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Gibberellins (GA) and paclobutrazol (PBZ) are plant growth regulators. GA promotes plant growth and development while PBZ retards plant growth. Little is known about their effects on chlorophyll synthesis and photosynthesis in young oil palm plantlets. In this study, ten-month old young clonal palms were treated with 0.02 g/palm either gibberellic acid (GA3) or PBZ. The PBZ-treated palms were shorter with compact crown, shorter fronds and leaflets, more fronds and higher Soil Plant Analysis Development (SPAD) units, particularly at time point T1. Thus, PBZ suppressed elongation in leaflets, rachis and trunk but increased fronds production and leaf chlorophyll content. Contrastingly, GA3 promoted oil palm height with significant inter-leaflet elongation and lower frond production. Chlorophyll content was also adversely affected in GA3-treated palms at time point T1. Transcriptome sequencing revealed that differentially expressed genes (DEGs) were enriched for metabolic related activities. These genes were mostly downregulated by GA3 treatment. The GA3 treatment also reduced expression of chlorophyll synthesis genes, DEGs encoding components of the photosystems I (PSI) and II (PSII) supercomplexes, cytochrome b6f, Adenosine tri-phosphate (ATP) synthase and Rubisco as well as their assembly factors, translocons and photoreceptors. Meanwhile, PBZ treatment increased expression of geranylgeranyl diphosphate reductase that may inhibit GA biosynthesis but increase chlorophyll synthesis, which was likely correlated to increased chlorophyll content in the darker green leaves of PBZ-treated palms. [ABSTRACT FROM AUTHOR]

In today's fast-shifting climate change scenario, crops are exposed to environmental pressures, abiotic and biotic stress. Hence, these will affect the production of agricultural products and give rise to a worldwide economic crisis. The increase in world population has exacerbated the situation with increasing food demand. The use of chemical agents is no longer recommended due to adverse effects towards the environment and health. Biocontrol agents (BCAs) and biostimulants, are feasible options for dealing with yield losses induced by plant stresses, which are becoming more intense due to climate change. BCAs and biostimulants have been recommended due to their dual action in reducing both stresses simultaneously. Although protection against biotic stresses falls outside the generally accepted definition of biostimulant, some microbial and non-microbial biostimulants possess the biocontrol function, which helps reduce biotic pressure on crops. The application of synergisms using BCAs and biostimulants to control crop stresses is rarely explored. Currently, a combined application using both agents offer a great alternative to increase the yield and growth of crops while managing stresses. This article provides an overview of crop stresses and plant stress responses, a general knowledge on synergism, mathematical modelling used for synergy evaluation and type of in vitro and in vivo synergy testing, as well as the application of synergism using BCAs and biostimulants in reducing crop stresses. This review will facilitate an understanding of the combined effect of both agents on improving crop yield and growth and reducing stress while also providing an eco-friendly alternative to agroecosystems. [ABSTRACT FROM AUTHOR]

Key message: Salicylic acid-mediated early defense response in asymptomatic oil palm roots infected by Ganoderma boninense. Jasmonic acid-mediated defense response in oil palm with root lesions caused by Ganoderma boninense. The oil palm defense responses could not eradicate basal stem rot but may delay deterioration of infected oil palms. Basal stem rot is an oil palm disease which causes substantial loss to the oil palm industry in Southeast Asia. Temporal gene expression analysis of oil palms infected with Ganoderma boninense is important to identify the defense pathways at biotrophic and necrotrophic phases of fungal infection. The aim of this study was to analyze the gene expression of oil palm genes related to respiratory burst oxidation, phytohormone biosynthesis, salicylic acid- and jasmonic acid-mediated defense pathways in oil palm roots infected by G. boninense at different time points. The findings of this study confirmed that salicylic acid mediated the early defense response from infected oil palm during the biotrophic phase of fungal infection, while the JA-mediated defense response was triggered when the root lesions occurred in the infected oil palm root tissues during the necrotrophic phase of Ganoderma infection. The oil palm defense responses may play a role in delaying the progression of basal stem rot but is insufficiently effective to eradicate Ganoderma infection. Temporal gene expression may help in finding methods to ameliorate the impact of basal stem rot by prolonging the productive lifespan of diseased trees and to reduce the economic loss due to this disease. [ABSTRACT FROM AUTHOR]

Basal stem rot (BSR) of oil palm is a disastrous disease caused by a white-rot fungus Ganoderma boninense Pat. Non-ribosomal peptides (NRPs) synthesized by non-ribosomal peptide synthetases (NRPSs) are a group of secondary metabolites that act as fungal virulent factors during pathogenesis in the host. In this study, we aimed to isolate NRPS gene of G. boninense strain UPMGB001 and investigate the role of this gene during G. boninense-oil palm interaction. The isolated NRPS DNA fragment of 8322 bp was used to predict the putative peptide sequence of different domains and showed similarity with G. sinense (85%) at conserved motifs of three main NRPS domains. Phylogenetic analysis of NRPS peptide sequences demonstrated that NRPS of G. boninense belongs to the type VI siderophore family. The roots of 6-month-old oil palm seedlings were artificially inoculated for studying NRPS gene expression and disease severity in the greenhouse. The correlation between high disease severity (50%) and high expression (67-fold) of G. boninense NRPS gene at 4 months after inoculation and above indicated that this gene played a significant role in the advancement of BSR disease. Overall, these findings increase our knowledge on the gene structure of NRPS in G. boninense and its involvement in BSR pathogenesis as an effector gene. [ABSTRACT FROM AUTHOR]

Due to the limitations in the range of antibodies recognising avian viruses, quantitative real-time PCR (RT-qPCR) is still the most widely used method to evaluate the expression of immunologically related genes in avian viruses. The objective of this study was to identify suitable reference genes for mRNA expression analysis in chicken intraepithelial lymphocyte natural killer (IEL-NK) cells after infection with very-virulent infectious bursal disease virus (vvIBDV). Fifteen potential reference genes were selected based on the references available. The coefficient of variation percentage (CV%) and average count of these 15 genes were determined by NanoString technology for control and infected samples. The M and V values for shortlisted reference genes (ACTB, GAPDH, HMBS, HPRT1, SDHA, TUBB1 and YWHAZ) were calculated using geNorm and NormFinder. GAPDH, YWHAZ and HMBS were the most stably expressed genes. The expression levels of three innate immune response related target genes, CASP8, IL22 and TLR3, agreed in the NanoString and RNA sequencing (RNA-Seq) results using one or two reference genes for normalisation (not HMBS). In conclusion, GAPDH and YWHAZ could be used as reference genes for the normalisation of chicken IEL-NK cell gene responses to infection with vvIBDV. [ABSTRACT FROM AUTHOR]

In this study, we analyzed the Rc and Rd genes that are responsible for the coloration of rice pericarps from six upland rice varieties. We also examined the association of pericarp coloration to the single nucleotide polymorphism in 9-cis-epoxycarotenoid dioxygenase 2 (NCED2), a key gene involved in abscisic acid (ABA) biosynthesis. Our findings demonstrated that all the upland rice varieties analyzed have a Rd gene which encodes a complete dihydroflavonol-4-reductase without early translational termination codon irrespective of their pericarp colors. However, the upland rice varieties with white pericarps were found to have a defective Rc gene with a 14-base deletion at exon 7 which could disrupt the function of a positive regulator of proanthocyanidin biosynthesis. In addition, the NCED2 genes from the upland rice varieties with white pericarps in this study have a C-allele while the NCED2 genes from Pandasan Red, Tomou and Taragang varieties that bear red pericarps were found to have a T-allele which was reported to be associated with a higher ABA level in upland rice. A better understanding of the gene sequences of upland rice varieties with red pericarp may provide important information for rice breeding programs. [ABSTRACT FROM AUTHOR]

Key message: Oil palm leaves prioritize defense during basal stem rot. Oil palm is susceptible to Ganoderma infection which causes basal stem rot (BSR). Induced defense gene profiles in oil palm leaves will assist the identification of markers for detection of infected oil palms. In this study, we have sequenced the mRNA samples from the leaves of G. boninense infected oil palm seedlings (LG) and in control treatment (LC). Differential gene expression analysis showed 711 and 482 genes that were up-and down-regulated more than fourfold in LG, respectively, compared to the LC. Differential gene expression analyses revealed the modulation of oil palm genes involved in defense response such as chitinases, glucanases, and thaumatin-like proteins that showed up-regulation in LG. In addition, genes for enzymes related to the biosynthesis of flavonoids, alkaloids, and terpenes were up-regulated, while many genes involved in photosynthesis were found to be suppressed in LG. Our findings provided information on how infected oil palm leaves diverting their resources into defense at the cost of other biological processes, contributing towards identification of candidate markers for the detection of infected oil palms. [ABSTRACT FROM AUTHOR]

The somatic embryogenesis receptor kinase (SERK) gene has been extensively studied in many plant species due to its role in conferring embryogenic competence to somatic cells. The oil palm (Elaeis guineensis Jacq.) full-length SERK I (EgSERK I) cDNA was first isolated from cell suspension culture using RACE-PCR. Total length of EgSERK I cDNA was 2378 bp in length with a 5'UTR region (358 bp) longer than 3'UTR region (130 bp) and the ORF was 1890 bp (629aa). The deduced amino acid sequence of EgSERK I contained protein domains commonly present in reported SERK proteins, including the hallmark proline-rich region and C-terminal domains. EgSERK I was most highly expressed in leaf explants and also detected in all tested tissues, including vegetative tissues, reproductive tissues, embryogenic tissues, and non-embryogenic tissues, suggesting that it may have a broad role in plant growth and development. Expression of EgSERK I in leaf explant was upregulated by minimal auxin concentration at the initial 6 h of incubation in callus induction media. EgSERK I mRNA was detected in the adjacent cells of the vascular tissues in the midvein region of leaf explants which serves as the callus initiation point of callogenesis in oil palm. Collectively, our findings suggest that the EgSERK I gene is involved in the callus initiation stage of oil palm somatic embryogenesis by transducing the signal to switch on the dedifferentiation process, triggering cellular reprogramming to form callus. [ABSTRACT FROM AUTHOR]

Agar, a gelatinous polysaccharide in the cell wall of many red algal species, is widely used as a gelling, thickening and stabilizing agent. The commercial value of seaweed is judged by their agar content and gel quality. Seaweed materials with higher agar yield and better gelling properties are desired due to the growing demand for agar in the global market. Agar biosynthesis in seaweeds is affected by genetic variations, developmental stages and environmental conditions, while different agar extraction techniques can also affect the yield and quality of agar. In this paper, the effects of different physiological states of seaweed, abiotic and biotic factors, seaweed storage and agar extraction techniques on the agar yield and gelling characteristics, are reviewed. This information is important as a guide for marine aquaculture of potential agarophytes and the possible effects of climate change on the stock of this natural resource. [ABSTRACT FROM AUTHOR]

African oil palm ( Elaeis guineensis) is an important oil bearing tree commercially cultivated in Malaysia. Palm oil is an important product for local consumption, provides enormous socio-economic benefits of trade and employment opportunities, and fulfilling the growing global demand for vegetable oils. The monoculture system has fostered the outbreak of basal stem rot (BSR) disease caused by the fungus Ganoderma boninense. Quantitative real-time PCR (qRT-PCR) is a widely used molecular technique to examine the infection effect on gene expression in oil palm. The selection of appropriate reference genes is vital for accurate data normalization. In this study, the expression stability of six housekeeping genes- β-actin, cyclophilin, GAPDH, MSD, NAD and ubiquitin were validated in oil palm root tissue after fungal infection. NormFinder and BestKeeper algorithms were used to cross-validate the expression stability of the candidate reference genes. MSD, NAD and ubiquitin were shown to exhibit the highest expression stability. These genes were recommended as reference genes for gene expression studies of oil palm root tissue at early fungal infection stage. [ABSTRACT FROM AUTHOR]

Salinity has been shown to be a major factor contributing to low nitrogen availability in plants. To verify the changes in nitrogen metabolism activity as affected by the exogenous application of proline under salt stress and its relation to salt tolerance, in vitro rice shoot apices were used as a model to study the growth performance and changes in nitrogen assimilation activities in two Malaysian rice cultivars MR 220 and MR 253. Results revealed that salt stress greatly reduced the plant height, shoot nitrate (NO ) content, shoot glutamine synthetase (GS), and root nitrate reductase (NR) activities in both cultivars. Supplementation of proline significantly increased the plant height, number of roots, root NO content, root NR, and root GS activities under salt stress in both cultivars with greater enhancement in MR 253 than MR 220. The results also indicated that MR 253 possessed higher nitrite reductase (NiR) and glutamate synthase (NADH-GOGAT) activities as compared with MR 220 in all tested treatments. It was suggested that the NO content, NR, and GS activities played important roles in regulating nitrogen metabolism under salt stress. Taken together, it was concluded that the ability of proline in mitigating salt stress-induced damages was correlated with the changes in nitrogen assimilation activities. [ABSTRACT FROM AUTHOR]

Many bacterial epiphytes of agar-producing seaweeds secrete agarase that degrade algal cell wall matrix into oligoagars which elicit defense-related responses in the hosts. The molecular defense responses of red seaweeds are largely unknown. In this study, we surveyed the defense-related transcripts of an agarophyte, Gracilaria changii, treated with β-agarase through next generation sequencing (NGS). We also compared the defense responses of seaweed elicited by agarase with those elicited by an agarolytic bacterium isolated from seaweed, by profiling the expression of defense-related genes using quantitative reverse transcription real-time PCR (qRT-PCR). NGS detected a total of 391 differentially expressed genes (DEGs) with a higher abundance (>2-fold change with a p value <0.001) in the agarase-treated transcriptome compared to that of the non-treated G. changii. Among these DEGs were genes related to signaling, bromoperoxidation, heme peroxidation, production of aromatic amino acids, chorismate, and jasmonic acid. On the other hand, the genes encoding a superoxide-generating NADPH oxidase and related to photosynthesis were downregulated. The expression of these DEGs was further corroborated by qRT-PCR results which showed more than 90 % accuracy. A comprehensive analysis of their gene expression profiles between 1 and 24 h post treatments (hpt) revealed that most of the genes analyzed were consistently upregulated or downregulated by both agarase and agarolytic bacterial treatments, indicating that the defense responses induced by both treatments are highly similar except for genes encoding vanadium bromoperoxidase and animal heme peroxidase. Our study has provided the first glimpse of the molecular defense responses of G. changii to agarase and agarolytic bacterial treatments. [ABSTRACT FROM AUTHOR]

EgT2RIP is a type 2 ribosome-inactivating protein isolated from oil palm ( Elaeis guineensis Jacq.). Its transcript abundance was reported to be up-regulated in oil palm roots upon inoculation of pathogenic fungus Ganoderma boninense in a recent study. This study aims to produce an active recombinant EgT2RIP protein for biological studies. The DNA fragments encoding Chain A (CA) and Chain B (CB) of EgT2RIP were cloned individually in an expression vector. Soluble CA and partially soluble CB were expressed in Escherichia coli Rosetta-gami 2 (DE3). Purified recombinant CA and CB were associated in a cysteine/cystine reduced/oxidized system, yielding a heterodimer protein (AB). The AB protein showed growth inhibitory activity against breast cancer cell lines (MCF-7) as well as non-tumorigenic breast epithelial cell line (MCF-10A) at IC = 1.4 and 10.9 μg mL, respectively. The active protein produced from this study may have the potential to be used for treatment in medical and agricultural fields. [ABSTRACT FROM AUTHOR]

9-Cis-epoxycarotenoid dioxygenase (NCED) is an important enzyme which catalyzes the oxidative cleavage of abscisic acid (ABA), a plant growth regulator which plays a vital role in stress tolerance. In this study, a cDNA sequence encoding NCED from a mangrove plant ( Acanthus ebracteatus) was analyzed and overexpressed in rice. Analysis of the deduced amino acid sequence of AeNCED revealed an open reading frame of 1,638 bp encoding a protein of 545 amino acids, with a 123 bp 5'-untranslated region (UTR) and a 259 bp 3'-UTR. The deduced amino acid sequence of AeNCED is more than 80% identical to the amino acid sequences of carotenoid cleavage dioxygenase from carrot, tomato, and coffee. The RNA encoding AeNCED was detected in transgenic rice ( Oryza sativa cv. BRRI dhan29) plants overexpressing this cDNA. These plants only showed significantly higher tolerance to salinity at germination and better performance at seedling stages. The levels of ABA in transgenic rice seedlings overexpressing AeNCED treated with 100 mM NaCl for 24 hours were higher than those of untransformed plants. However, a higher level of dihydrophaseic acid (DPA) and ABA glucose ester (ABA-GE) were also observed in these transgenic plants suggesting that rapid degradation of ABA through a self-regulation mechanism. [ABSTRACT FROM AUTHOR]

The effects of sulfate starvation on the agar characteristics of Gracilaria species was investigated by culturing two red algae from Morib, Malaysia, Gracilaria changii and Gracilaria salicornia in sulfate-free artificial seawater for 5 days. The seaweed samples were collected in October 2012 and March 2013, periods which have significant variation in the amount of rainfall. The agar yields were shown to be independent of sulfate availability, with only 0.60-1.20 % increment in treated G. changii and 0.31-1.40 % increment in treated G. salicornia while their gel strengths did not increase significantly (approximately 5-7 %) after sulfate starvation for both species. The gelling and melting temperatures did not vary between control and treated samples from both species, except for the treated G. changii collected in March 2013. The gel syneresis index of G. salicornia collected in March 2013 increased significantly after sulfate deprivation. Sulfate starvation introduced some variations in the content of 3, 6-anhydrogalactose and total sulfate esters, but the changes did not have a pronounced effect on the physical properties of agar. [ABSTRACT FROM AUTHOR]

Short-chain dehydrogenases (SDRs) which catalyze the dehydrogenation/reduction reaction have a wide range of substrate specificities. In this study, we report the molecular characterization of a transcript encoding SDR from the red seaweed, Gracilaria changii (Rhodophyta) as part of our effort to elucidate the functions of novel transcripts from this marine alga. The transcript, denoted as GcSDR, encodes a protein of 282 amino acids with a predicted size of approximately 31 kDa. The GxxxGxG coenzyme binding motif and YxxxK active-site motif of SDRs are well conserved in GcSDR. The coding sequence of GcSDR was cloned and expressed as recombinant protein in Escherichia coli BL21 (DE3) pLysS. Kinetic analysis of recombinant GcSDR using pyruvaldehyde dimethyl acetal as a substrate has a K value of 116.52 mM and a V value of 720 nmol product formed per minute per milligram. It has a higher affinity towards NADPH compared to NADP as a cofactor. Homology modeling showed that the three-dimensional structure of GcSDR has 34.5 % sequence identity to the SDR from a soil bacterium. Virtual screening of the possible substrates for GcSDR revealed that CMP-N-acetyl-beta-neuraminate (2-) which belongs to a group of amino sugars has the lowest binding energy among the compounds examined. The predicted cis-acting regulatory elements (CREs) at the 5′-flanking genomic sequence of GcSDR include CREs associated with abscisic acid, methyl jasmonic acid, light, anoxia, endosperm, low-temperature stress, and heat stress. The transcripts of GcSDR were found to accumulate in seaweed samples treated under low-salinity stress, thus suggesting its involvement during saline deprivation. [ABSTRACT FROM AUTHOR]

The isolation of high-quality RNA from brown seaweeds has always been problematic due to a high content of polyphenolic compounds and polysaccharides in their tissues. This study presents a simple and effective method for isolating high-quality RNA from the brown seaweeds Sargassum ( Sargassum polycystum, Sargassum siliquosum, Sargassum baccularia, and Sargassum binderi), Padina tetrastromatica, Turbinaria conoides, Dictyota sp., and Hormophysa cuneiformis using cetyltrimethylammonium bromide and selective lithium chloride precipitation. Approximately 25-43 μg g fresh weight of total RNA was obtained from these brown algae. The A/ A absorbance ratio of these RNA samples are between 1.995 ± 0.027 and 2.122 ± 0.013, with distinct 28S and 18S ribosomal RNA bands visible on a formaldehyde agarose gel. The RNA obtained from S. polycystum was found to be suitable for many downstream applications such as reverse transcription polymerase chain reaction, cloning, synthesis of cDNA, and construction of cDNA library for the generation of expressed sequence tags. [ABSTRACT FROM AUTHOR]

GDP-mannose-3′,5′-epimerase (GME) is an enzyme involved in the biosynthesis of GDP- l-galactose which is a building unit of agar and cell wall polysaccharides. GME catalyzes the formation of GDP-β- l-galactose and GDP- l-gulose from GDP-mannose. In this study, the gene and transcript encoding GME from the red alga Gracilaria changii (GcGME) were cloned. The structural gene sequence of GcGME is devoid of an intron. The cis-acting regulatory element involved in light response is the most abundant element at the 5′-flanking region of GcGME. The open reading frame of GcGME consists of 1,053 nucleotides with 351 amino acids. This cDNA was cloned into pET32a expression vector for recombinant protein production in Escherichia coli. High yield of soluble recombinant GcGME (55 kDa) was expressed upon isopropyl β- d-1-thiogalactopyranoside induction. The enzyme activity of recombinant GcGME was detected using thin layer chromatography and high-performance liquid chromatography. The transcript abundance of GcGME was the highest in G. changii and the lowest in Gracilaria salicornia corresponding to their agar contents. The characterization of GcGME from G. changii is important to facilitate the understanding of its role in agar production of this seaweed. [ABSTRACT FROM AUTHOR]

Basal stem rot (BSR) is the most devastating disease of oil palm. In this study, we examined the transcriptional responses of oil palm roots treated with a causal agent of BSR, Ganoderma boninense using a cDNA microarray approach. A total of 61 from 3,748 transcripts examined were found to be significantly up- or down-regulated in oil palm roots infected with G. boninense at 3 and 6 weeks post inoculation compared to those from uninfected roots. The differentially expressed genes identified in the artificially infected oil palm roots included genes encoding isoflavone reductase, Em protein H2, SPX domain-containing protein 1, pathogenesis-related protein 1, vicilin-like antimicrobial peptide. The gene expression of isoflavone reductase, which is involved in the production of phytoalexin and three related genes in the phenylpropanoid biosynthetic pathway was also profiled in the treated oil palms using real-time quantitative reverse transcription PCR. This information has contributed to our understanding of the defense mechanisms of oil palm in response to G. boninense, the future development of molecular markers for marker assisted breeding and screening of oil palms that are tolerant to G. boninense. [ABSTRACT FROM AUTHOR]

Contents RNA-binding proteins (RBPs) have been implicated as regulatory proteins involved in the post-transcriptional processes of gene expression in plants under various stress conditions. In this study, we report the cloning and characterization of a gene, designated as EgRBP42, encoding a member of the plant heterogeneous nuclear ribonucleoprotein (hnRNP)-like RBP family from oil palm ( Elaeis guineensis Jacq.). EgRBP42 consists of two N-terminal RNA recognition motifs and a glycine-rich domain at the C-terminus. The upstream region of EgRBP42 has multiple light-responsive, stress-responsive regulatory elements and regulatory elements associated with flower development. Real-time RT-PCR analysis of EgRBP42 showed that EgRBP42 was expressed in oil palm tissues tested, including leaf, shoot apical meristem, root, female inflorescence, male inflorescence and mesocarp with the lowest transcript level in the roots. EgRBP42 protein interacted with transcripts associated with transcription, translation and stress responses using pull-down assay and electrophoretic mobility shift assay. The accumulation of EgRBP42 and its interacting transcripts were induced by abiotic stresses, including salinity, drought, submergence, cold and heat stresses in leaf discs. Collectively, the data suggested that EgRBP42 is a RBP, which responds to various abiotic stresses and could be advantageous for oil palm under stress conditions. Key message EgRBP42 may be involved in the post-transcriptional regulation of stress-related genes important for plant stress response and adaptation. [ABSTRACT FROM AUTHOR]

Grain filling is an important agronomic trait, which directly affects the final yield of rice. Partially filled and empty rice grains are among the factors that limit the yield of MR219, one of the highest yielding rice varieties in Malaysia. In this study, the NSF 20 K rice oligonucleotide array, which contains 20,000 70-mer oligonucleotide probes, was used for direct comparison of the transcriptomes of MR219 and MR84 (a rice variety that has higher percentage of filled grains compared to MR219), during rapid grain-filling period at 5 and 10 days after fertilization (DAF). A total of 155 and 233 genes were differentially expressed in MR219 compared to MR84 at 5 and 10 DAF, respectively; and 9 of these expression ratios were tested using quantitative real-time RT PCR. Among the differentially expressed genes identified were those encoding hexokinase, various sugar transporters, GSDL-like lipase/acylhydrolase, brassinosteroid-insensitive 1-associated receptor kinase 1 precursor and homeobox protein GLABRA2, which were analyzed by real-time RT PCR in this study. The differences demonstrated by these genes in their transcript levels and profiles, between the two rice varieties understudied at different stages of grain filling may contribute to the formulation of hypotheses toward the understanding of poor percentage of filled grains in MR219. [ABSTRACT FROM AUTHOR]

Type III polyketide synthases (PKSs) produce an array of metabolites with diverse functions. In this study, we have cloned the complete reading frame encoding type III PKS (SbPKS) from a brown seaweed, Sargassum binderi, and characterized the activity of its recombinant protein biochemically. The deduced amino acid sequence of SbPKS is 414 residues in length, sharing a higher sequence similarity with bacterial PKSs (38% identity) than with plant PKSs. The Cys-His-Asn catalytic triad of PKS is conserved in SbPKS with differences in some of the residues lining the active and CoA binding sites. The wild-type SbPKS displayed broad starter substrate specificity to aliphatic long-chain acyl-CoAs (C-C) to produce tri- and tetraketide pyrones. Mutations at H and N caused complete loss of its activity, thus suggesting that these two residues are the catalytic residues for SbPKS as in other type III PKSs. Furthermore, H227G, H227G/L366V substitutions resulted in increased tetraketide-forming activity, while wild-type SbPKS produces triketide α-pyrone as a major product. On the other hand, mutant H227G/L366V/F93A/V95A demonstrated a dramatic decrease of tetraketide pyrone formation. These observations suggest that His and Leu play an important role for the polyketide elongation reaction in SbPKS. The conformational changes in protein structure especially the cavity of the active site may have more significant effect to the activity of SbPKS compared with changes in individual residues. [ABSTRACT FROM AUTHOR]

In this study, we report the molecular characterization of clone Eg707 isolated from cell suspension culture of the oil palm. The deduced polypeptide of clone Eg707 is highly similar to an unknown protein from Arabidopsis thaliana. The presence of an Ald-Xan-dh-C2 superfamily domain in the deduced protein sequence suggested that Eg707 protein might be involved in abscisic acid biosynthesis. Eg707 might be present as a single copy gene in the oil palm genome. This gene is highly expressed in tissue cultured materials compared to vegetative and reproductive tissues, suggesting a role of this gene during oil palm somatic embryogenesis or at the early stages of embryo development. Expression analysis of Eg707 by RNA in situ hybridization showed that Eg707 transcripts were present throughout somatic embryo development starting from proembryo formation at the embryogenic callus stages till the maturing embryo stages. Since proembryo formation within the embryogenic callus is one of the first key factors in oil palm somatic embryo development, it is suggested that Eg707 could be used as a reliable molecular marker for detecting early stage of oil palm somatic embryogenesis. [ABSTRACT FROM AUTHOR]

Plant growth-promoting bacteria (PGPB) promote plant growth through a combination of mechanisms which affect mineral nutrition and root development. In this study, we profiled the transcripts in oil palm roots inoculated with a PGPB, Bacillus sphaericus UPMB10, upon the establishment of a stable inoculum on the root surface by cDNA microarray analysis. A total of 70 from more than 3,700 transcripts examined were found to be significantly upregulated in the roots of oil palm inoculated with B. sphaericus UPMB10 compared to those from un-inoculated oil palm roots. Majority of these genes were related to protein synthesis and processing, stress, primary metabolism, and membrane transport. Many ribosomal proteins were upregulated in the roots of B. sphaericus-inoculated oil palm plantlets. In addition, B. sphaericus UPMB10 were able to upregulate the expression of a gene encoding low affinity nitrate transporter, independent of root morphogenesis. These rhizosphere bacteria were also demonstrated to induce stress-related proteins that may lead to tolerance to biotic and abiotic stresses. [ABSTRACT FROM AUTHOR]

Oil palm suspension cultures were initiated by transferring the gel-like friable embryogenic tissue onto liquid medium supplemented with auxins. In this study, transcripts that were differentially expressed in oil palm suspension cells cultured at different auxin concentrations were examined using suppression subtractive hybridization. Total RNA was first isolated from oil palm suspension cells proliferated in liquid medium with different hormone concentrations for 6 months. Four different hormone combinations: T1 (0.1 mg/l 2,4-D and 1.0 mg/l NAA), T2 (0.4 mg/l 2,4-D and 1.0 mg/l NAA), T3 (1.0 mg/l NAA), and T4 (0.4 mg/l 2,4-D) were used for the treatments. The first and second subtractions were performed using samples T1 and T2 in forward and reverse order. The other two subtractions were forward and reverse subtractions of T3 and T4, respectively. Reverse northern analyses showed that 14.13% of these clones were preferentially expressed in T1, 13.70% in T2, 14.75% in T3, and 15.70% in T4. Among the 294 cDNA clones that were sequenced, 61 contigs (assembled from 165 sequences) and 129 singletons were obtained. Among the 61 contigs, 10 contigs consist of sequences from treatment T1, 8 contigs were from treatment T2, 10 contigs were contains sequences of treatment T3 and 13 contigs contains sequences of treatment T4. Northern analyses of five transcripts that were shown to be differentially expressed in the oil palm suspension cells by reverse northern analysis revealed that transcripts 16A1 (a putative lignostilbene-α,β-dioxygenase, EgLSD) and 16H12 (a putative ethylene responsive 6, EgER6) were differentially expressed in oil palm suspension cells treated with different levels of auxin. [ABSTRACT FROM AUTHOR]

Light regulates photosynthesis, growth and reproduction, yield and properties of phycocolloids, and starch contents in seaweeds. Despite its importance as an environmental cue that regulates many developmental, physiological, and biochemical processes, the network of genes involved during light deprivation are obscure. In this study, we profiled the transcriptome of Gracilaria changii at two different irradiance levels using a cDNA microarray containing more than 3,000 cDNA probes. Microarray analysis revealed that 93 and 105 genes were up- and down-regulated more than 3-fold under light deprivation, respectively. However, only 50% of the transcripts have significant matches to the nonredundant peptide sequences in the database. The transcripts that accumulated under light deprivation include vanadium chloroperoxidase, thioredoxin, ferredoxin component, and reduced nicotinamide adenine dinucleotide dehydrogenase. Among the genes that were down-regulated under light deprivation were genes encoding light harvesting protein, light harvesting complex I, phycobilisome 7.8 kDa linker polypeptide, low molecular weight early light-inducible protein, and vanadium bromoperoxidase. Our findings also provided important clues to the functions of many unknown sequences that could not be annotated using sequence comparison. [ABSTRACT FROM AUTHOR]

In this study, we report the sequence, Southern analyses and spatial distribution of four cDNA sequences related to reactive oxygen species (ROS) scavenging systems from a mangrove plant, Acanthus ebracteatus. These four complementary DNA (cDNA) sequences encode cytosolic ascorbate peroxidase (AeAPX), monodehydroascorbate reductase (AeMDHR), glutathione- S-transferase (AeGST), and mitochondrial manganese superoxide dismutase (AeMnSOD), respectively. Experimental results indicated that AeAPX and AeGST belong to multigene families, whereas AeMDHAR and AeMnSOD exhibited substantial differences from other members of the same families. Transcript analyses indicated that all these genes were expressed in flowers. However, only AeAPX, AeMDHAR, and AeMnSOD were expressed in all tissues examined. Although both AeMDHAR and AeMnSOD were highly expressed in flowers, the highest expression of AeMnSOD was in the leaf tissue. The expression of AeMDHAR and AeMnSOD in stem was slightly higher than in the root. AeAPX was expressed at low levels in root and stem tissues and its expression in leaf was slightly higher than in the flower. On the other hand, the transcripts of AeGST were not detected in root and leaf. Its expression was almost equal in stem and flower. The information on spatial distribution and predicted subcellular locations of these antioxidant proteins are important for comprehensive analysis and characterization of ROS scavenging and signaling mechanisms in various plant compartments and tissues. [ABSTRACT FROM AUTHOR]

Salinity is a major abiotic stress that greatly affects plant growth and crop production. Sodium ions in saline soil are toxic to plants because of their adverse effects on potassium nutrition, cytosolic enzyme activities, photosynthesis, and metabolism. It is important to identify genes involved in salinity tolerance from mangrove plants that survive under saline conditions. In this study, a total of 864 randomly selected cDNA clones were isolated and sequenced from the primary cDNA library of Acanthus ebracteatus. Among the 521 readable sequences, 138 of them were assembled into 43 contigs, whereas 383 were singletons. Sequence analyses demonstrated that 349 of these expressed sequence tags showed significant homology to functional proteins, of which 18% are particularly interesting as they correspond to genes involved in stress response. Some of these clones, including putative mannitol dehydrogenase, plastidic aldolase, secretory peroxidase, ascorbate peroxidase, and vacuolar H+-ATPase, may be related to osmotic homeostasis, ionic homeostasis, and detoxification. [ABSTRACT FROM AUTHOR]

The infectious bursal disease (IBD) is an acute immunosuppressive viral disease that significantly affects the economics of the poultry industry. The IBD virus (IBDV) was known to infect B lymphocytes and activate macrophage and T lymphocytes, but there are limited studies on the impact of IBDV infection on chicken intraepithelial lymphocyte natural killer (IEL-NK) cells. This study employed an mRNA sequencing approach to investigate the early regulation of gene expression patterns in chicken IEL-NK cells after infection with very virulent IBDV strain UPM0081. A total of 12,141 genes were expressed in uninfected chicken IEL-NK cells, and most of the genes with high expression were involved in the metabolic pathway, whereas most of the low expressed genes were involved in the cytokine-cytokine receptor pathway. A total of 1,266 genes were differentially expressed (DE) at 3 day-post-infection (dpi), and these DE genes were involved in inflammation, antiviral response and interferon stimulation. The innate immune response was activated as several genes involved in inflammation, antiviral response and recruitment of NK cells to the infected area were up-regulated. This is the first study to examine the whole transcriptome profile of chicken NK cells towards IBDV infection and provides better insight into the early immune response of chicken NK cells. [ABSTRACT FROM AUTHOR]

Proteomic analysis was conducted to identify the rice root proteins induced by exogenous proline and their involvement in root growth. Proteins were extracted from the root tissues grown under two conditions, T1 (control) and T2 (10 mM proline), and profiled by two-dimensional polyacrylamide gel electrophoresis. Seventeen of 30 differentially expressed proteins were identified by mass spectrometry. Proline-treated rice roots showed up-regulation and down-regulation of nine and eight proteins, respectively, when compared to those in the control. Among the differentially expressed proteins, the down-regulation of glutathione reductase and peroxidase could be involved in the regulation of cellular hydrogen peroxide and reactive oxygen species levels that modulate the root cell wall structure. Differentially expressed proteins identified as pathogenesis-related proteins might be related to stress adaptive mechanisms in response to exogenous proline treatment. In addition, differentially expressed protein identified as the fructose-bisphosphate aldolases and cytochrome c oxidase might be associated with energy metabolism, which is needed during root developmental process. This is the first attempt to study the changes in rice root proteome treated with proline. The acquired information could open new avenues for further functional studies on the involvement of proline in modulating root development and its relation to stress adaptation of plants. [ABSTRACT FROM AUTHOR]

Seaweeds survive in marine waters with high sulfate concentration compared to those living at freshwater habitats. The cell wall polymer of Gracilaria spp. which supplies more than 50% of the world agar is heavily sulfated. Since sulfation reduces the agar quality, it is interesting to investigate the effects of sulfate deprivation on the sulfate contents of seaweed and agar, as well as the metabolic pathways of these seaweeds. In this study, two agarophytes G. changii and G. salicornia were treated under sulfate deprivation for 5 days. The sulfate contents in the seaweed/agar were generally lower in sulfate-deprivated samples compared to those in the controls, but the differences were only statistically significant for seaweed sample of G. changii and agar sample of G. salicornia. RNA sequencing (RNA-Seq) of sulfate-deprivated and untreated seaweed samples revealed 1,292 and 3,439 differentially expressed genes (DEGs; ≥1.5-fold) in sulfate-deprivated G. changii and G. salicornia, respectively, compared to their respective controls. Among the annotated DEGs were genes involved in putative agar biosynthesis, sulfur metabolism, metabolism of sulfur-containing amino acids, carbon metabolism and oxidative stress. These findings shed light on the sulfate deprivation responses in agarophytes and help to identify candidate genes involved in agar biosynthesis. [ABSTRACT FROM AUTHOR]