Identification and characterization of genes from Streptomyces sp. strain K30 responsible for clear zone formation on natural rubber latex and poly(cis-1,4-isoprene) rubber degradation

Toward Sustainable Polydienes

The sustainable management of polydiene waste represents a formidable challenge in the realm of polymer chemistry, given the extensive industrial utilization of polydienes due to their superior elastomeric properties. This comprehensive Perspective addresses the multifaceted obstacles hindering efficient recycling of polydienes, encompassing environmental concerns, technical limitations, and economic disincentives. We systematically dissect the influence of polydienes' chemical structures on their recyclability, tracing the evolution of polydiene utilization and disposal practices while assessing the current landscape of waste management strategies. Our investigation reveals the primary technical challenges associated with polydiene recycling, notably the energy-intensive nature of modification processes and the environmental detriments of prevailing disposal techniques. Furthermore, we critically evaluate existing recycling methodologies─including mechanical recycling, energy recovery, and chemical recycling─highlighting their respective merits, constraints, and environmental implications. Pioneering advancements in recycling technology, such as topochemical polymerization and computational prediction models, are spotlighted for their potential to revolutionize polydiene recycling. Looking forward, we delineate an optimistic trajectory for polydiene waste management, advocating for innovative polymerization methods, the exploration of milder recycling conditions, and the adoption of interdisciplinary approaches to bolster recycling efficiency. The Perspective culminates in a discussion on the pivotal role of policy frameworks, life cycle assessments, and economic analyses in shaping the future of polydiene recycling. Through this scholarly examination, we aim to catalyze further research and development efforts aimed at mitigating the environmental impact of polydiene waste, thereby contributing to the broader objective of sustainable chemistry.

The biochemical mechanisms of plastic biodegradation

Since the invention of the first synthetic plastic, an estimated 12 billion metric tons of plastics have been manufactured, 70% of which was produced in the last 20 years. Plastic waste is placing new selective pressures on humans and the organisms we depend on, yet it also places new pressures on microorganisms as they compete to exploit this new and growing source of carbon. The limited efficacy of traditional recycling methods on plastic waste, which can leach into the environment at low purity and concentration, indicates the utility of this evolving metabolic activity. This review will categorize and discuss the probable metabolic routes for each industrially relevant plastic, rank the most effective biodegraders for each plastic by harmonizing and reinterpreting prior literature, and explain the experimental techniques most often used in plastic biodegradation research, thus providing a comprehensive resource for researchers investigating and engineering plastic biodegradation.

Rubber Oxygenase Degradation Assay by UV-Labeling and Gel Permeation Chromatography

A versatile and robust end-group derivatization approach using oximes has been developed for the detection of oxidative degradation of synthetic polyisoprenes and polybutadiene. This method demonstrates broad applicability, effectively monitoring degradation across a wide molecular weight range through ultraviolet (UV)-detection coupled to gel permeation chromatography. Importantly, it enables the effective monitoring of degradation via derivatization-induced UV-maximum shifts, even in the presence of an excess of undegraded polyene, overcoming limitations previously reported with refractive index detectors. Notably, this oxime-based derivatization methodology is used in enzymatic degradation experiments of synthetic polyisoprenes characterized by a cis: trans ratio with the rubber oxygenase LcpK30. It reveals substantial UV absorption in derivatized enzymatic degradation products of polyisoprene with molecular weights exceeding 1000 g mol-1 - an unprecedented revelation for this enzyme's activity on such synthetic polyisoprenes. This innovative approach holds promise as a valuable tool for advancing research into the degradation of synthetic polyisoprenes and polybutadiene, particularly under conditions of low organocatalytic or enzymatic degradation activity. With its broad applicability and capacity to reveal previously hidden degradation processes, it represents a noteworthy contribution to sustainable polymer chemistry.

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.

Characterization of Latex-Clearing Protein and Aldehyde Dehydrogenases Involved in the Utilization of poly(cis-1,4-isoprene) by Nocardia farcinica NBRC 15532

Microbial degradation of natural rubber and synthetic poly(cis-1,4-isoprene) is expected to become an alternative treatment system for waste from poly(cis-1,4-isoprene) products including scrap tires. Nocardia farcinica NBRC 15,532, a gram-positive rubber-degrading bacterium, can utilize poly(cis-1,4-isoprene) as the sole source of carbon and energy to produce oligo-isoprene metabolites containing aldehyde and keto end groups. A homology-based search of the genome revealed a gene encoding a latex-clearing protein (Lcp). Gene disruption analysis indicated that this gene is essential for the utilization of poly(cis-1,4-isoprene) in this strain. Further analysis of the genome sequence identified aldehyde dehydrogenase (ALDH) genes as potential candidates for oxidative degradation of oligo-isoprene aldehydes. Based on the enzymatic activity of the ALDH candidates, NF2_RS14000 and NF2_RS14385 may be involved in the degradation of oligo-isoprene aldehydes. Analysis of the reaction products revealed that these ALDHs oxidized tri- to penta-isoprene aldehydes, which were generated by the reaction of Lcp. Based on the inability of ALDH gene deletion mutants, we concluded that NF2_RS14000 is mainly involved in the utilization of poly(cis-1,4-isoprene) and the oxidative degradation of oligo-isoprene aldehydes in Nocardia farcinica NBRC 15,532.

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.

Thermal Properties and Dynamic Characteristics of Electrospun Polylactide/Natural Rubber Fibers during Disintegration in Soil

In this work, PLA/NR electrospun fibers were used as substrates for growing basil. Thermal characteristics of initial samples and after 60 and 220 days of degradation were determined using differential scanning calorimetry. In the process of disintegration, the melting and glass transition temperatures in PLA/NR composites decreased, and in PLA fibers these values increased slightly. TGA analysis in an argon environment confirmed the effect of NR on the thermal degradation of PLA/NR fibers. After exposure to the soil for 220 days, the beginning of degradation shifted to the low-temperature region. The dynamic characteristics of the fibers were determined by the EPR method. A decrease in the correlation time of the probe-radical in comparison with the initial samples was shown. FTIR spectroscopy was used to analyze the chemical structure before and after degradation in soil. In PLA/NR fibrous substrates, there was a decrease in the intensity of the bands corresponding to the PLA matrix and the appearance of N-H C-N groups due to biodegradation by soil microorganisms.

Identification and transcriptional analysis of poly(cis-1,4-isoprene) degradation gene in Rhodococcus sp. strain RDE2

The microbial degradation of synthetic and natural poly(cis-1,4-isoprene) rubber is expected to become an alternative treatment technique for waste from poly(cis-1,4-isoprene) products, such as scrap tires. A gram-positive rubber-degrading bacterium, Rhodococcus sp. strain RDE2, was isolated from the waste of a rubber-processing factory in Vietnam. This strain grew on natural rubber as a sole source of carbon and energy and produced oligo-isoprenoid metabolites containing aldehyde groups from poly(cis-1,4-isoprene). To identify the genes responsible for poly(cis-1,4-isoprene) degradation, the complete genome sequence of this strain was determined. The complete genome sequence consists of a 5,715,406 bp chromosome and 6 plasmids (GenBank accession numbers AP025186.1 to AP025192.1) with an average GC content of 67.9%. The genome contains 5358 protein-coding sequences and 12 and 68 copies of rRNA and tRNA genes, respectively. Based on genome sequence analysis, the lcp gene (RDE2_08,770), responsible for the initial step of poly(cis-1,4-isoprene) degradation, was identified. The gene product obtained from Escherichia coli depolymerizes poly(cis-1,4-isoprene) to low-molecular-weight oligo-isoprenoids. The transcription of this gene is activated during the utilization of poly(cis-1,4-isoprene) in strain RDE2. The lcpR gene (RDE2_08,760), which encodes a putative transcriptional regulator, is located upstream of lcp. The lcpR gene product recognizes the promoter region of lcp. When the lcpR gene is deleted, the constitutive transcription of lcp is observed. Thus, it is inferred that the LcpR negatively regulates lcp transcription. These results strongly suggest that the lcp and lcpR genes are involved in poly(cis-1,4-isoprene) utilization in strain RDE2.

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.

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.

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 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.

Streptomycetes: Attractive Hosts for Recombinant Protein Production

Enzymes are increasingly applied as biocatalysts for fulfilling industrial needs in a variety of applications and there is a bursting of interest for novel therapeutic proteins. Consequently, developing appropriate expression platforms for efficiently producing such recombinant proteins represents a crucial challenge. It is nowadays widely accepted that an ideal ‘universal microbial host’ for heterologous protein expression does not exist. Indeed, the first-choice microbes, as Escherichia coli or yeasts, possess known intrinsic limitations that inevitably restrict their applications. In this scenario, bacteria belonging to the Streptomyces genus need to be considered with more attention as promising, alternative, and versatile platforms for recombinant protein production. This is due to their peculiar features, first-of-all their natural attitude to secrete proteins in the extracellular milieu. Additionally, streptomycetes are considered robust and scalable industrial strains and a wide range of tools for their genetic manipulation is nowadays available. This mini-review includes an overview of recombinant protein production in streptomycetes, covering nearly 100 cases of heterologous proteins expressed in these Gram-positives from the 1980s to December 2019. We investigated homologous sources, heterologous hosts, and molecular tools (promoters/vectors/signal peptides) used for the expression of these recombinant proteins. We reported on their final cellular localization and yield. Thus, this analysis might represent a useful source of information, showing pros and cons of using streptomycetes as platform for recombinant protein production and paving the way for their more extensive use in future as alternative heterologous hosts.

Biodegradation of natural rubber and deproteinized natural rubber by enrichment bacterial consortia

This study examined the biodegradation of natural rubber (NR) and deproteinized natural rubber (DPNR) by bacterial consortia enriched from a rubber-processing factory's waste in Vietnam. The results reveal the degradation in both NR and DPNR, and the DPNR was degraded easier than NR. The highest weight loss of 48.37% was obtained in the fourth enrichment consortium with DPNR, while 35.39% was obtained in the fifth enrichment consortium with NR after 14 days of incubation. Nitrogen content and fatty acid content determined by Kjeldahl method and fourier transform infrared spectroscopy (FTIR), respectively, were decreased significantly after being incubated with the consortia. Structure of degraded rubber film analyzed by nuclear magnetic resonance spectroscopy showed the presence of aldehyde group, a sign of rubber degradation. Bacterial cells tightly adhering and embedding into NR and DPNR films were observed by scanning electron microscopy. There were differences in the bacterial composition of the consortia with NR and DPNR, which were determined by metagenomic analysis using 16S rRNA gene sequencing. The phyla Bacteroidetes and Proteobacteria may play a role in the degradation of non-isoprene compounds such as protein or lipid, while the phylum Actinobacteria plays a crucial role in the degradation of rubber hydrocarbon in all consortia.

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.

Complete Genome of Isoprene Degrading Nocardioides sp. WS12

Isoprene is a climate-active gas whose wide-spread global production stems mostly from terrestrial plant emissions. The biodegradation of isoprene is carried out by a number of different bacteria from a wide range of environments. This study investigates the genome of a novel isoprene degrading bacterium Nocardioides sp. WS12, isolated from soil associated with Salix alba (Willow), a tree known to produce high amounts of isoprene. The Nocardioides sp. WS12 genome was fully sequenced, revealing the presence of a complete isoprene monooxygenase gene cluster, along with associated isoprene degradation pathway genes. Genes associated with rubber degradation were also present, suggesting that Nocardioides sp. WS12 may also have the capacity to degrade poly-cis-1,4-isoprene.

Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions

Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.

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.

Biodegradation of Vulcanized SBR: A Comparison between Bacillus subtilis, Pseudomonas aeruginosa and Streptomyces sp

Rubber residues present harmful impacts on health and environment, besides wasting valuable and huge amounts of rubber. Biological recycling technique is focused here to minimize this problem. A comparison of the biodegradation effect caused by Bacillus subtilis, Pseudomonas aeruginosa, and Streptomyces sp., separately, on vulcanized SBR-rubber during 4 weeks is reported. The surface and molecular analyses were studied by FTIR-ATR, TGA, DSC, TC and SEM/EDS, in addition to the contact angle and crosslinking tests. B. subtilis, P. aeruginosa, and Streptomyces sp. evoked after 4 weeks a loss in v-SBR crosslinks by 17.15, 10.68 and 43.39% and also in the contact angle with water by 14.10, 12.86 and 15.71%, respectively., if compared to Control samples. FTIR findings indicate that the polymeric chain has been partially consumed causing C-C bonds scission indicating the biodegradation and bio-devulcanization phenomena. The bacterial strains caused a carbon loss by 9.15, 5.97 and 4.55% after one week and 16.09, 16.79 and 18.13% after four weeks for B. subtilis, P. aeruginosa, and Streptomyces sp. mediums, respectively. DSC and EDS results are also promising and highlighting Streptomyces sp. strain as the most effective biodegradative one as an alternative and natural mean of degrading vulcanized rubber residues.

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.

Response of bacterial communities in rubber plantations to different fertilizer treatments

In the present study, the effects of chemical fertilizer (CF) and organic fertilizer plus chemical fertilizer application (OF-CF) on natural rubber yield, soil properties, and soil bacterial community were systematically investigated in rubber plantations. The rubber dry yield was 26.3% more in the OF treatment group than in the CF treatment group. The contents of total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AK) as well as soil organic matter (SOM) and pH value were higher following OF-CF treatment. Using Illumina sequencing, a total of 927 operational taxonomic units (OTUs) were obtained following CF treatment, while 955 OTUs were obtained after OF-CF treatment. Relative abundance analysis showed the relative abundances of four phyla (Acidobacteria, Proteobacteria, Actinobacteria, Gemmatimonadetes) were different between the two treatment groups. Correlation analysis revealed Acidobacteria, Bacteroidetes, Thaumarchaeota, Elusimicrobia, Verrucomicrobia were the key taxa that determined the soil properties. Additionally, five OTUs (OTU_506, OTU_391, OTU_189, OTU_278, OTU_1057) were thought to be related to the biodegradation of natural rubber. Taken together, these results improve our understanding of the OF-mediated improvement in soil fertility and contribute to the identification of rubber-degrading bacteria in rubber plantations.

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.

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.

Genome analysis and -omics approaches provide new insights into the biodegradation potential of Rhodococcus

The past few years observed a breakthrough of genome sequences of bacteria of Rhodococcus genus with significant biodegradation abilities. Invaluable knowledge from genome data and their functional analysis can be applied to develop and design strategies for attenuating damages caused by hydrocarbon contamination. With the advent of high-throughput -omic technologies, it is currently possible to utilize the functional properties of diverse catabolic genes, analyze an entire system at the level of molecule (DNA, RNA, protein, and metabolite), simultaneously predict and construct catabolic degradation pathways. In this review, the genes involved in the biodegradation of hydrocarbons and several emerging plasticizer compounds in Rhodococcus strains are described in detail (aliphatic, aromatics, PAH, phthalate, polyethylene, and polyisoprene). The metabolic biodegradation networks predicted from omics-derived data along with the catabolic enzymes exploited in diverse biotechnological and bioremediation applications are characterized.

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.

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.

Rubber gloves biodegradation by a consortium, mixed culture and pure culture isolated from soil samples

An increasing production of natural rubber (NR) products has led to major challenges in waste management. In this study, the degradation of rubber latex gloves in a mineral salt medium (MSM) using a bacterial consortium, a mixed culture of the selected bacteria and a pure culture were studied. The highest 18% weight loss of the rubber gloves were detected after incubated with the mixed culture. The increased viable cell counts over incubation time indicated that cells used rubber gloves as sole carbon source leading to the degradation of the polymer. The growth behavior of NR-degrading bacteria on the latex gloves surface was investigated using the scanning electron microscope (SEM). The occurrence of the aldehyde groups in the degradation products was observed by Fourier Transform Infrared Spectroscopy analysis. Rhodococcus pyridinivorans strain F5 gave the highest weight loss of rubber gloves among the isolated strain and posses latex clearing protein encoded by lcp gene. The mixed culture of the selected strains showed the potential in degrading rubber within 30 days and is considered to be used efficiently for rubber product degradation. This is the first report to demonstrate a strong ability to degrade rubber by Rhodococcus pyridinivorans.

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.

Oligo(cis-1,4-isoprene) aldehyde-oxidizing dehydrogenases of the rubber-degrading bacterium Gordonia polyisoprenivorans VH2

The actinomycete Gordonia polyisoprenivorans strain VH2 is well-known for its ability to efficiently degrade and catabolize natural rubber [poly(cis-1,4-isoprene)]. Recently, a pathway for the catabolism of rubber by strain VH2 was postulated based on genomic data and the analysis of mutants (Hiessl et al. in Appl Environ Microbiol 78:2874-2887, 2012). To further elucidate the degradation pathway of poly(cis-1,4-isoprene), 2-dimensional-polyacrylamide gel electrophoresis was performed. The analysis of the identified protein spots by matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry confirmed the postulated intracellular pathway suggesting a degradation of rubber via β-oxidation. In addition, other valuable information on rubber catabolism of G. polyisoprenivorans strain VH2 (e.g. oxidative stress response) was provided. Identified proteins, which were more abundant in cells grown with rubber than in cells grown with propionate, implied a putative long-chain acyl-CoA-dehydrogenase, a 3-ketoacyl-CoA-thiolase, and an aldehyde dehydrogenase. The amino acid sequence of the latter showed a high similarity towards geranial dehydrogenases. The expression of the corresponding gene was upregulated > 10-fold under poly(cis-1,4-isoprene)-degrading conditions. The putative geranial dehydrogenase and a homolog were purified and used for enzyme assays. Deletion mutants for five aldehyde dehydrogenases were generated, and growth with poly(cis-1,4-isoprene) was investigated. While none of the mutants had an altered phenotype regarding growth with poly(cis-1,4-isoprene) as sole carbon and energy source, purified aldehyde dehydrogenases were able to catalyze the oxidation of oligoisoprene aldehydes indicating an involvement in rubber degradation.

Identification of three homologous latex-clearing protein (lcp) genes from the genome of Streptomyces sp. strain CFMR 7

Rubber materials have greatly contributed to human civilization. However, being a polymeric material does not decompose easily, it has caused huge environmental problems. On the other hand, only few bacteria are known to degrade rubber, with studies pertaining them being intensively focusing on the mechanism involved in microbial rubber degradation. The Streptomyces sp. strain CFMR 7, which was previously confirmed to possess rubber-degrading ability, was subjected to whole genome sequencing using the single molecule sequencing technology of the PacBio® RS II system. The genome was further analyzed and compared with previously reported rubber-degrading bacteria in order to identify the potential genes involved in rubber degradation. This led to the interesting discovery of three homologues of latex-clearing protein (Lcp) on the chromosome of this strain, which are probably responsible for rubber degrading activities. Genes encoding oxidoreductase α-subunit (oxiA) and oxidoreductase β-subunit (oxiB) were also found downstream of two lcp genes which are located adjacent to each other. In silico analysis reveals genes that have been identified to be involved in the microbial degradation of rubber in the Streptomyces sp. strain CFMR 7. This is the first whole genome sequence of a clear-zone-forming natural rubber- degrading Streptomyces sp., which harbours three Lcp homologous genes with the presence of oxiA and oxiB genes compared to the previously reported Gordonia polyisoprenivorans strain VH2 (with two Lcp homologous genes) and Nocardia nova SH22a (with only one Lcp gene).

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.

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.

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.