the progress in understanding the initiation and formation of the PHA granule complex at the example of Ralstonia eutropha H16 (model organism of PHB-accumulating bacteria). Where appropriate, we include information on PHA granules of Pseudomonas putida as a representative species for medium-chain-length PHA-accumulating bacteria. We suggest to replace the previous micelle mode of PHB granule formation by the Scaffold Model in which the PHB synthase initiation complex is bound to the bacterial nucleoid. In the second part, we highlight data on other forms of PHB: oligo-PHB with ≈100 to 200 3-hydroxybutyrate (3HB) units and covalently bound PHB (cPHB) are unrelated in function to storage PHB but are presumably present in all living organisms, and therefore must be of fundamental importance.