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

Genomic insights into Dactylosporangium sp. AC04546, a rubber degrader with three latex clearing proteins

With more than 100 rubber-degrading strains being reported, only 9 Lcp proteins isolated from Nocardia, Gordonia, Streptomyces, Rhodococcus, Actinoplanes, and Solimonas have been purified and biochemically characterized. A new strain, Dactylosporangium sp. AC04546 (strain JCM34239), isolated from soil samples collected in Sarawak Forest, was able to grow and utilize natural or synthetic rubber as the sole carbon source. Complete genome of Strain AC04546 was obtained from the hybrid assembly of PacBio Sequel II and Illumina MiSeq. Strain AC04546 has a large circular genome of 13.08 Mb with a G+C content of 72.1%. The genome contains 11,865 protein-coding sequences with 3 latex clearing protein (lcp) genes located on its chromosome. The genetic organization of the lcp gene cluster is similar to two other reported rubber-degrading strains-Actinoplanes sp. OR16 and Streptomyces sp. CFMR 7. All 3 Lcp from strain AC04546 were expressed in Escherichia coli and exhibited degrading activity against natural rubber. The distinctiveness of strain AC04546, along with other characterized rubber-degrading strains, is reported here.

Study of sequential abiotic and biotic degradation of styrene butadiene rubber

Styrene butadiene rubber is one of the main constituents of tire tread. During tire life, the tread material undergoes different stresses that impact its structure and chemical composition. Wear particles are then released into the environment as weathered material. To understand their fate, it is important to start with a better characterization of abiotic and biotic degradation of the elastomer material. A multi-disciplinary approach was implemented to study the photo- and thermo- degradation of non-vulcanized SBR films containing 15 w% styrene as well as their potential biodegradation by Rhodoccocus ruber and Gordonia polyisoprenivorans bacterial strains. Each ageing process leads to crosslinking reactions, much surface oxidation of the films and the production of hundreds of short chain compounds. These degradation products present a high level of unsaturation and oxidation and can be released into water to become potential substrates for microorganisms. Both strains were able to degrade from 0.2 to 1.2 % (% ThOD) of the aged SBR film after 30-day incubation while no biodegradation was observed on the pristine material. A 25-75 % decrease in the signal intensity of water extractable compounds was observed, suggesting that biomass production was linked to the consumption of low-molecular-weight degradation products. These results evidence the positive impact of abiotic degradation on the biodegradation process of styrene butadiene rubber.

Cleavage of natural rubber by rubber oxygenases in Gram-negative bacteria

Bacterial degradation of natural rubber (NR) in an oxic environment is initiated by oxidative cleavage of double bonds in the NR-carbon backbone and is catalyzed by extracellular haem-containing rubber oxygenases. NR-cleavage products of sufficiently low molecular mass are taken up by the cells and metabolized for energy and biomass formation. Gram-negative and Gram-positive NR-degrading bacteria (usually) employ different types of rubber oxygenases such as RoxA and/or RoxB (most Gram-negative NR-degraders) or latex clearing protein Lcp (most Gram-positive NR-degraders). In order to find novel orthologues of Rox proteins, we have revisited databases and provide an update of Rox-like proteins. We describe the putative evolution of rubber oxygenases and confirm the presence of a third subgroup of Rox-related proteins (RoxCs), the biological function of which remains, however, unclear. We summarize the knowledge on the taxonomic position of Steroidobacter cummioxidans 35Y and related species. Comparison of genomic and biochemical features of strain 35Y with other species of the genus Steroidobacter suggests that strain 35Y represents a species of a novel genus for which the designation Aurantibaculum gen. nov. is proposed. A short summary on the capabilities of NR-degrading consortia, that could be superior in biotechnological applications compared to pure cultures, is also provided. KEY POINTS: • Three types of rubber oxygenases exist predominantly in Gram-negative microbes • S. cummioxidans 35Y contains RoxA and RoxB which are superior in activity • S. cummioxidans 35Y represents a species of a novel genus.

Investigation of potential rubber-degrading bacteria and genes involved

COVID-19 pandemic has generated high demand for natural rubber gloves (NR) leading to crucial issues of rubber waste and waste management such as burning, dumping, stockpiling, discarding waste in landfills. Hence, rubber biodegradation by microorganisms is an alternative solution to the problem. The biodegradation method is environmentally friendly but normally extremely slow. Numerous microorganisms can degrade NR as a source of carbon and energy. In this study, Rhodococcus pyridinivorans KU1 was isolated from the consortium CK from previous study. The 40% rubber weight loss was detected after incubated for 2 months. The bacterial colonization and cavities on the surface of rubber were identified using a scanning electron microscope (SEM). The result demonstrated the critical degradation of the rubber surface, indicating that bacteria can degrade rubber and use it as their sole carbon source. The result of whole-genome sequencing (WGS) revealed a gene that is 99.9% identical to lcp which is responsible for poly (cis-1,4-isoprene) degradation. The results from Meta16S rRNA sequencing showed that the microbial communities were slightly shifted during the 2-month degradation, depending on the presence of monomers or oligomers appeared during the degradation process. The majority of species were soil bacteria such as phylum Proteobacteria, Actinobacteria, and Firmicutes. Members of Pseudoxanthomonas seemed to be the dominant degraders throughout the degradation.

Assembly strategies for rubber-degrading microbial consortia based on omics tools

Numerous microorganisms, including bacteria and fungus, have been identified as capable of degrading rubber. Rubber biodegradation is still understudied due to its high stability and the lack of well-defined pathways and efficient enzymes involved in microorganism metabolism. However, rubber products manufacture and usage cause substantial environmental issues, and present physical-chemical methods involve dangerous chemical solvents, massive energy, and trash with health hazards. Eco-friendly solutions are required in this context, and biotechnological rubber treatment offers considerable promise. The structural and functional enzymes involved in poly (cis-1,4-isoprene) rubber and their cleavage mechanisms have been extensively studied. Similarly, novel bacterial strains capable of degrading polymers have been investigated. In contrast, relatively few studies have been conducted to establish natural rubber (NR) degrading bacterial consortia based on metagenomics, considering process optimization, cost effective approaches and larger scale experiments seeking practical and realistic applications. In light of the obstacles encountered during the constructing NR-degrading consortia, this study proposes the utilization of multi-omics tools to discern the underlying mechanisms and metabolites of rubber degradation, as well as associated enzymes and effective synthesized microbial consortia. In addition, the utilization of omics tool-based methods is suggested as a primary research direction for the development of synthesized microbial consortia in the future.

Enzymatic reactions towards aldehydes: An overview

Many aldehydes are volatile compounds with distinct and characteristic olfactory properties. The aldehydic functional group is reactive and, as such, an invaluable chemical multi-tool to make all sorts of products. Owing to the reactivity, the selective synthesis of aldehydic is a challenging task. Nature has evolved a number of enzymatic reactions to produce aldehydes, and this review provides an overview of aldehyde-forming reactions in biological systems and beyond. Whereas some of these biotransformations are still in their infancy in terms of synthetic applicability, others are developed to an extent that allows their implementation as industrial biocatalysts.

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.

Degradation of UV-pretreated polyolefins by latex clearing protein from Streptomyces sp. Strain K30

Plastic products made of polyethylene (PE), polypropylene (PP), and polystyrene (PS) are widely used in daily life and industrial production. Polyolefins-which have a very stable structure and do not contain any active molecular groups-are difficult to degrade and pose a serious global environment threat. This study selected latex clearing protein (Lcp_K30) derived from Streptomyces sp. Strain K30. The natural substrate of the enzyme is rubber (cis-1, 4-polyisoprene), and the site of action is the carbon‑carbon double bond. Lcp_K30 was incubated with UV-irradiated polyolefin PE, PP and PS (UV-PE, UV-PP, and UV-PS containing carbon‑carbon double bonds) for 5 d at 37 °C. The results showed that UV-PE-Lcp_K30 was more fragmented than UV-PE-blank; the Fourier transform infrared spectroscopy results showed that UV-PE-Lcp_K30 and UV-PP-Lcp_K30 produced new active groups (e.g., -OH and -C=O); however, the effect on UV-PS was not significant. Scanning electron microscopy results showed that the treated group had more obvious roughness, cracks, and pits than the control group. The results of high-temperature gel permeation chromatography showed that the average molecular weight (M_w) of UV-PE-Lcp_K30 and UV-PP-Lcp_K30 decreased; the M_w of UV-PE5-Lcp_K30 was reduced by 42.02%. The results of gas chromatography-mass spectrometry showed the production of ketones. Therefore, the Lcp_K30 latex clearing protein degrade UV-oxidized polyolefin plastics and has great potential for PE and PP degradation but may not be suitable for PS. Furthermore, other Lcps (such as Lcp_NRRL, Lcp_NVL3) can also degrade UV-PE.

Enzymatic and Chemical Approaches for Post-Polymerization Modifications of Diene Rubbers: Current state and Perspectives

Diene rubbers are polymeric materials which present elastic properties and have double bonds in the macromolecular backbone after the polymerization process. Post-polymerization modifications of rubbers can be conducted by enzymatic or chemical methods. Enzymes are environmentally friendly catalysts and with the increasing demand for rubber waste management, biodegradation and biomodifications have become hot topics of research. Some rubbers are renewable materials and are a source of organic molecules, and biodegradation can be conducted to obtain either oligomers or monomers. On the other hand, chemical modifications of rubbers by click-chemistry are important strategies for the creation and combination of new materials. In a way to expand the scope of uses to other non-traditional applications, several and effective modifications can be conducted with diene rubbers. Two groups of efficient tools, enzymatic, and chemical modifications in diene rubbers, are summarized in this review. By analyzing stereochemical and reactivity aspects, the authors also point to some applications perspectives for biodegradation products and to rational modifications of diene rubbers by combining both methodologies.

In vitro studies on the degradation of common rubber waste material with the latex clearing protein (Lcp1VH2) of Gordonia polyisoprenivorans VH2

The enzymatic degradation of the rubber polymer poly(cis-1,4-isoprene), e.g. by the latex clearing protein Lcp1_VH2 of Gordonia polyisoprenivorans VH2 has been demonstrated with latex milk or pure isoprene-rubber particles, recently. Unfortunately, carbon black filled vulcanized rubber (CFVR) making the biggest part of worldwide rubber wastes, contains several harmful additives making microbial and enzymatic rubber degradation challenging. However, this study demonstrates the successful enzymatic cleavage of industrially produced CFVR. The formation of the cleavage products, oligo(cis-1,4-isoprenoids), from incubating CFVR particles with Lcp1_VH2 was detected by HPLC-MS. Various organic solvents were tested to remove harmful or inhibiting additives like antioxidants to enhance product formation. The pretreatment of CFVR particles, especially with chloroform or cyclohexane, significantly improved the degradation. It was also demonstrated that reducing the particles size and thus increasing the enzymatically accessible surface area of the particles led to a strong acceleration of the degradation process. Furthermore, ATR-IR analyses showed that Lcp1_VH2 led to the functionalization of the rubber particle surface with carbonyl groups by cleaving isoprene chains, still linked to the particle. Both, the oligo(cis-1,4-isoprenoids) as well as the functionalized rubber particles, are potentially important products, which can be reused as fine chemicals or as additives in rubber production. The present study, showing the enzymatic degradation of common CFVR for the first time, takes an important step towards a new way of rubber waste disposal and indicates the economic feasibility of an efficient and environmentally friendly recycling process by using the rubber oxygenase Lcp1_VH2.

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.

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.

Enzymatic degradation of plant biomass and synthetic polymers

Plant biomass is an abundant renewable resource on Earth. Microorganisms harvest energy from plant material by means of complex enzymatic systems that efficiently degrade natural polymers. Intriguingly, microorganisms have evolved to exploit these ancient mechanisms to also decompose synthetic plastic polymers. In this Review, we summarize the mechanisms by which they decompose non-starch plant biomass and the six major types of synthetic plastics. We focus on the structural features of the enzymes that contribute to substrate recognition and then describe the catalytic mechanisms of polymer metabolism. An understanding of these natural biocatalysts is valuable if we are to exploit their potential for the degradation of synthetic polymers.

High yield production of the latex clearing protein from Gordonia polyisoprenivorans VH2 in fed batch fermentations using a recombinant strain of Escherichia coli

The enzymatic degradation of rubber with the latex clearing protein (Lcp1_VH2) from Gordonia polyisoprenivorans VH2, is a promising option as an environmentally friendly and economical solution to treat the enormous amount of rubber waste. Here we present a fed batch fermentation process on a 10 L scale, using E.coli C41 pET23a(+)::Hislcp1_VH2 and a modified defined mineral salt medium, designed for high cell densities, for a proper synthesis of Lcp1_VH2. Particularly, providing complex media components, as well as hemin, as precursor of the essential heme b cofactor, resulted in a 2.9-fold higher yield of active Lcp1_VH2 with increased specific activity, due to a better occupancy of the enzyme with the cofactor. Based on this optimization, the fed batch fermentation with an initial glucose feed, followed by a lactose-glycerol feed, finally gained a cell dry weight of 60 g L^-1 and a yield of 223 mg L^-1 of soluble, active Lcp1_VH2. Compared to a recently published fermentation process, which used a complex auto-induction medium, we significantly increased the biomass up to nearly 10-fold and the total Lcp1_VH2 yield up to 3.7-fold. Thereby we reduced the costs for the medium by 75 %, taking the next step towards industrial production of rubber degrading 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.

First report of cis-1,4-polyisoprene degradation by Gordonia paraffinivorans

The use of rubber has increased over the years, leading to a series of environmental problems due to its indefinite decomposition time. Bioremediation employing microorganisms have drawn an increasing interest and originated several studies of microbial rubber degradation. Genome sequencing and in silico analysis demonstrated that G. paraffinivorans MTZ041 isolate encodes the lcp gene (Latex Clearing Protein), responsible for expressing an enzyme that performs the first step in the assimilation of synthetic and natural rubber. Growth curves and scanning electron microscopy (SEM) were conducted for MTZ041 in natural (NR) and synthetic rubber (IR) as sole carbon source during 11 weeks. After 80 days, robust growth was observed and SEM analysis revealed the presence of bacilli and the formation of biofilm-like structures on natural and synthetic rubber. This is the first report of a G. paraffinivorans rubber degrader. Given the complexity of this substrate and the relative small number of microorganisms with this ability, the description and characterization of MTZ041 is of great importance on bioremediation processes of rubber products.

Characterization of the latex clearing protein of the poly(cis-1,4-isoprene) and poly(trans-1,4-isoprene) degrading bacterium Nocardia nova SH22a

Nocardia nova SH22a is an actinobacterium capable of degrading the polyisoprenes poly(cis-1,4-isoprene) and poly(trans-1,4-isoprene). Sequencing and annotating the genome of this strain led to the identification of a single gene coding for the key enzyme for the degradation of rubber: the latex clearing protein (Lcp). In this study, we showed that Lcp_SH22a-contrary to other already characterized rubber cleaving enzymes-is responsible for the initial cleavage of both polyisoprene isomers. For this purpose, lcp_SH22a was heterologously expressed in an Escherichia coli strain and purified with a functional His₆- or Strep-tag. Applying liquid chromatography electrospray ionization time-of-flight mass spectrometry (LC/ESI-ToF-MS) and a spectrophotometric pyridine hemochrome assay, heme b was identified as a cofactor. Furthermore, heme-associated iron was identified using total reflection X-ray fluorescence (TXRF) analysis and inhibition tests. The enzyme's temperature and pH optima at 30°C and 7, respectively, were determined using an oxygen consumption assay. Cleavage of poly(cis-1,4-isoprene) and poly(trans-1,4-isoprene) by the oxygenase was confirmed via detection of carbonyl functional groups containing cleavage products, using Schiff's reagent and electrospray ionization mass spectrometry (ESI-MS).

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.

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.

Metabolic and Biosynthetic Diversity in Marine Myxobacteria

Prior to 2005, the vast majority of characterized myxobacteria were obtained from terrestrial habitats. Since then, several species of halotolerant and even obligate marine myxobacteria have been described. Chemical analyses of extracts from these organisms have confirmed their ability to produce secondary metabolites with unique chemical scaffolds. Indeed, new genera of marine-derived myxobacteria, particularly Enhygromyxa, have been shown to produce novel chemical scaffolds that differ from those observed in soil myxobacteria. Further studies have shown that marine sponges and terrestrial myxobacteria are capable of producing similar or even identical secondary metabolites, suggesting that myxobacterial symbionts may have been the true producers. Recent in silico analysis of the genome sequences available from six marine myxobacteria disclosed a remarkably versatile biosynthetic potential. With access to ever-advancing tools for small molecule and genetic evaluation, these studies suggest a bright future for expeditions into this yet untapped resource for secondary metabolites.

Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y

The pathway of rubber (poly [cis-1,4-isoprene]) catabolism is well documented for Gram-positive rubber degraders but only little information exists for Gram-negative species. The first documented potent rubber degrading Gram-negative strain is Xanthomonas sp. strain 35Y that uses extracellular rubber oxygenases for the initial cleavage of the polyisoprene molecule. However, neither the exact phylogenetic position of Xanthomonas sp. strain 35Y nor the catabolic pathway of the primary polyisoprene cleavage products have been investigated. In this contribution, we started to address both these issues by a comprehensive taxonomic characterization and by the analysis of the draft genome sequence of strain 35Y. Evaluation of the 16S rRNA gene sequence pointed to a borderline taxonomic position of strain 35Y as a novel species of the genus Steroidobacter. Further, substantial differences in the genotypic properties of strain 35Y and the members of the genus Steroidobacter, including average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), resolved the taxonomic position of strain 35Y and suggested its positioning as a novel species of the genus Steroidobacter. This was further confirmed by comparative analysis of physiological and biochemical features of strain 35Y with other members of the genus Steroidobacter. Thus, we conclude that strain 35Y represents a novel species of the genus Steroidobacter, for which we propose the designation Steroidobacter cummioxidans sp. nov., strain 35YT. A comprehensive analysis of the draft genome of S. cummioxidans strain 35Y revealed similarities but also substantial differences to rubber degrading Gram-positive counterparts. In particular, the putative transporters for the uptake of polyisoprene cleavage products differ from Gram-positive rubber degrading species. The draft genome sequence of S. cummioxidans strain 35Y will be useful for researchers to experimentally verify the predicted similarities and differences in the pathways of polyisoprene catabolism in Gram-positive and Gram-negative rubber degrading species.

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.

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.