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Hoe-Han Goh

Universiti Kebangsaan Malaysia, Institute of Systems Biology, Faculty Member

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I'm a research fellow at INBIOSIS, UKM where my research interests are in the field of plant molecular biology and functional genomics for crop improvement and molecular discovery, particularly on plant development, secondary metabolites and phytonutrients.I'm looking for opportunity for collaborative research with like-minded researchers from around the world.
Address: Bangi, Selangor, Malaysia

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Papers by Hoe-Han Goh

Ten simple rules for writing scientific op-ed articles

PLOS Computational Biology, Sep 17, 2020

Methyl jasmonate-induced compositional changes of volatile organic compounds in Polygonum minus leaves

Journal of Plant Physiology, Sep 1, 2019

Polygonum minus Huds. is a medicinal aromatic plant rich in terpenes, aldehydes, and phenolic com... more 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. Timecourse 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. 1. Introduction Plant interactions with the environment lead to the accumulation of diverse natural products that are believed to influence plant fitness (Bourgaud et al., 2001). These natural products are secondary metabolites that mostly function as defense molecules against adverse conditions and play a role in plant communications with other plants, animals, and/or microbes (Spinelli et al., 2011). Volatile organic compounds (VOCs) are a large group of secondary metabolites. VOCs play a role in mediating plant responses to stress, defense, and reproduction (Pierik et al., 2014). VOCs help plants attract pollinators and seed dispersers, defend against herbivores and pathogens (below-and above-ground), protect against fungi and parasites, and protect against abiotic stresses, such as extreme light and temperature (Dudareva et al., 2013). Terpenoids, phenylpropanoids, and C6 green-leaf volatiles (GLVs) are the dominant compounds among the VOCs in many plants (Holopainen and Gershenzon, 2010; ul Hassan et al., 2015). Elicitation is the most practical way of inducing the biosynthesis of various defense metabolites in plants or tissue cultures (Angelova et al., 2006; Namdeo, 2007). Elicitation using chemicals related to plant signaling molecules is the most effective way to increase secondary metabolite production (Hussain et al., 2012). Jasmonates (JAs), which comprise jasmonic acid (JA) and its volatile methyl ester (methyl jasmonate, MeJA), are plant signaling molecules commonly applied as elicitors (Pauwels et al., 2009). Most studies, such as those in Norway spruce (Martin et al., 2003), Scots pine, and evergreen oak (Semiz et al., 2012), have focused on the emissions compared to the content of VOCs after MeJA elicitation. This is in contrast to studies on the MeJA-elicited roots of P. minus (Ismail et al., 2011) and exogenous application of JAs to stimulate the production of bioactive compounds, such as terpenes in Centella asiatica (Tugizimana et al., 2015), anthocyanin in Vitis vinifera(Tassoni et al., 2012), rosmarinic acid in Mentha piperita (Krzyzanowska et al., 2012), bacoside A in Bacopa monnieri(Sharma et al., 2013), andrographolide in Andrographis paniculata (Sharma et al., 2015), and plumbagin in the hairy roots of Plumbago indica (Gangopadhyay et al., 2011).

Omics Approaches in Uncovering Molecular Evolution and Physiology of Botanical Carnivory

Plants, Jan 15, 2023

This article is an open access article distributed under the terms and conditions of the Creative... more

Transformation of PRT6 RNAi construct into tomato (Solanum lycopersicum) cv. Micro-Tom

Nucleation and Atmospheric Aerosols, 2018

PROTEOLYSIS 6 plays major role in the N-end rule pathway as N-recognin which functions as E3 liga... more PROTEOLYSIS 6 plays major role in the N-end rule pathway as N-recognin which functions as E3 ligase enzyme. It mediates ubiquitin processes that lead to degradation of unstable substrate protein. The aim of the current study is to transform the PRT6 gene into tomato (Solanum lycopersicum) from the cultivar Micro-Tom and to investigate its function in regulating ripening in tomato fruits. The PRT6_RNAi construct was successfully transformed into Agrobacterium C58 via heat shock method and transformed into seven days old cotyledon explants. Factors affecting transformation efficiency such as co-cultivation time and type of plant growth regulator combination were evaluated. Results from this study found that pre-cultured cotyledons from seven days old seedlings incubated for 2 days in co-cultivation medium increased shoot regeneration. Plant growth hormones zeatin combine with auxin produced a higher number of callus formation but lower shoot proliferation and transformation frequency compared to treatments of single plant hormone in the selection medium. Polymerase chain reaction (PCR) was performed on the regenerated shoots to confirm the integration of PRT6 fragment into the genome of transgenic plants. Based on PCR analysis, all putative shoots were positive transformants.PROTEOLYSIS 6 plays major role in the N-end rule pathway as N-recognin which functions as E3 ligase enzyme. It mediates ubiquitin processes that lead to degradation of unstable substrate protein. The aim of the current study is to transform the PRT6 gene into tomato (Solanum lycopersicum) from the cultivar Micro-Tom and to investigate its function in regulating ripening in tomato fruits. The PRT6_RNAi construct was successfully transformed into Agrobacterium C58 via heat shock method and transformed into seven days old cotyledon explants. Factors affecting transformation efficiency such as co-cultivation time and type of plant growth regulator combination were evaluated. Results from this study found that pre-cultured cotyledons from seven days old seedlings incubated for 2 days in co-cultivation medium increased shoot regeneration. Plant growth hormones zeatin combine with auxin produced a higher number of callus formation but lower shoot proliferation and transformation frequency compared to treatments ...

Sequence analysis of PROTEOLYSIS 6 from Solanum lycopersicum

Nucleation and Atmospheric Aerosols, 2018

Transcriptome analysis of Carica papaya embryogenic callus upon De-etiolated 1 ( DET 1) gene suppression

Genomics data, Jun 1, 2017

Identification of calcium-dependent protein kinase (CDPK): A multi-functional gene family in Rafflesia cantleyi

Nucleation and Atmospheric Aerosols, 2016

Rafflesia, a parasitic plant that belongs to the Rafflesiaceae family, is notable for producing t... more Rafflesia, a parasitic plant that belongs to the Rafflesiaceae family, is notable for producing the largest flowers in the world. This study focused on identification of Calcium-dependent protein kinases (CDPKs) due to their vital roles in plant growth and development, biotic and abiotic stress responses, and hormone signaling. RNA-seq data generated from three bud stages of Rafflesia cantleyi ie BS1, BS2, and BS3 and were assembled. Based on the BLAST searches of Rafflesia unique transcripts (UTs) to Arabidopsis TAIR database, a total of 14 unique transcripts (UTs) were identified as CDPK1 to CDPK5, CDPK7 to CDPK11, CDPK16, CDPK18, CDPK19, and CDPK28. These genes are expressed at all three bud stages of R. cantleyi with up-regulation pattern at BS1 vs. BS2 and BS2 vs. BS3. This result shows that the expression of CDPK gene family increases by developmental progress in Rafflesia in order to regulate biochemical and molecular changes at the cellular level in response to exposure to environmental changes. H...

Transformasi Gen Proteolisis 6 (PRT6) Berperantarakan Agrobacterium tumefaciens ke dalam Kotiledon Tomato kultivar Micro Tom

Sains Malaysiana, Jul 31, 2018

Transformasi Gen Proteolisis 6 (PRT6) Berperantarakan Agrobacterium tumefaciens ke dalam Kotiledo... more Transformasi Gen Proteolisis 6 (PRT6) Berperantarakan Agrobacterium tumefaciens ke dalam Kotiledon Tomato kultivar Micro Tom (Agrobacterium tumefaciens Mediated Transformation of the Proteolysis 6 (PRT6) Gene into Cotyledons of Tomato cv. Micro Tom) INTAN ELYA SUKA, NUR FARHANA ROSLAN, BEE LYNN CHEW, HOE HAN GOH, ZAMRI ZAINAL & NURULHIKMA MD ISA* ABSTRAK Gen Proteolisis 6 (PRT6) merupakan gen yang memainkan peranan penting dalam tapak jalan N-end rule dan berfungsi sebagai enzim E3 ligase. PRT6 berperanan dalam pengenalan protein sasaran bagi proses degradasi. Objektif utama kajian ini adalah untuk mentransformasi konstruk RNAi PRT6 ke dalam tomato berperantarakan Agrobacterium tumefaciens. Ini bertujuan untuk memahami peranan tapak jalan N-end rule semasa proses pemasakan buah. Beberapa faktor yang memberi kesan kepada transformasi seperti masa ko-penanaman dan juga kepekatan antibiotik yang digunakan telah dioptimumkan. Keputusan kajian menunjukkan pengeraman kotiledon selama 48 jam pada medium ko-penanaman dapat meningkatkan penghasilan kalus sebanyak 61% manakala penggunaan 500 mg/L antibiotik karbenisilin dalam medium regenerasi pucuk dapat mengurangkan kontaminasi A. tumefaciens sehingga 5.2%. Selain itu, strain A. tumefaciens C58 merupakan strain A. tumefaciens yang paling sesuai digunakan sebagai perantara dalam kajian ini. Tindak balas berantai polimerase (PCR) telah dijalankan pada pucuk yang terhasil untuk mengesahkan integrasi fragmen PRT6 ke dalam genom tomato. Berdasarkan analisis PCR, kesemua tujuh pucuk putatif transgenik adalah merupakan transforman positif.

Microarray dataset of transgenic rice overexpressing Abp57

Data in Brief, Oct 1, 2017

Data on RNA-seq analysis of Garcinia mangostana L. seed development

Data in Brief, Feb 1, 2018

Table 2 Statistics of raw and clean reads and bases of mangosteen seed development transcriptome.... more

Protease activity is maintained in <scp> <i>Nepenthes ampullaria</i> </scp> digestive fluids depleted of endogenous proteins with compositional changes

Physiologia Plantarum, Sep 7, 2021

Nepenthes ampullaria is a unique carnivorous tropical pitcher plant with the detritivorous capabi... more Nepenthes ampullaria is a unique carnivorous tropical pitcher plant with the detritivorous capability of sequestering nutrients from leaf litter apart from being insectivorous. The changes in the protein composition and protease activity of its pitcher fluids during the early opening of pitchers (D0 and D3C) were investigated via a proteomics approach and a controlled protein depletion experiment (D3L). A total of 193 proteins were identified. Common proteins such as pathogenesis‐related protein, proteases (Nep [EC:3.4.23.12], SCP [EC:3.4.16.‐]), peroxidase [EC:1.11.1.7], GDSL esterase/lipase [EC:3.1.1.‐], and purple acid phosphatase [EC:3.1.3.2] were found in high abundance in the D0 pitchers and were replenished in D3L samples. This reflects their importance for biological processes upon pitcher opening. Meanwhile, prey‐inducible chitinases [EC:3.2.1.14] were found in D0 but not in D3C and D3L samples, which suggests their degradation in the absence of prey. Protease activity assays demonstrated the replenishment of proteases in D3L with similar levels of proteolytic activities to that of D3C samples. This supports a feedback mechanism and signaling in the molecular regulation of endogenous protein secretion, turnover, and activity in Nepenthes pitcher fluids. Furthermore, we also discovered several new enzymes (XTH [EC:2.4.1.207], PAE [EC:3.1.1.98]) with possible functions in cell wall degradation that could contribute to the detritivory habit of N. ampullaria.

Transcriptomic data of Arabidopsis thaliana hypocotyl upon suppression of expansin genes

Genomics data, Jun 1, 2017

DNA-seq analysis of Garcinia mangostana

Genomics data, Mar 1, 2016

Mangosteen (Garcinia mangostana Linn.) is a tropical tree mainly found in South East Asia and con... more Mangosteen (Garcinia mangostana Linn.) is a tropical tree mainly found in South East Asia and considered as "the queen of fruits". The asexually produced fruit is dark purple or reddish in color, with white flesh which is slightly acidic with sweet flavor and a pleasant aroma. The purple pericarp tissue is rich in xanthones which are useful for medical purposes. We performed the first genome sequencing of this commercially important fruit tree to study its genome composition and attempted draft genome assembly. Raw reads of the DNA sequencing project have been deposited to SRA database with the accession number SRX1426419.

Proteomic analysis of pitcher fluid from Nepenthes × ventrata

Data in Brief, Apr 1, 2018

The carnivorous plants of genus Nepenthes produce unique pitchers containing secretory glands, wh... more The carnivorous plants of genus Nepenthes produce unique pitchers containing secretory glands, which secrete proteins into the digestive fluid. We investigated protein profile in the pitcher fluid during the first three days of opening to understand carnivory trait of Nepenthes × ventrata. The proteome analysis of pitcher fluid from N. × ventrata was performed by label-free quantitative liquid chromatography mass spectrometry (nLC-MS/MS ALL). Raw MS data have been deposited to the ProteomeXchange with identifier PXD007251. This dataset allows the identification and quantification of proteins from pitcher fluids to elucidate proteins involved in carnivory physiology of Nepenthes species.

Mass spectrometry data of metabolomics analysis of Nepenthes pitchers

Data in Brief, Oct 1, 2017

Hybridisation plays a significant role in the evolution and diversification of plants. Hybridisat... more 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.

Production of Transgenic Rice (indica 1 cv. MR219) Overexpressing Abp57 Gene through Agrobacterium-Mediated Transformation

Sains Malaysiana, May 31, 2017

Agrobacterium-mediated transformation of indica rice is undoubtedly a challenging task due to the... more Agrobacterium-mediated transformation of indica rice is undoubtedly a challenging task due to the rice recalcitrant nature to transformation process. Therefore, optimization of the transformation protocol is important for specific indica rice cultivar to ensure effectiveness of the transformation. In this study, crucial parameters affecting Agrobacteriummediated transformation were optimized to obtain transgenic rice of local rice cultivar (indica MR219). Embryogenic calli were chosen for inoculation with Agrobacterium tumefaciens strain LBA4404 harbouring a binary vector pH2GW7-ABP57 containing gene of interest, Auxin binding protein 57 (Abp57). The parameters that have been optimized were the immersion time, co-cultivation period, acetosyringone concentration and co-cultivation temperature. A total of four days co-cultivation period and 30 min immersion of embryogenic callus are optimum for the transformation of MR219 with transformation efficiency of 26.4% and 16.0%, respectively. Acetosyringone at 200 μM and co-cultivation at 28°C also gave the highest transformation efficiency (14.4 and 18.4%, respectively). Meanwhile, inclusion of 20 g/L maltose+20 g/L sorbitol into the regeneration media has significantly improve the transformed somatic embryos growth and increase the regeneration efficiency up to 40.0%. The results of polymerase chain reaction (PCR) and reverse transcription-polymerase chain reaction (RT-PCR) indicated that the transgene was successfully integrated and overexpressed in transgenic rice of MR219. In conclusion, significant improvement in transformation efficiency for rice cv. MR219 has been obtained by using the optimised protocol for transformation and regeneration developed in this study.

RNA-seq analysis of mangosteen ( Garcinia mangostana L.) fruit ripening

Genomics data, Jun 1, 2017

Protein replenishment in pitcher fluids of Nepenthes × ventrata revealed by quantitative proteomics (SWATH-MS) informed by transcriptomics

Journal of Plant Research, Aug 17, 2019

Carnivorous plants capture and digest insects for nutrients, allowing them to survive in soil dep... more Carnivorous plants capture and digest insects for nutrients, allowing them to survive in soil deprived of nitrogenous nutrients. Plants from the genus Nepenthes produce unique pitchers containing secretory glands, which secrete enzymes into the digestive fluid. We performed RNA-seq analysis on the pitcher tissues and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis on the pitcher fluids of Nepenthes × ventrata to study protein expression in this carnivory organ during early days of pitcher opening. This transcriptome provides a sequence database for pitcher fluid protein identification. A total of 32 proteins of diverse functions were successfully identified in which 19 proteins can be quantified based on label-free quantitative proteomics (SWATH-MS) analysis while 16 proteins were not reported previously. Our findings show that certain proteins in the pitcher fluid were continuously secreted or replenished after pitcher opening, even without any prey or chitin induction. We also discovered a new aspartic proteinase, Nep6, secreted into pitcher fluid. This is the first SWATH-MS analysis of protein expression in Nepenthes pitcher fluid using a species-specific reference transcriptome. Taken together, our study using a gel-free shotgun proteomics informed by transcriptomics (PIT) approach showed the dynamics of endogenous protein secretion in the digestive organ of N. × ventrata and provides insights on protein regulation during early pitcher opening prior to prey capture.

Integrative Multi-Omics Through Bioinformatics

Advances in Experimental Medicine and Biology, 2018

This chapter introduces different aspects of bioinformatics with a brief discussion in the system... more 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.

Transcriptome analysis of<i>Polygonum minus</i>reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids

PeerJ, Feb 28, 2017

Background: Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnom... more Background: Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this important family of medicinal plants. The limited genetic information from the public expressed sequences tag (EST) library hinders further study on molecular mechanisms underlying secondary metabolite production. Methods: In this study, we performed a hybrid assembly of 454 and Illumina sequencing reads from Polygonum minus root and leaf tissues, respectively, to generate a combined transcriptome library as a reference. Results: A total of 34.37 million filtered and normalized reads were assembled into 188,735 transcripts with a total length of 136.67 Mbp. We performed a similarity search against all the publicly available genome sequences and found similarity matches for 163,200 (86.5%) of Polygonum minus transcripts, largely from Arabidopsis thaliana (58.9%). Transcript abundance in the leaf and root tissues were estimated and validated through RT-qPCR of seven selected transcripts involved in the biosynthesis of phenylpropanoids and flavonoids. All the transcripts were annotated against KEGG pathways to profile transcripts related to the biosynthesis of secondary metabolites. Discussion: This comprehensive transcriptome profile will serve as a useful sequence resource for molecular genetics and evolutionary research on secondary metabolite biosynthesis in Polygonaceae family. Transcriptome assembly of Polygonum minus can be accessed at http://prims.researchfrontier.org/index.php/ dataset/transcriptome.