Benjamin Lau Yii Chung

@mpob.gov.my

Advanced Biotechnology and Breeding Centre
Malaysian Palm Oil Board

Benjamin completed his Bachelor's and Master’s Degrees with the National University of Malaysia from 1999 – 2006. He started his career with the Malaysian Palm Oil Board (MPOB) in 2007 as a research scientist for the then Biochemistry Group. From 2007-2011, he was tasked with setting up the first proteomics-based core facility in MPOB and trained personnel in proteomics-based research. Towards the end of 2011, Benjamin was awarded a scholarship under Malaysian Plan (RMK) for a Ph.D. program at Lincoln University – AgResearch, Christchurch, New Zealand. He completed his Ph.D. in Biochemistry, specializing in plant proteomics, in June 2015. Thereafter, he continues his position as a research scientist at Proteomics and Metabolomics Unit, MPOB, until today. He is currently the Principal Research Scientist and Group Leader for Proteomics.

EDUCATION

Ph.D. (Biochemistry), New Zealand

RESEARCH INTERESTS

Mechanism of fatty acid production in oil palm using the proteomics approach and industrial-related problems such as oil palm disease and the production of bioactive compounds from industrial waste.

Scopus Publications

203

Scholar Citations

Scholar h-index

Scholar i10-index

Scopus Publications

Geographical Diversity of Proteomic Responses to Cold Stress in the Fungal Genus Pseudogymnoascus
Nurlizah Abu Bakar, Benjamin Yii Chung Lau, Marcelo González-Aravena, Jerzy Smykla, Beata Krzewicka, Saiful Anuar Karsani, and Siti Aisyah Alias
Springer Science and Business Media LLC
AbstractIn understanding stress response mechanisms in fungi, cold stress has received less attention than heat stress. However, cold stress has shown its importance in various research fields. The following study examined the cold stress response of six Pseudogymnoascus spp. isolated from various biogeographical regions through a proteomic approach. In total, 2541 proteins were identified with high confidence. Gene Ontology enrichment analysis showed diversity in the cold stress response pathways for all six Pseudogymnoascus spp. isolates, with metabolic and translation-related processes being prominent in most isolates. 25.6% of the proteins with an increase in relative abundance were increased by more than 3.0-fold. There was no link between the geographical origin of the isolates and the cold stress response of Pseudogymnoascus spp. However, one Antarctic isolate, sp3, showed a distinctive cold stress response profile involving increased flavin/riboflavin biosynthesis and methane metabolism. This Antarctic isolate (sp3) was also the only one that showed decreased phospholipid metabolism in cold stress conditions. This work will improve our understanding of the mechanisms of cold stress response and adaptation in psychrotolerant soil microfungi, with specific attention to the fungal genus Pseudogymnoascus.

Proteomic and Morphological Analysis of Bone and Articular Cartilage Changes in Osteoarthritic Rabbits Supplemented with Edible Bird’s Nest (EBN)
Sharifah Zakiah Syed Sulaiman, Nor Shahira Solehah Umran, Suhaila Mohamed, Jalila Abu, Angela Min Hwei Ng, Benjamin Yii Chung Lau, Kok Song Lai, Nazhan Ilias, Seng Fong Lau, and Mokrish Ajat
Penerbit UTM Press
This study is aimed at assessing the effects of Edible Bird’s Nest (EBN) on subchondral bone, articular cartilage and the expression of proteins in synovial fluid by micro-CT evaluation and histological analysis. 54 New Zealand white rabbits were induced by intra-articular injection of monosodium iodoacetate (8 mg) and divided into four groups: negative control (n=9): non-treated osteoarthritis; positive control (n=15): OA + diclofenac sodium 2 mg/kg daily orally; low dosage (n=15): OA + 75 mg/kg hydrolyzed EBN; and high dosage (n=15): OA + 150 mg/kg hydrolyzed EBN. The joints were harvested and subjected to micro-CT analysis and histological evaluation, and the synovial fluid was subjected to LCMS/MS analysis. Micro-CT analysis showed an increase in bone volume and a decrease in total porosity in the treatment group that showed bone integrity improvement. Histopathological results revealed comparable changes between the positive control group and the EBN treatment group. There was upregulation of proteins involved in the resolution of inflammation and downregulation of proteins associated with the bone resorption process. Morphology evaluation showed that EBN supplementation has a bone-improving effect by inhibiting osteoclastic activity. Protein expression showed chondroprotection and bone improvement through the action of several proteins via various signaling pathways. The morphological and molecular findings suggest the potential use of EBN as beneficial alternative for osteoarthritis treatment by improving bone quality and modulating inflammatory responses.

Integrative tissue-resolved proteomics and metabolomics analysis of oil palm (Elaeis guineensis Jacq.) fruit provides insights into stilbenoid biosynthesis at the interface of primary and secondary metabolism
Hasliza Hassan, Noor Idayu Tahir, Nurul Liyana Rozali, Benjamin Yii Chung Lau, Abrizah Othman, Wolfram Weckwerth, and Umi Salamah Ramli
Elsevier BV

Enhanced azadirachtin production in neem (Azadirachta indica) callus through NaCl elicitation: Insights into differential protein regulation via shotgun proteomics
Siti Ainnsyah Omar, Sharmilla Ashokhan, Nazia Abdul Majid, Saiful Anuar Karsani, Benjamin Yii Chung Lau, and Jamilah Syafawati Yaacob
Elsevier BV

Proteomic characterization of Pseudogymnoascus spp. isolates from polar and temperate regions
Nurlizah Abu Bakar, Benjamin Lau Yii Chung, Jerzy Smykla, Saiful Anuar Karsani, and Siti Aisyah Alias
Informa UK Limited
Proteomics has been used extensively in the field of mycology, mainly in trying to understand the complex network of protein-protein interactions that has been implicated in the molecular functions of fungi. It is also a useful tool to compare metabolic differences within a genus. Species of Pseudogymnoascus, a genus under the phyla Ascomycota, have been shown to play an important role in the soil environment. They have been found in both polar and temperate regions and are a known producer of many extracellular hydrolases that contribute to soil decomposition. Despite the apparent importance of Pseudogymnoascus spp. in the soil ecosystem, investigations into their molecular functions are still very limited. In the present study, proteomic characterization of six Pseudogymnoascus spp. isolated from three biogeographic regions (the Arctic, Antarctic, and temperate regions) was carried out using tandem mass spectrometry. Prior to proteomic analysis, the optimization for protein extraction was carried out. Trichloroacetic acid‑acetone‑phenol was found to be the best extraction method to be used for proteomic profiling of Pseudogymnoascus spp. The proteomic analysis identified 2003 proteins that were successfully mapped to the UniProtKB database. The identified proteins were clustered according to their biological processes and molecular functions. The shared proteins found in all Pseudogymnoascus spp. (1201 proteins) showed a significantly close relationship in their basic cellular functions, despite differences in morphological structures. Analysis of Pseudogymnoascus spp. proteome also identified proteins that were unique to each region. However, a high number of these proteins belonged to protein families of similar molecular functions, namely, transferases and hydrolases. Our proteomic data can be used as a reference for Pseudogymnoascus spp. across different global regions and a foundation for future soil ecosystem function research.

Comparative proteomic and metabolomic studies between partial resistant and susceptible oil palm reveal the molecular mechanism associated with Ganoderma boninense infection
Abrizah Othman, Benjamin Yii Chung Lau, Zain Nurazah, Syahanim Shahwan, Mohd Hefni Rusli, Rajinder Singh, Meilina Ong Abdullah, Marhalil Marjuni, Zulkifli Yaakub, Shamala Sundram,et al.
Elsevier BV

Quantitative proteomics analysis of permethrin and temephos-resistant Ae. aegypti revealed diverse differentially expressed proteins associated with insecticide resistance from Penang Island, Malaysia
Abubakar Shettima, Intan Haslina Ishak, Benjamin Lau, Hadura Abu Hasan, Noorizan Miswan, and Nurulhasanah Othman
Public Library of Science (PLoS)
Synthetic insecticides are the primary vector control method used globally. However, the widespread use of insecticides is a major cause of insecticide-resistance in mosquitoes. Hence, this study aimed at elucidating permethrin and temephos-resistant protein expression profiles in Ae. aegypti using quantitative proteomics. In this study, we evaluated the susceptibility of Ae. aegypti from Penang Island dengue hotspot and non-hotspot against 0.75% permethrin and 31.25 mg/l temephos using WHO bioassay method. Protein extracts from the mosquitoes were then analysed using LC–ESI–MS/MS for protein identification and quantification via label-free quantitative proteomics (LFQ). Next, Perseus 1.6.14.0 statistical software was used to perform differential protein expression analysis using ANOVA and Student’s t-test. The t-test selected proteins with≥2.0-fold change (FC) and ≥2 unique peptides for gene expression validation via qPCR. Finally, STRING software was used for functional ontology enrichment and protein-protein interactions (PPI). The WHO bioassay showed resistance with 28% and 53% mortalities in adult mosquitoes exposed to permethrin from the hotspot and non-hotspot areas. Meanwhile, the susceptibility of Ae. aegypti larvae revealed high resistance to temephos in hotspot and non-hotspot regions with 80% and 91% mortalities. The LFQ analyses revealed 501 and 557 (q-value <0.05) differentially expressed proteins in adults and larvae Ae. aegypti. The t-test showed 114 upregulated and 74 downregulated proteins in adult resistant versus laboratory strains exposed to permethrin. Meanwhile, 13 upregulated and 105 downregulated proteins were observed in larvae resistant versus laboratory strains exposed to temephos. The t-test revealed the upregulation of sodium/potassium-dependent ATPase β2 in adult permethrin resistant strain, H15 domain-containing protein, 60S ribosomal protein, and PB protein in larvae temephos resistant strain. The downregulation of troponin I, enolase phosphatase E1, glucosidase 2β was observed in adult permethrin resistant strain and tubulin β chain in larvae temephos resistant strain. Furthermore, the gene expression by qPCR revealed similar gene expression patterns in the above eight differentially expressed proteins. The PPI of differentially expressed proteins showed a p-value at <1.0 x 10−16 in permethrin and temephos resistant Ae. aegypti. Significantly enriched pathways in differentially expressed proteins revealed metabolic pathways, oxidative phosphorylation, carbon metabolism, biosynthesis of amino acids, glycolysis, and citrate cycle. In conclusion, this study has shown differentially expressed proteins and highlighted upregulated and downregulated proteins associated with insecticide resistance in Ae. aegypti. The validated differentially expressed proteins merit further investigation as a potential protein marker to monitor and predict insecticide resistance in field Ae. aegypti. The LC-MS/MS data were submitted into the MASSIVE database with identifier no: MSV000089259.

Understanding the effects of carbon and nitrogen starvation on the comparative secretomes of Ganoderma boninense and Ganoderma tornatum
Shahirah Balqis Dzulkafli, Abrizah Othman, Benjamin Yii Chung Lau, Zain Nurazah, Jayanthi Nagappan, Umi Salamah Ramli, and Saiful Anuar Karsani
Elsevier BV

Cross-reactivity analysis of milk proteins from different goat breeds with cow's milk allergens using a proteomic approach
Muzammeer Mansor, Jameel R. Al-Obaidi, Intan Hakimah Ismail, Muhammad Azri Zainal Abidin, Atiqah Farah Zakaria, Benjamin Yii Chung Lau, Aliah Zannierah Mohsin, Rashidah Sukor, Jinap Selamat, Nor Khaizura Mahmud,et al.
Elsevier BV

Higher resolution protein band visualisation via improvement of colloidal CBB-G staining by gel fixation
Nikson Fatt-Ming Chong, Hasnain Hussain, Nur Ezzati Hamdin, David Hong-Sheng Wee, Mehvish Nisar, Wei-Jie Yan, Benjamin Yii Chung Lau, and Norasfaliza Rahmad
Springer Science and Business Media LLC
Abstract Background Gel staining is a crucial step that allows the visualisation of proteins separated through SDS-PAGE. Colloidal Coomassie Brilliant Blue-G (CBB-G) staining is among the commonly used visualisation methods due to several factors such as compatibility with mass spectrometry (MS) analysis, sensitivity, reproducibility, and simplicity of the staining process. However, the standard colloidal CBB-G staining has a drawback: the resolution of protein bands is compromised because of diffusion of proteins during the washing step. Results A modification to an established colloidal CBB-G staining method, which greatly increases the resolution of protein bands, is described. The addition of a fixation step, which prevents the diffusion of proteins during the washing step, is shown to increase protein band resolution. Conclusion The fixation step is fast, flexible, and also retains all the advantages of the standard colloidal CBB-G staining methods. As there are no drawbacks, incorporating this fixation step into the standard colloidal CBB-G staining is an easy way to improve protein visualisation in SDS-PAGE. Graphical Abstract

Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in Vibrio parahaemolyticus
Nur Afiqah Md Yusof, Siti Aisyah Razali, Azyyati Mohd Padzil, Benjamin Yii Chung Lau, Syarul Nataqain Baharum, Nor Azlan Nor Muhammad, Nurul Hanun Ahmad Raston, Chou Min Chong, Natrah Fatin Mohd Ikhsan, Magdalena Lenny Situmorang,et al.
MDPI AG
(1) Background: Quorum sensing (QS) is the chemical communication between bacteria that sense chemical signals in the bacterial population to control phenotypic changes through the regulation of gene expression. The inhibition of QS has various potential applications, particularly in the prevention of bacterial infection. QS can be inhibited by targeting the LuxP, a periplasmic receptor protein that is involved in the sensing of the QS signaling molecule known as the autoinducer 2 (AI-2). The sensing of AI-2 by LuxP transduces the chemical information through the inner membrane sensor kinase LuxQ protein and activates the QS cascade. (2) Methods: An in silico approach was applied to design DNA aptamers against LuxP in this study. A method combining molecular docking and molecular dynamics simulations was used to select the oligonucleotides that bind to LuxP, which were then further characterized using isothermal titration calorimetry. Subsequently, the bioactivity of the selected aptamer was examined through comparative transcriptome analysis. (3) Results: Two aptamer candidates were identified from the ITC, which have the lowest dissociation constants (Kd) of 0.2 and 0.5 micromolar. The aptamer with the lowest Kd demonstrated QS suppression and down-regulated the flagellar-assembly-related gene expression. (4) Conclusions: This study developed an in silico approach to design an aptamer that possesses anti-QS properties.

Skin Mucus Proteome Analysis Reveals Disease-Resistant Biomarker Signatures in Hybrid Grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) against Vibrio alginolyticus
Nurhikmah, Annie Christianus, Wan Mohd Syazwan Wan Solahudin, Benjamin Yii Chung Lau, Intan Safinar Ismail, and Low Chen Fei
MDPI AG
Fish skin mucus is the first line of defense that provides physical and chemical barriers against pathogens and toxins. The mucus is produced continuously and sloughed off regularly from the skin to defend against infections through the skin. However, the molecular properties of the mucus content that prevent pathogen invasion are yet to be fully understood. In this study, a proteomic approach using liquid chromatography–mass spectrometry (LCMS) was applied to explore the changes in the mucus protein content of resistant and susceptible groupers in response to Vibrio alginolyticus. The Vibrio-resistant groupers showed no observable clinical sign of infection after the immersion challenge, while the Vibrio-susceptible groupers presented either hemorrhagic- or non-hemorrhagic ulceration of the skin. A comparative proteome analysis on the mucus samples yielded 1488 identified proteins. The immune-related proteins, namely Cystatin B, Complement Component C6, Complement factor 1, Allograft inflammatory factor 1, Deleted in malignant brain tumors protein, MHC class 1 and Annexin A1, that were significantly abundant in the resistant group responded to V. alginolyticus infection. Interestingly, there was an expression of immune-related proteins that possibly could be the non-invasive biomarkers, namely 3-hydroxybutyrate dehydrogenase type 2 and L-rhamnose-binding lectin SML.

ANTIFUNGAL AND ANTIOXIDANT PEPTIDES FROM OIL PALM MESOCARPS
BENJAMIN LAU YII CHUNG
Malaysian Palm Oil Board
Phytochemicals and bioactive peptides have been discovered in oil palm organs such as kernel and leaf, but there is no documented study in isolating peptides with bioactivities from fruit mesocarps. In this work, we aimed to determine the bioactivity of the peptides derived from hydrolysis of oil palm fruit mesocarps. The fruit mesocarps were subjected to enzyme hydrolysis using trypsin and pepsin, followed by separation of these peptides through liquid chromatography-tandem mass spectrometry (LC-MS/MS) and database searching. Analysis of bioactivity from 25% and 30% fractions (trypsinised), and 10% and 30% fractions (pepsinised) showed inhibitory effect towards the growth of Ganoderma boninense . In antioxidant assay, only non-fractionated protein hydrolysate with trypsin and pepsin showed a scavenging activity of 17.7%-22.3% for 2,2-diphenyl-1-picrylhydrazyl. We further determined the possible occurrence of antimicrobial activity in silico by matching the experimental peptide sequences to known bioactive peptides. Four antimicrobial peptides were found in fractionated mesocarp hydrolysates using trypsin and pepsin. These bioactive peptides had molecular masses of less than 4-5 kiloDalton (kDa) and made of 11-39 amino acid residues. A total of 23%-54% hydrophobic amino acids were found within these sequences. The results showed that the oil palm mesocarps contained peptides with various bioactivities that could be bioprospected into functional constituents with health and crop protection benefits.

ANALYSIS OF Pseudomonas sp. POLYCYCLIC AROMATIC HYDROCARBONS DEGRADATION PROTEINS BY LC-MS/MS

Protein homeostasis, regulation of energy production and activation of DNA damage-repair pathways are involved in the heat stress response of Pseudogymnoascus spp.
Nurlizah Abu Bakar, Benjamin Yii Chung Lau, Jerzy Smykla, Saiful Anuar Karsani, and Siti Aisyah Alias
Wiley
Proteome changes can be used as an instrument to measure the effects of climate change, predict the possible future state of an ecosystem and the direction in which is headed. In this study, proteomic and GO functional enrichment analysis of six Pseudogymnoascus spp. isolated from various global biogeographical regions were carried out to determine their response to heat stress. In total, 2,122 proteins were identified with high confidence. Comparative quantitative analysis showed that changes in proteome profiles varied greatly between isolates from different biogeographical regions. Although the identities of the proteins that changed varied between the different regions, the functions they governed were similar. Gene Ontology analysis showed enrichment of proteins involved in multiple protective mechanisms, including the modulation of protein homeostasis, regulation of energy production, and activation of DNA damage and repair pathways. Our proteomic analysis did not show any clear relationship between protein changes and the strains' biogeographical origins. This article is protected by copyright. All rights reserved.

OMICS PLATFORM TECHNOLOGIES FOR DISCOVERY AND UNDERSTANDING THE SYSTEMS BIOLOGY OF OIL PALM
UMI SALAMAH RAMLI
Malaysian Palm Oil Board
Palm oil is the leading vegetable oil in terms of volume in the world market. Indonesia and Malaysia are the top producers and exporters of the commodity. The global production of palm oil reached 73.5 million tonnes in the period 2018/2019, up from approximately 70.5 million tonnes in 2017/2018. Oil palm is the most productive crop in the world being 10 times more productive than soybean which produces only about 0.45 t oil per hectare. Nonetheless, the industry is continuously under pressure to improve productivity and sustainability. This will require concerted innovations across the entire palm oil supply chain and fully committed research efforts including upstream technologies to expedite crop improvement. At the Malaysian Palm Oil Board (MPOB), research efforts at development of tools for improving oil palm traits by genetic modification have been augmented more recently with omics-based approaches and all of these innovations are synchronised towards improved product quality. Omics is a multi-disciplinary field encompassing genomics, epigenomics, transcriptomics, proteomics and metabolomics. Each of these fields provides an opportunity to understand and view oil palm biology from a global perspective, enabling accelerated discoveries for improved productivity and the development of new and improved varieties. An integrative omics approach promises great value in both phenotyping and diagnostic analyses. With the current technological capabilities, metabolomics is also being exploited for identifying unique chemical fingerprints to detect product contamination and adulteration in oil palm. This effort is actively being conducted in order to position the oil palm industry to meet and optimise the delivery of the highest quality oil with minimum environmental and social concerns . In this review, an overview is given on the current knowledge and progress made in oil palm research, focusing on the application of omics strategies and their integration with high-throughput technologies for oil palm crop improvement, development of geographical traceability system and ensuring that palm oil is free from residual oil contamination.

Comparative proteome analysis of mycelial proteins from G. boninense vs G. tornatum: Identification of proteins potentially involved in the pathogenicity of G. boninense
Shahirah Balqis Dzulkafli, Abrizah Othman, Benjamin Yii Chung Lau, Umi Salamah Ramli, and Saiful Anuar Karsani
Elsevier BV

Transcriptomic and proteomic profiling revealed reprogramming of carbon metabolism in acetate-grown human pathogen Candida glabrata
Shu Yih Chew, Alistair J. P. Brown, Benjamin Yii Chung Lau, Yoke Kqueen Cheah, Kok Lian Ho, Doblin Sandai, Hassan Yahaya, and Leslie Thian Lung Than
Springer Science and Business Media LLC
AbstractBackgroundEmergence ofCandida glabrata, which causes potential life-threatening invasive candidiasis, has been widely associated with high morbidity and mortality. In order to cause disease in vivo, a robust and highly efficient metabolic adaptation is crucial for the survival of this fungal pathogen in human host. In fact, reprogramming of the carbon metabolism is believed to be indispensable for phagocytosedC. glabratawithin glucose deprivation condition during infection.MethodsIn this study, the metabolic responses ofC. glabrataunder acetate growth condition was explored using high-throughput transcriptomic and proteomic approaches.ResultsCollectively, a total of 1482 transcripts (26.96%) and 242 proteins (24.69%) were significantly up- or down-regulated. Both transcriptome and proteome data revealed that the regulation of alternative carbon metabolism inC. glabrataresembled other fungal pathogens such asCandida albicansandCryptococcus neoformans, with up-regulation of many proteins and transcripts from the glyoxylate cycle and gluconeogenesis, namely isocitrate lyase (ICL1), malate synthase (MLS1), phosphoenolpyruvate carboxykinase (PCK1) and fructose 1,6-biphosphatase (FBP1). In the absence of glucose,C. glabratashifted its metabolism from glucose catabolism to anabolism of glucose intermediates from the available carbon source. This observation essentially suggests that the glyoxylate cycle and gluconeogenesis are potentially critical for the survival of phagocytosedC. glabratawithin the glucose-deficient macrophages.ConclusionHere, we presented the first global metabolic responses ofC. glabratato alternative carbon source using transcriptomic and proteomic approaches. These findings implicated that reprogramming of the alternative carbon metabolism during glucose deprivation could enhance the survival and persistence ofC. glabratawithin the host.

Optimization of protein extraction for proteomic analyses of fresh and frozen “Musang King” durian pulps
Xue Yi Tan, Azizah Misran, Leona Daniela Jeffery Daim, and Benjamin Yii Chung Lau
Elsevier BV

Proteomics analysis on lipid metabolism in Elaeis guineensis and Elaeis oleifera
Benjamin Yii Chung Lau, Mohd Din Amiruddin, and Abrizah Othman
Elsevier BV

Evaluation of sodium deoxycholate as solubilization buffer for oil palm proteomics analysis
Benjamin Yii Chung Lau and Abrizah Othman
Public Library of Science (PLoS)
Protein solubility is a critical prerequisite to any proteomics analysis. Combination of urea/thiourea and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) have been routinely used to enhance protein solubilization for oil palm proteomics studies in recent years. The goals of these proteomics analysis are essentially to complement the knowledge regarding the regulation networks and mechanisms of the oil palm fatty acid biosynthesis. Through omics integration, the information is able to build a regulatory model to support efforts in improving the economic value and sustainability of palm oil in the global oil and vegetable market. Our study evaluated the utilization of sodium deoxycholate as an alternative solubilization buffer/additive to urea/thiourea and CHAPS. Efficiency of urea/thiourea/CHAPS, urea/CHAPS, urea/sodium deoxycholate and sodium deoxycholate buffers in solubilizing the oil palm (Elaeis guineensis var. Tenera) mesocarp proteins were compared. Based on the protein yields and electrophoretic profile, combination of urea/thiourea/CHAPS were shown to remain a better solubilization buffer and additive, but the differences with sodium deoxycholate buffer was insignificant. A deeper mass spectrometric and statistical analyses on the identified proteins and peptides from all the evaluated solubilization buffers revealed that sodium deoxycholate had increased the number of identified proteins from oil palm mesocarps, enriched their gene ontologies and reduced the number of carbamylated lysine residues by more than 67.0%, compared to urea/thiourea/CHAPS buffer. Although only 62.0% of the total identified proteins were shared between the urea/thiourea/CHAPS and sodium deoxycholate buffers, the importance of the remaining 38.0% proteins depends on the applications. The only observed limitations to the application of sodium deoxycholate in protein solubilization were the interference with protein quantitation and but it could be easily rectified through a 4-fold dilution. All the proteomics data are available via ProteomeXchange with identifier PXD013255. In conclusion, sodium deoxycholate is applicable in the solubilization of proteins extracted from oil palm mesocarps with higher efficiency compared to urea/thiourea/CHAPS buffer. The sodium deoxycholate buffer is more favorable for proteomics analysis due to its proven advantages over urea/thiourea/CHAPS buffer.

Application of Proteomics Technologies in Oil Palm Research
Benjamin Yii Chung Lau, Abrizah Othman, and Umi Salamah Ramli
Springer Science and Business Media LLC
Proteomics technologies were first applied in the oil palm research back in 2008. Since proteins are the gene products that are directly correspond to phenotypic traits, proteomic tools hold a strong advantage above other molecular tools to comprehend the biological and molecular mechanisms in the oil palm system. These emerging technologies have been used as non-overlapping tools to link genome-wide transcriptomics and metabolomics-based studies to enhance the oil palm yield and quality through sustainable plant breeding. Many efforts have also been made using the proteomics technologies to address the oil palm’s Ganoderma disease; the cause and management. At present, the high-throughput screening technologies are being applied to identify potential biomarkers involved in metabolism and cellular development through determination of protein expression changes that correlate with oil production and disease. This review highlights key elements in proteomics pipeline, challenges and some examples of their implementations in plant studies in the context of oil palm in particular. We foresee that the proteomics technologies will play more significant role to address diverse issues related to the oil palm in the effort to improve the oil crop.

Differential expression analysis of oil palm fatty acid biosynthetic enzymes with gel-free quantitative proteomics
LAU BENJAMIN YII CHUNG
Malaysian Palm Oil Board
The control mechanisms of de novo fatty acid biosynthesis continue to intrigue, particularly at protein level. The cross talk between transcriptional and metabolic regulatory networks remains undefined. In order to understand the metabolic factors affecting oleic acid biosynthesis in Elaeis guineensis var. tenera (oil palm), two-dimensional liquid chromatography-tandem mass spectrometry (2DLC-MS/MS) was attempted to capture the main fatty acid biosynthetic enzymes involved in oleic acid production. These enzymes were extracted from the chromoplast of low and high oleic mesocarps of 20th week after anthesis. Chromoplast proteins were separated using offline 2DLC for mass spectrometric analysis. Two subunits of acetyl-CoA carboxylase, β-ketoacyl-acyl carrier protein (ACP) reductase, β-hydroxyacyl-ACP dehydrogenase, 3-enoylACP reductase, β-ketoacyl-ACP synthase and stearoyl-ACP desaturase were identified. The relative expression of these fatty acid biosynthetic enzymes was determined using isobaric tags labelling. Initial assessment revealed that β-hydroxyacyl-ACP dehydrogenase and β-ketoacyl-ACP synthase were present in a higher abundance in the high oleic acid mesocarps while the accumulation of 3-enoyl-ACP reductase was lower relative to the other fatty acid biosynthetic enzymes investigated. The existence of other differentially expressed metabolic enzymes suggests that the control mechanism of fatty acid production, in particular oleic acid, might involve more than just the main fatty acid biosynthetic enzymes.

Application of a Mass Spectrometric Approach to Detect the Presence of Fatty Acid Biosynthetic Phosphopeptides
Benjamin Yii Chung Lau, Stefan Clerens, James D. Morton, Jolon M. Dyer, Santanu Deb-Choudhury, and Umi Salamah Ramli
Springer Science and Business Media LLC
The details of plant lipid metabolism are relatively well known but the regulation of fatty acid production at the protein level is still not understood. Hence this study explores the importance of phosphorylation as a mechanism to control the activity of fatty acid biosynthetic enzymes using low and high oleic acid mesocarps of oil palm fruit (Elaeis guineensis variety of Tenera). Adaptation of neutral loss-triggered tandem mass spectrometry and selected reaction monitoring to detect the neutral loss of phosphoric acid successfully found several phosphoamino acid-containing peptides. These peptides corresponded to the peptides from acetyl-CoA carboxylase and 3-enoyl-acyl carrier protein reductase as identified by their precursor ion masses. These findings suggest that these enzymes were phosphorylated at 20th week after anthesis. Phosphorylation could have reduce their activities towards the end of fatty acid biosynthesis at ripening stage. Implication of phosphorylation in the regulation of fatty acid biosynthesis at protein level has never been reported.

Method developments to extract proteins from oil palm chromoplast for proteomic analysis
Benjamin Yii Chung Lau, Santanu Deb-Choudhury, James D. Morton, Stefan Clerens, Jolon M. Dyer, and Umi Salamah Ramli
Springer Science and Business Media LLC
Abstract Proteins from the plant chromoplast are essential for many physiological processes such as fatty acid biosynthesis. Different protein extraction methods were tested to find the most robust method to obtain oil palm chromoplast proteins for mass spectrometry analysis. Initially, two different solvents were employed to reduce the fruit lipids. Then, two plant cell wall digestive enzymes were used to acquire the protoplasts to increase the protein extraction effectiveness. A two-stage centrifugation-based fractionation approach enhanced the number of identified proteins, particularly the fatty acid biosynthetic enzymes. The effectiveness of each extraction method was assessed using protein yields and 2DE gel profiles. The ideal method was successfully used to establish the 2DE chromoplast proteome maps of low and high oleic acid mesocarps of oil palm. Further nanoLC–MS/MS analysis of the extracted chromoplast proteins led to the identification of 162 proteins, including some of the main enzymes involved in the fatty acid biosynthesis. The established procedures would provide a solid foundation for further functional studies, including fatty acid biosynthetic expression profiling and evaluation of regulatory function.

RECENT SCHOLAR PUBLICATIONS

Proteomic and Morphological Analysis of Bone and Articular Cartilage Changes in Osteoarthritic Rabbits Supplemented with Edible Bird’s Nest (EBN)
SZS Sulaiman, NSS Umran, S Mohamed, J Abu, AMH Ng, BYC Lau, ...
Malaysian Journal of Fundamental and Applied Sciences 20 (6), 1274-1287 2024

Geographical Diversity of Proteomic Responses to Cold Stress in the Fungal Genus Pseudogymnoascus
N Abu Bakar, BYC Lau, M Gonzlez-Aravena, J Smykla, B Krzewicka, ...
Microbial Ecology 87 (1), 11 2024

Integrative tissue-resolved proteomics and metabolomics analysis of oil palm (Elaeis guineensis Jacq.) fruit provides insights into stilbenoid biosynthesis at the interface of
H Hassan, NI Tahir, NL Rozali, BYC Lau, A Othman, W Weckwerth, ...
Biocatalysis and Agricultural Biotechnology 60, 103308 2024

Proteomic characterization of Pseudogymnoascus spp. isolates from polar and temperate regions
SAA Nurlizah Abu Bakar, Benjamin Lau Yii Chung, Jerzy Smykla, Saiful Anuar ...
Mycologia 2024

Enhanced azadirachtin production in neem (Azadirachta indica) callus through NaCl elicitation: Insights into differential protein regulation via shotgun proteomics
SA Omar, S Ashokhan, NA Majid, SA Karsani, BYC Lau, JS Yaacob
Pesticide Biochemistry and Physiology 199, 105778 2024

A Study on the Effect of Administration of 500mg/kg Tocotrienol-Rich Fraction (TRF) on Liver Membrane Protein Expression in Mice Using Label-Free Quantitative Proteomics
MK Md. Yusof, MF Rusli, B Yii Chung Lau, NA Mohd Fahami, ...
Malaysian Journal of Medicine & Health Sciences 20, 76 2024

Comparative proteomic and metabolomic studies between partial resistant and susceptible oil palm reveal the molecular mechanism associated with Ganoderma boninense infection
A Othman, BYC Lau, Z Nurazah, S Shahwan, MH Rusli, R Singh, ...
Physiological and Molecular Plant Pathology 129, 102198 2024

Quantitative proteomics analysis of permethrin and temephos-resistant Ae. aegypti revealed diverse differentially expressed proteins associated with insecticide
A Shettima, IH Ishak, B Lau, H Abu Hasan, N Miswan, N Othman
PLOS Neglected Tropical Diseases 17 (9), e0011604 2023

Understanding the effects of carbon and nitrogen starvation on the comparative secretomes of Ganoderma boninense and Ganoderma tornatum
SB Dzulkafli, A Othman, BYC Lau, Z Nurazah, J Nagappan, US Ramli, ...
Physiological and Molecular Plant Pathology 127, 102084 2023

Cross-reactivity analysis of milk proteins from different goat breeds with cow’s milk allergens using a proteomic approach
M Mansor, JR Al-Obaidi, IH Ismail, MAZ Abidin, AF Zakaria, BYC Lau, ...
Molecular Immunology 155, 44-57 2023

Skin Mucus Proteome Analysis Reveals Disease-Resistant Biomarker Signatures in Hybrid Grouper (Epinephelus fuscoguttatus ♀ Epinephelus lanceolatus ♂) against Vibrio
LCF Nurhikmah Abu Aziz, Annie Christianus, Wan Mohd Syazwan Wan Solahudin ...
Fishes 7 (5), 278 2022

Higher resolution protein band visualisation via improvement of colloidal CBB‑G staining by gel fixation
NR Nikson Fatt‑Ming Chong, Hasnain Hussain, Nur Ezzati Hamdin, David Hong ...
Chemical and Biological Technologies in Agriculture 9 (32) 2022

Analysis of Pseudomonas sp. polycyclic aromatic hydrocarbons degradation proteins by LC-MS/MS
BYCL Suzana Adenan, Chee Fah Wong, Saripah Salbiah Syed Abdul Azziz, Som Cit ...
Malaysian Journal of Microscopy 18 (1), 66-76 2022

Protein homeostasis, regulation of energy production and activation of DNA damage‐repair pathways are involved in the heat stress response of Pseudogymnoascus spp.
N Abu Bakar, BYC Lau, J Smykla, SA Karsani, SA Alias
Environmental Microbiology 24 (4), 1849-1864 2022

Antifungal and antioxidant peptides from oil palm mesocarps
L Benjamin Yii Chung, A Othman, US Ramli
Journal of Oil Palm Research 34 (3), 453-464 2022

Omics platform technologies for discovery and understanding the systems biology of oil palm
NAM Ishak, MA Abd Manaf, S Shahwan, O Abd Rasid, A Othman, ...
Journal of Oil Palm Research (Malaysia) 2022

Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in Vibrio parahaemolyticus
LCF Nur Afiqah Md Yusof, Siti Aisyah Razali, Azyyati Mohd Padzil, Benjamin ...
Biology 11 (11), 1600 2022

Comparative proteome analysis of mycelial proteins from G. boninense vs G. tornatum: Identification of proteins potentially involved in the pathogenicity of G. boninense
SB Dzulkafli, A Othman, BYC Lau, US Ramli, SA Karsani
Physiological and Molecular Plant Pathology 117, 101736 2022

Transcriptomic and proteomic profiling revealed reprogramming of carbon metabolism in acetate-grown human pathogen Candida glabrata
LTLT Shu Yih Chew, Alistair J. P. Brown, Benjamin Yii Chung Lau, Yoke Kqueen ...
Journal of Biomedical Science 28 (1) 2021

Optimization of protein extraction for proteomic analyses of fresh and frozen “musang king” durian pulps
T Xue Yi, A Misran, LDJ Daim, BYC Lau
Food Chemistry 2020

MOST CITED SCHOLAR PUBLICATIONS

Evaluation of sodium deoxycholate as solubilization buffer for oil palm proteomics analysis
A Lau, Benjamin Yii Chung, Othman
PLoS ONE 14 (8), e0221052 2019
Citations: 28

Method developments to extract proteins from oil palm chromoplast for proteomic analysis
BYC Lau, S Deb-Choudhury, JD Morton, S Clerens, JM Dyer, US Ramli
Springerplus 4, 1-13 2015
Citations: 19

Combination of acid labile detergent and C18 Empore™ disks for improved identification and sequence coverage of in-gel digested proteins
H Koehn, B Lau, S Clerens, JE Plowman, JM Dyer, US Ramli, ...
Analytical and bioanalytical chemistry 400, 415-421 2011
Citations: 15

Application of a mass spectrometric approach to detect the presence of fatty acid biosynthetic phosphopeptides
BYC Lau, S Clerens, JD Morton, JM Dyer, S Deb-Choudhury, US Ramli
The Protein Journal 35, 163-170 2016
Citations: 13

The oil palm genome
M Ithnin, A Kushairi
Springer 2020
Citations: 12

Optimization of protein extraction for proteomic analyses of fresh and frozen “musang king” durian pulps
T Xue Yi, A Misran, LDJ Daim, BYC Lau
Food Chemistry 2020
Citations: 8

Application of proteomics technologies in oil palm research
BYC Lau, A Othman, US Ramli
The Protein Journal 37 (6), 473-499 2018
Citations: 8

Extraction Methods for Analysis of Oil Palm Leaf and Root Proteins By Two-Dimensional Gel Electrophoresis
US Hassan Hasliza, Lau, Benjamin Yii Chung, Ramli
Journal of Oil Palm Research 26 (1), 54-61 2014
Citations: 7

Proteomics analysis on lipid metabolism in Elaeis guineensis and Elaeis oleifera
A Lau, Benjamin Yii Chung, Amiruddin, Mohd Din, Othman
Data in Brief 2020
Citations: 6

Differential Expression Analysis of Oil Palm Fatty Acid Biosynthetic Enzymes With Gel-free Quantitative Proteomics
USR Benjamin Lau Yii Chung, James D Morton, Santanu Deb-Choudhury, Stefan ...
Journal of Oil Palm Research 29 (1), 23-34 2017
Citations: 6

Integrative tissue-resolved proteomics and metabolomics analysis of oil palm (Elaeis guineensis Jacq.) fruit provides insights into stilbenoid biosynthesis at the interface of
H Hassan, NI Tahir, NL Rozali, BYC Lau, A Othman, W Weckwerth, ...
Biocatalysis and Agricultural Biotechnology 60, 103308 2024
Citations: 4

Comparative proteomic and metabolomic studies between partial resistant and susceptible oil palm reveal the molecular mechanism associated with Ganoderma boninense infection
A Othman, BYC Lau, Z Nurazah, S Shahwan, MH Rusli, R Singh, ...
Physiological and Molecular Plant Pathology 129, 102198 2024
Citations: 4

Omics—A potential tool for oil palm improvement and productivity
US Ramli, A Othman, NIM Tahir, BYC Lau, S Shahwan, H Hassan, ...
The Oil Palm Genome, 141-157 2020
Citations: 4