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Fulltext Cross-Kingdom Regulation by Plant microRNAs Provides Novel Insight into Gene Regulation

Samad AFA, Kamaroddin MF, Sajad M

Adv Nutr, 2021 Feb 01;12(1):197-211.
PMID: 32862223 DOI: 10.1093/advances/nmaa095

microRNAs (miRNAs) are well known as major players in mammalian and plant genetic systems that act by regulating gene expression at the post-transcriptional level. These tiny molecules can regulate target genes (mRNAs) through either cleavage or translational inhibition. Recently, the discovery of plant-derived miRNAs showing cross-kingdom abilities to regulate mammalian gene expression has prompted exciting discussions among researchers. After being acquired orally through the diet, plant miRNAs can survive in the digestive tract, enter the circulatory system, and regulate endogenous mRNAs. Here, we review current knowledge regarding the cross-kingdom mechanisms of plant miRNAs, related controversies, and potential applications of these miRNAs in dietary therapy, which will provide new insights for plant miRNA investigations related to health issues in humans.
Fulltext Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

Samad AFA, Rahnamaie-Tajadod R, Sajad M, Jani J, Murad AMA, Noor NM, et al.

BMC Genomics, 2019 07 16;20(1):586.
PMID: 31311515 DOI: 10.1186/s12864-019-5954-0

BACKGROUND: Persicaria minor (kesum) is an herbaceous plant with a high level of secondary metabolite compounds, particularly terpenoids. These terpenoid compounds have well-established roles in the pharmaceutical and food industries. Although the terpenoids of P. minor have been studied thoroughly, the involvement of microRNA (miRNA) in terpenoid regulation remains poorly understood and needs to be explored. In this study, P. minor plants were inoculated with the pathogenic fungus Fusarium oxysporum for terpenoid induction.
RESULT: SPME GC-MS analysis showed the highest terpenoid accumulation on the 6th day post-inoculation (dpi) compared to the other treatment time points (0 dpi, 3 dpi, and 9 dpi). Among the increased terpenoid compounds, α-cedrene, valencene and β-bisabolene were prominent. P. minor inoculated for 6 days was selected for miRNA library construction using next generation sequencing. Differential gene expression analysis showed that 58 miRNAs belonging to 30 families had significantly altered regulation.
Among these 58 differentially expressed genes (DEGs), 27 [corrected] miRNAs were upregulated, whereas 31 [corrected] miRNAs were downregulated. Two putative novel pre-miRNAs were identified and validated through reverse transcriptase PCR. Prediction of target transcripts potentially involved in the mevalonate pathway (MVA) was carried out by psRobot software, resulting in four miRNAs: pmi-miR530, pmi-miR6173, pmi-miR6300 and a novel miRNA, pmi-Nov_13. In addition, two miRNAs, miR396a and miR398f/g, were predicted to have their target transcripts in the non-mevalonate pathway (MEP). In addition, a novel miRNA, pmi-Nov_12, was identified to have a target gene involved in green leaf volatile (GLV) biosynthesis. RT-qPCR analysis showed that pmi-miR6173, pmi-miR6300 and pmi-nov_13 were downregulated, while miR396a and miR398f/g were upregulated. Pmi-miR530 showed upregulation at 9 dpi, and dynamic expression was observed for pmi-nov_12. Pmi-6300 and pmi-miR396a cleavage sites were detected through degradome sequence analysis. Furthermore, the relationship between miRNA metabolites and mRNA metabolites was validated using correlation analysis.
CONCLUSION: Our findings suggest that six studied miRNAs post-transcriptionally regulate terpenoid biosynthesis in P. minor. This regulatory behaviour of miRNAs has potential as a genetic tool to regulate terpenoid biosynthesis in P. minor.
Fulltext Correction to: Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

Samad AFA, Rahnamaie-Tajadod R, Sajad M, Jani J, Murad AMA, Noor NM, et al.

BMC Genomics, 2019 08 01;20(1):627.
PMID: 31370802 DOI: 10.1186/s12864-019-5994-5

Following publication of the original article [1], the authors reported a number of errors, which are listed in this Correction article. The corrections are marked in bold.
Fulltext MicroRNA and Transcription Factor: Key Players in Plant Regulatory Network

Samad AFA, Sajad M, Nazaruddin N, Fauzi IA, Murad AMA, Zainal Z, et al.

Front Plant Sci, 2017;8:565.
PMID: 28446918 DOI: 10.3389/fpls.2017.00565

Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions. This present review focuses on the regulatory relationships between miRNAs and different families of TFs like; NF-Y, MYB, AP2, TCP, WRKY, NAC, GRF, and SPL. For instance NF-Y play important role during drought tolerance and flower development, MYB are involved in signal transduction and biosynthesis of secondary metabolites, AP2 regulate the floral development and nodule formation, TCP direct leaf development and growth hormones signaling. WRKY have known roles in multiple stress tolerances, NAC regulate lateral root formation, GRF are involved in root growth, flower, and seed development, and SPL regulate plant transition from juvenile to adult. We also studied the relation between miRNAs and TFs by consolidating the research findings from different plant species which will help plant scientists in understanding the mechanism of action and interaction between these regulators in the plant growth and development under normal and stress environmental conditions.
Fulltext Data on degradome sequencing and analysis from mock-inoculated and Fusarium oxysporum treated leaves samples in Persicaria minor

Samad AFA, Sajad M, Jani J, Murad AMA, Ismail I

Data Brief, 2018 Oct;20:555-557.
PMID: 30197911 DOI: 10.1016/j.dib.2018.08.034

Degradome sequencing referred as parallel analysis of RNA ends (PARE) by modifying 5'-rapid amplification of cDNA ends (RACE) with deep sequencing method. Deep sequencing of 5' products allow the determination of cleavage sites through the mapping of degradome fragments against small RNAs (miRNA or siRNA) on a large scale. Here, we carried out degradome sequencing in medicinal plant, Persicaria minor, to identify cleavage sites in small RNA libraries in control (mock-inoculated) and Fusarium oxysporum treated plants. The degradome library consisted of both control and treated samples which were pooled together during library preparation and named as D4. The D4 dataset have been deposited at GenBank under accession number SRX3921398, https://www.ncbi.nlm.nih.gov/sra/SRX3921398.
Fulltext Small RNA-seq analysis in response to methyl jasmonate and abscisic acid treatment in Persicaria minor

Nazaruddin N, Samad AFA, Sajad M, Jani J, Zainal Z, Ismail I

Genom Data, 2017 Jun;12:157-158.
PMID: 28560166 DOI: 10.1016/j.gdata.2017.05.011

Persicaria minor (Kesum) is an important medicinal plant with high level of secondary metabolite contents, especially, terpenoids and flavonoids. Previous studies have revealed that application of exogenous phytohormone could increase secondary metabolite contents of the plant. MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in various biological processes. In order to explore the possible role of miRNA in the regulation of these phytohormones signaling pathway and uncovering their potential correlation, we, for the first time, have generated the smallRNA library of Kesum plant. The library was developed in response to methyl jasmonate (MJ) and abscisic acid (ABA) treatment by using next-generation sequencing technology. Raw reads have been deposited to SRA database with the accession numbers, SRX2655642 and SRX2655643 (MJ-treated), SRXSRX2655644 and SRX2655645 (ABA-treated) and SRX2655646and SRX2655647 (Control).
Fulltext Small RNA sequencing for secondary metabolite analysis in Persicaria minor

Samad AFA, Nazaruddin N, Sajad M, Jani J, Murad AMA, Zainal Z, et al.

Genom Data, 2017 Sep;13:3-4.
PMID: 28560169 DOI: 10.1016/j.gdata.2017.05.014

Persicaria minor (kesum) is an important medicinal plant and commonly found in southeast countries; Malaysia, Thailand, Indonesia, and Vietnam. This plant is enriched with a variety of secondary metabolites (SMs), and among these SMs, terpenoids are in high abundance. Terpenoids are comprised of many valuable biomolecules which have well-established role in agriculture and pharmaceutical industry. In P. minor, for the first time, we have generated small RNAs data sets, which can be used as tool in deciphering their roles in terpenoid biosynthesis pathways. Fungal pathogen, Fusarium oxysporum was used as elicitor to trigger SMs biosynthesis in P. minor. Raw reads and small RNA analysis data have already been deposited at GenBank under the accessions; SRX2645684 (Fusarium-treated), SRX2645685 (Fusarium-treated), SRX2645686 (mock-infected), and SRX2645687 (mock-infected).
Assessment of hepatotoxicity and nephrotoxicity in Cirrhinus mrigala induced by trypan blue - An azo dye

Hussain B, Sajad M, Usman H, A Al-Ghanim K, Riaz MN, Berenjian A, et al.

Environ Res, 2022 Dec;215(Pt 1):114120.
PMID: 36029837 DOI: 10.1016/j.envres.2022.114120

Cytotoxicity in freshwater fishes induced by industrial effluents and dyes is a global issue. Trypan blue dye has many applications in different sectors, including laboratories and industries. This study determines to detect the cytotoxic effects of trypan blue dye in vivo. The objective of this study was to estimate the sub-lethal effects of azodye in fish. Cirrhinus mrigala, a freshwater fish, was exposed to three different grading concentrations of dye 5 mg/L, 10 mg/L, and 20 mg/L in a glass aquarium. Significant (p