Rubber oxygenase and latex clearing protein cleave rubber to different products and use different cleavage mechanisms

Computational investigation of cis-1,4-polyisoprene binding to the latex-clearing protein LcpK30

Latex clearing proteins (Lcps) catalyze the oxidative cleavage of the C = C bonds in cis-1,4-polyisoprene (natural rubber), producing oligomeric compounds that can be repurposed to other materials. The active catalytic site of Lcps is buried inside the protein structure, thus raising the question of how the large hydrophobic rubber chains can access the catalytic center. To improve our understanding of hydrophobic polymeric substrate binding to Lcps and subsequent catalysis, we investigated the interaction of a substrate model containing ten carbon-carbon double bonds with the structurally characterized LcpK30, using multiple computational tools. Prediction of the putative tunnels and cavities in the LcpK30 structure, using CAVER-Pymol plugin 3.0.3, fpocket and Molecular Dynamic (MD) simulations provided valuable insights on how substrate enters from the surface to the buried active site. Two dominant tunnels were discovered that provided feasible routes for substrate binding, and the presence of two hydrophobic pockets was predicted near the heme cofactor. The larger of these pockets is likely to accommodate the substrate and to determine the size distribution of the oligomers. Protein-ligand docking was carried out using GOLD software to predict the conformations and interactions of the substrate within the protein active site. Deeper insight into the protein-substrate interactions, including close-contacts, binding energies and potential cleavage sites in the cis-1,4-polyisoprene, were obtained from MD simulations. Our findings provide further justification that the protein-substrate complexation in LcpK30 is mainly driven by the hydrophobic interactions accompanied by mutual conformational changes of both molecules. Two potential binding modes were identified, with the substrate in either extended or folded conformations. Whilst binding in the extended conformation was most favorable, the folded conformation suggested a preference for cleavage of a central double bond, leading to a preference for oligomers with 5 to 6 C = C bonds. The results provide insight into further enzyme engineering studies to improve catalytic activity and diversify the substrate and product scope of Lcps.

Enhancing the heterologous expression of latex clearing protein from Streptomyces sp. strain K30 in Escherichia coli through fermentation condition optimization and molecular modification

Latex clearing protein from Streptomyces sp. strain K30 (LcpK30) is a natural oxidoreductase that can catalyse the cleavage of rubber through dioxygenation. It has significant potential applications in polymer degradation. However, its limited expression in engineered strains restricts its utility. This study aimed to enhance the soluble expression and enzyme activity of LcpK30 in E. coli BL21 (DE3) by optimizing fermentation conditions and making molecular modifications. The enzyme activity reached 5.05 U·mL-1 by optimizing the induction conditions, adding cofactors, and using chemical chaperones, which was 237.1 % of the initial case. Further enhancements in soluble expression were achieved through site mutations guided by the PROSS server, resulting in 8 out of 13 mutants with increased protein expression, a high positive mutation rate of 61.5 %. Subsequently, combined mutants were created by merging single mutants with enhanced protein expression and enzyme activity. The top three double mutants, G91D/S149A, G91D/A210H, and G91D/H296P, displayed expression levels at 173.3 %, 173.3 %, and 153.3 % of the wild-type LcpK30, respectively. These mutants also exhibited enhanced fermentation enzyme activity, reaching 149.5 %, 250.0 %, and 420.2 % compared to the wild-type, along with improved specific activities. This study provides insights for the efficient production of LcpK30 and a practical foundation for its application.

Biodegradation of rubber in cultures of Rhodococcus rhodochrous and by its enzyme latex clearing protein

The biodegradation of rubber materials is considered as a sustainable recycling alternative, highlighting the use of microorganisms and enzymes in oxidative processes of natural rubber. Currently, the main challenge is the treatment of rubber materials such as waste tyres, where the mixture of rubber polymers with different additives and the cross-linked structure obtained due to the vulcanisation process positions them as highly persistent materials. This study characterises the degradation of different rubber-containing substrates in in vivo and in vitro processes using the bacterium Rhodococcus rhodochrous and the oxygenase latex clearing protein (Lcp) from the same strain. For the first time, the degradation of polyisoprene particles in liquid cultures of R. rhodochrous was analysed, obtaining up to 19.32% mass loss of the polymer when using it as the only carbon source. Scanning electron microscopy analysis demonstrated surface alteration of pure polyisoprene and vulcanised rubber particles after 2 weeks of incubation. The enzyme Lcp_RR was produced in bioreactors under rhamnose induction and its activity characterised in oxygen consumption assays at different enzyme concentrations. A maximum consumption of 28.38 µmol_O2/min was obtained by adding 100 µg/mL Lcp_RR to a 2% (v/v) latex emulsion as substrate. The bioconversion of natural rubber into reaction degradation products or oligoisoprenoids was calculated to be 32.54%. Furthermore, the mass distribution of the oligoisoprenoids was analysed by liquid chromatography coupled to mass spectrometry (LC-MS) and 17 degradation products, ranging from C20 to C100 oligoisoprenoids, were identified. The multi-enzymatic degradation capacity of R. rhodochrous positions it as a model microorganism in complex degradation processes such as in the case of tyre waste.

Streptomyces sp. AC04842: Genomic Insights and Functional Expression of Its Latex Clearing Protein Genes (lcp1 and lcp2) When Cultivated With Natural and Vulcanized Rubber as the Sole Carbon Source

Rubber-degrading Actinobacteria have been discovered and investigated since 1985. Only recently, through the advancement of genomic sequencing and molecular techniques, genes and pathways involved in rubber degradation are being revealed; however, the complete degradation pathway remains unknown. Streptomyces sp. AC04842 (JCM 34241) was discovered by screening at a Culture Collection Centre in Sarawak for Actinomycetes forming a clear zone on natural rubber latex agar. Streptomyces is a dominant and well-studied soil bacterium playing an important role in soil ecology including carbon recycling and biodegradation. Streptomyces sp. AC04842 draft genome revealed the presence of 2 putative latex clearing protein (lcp) genes on its chromosome and is closely related to Streptomyces cellulosae. Under the Streptomyces genus, there are a total of 64 putative lcp genes deposited in the GenBank and UniProt database. Only 1 lcp gene from Streptomyces sp. K30 has been characterized. Unlike Streptomyces sp. K30 which contained 1 lcp gene on its chromosome, Streptomyces sp. AC04842 contained 2 lcp genes on its chromosome. Streptomyces sp. AC04842 lcp1 and lcp2 amino acid sequences showed 46.13 and 69.11%, respectively, similarity to lcp sequences of Streptomyces sp. K30. Most rubber degrading strains were known to harbor only 1 lcp gene, and only recently, 2–3 lcp homologs have been reported. Several studies have shown that lcp-homolog expression increased in the presence of rubber. To study the expression of lcp1 and lcp2 genes for Streptomyces sp. AC04842, the strain was incubated in different types of rubber as the sole carbon source. In general, the lcp1 gene was highly expressed, while the lcp2 gene expression was upregulated in the presence of vulcanized rubber. Mixtures of natural and vulcanized rubber did not further increase the expression of both lcp genes compared with the presence of a specific rubber type. In this study, we paved the way to the exploration of lcp homologs and their function in degrading different types of rubber.

Rubber Degrading Strains: Microtetraspora and Dactylosporangium

Rubber composed of highly unsaturated hydrocarbons, modified through addition of chemicals and vulcanization are widely used to date. However, the usage of rubber, faces many obstacles. These elastomeric materials are difficult to be re-used and recovered, leading to high post-consumer waste and vast environmental problems. Tyres, the major rubber waste source can take up to 80 years to naturally degrade. Experiments show that the latex clearing proteins (Lcp) found in Actinobacteria were reportedly critical for the initial oxidative cleavage of poly(cis-1,4-isoprene), the major polymeric unit of rubber. Although, more than 100 rubber degrading strains have been reported, only 8 Lcp proteins isolated from Nocardia (3), Gordonia (2), Streptomyces (1), Rhodococcus (1), and Solimonas (1) have been purified and biochemically characterized. Previous studies on rubber degrading strains and Lcp enzymes, implied that they are distinct. Following this, we aim to discover additional rubber degrading strains by randomly screening 940 Actinobacterial strains isolated from various locations in Sarawak on natural rubber (NR) latex agar. A total of 18 strains from 5 genera produced clearing zones on NR latex agar, and genes encoding Lcp were identified. We report here lcp genes from Microtetraspora sp. AC03309 (lcp1 and lcp2) and Dactylosporangium sp. AC04546 (lcp1, lcp2, lcp3), together with the predicted genes related to rubber degradation. In silico analysis suggested that Microtetraspora sp. AC03309 is a distinct species closely related to Microtetraspora glauca while Dactylosporangium sp. AC04546 is a species closely related to Dactylosporangium sucinum. Genome-based characterization allowed the establishment of the strains taxonomic position and provided insights into their metabolic potential especially in biodegradation of rubber. Morphological changes and the spectrophotometric detection of aldehyde and keto groups indicated the degradation of the original material in rubber samples incubated with the strains. This confirms the strains’ ability to utilize different rubber materials (fresh latex, NR product and vulcanized rubber) as the sole carbon source. Both strains exhibited different levels of biodegradation ability. Findings on tyre utilization capability by Dactylosporangium sp. AC04546 is of interest. The final aim is to find sustainable rubber treatment methods to treat rubber wastes.

Microbial Degradation of Rubber: Actinobacteria

Rubber is an essential part of our daily lives with thousands of rubber-based products being made and used. Natural rubber undergoes chemical processes and structural modifications, while synthetic rubber, mainly synthetized from petroleum by-products are difficult to degrade safely and sustainably. The most prominent group of biological rubber degraders are Actinobacteria. Rubber degrading Actinobacteria contain rubber degrading genes or rubber oxygenase known as latex clearing protein (lcp). Rubber is a polymer consisting of isoprene, each containing one double bond. The degradation of rubber first takes place when lcp enzyme cleaves the isoprene double bond, breaking them down into the sole carbon and energy source to be utilized by the bacteria. Actinobacteria grow in diverse environments, and lcp gene containing strains have been detected from various sources including soil, water, human, animal, and plant samples. This review entails the occurrence, physiology, biochemistry, and molecular characteristics of Actinobacteria with respect to its rubber degrading ability, and discusses possible technological applications based on the activity of Actinobacteria for treating rubber waste in a more environmentally responsible manner.

In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB)

The study presents an in silico identification of poly (cis-1,4-isoprene) cleaving enzymes, viz., RoxA and RoxB in bacteria, followed by their functional and evolutionary exploration using comparative genomics. The orthologs of these proteins were found to be restricted to Gram-negative beta-, gamma-, and delta-proteobacteria. Toward the evolutionary propagation, the RoxA and RoxB genes were predicted to have evolved via a common interclass route of horizontal gene transfer in the phylum Proteobacteria (delta → gamma → beta). Besides, recombination, mutation, and gene conversion were also detected in both the genes leading to their diversification. Further, the differential selective pressure is predicted to be operating on entire RoxA and RoxB genes such that the former is diversifying further, whereas the latter is evolving to reduce its genetic diversity. However, the structurally and functionally important sites/residues of these genes were found to be preventing changes implying their evolutionary conservation. Further, the phylogenetic analysis demonstrated a sharp split between the RoxA and RoxB orthologs and indicated the emergence of their variant as another type of putative rubber oxygenase (RoxC) in the class Gammaproteobacteria. A detailed in silico analysis of the signature motifs and residues of Rox sequences exhibited important differences as well as similarities among the RoxA, RoxB, and putative RoxC sequences. Although RoxC appears to be a hybrid of RoxA and RoxB, the signature motifs and residues of RoxC are more similar to RoxB.

Bacterial and enzymatic degradation of poly(cis-1,4-isoprene) rubber: Novel biotechnological applications

Poly(cis-1,4-isoprene) rubber is a highly demanded elastomeric material mainly used for the manufacturing of tires. The end-cycle of rubber-made products is creating serious environmental concern and, therefore, different recycling processes have been proposed. However, the current physical-chemical processes include the use of hazardous chemical solvents, large amounts of energy, and possibly generations of unhealthy micro-plastics. Under this scenario, eco-friendly alternatives are needed and biotechnological rubber treatments are demonstrating huge potential. The cleavage mechanisms and the biochemical pathways for the uptake of poly(cis-1,4-isoprene) rubber have been extensively reported. Likewise, novel bacterial strains able to degrade the polymer have been studied and the involved structural and functional enzymes have been analyzed. Considering the fundamentals, biotechnological approaches have been proposed considering process optimization, cost-effective methods and larger-scale experiments in the search for practical and realistic applications. In this work, the latest research in the rubber biodegradation field is shown and discussed, aiming to analyze the combination of detoxification, devulcanization and polymer-cleavage mechanisms to achieve better degradation yields. The modified superficial structure of rubber materials after biological treatments might be an interesting way to reuse old rubber for re-vulcanization or to find new materials.

Global Regulator of Rubber Degradation in Gordonia polyisoprenivorans VH2: Identification and Involvement in the Regulation Network

A cAMP receptor protein (CRP_VH2) was detected as a global regulator in Gordonia polyisoprenivorans VH2 and was proposed to participate in the network regulating poly(cis-1,4-isoprene) degradation as a novel key regulator. CRP_VH2 shares a sequence identity of 79% with GlxR, a well-studied global regulator of Corynebacterium glutamicum Furthermore, CRP_VH2 and GlxR have a common oligomerization state and similar binding motifs, and thus most likely have similar functions as global regulators. Size exclusion chromatography of purified CRP_VH2 confirmed the existence as a homodimer with a native molecular weight of 44.1 kDa in the presence of cAMP. CRP_VH2 bound to the TGTGAN₆TCACT motif within the 131-bp intergenic region of divergently oriented lcp1 _VH2 and lcpR _VH2, encoding a latex clearing protein and its putative repressor, respectively. DNase I footprinting assays revealed the exact operator size of CRP_VH2 in the intergenic region (25 bp), which partly overlapped with the proposed promoters of lcpR _VH2 and lcp1 _VH2 Our findings indicate that CRP_VH2 represses the expression of lcpR _VH2 while simultaneously directly or indirectly activating the expression of lcp1 _VH2 by binding the competing promoter regions. Furthermore, binding of CRP_VH2 to upstream regions of additional putative enzymes of poly(cis-1,4-isoprene) degradation was verified in vitro. In silico analyses predicted 206 CRP_VH2 binding sites comprising 244 genes associated with several functional categories, including carbon and peptide metabolism, stress response, etc. The gene expression regulation of several subordinated regulators substantiated the function of CRP_VH2 as a global regulator. Moreover, we anticipate that the novel lcpR regulation mechanism by CRPs is widespread in other rubber-degrading actinomycetes.IMPORTANCE In order to develop efficient microbial recycling strategies for rubber waste materials, it is required that we understand the degradation pathway of the polymer and how it is regulated. However, only little is known about the transcriptional regulation of the rubber degradation pathway, which seems to be upregulated in the presence of the polymer. We identified a novel key regulator of rubber degradation (CRP_VH2) that regulates several parts of the pathway in the potent rubber-degrader G. polyisoprenivorans VH2. Furthermore, we provide evidence for a widespread involvement of CRP regulators in the degradation of rubber in various other rubber-degrading actinomycetes. Thus, these novel insights into the regulation of rubber degradation are essential for developing efficient microbial degradation strategies for rubber waste materials by this group of actinomycetes.

Characterization of the genes responsible for rubber degradation in Actinoplanes sp. strain OR16

A Gram-positive rubber-degrading bacterium, Actinoplanes sp. strain OR16 (strain NBRC 114529), is able to grow on agar plates containing natural and synthetic rubber as the sole sources of carbon and energy. When this strain was grown on natural rubber latex overlay agar plates, translucent halos around the cells were observed. To identify the natural rubber degradation genes and other features of its metabolism, its complete genome sequence was determined. The genome of OR16 consists of 9,293,892 bp and comprises one circular chromosome (GenBank accession number AP019371.1) with a G + C content of 70.3%. The genome contains 8238 protein-coding and 18 rRNA genes. A homology search of the genome sequence revealed that three genes (lcp1, lcp2, and lcp3) are homologous to an extracellular latex-clearing protein (Lcp) of Streptomyces sp. K30. RT-PCR analysis revealed that lcp1 and lcp2 seem to constitute an operon. Purified lcp gene products have oxygen consumption activity toward natural rubber latex, suggesting that all these genes encode rubber-degrading enzymes in OR16. Quantitative reverse transcription-PCR analysis indicated that the transcription of these genes is induced during the growth of OR16 on natural rubber. The genes located adjacent to lcp1 and lcp3, which code for a TetR/AcrR-type transcriptional regulator, can bind to the promoter regions of these lcp genes. It is suggested that the putative regulators play a role in regulating the transcription of the lcp genes. These results strongly suggested that three lcp genes are required for the utilization of natural rubber in strain OR16. Key Points • The complete genome sequence of Actinoplanes sp. strain OR16 was determined. • Three lcp genes which are involved in the natural rubber degradation in OR16 were identified. • Transcription of these lcp genes is induced during utilization of rubber in OR16. • Two regulators, which bind to the promoter regions of lcp, were determined.

Mechanical Insights into the Enzymatic Cleavage of Double C-C Bond in Poly(cis-1,4-isoprene) by the Latex Clearing Protein

The b-type cytochrome Lcp_K30 is a latex clearing protein (Lcp), which acts as an endotype dioxygenase to catalyze the extracellular cleavage of the chemically inert aliphatic polymer poly(cis-1,4-isoprene), producing oligo-isoprenoids with different terminal carbonyl groups (aldehyde and ketone, -CH₂-CHO and -CH₂-COCH₃). On the basis of the fact that the muteins of E148A, E148Q, and E148H have substantially reduced reactivity, and the E148-initiated reaction mechanism has been previously proposed, in which a cyclic dioxetane intermediate or an epoxide intermediate may be involved, however, open questions still remain. In this paper, on the basis of the crystal structure of Lcp_K30, the enzyme-substrate reactant model was constructed, and the cleavage mechanism of the central double bond of poly(cis-1,4-isoprene) was elucidated by performing quantum mechanics/molecular mechanics calculations. Our calculation results revealed that the oxidative cleavage reaction is triggered by the addition of the heme-bound dioxygen to the double bond of the polymer, and E148 does not act as the catalytic base to extract the allylic proton to assist the reaction as previously suggested. Of the two considered pathways, the pathway that involves the dioxetane intermediate was calculated to be more favorable. During the catalysis, the distal oxygen first adds to the double bond of the substrate to form a radical intermediate, and then the Fe-O1 (proximal oxygen) bond cleaves to generate the dioxetane intermediate, which can easily collapse affording the final ketone and aldehyde products. In general, the cleavage mechanism of double C-C bond catalyzed by Lcp_K30 is similar to those of indoleamine 2,3-dioxygenase, tryptophan 2,3-dioxygenase, and the nonheme stilbene cleavage oxygenase NOV1 that all depend on the iron-bound dioxygen to initiate the cleavage reaction.

Poly(cis-1,4-isoprene)-cleavage enzymes from natural rubber-utilizing bacteria

Natural rubber and synthetic poly(cis-1,4-isoprene) are used industrially in the world. Microbial utilization for the isoprene rubbers has been reported in gram-positive and gram-negative bacteria. Poly(cis-1,4-isoprene)-cleavage enzymes that are secreted by rubber-utilizing bacteria cleave the poly(cis-1,4-isoprene) chain to generate low-molecular-weight oligo(cis-1,4-isoprene) derivatives containing aldehyde and ketone groups. The resulting products are converted to the compounds including carboxyl groups, which could then be further catabolized through β-oxidation pathway. One of poly(cis-1,4-isoprene)-cleavage enzymes is latex-clearing protein (Lcp) that was found in gram-positive rubber degraders including Streptomyces, Gordonia, Rhodococcus, and Nocardia species. The other one is rubber oxygenase A and B (RoxA/RoxB) which have been identified from gram-negative rubber degraders such as Steroidobacter cummioxidans and Rhizobacter gummiphilus. Recently, the transcriptional regulation mechanisms for Lcp-coding genes in gram-positive bacteria have been characterized. Here, the current knowledge of genes and enzymes for the isoprene rubber catabolism were summarized.

Immunosuppressant mycophenolic acid biosynthesis employs a new globin-like enzyme for prenyl side chain cleavage

Mycophenolic acid (MPA, 1) and its derivatives are first-line immunosuppressants used in organ transplantation and for treating autoimmune diseases. Despite chemical synthetic achievements, the biosynthetic formation of a seven-carbon carboxylic acid pharmacophore side chain of 1, especially the processes involving the cleavage of the prenyl side chain between DHMP (4) and DMMPA (5), remains unknown. In this work, we identified a membrane-bound prenyltransferase, PgMpaA, that transfers FPP to 4 to yield FDHMP (6). Compound 6 undergoes the first cleavage step via a new globin-like enzyme PgMpaB to form a cryptic intermediate 12. Heterologous expression of PgMpa genes in Aspergillus nidulans demonstrates that the second cleavage step (from 12 to 5) of 1 is a PgMpa cluster-independent process in vivo. Our results, especially the discovery of the broad tolerance of substrates recognized by PgMpaB, set up a strategy for the formation of "pseudo-isopentenyl" natural products using fungal globin-like enzymes.

Towards the understanding of the enzymatic cleavage of polyisoprene by the dihaem-dioxygenase RoxA

Utilization of polyisoprene (natural rubber) as a carbon source by Steroidobacter cummioxidans 35Y (previously Xanthomonas sp. strain 35Y) depends on the formation and secretion of rubber oxygenase A (RoxA). RoxA is a dioxygenase that cleaves polyisoprene to 12-oxo-4,8-dimethyl-trideca-4,8-diene-1-al (ODTD), a suitable growth substrate for S. cummioxidans. RoxA harbours two non-equivalent, spectroscopically distinguishable haem centres. A dioxygen molecule is bound to the N-terminal haem of RoxA and identifies this haem as the active site. In this study, we provide insights into the nature of this unusually stable dioxygen-haem coordination of RoxA by a re-evaluation of previously published together with newly obtained biophysical data on the cleavage of polyisoprene by RoxA. In combination with the meanwhile available structure of RoxA we are now able to explain several uncommon and previously not fully understood features of RoxA, the prototype of rubber oxygenases in Gram-negative rubber-degrading bacteria.

Solimonas fluminis has an active latex-clearing protein

The utilization of rubber (poly (cis-1,4-isoprene)) by rubber-degrading bacteria depends on the synthesis of rubber oxygenases that cleave the polymer extracellularly to low molecular weight products that can be taken up and used as a carbon source. All so far described Gram-negative rubber-degrading species use two related ≈ 70 kDa rubber oxygenases (RoxA and RoxB) for the primary attack of rubber while all described Gram-positive rubber-degrading strains use RoxA/RoxB-unrelated latex-clearing proteins (Lcps, ≈ 40 kDa) as rubber oxygenase(s). In this study, we identified an lcp orthologue in a Gram-negative species (Solimonas fluminis). We cloned and heterologously expressed the lcp gene of S. fluminis HR-BB, purified the corresponding Lcp protein (Lcp_HR-BB) from recombinant Escherichia coli, and biochemically characterised the Lcp_HR-BB activity. Lcp_HR-BB cleaved polyisoprene to a mixture of C₂₀ and higher oligoisoprenoids at a specific activity of 1.5 U/mg. Furthermore, spectroscopic investigation identified Lcp_HR-BB as a b-haem-containing protein with an oxidised, fivefold coordinated (open) haem centre. To the best of our knowledge, this is the first report that Gram-negative bacteria can have an active rubber oxygenase of the Lcp type.

Identification of LcpRBA3(2), a novel regulator of lcp expression in Streptomyces coelicolor A3(2)

Streptomyces coelicolor A3(2) is a rubber-degrading actinomycete that harbors one gene coding for a latex clearing protein (lcp_A3(2)). Within the genome of S. coelicolor A3(2), we identified a gene coding for a novel protein of the TetR family (LcpRB_A3(2)) downstream of lcp_A3(2) and demonstrated its binding upstream of lcp_A3(2). This indicates a role of LcpRB_A3(2) in the regulation of lcp expression. LcpRB_A3(2) shows no homology to LcpR_VH2, a putative regulator of lcp expression in Gordonia polyisoprenivorans VH2. Additionally, LcpR_VH2 homologs did not occur in the genome of S. coelicolor A3(2). Reverse transcriptase (RT) experiments showed that the expression of lcp_A3(2) and lcpRB_A3(2) is induced with poly(cis-1,4-isoprene) as sole carbon source. For further experiments, we heterologously expressed lcpRB_A3(2) in Escherichia coli, purified the protein, and subsequently verified a binding of LcpRB_A3(2) upstream of lcp_A3(2). The operator site was examined by a DNase I footprinting assay: it comprises 31 bp and exhibits an inverted repeat of nine bases for the putative binding region. Interestingly, two N-terminal DNA-binding HTH domains of the TetR-type (PF00440) were identified within the sequence of LcpRB_A3(2). The native molecular weight of LcpRB_A3(2) was determined as 44 kDa by size exclusion chromatography which correlates to the molecular weight of a monomer. Normally, proteins of the TetR family occur as dimers so that the monomeric state is a novelty. Furthermore, LcpRB_A3(2) homologs were identified in silico in several Lcp-containing actinomycetes, suspecting a conserved regulation mechanism. Apparently, the expression of lcps is regulated either by an LcpRB or by an LcpR.

Complete genome sequence of natural rubber-degrading, gram-negative bacterium, Rhizobacter gummiphilus strain NS21T

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The genome sequence of rubber-degrading Rhizobacter gummiphilus NS21^T was determined.

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An alternative rubber-degrading gene (latA2) was identified.

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β-oxidation pathway genes which is involved in the rubber degradation were predicted.

Gram-negative natural rubber-degrader, Rhizobacter gummiphilus NS21^T, which was isolated from soil in the botanical garden in Japan, is a newly proposed species of genus of Rhizobacter. It has been reported that the latA1 gene is involved in the natural rubber degradation in this strain. To gain novel insights into natural rubber degradation pathway, the complete genome sequence of this strain was determined. The genome of strain NS21^T consists of 6,398,096 bp of circular chromosome (GenBank accession number CP015118.1) with G + C content of 69.72%. The genome contains 5687 protein-coding and 68 RNA genes. Among the predicted genes, 4810 genes were categorized as functional COGs. Homology search revealed that existence of latA1 homologous gene (latA2) in this genome. Quantitative reverse-transcription-PCR and deletion analyses indicated that natural rubber degradation of this strain requires latA2 as well as latA1.

LcpRVH2 - regulating the expression of latex-clearing proteins in Gordonia polyisoprenivorans VH2

Gordonia polyisoprenivorans VH2 harbours two latex clearing proteins, which are responsible for the cleavage of poly(cis-1,4-isoprene) into oligoisoprenes, thereby allowing growth in presence of, e.g. natural rubber. A gene coding for a putative regulator of the TetR-family (lcpRVH2) is located 131 bp upstream of lcp1VH2. We heterologously expressed lcpRVH2 in Escherichia coli, and purified and characterized the protein with respect to its ability to bind to the operator region of lcp1VH2. LcpRVH2 forms a dimer in its native state. The size of the dimer was determined to be 52.7 kDa by size exclusion chromatography, whereas the calculated size of a monomer was 24.1 kDa. Electrophoretic mobility shift assays (EMSAs) with the purified protein revealed a shift upon binding to the intergenic region between lcpRVH2 and lcp1VH2. Within this region, an inverted repeat was identified in silico, probably being the binding site of LcpRVH2. This binding sequence was confirmed by a DNase I footprinting assay. A shift also occurred in EMSAs with this 44 bp sequence only. Interestingly, no regulator was detected upstream of the second lcp (lcp2VH2). Therefore, we performed EMSA studies with LcpRVH2 and the putative operator region upstream of lcp2VH2, and discovered by DNase I footprinting another binding sequence upstream of lcp2VH2. Hence, we concluded that LcpRVH2 binds the operator region of both lcps and, most likely, regulates their expression in G. polyisoprenivorans VH2.

Rubber oxygenases

Natural rubber (NR), poly(cis-1,4-isoprene), is used in an industrial scale for more than 100 years. Most of the NR-derived materials are released to the environment as waste or by abrasion of small particles from our tires. Furthermore, compounds with isoprene units in their molecular structures are part of many biomolecules such as terpenoids and carotenoids. Therefore, it is not surprising that NR-degrading bacteria are widespread in nature. NR has one carbon-carbon double bond per isoprene unit and this functional group is the primary target of NR-cleaving enzymes, so-called rubber oxygenases. Rubber oxygenases are secreted by rubber-degrading bacteria to initiate the break-down of the polymer and to use the generated cleavage products as a carbon source. Three main types of rubber oxygenases have been described so far. One is rubber oxygenase RoxA that was first isolated from Xanthomonas sp. 35Y but was later also identified in other Gram-negative rubber-degrading species. The second type of rubber oxygenase is the latex clearing protein (Lcp) that has been regularly found in Gram-positive rubber degraders. Recently, a third type of rubber oxygenase (RoxB) with distant relationship to RoxAs was identified in Gram-negative bacteria. All rubber oxygenases described so far are haem-containing enzymes and oxidatively cleave polyisoprene to low molecular weight oligoisoprenoids with terminal CHO and CO-CH3 functions between a variable number of intact isoprene units, depending on the type of rubber oxygenase. This contribution summarises the properties of RoxAs, RoxBs and Lcps.

Impact of additives of commercial rubber compounds on the microbial and enzymatic degradation of poly(cis-1,4-isoprene)

Much fundamental research has already been performed to understand the mechanism of microbial rubber degradation. Due to the increasing amount of rubber waste, biotechnical methods to degrade that particular waste are strongly needed. The present study evaluates whether a microbial or an enzymatic process is more suitable for efficient biodegradation, due to less sensitivity towards rubber additives. Therefore we investigated the impact of 15 different frequently used rubber additives on cells of the potent rubber degrader Gordonia polyisoprenivorans VH2 and the enzyme Lcp1_VH2. For this, cells were grown on poly(cis-1,4-isoprene) in presence of these rubber additives. Furthermore, the effect of those additives on the enzymatic cleavage of poly(cis-1,4-isoprene) by Lcp1_VH2 was determined by in vitro studies. It was observed that additives, used to accelerate the vulcanization process, like N-cyclohexyl-2-benzothiazolesulfenamide and zinc-bis(N,N-dibenzyl-dithiocarbamate), are diminishing the growth of the microorganism depending on their concentration-higher toxicity with increasing concentration. In contrast, sulfur prevents cell growth, but does not affect Lcp1_VH2. Stearic acid and paraffin wax were found to be consumed by G. polyisoprenivorans VH2. Plasticizers mainly prevent growth, but do not interfere with the enzyme activity. This study identified antioxidants as the most interfering group of additives for microbial and enzymatic rubber degradation. It was found that the in vitro degradation by Lcp1_VH2 is much more resistant and less sensitive towards the investigated rubber additives, when compared to the in vivo approach. Therefore, an enzymatic process might be a promising method to enhance rubber degradation.

Rhizobacter gummiphilus NS21 has two rubber oxygenases (RoxA and RoxB) acting synergistically in rubber utilisation

Biodegradation of poly(cis-1,4-isoprene) (rubber) by Gram-negative bacteria has been investigated on the enzymatic level only in Steroidobacter cummioxidans 35Y (previously Xanthomonas sp. 35Y). This species produces two kinds of rubber oxygenases, RoxA_35Y and RoxB_35Y, one of which (RoxB_35Y) cleaves polyisoprene to a mixture of C₂₀- and higher oligoisoprenoids while the other (RoxA_35Y) cleaves polyisoprene and RoxB_35Y-derived oligoisoprenoids to the C₁₅-oligoisoprenoid 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD). ODTD can be taken up by S. cummioxidans and used as a carbon source. Gram-positive rubber-degrading bacteria employ another type of rubber oxygenase, latex clearing protein (Lcp), for the initial oxidative attack of the polyisoprene molecule. In this contribution, we examined which type of rubber oxygenase is present in the only other well-documented Gram-negative rubber-degrading species, Rhizobacter gummiphilus NS21. No homologue for an Lcp protein but homologues for a putative RoxA and a RoxB protein (the latter identical to a previously postulated LatA-denominated rubber cleaving enzyme) were identified in the genome of strain NS21. The roxA_NS21 and roxB_NS21 genes were separately expressed in a ∆roxA_35Y/∆roxB_35Y background of S. cummioxidans 35Y and restored the ability of the mutant to produce oligoisoprenoids. The RoxA_NS21 and RoxB_NS21 proteins were each purified and biochemically characterised. The results-in combination with in silico analysis of databases-indicate that Gram-negative rubber-degrading bacteria generally utilise two synergistically acting rubber oxygenases (RoxA/RoxB) for efficient cleavage of polyisoprene to ODTD.

In vitro studies on the degradation of poly(cis-1,4-isoprene)

Cleavage of the backbone of poly(cis-1,4-isoprene) (IR) in solid rubber material was accomplished by the addition of partially purified latex clearing protein (Lcp1_VH2 ) using a 200-mL enzyme reactor. Two strategies for the addition of Lcp1_VH2 were studied revealing that the daily addition of 50 µg mL^-1 of Lcp1_VH2 for 5 days was clearly a more efficient regime in comparison to a one-time addition of 250 µg of Lcp1_VH2 at the beginning. Soluble oligo(cis-1,4-isoprene) molecules occurred as degradation products and were identified by ESI-MS and GPC. Oxygenase activity of Lcp1_VH2 with solid IR particles as substrate was shown for the first time by measuring the oxygen consumption in the reaction medium. A strong decrease of the dissolved oxygen concentration was detected at the end of the assay, which indicates an increase in the number of cleavage reactions. The oligo(cis-1,4-isoprene) molecules comprised 1 to 11 isoprene units and exhibited an average molecular weight (M_n ) of 885 g mol^-1 . Isolation of the oligo(cis-1,4-isoprene) molecules was achieved by using silica gel column chromatography. The relative quantification of the isolated products was performed by HPLC-MS after derivatization with 2,4-dinitrophenilhydrazyne yielding a concentration of total degradation products of 1.62 g L^-1 . Analysis of the polymer surface in samples incubated for 3 days with Lcp1_VH2 via ATR-FTIR indicated the presence of carbonyl groups, which occurred upon the cleavage reaction. This study presents a cell-free bioprocess as an alternative rubber treatment that can be applied for the partial degradation of the polymer. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:890-899, 2018.

Cleavage of poly(cis-1,4-isoprene) rubber as solid substrate by cultures of Gordonia polyisoprenivorans

Potential biotechnological recycling processes for rubber products include the bacterial degradation of poly(cis-1,4-isoprene) (IR) in order to achieve its total biodegradation or its biotransformation into useful products. The actinomycete Gordonia polyisoprenivorans strain VH2 catalyzes the degradation of IR and enables its use as a sole carbon source via β-oxidation. The initial cleavage reaction is catalyzed by the extracellular latex clearing protein (Lcp). This dioxygenase is the key enzyme for the formation of oligo(cis-1,4-isoprene) molecules with different lengths, i.e., numbers of isoprene units. For the first time, IR was used as a solid substrate in 2-l fermenters. Two different particle size fractions (63-500 and 500-1000 μm) and three stirring rates (300, 400 and 500 rpm) were evaluated in the process. An increase of the cell concentration was achieved by using smaller particles and by using lower stirring rates, reaching a final biomass concentration of 0.52 g l^-1 at 300 rpm after 12 days of cultivation. In order to enhance the formation of oligo(cis-1,4-isoprene) molecules, a transposon insertion mutant (TH5) of G. polyisoprenivorans strain VH2 that has lost the ability to transport the partial degradation products into the cells was used, thereby allowing the accumulation of the degradation products in the culture supernatants. Propionate, glucose and glycerol were evaluated as additional carbon sources besides IR, and the highest yields were observed on propionate. In 2-l bioreactors with pH control, different feeding regimes were performed during cultivation by the addition of propionate every 24 or 48 h for 16 days. After liquid-liquid extraction and a derivatization with Girard's T reagent, the oligo(cis-1,4-isoprene) molecules were detected by ESI-MS. The mass distribution of the degradation products was affected by the selection of the extraction solvent, but no influence of longer cultivation periods was detected.

Production of functionalized oligo-isoprenoids by enzymatic cleavage of rubber

In this study, we show the proof of concept for the production of defined oligo-isoprenoids with terminal functional groups that can be used as starting materials for various purposes including the synthesis of isoprenoid-based plastics. To this end, we used three types of rubber oxygenases for the enzymatic cleavage of rubber [poly(cis-1,4-isoprene)]. Two enzymes, rubber oxygenase RoxAXsp and rubber oxygenase RoxBXsp , originate from Xanthomonas sp. 35Y; the third rubber oxygenase, latex-clearing protein (LcpK30 ), is derived from Gram-positive rubber degraders such as Streptomyces sp. K30. Emulsions of polyisoprene (latex) were treated with RoxAXsp , RoxBXsp , LcpK30 or with combinations of the three proteins. The cleavage products were purified by solvent extraction and FPLC separation. All products had the same general structure with terminal functions (CHO-CH2 - and -CH2 -COCH3 ) but differed in the number of intact isoprene units in between. The composition and m/z values of oligo-isoprenoid products were determined by HPLC-MS analysis. Our results provide a method for the preparation of reactive oligo-isoprenoids that can likely be used to convert polyisoprene latex or rubber waste materials into value-added molecules, biofuels, polyurethanes or other polymers.

Characterization of oxidized oligomers from polyethylene films by mass spectrometry and NMR spectroscopy before and after biodegradation by a Rhodococcus rhodochrous strain

The objective of this work was to develop a new approach to assess the specificity and the efficiency of biodegradation of oxidized oligomers extracted from aged HDPE polyethylene films and to bring insight on the mechanisms occurring during biodegradation. ¹H NMR spectroscopy and LC Orbitrap™ mass spectrometry were combined together with data processing using Kendrick mass defect calculation and Van Krevelen Diagram. We showed that the molecular weight of extracted oligomers was lower than 850 Da with maximum chain length of 55 carbon atoms. The oligomers were divided into 11 classes of molecules with different oxidation state ranging from 0 to 10. All classes included series of chemically related compounds including up to 19 molecules. 95% of the soluble oligomers were assimilated by a strain of Rhodococcus rhodocchrous after 240 days of incubation. Large highly oxidized molecules completely disappeared while the other classes of molecules were still represented. Molecules containing 0-1 oxygen atom were less degraded. A strong shift to smaller molecules (<450 Da, 25 carbon atoms) was observed suggesting that longer molecules disappeared more rapidly than the smaller ones. It opens new perspectives on biodegradation processes as not only intracellular β-oxidation must be considered but also extracellular mechanisms leading to chain cleavages.

Structural and Functional Analysis of Latex Clearing Protein (Lcp) Provides Insight into the Enzymatic Cleavage of Rubber

Latex clearing proteins (Lcps) are rubber oxygenases that catalyse the extracellular cleavage of poly (cis-1,4-isoprene) by Gram-positive rubber degrading bacteria. Lcp of Streptomyces sp. K30 (LcpK30) is a b-type cytochrome and acts as an endo-type dioxygenase producing C20 and higher oligo-isoprenoids that differ in the number of isoprene units but have the same terminal functions, CHO-CH2- and -CH2-COCH3. Our analysis of the LcpK30 structure revealed a 3/3 globin fold with additional domains at the N- and C-termini and similarities to globin-coupled sensor proteins. The haem group of LcpK30 is ligated to the polypeptide by a proximal histidine (His198) and by a lysine residue (Lys167) as the distal axial ligand. The comparison of LcpK30 structures in a closed and in an open state as well as spectroscopic and biochemical analysis of wild type and LcpK30 muteins provided insights into the action of the enzyme during catalysis.

RoxB Is a Novel Type of Rubber Oxygenase That Combines Properties of Rubber Oxygenase RoxA and Latex Clearing Protein (Lcp)

Only two types of rubber oxygenases, rubber oxygenase (RoxA) and latex clearing protein (Lcp), have been described so far. RoxA proteins (RoxAs) are c-type cytochromes of ≈70 kDa produced by Gram-negative rubber-degrading bacteria, and they cleave polyisoprene into 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD), a C15 oligo-isoprenoid, as the major end product. Lcps are common among Gram-positive rubber degraders and do not share amino acid sequence similarities with RoxAs. Furthermore, Lcps have much smaller molecular masses (≈40 kDa), are b-type cytochromes, and cleave polyisoprene to a mixture of C20, C25, C30, and higher oligo-isoprenoids as end products. In this article, we purified a new type of rubber oxygenase, RoxB Xsp (RoxB of Xanthomonas sp. strain 35Y). RoxB Xsp is distantly related to RoxAs and resembles RoxAs with respect to molecular mass (70.3 kDa for mature protein) and cofactor content (2 c-type hemes). However, RoxB Xsp differs from all currently known RoxAs in having a distinctive product spectrum of C20, C25, C30, and higher oligo-isoprenoids that has been observed only for Lcps so far. Purified RoxB Xsp revealed the highest specific activity of 4.5 U/mg (at 23°C) of all currently known rubber oxygenases and exerts a synergistic effect on the efficiency of polyisoprene cleavage by RoxA Xsp RoxB homologs were identified in several other Gram-negative rubber-degrading species, pointing to a prominent function of RoxB for the biodegradation of rubber in Gram-negative bacteria.IMPORTANCE The enzymatic cleavage of rubber (polyisoprene) is of high environmental importance given that enormous amounts of rubber waste materials are permanently released (e.g., by abrasion of tires). Research from the last decade has discovered rubber oxygenase A, RoxA, and latex clearing protein (Lcp) as being responsible for the primary enzymatic attack on the hydrophobic and water-insoluble biopolymer poly(cis-1,4-isoprene) in Gram-negative and Gram-positive rubber-degrading bacteria, respectively. Here, we provide evidence that a third type of rubber oxygenase is present in Gram-negative rubber-degrading species. Due to its characteristics, we suggest the designation RoxB for the new type of rubber oxygenase. Bioinformatic analysis of genome sequences indicates the presence of roxB homologs in other Gram-negative rubber degraders.

Assays for the Detection of Rubber Oxygenase Activities

Microbial biodegradation of rubber relies on extracellular rubber oxygenases that catalyze the oxidative cleavage of the double bond of the polyisoprene backbone into oligo-isoprenoids. This protocol describes the determination of rubber oxygenase activities by an online measurement of molecular oxygen consumption via a non-invasive fluorescence-based assay. The produced oligo-isoprenoid cleavage products with terminal keto- and aldehyde-groups are identified qualitatively and quantitatively by HPLC. Our method allows for the characterization of homologue rubber oxygenases, and can likely be adapted to assay other oxygenases consuming dioxygen. Here we describe the determination of rubber oxygenase activities at the examples of the so far two known types of rubber oxygenases, namely rubber oxygenase A (RoxA) and latex clearing protein (Lcp).

Identification of natural rubber degradation gene in Rhizobacter gummiphilus NS21

A Gram-negative rubber-degrading bacterium, Rhizobacter gummiphilus NS21 grew and produced aldehyde metabolites on a deproteinized natural rubber (DPNR)-overlay agar medium forming a clearing zone. A transposon-insertion mutant, which had lost the ability to degrade DPNR, was isolated to identify the rubber degradation genes. Sequencing analysis indicated that the transposon was inserted into a putative oxygenase gene, latA. The deduced amino acid sequence of latA has 36% identity with that of roxA, which encodes a rubber oxygenase of Xanthomonas sp. strain 35Y. Phylogenetic analysis revealed that LatA constitutes a distinct group from RoxA. Heterologous expression in a Methylibium host and deletion analysis of latA indicated that the latA product is responsible for the depolymerization of DPNR. The quantitative reverse transcription-PCR analysis indicated that the transcription of latA is induced during the growth on DPNR. These results strongly suggest that latA is directly involved in the degradation of rubber in NS21.

Characterization and functional expression of a rubber degradation gene of a Nocardia degrader from a rubber-processing factory

A rubber-degrading bacterial consortium named H2DA was obtained from an enrichment culture with natural rubber latex and rubber-processing factory waste in Vietnam. Gel permeation chromatography analysis revealed that only the strain NVL3 degraded synthetic poly(cis-1,4-isoprene) into low-molecular-weight intermediates among the three strains found in the H2DA. The 16S-rRNA gene sequence of NVL3 showed the highest identity with that of Nocardia farcinica DSM 43665^T. NVL3 accumulated aldehyde intermediates from synthetic poly(cis-1,4-isoprene) on a rubber-overlay plate as indicated by Schiff's staining. NVL3 also degraded deproteinized natural rubber into low-molecular-weight aldehyde intermediates. A latex-clearing protein (lcp) gene ortholog was identified within the genome sequence of NVL3, and it showed a moderate amino-acid identity (54-75%) with the lcp genes from previously reported rubber degraders. The heterologous expression of the NVL3 lcp in Escherichia coli BL21(DE3) allowed us to purify the 46.8-kDa His-tagged lcp gene product (His-Lcp). His-Lcp degraded synthetic poly(cis-1,4-isoprene) and accumulated aldehyde intermediates from deproteinized natural rubber suggesting the functional expression of the lcp gene from a Nocardia degrader in E. coli. Quantitative reverse transcription PCR analysis indicated the strong transcriptional induction of the lcp gene in NVL3 in the presence of synthetic poly(cis-1,4-isoprene). These results suggest the involvement of the lcp gene in rubber degradation in NVL3.

A simple, rapid and cost-effective process for production of latex clearing protein to produce oligopolyisoprene molecules

Aiming at finding feasible alternatives for rubber waste disposal, the partial enzymatic degradation of poly(cis-1,4-isoprene)-containing materials represents a potential solution. The use of rubber-degrading enzymes and the biotransformation of rubber into new materials is limited by the high costs associated with the production and purification of the enzyme and the complexity of the process. This study presents a simple and low-cost procedure to obtain purified latex clearing protein (Lcp), an enzyme capable of cleaving the double bonds of poly(cis-1,4-isoprene) in presence of oxygen to produce different size of oligomers with terminal aldehyde and ketone groups, respectively. The gene coding for Lcp1_VH2 from Gordonia polyisoprenivorans strain VH2 was overexpressed in Escherichia coli C41 (DE3), and by using an auto-induction medium high protein yields were obtained. The cultivation process was described and compared with an IPTG-inducible medium previously used. Purification of the enzyme was performed using salting out precipitation with ammonium sulfate. Different salt concentrations and pH were tested in order to find the optimal for purification, obtaining a concentration of 60mg Lcp per l. The enzymatic activity of the purified enzyme was measured by an oxygen consumption assay in the presence of polyisoprene latex. Volumetric activities of 0.16Uml^-1 were obtained at optimal conditions of temperature and pH. The results showed an active and partial purified fraction of Lcp1_VH2, able to cleave the backbone of poly(cis-1,4-isoprene) and to produce degradation products that were identified with staining methodologies (Schiff reagent for aldehyde groups and 2,4-DNPH for carbonyl groups) and characterized using nuclear magnetic resonance (NMR). Thirteen different storage conditions were tested for the purified enzyme analyzing the enzymatic activity after 1 and 3 months. Lcp1_VH2, as an ammonium sulfate precipitate, was stable, easy to handle and sufficiently active for further analysis. The described methodology offers the possibility to upscale the process and to produce large amounts of this protein.

Cleavage of Rubber by the Latex Clearing Protein (Lcp) of Streptomyces sp. Strain K30: Molecular Insights

Gram-positive rubber degraders such as Streptomyces sp. strain K30 cleave rubber [poly(cis-1,4-isoprene)] to low-molecular-mass oligoisoprenoid products with terminal keto and aldehyde groups by the secretion of a latex clearing protein (Lcp) designated rubber oxygenase. Lcp_K30 is a heme b cytochrome and has a domain of unknown function (DUF2236) that is characteristic of orthologous Lcps. Proteins with a DUF2236 domain are characterized by three highly conserved residues (R164, T168, and H198 in Lcp_K30). Exchange of R164 or T168 by alanine and characterization of the purified Lcp_K30 muteins revealed that both were stable and contained a heme group (red color) but were inactive. This finding identifies both residues as key residues for the cleavage reaction. The purified H198A mutein was also inactive and stable but was colorless due to the absence of heme. We constructed and characterized alanine muteins of four additional histidine residues moderately conserved in 495 Lcp_K30 homologous sequences (H203A, H232A, H259A, H266A). All muteins revealed wild-type properties, excluding any importance for activity and/or heme coordination. Since Lcp_K30 has only eight histidines and the three remaining residues (H103, H184, and H296) were not conserved (<11%), H198 presumably is the only essential histidine, indicating its putative function as a heme ligand. The second axial position of the heme is likely occupied by a not yet identified molecule. Mutational analysis of three strictly conserved arginine residues (R195, R202, R328) showed that R195A and R202A muteins were colorless and instable, suggesting that these residues are important for the protein stability.

IMPORTANCE

Large amounts of rubber waste materials have been permanently released into the environment for more than a century, yet accumulation of rubber particles released, e.g., by abrasion of tires along highways has not been observed. This is indicative of the ubiquitous presence and activity of rubber-degrading microorganisms. Despite increasing research activities on rubber biodegradation during the last 2 decades, the knowledge of the enzymatic cleavage mechanism of rubber by latex clearing protein (Lcp) still is limited. In particular, the catalytic cleavage mechanism and the amino acids of Lcp proteins (Lcps) that are involved have not yet been identified for any Lcp. In this study, we investigated the importance of 10 amino acid residues of Lcp from Streptomyces sp. K30 (Lcp_K30) by mutagenesis, mutein purification, and biochemical characterization. We identified several essential residues, one of which most likely represents an axial heme ligand in Lcp of Streptomyces sp. K30.

Biochemical and spectroscopic characterization of purified Latex Clearing Protein (Lcp) from newly isolated rubber degrading Rhodococcus rhodochrous strain RPK1 reveals novel properties of Lcp

Background

Biodegradation of rubber (polyisoprene) is initiated by oxidative cleavage of the polyisoprene backbone and is performed either by an extracellular rubber oxygenase (RoxA) from Gram-negative rubber degrading bacteria or by a latex clearing protein (Lcp) secreted by Gram-positive rubber degrading bacteria. Only little is known on the biochemistry of polyisoprene cleavage by Lcp and on the types and functions of the involved cofactors.

Results

A rubber-degrading bacterium was isolated from the effluent of a rubber-processing factory and was taxonomically identified as a Rhodococcus rhodochrous species. A gene of R. rhodochrous RPK1 that coded for a polyisoprene-cleaving latex clearing protein (lcp_Rr) was identified, cloned, expressed in Escherichia coli and purified. Purified Lcp_Rr had a specific activity of 3.1 U/mg at 30 °C and degraded poly(1,4-cis-isoprene) to a mixture of oligoisoprene molecules with terminal keto and aldehyde groups. The pH optimum of Lcp_Rr was higher (pH 8) than for other rubber-cleaving enzymes (≈ pH 7). UVvis spectroscopic analysis of Lcp_Rr revealed a cytochrome-specific absorption spectrum with an additional feature at long wavelengths that has not been observed for any other rubber-cleaving enzyme. The presence of one b-type haem in Lcp_Rr as a co-factor was confirmed by (i) metal analysis, (ii) solvent extraction, (iii) bipyridyl assay and (iv) detection of haem-b specific m/z values via mass-spectrometry.

Conclusions

Our data point to substantial differences in the active sites of Lcp proteins obtained from different rubber degrading bacteria.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0703-x) contains supplementary material, which is available to authorized users.

Latex Clearing Protein (Lcp) of Streptomyces sp. Strain K30 Is a b-Type Cytochrome and Differs from Rubber Oxygenase A (RoxA) in Its Biophysical Properties

Specific polyisoprene-cleaving activities of 1.5 U/mg and 4.6 U/mg were determined for purified Strep-tagged latex clearing protein (Lcp) of Streptomyces sp. strain K30 at 23 °C and 37 °C, respectively. Metal analysis revealed the presence of approximately one atom of iron per Lcp molecule. Copper, which had been identified in Lcp1VH2 of Gordonia polyisoprenivorans previously, was below the detection limit in LcpK30. Heme was identified as a cofactor in purified LcpK30 by (i) detection of characteristic α-, β-, and γ (Soret)-bands at 562 nm, 532 nm, and 430 nm in the visible spectrum after chemical reduction, (ii) detection of an acetone-extractable porphyrin molecule, (iii) determination of a heme b-type-specific absorption maximum (556 nm) after chemical conversion of the heme group to a bipyridyl-heme complex, and (iv) detection of a b-heme-specific m/z value of 616.2 via mass spectrometry. Spectroscopic analysis showed that purified Lcp as isolated contains an oxidized heme-Fe(3+) that is free of bound dioxygen. This is in contrast to the rubber oxygenase RoxA, a c-type heme-containing polyisoprene-cleaving enzyme present in Gram-negative rubber degraders, in which the covalently bound heme firmly binds a dioxygen molecule. LcpK30 also differed from RoxA in the lengths of the rubber degradation cleavage products and in having a higher melting point of 61.5 °C (RoxA, 54.3 °C). In summary, RoxA and Lcp both are equipped with a heme cofactor and catalyze an oxidative C-C cleavage reaction but differ in the heme subgroup type and in several biochemical and biophysical properties. These findings suggest differences in the catalytic reaction mechanisms.