Tropical Rubber Research Articles

De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood.

BackgroundThe basidiomycete Rigidoporus microporus is a fungus that causes the white rot disease of the tropical rubber tree, Hevea brasiliensis, the major source of commercial natural rubber. Besides its lifestyle as a pathogen, the fungus is known to switch to saprotrophic growth on wood with the ability to degrade both lignin and cellulose. There is almost no genomic or transcriptomic information on the saprotrophic abilities of this fungus. In this study, we present the fungal transcriptomic profiles during saprotrophic growth on rubber wood.ResultsA total of 266.6 million RNA-Seq reads were generated from six libraries of the fungus growing either on rubber wood or without wood. De novo assembly produced 34, 518 unigenes with an average length of 2179 bp. Annotation of unigenes using public databases; GenBank, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups (COG) and Gene Ontology (GO) produced 25, 880 annotated unigenes. Transcriptomic profiling analysis revealed that the fungus expressed over 300 genes encoding lignocellulolytic enzymes. Among these, 175 genes were up-regulated in rubber wood. These include three members of the glycoside hydrolase family 43, as well as various glycosyl transferases, carbohydrate esterases and polysaccharide lyases. A large number of oxidoreductases which includes nine manganese peroxidases were also significantly up-regulated in rubber wood. Several genes involved in fatty acid metabolism and degradation as well as natural rubber degradation were expressed in the transcriptome. Four genes (acyl-CoA synthetase, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and acyl-CoA acetyltransferase) potentially involved in rubber latex degradation pathway were also induced. A number of ATP binding cassette (ABC) transporters and hydrophobin genes were significantly expressed in the transcriptome during saprotrophic growth. Some genes related to energy metabolism were also induced.ConclusionsThe analysed data gives an insight into the activation of lignocellulose breakdown machinery of R. microporus. This study also revealed genes with relevance in antibiotic metabolism (e.g. cephalosporin esterase) as well as those with potential applications in fatty acid degradation. This is the first study on the transcriptomic analysis of R. microporus on rubber wood and should serve as a pioneering resource for future studies of the fungus at the genomic or transcriptomic level.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2574-9) contains supplementary material, which is available to authorized users.

Soil CO2 efflux and soil carbon balance of a tropical rubber plantation

AbstractNatural rubber is a valuable source of income in many tropical countries and rubber trees are increasingly planted in tropical areas, where they contribute to land‐use changes that impact the global carbon cycle. However, little is known about the carbon balance of these plantations. We studied the soil carbon balance of a 15‐year‐old rubber plantation in Thailand and we specifically explored the seasonal dynamic of soil CO2 efflux (FS) in relation to seasonal changes in soil water content (WS) and soil temperature (TS), assessed the partitioning of FS between autotrophic (RA) and heterotrophic (RH) sources in a root trenching experiment and estimated the contribution of aboveground and belowground carbon inputs to the soil carbon budget. A multiplicative model combining both TS and WS explained 58 % of the seasonal variation of FS. Annual soil CO2 efflux averaged 1.88 kg C m−2 year−1 between May 2009 and April 2011 and RA and RH accounted for respectively 63 and 37 % of FS, after corrections of FS measured on trenched plots for root decomposition and for difference in soil water content. The 4‐year average annual aboveground litterfall was 0.53 kg C m−2 year−1 while a conservative estimate of belowground carbon input into the soil was much lower (0.17 kg C m−2 year−1). Our results highlighted that belowground processes (root and rhizomicrobial respiration and the heterotrophic respiration related to belowground carbon input into the soil) have a larger contribution to soil CO2 efflux (72 %) than aboveground litter decomposition.

The Hardware Design of Tropical Crop Monitoring System Based on ZigBee Wireless Sensor Network

This article has minutely designed the hardware structure of the tropical crop monitoring system in which Zigbee wireless sensor network is used to collect and monitor the information of tropical trop environments temperature and humidity. A system hardware circuit is also given in this article to meet the requirements of the tropical crop rubber monitoring.

Rubber plantations act as water pumps in tropical China

[1] Whether rubber plantations have the role of water pumps in tropical Southeast Asia is under active debate. Fifteen years (1994–2008) of paired catchments water observation data and one year paired eddy covariance water flux data in primary tropical rain forest and tropical rubber plantation was used to clarify how rubber plantation affects local water resources of Xishuangbanna, China. Both catchment water observations and direct eddy covariance estimates indicates that more water was evapotranspired from rubber plantation (1137 mm based on catchment water balance, 1125 mm based on eddy covariance) than from the rain forest (969 mm based on catchment water balance, 927 mm based on eddy covariance). Soil water storage during the rainy season is not sufficient to maintain such high evapotranspiration rates, resulting in zero flow and water shortages during the dry season in the rubber plantation. Therefore, this study supports the idea that rubber plantations act as water pumps as suggested by local inhabitants.

Alteration of soil labile organic carbon by invasive earthworms ( Pontoscolex corethrurus) in tropical rubber plantations

The invasive earthworm ( Pontoscolex corethrurus) is commonly found in rubber plantations of Xishuangbanna, southwestern China. To understand the long-term impact of this invasive earthworm on soil labile organic carbon (LOC), we examined changes in LOC that was protected and unprotected by soil aggregates during a worm-exclusion experiment in rubber plantations of Xishuangbanna. We found that the presence of this invasive earthworm for 20 months increased LOC (up to 35%) protected by aggregates in surface soil layer (0–5 cm). In contrast, the presence of this earthworm increased LOC unprotected by the aggregates and the turnover rate of LOC protected by the aggregates in subsurface soil layer (5–15 cm). Soil total LOC did not differ between the control and worm-exclusion treatments. These findings suggest that the invasion of P. corethrurus can redistribute LOC along soil vertical profiles with accumulation of protected LOC on surface soil layer and unprotected LOC on subsurface soil layer. Earthworms' redistribution of LOC between the protected and unprotected forms and along soil profile may affect long-term soil carbon cycling.

Adaptation to oxidative stress induced by polyunsaturated fatty acids in yeast

To create a conditional system for molecular analysis of effects of polyunsaturated fatty acids (PUFA) on cellular physiology, we have constructed a strain of yeast ( Saccharomyces cerevisiae) that functionally expresses, under defined conditions, the Δ12 desaturase gene from the tropical rubber tree, Hevea brasiliensis. This strain produces up to 15% PUFA, exclusively under inducing conditions resulting in production of 4-hydroxy-2-nonenal, one of the major end products of n − 6 polyunsaturated fatty acid peroxidation. The PUFA-producing yeast was initially more sensitive to oxidative stress than the wild-type strain. However, over extended time of cultivation it became more resistant to hydrogen peroxide indicating adaptation to endogenous oxidative stress caused by the presence of PUFA. Indeed, PUFA-producing strain showed an increased concentration of endogenous ROS, while initially increased hydrogen peroxide sensitivity was followed by an increase in catalase activity and adaptation to oxidative stress. The deletion mutants constructed to be defective in the catalase activity lost the ability to adapt to oxidative stress. These data demonstrate that the cellular synthesis of PUFA induces endogenous oxidative stress which is overcome by cellular adaptation based on the catalase activity.

Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis

The hydroxynitrile lyase from the tropical rubber tree Hevea brasiliensis (HbHNL) is utilized as a biocatalyst in stereospecific syntheses of alpha-hydroxynitriles from aldehydes and methyl-ketones. The catalyzed reaction represents one of the few industrially relevant examples of enzyme mediated C-C coupling reactions. In this work, we determined the X-ray crystal structures (at 1.54 and 1.76 Angstroms resolution) of HbHNL complexes with two chiral substrates -- mandelonitrile and 2,3-dimethyl-2-hydroxy-butyronitrile -- by soaking and rapid freeze quenching techniques. This is the first structural observation of the complex between a HNL and chiral substrates. Consistent with the known selectivity of the enzyme, only the S-enantiomers of the two substrates were observed in the active site. The binding modes of the chiral substrates were identical to that observed for the biological substrate acetone cyanohydrin. This indicates that the transformation of these non-natural substrates follows the same mechanism. A large hydrophobic pocket was identified in the active site of HbHNL which accommodates the more voluminous substituents of the two substrates. A three-point binding mode of the substrates -- hydrophobic pocket, hydrogen bonds between the hydroxyl group and Ser80 and Thr11, electrostatic interaction of the cyano group with Lys236 -- offers a likely structural explanation for the enantioselectivity of the enzyme. The structural data rationalize the observed (S)-enantioselectivity and form the basis for modifying the stereospecificity through rational design. The structures also revealed the necessity of considerable flexibility of the sidechain of Trp128 in order to bind and transform larger substrates.

A novel screening assay for hydroxynitrile lyases suitable for high-throughput screening

Hydroxynitrile lyases (Hnls) are important biocatalysts for the synthesis of optically pure cyanohydrins, which are used as precursors and building blocks for a wide range of high price fine chemicals. Although two Hnl enzymes, from the tropical rubber tree Hevea brasiliensis and from the almond tree Prunus amygdalus, are already used for large scale industrial applications, the enzymes still need to be improved and adapted to the special demands of industrial processes. In many cases directed evolution has been the method of choice to improve enzymes, which are applied as industrial biocatalysts. The screening procedure is the most crucial point in every directed evolution experiment. Herein, we describe the successful development of a novel screening assay for Hnls and its application in high-throughput screening of Escherichia coli mutant libraries. The new assay allows rapid screening of mutant libraries and facilitates the discovery of improved enzyme variants. Hnls catalyze the cleavage of cyanohydrins to hydrocyanic acid and the corresponding aldehyde or ketone. The enzyme assay is based on the detection of hydrocyanic acid produced, making it an all-purpose screening assay, without restriction to any kind of substrate. The gaseous HCN liberated within the Hnl reaction is detected by a visible colorimetric reaction. The facile, highly sensitive and reproducible screening method was validated by identifying new enzyme variants with novel substrate specificities.

A Biocatalytic Henry Reaction—The Hydroxynitrile Lyase from Hevea brasiliensis Also Catalyzes Nitroaldol Reactions

Novel enzyme activity: Biocatalytic Henry reactions with nitromethane and nitroethane yielded the corresponding nitroalcohols with good enantio- and diastereocontrol in the presence of the hydroxynitrile lyase from the tropical rubber tree Hevea brasiliensis. Molecular modeling and deuterated starting materials were used in mechanistic investigations.

Saccharomyces cerevisiae strain expressing a plant fatty acid desaturase produces polyunsaturated fatty acids and is susceptible to oxidative stress induced by lipid peroxidation

Although oxygen is essential for aerobic organisms, it also forms potentially harmful reactive oxygen species. For its simplicity, easy manipulation, and cultivation conditions, yeast is used as an attractive model in oxidative stress research. However, lack of polyunsaturated fatty acids in yeast membranes makes yeast unsuitable for research in the field of lipid peroxidation. Therefore, we have constructed a yeast strain expressing a Δ12 desaturase gene from the tropical rubber tree, Hevea brasiliensis. This yeast strain expresses the heterologous desaturase in an active form and, consequently, produces Δ9/Δ12 polyunsaturated fatty acids under inducing conditions. The functional expression of the heterologous desaturase did not affect cellular morphology or growth, indicating no general adverse effect on cellular physiology. However, the presence of polyunsaturated fatty acids changed the yeast's sensitivity to oxidative stress induced by addition of paraquat, tert-butylhydroperoxide, and hydrogen peroxide. This difference in sensitivity to the latter was followed by the formation of 4-hydroxy-2-nonenal, one of the end products of linoleic fatty acid peroxidation, which is known to play a role in cell growth control and signaling. Here we show that this yeast strain conditionally expressing the Δ12 desaturase gene provides a novel and well-defined eukaryotic model in lipid peroxidation research. Its potential to investigate the molecular basis of responses to oxidative stress, in particular the involvement of reactive aldehydes derived from fatty acid peroxidation, especially 4-hydroxy-2-nonenal, will be addressed.

Cloning and characterization of EstC from Burkholderia gladioli, a novel-type esterase related to plant enzymes.

By screening a genomic library of Burkholderia gladioli (formerly Pseudomonas marginata) for clones exhibiting esterolytic activity, the gene for a novel-type esterase (EstC) showing significant homology to plant enzymes could be isolated. High homology was found to two hydroxynitrile lyases originating from Hevea brasiliensis (tropical rubber tree) and Manihot esculenta (cassava), and to two proteins from Oryza sativa (rice) that are specifically induced upon infection by Pseudomonas syringae pv. syringae. The sequenced ORF encodes for a protein of 298 amino acids. The enzyme was efficiently overexpressed in Escherichia coli, purified and characterized with respect to enzymatic capabilities. The enzyme was able to hydrolyze a variety of esterase substrates of low to medium carbonic acid chain length, but no triglycerides were hydrolyzed. Despite the high sequence homology, no hydroxynitrile lyase activity could be recognized.

Bacteria Associated with Degradation of Wastes from Rubber Processing Industry

An investigation of bacteria found in rubber processing wastes was carried out. Rubber wastes which include effluents from washing tanks and natural rubber waste serum (NRWS) were obtained from Greenpark Rubber Industries Limited, Umutu, Delta State, Nigeria. Five bacterial species were isolated from the wastes. These include Arthrobacter sp., Bacillus sp., Lactobacillus sp., Psuedomonas sp. and Streptococcus sp. Apart from these a number of coliforms were also encountered. Arthrobacter sp. was found to be the dominant species and its potential to utilize rubber hydrocarbon was determined. It was found that the growth of Arthrobacter in both effluent and NRWS was related to pH with the highest growths recorded at pH of 8.5 and 7.5 for effluent and NRWS respectively. It was also found that at controlled pH of 7.5 in NRWS, the growth of Arthrobacter was consistent and was accompanied by a reduction in biological oxygen demand (BOD) which was the the main index for measuring pollution strength of the wastes. It is therefore being recommended that rubber wastes be treated with Arthrobacter under controlled pH to reduce their pollution potentials before disposal. It is however suggested that a combined biological treatment using both Arthrobacter and Mucor as was earlier suggested be used. It is also recommended that chemical flocculants should be used to remove suspended solids in the effluent. A combination of these two cheap methods will go a long way in alleviating the problems of pollution caused by rubber effluents from some tropical rubber processing factories.

High-Level Intracellular Expression of Hydroxynitrile Lyase from the Tropical Rubber TreeHevea brasiliensisin Microbial Hosts

(S)-Hydroxynitrile lyase (Hnl) from the tropical rubber treeHevea brasiliensiscatalyzes the formation of (S)-cyanohydrins from hydrocyanic acid and aldehydes or ketones. This enzyme accepts aliphatic, aromatic, and heterocyclic carbonyl compounds as substrates and is therefore considered a potent biocatalyst for the industrial production of optically active chemicals. Limitations in enzyme supply from natural resources were overcome by production of the enzyme in the microbial host systemsEscherichia coli, Saccharomyces cerevisiae,andPichia pastoris.Expression of Hnl in the prokaryotic system led to the formation of inclusion bodies whereas in both yeast hosts high levels of soluble protein were obtained. Highest yields were obtained in a high cell density batch fermentation of aP. pastoristransformant that expressed heterologous Hnl to about 50% of the soluble cytosolic protein. At a cell density of 100 g/liter cell dry weight, a volume yield of 22 g/liter of heterologous product was obtained. Attempts to produce the Hnl protein extracellularly with the yeast hosts by applying different leader peptide strategies were not successful. Immunofluorescence microscopy studies indicated that the secretion-directed heterologous Hnl protein accumulated in the plasma membrane forming aggregated clusters of inactive protein.

Microwave dielectric properties of rubber and oil palm leaf samples: Measurement and modelling

This paper contains the results of measured dielectric constants of leaves of two tropical crops, rubber ( Heavea brasiliensis ) and oil palm ( Elaeis guineensis ) at microwave frequency region. Using a microcomputer-based automated system consisting of a Wiltron 360B vector network analyser,measurements are conducted based on the waveguide thin sheet technique. Leaf samples are inserted within waveguide sections, and the dielectric constants are calculated from the complex reflection coefficients. The measurements cover a frequency range of 4-18GHz. In general, the dielectric constant of a leaf sample is a function of water content and frequency. Theoretical calculations from three dielectric mixing models, i.e., the Debye-Cole Dual-Dispersion dielectric model by Ulaby and Rayes, Matzler's Model and Carlson's Model are compared with the measurements. From the comparisons, the dual-dispersion model is found to show more promise in prediction of the dielectric constants, if proper physical parameters of the model, such as bound and free-water volume fractions, are used.

Hydroxynitrile lyase from Hevea brasiliensis: Molecular characterization and mechanism of enzyme catalysis

(S)-Hydroxynitrile lyase (Hnl) from the tropical rubber tree Hevea brasiliensis is a 29 kDa single chain protein that catalyses the breakdown or formation of a C--C bond by reversible addition of hydrocyanic acid to aldehydes or ketones. The primary sequence of Hnl has no significant homology to known proteins. Detailed homology investigations employing PROFILESEARCH and secondary structure prediction algorithms suggest that Hnl is a member of the alpha/beta hydrolase fold protein family and contains a catalytic triad as functional residues for catalysis. The significance of predicted catalytic residues was tested and confirmed by site-directed mutagenesis and expression of mutant and wild-type proteins in the yeast, Saccharomyces cerevisiae. Based on these data we suggest a mechanistic model for the (S)-cyanohydrin synthesis catalyzed by hydroxynitrile lyase from Hevea brasiliensis.

Hydroxynitrile lyase from Hevea brasiliensis: Molecular characterization and mechanism of enzyme catalysis

(S)-Hydroxynitrile lyase (Hnl) from the tropical rubber tree Hevea brasiliensis is a 29 kDa single chain protein that catalyses the breakdown or formation of a C--C bond by reversible addition of hydrocyanic acid to aldehydes or ketones. The primary sequence of Hnl has no significant homology to known proteins. Detailed homology investigations employing PROFILESEARCH and secondary structure prediction algorithms suggest that Hnl is a member of the alpha/beta hydrolase fold protein family and contains a catalytic triad as functional residues for catalysis. The significance of predicted catalytic residues was tested and confirmed by site-directed mutagenesis and expression of mutant and wild-type proteins in the yeast, Saccharomyces cerevisiae. Based on these data we suggest a mechanistic model for the (S)-cyanohydrin synthesis catalyzed by hydroxynitrile lyase from Hevea brasiliensis.

Molecular Cloning of the Full-length cDNA of (S)-Hydroxynitrile Lyase from Hevea brasiliensis: FUNCTIONAL EXPRESSION IN ESCHERICHIA COLI AND SACCHAROMYCES CEREVISIAE AND IDENTIFICATION OF AN ACTIVE SITE RESIDUE

The full-length cDNA of (S)-hydroxynitrile lyase (Hnl) from leaves of Hevea brasiliensis (tropical rubber tree) was cloned by an immunoscreening and sequenced. Hnl from H. brasiliensis is involved in the biodegradation of cyanogenic glycosides and also catalyzes the stereospecific synthesis of aliphatic, aromatic, and heterocyclic cyanohydrins, which are important as precursors for pharmaceutical compounds. The open reading frame identified in a 1. 1-kilobase cDNA fragment codes for a protein of 257 amino acids with a predicted molecular mass of 29.2 kDa. The derived protein sequence is closely related to the (S)-hydroxynitrile lyase from Manihot esculenta (Cassava) and also shows significant homology to two proteins of Oryza sativa with as yet unknown enzymatic function. The H. brasiliensis protein was expressed in Escherichia coli and Saccharomyces cerevisiae and isolated in an active form from the respective soluble fractions. Replacement of cysteine 81 by serine drastically reduced activity of the heterologous enzyme, suggesting a role for this amino acid residue in the catalytic action of Hnl.

Latex allergy in children

Natural latex, a product of the tropical rubber tree, Hevea brasiliensis, has been shown to cause allergic reactions in an increasing number of individuals. Severity of reaction has ranged from mild contact dermatitis to anaphylaxis. Individuals with spina bifida, congenital urogenital anomalies, health care workers, and those employed in the rubber industry are at highest risk for immediate hypersensitivity to latex. Health care workers should be aware of this high risk to minimize exposure of patients.

Tree Crops and Farming Systems Development in the Humid Tropics

SUMMARYExamples are presented of tropical tree commodity plantation crops, tea, coffee, rubber and oil palm, as models for farm system development. They are environmentally benign in comparison with annual food crops, have been organized on a large scale with smallholder participation, and make significant contributions to local and national economies. It is suggested that lessons learned in their development might be used in the large-scale development of other potentially major tree crops, including timber, fruit and nut producing species.

Monopolists and Speculators: British Investment in West African Rubber, 1905–1914

During the classical period of colonialism, from the 1890s to the 1940s, much private Western investment in Africa was conducted through investment waves – short-lived booms related to demands for, and prices of, particular raw materials. One such burst of foreign financial interest occurred between 1905 and 1914 when, against the background of a climacteric in tropical rubber, 55 companies with a total nominal capital of £5 9 million were floated in Britain to undertake rubber production in Africa. The article, seeking to understand why British capital, largely responsible for the dramatic growth of rubber planting in Asia, made such little lasting impact in Africa, focuses upon the 26 companies set up for West African operations. It notes their high failure rate, which was related to the predominance of interest in wild rather than planted rubber.Two principal reasons are adduced for the lack of commercial success of the 18 companies exploiting wild rubber concessions. The first, political and commercial opposition aroused by the exercise of monopoly rights over a natural forest product, is illustrated by the experience of three relatively large concerns in Liberia and the Ivory Coast. The second, an inadequate financial and managerial structure, is most obvious among companies with assets in the Gold Coast and Southern Nigeria, mainly fraudulent or near-fraudulent concerns floated to feed speculation in rubber shares during 1909–10. Their promotion involved the shadier fringes of the Edwardian capital market and was connected to the Gold Coast mining shares boom of 1900–1. These businesses made almost no contribution to the West African rubber trade.