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Integrative Multi-Omics Through Bioinformatics

Goh HH

Adv Exp Med Biol, 2018 11 2;1102:69-80.
PMID: 30382569 DOI: 10.1007/978-3-319-98758-3_5

This chapter introduces different aspects of bioinformatics with a brief discussion in the systems biology context. Example applications in network pharmacology of traditional Chinese medicine, systems metabolic engineering, and plant genome-scale modelling are described. Lastly, this chapter concludes on how bioinformatics helps to integrate omics data derived from various studies described in previous chapters for a holistic understanding of secondary metabolite production in P. minus.
Fulltext Ten simple rules for writing scientific op-ed articles

Goh HH, Bourne P

PLoS Comput Biol, 2020 09;16(9):e1008187.
PMID: 32941423 DOI: 10.1371/journal.pcbi.1008187
Fulltext Ten simple rules for researchers while in isolation from a pandemic

Goh HH, Bourne PE

PLoS Comput Biol, 2020 06;16(6):e1007946.
PMID: 32584810 DOI: 10.1371/journal.pcbi.1007946
Fulltext Genome-wide transcriptome profiling ofCarica papayaL. embryogenic callus

Jamaluddin ND, Mohd Noor N, Goh HH

Physiol Mol Biol Plants, 2017 Apr;23(2):357-368.
PMID: 28461724 DOI: 10.1007/s12298-017-0429-8

Genome-wide transcriptome profiling is a powerful tool to study global gene expression patterns in plant development. We report the first transcriptome profile analysis of papaya embryogenic callus to improve our understanding on genes associated with somatic embryogenesis. By using 3' mRNA-sequencing, we generated 6,190,687 processed reads and 47.0% were aligned to papaya genome reference, in which 21,170 (75.4%) of 27,082 annotated genes were found to be expressed but only 41% was expressed at functionally high levels. The top 10% of genes with high transcript abundance were significantly enriched in biological processes related to cell proliferation, stress response, and metabolism. Genes functioning in somatic embryogenesis such as SERK and LEA, hormone-related genes, stress-related genes, and genes involved in secondary metabolite biosynthesis pathways were highly expressed. Transcription factors such as NAC, WRKY, MYB, WUSCHEL, Agamous-like MADS-box protein and bHLH important in somatic embryos of other plants species were found to be expressed in papaya embryogenic callus. Abundant expression of enolase and ADH is consistent with proteome study of papaya somatic embryo. Our study highlights that some genes related to secondary metabolite biosynthesis, especially phenylpropanoid biosynthesis, were highly expressed in papaya embryogenic callus, which might have implication for cell factory applications. The discovery of all genes expressed in papaya embryogenic callus provides an important information into early biological processes during the induction of embryogenesis and useful for future research in other plant species.
Fulltext Transcriptome analysis of Carica papaya embryogenic callus upon De-etiolated 1 (DET1) gene suppression

Jamaluddin D, Mohd Noor N, Goh HH

Genom Data, 2017 Jun;12:120-121.
PMID: 28516036 DOI: 10.1016/j.gdata.2017.05.004

Papaya is considered to be one of the most nutritional fruits. It is rich in vitamins, carotenoids, flavonoids and other phytonutrient which function as antioxidant in our body [1]. Previous studies revealed that the suppression of a negative regulator gene in photomorphogenesis, De-etiolated 1 (DET1) can improve the phytonutrient in tomato and canola without affecting the fruit quality [2], [3]. This report contains the experimental data on high-throughput 3' mRNA sequencing of transformed papaya callus upon DET1 gene suppression.
Functional Genomics

Goh HH, Ng CL, Loke KK

Adv Exp Med Biol, 2018 11 2;1102:11-30.
PMID: 30382566 DOI: 10.1007/978-3-319-98758-3_2

Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.
Fulltext Omics Approaches in Uncovering Molecular Evolution and Physiology of Botanical Carnivory

Baharin A, Ting TY, Goh HH

Plants (Basel), 2023 Jan 15;12(2).
PMID: 36679121 DOI: 10.3390/plants12020408

Systems biology has been increasingly applied with multiple omics for a holistic comprehension of complex biological systems beyond the reductionist approach that focuses on individual molecules. Different high-throughput omics approaches, including genomics, transcriptomics, metagenomics, proteomics, and metabolomics have been implemented to study the molecular mechanisms of botanical carnivory. This covers almost all orders of carnivorous plants, namely Caryophyllales, Ericales, Lamiales, and Oxalidales, except Poales. Studies using single-omics or integrated multi-omics elucidate the compositional changes in nucleic acids, proteins, and metabolites. The omics studies on carnivorous plants have led to insights into the carnivory origin and evolution, such as prey capture and digestion as well as the physiological adaptations of trap organ formation. Our understandings of botanical carnivory are further enhanced by the discoveries of digestive enzymes and transporter proteins that aid in efficient nutrient sequestration alongside dynamic molecular responses to prey. Metagenomics studies revealed the mutualistic relationships between microbes and carnivorous plants. Lastly, in silico analysis accelerated the functional characterization of new molecules from carnivorous plants. These studies have provided invaluable molecular data for systems understanding of carnivorous plants. More studies are needed to cover the diverse species with convergent evolution of botanical carnivory.
Fulltext Discovery of digestive enzymes in carnivorous plants with focus on proteases

Ravee R, Mohd Salleh F', Goh HH

PeerJ, 2018;6:e4914.
PMID: 29888132 DOI: 10.7717/peerj.4914

BACKGROUND: Carnivorous plants have been fascinating researchers with their unique characters and bioinspired applications. These include medicinal trait of some carnivorous plants with potentials for pharmaceutical industry.
METHODS: This review will cover recent progress based on current studies on digestive enzymes secreted by different genera of carnivorous plants: Drosera (sundews), Dionaea (Venus flytrap), Nepenthes (tropical pitcher plants), Sarracenia (North American pitcher plants), Cephalotus (Australian pitcher plants), Genlisea (corkscrew plants), and Utricularia (bladderworts).
RESULTS: Since the discovery of secreted protease nepenthesin in Nepenthes pitcher, digestive enzymes from carnivorous plants have been the focus of many studies. Recent genomics approaches have accelerated digestive enzyme discovery. Furthermore, the advancement in recombinant technology and protein purification helped in the identification and characterisation of enzymes in carnivorous plants.
DISCUSSION: These different aspects will be described and discussed in this review with focus on the role of secreted plant proteases and their potential industrial applications.
Evaluation of electric vehicle response capability in power grid

Wong SY, Liang K, Goh HH

MethodsX, 2024 Jun;12:102783.
PMID: 38966713 DOI: 10.1016/j.mex.2024.102783

In recent years, frequent and substantial area-wide power outages have underscored the critical need for cities to possess robust backup power sources capable of swift response to prevent prolonged power system disruptions. Electric vehicles can contribute electricity to the power grid using vehicle-to-grid technology. The power delivered by electric vehicles in this context is termed as response capability. However, existing studies have overlooked response capability dynamics during transitions between electric vehicle states-such as the shift from charging or discharging to an idle state, thereby hindering a comprehensive understanding of this aspect. Hence, this paper introduces a multi-timescale response capability prediction model that evaluates the electric vehicle's state of charge to ensure users' requirements are met for upcoming trips. To better assess users' travel demand, the gravity model is employed as a precursor to response capability prediction to further enhance the validity of the prediction outcomes. Three neighborhoods in Los Angeles have been chosen for analysis: Downtown, Lincoln Heights, and Silver Lake. Predictions indicate that neglecting the response capability when electric vehicles undergo state transformation can lead to a differential response capability ranging from 2000 kWh to 4000 kWh, resulting in a loss of prediction accuracy by 20 % to 25 %.•The response capability of EV is non-zero during state transformations•Users' travel demand assessment•Seamless integration of vehicle-to-grid technology into the power grid.
Metabolite profiling reveals temperature effects on the VOCs and flavonoids of different plant populations

Goh HH, Khairudin K, Sukiran NA, Normah MN, Baharum SN

Plant Biol (Stuttg), 2016 Jan;18 Suppl 1:130-9.
PMID: 26417881 DOI: 10.1111/plb.12403

Temperature is one of the key factors in limiting the distribution of plants and controlling major metabolic processes. A series of simulated reciprocal transplant experiments were performed to investigate the effect of temperature on plant chemical composition. Polygonum minus of different lowland and highland origin were grown under a controlled environment with different temperature regimes to study the effects on secondary metabolites. We applied gas chromatography-mass spectrometry and liquid chromatography time-of-flight mass spectrometry to identify the chemical compounds. A total of 37 volatile organic compounds and 85 flavonoids were detected, with the largest response observed in the compositional changes of aldehydes and terpenes in highland plants under higher temperature treatment. Significantly less anthocyanidin compounds and larger amounts of flavonols were detected under higher temperature treatment. We also studied natural variation in the different plant populations growing under the same environment and identified compounds unique to each population through metabolite fingerprinting. This study shows that the origin of different plant populations influences the effects of temperature on chemical composition.
Transcriptome-wide effect of DE-ETIOLATED1 (DET1) suppression in embryogenic callus of Carica papaya

Jamaluddin ND, Rohani ER, Mohd Noor N, Goh HH

J Plant Res, 2019 Mar;132(2):181-195.
PMID: 30649676 DOI: 10.1007/s10265-019-01086-x

Papaya is one of the most nutritional fruits, rich in vitamins, carotenoids, flavonoids and other antioxidants. Previous studies showed phytonutrient improvement without affecting quality in tomato fruit and rapeseed through the suppression of DE-ETIOLATED-1 (DET1), a negative regulator in photomorphogenesis. This study is conducted to study the effects of DET1 gene suppression in papaya embryogenic callus. Immature zygotic embryos were transformed with constitutive expression of a hairpin DET1 construct (hpDET1). PCR screening of transformed calli and reverse transcription quantitative PCR (RT-qPCR) verified that DET1 gene downregulation in two of the positive transformants. High-throughput cDNA 3' ends sequencing on DET1-suppressed and control calli for transcriptomic analysis of global gene expression identified a total of 452 significant (FDR
ADAP is a possible negative regulator of glucosinolate biosynthesis in Arabidopsis thaliana based on clustering and gene expression analyses

Harun S, Rohani ER, Ohme-Takagi M, Goh HH, Mohamed-Hussein ZA

J Plant Res, 2021 Mar;134(2):327-339.
PMID: 33558947 DOI: 10.1007/s10265-021-01257-9

Glucosinolates (GSLs) are plant secondary metabolites consisting of sulfur and nitrogen, commonly found in Brassicaceae crops, such as Arabidopsis thaliana. These compounds are known for their roles in plant defense mechanisms against pests and pathogens. 'Guilt-by-association' (GBA) approach predicts genes encoding proteins with similar function tend to share gene expression pattern generated from high throughput sequencing data. Recent studies have successfully identified GSL genes using GBA approach, followed by targeted verification of gene expression and metabolite data. Therefore, a GSL co-expression network was constructed using known GSL genes obtained from our in-house database, SuCComBase. DPClusO was used to identify subnetworks of the GSL co-expression network followed by Fisher's exact test leading to the discovery of a potential gene that encodes the ARIA-interacting double AP2-domain protein (ADAP) transcription factor (TF). Further functional analysis was performed using an effective gene silencing system known as CRES-T. By applying CRES-T, ADAP TF gene was fused to a plant-specific EAR-motif repressor domain (SRDX), which suppresses the expression of ADAP target genes. In this study, ADAP was proposed as a negative regulator in aliphatic GSL biosynthesis due to the over-expression of downstream aliphatic GSL genes (UGT74C1 and IPMI1) in ADAP-SRDX line. The significant over-expression of ADAP gene in the ADAP-SRDX line also suggests the behavior of the TF that negatively affects the expression of UGT74C1 and IPMI1 via a feedback mechanism in A. thaliana.
A Comprehensive Gene Inventory for Glucosinolate Biosynthetic Pathway in Arabidopsis thaliana

Harun S, Abdullah-Zawawi MR, Goh HH, Mohamed-Hussein ZA

J Agric Food Chem, 2020 Jul 15;68(28):7281-7297.
PMID: 32551569 DOI: 10.1021/acs.jafc.0c01916

Glucosinolates (GSLs) are plant secondary metabolites comprising sulfur and nitrogen mainly found in plants from the order of Brassicales, such as broccoli, cabbage, and Arabidopsis thaliana. The activated forms of GSL play important roles in fighting against pathogens and have health benefits to humans. The increasing amount of data on A. thaliana generated from various omics technologies can be investigated more deeply in search of new genes or compounds involved in GSL biosynthesis and metabolism. This review describes a comprehensive inventory of A. thaliana GSLs identified from published literature and databases such as KNApSAcK, KEGG, and AraCyc. A total of 113 GSL genes encoding for 23 transcription components, 85 enzymes, and five protein transporters were experimentally characterized in the past two decades. Continuous efforts are still on going to identify all molecules related to the production of GSLs. A manually curated database known as SuCCombase (http://plant-scc.org) was developed to serve as a comprehensive GSL inventory. Realizing lack of information on the regulation of GSL biosynthesis and degradation mechanisms, this review also includes relevant information and their connections with crosstalk among various factors, such as light, sulfur metabolism, and nitrogen metabolism, not only in A. thaliana but also in other crucifers.
Temporal gene expression profiling of maslinic acid-treated Raji cells

Lau WM, Subramaniam M, Goh HH, Lim YM

Mol Omics, 2021 04 19;17(2):252-259.
PMID: 33346776 DOI: 10.1039/d0mo00168f

Maslinic acid is a novel phytochemical reported to target multiple signaling pathways. A complete gene expression profile was therefore constructed to illustrate the anti-tumourigenesis effects of maslinic acid in Raji cells across five time-points. Microarray analysis was used to identify genes that were differentially expressed in maslinic acid treated Raji cells at 0, 4, 8, 12, 24 and 48 h. Extracted RNA was hybridized using the AffymetrixGeneChip to obtain expression profiles. A total of 109 genes were found to be significantly expressed over a period of 48 hours. By 12 hours, maslinic acid regulates the majority of genes involved in the cell cycle, p53 and NF-κB signaling pathways. At the same time, XAF1, APAF1, SESN3, and TP53BP2 were evidently up-regulated, while oncogenes, FAIM, CD27, and RRM2B, were down-regulated by at least 2-fold. In conclusion, maslinic acid shows an hourly progression of gene expression in Raji cells.
Fulltext Transcriptomic data of Arabidopsis thaliana hypocotyl upon suppression of expansin genes

Ilias IA, Airianah OB, Baharum SN, Goh HH

Genom Data, 2017 Jun;12:132-133.
PMID: 28529882 DOI: 10.1016/j.gdata.2017.05.002

Expansin is a cell wall loosening protein without hydrolytic activity, which allows cell expansion by influencing cell wall extensibility. Previous studies showed that the suppression of expansin genes (EXPA1, EXPA3, EXPA5 and EXPA10) resulted in defective organ growth and altered cell wall chemical composition [1,2]. However, the molecular mechanism on how the suppression of non-enzymatic expansin expression can result in widespread effects on plant cell wall and organ growth is still unclear. In this study, we performed transcriptomic analysis on the hypocotyls of previously reported transgenic Arabidopsis line [1] to investigate the effects of expansin gene suppression on the global gene expression pattern, particularly on the cell wall related genes.
Fulltext Mass spectrometry data of metabolomics analysis of Nepenthes pitchers

Rosli MAF, Azizan KA, Baharum SN, Goh HH

Data Brief, 2017 Oct;14:295-297.
PMID: 28795107 DOI: 10.1016/j.dib.2017.07.068

Hybridisation plays a significant role in the evolution and diversification of plants. Hybridisation among Nepenthes species is extensive, either naturally or man-made. To investigate the effects of hybridisation on the chemical compositions, we carried out metabolomics study on pitcher tissue of Nepenthes ampullaria, Nepenthes rafflesiana and their hybrid, Nepenthes × hookeriana. Pitcher samples were harvested and extracted in methanol:chloroform:water via sonication-assisted extraction before analysed using LC-TOF-MS. MS data were analysed using XCMS online version 2.2.5. This is the first MS data report towards the profiling, identification and comprehensive comparison of metabolites present in Nepenthes species.
Fulltext Transcriptomic data of Arabidopsis hypocotyl overexpressing a heterologous CsEXPA1 gene

Ilias IA, Airianah OB, Baharum SN, Goh HH

Data Brief, 2017 Dec;15:320-323.
PMID: 29214193 DOI: 10.1016/j.dib.2017.09.050

Expansin increases cell wall extensibility to allow cell wall loosening and cell expansion even in the absence of hydrolytic activity. Previous studies showed that excessive overexpression of expansin gene resulted in defective growth (Goh et al., 2014; Rochange et al., 2001) [1,2] and altered cell wall chemical composition (Zenoni et al., 2011) [3]. However, the molecular mechanism on how the overexpression of non-enzymatic cell wall protein expansin can result in widespread effects on plant cell wall and organ growth remains unclear. We acquired transcriptomic data on previously reported transgenic Arabidopsis line (Goh et al., 2014) [1] to investigate the effects of overexpressing a heterologus cucumber expansin gene (CsEXPA1) on the global gene expression pattern during early and late phases of etiolated hypocotyl growth.
Methyl jasmonate-induced compositional changes of volatile organic compounds in Polygonum minus leaves

Rahnamaie-Tajadod R, Goh HH, Mohd Noor N

J Plant Physiol, 2019 Sep;240:152994.
PMID: 31226543 DOI: 10.1016/j.jplph.2019.152994

Polygonum minus Huds. is a medicinal aromatic plant rich in terpenes, aldehydes, and phenolic compounds. Methyl jasmonate (MeJA) is a plant signaling molecule commonly applied to elicit stress responses to produce plant secondary metabolites. In this study, the effects of exogenous MeJA treatment on the composition of volatile organic compounds (VOCs) in P. minus leaves were investigated by using a metabolomic approach. Time-course changes in the leaf composition of VOCs on days 1, 3, and 5 after MeJA treatment were analyzed through solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS). The VOCs found in MeJA-elicited leaves were similar to those found in mock-treated leaves but varied in quantity at different time points. We focused our analysis on the content and composition of monoterpenes, sesquiterpenes, and green leaf volatiles (GLVs) within the leaf samples. Our results suggest that MeJA enhances the activity of biosynthetic pathways for aldehydes and terpenes in P. minus. Hence, the production of aromatic compounds in this medicinal herb can be increased by MeJA elicitation. Furthermore, the relationship between MeJA elicitation and terpene biosynthesis in P. minus was shown through SPME-GC-MS analysis of VOCs combined with transcriptomic analysis of MeJA-elicited P. minus leaves from our previous study.
Variable expansin expression in Arabidopsis leads to different growth responses

Goh HH, Sloan J, Malinowski R, Fleming A

J Plant Physiol, 2014 Feb 15;171(3-4):329-39.
PMID: 24144490 DOI: 10.1016/j.jplph.2013.09.009

Expansins have long been implicated in the control of cell wall extensibility. However, despite ample evidence supporting a role for these proteins in the endogenous mechanism of plant growth, there are also examples in the literature where the outcome of altered expansin gene expression is difficult to reconcile with a simplistic causal linkage to growth promotion. To investigate this problem, we report on the analysis of transgenic Arabidopsis plants in which a heterologous cucumber expansin can be inducibly overexpressed. Our results indicate that the effects of expansin expression on growth depend on the degree of induction of expansin expression and the developmental pattern of organ growth. They support the role of expansin in directional cell expansion. They are also consistent with the idea that excess expansin might itself impede normal activities of cell wall modifications, culminating in both growth promotion and repression depending on the degree of expression.
Fulltext Differential Gene Expression Analysis in Polygonum minus Leaf upon 24 h of Methyl Jasmonate Elicitation

Rahnamaie-Tajadod R, Loke KK, Goh HH, Noor NM

Front Plant Sci, 2017;8:109.
PMID: 28220135 DOI: 10.3389/fpls.2017.00109

Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used as medicine. This plant produces diverse secondary metabolites such as phenolic compounds and their derivatives, which are known to have roles in plant abiotic and biotic stress responses. Methyl jasmonate (MeJA) is a plant signaling molecule that triggers transcriptional reprogramming in secondary metabolism and activation of defense responses against many biotic and abiotic stresses. However, the effect of MeJA elicitation on the genome-wide expression profile in the leaf tissue of P. minus has not been well-studied due to the limited genetic information. Hence, we performed Illumina paired-end RNA-seq for de novo reconstruction of P. minus leaf transcriptome to identify differentially expressed genes (DEGs) in response to MeJA elicitation. A total of 182,111 unique transcripts (UTs) were obtained by de novo assembly of 191.57 million paired-end clean reads using Trinity analysis pipeline. A total of 2374 UTs were identified to be significantly up-/down-regulated 24 h after MeJA treatment. These UTs comprising many genes related to plant secondary metabolite biosynthesis, defense and stress responses. To validate our sequencing results, we analyzed the expression of 21 selected DEGs by quantitative real-time PCR and found a good correlation between the two analyses. The single time-point analysis in this work not only provides a useful genomic resource for P. minus but also gives insights on molecular mechanisms of stress responses in P. minus.

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