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

Superior sequence-controlled poly(L-lactide)-based bioplastic with tunable seawater biodegradation

Developing superior-performance marine-biodegradable plastics remains a critical challenge in mitigating marine plastic pollution. Commercially available biodegradable polymers, such as poly(L-lactide) (PLA), undergo slow degradation in complex marine environments. This study introduces an innovative bioplastic design that employs a facile ring-opening and coupling reaction to incorporate hydrophilic polyethylene glycol (PEG) into PLA, yielding PEG-PLA copolymers with either sequence-controlled alternating or random structures. These materials exhibit exceptional toughness in both wet and dry states, with an elongation at break of 1446.8% in the wet state. Specifically, PEG4kPLA2k copolymer biodegraded rapidly in proteinase K enzymatic solutions and had a significant weight loss of 71.5% after 28 d in seawater. The degradation primarily affects the PLA segments within the PEG-PLA copolymer, as evidenced by structural changes confirmed through comprehensive characterization techniques. The seawater biodegradability, in line with the Organization for Economic Cooperation and Development 306 Marine biodegradation test guideline, reached 72.63%, verified by quantitative biochemical oxygen demand analysis, demonstrating rapid chain scission in marine environments. The capacity of PEG-PLA bioplastic to withstand DI water and rapidly biodegrade in seawater makes it a promising candidate for preventing marine plastic pollution.

Molecular Chirality of Biosynthesized PHB Translates into Uniformly Curved Single Crystals in Langmuir Films

While in nature, molecular chirality enables the formation of chiral macroscopic structures through crystallization and self-organization, such a transfer of molecular information to higher hierarchical levels is rarely observed in vitro. Here, the study reports on single crystals of microbially synthesized polyester poly[(R)-3-hydroxybutyrate], which have chiral habits when grown at the air-water interface, in analogy to the 2D crystallization of chiral lipids such as DPPC. Depending on the crystallization conditions, the chiral single crystals either undergo a transition into fiber-like structures, orassemble into larger superstructures with a uniform sense of rotation.

Poly(lactic acid)/Poly(3-hydroxybutyrate) Biocomposites with Differently Treated Cellulose Fibers

The growing concern about environmental pollution has generated an increased demand for biobased and biodegradable materials intended particularly for the packaging sector. Thus, this study focuses on the effect of two different cellulosic reinforcements and plasticized poly(3-hydroxybutyrate) (PHB) on the properties of poly(lactic acid) (PLA). The cellulose fibers containing lignin (CFw) were isolated from wood waste by mechanical treatment, while the ones without lignin (CF) were obtained from pure cellulose by acid hydrolysis. The biocomposites were prepared by means of a melt compounding-masterbatch technique for the better dispersion of additives. The effect of the presence or absence of lignin and of the size of the cellulosic fibers on the properties of PLA and PLA/PHB was emphasized by using in situ X-ray diffraction, polarized optical microscopy, atomic force microscopy, and mechanical and thermal analyses. An improvement of the mechanical properties of PLA and PLA/PHB was achieved in the presence of CF fibers due to their smaller size, while CFw fibers promoted an increased thermal stability of PLA/PHB, owing to the presence of lignin. The overall thermal and mechanical results show the great potential of using cheap cellulose fibers from wood waste to obtain PLA/PHB-based materials for packaging applications as an alternative to using fossil based materials. In addition, in situ X-ray diffraction analysis over a large temperature range has proven to be a useful technique to better understand changes in the crystal structure of complex biomaterials.

A Review on Biological Synthesis of the Biodegradable Polymers Polyhydroxyalkanoates and the Development of Multiple Applications

Polyhydroxyalkanoates, or PHAs, belong to a class of biopolyesters where the biodegradable PHA polymer is accumulated by microorganisms as intracellular granules known as carbonosomes. Microorganisms can accumulate PHA using a wide variety of substrates under specific inorganic nutrient limiting conditions, with many of the carbon-containing substrates coming from waste or low-value sources. PHAs are universally thermoplastic, with PHB and PHB copolymers having similar characteristics to conventional fossil-based polymers such as polypropylene. PHA properties are dependent on the composition of its monomers, meaning PHAs can have a diverse range of properties and, thus, functionalities within this biopolyester family. This diversity in functionality results in a wide array of applications in sectors such as food-packaging and biomedical industries. In order for PHAs to compete with the conventional plastic industry in terms of applications and economics, the scale of PHA production needs to grow from its current low base. Similar to all new polymers, PHAs need continuous technological developments in their production and material science developments to grow their market opportunities. The setup of end-of-life management (biodegradability, recyclability) system infrastructure is also critical to ensure that PHA and other biobased biodegradable polymers can be marketed with maximum benefits to society. The biobased nature and the biodegradability of PHAs mean they can be a key polymer in the materials sector of the future. The worldwide scale of plastic waste pollution demands a reformation of the current polymer industry, or humankind will face the consequences of having plastic in every step of the food chain and beyond. This review will discuss the aforementioned points in more detail, hoping to provide information that sheds light on how PHAs can be polymers of the future.

Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates

Biodegradable and compostable plastics are getting more attention as the environmental impacts of fossil-fuel-based plastics are revealed. Microbes can consume these plastics and biodegrade them within weeks to months under the proper conditions. The biobased polyhydroxyalkanoate (PHA) polymer family is an attractive alternative due to its physicochemical properties and biodegradability in soil, aquatic, and composting environments. Standard test methods are available for biodegradation that employ either natural inocula or defined communities, the latter being preferred for standardization and comparability. The original marine biodegradation standard test method ASTM D6691 employed such a defined consortium for testing PHA biodegradation. However, the taxonomic composition and metabolic potential of this consortium have never been confirmed using DNA sequencing technologies. To this end, we revived available members of this consortium and determined their phylogenetic placement, genomic sequence content, and metabolic potential. The revived members belonged to the Bacillaceae, Rhodobacteraceae, and Vibrionaceae families. Using a comparative genomics approach, we found all the necessary enzymes for both PHA production and utilization in most of the members. In a clearing-zone assay, three isolates also showed extracellular depolymerase activity. However, we did not find classical PHA depolymerases, but identified two potentially new extracellular depolymerases that resemble triacylglycerol lipases.

Surface Analysis of Native Spider Draglines by FE-SEM and XPS

Although the physical and biological functions of the skin layer of spider dragline have been studied and partially clarified, the morphology and elemental contents of the skin layer of silk fibers have not been investigated in detail to date. Here, the surface of Nephila clavata spider dragline was evaluated by field emission scanning electron microscopy (FE-SEM) and X-ray photoelectron spectroscopy (XPS) to obtain clear surface morphological and molecular information. The FE-SEM images of the spider dragline indicate that the spider dragline forms a bundle of microfibrils. This hierarchical structure might induce faint fibrilar and network-like patterns on the surface of the dragline. XPS analysis revealed the presence of Na, P, and S, which are reasonably explained by considering the biological components of the major ampullate gland of spiders. The results obtained here are preliminary but will be important to consider the molecular transition of silk proteins to form excellent hierarchical structures during the spider dragline spinning process.

Peptide-derived Method to Transport Genes and Proteins Across Cellular and Organellar Barriers in Plants

The capacity to introduce exogenous proteins and express (or down-regulate) specific genes in plants provides a powerful tool for fundamental research as well as new applications in the field of plant biotechnology. Viable methods that currently exist for protein or gene transfer into plant cells, namely Agrobacterium and microprojectile bombardment, have disadvantages of low transformation frequency, limited host range, or a high cost of equipment and microcarriers. The following protocol outlines a simple and versatile method, which employs rationally-designed peptides as delivery agents for a variety of nucleic acid- and protein-based cargoes into plants. Peptides are selected as tools for development of the system due to their biodegradability, reduced size, diverse and tunable properties as well as the ability to gain intracellular/organellar access. The preparation, characterization and application of optimized formulations for each type of the wide range of delivered cargoes (plasmid DNA, double-stranded DNA or RNA, and protein) are described. Critical steps within the protocol, possible modifications and existing limitations of the method are also discussed.

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.

Enzyme-Mimic Peptide Assembly To Achieve Amidolytic Activity

Amyloid fibers are classified as a new generation of tunable bionanomaterials that exhibit new functions related to their distinctive characteristics, such as their universality, tunability, and stiffness. Here, we introduce the catalytic residues of serine protease into a peptide catalyst (PC) via an enzyme-mimic approach. The rational design of a repeating pattern of polar and nonpolar amino acids favors the conversion of the peptides into amyloid-like fibrils via self-assembly. Distinct fibrous morphologies have been observed at different pH values and temperatures, which indicates that different fibril packing schemes can be designed; hence, fibrillar peptides can be used to generate efficient artificial catalysts for amidolytic activities at mild pH values. The results of atomic force microscopy, Raman spectroscopy, and wide-angle X-ray scattering analyses are used to discuss and compare the fibril structure of a fibrillar PC with its amidolytic activity. The pH of the fibrillation reaction crucially affects the pK_a of the side chains of the catalytic triads and is important for stable fibril formation. Temperature is another important parameter that controls the self-assembly of peptides into highly stacked and laminated morphologies. The morphology and stability of fibrils are crucial and represent important factors for demonstrating the capability of the peptides to exert amidolytic activity. The observed amidolytic activity of PC4, one of the PCs, was validated using an inhibition assay, which revealed that PC4 can perform enzyme-like amidolytic catalysis. These results provide insights into the potential use of designed peptides in the generation of efficient artificial enzymes.

Synthesis of High-Molecular-Weight Polyhydroxyalkanoates by Marine Photosynthetic Purple Bacteria

Polyhydroxyalkanoate (PHA) is a biopolyester/bioplastic that is produced by a variety of microorganisms to store carbon and increase reducing redox potential. Photosynthetic bacteria convert carbon dioxide into organic compounds using light energy and are known to accumulate PHA. We analyzed PHAs synthesized by 3 purple sulfur bacteria and 9 purple non-sulfur bacteria strains. These 12 purple bacteria were cultured in nitrogen-limited medium containing acetate and/or sodium bicarbonate as carbon sources. PHA production in the purple sulfur bacteria was induced by nitrogen-limited conditions. Purple non-sulfur bacteria accumulated PHA even under normal growth conditions, and PHA production in 3 strains was enhanced by nitrogen-limited conditions. Gel permeation chromatography analysis revealed that 5 photosynthetic purple bacteria synthesized high-molecular-weight PHAs, which are useful for industrial applications. Quantitative reverse transcription polymerase chain reaction analysis revealed that mRNA levels of phaC and PhaZ genes were low under nitrogen-limited conditions, resulting in production of high-molecular-weight PHAs. We conclude that all 12 tested strains are able to synthesize PHA to some degree, and we identify 5 photosynthetic purple bacteria that accumulate high-molecular-weight PHA molecules. Furthermore, the photosynthetic purple bacteria synthesized PHA when they were cultured in seawater supplemented with acetate. The photosynthetic purple bacteria strains characterized in this study should be useful as host microorganisms for large-scale PHA production utilizing abundant marine resources and carbon dioxide.

Local gene silencing in plants via synthetic dsRNA and carrier peptide

Quick and facile transient RNA interference (RNAi) is one of the most valuable plant biotechnologies for analysing plant gene functions. To establish a novel double-strand RNA (dsRNA) delivery system for plants, we developed an ionic complex of synthetic dsRNA with a carrier peptide in which a cell-penetrating peptide is fused with a polycation sequence as a gene carrier. The dsRNA-peptide complex is 100-300 nm in diameter and positively charged. Infiltration of the complex into intact leaf cells of Arabidopsis thaliana successfully induced rapid and efficient down-regulation of exogenous and endogenous genes such as yellow fluorescent protein and chalcone synthase. The present method realizes quick and local gene silencing in specific tissues and/or organs in plants.

Rapid and efficient gene delivery into plant cells using designed peptide carriers

To develop a new easy and quick gene delivery system for any types of plants, we prepared ionic complexes of plasmid DNA with designed peptide carriers, each of which combined a cell-penetrating peptide (Bp100 or Tat(2)) with a polycation (nona-arginine or a copolymer of histidine and lysine). The present system via the designed peptides demonstrated rapid and efficient transient transfections into intact leaf cells of Nicotiana benthamiana and Arabidopsis thaliana without protoplast preparations. The designed peptides demonstrated significantly higher transfection efficiency in comparison to the nonfusion peptides (Bp100, Tat2, nona-arginine, and copolymer of histidine and lysine), indicating that the combination of functional peptides was a key to develop an efficient peptide-based gene delivery system. On the basis of the results, we exhibited the versatility of the designed peptide-based gene delivery system, which will explore the application of plant biotechnology.

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.

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.

Microscopic examination in vivo and in vitro of natural and cross-linked polyunsaturated mclPHA

Pseudomonas aeruginosa 42A2 produces a polyunsaturated polyhydroxyalkanoates (PHA-L) when grown on linseed oil as a substrate. Its high unsaturation content (36.5%) provides highly reactive PHA-L, generating a cross-linked biopolymer after ultraviolet (UV) irradiation. Both PHAs (PHA-L and uvPHA-L) were characterized by nuclear magnetic resonance, Fourier transform infrared spectroscopy, gel permeation chromatography, gas chromatography-mass spectrometry and differential scanning calorimetry-thermogravimetric analysis. The structural analysis of the new polymer revealed a dramatic decrease in unsaturated monomer content (8.5%), due to the complete disappearance of the polyunsaturated monomers (C(12:2), C(14:2), and C(14:3)). The cross-linking reaction was also confirmed by atomic force microscopy (AFM) and transmission electron microscopy. AFM showed morphological changes in bacteria cells with and without PHA granules. The microscope techniques provided us with micrographs of the native and cross-linked polymers, showing the formation of a reticular structure as the consequence of the cross-linking reaction.

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.

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.

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.