Enzymatic Degradation of Bacterial Poly(3-hydroxybutyrate) by a Depolymerase from Pseudomonas lemoignei

Deciphering heterogeneous enzymatic surface reactions on xylan using surface plasmon resonance spectroscopy

Xylans' unique properties make it attractive for a variety of industries, including paper, food, and biochemical production. While for some applications the preservation of its natural structure is crucial, for others the degradation into monosaccharides is essential. For the complete breakdown, the use of several enzymes is required, due to its structural complexity. In fact, the specificity of enzymatically-catalyzed reactions is guided by the surface, limiting or regulating accessibility and serving structurally encoded input guiding the actions of the enzymes. Here, we investigate enzymes at surfaces rich in xylan using surface plasmon resonance spectroscopy. The influence of diffusion and changes in substrate morphology is studied via enzyme surface kinetics simulations, yielding reaction rates and constants. We propose kinetic models, which can be applied to the degradation of multilayer biopolymer films. The most advanced model was verified by its successful application to the degradation of a thin film of polyhydroxybutyrate treated with a polyhydroxybutyrate-depolymerase. The herein derived models can be employed to quantify the degradation kinetics of various enzymes on biopolymers in heterogeneous environments, often prevalent in industrial processes. The identification of key factors influencing reaction rates such as inhibition will contribute to the quantification of intricate dynamics in complex systems.

Comprehensive Biodegradation Analysis of Chemically Modified Poly(3-hydroxybutyrate) Materials with Different Crystal Structures

This work presents a comprehensive analysis of the biodegradation of polyhydroxybutyrate (PHB) and chemically modified PHB with different chemical and crystal structures in a soil environment. A polymer modification reaction was performed during preparation of the chemically modified PHB films, utilizing 2,5-dimethyl-2,5-di(tert-butylperoxy)-hexane as a free-radical initiator and maleic anhydride. Films of neat PHB and chemically modified PHB were prepared by extrusion and thermocompression. The biological agent employed was natural mixed microflora in the form of garden soil. The course and extent of biodegradation of the films was investigated by applying various techniques, as follows: a respirometry test to determine the production of carbon dioxide through microbial degradation; scanning electron microscopy (SEM); optical microscopy; fluorescence microscopy; differential scanning calorimetry (DSC); and X-ray diffraction (XRD). Next-generation sequencing was carried out to study the microbial community involved in biodegradation of the films. Findings from the respirometry test indicated that biodegradation of the extruded and chemically modified PHB followed a multistage (2-3) course, which varied according to the spatial distribution of amorphous and crystalline regions and their spherulitic morphology. SEM and polarized optical microscopy (POM) confirmed that the rate of biodegradation depended on the availability of the amorphous phase in the interspherulitic region and the width of the interlamellar region in the first stage, while dependence on the size of spherulites and thickness of spherulitic lamellae was evident in the second stage. X-ray diffraction revealed that orthorhombic α-form crystals with helical chain conformation degraded concurrently with β-form crystals with planar zigzag conformation. The nucleation of PHB crystals after 90 days of biodegradation was identified by DSC and POM, a phenomenon which impeded biodegradation. Fluorescence microscopy evidenced that the crystal structure of PHB affected the physiological behavior of soil microorganisms in contact with the surfaces of the films.

Isolation of a polyethylene-degrading bacterium, Acinetobacter guillouiae, using a novel screening method based on a redox indicator

Plastic, a polymer synthesized from petrochemicals, is used worldwide. However, natural degradation of plastic is difficult, causing environmental pollution, with microplastics posing a serious threat to human health. In this study, we aimed to use a new screening method based on the oxidation-reduction indicator, 2,6-dichlorophenolindophenol, to isolate a polyethylene-degrading bacterium, Acinetobacter guillouiae, from insect larvae. Plastic-degrading strains are identified by the color change in the redox indicator from blue to colorless as plastic metabolism occurs. Polyethylene biodegradation by A. guillouiae was verified through weight loss, surface erosion, physiological evidence, and chemical changes on the plastic surface. In addition, we analyzed the characteristics of hydrocarbon metabolism in polyethylene-degrading bacteria. Results suggested that alkane hydroxylation and alcohol dehydrogenation were key steps in polyethylene degradation. This novel screening method will pave the way for high-throughput screening of polyethylene-degrading microorganisms and extending its application to other types of plastics may potentially address plastic pollution.

A sensitive pH indicator-based spectrophotometric assay for PHB depolymerase activity on microtiter plates

A continuous spectrophotometric assay for the screening of PHB depolymerase activity in microtiter plates was developed. We evaluated crystalline PHB in the suspension and coated it with the addition of a pH indicator to detect the breakage of the ester bond by proton titration. The reaction rate and the concentration of the recombinant PhaZ1 from Paucimonas lemoignei PHB depolymerase presented a linear correlation. A comparison of the proposed method with the turbidimetric method adapted to the microtiter plates revealed that the use of indicators increases the response signal by at least 5-fold, resulting in increased sensitivity and better signal-to-noise ratio. Furthermore, the proposed method offers a wide range of pH from 5.0 to 9.2 by using different buffer-indicator pairs and was employed for the screening of PHB-depolymerase activity on 140 bacterial strains isolated from Lake Chapala. Eleven strains were positive for PHB-depolymerase activity, which were ACSLRF-27, ACPLRF-6, and ACPLRF-5 (16S rRNA sequence alignment revealed 99-100% similarity with Actinomadura geliboluensis strain A8036, Streptomyces cavourensis strain NRRL 2740, and Streptomyces coelicolor strain DSM 40233, respectively); these that showed the highest activities. In conclusion, the method was successfully applied for finding new strains and for quantifying the PHB depolymerases activity with crystalline PHB.

Difference in solid-state properties and enzymatic degradation of three kinds of poly(butylene succinate)/cellulose blends

Mechanical and crystalline properties of PBS/CMC and PBS/CA blends were improved and their enzymolysis was better than for a PBS/CTA blend.

Laser microperforated biodegradable microbial polyhydroxyalkanoate substrates for tissue repair strategies: an infrared microspectroscopy study

Flexible and biodegradable film substrates prepared by solvent casting from poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBHV) solutions in chloroform were microperforated by ultraviolet laser ablation and subsequently characterized using infrared (IR) microspectroscopy and imaging techniques and scanning electron microscopy (SEM). Both transmission synchrotron IR microspectroscopy and attenuated total reflectance microspectroscopy measurements demonstrate variations in the polymer at the ablated pore rims, including evidence for changes in chemical structure and crystallinity. SEM results on microperforated PHBHV substrates after cell culture demonstrated that the physical and chemical changes observed in the biomaterial did not hinder cell migration through the pores.

Biosynthesis and biodegradation of 3-hydroxypropionate-containing polyesters

3-Hydroxypropionate (3HP) is an important compound in the chemical industry, and the polymerized 3HP can be used as a bioplastic. In this review, we focus on polyesters consisting of 3HP monomers, including the homopolyester poly(3-hydroxypropionate) and copolyesters poly(3-hydroxybutyrate-co-3-hydroxypropionate), poly(3-hydroxypropionate-co-3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate), poly(4-hydroxybutyrate-co-3-hydroxypropionate-co-lactate), and poly(3-hydroxybutyrate-co-3-hydroxypropionate-co-4-hydroxybutyrate-co-lactate). Homopolyesters like poly(3-hydroxybutyrate) are often highly crystalline and brittle, which limits some of their applications. The incorporation of 3HP monomers reduces the glass transition temperature, the crystallinity, and also, at up to 60 to 70 mol% 3HP, the melting point of the copolymer. This review provides a survey of the synthesis and physical properties of different polyesters containing 3HP.

Enzymatic processes for biodegradation of poly(hydroxyalkanoate)s crystals

Poly(hydroxyalkanoate)s (PHAs) have attracted much attention as environmentally compatible polymeric materials that can be produced from renewable carbon resources. Biodegradation of PHA materials occurs by the function of extracellular PHA depolymerase secreted from microorganisms. Thus, elucidation of the enzymatic degradation mechanism for PHA materials is important to design PHA materials with desirable properties and controlled biodegradability. The solid PHA polymer is a water-insoluble substrate but PHA depolymerases are soluble in water. Therefore, the enzymatic degradation of PHA materials is a heterogeneous reaction on the material’s surface. Two distinct processes are involved during the degradation, namely, adsorption of the enzyme on the surface of PHA material and the subsequent hydrolysis of polymer chains. Atomic force microscopy (AFM) is a powerful tool that has been used for the quantitative analysis of PHA crystal degradation. AFM enables the characterization of the crystal surface nanostructure in a buffer solution. By using in-situ (real-time) AFM observations, we recently succeeded in observing the degradation processes of PHA crystals. Subsequently, we were also able to investigate the degradation rates of PHA crystals using the same technique. In this review, we have attempted to give an overview concerning the direct visualization of the adsorption, as well as the hydrolysis reactions of PHA depolymerases at the nanometer scale. In addition, we present other analytical techniques besides AFM as a complimentary approach to analyze the effect of enzyme adsorption on PHA crystals.Key words: poly(hydroxyalkanoate) (PHA), enzymatic degradation, lamellar crystal, PHA depolymerase.

Peculiarities of PHA granules preparation and PHA depolymerase activity determination

An extensive amount of knowledge on biochemistry of poly(3-hydroxyalkanoic acid) (PHA) synthesis and on its biodegradation has accumulated during the last two decades. Numerous genes encoding enzymes involved in the formation of PHA and in PHA degradation (PHA depolymerases) were cloned and characterized from many microorganisms. A large variety of methods exists for determination of PHA depolymerase activity and for preparation of the polymeric substrate (PHA). Unfortunately, results obtained with these different methods cannot be compared directly because they highly depend on the assay method applied and on the history of PHA granules preparation. In this contribution, the peculiarities, advantages, disadvantages and limitations of existing PHA depolymerase assay methods are described.

Assay of poly(3-hydroxybutyrate) depolymerase activity and product determination

Two methods for accurate poly(3-hydroxybutyrate) (PHB) depolymerase activity determination and quantitative and qualitative hydrolysis product determination are described. The first method is based on online determination of NaOH consumption rates necessary to neutralize 3-hydroxybutyric acid (3HB) and/or 3HB oligomers produced during the hydrolysis reaction and requires a pH-stat apparatus equipped with a software-controlled microliter pump for rapid and accurate titration. The method is universally suitable for hydrolysis of any type of polyhydroxyalkanoate or other molecules with hydrolyzable ester bonds, allows the determination of hydrolysis rates of as low as 1 nmol/min, and has a dynamic capacity of at least 6 orders of magnitude. By applying this method, specific hydrolysis rates of native PHB granules isolated from Ralstonia eutropha H16 were determined for the first time. The second method was developed for hydrolysis product identification and is based on the derivatization of 3HB oligomers into bromophenacyl derivates and separation by high-performance liquid chromatography. The method allows the separation and quantification of 3HB and 3HB oligomers up to the octamer. The two methods were applied to investigate the hydrolysis of different types of PHB by selected PHB depolymerases.

Interaction between poly[(R)-3-hydroxybutyrate] depolymerase and biodegradable polyesters evaluated by atomic force microscopy

Adsorption of PHB depolymerase from Ralstonia pickettii T1 to biodegradable polyesters such as poly[(R)-3-hydroxybutyrate] (PHB) and poly(l-lactic acid) (PLLA) was investigated by atomic force microscopy (AFM). The substrate-binding domain (SBD) with histidines within the N-terminus was prepared and immobilized on the AFM tip surface via a self-assembled monolayer with a nitrilotriacetic acid group. Using the functionalized AFM tips, the force-distance measurements for polyesters were carried out at room temperature in a buffer solution. In the case of AFM tips with immobilized SBD and their interaction with polyesters, multiple pull-off events were frequently recognized in the retraction curves. The single rupture force was estimated at approximately 100 pN for both PLLA and PHB. The multiple pull-off events were recognized even in the presence of a surfactant, which will prevent nonspecific interactions, but reduced when using polyethylene instead of polyesters as a substrate. The present results provide that the PHB depolymerase adsorbs specifically to the surfaces of polyesters and that the single unbinding event evaluated here is mainly associated with the interaction between one molecule of SBD and the polymer surface.

Enzymatic degradation processes of lamellar crystals in thin films for poly[(R)-3-hydroxybutyric acid] and its copolymers revealed by real-time atomic force microscopy

Enzymatic degradation processes of flat-on lamellar crystals in melt-crystallized thin films of poly[(R)-3-hydroxybutyric acid] (P(3HB)) and its copolymers were characterized by real-time atomic force microscopy (AFM) in a phosphate buffer solution containing PHB depolymerase from Ralstonia pickettii T1. Fiberlike crystals with regular intervals were generated along the crystallographic a axis at the end of lamellar crystals during the enzymatic degradation. The morphologies and sizes of the fiberlike crystals were markedly dependent on the compositions of comonomer units in the polyesters. Length, width, interval, and thickness of the fiberlike crystals after the enzymatic degradation for 2 h were measured by AFM, and the dimensions were related to the solid-state structures of P(3HB) and its copolymers. The width and thickness decreased at the tip of fiberlike crystals, indicating that the enzymatic degradation of crystals takes place not only along the a axis but also along the b and c axes. These results from AFM measurement were compared with the data on crystal size by wide-angle X-ray diffraction, and on lamellar thickness and long period by small-angle X-ray scattering. In addition, the enzymatic erosion rate of flat-on lamellar crystals along the a axis was measured from real-time AFM height images. A schematic glacier model for the enzymatic degradation of flat-on lamellar crystals of P(3HB) by PHB depolymerase has been proposed on the basis of the AFM observations.

Degradation of polyesters by a novel marine Nocardiopsis aegyptia sp. nov.: Application of Plackett-Burman experimental design for the improvement of PHB depolymerase activity

This is the first report on the degradation of poly(3-hydroxybutyrate) (PHB), and its copolymers poly(3-hydroxyvalerate) P(3HB-co-10-20% HV) by Nocardiopsis aegyptia, a new species isolated from marine seashore sediments. The strain excreted an extracellular PHB depolymerase and grew efficiently on PHB or its copolymers as the sole carbon sources. The degradation activity was detectable by the formation of a transparent clearing zone around the colony on an agar Petri plate after 25 days, or a clearing depth under the colony in test tubes within 3 weeks. The previous techniques proved that the bacterium was able to assimilate the monomeric components of the shorter alkyl groups of the polymers. Nocardiopsis aegyptia hydrolyzed copolymers 10-20% PHBV more rapidly than the homopolymer PHB. The bacterial degradation of the naturally occurring sheets of poly(3-hydroxybutyrate), and its copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) was observed by scanning electron microscopy (SEM). The samples were degraded at the surface and proceeded to the inner part of the materials. Clear morphological alterations of the polymers were noticed, indicating the degradative capability of the bacterium. Plackett-Burman statistical experimental design has been employed to optimize culture conditions for maximal enzyme activity. The main factors that had significant positive effects on PHB depolymerase activity of Nocardiopsis aegyptia were sodium gluconate, volume of medium/flask and age of inoculum. On the other hand, MgSO4.7H2O, KH2PO4, K2HPO4 and NH4NO3 exhibited negative effects. Under optimized culture conditions, the highest activity (0.664 U/mg protein) was achieved in a medium predicted to be near optimum containing (in g/L): PHB, 0.5; C6H11O7Na, 7.5; MgSO4.7H2O, 0.35; K2HPO4, 0.35; NH4NO3, 0.5; KH2PO4, 0.35; malt extract, 0.5 and prepared with 50% seawater. The medium was inoculated with 1% (v/v) spore suspension of 7 days old culture. Complete clarity of the medium was achieved after 3 days at 30 degrees C.

Change of surface structure of poly(3-hydroxybutyrate) film upon enzymatic hydrolysis by PHB depolymerase

The change in the surface structure of poly[(R)-3-hydroxybutyrate] [PHB] films upon the enzymatic hydrolysis was analyzed by attenuated total reflection infrared [ATR/IR] spectrometry. As enzymes, PHB depolymerases isolated from Ralstonia pickettii T1 and Pseudomonas stutzeri were used. By curve decomposition of the carbonyl stretching band of ATR/IR spectra, the change in the surface crystallinity of PHB films by exposure to buffer containing 0, 1, and 4 microg of PHB depolymerases was estimated. It has been widely believed that the enzymatic hydrolysis first occurs in the amorphous phase, followed by the degradation in the crystalline phase, and extracellular PHB depolymerase can degrade only polymer chains in the surface layer of the film. Therefore, the surface crystallinity had been expected to increase upon the enzymatic degradation. However, the results were contrary to this expectation. The surface crystallinity was decreased by the enzymatic attack. Because ATR/IR spectrometry is sensitive to a small change in molecular structure of the sample surface, the decrease in the crystallinity shown by ATR/IR experiments probably does not indicate the complete loss of regularity of the crystalline phase. Because the chains at crystalline surface are more mobile than those inside the crystals, the C=O band for crystalline surface may appear at a position similar to those of the amorphous or interfacial phase in ATR/IR spectra of PHB. Only the chains inside the crystals may contribute to the C=O band of the crystalline phase. Thus, we rather suppose that the decrease in the crystalline peak of the ATR/IR spectra reflects the change in chain mobility or the increase of crystalline surface area by cracking of lamellas at the surface layers of PHB films or both.

Enzymatic hydrolysis of chemosynthesized atactic poly(3-hydroxybutyrate) by poly(3-hydroxyalkanoate) depolymerase from Acidovorax Sp. TP4 and Ralstonia pickettii T1

The enzymatic degradability of chemosynthesized atactic poly([R,S]-3-hydroxybutyrate) [a-P(3HB)] by two types of extracellular poly(3-hydroxyalkanoate) (PHA) depolymerases purified from Ralstonia pickettii T1 (PhaZ(ral)) and Acidovorax Sp. TP4 (PhaZ(aci)), defined respectively as PHA depolymerase types I and II according to the position of the lipase box in the catalytic domain, were studied. The enzymatic degradation of a-P(3HB) by PhaZ(aci) depolymerase was confirmed from the results of weight loss and the scanning electron micrographs. The degradation products were characterized by one- and two-dimension (1)H NMR spectroscopy. It was found that a-P(3HB) could be degraded into monomer, dimer, and trimer by PhaZ(aci) depolymerase at temperatures ranging from 4 to 20 degrees C, while a-P(3HB) could hardly be hydrolyzed by PhaZ(ral) depolymerase in the same temperature range. These results suggested that the chemosynthesized a-P(3HB) could be degraded in the pure state by natural PHA depolymerase.

Enzymatic hydrolysis of bacterial poly(3-hydroxybutyrate-co-3-hydroxypropionate)s by poly(3-hydroxyalkanoate) depolymerase from Acidovorax Sp. TP4

Enzymatic degradability has been investigated for a series of bacterial poly(3-hydroxybutyrate-co-3-hydroxypropionate)s (P(3HB-co-3HP)s) with 3-hydroxypropionate (3HP) unit contents from 11 to 86 mol % as well as poly(3-hydroxybutyrate) (P(3HB)) and chemosynthesized poly(3-hydroxypropionate) (P(3HP)). The behavior of degradation by two types of extracellular poly(3-hydroxyalkanoate) (PHA) depolymerases purified from Ralstonia pikettii T1 and Acidovorax Sp. TP4, defined respectively as PHA depolymerase types I and II according to the position of the lipase box in the catalytic domain, were compared in relation to the thermal properties and crystalline structures of the PHA samples elucidated by differential scanning calorimetry and wide-angle X-ray diffraction. The degradation products were characterized by high-performance liquid chromatography and one- (1D) and two-dimension (2D) (1)H NMR spectroscopy. It was found that the PHA depolymerase of Acidovorax Sp. TP4 showed degradation behavior different from that shown by depolymerase of R. pikettii T1. PHA depolymerase from Acidovorax Sp. TP4 degraded the P(3HB-co-3HP) films with lower crystallinity in higher rates than those with higher crystallinity, no matter what kinds of crystalline structures they formed. In contrast, PHA depolymerase from R. pikettii T1 degraded P(3HB-co-3HP) films forming P(3HB) crystalline structure in higher rates than those forming P(3HP)s. The increase in amorphous nature of the P(3HB-co-3HP) films with P(3HB)-homopolymer-like crystalline structure increases and then decreases the rate of degradation by depolymerase from R. pikettii T1. The 3-hydroxybutyrate (3HB) monomer was produced as a major product by the hydrolysis of P(3HB) film by PHA depolymerase from Acidovorax Sp. TP4. The P(3HB-co-3HP) films could be degraded into 3HB and 3-hydroxypropionate (3HP) monomer at last, indicating that the catalytic domain of the enzyme recognized at least two monomeric units as substrates. While the PHA depolymerase from R. pikettii T1 hydrolyzed P(3HB) film into 3HB dimer as a major product, and the catalytic domain recognized at least three monomeric units. The degradation behavior of P(3HB-co-3HP) films by the PHA depolymerase of Acidovorax Sp. TP4 could be distinguished from that by the depolymerase of R. pikettii T1.