Bacterial synthesis of biodegradable polyhydroxyalkanoates

Analysis of two polyhydroxyalkanoate synthases in Bradyrhizobium japonicum USDA 110

Bradyrhizobium japonicum USDA 110 has five polyhydroxyalkanoate (PHA) synthases (PhaC) annotated in its genome: bll4360 (phaC1), bll6073 (phaC2), blr3732 (phaC3), blr2885 (phaC4), and bll4548 (phaC5). All these proteins possess the catalytic triad and conserved amino acid residues of polyester synthases and are distributed into four different PhaC classes. We obtained mutants in each of these paralogs and analyzed phaC gene expression and PHA production in liquid cultures. Despite the genetic redundancy, only phaC1 and phaC2 were expressed at significant rates, while PHA accumulation in stationary-phase cultures was impaired only in the ΔphaC1 mutant. Meanwhile, the ΔphaC2 mutant produced more PHA than the wild type under this condition, and surprisingly, the phaC3 transcript increased in the ΔphaC2 background. A double mutant, the ΔphaC2 ΔphaC3 mutant, consistently accumulated less PHA than the ΔphaC2 mutant. PHA accumulation in nodule bacteroids followed a pattern similar to that seen in liquid cultures, being prevented in the ΔphaC1 mutant and increased in the ΔphaC2 mutant in relation to the level in the wild type. Therefore, we used these mutants, together with a ΔphaC1 ΔphaC2 double mutant, to study the B. japonicum PHA requirements for survival, competition for nodulation, and plant growth promotion. All mutants, as well as the wild type, survived for 60 days in a carbon-free medium, regardless of their initial PHA contents. When competing for nodulation against the wild type in a 1:1 proportion, the ΔphaC1 and ΔphaC1 ΔphaC2 mutants occupied only 13 to 15% of the nodules, while the ΔphaC2 mutant occupied 81%, suggesting that the PHA polymer is required for successful competitiveness. However, the bacteroid content of PHA did not affect the shoot dry weight accumulation.

Bioplastics from Blends of Cassava and Rice Flours: The Effect of Blend Composition

Bioplastics from melt-mixing of cassava flour, rice flour and their blends with compositions of between 0/100 and 100/0 %wt were successfully obtained using twin-screw extrusion and compression molding processes. The influence of blend composition on the bioplastic's properties was studied. It was found that the flour blends were uniformly mixed. The tensile properties and dynamic properties of the flour bioplastics were examined. The tensile strength and storage modulus of compression molded bioplastics based on rice flour was greater than those of the cassava flour, but their flexibility was lower. The tensile strength and storage modulus of the flour blend bioplastics increased with increasing rice flour content. The flour bioplastics showed two glass transitions, one corresponding to glycerol rich phase and the other corresponding to plasticized starch. For plasticized flour blends, the glass transitions were not affected by the blend composition. The improvement in the mechanical properties of the bioplastics produced from the cassava/rice flour blend could be explained by an increase in the crystallinity level resulting from the higher concentration of rice flour. Using flour blends derived from cassava and rice flours, the bioplastics developed in this study offer a greater performance while maintaining environmental compatibility and sustainability, which allows for a substitution of tradition bioplastics from cassava starch.

The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4

The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.

Polyhydroxyalkanoates production by a mixed photosynthetic consortium of bacteria and algae

For the first time, a mixed photosynthetic culture (MPC) consisting of a consortium of bacteria and algae was investigated for its capacity to accumulate polyhydroxyalkanoates (PHA). The culture was subjected to a feast and famine regime in an illuminated environment without supplying oxygen or any other electron acceptor. The MPC accumulated PHA during the feast phase and consumed it in the famine phase, where the PHA consumption was made possible due to oxygen production by algae. The internal cycling of carbohydrates was also observed, which was likely linked to bacterial glycogen being used as an additional source of energy for acetate uptake during the feast phase, and restored in the famine phase via PHA degradation. The MPC reached a PHA content of 20%, with a PHA storage yield per acetate similar to aerobic systems, opening up the possibility of a new sunlight-driven PHA production process without the need for aeration.

Escherichia coli redox mutants as microbial cell factories for the synthesis of reduced biochemicals

Bioprocesses conducted under conditions with restricted O₂ supply are increasingly exploited for the synthesis of reduced biochemicals using different biocatalysts. The model facultative aerobe Escherichia coli, the microbial cell factory par excellence, has elaborate sensing and signal transduction mechanisms that respond to the availability of electron acceptors and alternative carbon sources in the surrounding environment. In particular, the ArcBA and CreBC two-component signal transduction systems are largely responsible for the metabolic regulation of redox control in response to O₂ availability and carbon source utilization, respectively. Significant advances in the understanding of the biochemical, genetic, and physiological duties of these regulatory systems have been achieved in recent years. This situation allowed to rationally-design novel engineering approaches that ensure optimal carbon and energy flows within central metabolism, as well as to manipulate redox homeostasis, in order to optimize the production of industrially-relevant metabolites. In particular, metabolic flux analysis provided new clues to understand the metabolic regulation mediated by the ArcBA and CreBC systems. Genetic manipulation of these regulators proved useful for designing microbial cells factories tailored for the synthesis of reduced biochemicals with added value, such as poly(3-hydroxybutyrate), under conditions with restricted O₂ supply. This network-wide strategy is in contrast with traditional metabolic engineering approaches, that entail direct modification of the pathway(s) at stake, and opens new avenues for the targeted modulation of central catabolic pathways at the transcriptional level.

Microbial cultivation and the role of microbial resource centers in the omics era

Despite tremendous advances in microbial ecology over the past two decades, traditional cultivation methods have failed to grow ecologically more relevant microorganisms in the laboratory, leading to a predominance of weed-like species in the world's culture collections. In this review, we highlight the gap between culture-based and culture-independent methods of microbial diversity analysis, especially in investigations of slow growers, oligotrophs, and fastidious and recalcitrant microorganisms. Furthermore, we emphasize the importance of microbial cultivation and the acquisition of the cultivation-based phenotypic data for the testing of hypotheses arising from genomics and proteomics approaches. Technical difficulties in cultivating novel microorganisms and how modern approaches have helped to overcome these limitations are highlighted. After cultivation, adequate preservation without changes in genotypic and phenotypic features of these microorganisms is necessary for future research and training. Hence, the contribution of microbial resource centers in the handling, preservation, and distribution of this novel diversity is discussed. Finally, we explore the concept of microbial patenting and requisite guidelines of the "Budapest Treaty" for establishment of an International Depositary Authority.

Bionanocomposites: Green sustainable materials for the near future

Bionanocomposites are a novel class of nanosized materials. They contain the constituent of biological origin and particles with at least one dimension in the range of 1–100 nm. There are similarities with nanocomposites but also fundamental differences in the methods of preparation, properties, functionalities, biodegradability, biocompatibility, and applications. The article includes two parts. Bionanocomposite definition and classification along with nanoparticles, biomaterials, and methods of their preparation are initially reviewed. Then, novel approaches developed by our team are presented. The first approach concerns the preparation of bionanocomposites from chitosan and nanoparticles. It is based on the regulated charging of polysaccharide by the gradual shift of solution pH. When charges appear, the biomacromolecules come into the electrostatic interactions with negatively charged nanoparticles that cause the jellification of solutions. It is also applied to form films. They have a nacre-like structure from stacked planar nanoparticles separated by aligned biomacromolecules. The second approach deals with the biomimicking mineralization of biopolymers by using a novel silica precursor. Its advantage over the current sol-gel processing is in the compatibility and regulation of processes and structure of generated silica. Another example of the mineralization is presented by titania. Syntheses are performed in anhydrous ethylene glycol. Processes and structure of bionanocomposites are regulated by water that is added in an amount to only hydrate functional groups in the carbohydrate macromolecule.

Cytosolic lipid inclusions formed during infection by viral and bacterial pathogens

Lipid inclusions play an important role in several pathological processes. Intracellular bacterial pathogens, such as members of the Mycobacterium and Chlamydia species are able to trigger the formation of lipid-laden foamy macrophages. Lipid droplet accumulation in the host constitutes a reservoir used by the bacilli for long-term persistence. Viruses need lipid droplets as assembly platform. We present the current knowledge about structural, functional and regulatory aspects of lipid inclusions.

Introduction of environmentally degradable parameters to evaluate the biodegradability of biodegradable polymers

Environmentally Degradable Parameter (^EdK) is of importance in the describing of biodegradability of environmentally biodegradable polymers (BDPs). In this study, a concept ^EdK was introduced. A test procedure of using the ISO 14852 method and detecting the evolved carbon dioxide as an analytical parameter was developed, and the calculated ^EdK was used as an indicator for the ultimate biodegradability of materials. Starch and polyethylene used as reference materials were defined as the ^EdK values of 100 and 0, respectively. Natural soil samples were inoculated into bioreactors, followed by determining the rates of biodegradation of the reference materials and 15 commercial BDPs over a 2-week test period. Finally, a formula was deduced to calculate the value of ^EdK for each material. The ^EdK values of the tested materials have a positive correlation to their biodegradation rates in the simulated soil environment, and they indicated the relative biodegradation rate of each material among all the tested materials. Therefore, the ^EdK was shown to be a reliable indicator for quantitatively evaluating the potential biodegradability of BDPs in the natural environment.

Characterization of polyhydroxyalkanoates (PHAs) biosynthesis by isolated Novosphingobium sp. THA_AIK7 using crude glycerol

Biodiesel-contaminated wastewater was used to screen for PHAs-producing bacteria by using crude glycerol as the sole carbon source. A gram-negative THA_AIK7 isolate was chosen as a potential PHAs producer. The 16S rRNA phylogeny indicated that THA_AIK7 isolate is a member of Novosphingobium genus which is supported by a bootstrap percentage of 100% with Novosphingobium capsulatum. The 1,487 bp of 16S rRNA gene sequence of THA_AIK7 isolate has been deposited in the GenBank database under the accession number HM031593. Polymer content of 45% cell dry weight was achieved in 72 h with maximum product yield coefficient of 0.29 g PHAs g−1 glycerol. Transmission electron micrograph results exhibited the PHAs granules accumulated inside the bacterial cell. PHAs polymer production in mineral salt media supplemented with 2% (w/v) of crude glycerol at initial pH 7 was extracted by the sodium hypochlorite method. Polymer film spectrographs from Nuclear magnetic resonance displayed a pattern of signal virtually identical to spectra of commercial PHB. Thermal analysis by Differential scanning calorimeter showed a melting temperature at 179°C. Molecular weight analysis by Gel permeation chromatography showed two main peaks of 133,000 and 700 g mol−1 with weight-average molecular weight value of 23,800 and number-average molecular weight value of 755. Endotoxin-free of PHAs polymer was preliminarily assessed by a negative result of the gel-clot formation, Pyrotell® Single test vial, at sensitivity of 0.25 EU ml−1. To our knowledge, this is the first reported test of endotoxin-free PHAs naturally produced from gram-negative bacteria which could be used for biomedical application.

Molecular characterisation of phaCAB from Comamonas sp. EB172 for functional expression in Escherichia coli JM109

In this study, PHA biosynthesis operon of Comamonas sp. EB172, an acid-tolerant strain, consisting of three genes encoding acetyl-CoA acetyltransferase (phaA(Co) gene, 1182 bp), acetoacetyl-CoA reductase (phaB(Co) gene, 738 bp) and PHA synthase, class I (phaC(Co) gene, 1694 bp) were identified. Sequence analysis of the phaA(Co), phaB(Co) and phaC(Co) genes revealed that they shared more than 85%, 89% and 69% identity, respectively, with orthologues from Delftia acidovorans SPH-1 and Acidovorax ebreus TPSY. The PHA biosynthesis genes (phaC(Co) and phaAB(Co)) were successfully cloned in a heterologous host, Escherichia coli JM109. E. coli JM109 transformants harbouring pGEM'-phaC(Co)AB(Re) and pGEM'-phaC(Re)AB(Co) were shown to be functionally active synthesising 33 wt.% and 17 wt.% of poly(3-hydroxybutyrate) [P(3HB)]. E. coli JM109 transformant harbouring the three genes from the acid-tolerant Comamonas sp. EB172 (phaCAB(Co)) under the control of native promoter from Cupriavidus necator, in vivo polymerised P(3HB) when fed with glucose and volatile mixed organic acids (acetic acid:propionic acid:n-butyric acid) in ration of 3:1:1, respectively. The E. coli JM109 transformant harbouring phaCAB(Co) could accumulate P(3HB) at 2g/L of propionic acid. P(3HB) contents of 40.9% and 43.6% were achieved by using 1% of glucose and mixed organic acids, respectively.

Increased Performance of Thermoplastic Packaging Materials by Using a Mild Oxidizing Biobased Additive

Green additives such as prodegradants based on natural fatty acids and iron can improve the environmental profile of thermoplastic packaging materials. We present two studies in which this is demonstrated. In the first study, the addition of a green prodegradant to a 5-layer gas barrier laminate during processing provided a laminate with significantly reduced oxygen transmission due to the resulting oxygen-consuming degradation process. The result shows that material reduction and cost efficiency of packaging laminates can be combined, since 5-layer laminates with reduced oxygen barrier layer thickness and retained gas barrier properties are feasible. The products are interesting from an ecological and economic aspect. In the second study, the addition of a green prodegradant to several qualities of polypropylene that are used in packaging applications leads to materials that are readily degraded in accelerated weathering. The molecular weight of the modified polypropylenes after 830 hours of accelerated weathering is reduced from typically 80.000 g/mole to 1.500–2.500 g/mole. At such molecular weight levels, digestion by microorganisms is feasible. The mild prodegradant used in the study does not lead to degradation during processing. Thermoplastics containing such additives are therefore fully recyclable provided that they have not been exposed to a long period of weathering.

Exploiting metagenomic diversity for novel polyhydroxyalkanoate synthases: production of a terpolymer poly(3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate) with a recombinant Pseudomonas putida strain

A metagenomic library of 2.1×10(6) clones was constructed using oil-contaminated soil from Gujarat (India). One of the fosmid clones, 40N22, encodes a polyhydroxyalkanoate synthase showing 76% identity with an Alcaligenes sp. synthase. The corresponding gene was expressed in Pseudomonas putida KT2440 ΔphaC1 which is impaired in PHA production. The gene conferred the recombinant strain PpKT-40N22 with the ability to produce copolymers with up to 21% in medium-chain-length content. Thus, 37% and 45% of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) and poly(3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate), respectively were obtained when using sodium heptanoate and oleic acid as carbon sources. These 3-hydroxybutyrate-(3HB)-based polymers are of interest since they incorporate the properties of medium chain length polymers and thus increase the range of applications of PHAs.

Examining the feasibility of bulk commodity production in Escherichia coli

Escherichia coli is currently used by many research institutions and companies around the world as a platform organism for the development of bio-based production processes for bulk biochemicals. A given bulk biochemical bioprocess must be economically competitive with current production routes. Ideally the viability of each bioprocess should be evaluated prior to commencing research, both by metabolic network analysis (to determine the maximum theoretical yield of a given biocatalyst) and by techno-economic analysis (TEA; to determine the conditions required to make the bioprocess cost-competitive). However, these steps are rarely performed. Here we examine theoretical yields and review available TEA for bulk biochemical production in E. coli. In addition, we examine fermentation feedstocks and review recent strain engineering approaches to achieve industrially-relevant production, using examples for which TEA has been performed: ethanol, poly-3-hydroxybutyrate, and 1,3-propanediol.

Expression of Aeromonas caviae polyhydroxyalkanoate synthase gene in Burkholderia sp. USM (JCM15050) enables the biosynthesis of SCL-MCL PHA from palm oil products

AIMS

Burkholderia sp. USM (JCM15050) isolated from oil-polluted wastewater is capable of utilizing palm oil products and glycerol to synthesize poly(3-hydroxybutyrate) [P(3HB)]. To confer the ability to produce polymer containing 3-hydroxyhexanoate (3HHx), plasmid (pBBREE32d13) harbouring the polyhydroxyalkanoate (PHA) synthase gene of Aeromonas caviae (phaC(Ac)) was transformed into this strain.

METHODS AND RESULTS

  The resulting transformant incorporated approximately 1 ± 0·3 mol% of 3HHx in the polymer when crude palm kernel oil (CPKO) or palm kernel acid oil was used as the sole carbon source. In addition, when the transformed strain was cultivated in the mixtures of CPKO and sodium valerate, PHA containing 69 mol% 3HB, 30 mol% 3-hydroxyvalerate and 1 mol% 3HHx monomers was produced. Batch feeding of carbon sources with 0·5% (v/v) CPKO at 0 h and 0·25% (w/v) sodium valerate at 36 h yielded 6 mol% of 3HHx monomer by controlled-feeding strategies.

CONCLUSIONS

Burkholderia sp. USM (JCM15050) has the metabolic pathways to supply both the short-chain length (SCL) and medium-chain length (MCL) PHA monomers. By transforming the strain with the Aer. caviae PHA synthase with broader substrate specificity, SCL-MCL PHA was produced.

SIGNIFICANCE AND IMPACT OF THE STUDY

  This is the first study demonstrating the ability of transformant Burkholderia to produce P(3HB-co-3HHx) from a single carbon source.

Group 4 initiators for the stereoselective ROP of rac-β-butyrolactone and its copolymerization with rac-lactide

In this paper we demonstrate the utility of Group 4 metals for the well-controlled and stereoselective (syndiotactic) ring opening polymerization (ROP) of rac-β-butyrolactone (BBL) and their ability to form copolymers.

Hydrogen and Polyhydroxybutyrate Producing Abilities of Bacillus spp. From Glucose in Two Stage System

Metabolic activities of four Bacillus strains to transform glucose into hydrogen (H(2)) and polyhydroxybutyrate (PHB) in two stages were investigated in this study. Under batch culture conditions, Bacillus thuringiensis EGU45 and Bacillus cereus EGU44 evolved 1.67-1.92 mol H(2)/mol glucose, respectively during the initial 3 days of incubation at 37°C. In the next 2 days, the residual glucose solutions along with B. thuringiensis EGU45 shaken at 200 rpm was found to produce PHB yield of 11.3% of dry cell mass. This is the first report among the non-photosynthetic microbes, where the Bacillus spp.-B. thuringiensis and B. cereus strains have been shown to produce H(2) and PHB in same medium under different conditions.

Production and characterization of PHA from recombinant E. coli harbouring phaC1 gene of indigenous Pseudomonas sp. LDC-5 using molasses

Polyhydroxyalkanoates (PHA) are biodegradable and biocompatible green thermoplastics, synthesized by wide variety of bacteria as an intracellular carbon and energy storage intermediate. They are used as an alternative to nonrenewable petroleum derived plastics. The current interest in these biopolyesters is stimulated by the search for cost-effective capitalized production. This paper attempts to achieve maximized production rate from recombinant system using inexpensive substrate. Molasses from agro-industrial waste was used to produce PHA from recombinant E.coli in batch culture. PHA yield in molasses (3.06g/L ± 0.05‒75.5%) was higher than that of sucrose (2.5g/L ± 0.05 - 65.1%). Properties of the polymer produced from molasses and sucrose were analyzed by DSC, TGA, DTA, GC/MS, TLC and optical rotation studies. The findings suggested that molasses enhanced PHA production in recombinant E.coli.

Elimination of D-lactate synthesis increases poly(3-hydroxybutyrate) and ethanol synthesis from glycerol and affects cofactor distribution in recombinant Escherichia coli

The effect of eliminating D-lactate synthesis in poly(3-hydroxybutyrate) (PHB)-accumulating recombinant Escherichia coli (K24K) was analyzed using glycerol as a substrate. K24KL, an ldhA derivative, produced more biomass and had altered carbon partitioning among the metabolic products, probably due to the increased availability of carbon precursors and reducing power. This resulted in a significant increase of PHB and ethanol synthesis and a decrease in acetate production. Cofactor measurements revealed that cultures of K24K and K24KL had a high intracellular NADPH content and that the NADPH/NADP(+) ratio was higher than the NADH/NAD(+) ratio. The ldhA mutation affected cofactor distribution, resulting in a more reduced intracellular state, mainly due to a further increase in NADPH/NADP(+). In 60-h fed-batch cultures, K24KL reached 41.9 g·liter⁻¹ biomass and accumulated PHB up to 63% ± 1% (wt/wt), with a PHB yield on glycerol of 0.41 ± 0.03 g·g⁻¹, the highest reported using this substrate.