Upstream open reading frames (uORFs) are often found in the 5′-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be independent of their encoded peptide sequences, certain uORFs control translation of the main ORF in a peptide sequence-dependent manner. For genome-wide identification of such peptide sequence-dependent regulatory uORFs, exhaustive searches for uORFs with conserved amino acid sequences have been conducted using bioinformatic analyses. However, whether the conserved uORFs identified by these bioinformatic approaches encode regulatory peptides has not been experimentally determined. Here we analyzed 16 recently identified Arabidopsis thaliana conserved uORFs for the effects of their amino acid sequences on the expression of the main ORF using a transient expression assay. We identified five novel uORFs that repress main ORF expression in a peptide sequence-dependent manner. Mutational analysis revealed that, in four of them, the C-terminal region of the uORF-encoded peptide is critical for the repression of main ORF expression. Intriguingly, we also identified one exceptional sequence-dependent regulatory uORF, in which the stop codon position is not conserved and the C-terminal region is not important for the repression of main ORF expression.

Many eukaryotic mRNAs contain one or more upstream open reading frames (uORFs) in their 5′ untranslated regions (5′-UTRs). Some uORFs encode regulatory peptides that repress translation of the main ORF. To comprehensively identify uORFs encoding regulatory peptides, genome-wide searches for uORFs with evolutionarily conserved amino acid sequences, referred to as conserved peptide uORFs (CPuORFs), have been conducted using bioinfomatic approaches. To date, more than 40 homology groups of CPuORFs have been identified in dicotyledonous plants. The Arabidopsis thaliana ANAC096 gene is one of the CPuORF-containing genes; however, the ANAC096 CPuORF exerts only little peptide sequence-dependent effect on expression of the main ORF. Here, we investigated the effect of the CPuORF sequence of a tomato ANAC096 homologue on expression of the main ORF, because it has a more highly conserved amino acid sequence than the ANAC096 CPuORF. Mutational analyses revealed that the CPuORF of the tomato ANAC096 homologue represses main ORF expression in a peptide sequence-dependent manner, and determined the critical amino acid residues of the CPuORF peptide responsible for the repression. This study identified a novel peptide sequence-dependent regulatory uORF and demonstrated that the level of uORF peptide-mediated repression can differ among closely related homologues.

Stevia rebaudiana (S. rebaudiana) is a herbaceous and perennial plant belonging to Asteraceae family. The genus stevia is well known as a natural producer of sweetener comprising non-caloric and non-carcinogenic steviol glycosides. In recent years, the capability in producing natural sweetner has increased the demand for S. rebaudiana as substitute of processed sugars. Flowering phase of S. rebaudiana has shown to affect the content of steviol glycosides in the leaves. Steviol glycosides level is the highest at the time of flower bud formation and lowest at time preceding and following flower bud formation. Therefore, sequencing and analysing the genes that are involved in flowering phase will provide platform for gene manipulation in increasing steviol glycosides content. The Stevia transcriptome data that include two stages of growth (before flowering and after flowering), were obtained using Illumina RNA-seq technology and can be accessed at NCBI Sequence Read Archive under Accession No. SRX6362785 and SRX6362784.

Stevia rebaudiana (Bertoni) is a commercially important plant worldwide. The leaves of Stevia rebaudiana contain steviol glycosides which are non-caloric, high-potency sweeteners. They are suitable for substituting sucrose and other artificial sweetening agents. Stevia rebaudiana also has many different therapeutic uses, with antidiabetic, anti-cariogenic, antimicrobial, anticancer and antioxidative properties. Rebaudioside A and stevioside are the major glycosides produced in its leaves. However, development of new varieties of Stevia rebaudiana with a greater content of rebaudioside A and decreased content of stevioside is the main concern lately. This is due to rebaudioside A having a more desirable sweet flavour taste than stevioside which possesses bitter aftertaste. In respect to that many biotechnological approaches are being used for the industrial improvement and manipulation of steviol glycosides content of Stevia rebaudiana. Transcriptome profiling has emerged as a useful tool to identify target genes involved in the steviol glycosides biosynthesis pathway. Understanding the mechanism and biosynthesis pathway of these compounds has further helped to improve the glycosides profile by up-regulating and down-regulating the desired genes. The aim of this paper is to describe the latest development in the transcriptome profiling in Stevia rebaudiana as well as to discuss the methods used in this endeavour.

Phytophthora palmivora is a destructive plant pathogenic oomycete that has caused lethal diseases in a wide range of hosts. It is a pan-tropical distributed pathogen that can infect plants at all growth stages. Extensive studies have linked P. palmivora to severe diseases in several crops, such as black pepper, rubber, cocoa, and durian, causing global economic losses. This review covers the following topics in depth: (i) P. palmivora as phytopathogen; (ii) identification and infection mechanism in rubber, cocoa, and durian; and (iii) management and control applied for P. palmivora diseases. Effective management strategies were studied and practiced to prevent the spread of P. palmivora disease. Genetic resistance and biocontrol are the best methods to control the disease. A better understanding of P. palmivora infection mechanisms in our main crops and early disease detection can reduce the risk of catastrophic pandemics.

AbstractAzolla pinnata is an aquatic plant that comes from the order of Pteridophyta and family of Azollaceae that can be found floating on the surface of waters and can only grow at non-moving or slow-moving water areas. This research aims to understand the effect of different extraction methods and fertilizers on Azolla pinnata and its secondary metabolites. The fertilizers treatments that were tested were chicken manure and AB. The different extraction methods that were tested were SFE and Soxhlet extraction. In the test, the amount of dry weight of A.pinnata obtained from using AB fertilizer was higher compared to chicken manure. For the extraction, both SFE and Soxhlet extraction produced an almost similar amount of extracts but different amounts of secondary metabolites. The amounts of the secondary metabolites were determined and analyzed using GC-MS. The metabolites identified were theamine, bioxirane, acetic acid, 9 methyl-1-decene, glycerine, dihydroxyacetone, thymine, pyranone, 6-fluoro-2-trifluoromethylbenzoic acid, 2-formyl-4,6 dichlorophenyl ester, and isoglutamine. Based on the result, treatment with AB fertilizer provides higher amounts of secondary metabolites in A.pinnata compared to chicken manure, while for extraction methods, SFE provides higher amounts of secondary metabolites in A.pinnata compared to Soxhlet extraction.

This study explored the potential of Acacia mangium to remediate arsenic present in mine wastes and to determine the remediation mechanism of this plant for removing arsenic. A preliminary test using soil spiked with various arsenic concentrations showed that Acacia mangium was able to survive on arsenic‐contaminated soil with concentrations up to 500 mg kg−1 arsenic. Ex situ phytoremediation studies using mine wastes containing approximately 790 mg kg−1 arsenic also showed no toxicity effect on Acacia mangium throughout 5 months of treatment. Bioconcentration and translocation factors indicate that Acacia mangium utilizes phytostabilization as its main mechanism to uptake arsenic into the plant tissues. The use of the chemical lixiviants monoammonium phosphate and citric acid was also found to increase the translocation of arsenic from roots to stems of Acacia mangium with a 12‐ and six‐fold increase, respectively, compared with the un‐dosed plants. Further speciation analysis revealed that arsenic in the form of arsenate was the only arsenic species detected in the stems after being amended with monoammonium phosphate; thereby, suggesting a sensible strategy for more efficient targeted arsenic phytoremediation by Acacia mangium.

The propagation, extraction, and antibacterial studies of Azolla pinnata were carried out in this study. The propagation involved two fertilizers, which were chicken manure and inorganic AB fertilizer. The dry yield was extracted using two methods, which were Soxhlet and supercritical fluid extraction (SFE). Methanolic extracts were obtained and subjected to several antibacterial tests, which include the disk diffusion assay, minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) tests, against Bacillus subtilis, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. The results showed that AB fertilizer produced more dry yield compared to chicken manure. The extract yield from Soxhlet exhibited a higher yield than that of SFE, recording its highest at 21.20%. The findings of antibacterial tests revealed that all extracts inhibited the growth of B. subtilis and S. aureus, but none showed inhibition against E. coli and P. aeruginosa. The largest diameter of inhibition zone of 2.67 ± 1.53 mm was obtained by E2 (CM-SFE), with a MIC value of 0.125 mg/mL against B. subtilis. High MBC values further confirm that the mechanism of inhibition against B. subtilis and S. aureus were due to the bacteriostatic properties of the extracts tested.