New pathways for bacterial polythioesters

Sustainable Polythioesters via Thio(no)lactones: Monomer Synthesis, Ring-Opening Polymerization, End-of-Life Considerations, and Industrial Perspectives

As the environmental effects of plastics are of ever greater concern, the industry is driven towards more sustainable polymers. Besides sustainability, our fast-developing society imposes the need for highly versatile materials. Whereas aliphatic polyesters (PEs) are widely adopted and studied as next-generation biobased and (bio)degradable materials, their sulfur-containing analogs, polythioesters (PTEs), only recently gained attention. Nevertheless, the introduction of S atoms is known to often enhance thermal, mechanical, electrochemical, and optical properties, offering prospects for broad applicability. Furthermore, thanks to their thioester-based backbone, PTEs are inherently susceptible to degradation, giving them a high sustainability potential. The key route to PTEs is through ring-opening polymerization (ROP) of thio(no)lactones. This Review critically discusses the (potential) sustainability of the most relevant state-of-the-art in every step from sulfur source to end-of-life treatment options of PTEs, obtained through ROP of thio(no)lactones. The benefits and drawbacks of PTEs versus PEs are highlighted, including their industrial perspective.

Biosynthesis and Properties of Sulfur-Containing Polyhydroxyalkanoates (PHAs) Produced by Wild-Type Strain Cupriavidus necator B-10646

The study addresses the growth of the wild-type strain Cupriavidus necator B-10646 and the synthesis of sulfur-containing polyhydroxyalkanoates (PHA) by this strain on media containing fructose and three different precursors (3-mercaptopropionic acid, 3',3'-dithiodipropionic acid and 3',3'-thiodipropionic acid). By varying the concentration and number of doses of the precursors added into the bacterial culture, it was possible to find conditions that ensure the formation of 3-mercaptopropionate (3MP) monomers from the precursors and their incorporation into the C-chain of poly(3-hydroxybutyrate). A series of P(3HB-co-3MP) copolymer samples with different content of 3MP monomers (from 2.04 to 39.0 mol.%) were synthesized and the physicochemical properties were studied. The effect of 3MP monomers is manifested in a certain decrease in the molecular weight of the samples and an increase in polydispersity. Temperature changes are manifested in the appearance of two peaks in the melting region with different intervals regardless of the 3MP content. The studied P(3HB-co-3MP) samples, regardless of the content of 3MP monomers, are characterized by equalization of the ratio of the amorphous and crystalline phases and have a close degree of crystallinity with a minimum of 42%, = and a maximum of 54%.

Advances in Polyhydroxyalkanoate (PHA) Production, Volume 3

Steadily increasing R&D activities in the field of microbial polyhydroxyalkanoate (PHA) biopolyesters are committed to growing global threats from climate change, aggravating plastic pollution, and the shortage of fossil resources. These prevailing issues paved the way to launch the third Special Issue of Bioengineering dedicated to future-oriented biomaterials, characterized by their versatile plastic-like properties. Fifteen individual contributions to the Special Issue, written by renowned groups of researchers from all over the world, perfectly mirror the current research directions in the PHA sector: inexpensive feedstock like carbon-rich waste from agriculture, mitigation of CO2 for PHA biosynthesis by cyanobacteria or wild type and engineered “knallgas” bacteria, powerful extremophilic PHA production strains, novel tools for rapid in situ determination of PHA in photobioreactors, modelling of the dynamics of PHA production by mixed microbial cultures from inexpensive raw materials, enhanced bioreactor design for high-throughput PHA production by sophisticated cell retention systems, sustainable and efficient PHA recovery from biomass assisted by supercritical water, enhanced processing of PHA by application of novel antioxidant additives, and the development of compatible biopolymer blends. Moreover, elastomeric medium chain length PHA (mcl-PHA) are covered in-depth, inter alia, by introduction of a novel class of bioactive mcl-PHA-based networks, in addition to the first presentation of the new rubber-like polythioester poly(3-mercapto-2-methylpropionate). Finally, the present Special Issue is concluded by a critical essay on past, ongoing, and announced global endeavors for PHA commercialization.

Unveiling steps of the TDP degradation pathway in Variovorax paradoxus TBEA6

Since the role of biobased plastics increases every year, the search for alternatives to petrol-based polymers is very important. Variovorax paradoxus TBEA6 is able to grow with 3,3'-thiodipropionic acid (TDP) as sole source for carbon and energy. TDP can be used as a precursor substrate for the synthesis of polythioesters (PTE). To increase the feasibility of PTE synthesis, a good understanding of the degradation pathway of TDP in V. paradoxus TBEA6 is essential. Therefore, two putative 3-hydroxyisobutyryl-CoA hydrolases (VPARA_03110 & VPARA_05510) and two putative 3-hydroxypropionate dehydrogenases (VPARA_41140 & VPARA_54550) were investigated in this study. The deletion mutant V. paradoxus ∆VPARA_05510 showed a TDP-negative phenotype during growth experiments. The ability to grow with TDP as sole carbon source was successfully restored by complementation. Supernatant analysis revealed that the deletion mutant did not metabolize TDP or 3MP anymore. A specific enzyme activity up to 0.032 U/mg for the purified 3-hydroxyisobutyryl-CoA hydrolase VPARA_05510 was determined. A shift in the proteins (VPARA_54550) melting temperature of 6 °C with 2000 µM 3HP in comparison to protein without ligand was observed during thermal shift assays with the putative 3-hydroxypropionate dehydrogenase.

Biocompatibility and Physiological Thiolytic Degradability of Radically Made Thioester-Functional Copolymers: Opportunities for Drug Release

Being nondegradable, vinyl polymers have limited biomedical applicability. Unfortunately, backbone esters incorporated through conventional radical ring-opening methods do not undergo appreciable abiotic hydrolysis under physiologically relevant conditions. Here, PEG acrylate and di(ethylene glycol) acrylamide-based copolymers containing backbone thioesters were prepared through the radical ring-opening copolymerization of the thionolactone dibenzo[c,e]oxepin-5(7H)-thione. The thioesters degraded fully in the presence of 10 mM cysteine at pH 7.4, with the mechanism presumed to involve an irreversible S-N switch. Degradations with N-acetylcysteine and glutathione were reversible through the thiol-thioester exchange polycondensation of R-SC(═O)-polymer-SH fragments with full degradation relying on an increased thiolate/thioester ratio. Treatment with 10 mM glutathione at pH 7.2 (mimicking intracellular conditions) triggered an insoluble-soluble switch of a temperature-responsive copolymer at 37 °C and the release of encapsulated Nile Red (as a drug model) from core-degradable diblock copolymer micelles. Copolymers and their cysteinolytic degradation products were found to be noncytotoxic, making thioester backbone-functional polymers promising for drug delivery applications.

A tripartite tricarboxylate transporter (MIM_c39170-MIM_c39210) of Advenella mimigardefordensis DPN7T is involved in citrate uptake

To date, tripartite tricarboxylate transport (TTT) systems are not well characterized in most organisms. To investigate which carbon sources are transported by the TTT system of A. mimigardefordensis DPN7^T, single deletion mutants were generated lacking either completely both sets of genes encoding for these transport systems tctABCDE1 and tctABDE2 in the organism or the two genes encoding for the regulatory components of the third chosen TTT system, tctDE3. Deletion of tctABCDE1 (MIM_c39170-MIM_c39210) in Advenella mimigardefordensis strain DPN7^T led to inhibition of growth of the cells with citrate indicating that TctABCDE1 is the transport system for the uptake of citrate. Because of the negative phenotype, it was concluded that this deletion cannot be substituted by other transporters encoded in the genome of strain DPN7^T. A triple deletion mutant of A. mimigardefordensis lacking both complete TTT transport systems and the regulatory components of the third chosen system (ΔTctABCDE1 ΔTctABDE2 ΔTctDE3) showed a leaky growth with α-ketoglutarate in comparison with the wild type. The other investigated TTT (TctABDE3, MIM_c17190-MIM_c17220) is most probably involved in the transport of α-ketoglutarate. Additionally, thermoshift assays with TctC1 (MIM_c39190) showed a significant shift in the melting temperature of the protein in the presence of citrate whereas no shift occurred with α-ketoglutarate. A dissociation constant K_d for citrate of 41.7 μM was determined. Furthermore, alternative α-ketoglutarate transport was investigated via in silico analysis.

The catabolism of 3,3'-thiodipropionic acid in Variovorax paradoxus strain TBEA6: A proteomic analysis

Variovorax paradoxus strain TBEA6 is one of the few organisms known to utilize 3,3'-thiodipropionate (TDP) as the only source of carbon and energy. It cleaves TDP to 3-mercaptopropionate (3MP), which is a direct precursor for polythioester synthesis. To establish this process in V. paradoxus TBEA6, it is crucial to unravel its TDP metabolism. Therefore, a proteomic approach with subsequent deletion of interesting genes in the bacterium was chosen. Cells were cultivated with D-gluconate, TDP or 3-sulfinopropionate as the only carbon sources. Proteins with high abundances in gels of cells cultivated with either of the organic sulfur compounds were analyzed further. Thereby, we did not only confirm parts of the already postulated TDP metabolism, but also eight new protein candidates for TDP degradation were detected. Deletions of the corresponding genes (two enoyl-CoA hydratases (Ech-20 and Ech-30), an FK506-binding protein, a putative acetolactate synthase, a carnitinyl-CoA dehydratase, and a putative crotonase family protein) were obtained. Only the deletions of both Ech-20 and Ech-30 led to a TDP negative phenotype. The deletion mutant of VPARA_05510, which encodes the putative crotonase family protein showed reduced growth with TDP. The three genes are located in one cluster with genes proven to be involved in TDP metabolism. Thermal shift assays showed an increased stability of Ech-20 with TDP-CoA but not with TDP. These results indicate that Ech-20 uses TDP-CoA as a substrate instead of TDP. Hence, we postulate a new putative pathway for TDP metabolism. Ech-30 interacts with neither TDP-CoA nor TDP but might interact with other CoA-activated intermediates of the proposed pathway. Further enzyme characterization is necessary to unravel the complete pathway from TDP to 3MP.

Functional analysis of active amino acid residues of the mercaptosuccinate dioxygenase of Variovorax paradoxus B4

Thiol dioxygenases are non-heme mononuclear-iron proteins and belong to the cupin superfamily. In 2014, mercaptosuccinate dioxygenase (Msdo) of Variovorax paradoxus B4 was identified as another bacterial cysteine dioxygenase (Cdo) homolog catalyzing the conversion of mercaptosuccinate (MS) into succinate and sulfite. To gain further insights into potentially important amino acid residues for enzyme activity, seven enzyme variants were generated and analyzed. (i) Three variants comprised the substitution of one conserved histidine residue each by leucine, either supposed to be mandatory for coordination of the Fe(II) cofactor (H93 and H95) or to be important for substrate positioning within the active site (H163). The corresponding enzyme variants were completely inactive confirming their essential roles for enzyme activity. (ii) Mutation C100S resulted as well in an inactive enzyme demonstrating its importance for either stability or activity of the protein. (iii) For eukaryotic Cdo, a hydrogen bond network for substrate positioning was postulated, and the corresponding amino acids are basically present in Msdo. Albeit the MsdoQ64A mutation exhibited an increased K_m of 0.29 mM when compared to the wildtype with 0.06 mM, it did not significantly affect the specific activity. (iv) The variant MsdoR66A showed only very low activity even when high amounts of enzyme were applied indicating that this residue might be important for catalysis. (v) No strong effect had the mutation Y165F for which a specific enzyme activity of 10.22 μmol min^-1 mg^-1 protein and a K_m value of 0.06 mM with high similarity to those of the wildtype enzyme were obtained. This residue corresponds to Y157 of human Cdo, which is part of the catalytic triad and is supposed to be involved in substrate positioning. Apparently, another residue could fulfill this role in Msdo, since the loss of Y165 did not have a strong effect.

Proteomic analysis of organic sulfur compound utilisation in Advenella mimigardefordensis strain DPN7T

2-Mercaptosuccinate (MS) and 3,3´-ditiodipropionate (DTDP) were discussed as precursor substance for production of polythioesters (PTE). Therefore, degradation of MS and DTDP was investigated in Advenella mimigardefordensis strain DPN7^T, applying differential proteomic analysis, gene deletion and enzyme assays. Protein extracts of cells cultivated with MS, DTDP or 3-sulfinopropionic acid (SP) were compared with those cultivated with propionate (P) and/or succinate (S). The chaperone DnaK (ratio DTDP/P 9.2, 3SP/P 4.0, MS/S 6.1, DTDP/S 6.2) and a Do-like serine protease (DegP) were increased during utilization of all organic sulfur compounds. Furthermore, a putative bacterioferritin (locus tag MIM_c12960) showed high abundance (ratio DTDP/P 5.3, 3SP/P 3.2, MS/S 4.8, DTDP/S 3.9) and is probably involved in a thiol-specific stress response. The deletion of two genes encoding transcriptional regulators (LysR (MIM_c31370) and Xre (MIM_c31360)) in the close proximity of the relevant genes of DTDP catabolism (acdA, mdo and the genes encoding the enzymes of the methylcitric acid cycle; prpC,acnD, prpF and prpB) showed that these two regulators are essential for growth of A. mimigardefordensis strain DPN7^T with DTDP and that they most probably regulate transcription of genes mandatory for this catabolic pathway. Furthermore, proteome analysis revealed a high abundance (ratio MS/S 10.9) of a hypothetical cupin-2-domain containing protein (MIM_c37420). This protein shows an amino acid sequence similarity of 60% to a newly identified MS dioxygenase from Variovorax paradoxus strain B4. Deletion of the gene and the adjacently located transcriptional regulator LysR, as well as heterologous expression of MIM_c37420, the putative mercaptosuccinate dioxygenase (Msdo) from A. mimigardefordensis, showed that this protein is the key enzyme of MS degradation in A. mimigardefordensis strain DPN7^T (K_M 0.2 mM, specific activity 17.1 μmol mg^-1 min^-1) and is controlled by LysR (MIM_c37410).

Genome and Proteome Analysis of Rhodococcus erythropolis MI2: Elucidation of the 4,4´-Dithiodibutyric Acid Catabolism

Rhodococcus erythropolis MI2 has the extraordinary ability to utilize the xenobiotic 4,4´-dithiodibutyric acid (DTDB). Cleavage of DTDB by the disulfide-reductase Nox, which is the only verified enzyme involved in DTDB-degradation, raised 4-mercaptobutyric acid (4MB). 4MB could act as building block of a novel polythioester with unknown properties. To completely unravel the catabolism of DTDB, the genome of R. erythropolis MI2 was sequenced, and subsequently the proteome was analyzed. The draft genome sequence consists of approximately 7.2 Mbp with an overall G+C content of 62.25% and 6,859 predicted protein-encoding genes. The genome of strain MI2 is composed of three replicons: one chromosome and two megaplasmids with sizes of 6.45, 0.4 and 0.35 Mbp, respectively. When cells of strain MI2 were cultivated with DTDB as sole carbon source and compared to cells grown with succinate, several interesting proteins with significantly higher expression levels were identified using 2D-PAGE and MALDI-TOF mass spectrometry. A putative luciferase-like monooxygenase-class F420-dependent oxidoreductase (RERY_05640), which is encoded by one of the 126 monooxygenase-encoding genes of the MI2-genome, showed a 3-fold increased expression level. This monooxygenase could oxidize the intermediate 4MB into 4-oxo-4-sulfanylbutyric acid. Next, a desulfurization step, which forms succinic acid and volatile hydrogen sulfide, is proposed. One gene coding for a putative desulfhydrase (RERY_06500) was identified in the genome of strain MI2. However, the gene product was not recognized in the proteome analyses. But, a significant expression level with a ratio of up to 7.3 was determined for a putative sulfide:quinone oxidoreductase (RERY_02710), which could also be involved in the abstraction of the sulfur group. As response to the toxicity of the intermediates, several stress response proteins were strongly expressed, including a superoxide dismutase (RERY_05600) and an osmotically induced protein (RERY_02670). Accordingly, novel insights in the catabolic pathway of DTDB were gained.

Substrate and Cofactor Range Differences of Two Cysteine Dioxygenases from Ralstonia eutropha H16

Cysteine dioxygenases (Cdos), which catalyze the sulfoxidation of cysteine to cysteine sulfinic acid (CSA), have been extensively studied in eukaryotes because of their roles in several diseases. In contrast, only a few prokaryotic enzymes of this type have been investigated. In Ralstonia eutropha H16, two Cdo homologues (CdoA and CdoB) have been identified previously. In vivo studies showed that Escherichia coli cells expressing CdoA could convert 3-mercaptopropionate (3MP) to 3-sulfinopropionate (3SP), whereas no 3SP could be detected in cells expressing CdoB. The objective of this study was to confirm these findings and to study both enzymes in detail by performing an in vitro characterization. The proteins were heterologously expressed and purified to apparent homogeneity by immobilized metal chelate affinity chromatography (IMAC). Subsequent analysis of the enzyme activities revealed striking differences with regard to their substrate ranges and their specificities for the transition metal cofactor, e.g., CdoA catalyzed the sulfoxidation of 3MP to a 3-fold-greater extent than the sulfoxidation of cysteine, whereas CdoB converted only cysteine. Moreover, the dependency of the activities of the Cdos from R. eutropha H16 on the metal cofactor in the active center could be demonstrated. The importance of CdoA for the metabolism of the sulfur compounds 3,3'-thiodipropionic acid (TDP) and 3,3'-dithiodipropionic acid (DTDP) by further converting their degradation product, 3MP, was confirmed. Since 3MP can also function as a precursor for polythioester (PTE) synthesis in R. eutropha H16, deletion of cdoA might enable increased synthesis of PTEs.

Biodegradation of the organic disulfide 4,4'-dithiodibutyric acid by Rhodococcus spp

Four Rhodococcus spp. exhibited the ability to use 4,4'-dithiodibutyric acid (DTDB) as a sole carbon source for growth. The most important step for the production of a novel polythioester (PTE) using DTDB as a precursor substrate is the initial cleavage of DTDB. Thus, identification of the enzyme responsible for this step was mandatory. Because Rhodococcus erythropolis strain MI2 serves as a model organism for elucidation of the biodegradation of DTDB, it was used to identify the genes encoding the enzymes involved in DTDB utilization. To identify these genes, transposon mutagenesis of R. erythropolis MI2 was carried out using transposon pTNR-TA. Among 3,261 mutants screened, 8 showed no growth with DTDB as the sole carbon source. In five mutants, the insertion locus was mapped either within a gene coding for a polysaccharide deacetyltransferase, a putative ATPase, or an acetyl coenzyme A transferase, 1 bp upstream of a gene coding for a putative methylase, or 176 bp downstream of a gene coding for a putative kinase. In another mutant, the insertion was localized between genes encoding a putative transcriptional regulator of the TetR family (noxR) and an NADH:flavin oxidoreductase (nox). Moreover, in two other mutants, the insertion loci were mapped within a gene encoding a hypothetical protein in the vicinity of noxR and nox. The interruption mutant generated, R. erythropolis MI2 noxΩtsr, was unable to grow with DTDB as the sole carbon source. Subsequently, nox was overexpressed and purified, and its activity with DTDB was measured. The specific enzyme activity of Nox amounted to 1.2 ± 0.15 U/mg. Therefore, we propose that Nox is responsible for the initial cleavage of DTDB into 2 molecules of 4-mercaptobutyric acid (4MB).

Engineering the heterotrophic carbon sources utilization range of Ralstonia eutropha H16 for applications in biotechnology

Ralstonia eutropha H16 is an interesting candidate for the biotechnological production of polyesters consisting of hydroxy- and mercaptoalkanoates, and other compounds. It provides all the necessary characteristics, which are required for a biotechnological production strain. Due to its metabolic versatility, it can convert a broad range of renewable heterotrophic resources into diverse valuable compounds. High cell density fermentations of the non-pathogenic R. eutropha can be easily performed. Furthermore, this bacterium is accessible to engineering of its metabolism by genetic approaches having available a large repertoire of genetic tools. Since the complete genome sequence of R. eutropha H16 has become available, a variety of transcriptome, proteome and metabolome studies provided valuable data elucidating its complex metabolism and allowing a systematic biology approach. However, high production costs for bacterial large-scale production of biomass and biotechnologically valuable products are still an economic challenge. The application of inexpensive raw materials could significantly reduce the expenses. Therefore, the conversion of diverse substrates to polyhydroxyalkanoates by R. eutropha was steadily improved by optimization of cultivation conditions, mutagenesis and metabolic engineering. Industrial by-products and residual compounds like glycerol, and substrates containing high carbon content per weight like palm, soybean, corn oils as well as raw sugar-rich materials like molasses, starch and lignocellulose, are the most promising renewable substrates and were intensively studied.

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.

The genome of Variovorax paradoxus strain TBEA6 provides new understandings for the catabolism of 3,3'-thiodipropionic acid and hence the production of polythioesters

The betaproteobacterium Variovorax paradoxus strain TBEA6 is capable of using 3,3'-thiodipropionic acid (TDP) as sole carbon and energy source for growth. This thioether is employed for several industrial applications. It can be applied as precursor for the biotechnical production of polythioesters (PTE), which represent persistent bioplastics. Consequently, the genome of V. paradoxus strain TBEA6 was sequenced. The draft genome sequence comprises approximately 7.2Mbp and 6852 predicted open reading frames. Furthermore, transposon mutagenesis to unravel the catabolism of TDP in strain TBEA6 was performed. Screening of 20,000 mutants mapped the insertions of Tn5::mob in 32 mutants, which all showed no growth with TDP as sole carbon source. Based on the annotated genome sequence together with transposon-induced mutagenesis, defined gene deletions, in silico analyses and comparative genomics, a comprehensive pathway for the catabolism of TDP is proposed: TDP is imported via the tripartite tricarboxcylate transport system and/or the TRAP-type dicarboxylate transport system. The initial cleavage of TDP into 3-hydroxypropionic acid (3HP) and 3-mercaptopropionic acid (3MP), which serves as precursor substrate for PTE synthesis, is most probably performed by the FAD-dependent oxidoreductase Fox. 3HP is presumably catabolized via malonate semialdehyde, whereas 3MP is oxygenated by the 3MP-dioxygenase Mdo yielding 3-sulfinopropionic acid (3SP). Afterwards, 3SP is linked to coenzyme A. The next step is the abstraction of sulfite by a desulfinase, and the resulting propionyl-CoA enters the central metabolism. Sulfite is oxidized to sulfate by the sulfite-oxidizing enzyme SoeABC and is subsequently excreted by the cells by the sulfate exporter Pse.