Khayalethu Ntushelo

Functional Roles of microRNAs in Agronomically Important Plants—Potential as Targets for Crop Improvement and Protection

MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic—or abiotic origin.

Chemical compositions and antimicrobial activities of Athrixia phylicoides DC. (bush tea), Monsonia burkeana (special tea) and synergistic effects of both combined herbal teas

OBJECTIVE To determine the chemical compositions and evaluate the antimicrobial activity of bush tea (Athrixia phylicoides DC.), special tea (Monsonia burkeana) and synergy (combination of bush tea and special tea). METHODS Total polyphenols were determined using the methods reported by Singleton and Rossi (1965) and modified by Waterman and Mole (1994). Tannins were determined using vanillin HCL methods described by Prince et al. (1978). Total antioxidants were determined using the methods described by Awika et al. (2004). The micro dilution technique using 96-well micro-plates, as described by Eloff (1998) was used to obtain the minimum inhibition concentration (MIC) and minimum microbicidal concentration (MMC) values of the ethanol extracts against the microorganisms under study. The microbes strain used was Gram negative bacteria such as Escherichia coli, Klebsiella oxytoca, Proteus vulgaris, Serratia marcescens, Salmonella typhi, Klebsiella pneumonia; Gram positive bacteria such as Bacillus cereus, Staphylococcus aureus and a fungus Candida albicans. RESULTS The results demonstrated that special tea contains significantly higher content of total polyphenols (8.34 mg/100 g) and total antioxidant (0.83 mg/100 g) as compared to bush tea [total polyphenols (6.41 mg/100g) and total antioxidant (0.63 mg/100g)] and combination of bush tea and special tea [total polyphenols (6.42 mg/100 g) and total antioxidant (0.64 mg/100 g)]. There was no significant difference in tannins between bush tea, special tea and synergy. The results of antimicrobial activity (MIC and MMC) demonstrated that the ethanol extracts of bush tea, special tea and synergy possessed antimicrobial activity against all microorganisms at different zones. The MIC of bush tea ranged from 1.56 to 12.50 mg/mL while the MMC ranged from 0.78 to 12.50 mg/mL. Special teas MIC ranged from 0.39 to 12.50 mg/mL while the MMC ranged from 0.01 to 12.50 mg/mL. The MIC of synergy ranged from 3.13 to 12.50 mg/mL while the MMC ranged from 3.13 to 12.50 mg/mL without positive synergistic effect recorded. CONCLUSIONS Both bush and special tea contain total polyphenols, total antioxidants and tannins with special tea containing a significantly higher total polyphenols and total antioxidant as compared to bush tea and synergy. Bush tea, special tea and synergy possess antimicrobial activity at various degrees.

Identification and characterization of protein coding genes in monsonia (Monsonia burkeana Planch. ex harv) using a combination of approaches

The advent of next generation sequencing has made possible massive availability of sequence information for in-depth structural and functional analysis of the genes and their encoded biological state in model and non-model organisms. In this study, we demonstrate a combinatorial approach for finding protein coding genes using ab initio and extrinsic evidence-based methods in monsonia (Monsonia burkeana Planch. ex harv). This is an important herbal tea crop, yet little is known about its coding genes. To our knowledge, this is the first description of protein coding genes with detailed functional annotation in M. burkeana. This study demonstrates that (1) regions of transcript assembly potentially encode protein coding genes, (2) homologous evidence with known functions reliably assigns functions to the identified genes (3) conserved domains suggest evolutionary and functional relationship of the crop with other lineage and (4) accuracy of finding coding genes in alignment free models and in RNA-seq alignment based transcript assembly performs well. This study provides a glimpse of functional information of the protein coding region at the transcriptome level and can be used as the basis for further investigation of the underlying genetic composition and molecular functions associated with M. burkeana.

De novo transcriptome sequencing in Monsonia burkeana revealed putative genes for key metabolic pathways involved in tea quality and medicinal value

Monsonia (Monsonia burkeana Planch. ex Harv) is one of the most valuable tea and traditional medicinal plants used in Southern Africa. In spite of this, there is no sequence information regarding this plant in literature. To provide understanding of the naturally occurring tea and drug-specific products and the key pathways for the biosynthesis of these molecules, we sequenced the leaf transcriptome using Illumina MiSeq platform and generated 2,590,652 paired-end reads that were assembled de novo into 45,450 high-quality transcripts. Annotation of these transcripts revealed best hits for homology to discover more than 17,800 functional genes and conserved domains. A total of 93 KEGG pathways and associated genes encoded by more than 90% of the coding transcripts are responsible for the biosynthesis of these life-saving metabolites. We validated and enriched the genes by GO annotation and linked this to enzyme-powered pathways through interactive network map. Caffeine metabolism, flavonoid, phenylpropanoid and terpenoids biosynthesis and xenobiotics degradation were typical in tea quality and drug therapy. The relatedness of more than 80 gene families encoding key enzymes was shown using unrooted phylogenetic tree. In conclusion, the M. burkeana leaf transcriptome gives insight into tea and drug-specific products, therefore representing basis in further investigation of the plant.

The potential of omics technologies as tools to understand the environmental factors influencing okra (Abelmoschus esculentus) growth and adaptation

Leading crops such as cotton, maize, rice and wheat were the first to be studied using omics technologies (genomics, transcriptomics, proteomics and metabolomics). Those crops that are considered less significant, such as okra (Abelmoschus esculentus (L.) Moench), are yet to follow. Okra, grown in tropical and subtropical regions, is an economically important vegetable crop with high nutritional qualities and health-related benefits. In this review, the justification for okra to benefit from omics technologies is highlighted and the discussion is limited to the influence of heat stress, aluminium toxicity and exposure to Bacillus subtilis as environmental factors, which can be studied to enhance our understanding of okra growth and adaptation. The implications of okra benefiting from the potential of omics technologies are also briefly discussed.

Influence of temperature, aluminium chloride toxicity and exposure to Bacillus subtilis on the germination of okra

Influences of heat, aluminium chloride concentration and exposure to Bacillus subtilis on germination of okra seed were investigated. A factorial experiment was conducted using Petri dish assays, and seed germination percentage and coleoptile length were recorded for the different treatments. Secondary metabolite shifts of five-day-old germinated seed were assessed using 1H nuclear magnetic resonance and ultra-high resolution mass analyses. Analysis of the experimental data indicated that, individually, temperature, aluminium chloride concentration and exposure of the germinating seed to B. subtilis influenced germination of okra. Germination phenotype was also influenced by the interactions of the treatments. No clear-cut spectral shifts were observed in the secondary metabolome of the germinated seeds.

Influence of environmental factors on biodegradation of quinalphos by Bacillus thuringiensis

BackgroundThe extensive and intensive uses of organophosphorus insecticide—quinalphos in agriculture, pose a health hazard to animals, humans, and environment because of its persistence in the soil and crops. However, there is no much information available on the biodegradation of quinalphos by the soil micro-organisms, which play a significant role in detoxifying pesticides in the environment; so research is initiated in biodegradation of quinalphos.ResultsA soil bacterium strain, capable of utilizing quinalphos as its sole source of carbon and energy, was isolated from soil via the enrichment method on minimal salts medium (MSM). On the basis of morphological, biochemical and 16S rRNA gene sequence analysis, the bacterium was identified as to be Bacillus thuringiensis. Bacillus thuringiensis grew on quinalphos with a generation time of 28.38 min or 0.473 h in logarithmic phase. Maximum degradation of quinalphos was observed with an inoculum of 1.0 OD, an optimum pH (6.5–7.5), and an optimum temperature of 35–37 °C. Among the additional carbon and nitrogen sources, the carbon source—sodium acetate and nitrogen source—a yeast extract marginally improved the rate of degradation of quinalphos.ConclusionsDisplay of degradation of quinalphos by B. thuringiensis in liquid culture in the present study indicates the potential of the culture for decontamination of quinalphos in polluted environment sites.

Draft genome of a South African strain of Pectobacterium carotovorum subsp. brasiliense

The draft genome of Pectobacterium carotovorum subsp. brasiliense (Pcb) which causes blackleg of potato was submitted to the NCBI and released with reference number NZ_LGRF00000000.1. The estimated genome size based on the draft genome assembly is 4,820,279 bp from 33 contigs ranging in length from 444 to 1,660,019 nucleotides. The genome annotation showed 4250 putative genes, 4114 CDS and 43 pseudo-genes. Three complete rRNA gene species were detected: nine 5S, one 16S and one 23S. Other partial rRNA gene fragments were also identified, nine 16S rRNA and three 23S rRNA. A total of 69 tRNA genes and one ncRNA gene were also annotated in this genome.