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

Biodegradation of Biodegradable Polymers in Mesophilic Aerobic Environments

Finding alternatives to diminish plastic pollution has become one of the main challenges of modern life. A few alternatives have gained potential for a shift toward a more circular and sustainable relationship with plastics. Biodegradable polymers derived from bio- and fossil-based sources have emerged as one feasible alternative to overcome inconveniences associated with the use and disposal of non-biodegradable polymers. The biodegradation process depends on the environment's factors, microorganisms and associated enzymes, and the polymer properties, resulting in a plethora of parameters that create a complex process whereby biodegradation times and rates can vary immensely. This review aims to provide a background and a comprehensive, systematic, and critical overview of this complex process with a special focus on the mesophilic range. Activity toward depolymerization by extracellular enzymes, biofilm effect on the dynamic of the degradation process, CO2 evolution evaluating the extent of biodegradation, and metabolic pathways are discussed. Remarks and perspectives for potential future research are provided with a focus on the current knowledge gaps if the goal is to minimize the persistence of plastics across environments. Innovative approaches such as the addition of specific compounds to trigger depolymerization under particular conditions, biostimulation, bioaugmentation, and the addition of natural and/or modified enzymes are state-of-the-art methods that need faster development. Furthermore, methods must be connected to standards and techniques that fully track the biodegradation process. More transdisciplinary research within areas of polymer chemistry/processing and microbiology/biochemistry is needed.

Biodegradation of Polymeric Mulch Films in Agricultural Soils: Concepts, Knowledge Gaps, and Future Research Directions

The agricultural use of conventional, polyethylene-based mulch films leads to the accumulation of remnant film pieces in agricultural soils with negative impacts for soil productivity and ecology. A viable strategy to overcome this accumulation is to replace conventional with biodegradable mulch films composed of polymers designed to be degraded by soil microorganisms. However, understanding polymer biodegradation in soils remains a significant challenge due to its dependence on polymer properties, soil characteristics, and prevailing environmental conditions. This perspective aims to advance our understanding of the three fundamental steps underlying biodegradation of mulch films in agricultural soils: colonization of the polymer film surfaces by soil microorganisms, depolymerization of the polymer films by extracellular microbial hydrolases, and subsequent microbial assimilation and utilization of the hydrolysis products for energy production and biomass formation. The perspective synthesizes the current conceptual understanding of these steps and highlights existing knowledge gaps. The discussion addresses future research and analytical advancements required to overcome the knowledge gaps and to identify the key polymer properties and soil characteristics governing mulch film biodegradation in agricultural soils.

Enzymatic degradation of dimensionally constrained polyhydroxybutyrate films

The effect of dimensional constraint, imparted by a variation in film thickness, on the enzymatic degradation of polyhydroxybutyrate (PHB) is reported. The characterization of the crystalline structure and the surface topography of solvent-cast PHB thin films revealed strong correlations between film thickness and both crystallinity and crystal anisotropy, with the polymer film becoming more amorphous with decreasing thickness. The enzymatic degradation of the PHB films was characterized using a high precision diffraction metrology, which enabled the visualization of small variations in the degradation behavior. The results show that the degradation rate increases with decreasing thickness due to the corresponding decrease in crystallinity. However, in a nanoscopic ultra-thin PHB specimen, produced by μ-transfer molding, enzymatic degradation was impeded. The enzymatic degradation rate of the PHB films therefore was found to exhibit a discontinuous trend with respect to film thickness: initially increasing as film thickness was reduced, and then decreasing dramatically once the thickness was reduced to tens of nanometers. In this regime, enzymatic degradation was hindered by the absence of crystalline regions in the films. These results show that a nano-dimensional constraint on PHB films can result in specimens with a tunable response to extracellular enzymes.

Biosynthesis of polyhydroxyalkanoates containing hydroxyl group from glycolate in Escherichia coli

Polyhydroxyalkanoates (PHAs) containing hydroxyl groups in a side chain were produced in recombinant Escherichia coli JM109 using glycolate as the sole carbon source. The propionate-CoA transferase (pct) gene from Megasphaera elsdenii and the β-ketothiolase (bktB) gene and phaCAB operon from Ralstonia eutropha H16 were introduced into E. coli JM109. A novel monomer containing a hydroxyl group, dihydroxybutyrate (DHBA), was the expected product of the condensation of glycolyl-CoA and acetyl-CoA by BktB. The recombinant strain produced a PHA containing 1 mol% DHBA. The incorporation of DHBA may have been restricted because the expression of phaAB1 competes for acetyl-CoA. The PHA containing DHBA units were evaluated regarding thermal properties, such as melting temperature, glass transition temperature and thermal degradation temperature. The current study demonstrates a potential use of PHA containing hydroxyl groups as renewable resources in biological materials.

Relationships between physical properties and sequence in silkworm silks

Silk has attracted widespread attention due to its superlative material properties and promising applications. However, the determinants behind the variations in material properties among different types of silk are not well understood. We analysed the physical properties of silk samples from a variety of silkmoth cocoons, including domesticated Bombyx mori varieties and several species from Saturniidae. Tensile deformation tests, thermal analyses, and investigations on crystalline structure and orientation of the fibres were performed. The results showed that saturniid silks produce more highly-defined structural transitions compared to B. mori, as seen in the yielding and strain hardening events during tensile deformation and in the changes observed during thermal analyses. These observations were analysed in terms of the constituent fibroin sequences, which in B. mori are predicted to produce heterogeneous structures, whereas the strictly modular repeats of the saturniid sequences are hypothesized to produce structures that respond in a concerted manner. Within saturniid fibroins, thermal stability was found to correlate with the abundance of poly-alanine residues, whereas differences in fibre extensibility can be related to varying ratios of GGX motifs versus bulky hydrophobic residues in the amorphous phase.

Spider silk-based gene carriers for tumor cell-specific delivery

The present study demonstrates pDNA complexes of recombinant silk proteins containing poly(L-lysine) and tumor-homing peptides (THPs), which are globular and approximately 150-250 nm in diameter, show significant enhancement of target specificity to tumor cells by additions of F3 and CGKRK THPs. We report herein the preparation and study of novel nanoscale silk-based ionic complexes containing pDNA able to home specifically to tumor cells. Particular focus was on how the THP, F3 (KDEPQRRSARLSAKPAPPKPEPKPKKAPAKK), and CGKRK, enhanced transfection specificity to tumor cells. Genetically engineered silk proteins containing both poly(L-lysine) domains to interact with pDNA and the THP to bind to specific tumor cells for target-specific pDNA delivery were prepared using Escherichia coli, followed by in vitro and in vivo transfection experiments into MDA-MB-435 melanoma cells and highly metastatic human breast tumor MDA-MB-231 cells. Non-tumorigenic MCF-10A breast epithelial cells were used as a control cell line for in vitro tumor-specific delivery studies. These results demonstrate that combination of the bioengineered silk delivery systems and THP can serve as a versatile and useful new platform for nonviral gene delivery.

Mechanisms of enzymatic degradation of amyloid Beta microfibrils generating nanofilaments and nanospheres related to cytotoxicity

Amyloid beta (Abeta) fibrils are found in the brain tissue of persons with Alzheimer's disease (AD), where they accumulate as plaques. One way to reduce the level of accumulation of Abeta in the brain and potentially treat AD is with Abeta-degrading enzymes such as neprilysin (NEP) and insulin-degrading enzyme (IDE). However, enzymatic responses and degradation mechanisms of Abeta fibrils (crystalline-state Abeta) have not been investigated, particularly with respect to how to avoid cytotoxicity of the degradation products to neuronal cells. Thus, insight into mechanisms of enzymatic degradation of Abeta fibrils would be instructive as a route to elucidating different structural features related to degradation and to cytotoxicity. We report mechanisms of enzymatic degradation of Abeta with cross-beta structures and show the series of steps involved in the digestion of Abeta microfibrils to nanospheres or nanofilaments by protease XIV or alpha-chymotrypsin, respectively. These degradation products, which contained almost the same secondary structures, exhibited different cytotoxicities, indicating that relationships between nanoassembled structures and cytotoxicity of Abeta peptides are more significant than the beta-sheet content. In addition, the enzymatic digestion at the Lys28 loop region linking the two beta-sheets in Abeta fibrils is suggested as a key target related to cytotoxicity, a feature that can be selectively targeted on the basis of the choice of protease.

Mechanism of enzymatic degradation of beta-sheet crystals

The anti-parallel beta pleated sheet is a fundamental secondary structure in proteins and a major component in silk fibers generated by silkworms and spiders, with a key role to stabilize these proteins via physical cross-links. Importantly, these beta-sheets are fully degradable and nontoxic structures in biology, in contrast for example to beta-amyloid structures formed in disease states. Thus, insight into mechanism of enzymatic degradation would be instructive as a route to elucidating differences among these stable yet different structural features in biological systems. We report on the mechanism of enzymatic degradation of anti-parallel beta pleated sheets with Bombyx mori silk structures, leading to fibrils and subsequently to nanofilaments (2nm thickness and 160nm length). These nanofilaments play a role as nucleators of the crystalline regions, an important feature of the system that can be exploited to design silk-based biomaterials with predictable biodegradability and mechanical properties. The potential toxicity of degradation products from these proteolytic enzymes was also assessed in vitro and no cell toxicity found in vitro for the protease found in vivo in the human body. The degradation mechanism of beta-sheet silk crystals provides additional insight into the significant differences in biological impact between the anti-parallel beta-sheet silk biomaterials reported in this work vs. amyloid structures in disease states, adding to prior descriptions of chemical and structural differences that are more extensively documented.

Biodegradability of Poly(hydroxyalkanoate) Materials

Poly(hydroxyalkanoate) (PHA), which is produced from renewable carbon resources by many microorganisms, is an environmentally compatible polymeric material and can be processed into films and fibers. Biodegradation of PHA material occurs due to the action of extracellular PHA depolymerase secreted from microorganisms in various natural environments. A key step in determining the overall enzymatic or environmental degradation rate of PHA material is the degradation of PHA lamellar crystals in materials; hence, the degradation mechanism of PHA lamellar crystals has been studied in detail over the last two decades. In this review, the relationship between crystal structure and enzymatic degradation behavior, in particular degradation rates, of films and fibers for PHA is described.

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.

The Oil-Absorbing Property of Polyhydroxyalkanoate Films and its Practical Application: A Refreshing New Outlook for an Old Degrading Material

Polyhydroxyalkanoates (PHAs) have attracted the attention of academia and industry because of their plastic-like properties and biodegradability. However, practical applications as a commodity material have not materialized because of their high production cost and unsatisfactory mechanical properties. PHAs are also believed to have high-value applications as an absorbable biomaterial for tissue engineering and drug-delivery devices because of their biocompatibility. However, research in these areas is still in its very early stages. The main problem faced by proponents of PHAs is the lack of a niche area where PHAs will be the most desired material in terms of its function during use rather than because of its eco-friendly virtues after use. Here, we report on the oil-absorbing property of PHA films and its potential applications. By comparing with some of the existing commercial products, the potential application of PHAs as cosmetic oil-blotting films is revealed for the first time. Besides having the ability to rapidly absorb and retain oil, PHA films also have a natural oil-indicator property, showing obvious changes in opacity following oil absorption. Surface analysis revealed that the surface structures such as porosity and smoothness exert great influence on the rapid oil-absorption properties of the PHA films. These newly discovered properties could be exploited to create a niche area for the practical applications of PHAs.

Adsorption and Hydrolysis Reactions of Poly(hydroxybutyric acid) Depolymerases Secreted fromRalstoniapickettiiT1 andPenicilliumfuniculosumonto Poly[(R)-3-hydroxybutyric acid]

Reaction processes of poly[(R)-3-hydroxybutyric acid] (P(3HB)) with two types of poly(hydroxybutyric acid) (PHB) depolymerases secreted from Ralstonia pickettii T1 and Penicillium funiculosum were characterized by means of atomic force microscopy (AFM) and quartz crystal microbalance (QCM). The PHB depolymerase from R. pickettii T1 consists of catalytic, linker, and substrate-binding domains, whereas the one from P. funiculosum lacks a substrate-binding domain. We succeeded in observing the adsorption of single molecules of the PHB depolymerase from R. pickettii T1 onto P(3HB) single crystals and the degradation of the single crystals in a phosphate buffer solution at 37 degrees C by real-time AFM. On the contrary, the enzyme molecule from P. funiculosum was hardly observed at the surface of P(3HB) single crystals by real-time AFM, even though the enzymatic degradation of the single crystals was surely progressed. On the basis of the AFM observations in air of the P(3HB) single crystals after the enzymatic treatments, however, not only the PHB depolymerase from R. pickettii T1 but also that from P. funiculosum adsorbed onto the surface of P(3HB) crystals, and both concentrations of the enzymes on the surface were nearly identical. This means both enzymes were adsorbed onto the surface of P(3HB) single crystals. Moreover, QCM measurements clarified quantitatively the differences in detachment behavior between two types of PHB depolymerases, namely the enzyme from R. pickettii T1 was hardly detached but the enzyme from P. funiculosum was released easily from the surface of P(3HB) crystals under an aqueous condition.

Adsorption of biopolyester depolymerase on silicon wafer and poly[(R)-3-hydroxybutyric acid] single crystal revealed by real-time AFM

The adsorption behavior of PHB depolymerase from R. pickettii T1 on a silicon wafer and on P(3HB) single crystals has been studied by real-time and AFM in air and a buffer solution. First, the morphology of PHB depolymerase adsorbed on a silicon wafer was characterized to show that one molecule of PHB depolymerase has dimensions of 2.2 +/- 0.7 nm height and 16 +/- 5 nm width. The observation of PHB depolymerase adsorbed on a P(3HB) single crystal indicated that the dimensions of enzyme on the crystalline surface in air were 1.2 +/- 0.5 nm high and 28 +/- 7 nm wide, while enzyme molecules with dimensions of 2.1 +/- 0.6 nm height and 16 +/- 7 nm width were detected in a buffer solution. Comparison of the dimensions of PHB depolymerase in air with those in a buffer solution showed that the enzyme was squashed in air, but not in a buffer solution. In addition, the influence of enzymatic adsorption on the molecular state of the P(3HB) crystalline surface was investigated. The AFM images of P(3HB) single crystals after enzymatic adsorption and washing with ethanol indicated that the adhesion of PHB depolymerase changed the molecular state and generated holes on the crystalline surface.

Enzymatic degradation processes of poly[(R)-3-hydroxybutyric acid] and poly[(R)-3-hydroxybutyric acid-co-(R)-3-hydroxyvaleric acid] single crystals revealed by atomic force microscopy: effects of molecular weight and second-monomer composition on erosion rates

Enzymatic degradation processes of poly[(R)-3-hydroxybutyric acid] (P(3HB)) and poly[(R)-3-hydroxybutyric acid-co-(R)-3-hydroxyvaleric acid] (P(3HB-co-3HV)) single crystals in the presence of PHB depolymerase from Ralstonia pickettii T1 were studied by real-time and static atomic force microscopy (AFM) observations. Fibril-like crystals were generated along the long axis of single crystals during the enzymatic degradation, and then the dimensions of fibril-like crystals were analyzed quantitatively. The morphologies and sizes of fibril-like crystals were dependent on the molecular weight and copolymer composition of polymers. For all samples, the crystalline thickness gradually decreased toward a tip from the root of a fibril-like crystal after enzymatic degradation for 1 h. The thinning of fibril-like crystals may be attributed to the destruction of chain-packing structure toward crystallographic c axis by the adsorption of enzyme. From the real-time AFM images, it was found that at the initial stage of degradation the enzymatic erosion started from the disordered chain-packing region in single crystals to form the grooves along the a axis. The generated fibril-like crystals deformed at a constant rate along the a axis with a constant rate after the induction time. The erosion rate at the grooves along the a axis increased with a decrease of molecular weight and with an increase of copolymer composition. On the other hand, the erosion rate along the a axis, at the tip of the fibril-like crystal, was dependent on only the copolymer composition, and the value increased with an increase in the copolymer composition. The morphologies and sizes of fibril-like crystals were governed by both the erosion rates along the a axis at the grooves and tip of fibril-like crystals. In addition, we were able to estimated the overall enzymatic erosion rate of single crystals by PHB depolymerase from the volumetric analysis.

Dynamic Adsorption Behavior of Poly(3-hydroxybutyrate) Depolymerase onto Polyester Surface Investigated by QCM and AFM

Time-dependent adsorption behavior of poly(3-hydroxybutyrate) (PHB) depolymerase from Ralstonia pickettiiT1 on a polyester surface was studied by complementary techniques of quarts crystal microbalance (QCM) and atomic force microscopy (AFM). Amorphous poly(l-lactide) (PLLA) thin films were used as adsorption substrates. Effects of enzyme concentration on adsorption onto the PLLA surface were determined time-dependently by QCM. Adsorption of PHB depolymerase took place immediately after replacement of the buffer solutions with the enzyme solutions in the cell, followed by a gradual increase in the amount over 30 min. The amount of PHB depolymerase molecules adsorbed on the surface of amorphous PLLA thin films increased with an increase in the enzyme concentration. Time-dependent AFM observation of enzyme molecules was performed during the adsorption of PHB depolymerase. The phase response of the AFM signal revealed that the nature of the PLLA surface around the PHB depolymerase molecule was changed due to the adsorption function of the enzyme and that PHB depolymerase adsorbed onto the PLLA surface as a monolayer at a lower enzyme concentration. The number of PHB depolymerase molecules on the PLLA surface depended on the enzyme concentration and adsorption time. In addition, the height of the adsorbed enzyme was found to increase with time when the PLLA surface was crowded with the enzymes. In the case of higher enzyme concentrations, multilayered PHB depolymerases were observed on the PLLA thin film. These QCM and AFM results indicate that two-step adsorption of PHB depolymerase occurs on the amorphous PLLA thin film. First, adsorption of PHB depolymerase molecules takes place through the characteristic interaction between the binding domain of PHB depolymerase and the free surface of an amorphous PLLA thin film. As the adsorption proceeded, the surface region of the thin film was almost covered with the enzyme, which was accompanied by morphological changes. Second, the hydrophobic interactions among the enzymes in the adlayer and the solution become more dominant to stack as a second layer.