Polyhydroxyalkanoate accumulation in Burkholderia sp.: a molecular approach to elucidate the genes involved in the formation of two homopolymers consisting of short-chain-length 3-hydroxyalkanoic acids

Secondary metabolite biosynthetic diversity in Arctic Ocean metagenomes

Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are mega enzymes responsible for the biosynthesis of a large fraction of natural products (NPs). Molecular markers for biosynthetic genes, such as the ketosynthase (KS) domain of PKSs, have been used to assess the diversity and distribution of biosynthetic genes in complex microbial communities. More recently, metagenomic studies have complemented and enhanced this approach by allowing the recovery of complete biosynthetic gene clusters (BGCs) from environmental DNA. In this study, the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples (NICE-2015 expedition), was assessed using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. In total, 149 KS domain OTU sequences were recovered, 36 % of which could not be assigned to any known BGC. In addition, 74 bacterial metagenome-assembled genomes were recovered, from which 179 BGCs were extracted. A network analysis identified potential new NP families, including non-ribosomal peptides and polyketides. Complete or near-complete BGCs were recovered, which will enable future heterologous expression efforts to uncover the respective NPs. Our study represents the first report of biosynthetic diversity assessed for Arctic Ocean metagenomes and highlights the potential of Arctic Ocean planktonic microbiomes for the discovery of novel secondary metabolites. The strategy employed in this study will enable future bioprospection, by identifying promising samples for bacterial isolation efforts, while providing also full-length BGCs for heterologous expression.

Statistical optimisation of polyhydroxyalkanoate production in Bacillus endophyticus using sucrose as sole source of carbon

Microorganisms have been contemplated as a promising source for the inexhaustible synthesis of many novel materials utilizing renewable sources. Among many of such products, polyhydroxyalkanoate (PHA) remains as an essential biodegradable polymer with functions similar to conventional plastics. Bacillus endophyticus is capable of accumulating biopolymer PHA in nutrient limiting conditions with excess of carbon source. Screening and optimizing the parameters for increased PHA production was done statistically. The optimized medium gave a maximum yield of 46.57% which was in well agreement with the given predicted value provided by response surface methodology model yield of 47.02%. Optimal media conditions when extrapolated in bioreactor gave an even higher production percentage of 49.9. This is the first report highlighting 49% of polyhydroxybutyrate statistically using sucrose as a source. The main highlight of the study was the use of wild type strain for producing high quality PHA using simple carbon source which can be a starting platform for using this strain for large scale PHA production industrially. FTIR and ¹HNMR analysis confirmed the polymer produced.

Polyhydroxyalkanoates (PHAs): Biopolymers for Biofuel and Biorefineries

Fossil fuels are energy recourses that fulfill most of the world's energy requirements. However, their production and use cause severe health and environmental problems including global warming and pollution. Consequently, plant and animal-based fuels (also termed as biofuels), such as biogas, biodiesel, and many others, have been introduced as alternatives to fossil fuels. Despite the advantages of biofuels, such as being renewable, environmentally friendly, easy to source, and reducing the dependency on foreign oil, there are several drawbacks of using biofuels including high cost, and other factors discussed in the fuel vs. food debate. Therefore, it is imperative to produce novel biofuels while also developing suitable manufacturing processes that ease the aforementioned problems. Polyhydroxyalkanoates (PHAs) are structurally diverse microbial polyesters synthesized by numerous bacteria. Moreover, this structural diversity allows PHAs to readily undergo methyl esterification and to be used as biofuels, which further extends the application value of PHAs. PHA-based biofuels are similar to biodiesel except for having a high oxygen content and no nitrogen or sulfur. In this article, we review the microbial production of PHAs, biofuel production from PHAs, parameters affecting the production of fuel from PHAs, and PHAs biorefineries. In addition, future work on the production of biofuels from PHAs is also discussed.

Genome analysis of the marine bacterium Kiloniella laminariae and first insights into comparative genomics with related Kiloniella species

Kiloniella laminariae is a true marine bacterium and the first member of the family and order, the Kiloniellaceae and Kiloniellales. K. laminariae LD81T (= DSM 19542T) was isolated from the marine macroalga Saccharina latissima and is a mesophilic, typical marine chemoheterotrophic aerobic bacterium with antifungal activity. Phylogenetic analysis of 16S rRNA gene sequence revealed the similarity of K. laminariae LD81T not only with three validly described species of the genus Kiloniella, but also with undescribed isolates and clone sequences from marine samples in the range of 93.6-96.7%. We report on the analysis of the draft genome of this alphaproteobacterium and describe some selected features. The 4.4 Mb genome has a G + C content of 51.4%, contains 4213 coding sequences including 51 RNA genes as well as 4162 protein-coding genes, and is a part of the Genomic Encyclopaedia of Bacteria and Archaea (GEBA) project. The genome provides insights into a number of metabolic properties, such as carbon and sulfur metabolism, and indicates the potential for denitrification and the biosynthesis of secondary metabolites. Comparative genome analysis was performed with K. laminariae LD81T and the animal-associated species Kiloniella majae M56.1T from a spider crab, Kiloniella spongiae MEBiC09566T from a sponge as well as Kiloniella litopenai P1-1 from a white shrimp, which all inhabit quite different marine habitats. The analysis revealed that the K. laminariae LD81T contains 1397 unique genes, more than twice the amount of the other species. Unique among others is a mixed PKS/NRPS biosynthetic gene cluster with similarity to the biosynthetic gene cluster responsible for the production of syringomycin.

Polyhydroxybutyrate and polyhydroxydodecanoate produced by Burkholderia contaminans IPT553

AIMS

In this paper, we introduce a new Burkholderia contaminans capable of producing a newly characterized polymer.

METHODS AND RESULTS

CG-MS and magnetic nuclear resonance ¹ H and ¹³ C were used to determine the constitution of polymers produced in glucose, glucose with casein, sucrose and sucrose with casein. Three pairs of primers were used to find the polyhydroxyalkanoates (PHA) synthase class and sequence. The synthesized polymers were composed by short-chain length PHA (scl-PHA), especially polyhydroxybutyrate (PHB), and medium chain length PHA (mcl-PHA), especially polyhydroxydodecanoate (PHDd), and their concentration, constitution and molecular weight depend on carbon source used. The bacterium showed only class I synthase which could not explain the mcl-PHA production.

CONCLUSIONS

Burkholderia contaminans has a class I PHA synthase and produces PHB combined to PHDd when cultivated in sucrose or glucose, and PHDd concentration is affected when casein is used.

SIGNIFICANCE AND IMPACT OF THE STUDY

PHA are natural polymers produced by a wide range of bacteria. The presence of PHDd monomers confers to the polymer elastomeric properties. Previously, PHDd was only obtained when bacteria were cultivated in related carbon source. In this work, B. contaminansIPT553 produced PHB with PHDd using simple and low-cost carbon sources that can make possible the cheaper production of a more flexible biopolymer with crystallinity and elasticity different from the more common PHAs.

Acyltransferases in bacteria

Long-chain-length hydrophobic acyl residues play a vital role in a multitude of essential biological structures and processes. They build the inner hydrophobic layers of biological membranes, are converted to intracellular storage compounds, and are used to modify protein properties or function as membrane anchors, to name only a few functions. Acyl thioesters are transferred by acyltransferases or transacylases to a variety of different substrates or are polymerized to lipophilic storage compounds. Lipases represent another important enzyme class dealing with fatty acyl chains; however, they cannot be regarded as acyltransferases in the strict sense. This review provides a detailed survey of the wide spectrum of bacterial acyltransferases and compares different enzyme families in regard to their catalytic mechanisms. On the basis of their studied or assumed mechanisms, most of the acyl-transferring enzymes can be divided into two groups. The majority of enzymes discussed in this review employ a conserved acyltransferase motif with an invariant histidine residue, followed by an acidic amino acid residue, and their catalytic mechanism is characterized by a noncovalent transition state. In contrast to that, lipases rely on completely different mechanism which employs a catalytic triad and functions via the formation of covalent intermediates. This is, for example, similar to the mechanism which has been suggested for polyester synthases. Consequently, although the presented enzyme types neither share homology nor have a common three-dimensional structure, and although they deal with greatly varying molecule structures, this variety is not reflected in their mechanisms, all of which rely on a catalytically active histidine residue.

Biosynthesis and mobilization of a novel polyhydroxyalkanoate containing 3-hydroxy-4-methylvalerate monomer produced by Burkholderia sp. USM (JCM15050)

We attempted to synthesize a polyhydroxyalkanoate (PHA) containing newly reported 3-hydroxy-4-methylvalerate (3H4MV) monomer by using wild type Burkholderia sp. USM (JCM15050) and its transformed strain harboring the PHA synthase gene of Aeromonas caviae (phaCAc). The introduction of 3H4MV as a second monomer will improve the material properties of 3HB-based polymers. To promote the accumulation of PHA containing 3H4MV monomer, isocaproic acid was provided as co-carbon source. Approximately 1mol% of 3H4MV was detected in wild type Burkholderia sp. cultures when they were fed glucose or fructose together with isocaproic acid. Thus, the wild type strain can synthesize the 3H4MV monomer. High 3H4MV fractions, of about 40mol%, were obtained when the transformed strain was cultivated on glucose or fructose together with isocaproic acid. In addition, the ability of the transformed strain to mobilize accumulated PHA containing 3H4MV monomer was demonstrated in this study. This is the first report on mobilization of the 3H4MV monomer.

PCR-based identification of Burkholderia pseudomallei

DNA amplification techniques are being used increasingly in clinical laboratories to confirm the identity of medically important bacteria. A PCR-based identification method has been in use in our centre for 10 years for Burkholderia pseudomallei and was used to confirm the identity of bacteria isolated from cases of melioidosis in Ceará since 2003. This particular method has been used as a reference standard for less discriminatory methods. In this study we evaluated three PCR-based methods of B. pseudomallei identification and used DNA sequencing to resolve discrepancies between PCR-based results and phenotypic identification methods. The established semi-nested PCR protocol for B. pseudomallei 16-23s spacer region produced a consistent negative result for one of our 100 test isolates (BCC #99), but correctly identified all 71 other B. pseudomallei isolates tested. Anomalous sequence variation was detected at the inner, reverse primer binding site for this method. PCR methods were developed for detection of two other B. pseudomallei bacterial metabolic genes. The conventional lpxO PCR protocol had a sensitivity of 0.89 and a specificity of 1.00, while a real-time lpxO protocol performed even better with sensitivity and specificity of 1.00, and 1.00. This method identified all B. pseudomallei isolates including the PCR-negative discrepant isolate. The phaC PCR protocol detected the gene in all B. pseudomallei and all but three B. cepacia isolates, making this method unsuitable for PCR-based identification of B. pseudomallei. This experience with PCR-based B. pseudomallei identification methods indicates that single PCR targets should be used with caution for identification of these bacteria, and need to be interpreted alongside phenotypic and alternative molecular methods such as gene sequencing.

Polyester synthases: natural catalysts for plastics

Polyhydroxyalkanoates (PHAs) are biopolyesters composed of hydroxy fatty acids, which represent a complex class of storage polyesters. They are synthesized by a wide range of different Gram-positive and Gram-negative bacteria, as well as by some Archaea, and are deposited as insoluble cytoplasmic inclusions. Polyester synthases are the key enzymes of polyester biosynthesis and catalyse the conversion of (R)-hydroxyacyl-CoA thioesters to polyesters with the concomitant release of CoA. These soluble enzymes turn into amphipathic enzymes upon covalent catalysis of polyester-chain formation. A self-assembly process is initiated resulting in the formation of insoluble cytoplasmic inclusions with a phospholipid monolayer and covalently attached polyester synthases at the surface. Surface-attached polyester synthases show a marked increase in enzyme activity. These polyester synthases have only recently been biochemically characterized. An overview of these recent findings is provided. At present, 59 polyester synthase structural genes from 45 different bacteria have been cloned and the nucleotide sequences have been obtained. The multiple alignment of the primary structures of these polyester synthases show an overall identity of 8-96% with only eight strictly conserved amino acid residues. Polyester synthases can been assigned to four classes based on their substrate specificity and subunit composition. The current knowledge on the organization of the polyester synthase genes, and other genes encoding proteins related to PHA metabolism, is compiled. In addition, the primary structures of the 59 PHA synthases are aligned and analysed with respect to highly conserved amino acids, and biochemical features of polyester synthases are described. The proposed catalytic mechanism based on similarities to alpha/beta-hydrolases and mutational analysis is discussed. Different threading algorithms suggest that polyester synthases belong to the alpha/beta-hydrolase superfamily, with a conserved cysteine residue as catalytic nucleophile. This review provides a survey of the known biochemical features of these unique enzymes and their proposed catalytic mechanism.

PCR cloning of polyhydroxyalkanoate biosynthesis genes from Burkholderia caryophylli and their functional expression in recombinant Escherichia coli

The PCR cloning strategy for type II polyhydroxyalkanoate (PHA) biosynthesis genes established previously for Pseudomonas was successfully applied to Burkholderia caryophylli strain AS 1.2741. The whole pha locus containing PHA synthase genes phaC1, phaC2 and PHA depolymerase gene phaZ was cloned. The complete open reading frames of phaC1(Bc), phaC2(Bc) and phaZ(Bc) were identified. Sequence analyses of the phaC1(Bc), phaZ(Bc) and phaC2(Bc) showed more than 77.7%, 73.7% and 68.5% identities compared with the corresponding pha loci of the known Pseudomonas strains, respectively. The functional expression of the phaC1(Bc) or phaC2(Bc) in Escherichia coli strain KM32B (fadB deleted mutant) showed the abilities of PHA production by the estimated PHA synthase genes. Over 1% PHA consisting of 3-hydroxyhexanoate (3HHx), 3-hydroxyoctanoate (3HO) and 3-hydroxydecanoate (3HD) was detected from cells of recombinant E. coli KM32B (pHXM11) harboring phaC1(Bc), grown on octanoate. At the same time over 3% of PHA consisting of 3HO and 3HD was produced from cells of recombinant E. coli KM32B (pHXM21) harboring phaC2(BC), grown on decanoate. Results showed the PCR cloning strategy developed previously can be applied to non-Pseudomonas strains such as Burkholderia in this case. This result also provided evidence for the presumption that the Burkholderia strain possesses not only polyhydroxybutyrate synthase genes, but also synthase for medium-chain-length polyhydroxyalkanoates consisting of 3HHx, 3HO and 3HD.

PhaR, a protein of unknown function conserved among short-chain-length polyhydroxyalkanoic acids producing bacteria, is a DNA-binding protein and represses Paracoccus denitrificans phaP expression in vitro

A putative regulatory protein, PhaR, which was identified in the polyhydroxyalkanoic acid synthetic locus (phaZCPR) in Paracoccus denitrificans, was investigated. The PhaR protein purified from a recombinant Escherichia coli was estimated to be 22 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, being consistent with the mass calculated from the nucleotide sequence. The molecular mass was determined to be 93 kDa by size-exclusion chromatography, suggesting that the protein formed a tetramer. A gel mobility shift assay showed that PhaR specifically bound to the intergenic region of phaC--phaP. In a cell-free protein synthesis system using E. coli S30 extract, the expression of the phaP gene was repressed by the addition of purified PhaR. These results suggest that PhaR is a DNA-binding protein and may play a role in the regulation of phaP gene expression.

Biochemical and molecular basis of microbial synthesis of polyhydroxyalkanoates in microorganisms

Intensive research on the physiology, biochemistry, and molecular genetics of the metabolism of polyhydroxyalkanoates (PHA) during the last 15 years has revealed a dramatic increase of our knowledge on the biosynthesis of these polyesters in bacteria. This mainly very basic research has revealed several new, hitherto not described enzymes and pathways. In addition, many genes encoding the enzymes of these pathways and in particular the key enzyme of PHA biosynthesis, PHA synthase, were cloned and characterized at a molecular level. This knowledge was utilized to establish PHA biosynthesis in many prokaryotic and eukaryotic organisms, which were unable to synthesize PHAs, and to apply the methodology of metabolic engineering, thus opening new perspectives for the production of various PHAs by fermentation biotechnology or agriculture in economically feasible processes. This contribution summarizes the properties of PHA synthases and gives an overview on the genes for these enzymes and other enzymes of PHA biosynthesis that have been cloned and are available. It also summarizes our current knowledge on the regulation at the enzyme and gene level of PHA biosynthesis in bacteria.

Studies on polyhydroxyalkanoate (PHA) accumulation in a PHA synthase I-negative mutant of Burkholderia cepacia generated by homogenotization

In the genome of Burkholderia cepacia strain IPT64, which accumulates a blend of the two homopolyesters poly(3-hydroxybutyrate), poly(3HB), and poly(3-hydroxy-4-pentenoic acid), poly(3H4PE), from sucrose or gluconate as single carbon source, the polyhydroxyalkanoate (PHA) synthase structural gene was disrupted by the insertion of a chloramphenicol-resistant gene cassette (phaC1::Cm). The suicide vector pSUP202 harboring phaC1::Cm was transferred to B. cepacia by conjugation. The inactivated gene was integrated into the chromosome of B. cepacia by homologous recombination. This mutant and also 15 N-methyl-N'-nitrosoguanidine (NMG)-induced mutants still accumulated low amounts of PHAs and expressed low PHA synthase activity. The analysis of the mutant phaC1::Cm showed that it accumulated about 1% of PHA consisting of 68.2 mol% 3HB and 31.8 mol% 3H4PE from gluconate. The wild-type, in contrast, accumulated 49.3% of PHA consisting of 96.5 mol% 3HB and 3. 5 mol% 3H4PE. Our results indicated that the genome of B. cepacia possesses at least two PHA synthase genes, which probably have different substrate specificities.