Ridha Wati

Bioinformatics analysis of the expressed sequence tags from Rhizophora stylosa Griff. genomic library

This present study describes the bioinformatics analysis of 14 expressed sequence tags (ESTs) of salt tolerance genes in mangrove plant, Rhizophora stylosa Griff. on DDBJ/EMBL/GenBank as well as physical and chemical properties, similarity, phylogenetic, potential peptide, and subcellular localization. The physical and chemical properties of 14 ESTs showed diversity among the fragment genes. The DNA sequence among the ESTs from R. stylosa exhibited 49 % to 99 % among themselves. The target peptide value of chloroplast and mitochondrial varied from 0.094 to 0.544 and from 0.016 to 0.314, respectively, indicated it was possible to exist. These results suggested the importance of understanding the diversity and function of properties of the salt tolerance genes in R. stylosa genomic library. To confirm the relationship among the ESTs in R. stylosa, a phylogenetic tree was constructed. The phylogenetic tree shows that there are three clusters, the first branch contained one EST, the second branch consists of 11 genes, in which the majority ESTs resides and the last group comprised of two ESTs. The present study, therefore, suggested the diversity of ESTs salt tolerance genes form distinct clusters in the phylogenetic tree.This present study describes the bioinformatics analysis of 14 expressed sequence tags (ESTs) of salt tolerance genes in mangrove plant, Rhizophora stylosa Griff. on DDBJ/EMBL/GenBank as well as physical and chemical properties, similarity, phylogenetic, potential peptide, and subcellular localization. The physical and chemical properties of 14 ESTs showed diversity among the fragment genes. The DNA sequence among the ESTs from R. stylosa exhibited 49 % to 99 % among themselves. The target peptide value of chloroplast and mitochondrial varied from 0.094 to 0.544 and from 0.016 to 0.314, respectively, indicated it was possible to exist. These results suggested the importance of understanding the diversity and function of properties of the salt tolerance genes in R. stylosa genomic library. To confirm the relationship among the ESTs in R. stylosa, a phylogenetic tree was constructed. The phylogenetic tree shows that there are three clusters, the first branch contained one EST, the second branch consists of ...

Characterization of cycloartenol synthase KcCAS promoter region from mangrove plant (Kandelia obovata Sheue, H. Y. Liu & J. Yong)

Cloning of Kandelia obovata (S. L.) Yong (2003) KcCAS gene from young roots (formerly known as Kandelia candel) has previously been reported and encoded a cycloartenol synthase. Fresh leaves of K. obovata that naturally grown in Okukubi River, Okinawa, Japan and used for DNA extraction. In this study, the KcCAS gene promoter was cloned through Genome walking, then sequenced and analyzed. An approximately 1 306u2005bp genomic DNA fragment of KcCAS promoter was obtained using the Universal Genome Walker kit. PLACE and PlantCARE analysis of the KcCAS promoter revealed that there was a number of regulatory elements in response to environmental signals and involved in the regulation of gene expression. Results showed that five kinds of cis-acting elements are regulated by hormone binding. These are the ABRE (TACGTG) involved in abscisic acid responsiveness, gibberellin-related GARE-motif (TCTGTTG), the P-box (CCTTTTG) involved in the gibberellin-responsive element, TCA-element (GAGAAGAATA) involved in salicylic acid responsiveness, and TGA-element (AACGAC) as an auxin-responsive element. Several important cis-acting elements in the KcCAS have been shown in other plants to be responsive to abiotic stress. These motifs were MBS (CAACTG), TC-rich repeats, and seven light responsive elements. The KcCAS promoter was also involved in the activation of defense genes in plants such as Box-W1 (TTGACC), dOCT (CaCGGATC), ARE (TGGTTT), and two circadian control elements (CAANNNNATC). The presence of multipotential regulatory motifs suggested that KcCAS may be involved in regulation of plant tolerance to several types of stresses.

Distribution of polyisoprenoids in various tissues of Bintaro (Cerbera manghas)

Bintaro (Cerbera manghas L, Apocynaceae) is a mangrove plant that has been described to have several important biological properties and pharmacological activities. In this study, the vegetative organs (leaves, roots, and stems) and the generative tissues (flowers and fruits) were analysed using two-plate thin layer chromatography to investigate the polyisoprenoid (polyprenol or dehydrodolichol and dolichol) profiles. It was found that in the vegetative tissues, there was two types (I and II) of polyprenols and dolichols detected. Type-I having a prevalence of dolichols over dehydrodolichols, was traced in the roots and stems, and type-II, having an occurrence of both polyprenols and dolichols, was found in the leaves. In contrast, in the generative organs only type-I was detected. Taken together, four out of five tissues tested showed a predominance of dolichols over polyprenols, suggesting the existence of polyprenol reductase in C. manghas. The varying polyisoprenoids in the different tissues of C. manghas indicating that these compounds have chemotaxonomic significance in C. manghas.Bintaro (Cerbera manghas L, Apocynaceae) is a mangrove plant that has been described to have several important biological properties and pharmacological activities. In this study, the vegetative organs (leaves, roots, and stems) and the generative tissues (flowers and fruits) were analysed using two-plate thin layer chromatography to investigate the polyisoprenoid (polyprenol or dehydrodolichol and dolichol) profiles. It was found that in the vegetative tissues, there was two types (I and II) of polyprenols and dolichols detected. Type-I having a prevalence of dolichols over dehydrodolichols, was traced in the roots and stems, and type-II, having an occurrence of both polyprenols and dolichols, was found in the leaves. In contrast, in the generative organs only type-I was detected. Taken together, four out of five tissues tested showed a predominance of dolichols over polyprenols, suggesting the existence of polyprenol reductase in C. manghas. The varying polyisoprenoids in the different tissues of C. man...

Protein modelling of triterpene synthase genes from mangrove plants using Phyre2 and Swiss-model

Molecular cloning of five oxidosqualene cyclases (OSC) genes from Bruguiera gymnorrhiza, Kandelia candel, and Rhizophora stylosa had previously been cloned, characterized, and encoded mono and -multi triterpene synthases. The present study analyzed protein modelling of triterpene synthase genes from mangrove using Phyre2 and Swiss-model. The diversity was noted within protein modelling of triterpene synthases using Phyre2 from sequence identity (38-43%) and residue (696-703). RsM2 was distinguishable from others for template structure; it used lanosterol synthase as a template (PDB ID: w6j.1.A). By contrast, other genes used human lanosterol synthase (1w6k.1.A). The predicted bind sites were correlated with the product of triterpene synthase, the product of BgbAS was β-amyrin, while RsM1 contained a significant amount of β-amyrin. Similarly BgLUS and KcMS, both main products was lupeol, on the other hand, RsM2 with the outcome of taraxerol. Homology modelling revealed that 696 residues of BgbAS, BgLUS, RsM1, and RsM2 (91-92% of the amino acid sequence) had been modelled with 100% confidence by the single highest scoring template using Phyre2. This coverage was higher than Swiss-model (85-90%). The present study suggested that molecular cloning of triterpene genes provides useful tools for studying the protein modelling related regulation of isoprenoids biosynthesis in mangrove forests.

Predicted cycloartenol synthase protein from Kandelia obovata and Rhizophora stylosa using online software of Phyre2 and Swiss-model

Cloning of Kandelia obovata KcCAS gene (previously known as Kandelia candel) and Rhizophora stylosa RsCAS have already have been reported and encoded cycloartenol synthases. In this study, the predicted KcCAS and RsCAS protein were analyzed using online software of Phyre2 and Swiss-model. The protein modelling for KcCAS and RsCAS cycloartenol synthases was determined using Pyre2 had similar results with slightly different in sequence identity. By contrast, the Swiss-model for KcCAS slightly had higher sequence identity (47.31%) and Qmean (0.70) compared to RsCAS. No difference of ligands binding site which is considered as modulators for both cycloartenol synthases. The range of predicted protein derived from 91-757 amino acid residues with coverage sequence similarities 0.86, respectively from template model of lanosterol synthase from the human. Homology modelling revealed that 706 residues (93% of the amino acid sequence) had been modelled with 100.0% confidence by the single highest scoring template for both KcCAS and RsCAS using Phyre2. This coverage was more elevated than swiss-model predicted (86%). The present study suggested that both genes are responsible for the genesis of cycloartenol in these mangrove plants.