Extracellular heme peroxidases in actinomycetes: a case of mistaken identity

Identification and characterization of lignin depolymerization enzymes in Bacillus subtilis strain S11Y isolated from a tropical environment in Malaysia

Biological pretreatment using microbial enzymes appears to be the most promising pre-treatment technology for the breakdown of recalcitrant lignin structure. This research focuses on the identification and characterization of lignin-depolymerizing enzymes in Bacillus subtilis strain S11Y, previously isolated from palm oil wastes in Malaysia. The draft genome sequences of this highly lignin-depolymerizing strain revealed that the genome lacked any of the well-known dye-decolorizing peroxidase or catalase-peroxidase that are commonly reported to be involved in lignin depolymerization by bacteria, indicating that strain S11Y has distinct sets of potential lignin depolymerization genes. The oxidative stress-related enzymes Cu/Zn type-superoxide dismutase (Sod2) and a heme-containing monofunctional catalase (Kat2) were identified in the genome sequences that are of interest. Their lignin-depolymerizing ability were evaluated by treating Alkali lignin (AL) with each enzyme and their degradation ability were evaluated using gel-permeation chromatography (GPC), ultrahigh-pressure liquid chromatography-mass spectrometry (UHPLC/MS), and gas chromatography-mass spectrometry (GC/MS), which successfully proved lignin depolymerizing ability. Successful evaluation of lignin depolymerizing enzymes can be applicable for lignin pretreatment process in green energy production and generation of valuable chemicals in bio-refinery.

Effects of different soil water holding capacities on vegetable residue return and its microbiological mechanism

With the gradual expansion of the protected vegetable planting area, dense planting stubbles and increasing labor cost, the treatment of vegetable residues has become an urgent problem to be solved. Soil bacterial community structure plays an important role in vegetable residue return and is susceptible to environmental changes. Therefore, understanding the influences of different soil water holding capacities on plant residue decomposition and soil bacterial communities is important for biodegradation. During the whole incubation period, the weight loss ratio of plant residue with 100% water holding capacity was 69.60 to 75.27%, which was significantly higher than that with 60% water holding capacity in clay and sandy soil, indicating that high water holding capacity promoted the decomposition of plant residue. The degradation of lignin and cellulose was also promoted within 14 days. Furthermore, with the increase in soil water holding capacity, the contents of NH4+ increased to 5.36 and 4.54 times the initial value in the clay and sandy soil, respectively. The increase in napA and nrfA resulted in the conversion of NO3- into NH4+. The increase in water holding capacity made the bacterial network structure more compact and changed the keystone bacteria. The increase in water holding capacity also increased the relative abundance of Firmicutes at the phylum level and Symbiobacterium, Clostridium at the genus level, which are all involved in lignin and cellulose degradation and might promote their degradation. Overall, these findings provide new insight into the effects of different soil water holding capacities on the degradation of plant residues in situ and the corresponding bacterial mechanisms.

Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms

Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecules in BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis sp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and that elucidating their role in complex communities should continue to be a priority.

Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms

Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecule mediated BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis spp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and their role in complex communities should continue to be a priority.

Cryptic specialized metabolites drive Streptomyces exploration and provide a competitive advantage during growth with other microbes

Streptomyces bacteria have a complex life cycle that is intricately linked with their remarkable metabolic capabilities. Exploration is a recently discovered developmental innovation of these bacteria, that involves the rapid expansion of a structured colony on solid surfaces. Nutrient availability impacts exploration dynamics, and we have found that glycerol can dramatically increase exploration rates and alter the metabolic output of exploring colonies. We show here that glycerol-mediated growth acceleration is accompanied by distinct transcriptional signatures and by the activation of otherwise cryptic metabolites including the orange-pigmented coproporphyrin, the antibiotic chloramphenicol, and the uncommon, alternative siderophore foroxymithine. Exploring cultures are also known to produce the well-characterized desferrioxamine siderophore. Mutational studies of single and double siderophore mutants revealed functional redundancy when strains were cultured on their own; however, loss of the alternative foroxymithine siderophore imposed a more profound fitness penalty than loss of desferrioxamine during coculture with the yeast Saccharomyces cerevisiae. Notably, the two siderophores displayed distinct localization patterns, with desferrioxamine being confined within the colony area, and foroxymithine diffusing well beyond the colony boundary. The relative fitness advantage conferred by the alternative foroxymithine siderophore was abolished when the siderophore piracy capabilities of S. cerevisiae were eliminated (S. cerevisiae encodes a ferrioxamine-specific transporter). Our work suggests that exploring Streptomyces colonies can engage in nutrient-targeted metabolic arms races, deploying alternative siderophores that allow them to successfully outcompete other microbes for the limited bioavailable iron during coculture.

Identification of Red Pigments Produced by Cheese-Ripening Bacterial Strains of Glutamicibacter arilaitensis Using HPLC

Glutamicibacter arilaitensis is one of the predominant bacterial species involved in the coloration of cheese rinds, especially smear-ripened cheeses. Besides well-known yellow-pigmented carotenoids, this species exhibits an ability to produce red pigments, as the occurrence of pink/red formation was previously found when co-cultured with a fungal strain. In this work, the red pigments synthesized by G. arilaitensis strains grown on cheese-based (curd) solid medium deacidified using Debaryomyces hansenii were identified. The analyses using HPLC equipped with both fluorescence and diode array detectors were performed to characterize the pigments extracted from a dry matter of the medium inoculated with either G. arilaitensis Re117, Po102, or Stp101. Based on the UV–vis absorption spectra, the elution order, and fluorescent property, compared to those of the porphyrin standards, eight metal-free porphyrins, including UPI, UPIII, 7PI, 6PI, 5PI, CPI, CPIII, and MPIX, were indicated as components of the red pigments produced by these G. arilaitensis strains. However, following the chromatographic profiles, the degree of porphyrins formed by each strain was apparently different. Regardless of precise quantitative measurement, the type strains Re117 and Po102 manifested a potential to produce a high amount of CPIII, whereas MPIX was formed by the strains Po102 and Stp101, but exceptionally high by the strain Stp101. The variation in both yield and form of the red pigments synthesized by the cheese-related bacterial G. arilaitensis has not previously been reported; therefore, our results provide the first information on these aspects.

Marine Actinobacteria Bioflocculant: A Storehouse of Unique Biotechnological Resources for Wastewater Treatment and Other Applications

The bioactive compounds produced by actinobacteria have played a major role in antimicrobials, bioremediation, biofuels, enzymes, and anti-cancer activities. Biodegradable microbial flocculants have been produced by bacteria, algae, and fungi. Microbial bioflocculants have also attracted biotechnology importance over chemical flocculants as a result of degradability and environmentally friendly attributes they possess. Though, freshwater actinobacteria flocculants have been explored in bioflocculation. Yet, there is a paucity of information on the application of actinobacteria flocculants isolated from the marine environment. Similarly, marine habitats that supported the biodiversity of actinobacteria strains in the field of biotechnology have been underexplored in bioflocculation. Hence, this review reiterates the need to optimize culture conditions and other parameters that affect bioflocculant production by using a response surface model or artificial neural network.

Role of different microorganisms in remediating PAH-contaminated soils treated with compost or fungi

Microbial degradation is the main responsible for polycyclic aromatic hydrocarbons (PAHs) removal from contaminated soils, and the understanding of this process is pivotal to define effective bioremediation approaches. To evaluate the contribution of several microbial groups in soil anthracene and benzo[a]pyrene degradation, the analysis of phospholipid fatty acid (PLFA) profiles and machine learning techniques were employed. To this end, PLFAs and PAH concentrations were analysed, along 274 days of incubation in mesocosms, in soils artificially contaminated with anthracene and benzo[a]pyrene, subjected to different treatments: untreated soil and soils treated with biowaste compost or fungal consortium. Random forest models, figuring anthracene or benzo[a]pyrene concentrations as dependent variables and PLFAs as predictors, were then built to evaluate the contribution of each variable in PAH degradation. PLFA profiles varied substantially among soil treatments and along time, with the increase of Actinomycetes in soils added with fungi and other Gram+ bacteria in compost amended soils. The former, together with fungi, are primarily responsible for anthracene and benzo[a]pyrene degradation in both treated soils, a process in which also metanotrophs and other Gram+ and Gram- bacteria participate. In untreated soil, the cooperation of a multitude of different microorganisms was, instead, responsible for PAH removal, a process with lower efficiency in respect to treated soils.

Coproporphyrin III Produced by the Bacterium Glutamicibacter arilaitensis Binds Zinc and Is Upregulated by Fungi in Cheese Rinds

Bacterium-fungus interactions play key roles in the assembly of cheese rind microbial communities, but the molecular mechanisms underlying these interactions are poorly characterized. Moreover, millions of people around the world enjoy eating cheeses and cheese rinds, but our understanding of the diversity of microbial metabolites ingested during cheese consumption is limited. The discovery of zinc coproporphyrin III as the cause of pink pigment production by Glutamicibacter arilaitensis suggests that secretion of this molecule is important for microbial acquisition of trace metals.

Microbial communities of fermented food microbiomes typically exhibit predictable patterns of microbial succession. However, the biochemical mechanisms that control the diversity and dynamics of these communities are not well described. Interactions between bacteria and fungi may be one mechanism controlling the development of cheese rind microbiomes. This study characterizes a specific bacterium-fungus interaction previously discovered on cheese rinds between the bacterium Glutamicibacter arilaitensis (formerly Arthrobacter arilaitensis) and fungi of the genus Penicillium and identifies the specialized metabolites produced during cocultures. G. arilaitensis was previously shown to produce an unknown pink pigment in response to the presence of Penicillium. Using a combination of mass spectrometry, nuclear magnetic resonance (NMR), and transcriptome sequencing (RNA-seq), we determined that this pigment production is associated with production of coproporphyrin III. The discovery that coproporphyrin III preferentially bound zinc over other trace metals found in cheese curds highlights the value of using analytical chemistry to confirm identity of predicted chemical species.

IMPORTANCE Bacterium-fungus interactions play key roles in the assembly of cheese rind microbial communities, but the molecular mechanisms underlying these interactions are poorly characterized. Moreover, millions of people around the world enjoy eating cheeses and cheese rinds, but our understanding of the diversity of microbial metabolites ingested during cheese consumption is limited. The discovery of zinc coproporphyrin III as the cause of pink pigment production by Glutamicibacter arilaitensis suggests that secretion of this molecule is important for microbial acquisition of trace metals.

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Enzymes From Rare Actinobacterial Strains

Actinobacteria constitute rich sources of novel biocatalysts and novel natural products for medical and industrial utilization. Although actinobacteria are potential source of economically important enzymes, the isolation and culturing are somewhat tough because of its extreme habitats. But now-a-days, the rate of discovery of novel compounds producing actinomycetes from soil, freshwater, and marine ecosystem has increased much through the developed culturing and genetic engineering techniques. Actinobacteria are well-known source of their bioactive compounds and they are the promising source of broad range of industrially important enzymes. The bacteria have the capability to degrade a range of pesticides, hydrocarbons, aromatic, and aliphatic compounds (Sambasiva Rao, Tripathy, Mahalaxmi, & Prakasham, 2012). Most of the enzymes are mainly derived from microorganisms because of their easy of growth, minimal nutritional requirements, and low-cost for downstream processing. The focus of this review is about the new, commercially useful enzymes from rare actinobacterial strains. Industrial requirements are now fulfilled by the novel actinobacterial enzymes which assist the effective production. Oxidative enzymes, lignocellulolytic enzymes, extremozymes, and clinically useful enzymes are often utilized in many industrial processes because of their ability to catalyze numerous reactions. Novel, extremophilic, oxidative, lignocellulolytic, and industrially important enzymes from rare Actinobacterial population are discussed in this chapter.

Actinomycetes: A Source of Lignocellulolytic Enzymes

Lignocellulose is the most abundant biomass on earth. Agricultural, forest, and agroindustrial activities generate tons of lignocellulosic wastes annually, which present readily procurable, economically affordable, and renewable feedstock for various lignocelluloses based applications. Lignocelluloses are the focus of present decade researchers globally, in an attempt to develop technologies based on natural biomass for reducing dependence on expensive and exhaustible substrates. Lignocellulolytic enzymes, that is, cellulases, hemicellulases, and lignolytic enzymes, play very important role in the processing of lignocelluloses which is prerequisite for their utilization in various processes. These enzymes are obtained from microorganisms distributed in both prokaryotic and eukaryotic domains including bacteria, fungi, and actinomycetes. Actinomycetes are an attractive microbial group for production of lignocellulose degrading enzymes. Various studies have evaluated the lignocellulose degrading ability of actinomycetes, which can be potentially implemented in the production of different value added products. This paper is an overview of the diversity of cellulolytic, hemicellulolytic, and lignolytic actinomycetes along with brief discussion of their hydrolytic enzyme systems involved in biomass modification.

Poly R decolorization and APPL production by Streptomyces violaceoruber and Streptomyces spiroverticillatus

Two mesophilic streptomycetes (S. violaceoruber and S. spiroverticillatus) were selected to study their Poly R-478 decolorization ability and lignocellulose solubilizing activity. Both strains were able to degrade Poly R-478 dye and ferulic acid during growth on a minimal salts medium. The Poly R-478 decolorizing activities of both strains were induced by adding different carbon sources to the culture media. S. violaceoruber could decolorize 63% of Poly R-478 after 24 h. Both strains could solubilize straw and produce acid-precipitable polymeric lignin (APPL) with different efficiency. From the major extracellular enzymes recovery of both strains on rice and wheat straw, we can predicate that the biodegradation process was partial indicating a possible utilization in biological delignification.

Distribution of live and dead cells in pellets of an actinomycete Amycolatopsis balhimycina and its correlation with balhimycin productivity

Secondary metabolites such as antibiotics are typically produced by actinomycetes as a response to growth limiting stress conditions. Several studies have shown that secondary metabolite production is correlated with changes observed in actinomycete pellet morphology. Therefore, we investigated the correlation between the production of balhimycin and the spatio-temporal distribution of live and dead cells in pellets of Amycolatopsis balhimycina in submerged cultures. To this end, we used laser scanning confocal microscopy to analyze pellets from balhimycin producing and nonproducing media containing 0.2 and 1.0 g l−1 of potassium di-hydrogen phosphate, respectively. We observed a substantially higher fraction of live cells in pellets from cultures yielding larger amounts of balhimycin. Moreover, in media that resulted in no balhimycin production, the pellets exhibit an initial death phase which commences from the centre of the pellet and extends in the radial direction. A second growth phase was observed in these pellets, where live mycelia are seen to appear in the dead core of the pellets. This secondary growth was absent in pellets from media producing higher amounts of balhimycin. These results suggest that distribution of live and dead cells and its correlation with antibiotic production in the non-sporulating A. balhimycina differs markedly than that observed in Streptomycetes.

Actinobacterial peroxidases: an unexplored resource for biocatalysis

Peroxidases are redox enzymes that can be found in all forms of life where they play diverse roles. It is therefore not surprising that they can also be applied in a wide range of industrial applications. Peroxidases have been extensively studied with particular emphasis on those isolated from fungi and plants. In general, peroxidases can be grouped into haem-containing and non-haem-containing peroxidases, each containing protein families that share sequence similarity. The order Actinomycetales comprises a large group of bacteria that are often exploited for their diverse metabolic capabilities, and with recent increases in the number of sequenced genomes, it has become clear that this metabolically diverse group of organisms also represents a large resource for redox enzymes. It is therefore surprising that, to date, no review article has been written on the wide range of peroxidases found within the actinobacteria. In this review article, we focus on the different types of peroxidases found in actinobacteria, their natural role in these organisms and how they compare with the more well-described peroxidases. Finally, we also focus on work remaining to be done in this research field in order for peroxidases from actinobacteria to be applied in industrial processes.

Spectroscopic properties of rubber oxygenase RoxA from Xanthomonas sp., a new type of dihaem dioxygenase

Natural rubber [poly-(cis-1,4-isoprene)] is cleaved to 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD) by rubber oxygenase A (RoxA) isolated from Xanthomonas sp. RoxA has two c-type haem centres that show two distinct alpha-bands at 549 and 553 nm in the dithionite-reduced state. A well-resolved midpoint potential (E(0)') of -65 mV was determined for one haem by spectrophotometric titrations in the absence of dioxygen with dithionite and ferricyanide as reductant and oxidant, respectively. The midpoint potential of the second haem was not resolvable (E(0)' about -130 to -160 mV). One of the two haems was reduced by NADH (549 nm alpha-band), similar to bacterial dihaem peroxidases. Evidence for an electron transfer between the two haems was provided by slow reduction of the second haem (553 nm alpha-band) upon incubation of the partially reduced enzyme at room temperature. Addition of imidazole or related compounds to RoxA led to UV/vis spectral features similar to those observed for partially reduced RoxA. Notably, reduction of RoxA with dithionite or NADH, or binding of compounds such as imidazole, resulted in a reversible inactivation of the enzyme, unlike dihaem peroxidases. In line with this result, RoxA did not show any peroxidase activity. EPR spectra of RoxA as isolated showed two low-spin Fe(III) haem centres, with apparent g-values of 3.39, 3.09, 2.23, 1.92 and 1.50. A weak signal in the g=6 region resulting from a high-spin Fe(III) haem was also observed with a preparation-dependent intensity that disappeared in the presence of imidazole. Attempts to provide spectroscopic evidence for binding of the natural substrate (polyisoprene latex) to RoxA failed. However, experimental data are presented that RoxA is able to subtract redox equivalents from its substrate or from model compounds. In conclusion, RoxA is a novel type of dihaem dioxygenase with features clearly different from classical cytochrome c peroxidases.

Cadmium biosorption by Streptomyces sp. F4 isolated from former uranium mine

46 actinomycetes were isolated from two polluted sites and one unpolluted site. One strain, F4, was selected through primary qualitative screening assays because of its cadmium resistance, and physiologically and taxonomically characterized. F4 was able to grow at 7.5% NaCl and 100 microg/ml lysozyme and at a pH between 6 and 10. 16S rDNA sequence analysis showed that F4 was closely related to Streptomyces tendae. Growth of Streptomyces sp. F4 on culture medium with 8 mg/l Cd(2+) for 8 days showed 80% inhibition. Maximum specific biosorption was 41.7 mg Cd(2+)/g dry weight after 7 days of growth and highest Cd(2+ )concentration was found in the cell wall (41.2%). The exopolysaccharide layer only contained 7.4%, whereas 39.4% of Cd(2+) was found in the cytosolic fraction. Twelve % was found in the ribosomes and membrane fraction. This was verified with TEM, showing Streptomyces sp. F4 cytoplasm with dark granulate appearance. This study could present the potential capacity of Streptomyces sp. F4 for Cd(2+) bioremediation.

A preliminary study of metalloproteins in CSF by CapLC-ICPMS and NanoLC-CHIP/ITMS

Cerebrospinal fluid (CSF) has frequently been studied to explore the total metal concentrations in patients with neurodegenerative diseases. Some examples of neurologic diseases include but are not limited to intracerebral hemorrhage, intraventricular hemorrhage, traumatic brain injury, subarachnoid hemorrhage and hydrocephalus. In this study, however, a comprehensive approach was begun using metallomics methods. First, two molecular weight cutoff filters were used to separate CSF constituents by molecular weight. The remaining CSF was then separated with capillary liquid chromatography/normal bore liquid chromatography and analyzed with inductively coupled mass spectrometry (ICPMS). With this ICPMS screening, a possible iron associated protein was suggested by nanoliquid chromatography-CHIP/ion trap mass spectrometry (nanoLC-CHIP/ITMS) identification in conjunction with a Spectrum Mill database search. In this preliminary study, three different types of pooled CSF were partially characterized by their metal (Pb, Mg, Zn, Fe and Cu) containing species with suggestions for fuller studies. Chemical 'differences' in the CSF and metal constituents suggests some utility in this analysis for understanding some of the complications observed following subarachnoid hemorrhage.

Actinomycetes in rice straw decomposition

Actinomycetes are well known as lignocellulose decomposers. Forty-two cellulolytic actinomycete isolates have been recovered from soil. Those were identified to the genus level as: Streptomyces (26 isolates), Nocardiopsis (5 isolates), Micromonospora (4 isolates), Nocardioides (4 isolates) in addition to three isolates tentatively identified as Nocardia, Kibdelosporangium and Saccharomonospora. These actinomycetes were examined for their cellulolytic activity using filter paper strips and rice straw pieces. Four isolates of the four genera Kibdelosporangium, Micromonospora, Streptomyces and Nocardioides were able to efficiently degrade rice straw pieces in minimal medium causing significant weight loss between 50 and 61%. Application of this knowledge may improve the management of waste rice straw.

Global regulation of photosynthesis and respiration by FnrL: the first two targets in the tetrapyrrole pathway

Fnr is a regulator that controls the expression of a variety of genes in response to oxygen limitation in bacteria. To assess the role of Fnr in photosynthesis in Rubrivivax gelatinosus, a strain carrying a null mutation in fnrL was constructed. It was unable to grow anaerobically in the light, but, intriguingly, it was able to produce photosynthetic complexes under high oxygenation conditions. The mutant lacked all c-type cytochromes normally detectable in microaerobically-grown wild type cells and accumulated coproporphyrin III. These data suggested that the pleiotropic phenotype observed in FNR is primarily due to the control at the level of the HemN oxygen-independent coproporphyrinogen III dehydrogenase. hemN expression in trans partially suppressed the FNR phenotype, as it rescued heme and cytochrome syntheses. Nevertheless, these cells were photosynthetically deficient, and pigment analyses showed that they were blocked at the level of Mg(2+)-protoporphyrin monomethyl ester. Expression of both hemN and bchE in the FNR mutant restored synthesis of Mg(2+)-protochlorophyllide. We, therefore, conclude that FnrL controls respiration by regulating hemN expression and controls photosynthesis by regulating both hemN and bchE expression. A comprehensive picture of the control points of microaerobic respiration and photosynthesis by FnrL is provided, and the prominent role of this factor in activating alternative gene programs after reduction of oxygen tension in facultative aerobes is discussed.

Novel type of heme-dependent oxygenase catalyzes oxidative cleavage of rubber (poly-cis-1,4-isoprene)

An extracellular protein with strong absorption at 406 nm was purified from cell-free culture fluid of latex-grown Xanthomonas sp. strain 35Y. This protein was identical to the gene product of a recently characterized gene cloned from Xanthomonas sp., as revealed by determination of m/z values and sequencing of selected isolated peptides obtained after trypsin fingerprint analysis. The purified protein degraded both natural rubber latex and chemosynthetic poly(cis-1,4-isoprene) in vitro by oxidative cleavage of the double bonds of poly(cis-1,4-isoprene). 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (m/z 236) was identified and unequivocally characterized as the major cleavage product, and there was a homologous series of minor metabolites that differed from the major degradation product only in the number of repetitive isoprene units between terminal functions, CHO-CH2--and--H2-COCH3. An in vitro enzyme assay for oxidative rubber degradation was developed based on high-performance liquid chromatography analysis and spectroscopic detection of product carbonyl functions after derivatization with dinitrophenylhydrazone. Enzymatic cleavage of rubber by the purified protein was strictly dependent on the presence of oxygen; it did not require addition of any soluble cofactors or metal ions and was optimal around pH 7.0 at 40 degrees C. Carbon monoxide and cyanide inhibited the reaction; addition of catalase had no effect, and peroxidase activity could not be detected. The purified protein was specific for natural rubber latex and chemosynthetic poly(cis-1,4-isoprene). Analysis of the amino acid sequence deduced from the cloned gene (roxA [rubber oxygenase]) revealed the presence of two heme-binding motifs (CXXCH) for covalent attachment of heme to the protein. Spectroscopic analysis confirmed the presence of heme, and approximately 2 mol of heme per mol of RoxA was found.