Taxonomic identification of Streptomyces exfoliatus K10 and characterization of its poly(3-hydroxybutyrate) depolymerase gene

Can bioplastics always offer a truly sustainable alternative to fossil-based plastics?

Bioplastics, comprised of bio-based and/or biodegradable polymers, have the potential to play a crucial role in the transition towards a sustainable circular economy. The use of biodegradable polymers not only leads to reduced greenhouse gas emissions but also might address the problem of plastic waste persisting in the environment, especially when removal is challenging. Nevertheless, biodegradable plastics should not be considered as substitutes for proper waste management practices, given that their biodegradability strongly depends on environmental conditions. Among the challenges hindering the sustainable implementation of bioplastics in the market, the development of effective downstream recycling routes is imperative, given the increasing production volumes of these materials. Here, we discuss about the most advisable end-of-life scenarios for bioplastics. Various recycling strategies, including mechanical, chemical or biological (both enzymatic and microbial) approaches, should be considered. Employing enzymes as biocatalysts emerges as a more selective and environmentally friendly alternative to chemical recycling, allowing the production of new bioplastics and added value and high-quality products. Other pending concerns for industrial implementation of bioplastics include misinformation among end users, the lack of a standardised bioplastic labelling, unclear life cycle assessment guidelines and the need for higher financial investments. Although further research and development efforts are essential to foster the sustainable and widespread application of bioplastics, significant strides have already been made in this direction.

Bioplastic degradation and assimilation processes by a novel bacterium isolated from the marine plastisphere

Biosourced and biodegradable plastics offer a promising solution to reduce environmental impacts of plastics for specific applications. Here, we report a novel bacterium named Alteromonas plasticoclasticus MED1 isolated from the marine plastisphere that forms biofilms on foils of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). Experiments of degradation halo, plastic matrix weight loss, bacterial oxygen consumption and heterotrophic biosynthetic activity showed that the bacterial isolate MED1 is able to degrade PHBV and to use it as carbon and energy source. The likely entire metabolic pathway specifically expressed by this bacterium grown on PHBV matrices was shown by further genomic and transcriptomic analysis. In addition to a gene coding for a probable secreted depolymerase, a gene cluster was located that encodes characteristic enzymes involved in the complete depolymerization of PHBV, the transport of oligomers, and in the conversion of the monomers into intermediates of central carbon metabolism. The transcriptomic experiments showed the activation of the glyoxylate shunt during PHBV degradation, setting the isocitrate dehydrogenase activity as regulated branching point of the carbon flow entering the tricarboxylic acid cycle. Our study also shows the potential of exploring the natural plastisphere to discover new bacteria with promising metabolic capabilities.

Biodegradation of Biodegradable Polymers in Mesophilic Aerobic Environments

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

Characterization of Streptomyces nymphaeiformis sp. nov., and its taxonomic relatedness to other polyhydroxybutyrate-degrading streptomycetes

A polyhydroxybutyrate (PHB)-degrading actinomycete, strain SFB5AT, was identified as a species of Streptomyces based on its membrane fatty acid profile and the presence of ll-diaminopimelic acid in the cell wall. It formed sporulating mycelia on most agar media, but flat or wrinkled, moist colonies on trypticase soy agar. Spores were smooth, cylindrical, and borne on long, straight to flexuous chains. It produced a light brown diffusible pigment, but not melanin. Comparison of genomic digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values indicated that strain SFB5AT was related to Streptomyces litmocidini JCM 4394T, Streptomyces vietnamensis GIMV4.0001T, Streptomyces nashvillensis JCM 4498T and Streptomyces tanashiensis JCM 4086T, plus 11 other species. However, the dDDH and ANI values were well below the species differentiation thresholds of <70 and <95 %, respectively; also, multilocus sequence analysis distances exceeded the species threshold of 0.007. Moreover, strain SFB5AT differed from the other species in pigmentation and its ability to catabolize arabinose. Strain SFB5AT and 11 of its 15 closest relatives degraded PHB and have genes for extracellular, short-chain-length denatured polyhydroxyalkanoate depolymerases. These enzymes from strain SFB5AT and its closest relatives had a type 1 catalytic domain structure, while those from other relatives had a type 2 structure, which differs from type one in the position of a consensus histidine in the active site. Thus, phenotypic and genotypic differences suggest that strain SFB5AT represents a new species of Streptomyces, for which we propose the name Streptomyces nymphaeiformis sp. nov. The type strain is SFB5AT (=NRRL B-65520T=DSM 112030T).

Enhanced polyhydroxybutyrate (PHB) production by newly isolated rare actinomycetes Rhodococcus sp. strain BSRT1-1 using response surface methodology

Poly-β-hydroxybutyrate (PHB) is a biodegradable polymer, synthesized as carbon and energy reserve by bacteria and archaea. To the best of our knowledge, this is the first report on PHB production by a rare actinomycete species, Rhodococcus pyridinivorans BSRT1-1. Response surface methodology (RSM) employing central composite design, was applied to enhance PHB production in a flask scale. A maximum yield of 3.6 ± 0.5 g/L in biomass and 43.1 ± 0.5 wt% of dry cell weight (DCW) of PHB were obtained when using RSM optimized medium, which was improved the production of biomass and PHB content by 2.5 and 2.3-fold, respectively. The optimized medium was applied to upscale PHB production in a 10 L stirred-tank bioreactor, maximum biomass of 5.2 ± 0.5 g/L, and PHB content of 46.8 ± 2 wt% DCW were achieved. Furthermore, the FTIR and ¹H NMR results confirmed the polymer as PHB. DSC and TGA analysis results revealed the melting, glass transition, and thermal decomposition temperature of 171.8, 4.03, and 288 °C, respectively. In conclusion, RSM can be a promising technique to improve PHB production by a newly isolated strain of R. pyridinivorans BSRT1-1 and the properties of produced PHB possessed similar properties compared to commercial PHB.

A sensitive pH indicator-based spectrophotometric assay for PHB depolymerase activity on microtiter plates

A continuous spectrophotometric assay for the screening of PHB depolymerase activity in microtiter plates was developed. We evaluated crystalline PHB in the suspension and coated it with the addition of a pH indicator to detect the breakage of the ester bond by proton titration. The reaction rate and the concentration of the recombinant PhaZ1 from Paucimonas lemoignei PHB depolymerase presented a linear correlation. A comparison of the proposed method with the turbidimetric method adapted to the microtiter plates revealed that the use of indicators increases the response signal by at least 5-fold, resulting in increased sensitivity and better signal-to-noise ratio. Furthermore, the proposed method offers a wide range of pH from 5.0 to 9.2 by using different buffer-indicator pairs and was employed for the screening of PHB-depolymerase activity on 140 bacterial strains isolated from Lake Chapala. Eleven strains were positive for PHB-depolymerase activity, which were ACSLRF-27, ACPLRF-6, and ACPLRF-5 (16S rRNA sequence alignment revealed 99-100% similarity with Actinomadura geliboluensis strain A8036, Streptomyces cavourensis strain NRRL 2740, and Streptomyces coelicolor strain DSM 40233, respectively); these that showed the highest activities. In conclusion, the method was successfully applied for finding new strains and for quantifying the PHB depolymerases activity with crystalline PHB.

Poly(hydroxy acids) derived from the self-condensation of hydroxy acids: from polymerization to end-of-life options

Poly(hydroxy acids) derived from the self-condensation of hydroxy acid are biodegradable and can be fully recycled in a Circular Economy approach.

Stenotrophomonas sp. RZS 7, a novel PHB degrader isolated from plastic contaminated soil in Shahada, Maharashtra, Western India

This paper reports an isolation and identification of novel poly-β-hydroxybutyrate (PHB) degrading bacterium Stenotrophomonas sp. RZS 7 and studies on its extracellular PHB degrading depolymerase enzyme. The bacterium isolated from soil samples of plastic contaminated sites of municipal area in Shahada, Maharashtra, Western India. It was identified as Stenotrophomonas sp. RZS 7 based on polyphasic approach. The bacterium grew well in minimal salt medium (MSM) and produced a zone (4.2 mm) of PHB hydrolysis on MSM containing PHB as the only source of nutrient. An optimum yield of enzyme was obtained on the fifth day of incubation at 37 °C and at pH 6.0. Further increase in enzyme production was recorded with Ca²⁺ ions, while other metal ions like Fe²⁺ (1 mM) and chemical viz. mercaptoethanol severally affected the production of enzyme.

Novel extracellular medium-chain-length polyhydroxyalkanoate depolymerase from Streptomyces exfoliatus K10 DSMZ 41693: a promising biocatalyst for the efficient degradation of natural and functionalized mcl-PHAs

Cloning and biochemical characterization of a novel extracellular medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase from Streptomyces exfoliatus K10 DSMZ 41693 are described. The primary structure of the depolymerase (PhaZSex2) includes the lipase consensus sequence (serine-histidine-aspartic acid) which is known for serine hydrolases. Secondary structure analysis shows 7.9 % α-helix, 43.9 % β-sheet, 19.4 % β-turns, and 31.2 % random coil, suggesting that this enzyme belongs to the α/β hydrolase fold family, in agreement with other PHA depolymerases and lipases. The enzyme was efficiently produced as an extracellular active form in Rhodococcus and purified by two consecutive hydrophobic chromatographic steps. Matrix-assisted laser desorption-time-of-flight (MALDI-TOF) analysis of the purified enzyme revealed a monomer of 27.6 kDa with a midpoint transition temperature of 44.2 °C. Remarkably, the activity is significantly enhanced by low concentrations of nonionic and anionic detergents and thermal stability is improved by the presence of 10 % glycerol. PhaZSex2 is an endo-exohydrolase that cleaves both large and small PHA molecules, producing (R)-3-hydroxyoctanoic acid monomers as the main reaction product. Markedly, PhaZSex2 is able to degrade functionalized polymers containing thioester groups in the side chain (PHACOS), releasing functional thioester-based monomers and oligomers demonstrating the potentiality of this novel biocatalyst for the industrial production of enantiopure (R)-3-hydroxyalkanoic acids.

Genome Sequence of Streptomyces exfoliatus DSMZ 41693, a Source of Poly(3-Hydroxyalkanoate)-Degrading Enzymes

Here we report the draft genome sequence of Streptomyces exfoliatus DSMZ 41693, which includes a gene encoding a poly(3-hydroxyoctanoate) depolymerase, an enzyme which can be used for the industrial synthesis of chiral (R)-3-hydroxyalkanoic acids. In addition, the genome carries numerous genes involved in the biosynthesis of secondary metabolites, including polyketides and terpenes.

Novel extracellular PHB depolymerase from Streptomyces ascomycinicus: PHB copolymers degradation in acidic conditions

The ascomycin-producer strain Streptomyces ascomycinicus has been proven to be an extracellular poly(R)-3-hydroxybutyrate (PHB) degrader. The fkbU gene, encoding a PHB depolymerase (PhaZ_Sa), has been cloned in E. coli and Rhodococcus sp. T104 strains for gene expression. Gram-positive host Rhodococcus sp. T104 was able to produce and secrete to the extracellular medium an active protein form. PhaZ_Sa was purified by two hydrophobic interaction chromatographic steps, and afterwards was biochemically as well as structurally characterized. The enzyme was found to be a monomer with a molecular mass of 48.4 kDa, and displayed highest activity at 45°C and pH 6, thus being the first PHB depolymerase from a gram-positive bacterium presenting an acidic pH optimum. The PHB depolymerase activity of PhaZ_Sa was increased in the presence of divalent cations due to non-essential activation, and also in the presence of methyl-β-cyclodextrin and PEG 3350. Protein structure was analyzed, revealing a globular shape with an alpha-beta hydrolase fold. The amino acids comprising the catalytic triad, Ser¹³¹-Asp²⁰⁹-His²⁶⁹, were identified by multiple sequence alignment, chemical modification of amino acids and site-directed mutagenesis. These structural results supported the proposal of a three-dimensional model for this depolymerase. PhaZ_Sa was able to degrade PHB, but also demonstrated its ability to degrade films made of PHB, PHBV copolymers and a blend of PHB and starch (7∶3 proportion wt/wt). The features shown by PhaZ_Sa make it an interesting candidate for industrial applications involving PHB degradation.

Degradation of Poly(ε-caprolactone) by thermophilic Streptomyces thermoviolaceus subsp. thermoviolaceus 76T-2

A thermophilic Streptomyces thermoviolaceus subsp. thermoviolaceus isolate 76T-2 that can degrade poly(ε-caprolactone) (PCL) was isolated from soil in Taiwan. Isolate 76T-2 grew well in urea fructose oatmeal medium and exhibited clear zones on agar plates containing PCL, indicating the presence of extracellular PCL depolymerases. The PCL powder present in culture medium was completely degraded within 6 h of culture at 45°C. Two PCL-degrading enzymes were purified to homogeneity from the culture supernatant. The molecular weights of these two enzymes were estimated to be 25 kDa and 55 kDa, respectively. A portion of the N-terminal region of the 25-kDa protein was determined, and the sequence Ala-Asn-Phe-Val-Val-Ser-Glu-Ala thus obtained was identical to that of A₆₄-A₇₁ of the Chi25 chitinase of Streptomyces thermoviolaceus OPC-520. The 25-kDa protein was shown to also degrade chitin, suggesting that isolate 76T-2 has the ability to degrade both PCL and chitin.

Characterization of a novel subgroup of extracellular medium-chain-length polyhydroxyalkanoate depolymerases from actinobacteria

Nineteen medium-chain-length (mcl) poly(3-hydroxyalkanoate) (PHA)-degrading microorganisms were isolated from natural sources. From them, seven Gram-positive and three Gram-negative bacteria were identified. The ability of these microorganisms to hydrolyze other biodegradable plastics, such as short-chain-length (scl) PHA, poly(ε-caprolactone) (PCL), poly(ethylene succinate) (PES), and poly(l-lactide) (PLA), has been studied. On the basis of the great ability to degrade different polyesters, Streptomyces roseolus SL3 was selected, and its extracellular depolymerase was biochemically characterized. The enzyme consisted of one polypeptide chain of 28 kDa with a pI value of 5.2. Its maximum activity was observed at pH 9.5 with chromogenic substrates. The purified enzyme hydrolyzed mcl PHA and PCL but not scl PHA, PES, and PLA. Moreover, the mcl PHA depolymerase can hydrolyze various substrates for esterases, such as tributyrin and p-nitrophenyl (pNP)-alkanoates, with its maximum activity being measured with pNP-octanoate. Interestingly, when poly(3-hydroxyoctanoate-co-3-hydroxyhexanoate [11%]) was used as the substrate, the main hydrolysis product was the monomer (R)-3-hydroxyoctanoate. In addition, the genes of several Actinobacteria strains, including S. roseolus SL3, were identified on the basis of the peptide de novo sequencing of the Streptomyces venezuelae SO1 mcl PHA depolymerase by tandem mass spectrometry. These enzymes did not show significant similarity to mcl PHA depolymerases characterized previously. Our results suggest that these distinct enzymes might represent a new subgroup of mcl PHA depolymerases.

Preparation and characterization of cross-linked enzyme aggregates (CLEAs) of recombinant poly-3-hydroxybutyrate depolymerase from Streptomyces exfoliatus

Cross-linked enzyme aggregates of poly-3-hydroxybutyrate (PHB) depolymerase from Streptomyces exfoliatus (PhaZ(Sex)-CLEAs) have been prepared. Acetone was used as the precipitating agent, while addition of bovine serum albumin (BSA) facilitated CLEAs formation. Conditions for enzyme precipitation and cross-linking have been optimized, and confocal scanning microscopy showed a homogeneous enzyme distribution in the biocatalyst. Obtained PhaZ(Sex)-CLEAs presented an average size of 50-300 μm, showing a high PHB depolymerase activity of 255 U/g wet biocatalyst at 40°C and pH 7.0. Temperature-activity profile of PhaZ(Sex)-CLEAs at pH 8.0 showed that the highest activity for pNPB hydrolysis was achieved at 60°C, whereas pH-activity profile at 40°C indicated that highest activity for PHB hydrolysis was achieved at pH 7.0. Additionally, immobilized biocatalyst could be recycled at least for 20 consecutive batch reactions without loss of catalytic activity, and showed higher pH and temperature stability, and better tolerance to several organic solvents than its soluble counterpart.

Polyester hydrolytic and synthetic activity catalyzed by the medium-chain-length poly(3-hydroxyalkanoate) depolymerase from Streptomyces venezuelae SO1

The extracellular medium-chain-length polyhydroxyalkanote (MCL-PHA) depolymerase from an isolate identified as Streptomyces venezuelae SO1 was purified to electrophoretic homogeneity and characterized. The molecular mass and pI of the purified enzyme were approximately 27 kDa and 5.9, respectively. The depolymerase showed its maximum activity in the alkaline pH range and 50 °C and retained more than 70 % of its initial activity after 8 h at 40 °C. The MCL-PHA depolymerase hydrolyzes various p-nitrophenyl-alkanoates and polycaprolactone but not polylactide, poly-3-hydroxybutyrate, and polyethylene succinate. The enzymatic activity was markedly enhanced by the presence of low concentrations of detergents and organic solvents, being inhibited by dithiothreitol and EDTA. The potential of using the enzyme to produce (R)-3-hydroxyoctanoate in aqueous media or to catalyze ester-forming reactions in anhydrous media was investigated. In this sense, the MCL-PHA depolymerase catalyzes the hydrolysis of poly-3-hydroxyoctanoate to monomeric units and the ring-opening polymerization of β-butyrolactone and lactides, while ε-caprolactone and pentadecalactone were hardly polymerized.

Identification and characterization of a novel class of extracellular poly(3-hydroxybutyrate) depolymerase from Bacillus sp. strain NRRL B-14911

The catalytic, linker, and denatured poly(3-hydroxybutyrate) (dPHB)-binding domains of bacterial extracellular PHB depolymerases (PhaZs) are classified into several different types. We now report a novel class of extracellular PHB depolymerase from Bacillus sp. strain NRRL B-14911. Its catalytic domain belongs to type 1, whereas its putative linker region neither possesses the sequence features of the three known types of linker domains nor exhibits significant amino acid sequence similarity to them. Instead, this putative linker region can be divided into two distinct linker domains of novel types: LD1 and LD2. LD1 shows significant amino acid sequence similarity to certain regions of a large group of PHB depolymerase-unrelated proteins. LD2 and its homologs are present in a small group of PhaZs. The remaining C-terminal portion of this PhaZ can be further divided into two distinct domains: SBD1 and SBD2. Each domain showed strong binding to dPHB, and there is no significant sequence similarity between them. Each domain neither possesses the sequence features of the two known types of dPHB-binding domains nor shows significant amino acid sequence similarity to them. These unique features indicate the presence of two novel and distinct types of dPHB-binding domains. Homologs of these novel domains also are present in the extracellular PhaZ of Bacillus megaterium and the putative extracellular PhaZs of Bacillus pseudofirmus and Bacillus sp. strain SG-1. The Bacillus sp. NRRL B-14911 PhaZ appears to be a representative of a novel class of extracellular PHB depolymerases.

The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases

Background

Polyhydroxyalkanoates (PHAs) can be degraded by many microorganisms using intra- or extracellular PHA depolymerases. PHA depolymerases are very diverse in sequence and substrate specificity, but share a common α/β-hydrolase fold and a catalytic triad, which is also found in other α/β-hydrolases.

Results

The PHA Depolymerase Engineering Database (DED, ) has been established as a tool for systematic analysis of this enzyme family. The DED contains sequence entries of 587 PHA depolymerases, which were assigned to 8 superfamilies and 38 homologous families based on their sequence similarity. For each family, multiple sequence alignments and profile hidden Markov models are provided, and functionally relevant residues are annotated.

Conclusion

The DED is a valuable tool which can be applied to identify new PHA depolymerase sequences from complete genomes in silico, to classify PHA depolymerases, to predict their biochemical properties, and to design enzyme variants with improved properties.

Polyhydroxyalkanoates in Gram-positive bacteria: insights from the genera Bacillus and Streptomyces

Gram-positive bacteria, notably Bacillus and Streptomyces, have been used extensively in industry. However, these microorganisms have not yet been exploited for the production of the biodegradable polymers, polyhydroxyalkanoates (PHAs). Although PHAs have many potential applications, the cost of production means that medical applications are currently the main area of use. Gram-negative bacteria, currently the only commercial source of PHAs, have lipopolysaccharides (LPS) which co-purify with the PHAs and cause immunogenic reactions. On the other hand, Gram- positive bacteria lack LPS, a positive feature which justifies intensive investigation into their production of PHAs. This review summarizes currently available knowledge on PHA production by Gram- positive bacteria especially Bacillus and Streptomyces. We hope that this will form the basis of further research into developing either or both as a source of PHAs for medical applications.

A novel PHB depolymerase from a thermophilic Streptomyces sp

A novel PHB depolymerase from a thermophilic Streptomyces sp. MG was purified to homogeneity by hydrophobic interaction chromatography and gel filtration. The molecular mass of the purified enzyme was 43 kDa as determined by size exclusion chromatography and 41 kDa by SDS-PAGE. The optimum pH and temperature were 8.5 and 60 degrees C respectively. The enzyme was stable at 50 degrees C and from pH 6.5-8.5. The enzyme hydrolyzed not only bacterial polyesters, i.e. poly(3-hydroxybutyric acid and poly(3-hydroxybutyrate-co-3-hydroxyvalerate), but also synthetic, aliphatic polyesters such as polypropiolactone, poly(ethylene adipate) and poly(ethylene succinate).

Microbial degradation of polyhydroxyalkanoates

Polyesters such as poly(3-hydroxybutyrate) (PHB) or other polyhydroxyalkanoates (PHA) have attracted commercial and academic interest as new biodegradable materials. The ability to degrade PHA is widely distributed among bacteria and fungi and depends on the secretion of specific extracellular PHA depolymerases (e-PHA depolymerases), which are carboxyesterases (EC 3.1.1.75 and EC 3.1.1.76), and on the physical state of the polymer (amorphous or crystalline). This contribution provides a summary of the biochemical and molecular biological characteristics of e-PHA depolymerases and focuses on the intracellular mobilization of storage PHA by intracellular PHA depolymerases (i-PHA depolymerases) of PHA-accumulating bacteria. The importance of different assay systems for PHA depolymerase activity is also discussed.

Bacterial degradation of natural and synthetic rubber

The degradation of natural rubber (NR), synthetic poly(cis-1,4-isoprene) (SR), and cross-linked NR (latex gloves) by Gram-positive and Gram-negative bacteria was analyzed by weight loss, gel permeation chromatography, and determination of the protein content. Weight losses of 11-18% and an increase in protein up to 850 microg/mL after incubation of Nocardia sp. DSMZ43191, Streptomyces coelicolor, Streptomyces griseus, bacterial isolate 18a, Acinetobacter calcoaceticus, and Xanthomonas sp. with latex gloves as a carbon source indicated degradation of the polymer. An increase of protein up to 1250 microg/mL was obtained upon incubation of the bacteria with SR. No or only little weight losses and no increase in the protein content were found for nondegrading control strains such as Streptomyces lividans and Streptomyces exfoliatus and for mutants of degrading strains of S. coelicolor and S. griseus, which have been identified by their inability to produce clearing zones on opaque latex agar. Measurement of the average molecular weight of synthetic rubber before and after degradation showed a time-dependent shift to lower values for the degrading strains. Diketone derivates of oligo(cis-1,4-isoprene) were identified as metabolites of rubber degradation. An oxidative degradation pathway of poly(cis-1,4-isoprene) to acetyl-coenzymeA and propionyl-coenzymeA by beta-oxidation is suggested for bacterial degradation of isoprene rubber.

Degradation of poly (3-hydroxybutyrate) and its copolymer poly (3-hydroxybutyrate-co-3-hydroxyvalerate) by a marine Streptomyces sp. SNG9

A marine Streptomyces sp. SNG9 was characterized by its ability to utilize poly(3-hydroxybutyrate) (PHB) and its copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate P (3HB-co-HV). The bacterium grew efficiently in a simple mineral liquid medium enriched with 0.1 % poly(3-hydroxybutyrate) powder as the sole carbon source. Cells excreted PHB depolymerase and degraded the polymer particles to complete clarity in 4 days. The degradation activity was detectable by the formation of a clear zone around the colony (petri plates) or a clear depth under the colony (test tubes). The expression of PHB depolymerase was repressed by the presence of simple soluble carbon sources. Bacterial degradation of the naturally occurring sheets of poly(3-hydroxybutyrate) and its copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) was observed by scanning electron microscopy (SEM). Morphological alterations of the polymers sheets were evidence for bacterial hydrolysis.

Function of the catalytic domain of poly(3-hydroxybutyrate) depolymerase from Pseudomonas stutzeri

The mechanism of enzymatic hydrolysis for (R)-3-hydroxybutyrate (3HB) oligomers with poly[(R)-3-hydroxybutyrate] [P(3HB)] depolymerase (PhaZpst) from Pseudomonas stutzeri was investigated by two deletion mutants lacking the substrate-binding domain and linker region, PhaZpst delta sbd and PhaZpstcore. The two deletion mutants had no ability for hydrolysis of water-insoluble P(3HB), while the hydrolysis activities of two deletion mutants for water-soluble 3HB oligomer and its derivatives (dimer, trimer, and tetramer) were identical with those of the wild type, indicating that the function of catalytic domain is independent of its substrate-binding domain and linker region. The hydrolyzed products analysis of 3HB oligomers by HPLC showed that the active site of catalytic domain recognizes at least two 3HB units for hydrolysis. The initial rates of hydrolysis of dimer derivative were lower by 2 orders of magnitude than those of trimer and tetramer derivatives, suggesting that 3HB oligomer derivatives larger than trimer are favorite substrates for PhaZpst.

Microbial degradation of polyesters

Polyesters, such as microbially produced poly[(R)-3-hydroxybutyric acid] [poly(3HB)], other poly[(R)-hydroxyalkanoic acids] [poly(HA)] and related biosynthetic or chemosynthetic polyesters are a class of polymers that have potential applications as thermoplastic elastomers. In contrast to poly(ethylene) and similar polymers with saturated, non-functionalized carbon backbones, poly(HA) can be biodegraded to water, methane, and/or carbon dioxide. This review provides an overview of the microbiology, biochemistry and molecular biology of poly(HA) biodegradation. In particular, the properties of extracellular and intracellular poly(HA) hydrolyzing enzymes [poly(HA) depolymerases] are described.

Poly(3-hydroxyvalerate) depolymerase of Pseudomonas lemoignei

Pseudomonas lemoignei is equipped with at least five polyhydroxyalkanoate (PHA) depolymerase structural genes (phaZ1 to phaZ5) which enable the bacterium to utilize extracellular poly(3-hydroxybutyrate) (PHB), poly(3-hydroxyvalerate) (PHV), and related polyesters consisting of short-chain-length hxdroxyalkanoates (PHA(SCL)) as the sole sources of carbon and energy. Four genes (phaZ1, phaZ2, phaZ3, and phaZ5) encode PHB depolymerases C, B, D, and A, respectively. It was speculated that the remaining gene, phaZ4, encodes the PHV depolymerase (D. Jendrossek, A. Frisse, A. Behrends, M. Andermann, H. D. Kratzin, T. Stanislawski, and H. G. Schlegel, J. Bacteriol. 177:596-607, 1995). However, in this study, we show that phaZ4 codes for another PHB depolymeraes (i) by disagreement of 5 out of 41 amino acids that had been determined by Edman degradation of the PHV depolymerase and of four endoproteinase GluC-generated internal peptides with the DNA-deduced sequence of phaZ4, (ii) by the lack of immunological reaction of purified recombinant PhaZ4 with PHV depolymerase-specific antibodies, and (iii) by the low activity of the PhaZ4 depolymerase with PHV as a substrate. The true PHV depolymerase-encoding structural gene, phaZ6, was identified by screening a genomic library of P. lemoignei in Escherichia coli for clearing zone formation on PHV agar. The DNA sequence of phaZ6 contained all 41 amino acids of the GluC-generated peptide fragments of the PHV depolymerase. PhaZ6 was expressed and purified from recombinant E. coli and showed immunological identity to the wild-type PHV depolymerase and had high specific activities with PHB and PHV as substrates. To our knowledge, this is the first report on a PHA(SCL) depolymerase gene that is expressed during growth on PHV or odd-numbered carbon sources and that encodes a protein with high PHV depolymerase activity. Amino acid analysis revealed that PhaZ6 (relative molecular mass [M(r)], 43,610 Da) resembles precursors of other extracellular PHA(SCL) depolymerases (28 to 50% identical amino acids). The mature protein (M(r), 41,048) is composed of (i) a large catalytic domain including a catalytic triad of S(136), D(211), and H(269) similar to serine hydrolases; (ii) a linker region highly enriched in threonine residues and other amino acids with hydroxylated or small side chains (Thr-rich region); and (iii) a C-terminal domain similar in sequence to the substrate-binding domain of PHA(SCL) depolymerases. Differences in the codon usage of phaZ6 for some codons from the average codon usage of P. lemoignei indicated that phaZ6 might be derived from other organisms by gene transfer. Multialignment of separate domains of bacterial PHA(SCL) depolymerases suggested that not only complete depolymerase genes but also individual domains might have been exchanged between bacteria during evolution of PHA(SCL) depolymerases.

Extracellular degradation of medium chain length poly(beta-hydroxyalkanoates) by Comamonas sp

The PHA-degrading isolate, strain P37C, was enriched from residential compost for its ability to hydrolyze the medium chain length PHA, poly(beta-hydroxyoctanoate) (PHO). It was subsequently found to grow on a wide range of PHAs, including both short chain length and medium chain length PHAs. The isolate was identified as belonging to the genus Comamonas. Strain P37C formed clear zones on poly(beta-hydroxybutyrate) (PHB), (PHO) and poly(beta-hydroxyphenylvalerate) (PHPV) overlay plates. PHA clear zone tubes were prepared using seven different kinds of PHAs, ranging from PHB with four-carbon repeating units, to poly(beta-hydroxyoctanoate-co-beta-hydroxyundecanoate) (PHOU) with 8- and 11-carbon repeating units. There was a direct correlation between PHA side chain length and rate of hydrolysis of the PHAs. A series of PHOUs containing varying percentages of unsaturated bonds were used to make a series of epoxidized PHOUs (PHOEs) with varying percentages of epoxy functions. Results of clear zone tube assays showed that these functionalized PHAs were all biodegradable by strain P37C, and there was no apparent correlation between rate of biodegradation and the proportion of functional groups in the PHAs. Biodegradability of these PHAs was verified using respirometry and enzyme assays. Cell-free supernatants containing activity toward PHAs were prepared, and strain P37C was shown to synthesize at least two distinct PHA depolymerases for the hydrolysis of SCL and MCL PHAs.

Cloning and characterization of the polyhydroxybutyrate depolymerase gene of Pseudomonas stutzeri and analysis of the function of substrate-binding domains

The extracellular polyhydroxybutyrate (PHB) depolymerase gene (phaZPst) of Pseudomonas stutzeri was cloned and sequenced. phaZPst was composed of 1,728 bp encoding a protein of 576 amino acids. Analyses of the N-terminal amino acid sequence and the matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrum of the purified enzyme showed that the mature enzyme consisted of 538 amino acids with a deduced molecular mass of 57,506 Da. Analysis of the deduced amino acid sequence of the protein revealed a domain structure containing a catalytic domain, putative linker region, and two putative substrate-binding domains (SBDI and SBDII). The putative linker region was similar to the repeating units of the cadherin-like domain of chitinase A from Vibrio harveyi and chitinase B from Clostridium paraputrificum. The binding characteristics of SBDs to poly([R]-3-hydroxybutyrate) [P(3HB)] and chitin granules were characterized by using fusion proteins of SBDs with glutathione S-transferase (GST). These GST fusion proteins with SBDII and SBDI showed binding activity toward P(3HB) granules but did not bind on chitin granules. It has been suggested that the SBDs of the depolymerase interact specifically with the surface of P(3HB). In addition, a kinetic analysis for the enzymatic hydrolysis of 3-hydroxybutyrate oligomers of various sizes has suggested that the catalytic domain of the enzyme recognizes at least two monomeric units as substrates.

The adsorption of substrate-binding domain of PHB depolymerases to the surface of poly(3-hydroxybutyric acid)

The binding characteristic of PHB depolymerase has been studied by using glutathione S-transferase (GST) fusion proteins with substrate-binding domain of three bacterial PHB depolymerases, Alcaligenes faecalis, Comamonas acidovorans and Comamonas testosteroni. Analysis using immuno-gold labeling technique and transmission electron microscopy indicated that a novel GST fusion protein derived from A. Faecalis enzyme adsorbed to the surface of poly(3-hydroxybutyric acid) (P(3HB)) single crystals like other fusion proteins. Comparison of inhibiting degree of P(3HB) powder hydrolysis activity of PHB depolymerase by fusion proteins indicated that three fusion proteins bind to P(3HB) powder in the same degree. The measurement of the surface hydrophobicity of proteins suggests that the interaction of the substrate-binding domain with insoluble P(3HB) may include not only a hydrophobic effect but also molecule-specific contacts.

Biochemical and molecular characterization of the polyhydroxybutyrate depolymerase of Comamonas acidovorans YM1609, isolated from freshwater

Comamonas acidovorans YM1609 secreted a polyhydroxybutyrate (PHB) depolymerase into the culture supernatant when it was cultivated on poly(3-hydroxybutyrate) [P(3HB)] or poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] as the sole carbon source. The PHB depolymerase was purified from culture supernatant of C. acidovorans by two chromatographic methods, and its molecular mass was determined as 45,000 Da by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The enzyme was stable at temperatures below 37 degrees C and at pH values of 6 to 10, and its activity was inhibited by diisopropyl fluorophosphonate. The liquid chromatography analysis of water-soluble products revealed that the primary product of enzymatic hydrolysis of P(3HB) was a dimer of 3-hydroxybutyric acid. Kinetics of enzymatic hydrolysis of P(3HB) film were studied. In addition, a gene encoding the PHB depolymerase was cloned from the C. acidovorans genomic library. The nucleotide sequence of this gene was found to encode a protein of 494 amino acids (M(r), 51,018 Da). Furthermore, by analysis of the N-terminal amino acid sequence of the purified enzyme, the molecular mass of the mature enzyme was calculated to be 48,628 Da. Analysis of the deduced amino acid sequence suggested a domain structure of the protein containing a catalytic domain, fibronectin type III module as linker, and a putative substrate-binding domain. Electron microscopic visualization of the mixture of P(3HB) single crystals and a fusion protein of putative substrate-binding domain with glutathione S-transferase demonstrated that the fusion protein adsorbed strongly and homogeneously to the surfaces of P(3HB) single crystals.

Cloning of the gene for poly(3-hydroxybutyric acid) depolymerase of Comamonas testosteroni and functional analysis of its substrate-binding domain

A poly(3-hydroxybutyric acid) (PHB) depolymerase gene of Comamonas testosteroni YM1004 was cloned on Sau3AI fragment from genomic DNA into Escherichia coli DH5. Nucleotide sequence analysis dedicated a 1539 bp open reading frame encoding a protein 513 amino acid with a putative 25 residue signal peptide for secretion. The deduced amino acid sequence was very similar to that of PHB depolymerase of Comamonas sp. In order to understand the characteristics of substrate-binding domain of the depolymerase, we constructed its glutathione S-transferase (GST) fusion protein and investigated the ability of adsorption on PHB single crystals by using gold-conjugated antibody and transmission electron microscopy. The fusion protein adsorbed on PHB single crystals tightly and homogeneously, suggesting that binding domain contributes to the adsorption of enzyme on solid PHB without site specificity.

Poly(3-hydroxybutyrate) depolymerases bind to their substrate by a C-terminal located substrate binding site

Binding of (i) purified wild-type poly(3-hydroxybutyrate) (PHB) depolymerase PhaZ4 of Pseudomonas lemoignei, (ii) a purified truncated form of PhaZ4, which lacked 55 C-terminal amino acids and (iii) commercial lactate dehydrogenase to aqueous suspensions of PHB, chitin or cellulose was studied. Only the wild-type PHB depolymerase was specifically able to bind to PHB granules. No other combination of protein and polymeric substrate resulted in polymer-bound protein. Similar results were obtained for other PHB depolymerases. We concluded that the C-terminal amino acids of PHB depolymerases represent a PHB-specific binding domain or at least an essential part of it.