Enzyme and metabolic engineering for the production of novel biopolymers: crossover of biological and chemical processes

Complete sequence randomness of lactate-based copolymers (LAHBs) with varied lactate monomer fractions employing a series of propionyl-CoA transferases

Previously, we biosynthesized an evolved version of a bio-based polylactide (PLA) on microbial platforms using our engineered lactate-polymerizing enzyme (LPE). This lactate (LA)-based copolyester, LAHB, has advantages over PLA, including improved flexibility and biodegradability, and its properties can be regulated through the LA fraction. To expand the LA-incorporation capacity and improve polymer properties, in the state of in vivo LAHB production, propionyl-CoA transferases (PCTs) that exhibited enhanced production of LA-CoA than the conventional PCTs were selected. Here, the present study has demonstrated that the LA fraction of LAHB could be altered using various PCTs. Enhanced PCT performance was achieved by balancing polymer production and cell growth. Both events are governed by the use of acetyl-CoA, a commonly shared key metabolite. This could be attributed to the different reactivities of individual PCTs towards acetyl-CoA, which serves both as a CoA donor and a leading compound in the TCA cycle. Interestingly, we found complete sequence randomness in the LAHB copolymers, independent of the LA fraction. The mechanism of LA fraction-independent sequence randomness is discussed. This new PCT-based strategy synergistically combines with the evolution of LPE to advance the LAHB project, and enables us to perform advanced applications other than LAHB production utilizing CoA-linked substrates.

Biodegradable polymers – research and applications

The major concern in ecology we are facing in this era of modernization is environmental pollution due to non-biodegradable plastics. Because of its low cost, readily available nature, light weight, corrosion resistance, and added additives, it is adaptable and suitable for a wide range of applications. But the problem is that most of the petroleum-based plastics are not recyclable. Recycling and degradation of plastics are time-consuming and also release harmful chemicals, which pose a great threat to the environment. It is the need of the modern era to focus on the production of biodegradable and eco-friendly polymers as alternatives to these plastics. Nowadays, plant-based polymers are coming onto the market, which are easily degraded into soil with the help of microorganisms. However, commercialization is less due to its high production costs and the requirement for large agricultural lands for production, and their degradation also necessitated the use of special composting techniques. It is urgently needed to produce good quality and a high quantity of biodegradable polymers. The microorganisms are often searched for and screened from the carbon-rich and nutrient-deficient environment, but the commercial value of the polymers from microorganisms is very costly. Moreover, the currently explored microbes like Ralstonia eutropha, Aspergillus eutrophus, Cupriavidus necator, etc. are producing polymers naturally as a carbon reserve. But the quality as well as quantity of production are low, which means they cannot meet our requirements. So, the main aim of this chapter is to focus on the wide applications of different biodegradable polymers from plants, animals and even microbes and recent advancements in their production and improvement of biopolymers to increase their quality and quantity from natural sources, as well as their applications in packaging, the medical field, aquaculture, and other various fields for the commercialization of the product.

Artificial polyhydroxyalkanoate poly[2-hydroxybutyrate-block-3-hydroxybutyrate] elastomer-like material

The first polyhydroxyalkanoate (PHA) block copolymer poly(2-hydroxybutyrate-b-3-hydroxybutyrate) [P(2HB-b-3HB)] was previously synthesized using engineered Escherichia coli expressing a chimeric PHA synthase PhaCAR with monomer sequence-regulating capacity. In the present study, the physical properties of the block copolymer and its relevant random copolymer P(2HB-ran-3HB) were evaluated. Stress-strain tests on the P(88 mol% 2HB-b-3HB) film showed an increasing stress value during elongation up to 393%. In addition, the block copolymer film exhibited slow contraction behavior after elongation, indicating that P(2HB-b-3HB) is an elastomer-like material. In contrast, the P(92 mol% 2HB-ran-3HB) film, which was stretched up to 692% with nearly constant stress, was stretchable but not elastic. The differential scanning calorimetry and wide-angle X-ray diffraction analyses indicated that the P(2HB-b-3HB) contained the amorphous P(2HB) phase and the crystalline P(3HB) phase, whereas P(2HB-ran-3HB) was wholly amorphous. Therefore, the elasticity of P(2HB-b-3HB) can be attributed to the presence of the crystalline P(3HB) phase and a noncovalent crosslinked structure by the crystals. These results show the potential of block PHAs as elastic materials.

Recent advances in the microbial synthesis of lactate-based copolymer

Due to the increasing environmental pollution of un-degradable plastics and the consumption of non-renewable resources, more attention has been attracted by new bio-degradable/based polymers produced from renewable resources. Polylactic acid (PLA) is one of the most representative bio-based materials, with obvious advantages and disadvantages, and has a wide range of applications in industry, medicine, and research. By copolymerizing to make up for its deficiencies, the obtained copolymers have more excellent properties. The development of a one-step microbial metabolism production process of the lactate (LA)-based copolymers overcomes the inherent shortcomings in the traditional chemical synthesis process. The most common lactate-based copolymer is poly(lactate-co-3-hydroxybutyrate) [P(LA-co-3HB)], within which the difference of LA monomer fraction will cause the change in the material properties. It is necessary to regulate LA monomer fraction by appropriate methods. Based on synthetic biology and systems metabolic engineering, this review mainly focus on how did the different production strategies (such as enzyme engineering, fermentation engineering, etc.) of P(LA-co-3HB) optimize the chassis cells to efficiently produce it. In addition, the metabolic engineering strategies of some other lactate-based copolymers are also introduced in this article. These studies would facilitate to expand the application fields of the corresponding materials.

Microbial Production of Biodegradable Lactate-Based Polymers and Oligomeric Building Blocks From Renewable and Waste Resources

Polyhydroxyalkanoates (PHAs) are naturally occurring biopolymers produced by microorganisms. PHAs have become attractive research biomaterials in the past few decades owing to their extensive potential industrial applications, especially as sustainable alternatives to the fossil fuel feedstock-derived products such as plastics. Among the biopolymers are the bioplastics and oligomers produced from the fermentation of renewable plant biomass. Bioplastics are intracellularly accumulated by microorganisms as carbon and energy reserves. The bioplastics, however, can also be produced through a biochemistry process that combines fermentative secretory production of monomers and/or oligomers and chemical synthesis to generate a repertoire of biopolymers. PHAs are particularly biodegradable and biocompatible, making them a part of today's commercial polymer industry. Their physicochemical properties that are similar to those of petrochemical-based plastics render them potential renewable plastic replacements. The design of efficient tractable processes using renewable biomass holds key to enhance their usage and adoption. In 2008, a lactate-polymerizing enzyme was developed to create new category of polyester, lactic acid (LA)-based polymer and related polymers. This review aims to introduce different strategies including metabolic and enzyme engineering to produce LA-based biopolymers and related oligomers that can act as precursors for catalytic synthesis of polylactic acid. As the cost of PHA production is prohibitive, the review emphasizes attempts to use the inexpensive plant biomass as substrates for LA-based polymer and oligomer production. Future prospects and challenges in LA-based polymer and oligomer production are also highlighted.

Bioconversion of biphenyl to a polyhydroxyalkanoate copolymer by Alcaligenes denitrificans A41

A polyhydroxyalkanoate (PHA) copolymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)], was biosynthesized from biphenyl as the sole carbon source using Alcaligenes (currently Achromobacter) denitrificans A41. This strain is capable of degrading polychlorinated biphenyls (PCBs) and biphenyl. This proof-of-concept of the conversion of aromatic chemicals such as the environmental pollutant PCBs/biphenyl to eco-friendly products such as biodegradable polyester PHA was inspired by the uncovering of two genes encoding PHA synthases in the A. denitrificans A41 genome. When the carbon/nitrogen (C/N) ratio was set at 21, the cellular P(3HB-co-3HV) content in strain A41 reached its highest value of 10.1% of the cell dry weight (CDW). A two-step cultivation protocol improved the accumulation of P(3HB-co-3HV) by up to 26.2% of the CDW, consisting of 13.0 mol % 3HV when grown on minimum salt medium without nitrogen sources. The highest cellular content of P(3HB-co-3HV) (47.6% of the CDW) was obtained through the two-step cultivation of strain A41 on biphenyl as the sole carbon source. The purified copolymer had ultra-high molecular weight (weight-average molecular weight of 3.5 × 106), as revealed through gel-permeation chromatography. Based on the genomic information related to both polymer synthesis and biphenyl degradation, we finally proposed a metabolic pathway for the production of P(3HB-co-3HV) associated with the degradation of biphenyl by strain A41.

The Place for Enzymes and Biologically Active Peptides from Marine Organisms for Application in Industrial and Pharmaceutical Biotechnology

Since the beginning of written history, diverse texts have reported the use of enzymatic preparations in food processing and have described the medicinal properties of crude and fractionated venoms to treat various diseases and injuries. With the biochemical characterization of enzymes from distinct sources and bioactive polypeptides from animal venoms, the last sixty years have testified the advent of industrial enzymology and protein therapeutics, which are currently applicable in a wide variety of industrial processes, household products, and pharmaceuticals. Bioprospecting of novel biocatalysts and bioactive peptides is propelled by their unsurpassed properties that are applicable for current and future green industrial processes, biotechnology, and biomedicine. The demand for both novel enzymes with desired characteristics and novel peptides that lead to drug development, has experienced a steady increase in response to the expanding global market for industrial enzymes and peptidebased drugs. Moreover, although largely unexplored, oceans and marine realms, with their unique ecosystems inhabited by a large variety of species, including a considerable number of venomous animals, are recognized as untapped reservoirs of molecules and macromolecules (enzymes and bioactive venom-derived peptides) that can potentially be converted into highly valuable biopharmaceutical products. In this review, we have focused on enzymes and animal venom (poly)peptides that are presently in biotechnological use, and considering the state of prospection of marine resources, on the discovery of useful industrial biocatalysts and drug leads with novel structures exhibiting selectivity and improved performance.

Production of bioplastic through food waste valorization

The tremendous amount of food waste from diverse sources is an environmental burden if disposed of inappropriately. Thus, implementation of a biorefinery platform for food waste is an ideal option to pursue (e.g., production of value-added products while reducing the volume of waste). The adoption of such a process is expected to reduce the production cost of biodegradable plastics (e.g., compared to conventional routes of production using overpriced pure substrates (e.g., glucose)). This review focuses on current technologies for the production of polyhydroxyalkanoates (PHA) from food waste. Technical details were also described to offer clear insights into diverse pretreatments for preparation of raw materials for the actual production of bioplastic (from food wastes). In this respect, particular attention was paid to fermentation technologies based on pure and mixed cultures. A clear description on the chemical modification of starch, cellulose, chitin, and caprolactone is also provided with a number of case studies (covering PHA-based products) along with a discussion on the prospects of food waste valorization approaches and their economic/technical viability.

Enhancement of lactate fraction in poly(lactate-co-3-hydroxybutyrate) synthesized by Escherichia coli harboring the D-lactate dehydrogenase gene from Lactobacillus acetotolerans HT

For enhancing the lactate (LA) fraction of poly(lactate-co-3-hydroxybutyrate)s [P(LA-co-3HB)s], an exogenous D-lactate dehydrogenase gene (ldhD) was introduced into Escherichia coli. Recombinant strains of E. coli DH5α, LS5218, and XL1-Blue harboring the ldhD gene from Lactobacillus acetotolerans HT, together with polyhydroxyalkanoate (PHA)-biosynthetic genes containing a lactate-polymerizing enzyme (modified PHA synthase) gene, accumulated the P(LA-co-3HB) copolymer from glucose under microaerobic conditions (100 strokes/min). The LA fraction of copolymers synthesized in the strains of DH5α, LS5218, and XL1-Blue were 19.8, 15.7, and 28.5 mol%, respectively, which were higher than those of the strains without the ldhD gene (<6.7 mol% of LA units). Introduction of the exogenous ldhD gene into E. coli strains resulted in an enhanced LA fraction in P(LA-co-3HB)s.

A high-sensitivity fluorescent probe with a self-immolative spacer for real-time ratiometric detection and imaging of alkaline phosphatase activity

The probe APW uses a self-immolative mechanism to achieve a ratio response to ALP, which has the following advantages: fast response (in less than 15 min), high quantum yield (Φ = 0.6), low detection limit (0.46 U L⁻¹) and excellent selectivity.

Crystal structure and kinetic analyses of a hexameric form of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum

(S)-3-Hydroxybutyryl-CoA dehydrogenase (HBD) has been gaining increased attention recently as it is a key enzyme in the enantiomeric formation of (S)-3-hydroxybutyryl-CoA [(S)-3HB-CoA]. It converts acetoacetyl-CoA to (S)-3HB-CoA in the synthetic metabolic pathway. (S)-3HB-CoA is further modified to form (S)-3-hydroxybutyrate, which is a source of biodegradable polymers. During the course of a study to develop biodegradable polymers, attempts were made to determine the crystal structure of HBD from Clostridium acetobutylicum (CacHBD), and the crystal structures of both apo and NAD⁺-bound forms of CacHBD were determined. The crystals belonged to different space groups: P2₁2₁2₁ and P2₁. However, both structures adopted a hexamer composed of three dimers in the asymmetric unit, and this oligomerization was additionally confirmed by gel-filtration column chromatography. Furthermore, to investigate the catalytic residues of CacHBD, the enzymatic activities of the wild type and of three single-amino-acid mutants were analyzed, in which the Ser, His and Asn residues that are conserved in the HBDs from C. acetobutylicum, C. butyricum and Ralstonia eutropha, as well as in the L-3-hydroxyacyl-CoA dehydrogenases from Homo sapiens and Escherichia coli, were substituted by alanines. The S117A and N188A mutants abolished the activity, while the H138A mutant showed a slightly lower K_m value and a significantly lower k_cat value than the wild type. Therefore, in combination with the crystal structures, it was shown that His138 is involved in catalysis and that Ser117 and Asn188 may be important for substrate recognition to place the keto group of the substrate in the correct position for reaction.

A non-naturally-occurring P(3HB-co-3HAMCL) is produced by recombinant Pseudomonas sp. from an unrelated carbon source

Pseudomonas sp. PHA^- was used as host for PHA biosynthesis genes from Aeromonas sp. to produce 3HB-co-3HA_MCL from glucose with no supply of co-substrates. A non-naturally-occurring PHA composed mainly of 3HB, 3HHx and 3HD (3HO, 3HDdΔ₅ and 3HDd monomers were detected in smaller amounts) was obtained. The polymer was extracted using two different solvents (acetone and chloroform) and subject to the following characterization tests: FTIR, DSC, TGA and GPC. The latter suggests a block copolymer since a single and narrow elution peak was observed for each sample. The DSC results ruled out the possibility of a random copolymer and agrees with a single copolymer composed of two blocks: one with the typical composition of PHA_MCL produced by Pseudomonas and another containing 3HB and 3HHx with a high 3HHx molar fraction. Thus, this study increases the perspectives of P(3HB-co-3HA_MCL) production from carbohydrates as the sole carbon source.

Lipases: An Overview

Lipases are ubiquitous enzymes, widespread in nature. They were first isolated from bacteria in the early nineteenth century, and the associated research continuously increased due to the characteristics of these enzymes. This chapter reviews the main sources, structural properties, and industrial applications of these highly studied enzymes.

Enhanced production of polyhydroxybutyrate by multiple dividing E. coli

BACKGROUND

Most bacteria are grown in a binary fission way meaning a bacterial cell is equally divided into two. Polyhydroxyalkanoates (PHA) can be accumulated as inclusion bodies by bacteria. The cell division way and morphology have been shown to play an important role in regulating the bacterial growth and PHA storages.

RESULTS

The common growth pattern of Escherichia coli was changed to multiple fission patterns by deleting fission related genes minC and minD together, allowing the formation of multiple fission rings (Z-rings) in several positions of an elongated cell, thus a bacterial cell was observed to be divided into more than two daughter cells at same time. To further improve cell growth and PHA production, some genes related with division process including ftsQ, ftsL, ftsW, ftsN and ftsZ, together with the cell shape control gene mreB, were all overexpressed in E. coli JM109 ∆minCD. The changing pattern of E. coli cell growth and morphology resulted in more cell dry weights (CDW) and more than 80 % polyhydroxybutyrate (PHB) accumulation increases compared to its binary fission control grown under the same conditions.

CONCLUSIONS

This study clearly demonstrated that combined over-expression genes ftsQ, ftsW, ftsN, ftsL and ftsZ together with shape control gene mreB in multiple division bacterial E. coli JM109 ∆minCD benefited PHA accumulation. Our study provides useful information on increasing the yield of PHA by changing the cell division pattern and cell morphology of E. coli.

Engineering cell factories for producing building block chemicals for bio-polymer synthesis

Synthetic polymers are widely used in daily life. Due to increasing environmental concerns related to global warming and the depletion of oil reserves, the development of microbial-based fermentation processes for the production of polymer building block chemicals from renewable resources is desirable to replace current petroleum-based methods. To this end, strains that efficiently produce the target chemicals at high yields and productivity are needed. Recent advances in metabolic engineering have enabled the biosynthesis of polymer compounds at high yield and productivities by governing the carbon flux towards the target chemicals. Using these methods, microbial strains have been engineered to produce monomer chemicals for replacing traditional petroleum-derived aliphatic polymers. These developments also raise the possibility of microbial production of aromatic chemicals for synthesizing high-performance polymers with desirable properties, such as ultraviolet absorbance, high thermal resistance, and mechanical strength. In the present review, we summarize recent progress in metabolic engineering approaches to optimize microbial strains for producing building blocks to synthesize aliphatic and high-performance aromatic polymers.

Advances and needs for endotoxin-free production strains

The choice of an appropriate microbial host cell and suitable production conditions is crucial for the downstream processing of pharmaceutical- and food-grade products. Although Escherichia coli serves as a highly valuable leading platform for the production of value-added products, like most Gram-negative bacteria, this bacterium contains a potent immunostimulatory lipopolysaccharide (LPS), referred to as an endotoxin. In contrast, Gram-positive bacteria, notably Bacillus, lactic acid bacteria (LAB), Corynebacterium, and yeasts have been extensively used as generally recognized as safe (GRAS) endotoxin-free platforms for the production of a variety of products. This review summarizes the currently available knowledge on the utilization of these representative Gram-positive bacteria for the production of eco- and bio-friendly products, particularly natural polyesters, polyhydroxyalkanoates, bacteriocins, and membrane proteins. The successful case studies presented here serve to inspire the use of these microorganisms as a main-player or by-player depending on their individual properties for the industrial production of these desirable targets.

Indirect positive effects of a sigma factor RpoN deletion on the lactate-based polymer production in Escherichia coli

The production of bacterial polyesters, polyhydroxyalkanoates (PHAs), has been improved by several rational approaches such as overexpression and/or engineering of the enzymes directly related to PHA biosynthetic pathways. In this study, a new approach at transcription level has been applied to a new category of the copolymer of lactate (LA) and 3-hydroxybutyrate (3HB), P(LA-co-3HB). When the 4 disrupting mutants of sigma factors in Escherichia coli, rpoN, rpoS, fliA, fecI, were used as platforms for production of P(LA-co-3HB), increases in the production level and LA fraction of the copolymer were observed for the mutant strain with rpoN disruption. These positive impacts on the polymer production were caused in an "indirect manner" via changes in the multiple genes governed by RpoN. A genome-wide engineering by sigma factors would be a versatile approach for the production of value-added products of interest and available for combination with the other beneficial tools.

Improved production of poly(lactic acid)-like polyester based on metabolite analysis to address the rate-limiting step

The biosynthesis of poly(lactic acid) (PLA)-like polymers, composed of >99 mol% lactate and a trace amount of 3-hydroxybutyrate, in engineered Corynebacterium glutamicum consists of two steps; the generation of the monomer substrate lactyl-coenzyme A (CoA) and the polyhydroxyalkanoate (PHA) synthase-catalyzed polymerization of lactyl-CoA. In order to increase polymer productivity, we explored the rate-limiting step in PLA-like polymer synthesis based on quantitative metabolite analysis using liquid chromatography mass spectroscopy (LC-MS). A significant pool of lactyl-CoA was found during polymer synthesis. This result suggested that the rate-limitation occurred at the polymerization step. Accordingly, the expression level of PHA synthase was increased by means of codon-optimization of the corresponding gene that consequently led to an increase in polymer content by 4.4-fold compared to the control. Notably, the codon-optimization did not significantly affect the concentration of lactyl-CoA, suggesting that the polymerization reaction was still the rate-limiting step upon the overexpression of PHA synthase. Another important finding was that the generation of lactyl-CoA was concomitant with a decrease in the acetyl-CoA level, indicating that acetyl-CoA served as a CoA donor for lactyl-CoA synthesis. These results show that obtaining information on the metabolite concentrations is highly useful for improving PLA-like polymer production. This strategy should be applicable to a wide range of PHA-producing systems.

Improved artificial pathway for biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) with high C6-monomer composition from fructose in Ralstonia eutropha

Poly((R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate) [P(3HB-co-3HHx)], a flexible and practical kind of polyhydroxyalkanoates, is generally produced from plant oils and fatty acids by several wild and recombinant bacteria. This study established an improved artificial pathway for the biosynthesis of P(3HB-co-3HHx) with high 3HHx composition from structurally unrelated fructose in Ralstonia eutropha. Depression of (R)-specific reduction of acetoacetyl-CoA by the deletion of phaB1 was an effective modification for formation of the C6-monomer unit from fructose driven by crotonyl-CoA carboxylase/reductase (Ccr). Co-overexpression of phaJ4a, which encodes medium-chain-length (R)-enoyl-CoA hydratase, with ccr promoted the incorporation of both 3HB and 3HHx units. Further introduction of emdMm, a synthetic gene encoding ethylmalonyl-CoA decarboxylase derived from mouse, was remarkably effective for P(3HB-co-3HHx) biosynthesis, probably by converting ethylmalonyl-CoA generated by the reductive carboxylase activity of Ccr back into butyryl-CoA. A high cellular content of P(3HB-co-3HHx) composed of 22mol% 3HHx could be produced from fructose by the engineered strain of R. eutropha with ΔphaB1 genotype expressing ccr, phaJ4a, and emd.

Fatty acid synthesis in Escherichia coli and its applications towards the production of fatty acid based biofuels

The idea of renewable and regenerative resources has inspired research for more than a hundred years. Ideally, the only spent energy will replenish itself, like plant material, sunlight, thermal energy or wind. Biodiesel or ethanol are examples, since their production relies mainly on plant material. However, it has become apparent that crop derived biofuels will not be sufficient to satisfy future energy demands. Thus, especially in the last decade a lot of research has focused on the production of next generation biofuels. A major subject of these investigations has been the microbial fatty acid biosynthesis with the aim to produce fatty acids or derivatives for substitution of diesel. As an industrially important organism and with the best studied microbial fatty acid biosynthesis, Escherichia coli has been chosen as producer in many of these studies and several reviews have been published in the fields of E. coli fatty acid biosynthesis or biofuels. However, most reviews discuss only one of these topics in detail, despite the fact, that a profound understanding of the involved enzymes and their regulation is necessary for efficient genetic engineering of the entire pathway. The first part of this review aims at summarizing the knowledge about fatty acid biosynthesis of E. coli and its regulation, and it provides the connection towards the production of fatty acids and related biofuels. The second part gives an overview about the achievements by genetic engineering of the fatty acid biosynthesis towards the production of next generation biofuels. Finally, the actual importance and potential of fatty acid-based biofuels will be discussed.