Impact of an intragenic retrotransposon on the structural integrity and evolution of a major isoprenoid biosynthesis pathway gene in Hevea brasiliensis

Isoprenoids belong to a large family of structurally and functionally different natural compounds found universally from prokaryotes to higher animals and plants. In Hevea brasiliensis, the commercially important cis-polyisoprene (rubber) is synthesised as part of its defence mechanism in addition to other common isoprenoids like phytosterols, growth hormones etc. Farnesyl diphosphate synthase (FDPS) is a key enzyme in this process which catalyses the conversion of isoprene units into polyisoprene. Although prior sequence information is available, the structural variants of the FDPS gene presently existing in Hevea population are largely unknown. Since gene structure has a major role in gene regulation, extensive sequence analysis of this gene from different genotypes was carried out to identify the prevailing structural variants. We identified several SNPs and large indels which were associated with a partial transposable element (TE). Modification of key regulatory motifs and splice sites induced by the retroelement was also identified in the first intron. Screening of popular rubber clones, wild germplasm accessions and Hevea species revealed that the retroelement is responsible for the generation of new alleles with varying degrees of sequence homology. Segregation analysis of a progeny population confirmed that the alleles are not paralogs and are inherited in a Mendelian mode. Our findings suggest that the first intron of the FDPS gene has been subjected to various chromosomal rearrangements due to the interaction of a retrotransposon, resulting in novel alleles which may substantially contribute towards the evolution of this major gene in rubber. Moreover, the results indicate the possible existence of a retrotransposon-mediated epigenetic gene regulatory mechanism in Hevea.

Lipid droplet-associated proteins (LDAPs) are involved in the compartmentalization of lipophilic compounds in plant cells

While lipid droplets have traditionally been considered as inert sites for the storage of triacylglycerols and sterol esters, they are now recognized as dynamic and functionally diverse organelles involved in energy homeostasis, lipid signaling, and stress responses. Unlike most other organelles, lipid droplets are delineated by a half-unit membrane whose protein constituents are poorly understood, except in the specialized case of oleosins, which are associated with seed lipid droplets. Recently, we identified a new class of lipid-droplet associated proteins called LDAPs that localize specifically to the lipid droplet surface within plant cells and share extensive sequence similarity with the small rubber particle proteins (SRPPs) found in rubber-accumulating plants. Here, we provide additional evidence for a role of LDAPs in lipid accumulation in oil-rich fruit tissues, and further explore the functional relationships between LDAPs and SRPPs. In addition, we propose that the larger LDAP/SRPP protein family plays important roles in the compartmentalization of lipophilic compounds, including triacylglycerols and polyisoprenoids, into lipid droplets within plant cells. Potential roles in lipid droplet biogenesis and function of these proteins also are discussed.

Characterization of HbWRKY1, a WRKY transcription factor from Hevea brasiliensis that negatively regulates HbSRPP

Small rubber particle protein (SRPP) is a major component of Hevea brasiliensis (H. brasiliensis) latex, which is involved in natural rubber (NR) biosynthesis. However, little information is available on the regulation of SRPP gene (HbSRPP) expression. To study the transcriptional regulation of HbSRPP, the yeast one-hybrid experiment was performed to screen the latex cDNA library using the HbSRPP promoter as bait. One cDNA that encodes the WRKY transcription factor, designated as HbWRKY1, was isolated from H. brasiliensis. HbWRKY1 contains a 1437 bp open reading frame that encodes 478 amino acids. The deduced HbWRKY1 protein was predicted to possess two conserved WRKY domains and a C2H2 zinc-finger motif. HbWRKY1 was expressed at different levels, with the highest transcription in the flower, followed by the bark, latex, and leaf. Furthermore, the co-expression of pHbSRP::GUS with CaMV35S::HbWRKY1 significantly decreased the GUS activity in transgenic tobacco, indicating that HbWRKY1 significantly suppressed the HbSRPP promoter. These results suggested that HbWRKY1 maybe a negative transcription regulator of HbSRPP involved in NR biosynthesis in H. brasiliensis.

Neofusicoccum ribis Associated with Leaf Blight on Rubber (Hevea brasiliensis) in Peninsular Malaysia

Hevea brasiliensis is a natural source of rubber and an important plantation tree species in Malaysia. Leaf blight disease caused by Fusicoccum substantially reduces the growth and performance of H. brasiliensis. The aim of this study was to use a combination of both morphological characteristics and molecular data to clarify the taxonomic position of the fungus associated with leaf blight disease. Fusicoccum species were isolated from infected leaves collected from plantations at 3 widely separated locations - Selangor, Perak, and Johor states - in Peninsular Malaysia in 2010. All the isolates were identified according to their conidial patterns and DNA sequences generated from internal transcribed spacers (ITS1 and ITS2), the 5.8S rRNA, and an unknown locus (BotF15) containing microsatellite repeats. Based on taxonomic and sequence data, Neofusicoccum ribis was identified as the main cause of leaf blight disease in H. brasiliensis in commercial plantations in Malaysia. A pathogenicity trial on detached leaves further confirmed that N. ribis causes leaf blight disease. N. ribis is an important leaf pathogen, and its detection in Malaysia has important implications for future planting of H. brasiliensis.

Effect of rubber wood biochar on nutrition and growth of nursery plants of Hevea brasiliensis established in an Ultisol

Application of biochar alters availability of nutrients and acidic cations in soils which in turn could affect growth of plant to different degrees. Effect of rubber wood biochar amendment on the growth and nutritional status of Hevea nursery plants was determined in this study. Biochar were applied at 1% and 2% (w/w) with and without the recommended rates of N and Mg liquid fertilizers (LF). Two control treatments with 0% biochar but with and without recommended levels of all N, P, K, and Mg LF were also included. Application of biochar alone has a significant positive effect on above ground dry matter accumulation of the rootstock seedling (81% over the 0% biochar + no LF control) while no effect on the scion growth. Growth of plants in LF added treatments were much higher. Combining 2% biochar with N and Mg significantly increased the above ground dry matter accumulation over N-P-K-Mg only treatment in both rootstock seedling (29%) and the scion (61%). Biochar only application did not affect the N and P and decreased K and Ca concentrations in leaves. When combined with N and Mg fertilizers however, biochar significantly increased total N, P, Mg and Ca uptake. Biochar only application (2%) significantly decreased the leaf Mn concentrations in the seedling probably due to decrease in Mn availability as a result of increase in soil pH. The increase in soil pH due to biochar addition decreased with time close to original values in soils that received LF, possibly due to sulfate of ammonia. We concluded that application of rubber wood biochar (upto 2% w/w) could improve the growth of Hevea plants with the use of only N and Mg fertilizers under nursery conditions tested in this experiment.

Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers

Genetic diversity of 60 Hevea genotypes, consisting of Asiatic, Amazonian, African and IAC clones, and pertaining to the genetic breeding program of the Agronomic Institute (IAC), Brazil, was estimated. Analyses were based on phenotypic multivariate parameters and microsatellites. Five agronomic descriptors were employed in multivariate procedures, such as Standard Euclidian Distance, Tocher clustering and principal component analysis. Genetic variability among the genotypes was estimated with 68 selected polymorphic SSRs, by way of Modified Rogers Genetic Distance and UPGMA clustering. Structure software in a Bayesian approach was used in discriminating among groups. Genetic diversity was estimated through Nei's statistics. The genotypes were clustered into 12 groups according to the Tocher method, while the molecular analysis identified six groups. In the phenotypic and microsatellite analyses, the Amazonian and IAC genotypes were distributed in several groups, whereas the Asiatic were in only a few. Observed heterozygosity ranged from 0.05 to 0.96. Both high total diversity (H_T' = 0.58) and high gene differentiation (G _st' = 0.61) were observed, and indicated high genetic variation among the 60 genotypes, which may be useful for breeding programs. The analyzed agronomic parameters and SSRs markers were effective in assessing genetic diversity among Hevea genotypes, besides proving to be useful for characterizing genetic variability.

Molecular cloning and characterization of a 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (hmgr1) gene from rubber tree (Hevea brasiliensis Muell. Arg.): A key gene involved in isoprenoid biosynthesis

Natural rubber (cis-1,4-polyisoprene) is a secondary metabolite produced in the laticiferous tissue of Hevea tree. Mevalonate synthesis, which is the first step in isoprenoid biosynthesis, is catalyzed by the enzyme 3-hydroxy-3-methylglutarylcoenzyme A reductase 1 (hmgr1). We have cloned and characterized a full-length cDNA as well as genomic DNA for hmgr1 gene from an elite Indian rubber clone (RRII 105). The nucleotide sequence of the genomic clone comprises 4 exons and 3 introns, giving a total length of 2440 bp. The sequences of 42 bp 5' UTR and 69 bp of the 3' UTR were also determined. The hmgr1 cDNA contained an open reading frame of 1838 bp coding for 575 amino acid protein with a theoretical pI value of 6.6 and the calculated protein M W was 61.6 kDa. The deduced amino acid sequence showed high identity with other plant hmgr1 sequences. The amino acid sequence of the Hevea hmgr1 revealed several motifs which are highly conserved and common to the other plant species. These sequence conservations suggest a strong evolutionary pressure to maintain amino acid residues at specific positions, indicating that the conserved motifs might play important roles in the structural and/or catalytic properties of the enzyme. Southern blot analysis of genomic DNA from Hevea probed with a genomic fragment indicated that there were at least three isoforms of hmgr in Hevea. This result reveals that hmgr1 is one of the members of a small gene family. (Northern blot analysis showed that hmgr1 mRNA transcripts were noticed in all tissues - latex, leaf, immature leaf, and seedlings), however, the abundance of transcript level was higher in latex cells. As one step towards a better understanding of the role that this enzyme plays in coordinating isoprenoid biosynthesis in plants, hmgr1 cDNA was over expressed in transgenic Arabidopsis plants. Transgenic plants were morphologically distinguishable from control wild-type plants and an increased expression level of hmgr1 mRNA was detected. These data suggest that hmgr1 gene expression is playing an important role in isoprenoid biosynthesis.