Roles of Poly(3-Hydroxybutyrate) Depolymerase and 3HB-Oligomer Hydrolase in Bacterial PHB Metabolism

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.

A (S)-3-Hydroxybutyrate Dehydrogenase Belonging to the 3-Hydroxyacyl-CoA Dehydrogenase Family Facilitates Hydroxyacid Degradation in Anaerobic Bacteria

Ketone bodies, including acetoacetate, 3-hydroxybutyrate, and acetone, are produced in the liver of animals during glucose starvation. Enzymes for the metabolism of (R)-3-hydroxybutyrate have been extensively studied, but little is known about the metabolism of its enantiomer (S)-3-hydroxybutyrate. Here, we report the characterization of a novel pathway for the degradation of (S)-3-hydroxybutyrate in anaerobic bacteria. We identify and characterize a stereospecific (S)-3-hydroxylbutyrate dehydrogenase (3SHBDH) from Desulfotomaculum ruminis, which catalyzes the reversible NAD(P)H-dependent reduction of acetoacetate to form (S)-3-hydroxybutyrate. 3SHBDH also catalyzes oxidation of d-threonine (2R, 3S) and l-allo-threonine (2S, 3S), consistent with its specificity for β-(3S)-hydroxy acids. Isothermal calorimetry experiments support a sequential mechanism involving binding of NADH prior to (S)-3-hydroxybutyrate. Homologs of 3SHBDH are present in anaerobic fermenting and sulfite-reducing bacteria, and experiments with Clostridium pasteurianum showed that 3SHBDH, acetate CoA-transferase (YdiF), and (S)-3-hydroxybutyryl-CoA dehydrogenase (Hbd) are involved together in the degradation of (S)-3-hydroxybutyrate as a carbon and energy source for growth. (S)-3-hydroxybutyrate is a human metabolic marker and a chiral precursor for chemical synthesis, suggesting potential applications of 3SHBDH in diagnostics or the chemicals industry. IMPORTANCE (R)-3-hydroxybutyrate is well studied as a component of ketone bodies produced by the liver and of bacterial polyesters. However, the biochemistry of its enantiomer (S)-3-hydroxybutyrate is poorly understood. This study describes the identification and characterization of a stereospecific (S)-3-hydroxylbutyrate dehydrogenase and its function in a metabolic pathway for the degradation of (S)-3-hydroxybutyrate as a carbon and energy source in anaerobic bacteria. (S)-3-hydroxybutyrate is a mammalian metabolic marker and a precursor for chemical synthesis and bioplastics, suggesting potential applications of these enzymes in diagnostics and biotechnology.

Biodegradation Studies of Polyhydroxybutyrate and Polyhydroxybutyrate-co-Polyhydroxyvalerate Films in Soil

Due to increased environmental pressures, significant research has focused on finding suitable biodegradable plastics to replace ubiquitous petrochemical-derived polymers. Polyhydroxyalkanoates (PHAs) are a class of polymers that can be synthesized by microorganisms and are biodegradable, making them suitable candidates. The present study looks at the degradation properties of two PHA polymers: polyhydroxybutyrate (PHB) and polyhydroxybutyrate-co-polyhydroxyvalerate (PHBV; 8 wt.% valerate), in two different soil conditions: soil fully saturated with water (100% relative humidity, RH) and soil with 40% RH. The degradation was evaluated by observing the changes in appearance, chemical signatures, mechanical properties, and molecular weight of samples. Both PHB and PHBV were degraded completely after two weeks in 100% RH soil conditions and showed significant reductions in mechanical properties after just three days. The samples in 40% RH soil, however, showed minimal changes in mechanical properties, melting temperatures/crystallinity, and molecular weight over six weeks. By observing the degradation behavior for different soil conditions, these results can pave the way for identifying situations where the current use of plastics can be replaced with biodegradable alternatives.

Exploiting Polyhydroxyalkanoates for Biomedical Applications

Polyhydroxyalkanoates (PHA) are biodegradable plastic. Numerous bacteria produce PHAs under environmental stress conditions, such as excess carbon-rich organic matter and limitations of other nutritional elements such as potassium, magnesium, oxygen, phosphorus, and nitrogen. In addition to having physicochemical properties similar to fossil-fuel-based plastics, PHAs have unique features that make them ideal for medical devices, such as easy sterilization without damaging the material itself and easy dissolution following use. PHAs can replace traditional plastic materials used in the biomedical sector. PHAs can be used in a variety of biomedical applications, including medical devices, implants, drug delivery devices, wound dressings, artificial ligaments and tendons, and bone grafts. Unlike plastics, PHAs are not manufactured from petroleum products or fossil fuels and are, therefore, environment-friendly. In this review, a recent overview of applications of PHAs with special emphasis on biomedical sectors, including drug delivery, wound healing, tissue engineering, and biocontrols, are discussed.

The protective role of PHB and its degradation products against stress situations in bacteria

Many bacteria produce storage biopolymers that are mobilized under conditions of metabolic adaptation, for example, low nutrient availability and cellular stress. Polyhydroxyalkanoates are often found as carbon storage in Bacteria or Archaea, and of these polyhydroxybutyrate (PHB) is the most frequently occurring PHA type. Bacteria usually produce PHB upon availability of a carbon source and limitation of another essential nutrient. Therefore, it is widely believed that the function of PHB is to serve as a mobilizable carbon repository when bacteria face carbon limitation, supporting their survival. However, recent findings indicate that bacteria switch from PHB synthesis to mobilization under stress conditions such as thermal and oxidative shock. The mobilization products, 3-hydroxybutyrate and its oligomers, show a protective effect against protein aggregation and cellular damage caused by reactive oxygen species and heat shock. Thus, bacteria should have an environmental monitoring mechanism directly connected to the regulation of the PHB metabolism. Here, we review the current knowledge on PHB physiology together with a summary of recent findings on novel functions of PHB in stress resistance. Potential applications of these new functions are also presented.

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

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

Microbial Polyhydroxyalkanoates and Nonnatural Polyesters

Microorganisms produce diverse polymers for various purposes such as storing genetic information, energy, and reducing power, and serving as structural materials and scaffolds. Among these polymers, polyhydroxyalkanoates (PHAs) are microbial polyesters synthesized and accumulated intracellularly as a storage material of carbon, energy, and reducing power under unfavorable growth conditions in the presence of excess carbon source. PHAs have attracted considerable attention for their wide range of applications in industrial and medical fields. Since the first discovery of PHA accumulating bacteria about 100 years ago, remarkable advances have been made in the understanding of PHA biosynthesis and metabolic engineering of microorganisms toward developing efficient PHA producers. Recently, nonnatural polyesters have also been synthesized by metabolically engineered microorganisms, which opened a new avenue toward sustainable production of more diverse plastics. Herein, the current state of PHAs and nonnatural polyesters is reviewed, covering mechanisms of microbial polyester biosynthesis, metabolic pathways, and enzymes involved in biosynthesis of short-chain-length PHAs, medium-chain-length PHAs, and nonnatural polyesters, especially 2-hydroxyacid-containing polyesters, metabolic engineering strategies to produce novel polymers and enhance production capabilities and fermentation, and downstream processing strategies for cost-effective production of these microbial polyesters. In addition, the applications of PHAs and prospects are discussed.

Polyhydroxyalkanoate Production and Degradation Patterns in Bacillus Species

Bacteria under stress conditions of excess of carbon (C) and limitations of nutrients divert its metabolism towards C storage as energy reservoir-polyhydroxyalkanoate (PHA). Different Bacillus species-B. cereus and B. thuringiensis, were monitored to produce PHA from different C sources-glucose, crude glycerol and their combination at 37 °C for period up to 192 h. PHA production and its composition was found to vary with feed and bacterial strains. PHA production on crude glycerol continued to increase up to 120 h, reaching a maximum of 2725 mg/L with an effective yield of 71% of the dry cell mass. Depolymerization of PHA was observe to initiate after 96 h of incubation up to 192 h. PHA degradation products have been envisaged to be applied in medical field: tissue engineering, drug carriers, memory enhancers, antiosteoporosis, biodegradable implants. The PHA production and degradation cycle for 192 h has not been reported previously in literature.

3-Hydroxybutyrate oligomer hydrolase and 3-hydroxybutyrate dehydrogenase participate in intracellular polyhydroxybutyrate and polyhydroxyvalerate degradation in Paracoccus denitrificans

Genes encoding 3-hydroxybutyrate oligomer hydrolase (PhaZc) and 3-hydroxybutyrate dehydrogenase (Hbd) were isolated from Paracoccus denitrificans. PhaZc and Hbd were overproduced as His-tagged proteins in Escherichia coli and purified by affinity and gel filtration chromatography. Purified His-tagged proteins had molecular masses of 31 kDa and 120 kDa (a tetramer of 29-kDa subunits). The His-tagged PhaZc hydrolyzed not only 3-hydroxybutyrate oligomers but also 3-hydroxyvalerate oligomers. The His-tagged Hbd catalyzed the dehydrogenation of 3-hydroxyvalerate as well as 3-hydroxybutyrate. When both enzymes were included in the same enzymatic reaction system with 3-hydroxyvalerate dimer, sequential reactions occurred, suggesting that PhaZc and Hbd play an important role in the intracellular degradation of poly(3-hydroxyvalerate). When the phaZc gene was disrupted in P. denitrificans by insertional inactivation, the mutant strain lost PhaZc activity. When the phaZc-disrupted P. denitrificans was complemented with phaZc, PhaZc activity was restored. These results suggest that P. denitrificans carries a single phaZc gene. Disruption of the phaZc gene in P. denitrificans affected the degradation rate of PHA.

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 complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments

Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals.

Purification and molecular cloning of an intracellular 3-hydroxybutyrate-oligomer hydrolase from Paucimonas lemoignei

An intracellular 3-hydroxybutyrate-oligomer hydrolase was purified from a poly(3-hydroxybutyrate)-degrading bacterium, Paucimonas lemoignei. It hydrolyzed the 3-hydroxybutyrate dimer with the highest specific activity of any of the enzymes reported so far. The gene was cloned and sequenced. The deduced amino acid sequence showed that the enzyme is a homolog of the PhaZc of Ralstonia eutropha H16.

Linear 3-hydroxybutyrate tetramer (HB4) produced by Sphingomonas sp. is characterized as a growth promoting factor for some rhizomicrofloral composers

Sphingomonas spp. of alpha-proteobacteria often play a role in assisting the development of microfloral communities under adverse soil conditions. Using a Frateuria sp. as an indicator for bacterial growth assay, we investigated the bacterial growth-promoting factor in the culture fluids of Sphingomonas sp. EC-K085. This factor was successfully isolated and identified as linear (R,R,R,R)-3-hydroxybutyrate tetramer (HB4), having a hydroxy-end and a carboxy-end group. When 28 mug of HB4 was charged on a paper disc, impregnated Frateuria sp. cells in modified Winogradsky agar medium exhibited a promoted cell growth to form a clear colony emerging zone after a 2-day incubation.

Properties of a novel intracellular poly(3-hydroxybutyrate) depolymerase with high specific activity (PhaZd) in Wautersia eutropha H16

A novel intracellular poly(3-hydroxybutyrate) (PHB) depolymerase (PhaZd) of Wautersia eutropha (formerly Ralstonia eutropha) H16 which shows similarity with the catalytic domain of the extracellular PHB depolymerase in Ralstonia pickettii T1 was identified. The positions of the catalytic triad (Ser190-Asp266-His330) and oxyanion hole (His108) in the amino acid sequence of PhaZd deduced from the nucleotide sequence roughly accorded with those of the extracellular PHB depolymerase of R. pickettii T1, but a signal peptide, a linker domain, and a substrate binding domain were missing. The PhaZd gene was cloned and the gene product was purified from Escherichia coli. The specific activity of PhaZd toward artificial amorphous PHB granules was significantly greater than that of other known intracellular PHB depolymerase or 3-hydroxybutyrate (3HB) oligomer hydrolases of W. eutropha H16. The enzyme degraded artificial amorphous PHB granules and mainly released various 3-hydroxybutyrate oligomers. PhaZd distributed nearly equally between PHB inclusion bodies and the cytosolic fraction. The amount of PHB was greater in phaZd deletion mutant cells than the wild-type cells under various culture conditions. These results indicate that PhaZd is a novel intracellular PHB depolymerase which participates in the mobilization of PHB in W. eutropha H16 along with other PHB depolymerases.