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Fulltext Volatile profiling of aromatic traditional medicinal plant, Polygonum minus in different tissues and its biological activities

Ahmad R, Baharum SN, Bunawan H, Lee M, Mohd Noor N, Rohani ER, et al.

Molecules, 2014 Nov 20;19(11):19220-42.
PMID: 25420073 DOI: 10.3390/molecules191119220

The aim of this research was to identify the volatile metabolites produced in different organs (leaves, stem and roots) of Polygonum minus, an important essential oil producing crop in Malaysia. Two methods of extraction have been applied: Solid Phase Microextraction (SPME) and hydrodistillation coupled with Gas Chromatography-Mass Spectrometry (GC-MS). Approximately, 77 metabolites have been identified and aliphatic compounds contribute significantly towards the aroma and flavour of this plant. Two main aliphatic compounds: decanal and dodecanal were found to be the major contributor. Terpenoid metabolites were identified abundantly in leaves but not in the stem and root of this plant. Further studies on antioxidant, total phenolic content, anticholinesterase and antimicrobial activities were determined in the essential oil and five different extracts. The plant showed the highest DPPH radical scavenging activity in polar (ethanol) extract for all the tissues tested. For anti-acetylcholinesterase activity, leaf in aqueous extract and methanol extract showed the best acetylcholinesterase inhibitory activities. However, in microbial activity, the non-polar extracts (n-hexane) showed high antimicrobial activity against Methicillin-resistant Staphylococcus aureus (MRSA) compared to polar extracts. This study could provide the first step in the phytochemical profiles of volatile compounds and explore the additional value of pharmacology properties of this essential oil producing crop Polygonum minus.
Fulltext UPLC-TOF-MS/MS-Based Metabolomics Analysis Reveals Species-Specific Metabolite Compositions in Pitchers of Nepenthes ampullaria, Nepenthes rafflesiana, and Their Hybrid Nepenthes × hookeriana

Rosli MAF, Mediani A, Azizan KA, Baharum SN, Goh HH

Front Plant Sci, 2021;12:655004.
PMID: 33968110 DOI: 10.3389/fpls.2021.655004

Hybridization is key to the evolution and diversity of plants in nature. Nepenthaceae comprises a family of diverse tropical carnivorous pitcher plant species with extensive hybridization. However, there is no study to date on the metabolite expression of hybrids in this family. We performed a non-targeted metabolomics analysis of the pitchers of two Nepenthes species with different dietary habits, namely, the semi-detritivorous N. ampullaria and carnivorous N. rafflesiana with their hybrid (N. × hookeriana) for a comparative study. The whole-pitcher samples were extracted in methanol:chloroform:water (3:1:1) via sonication-assisted extraction and analyzed using ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) followed by data analysis to profile chemical compositions. A total of 1,441 metabolite features were profiled from the three species in which 43.3% of features in the hybrid samples were not found in either of its parents. The partial least squares discriminant analysis (PLS-DA) found 324 metabolite features with variable in projection (VIP) values greater than one in which 55 features were statistically significant. This showed that the hybrid is closer to N. rafflesiana, which is consistent to the previous study on gene and protein expressions. A total of 105 metabolites were putatively identified with manual searches using public metabolite databases. Phenols were detected to be the most abundant secondary metabolites due to a high flavonoid content, especially in N. rafflesiana. The most abundant feature 476.3s:449.102 was found to be the most significant VIP for distinguishing between the three species as a chemical marker. This is the first study comparing metabolites in the carnivory organs of different Nepenthes species with comprehensive profiling and putative identification. The differential metabolite compositions in the pitchers of different species might have ecological implications with the hybrid showing intermediate phenotype between the parents as well as manifesting unique metabolites. However, there is no clear evidence of metabolites related to the differences in dietary habits between the hybrid and the two parent species.
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 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.
Transcriptome-wide effects of expansin gene manipulation in etiolated Arabidopsis seedling

Ilias IA, Negishi K, Yasue K, Jomura N, Morohashi K, Baharum SN, et al.

J Plant Res, 2019 Mar;132(2):159-172.
PMID: 30341720 DOI: 10.1007/s10265-018-1067-0

Expansin is a non-enzymatic protein which plays a pivotal role in cell wall loosening by inducing stress relaxation and extension in the plant cell wall. Previous studies on Arabidopsis, Petunia × hybrida, and tomato demonstrated that the suppression of expansin gene expression reduced plant growth but expansin overexpression does not necessarily promotes growth. In this study, both expansin gene suppression and overexpression in dark-grown transgenic Arabidopsis seedlings resulted in reduced hypocotyl length at late growth stages with a more pronounced effect for the overexpression. This defect in hypocotyl elongation raises questions about the molecular effect of expansin gene manipulation. RNA-seq analysis of the transcriptomic changes between day 3 and day 5 seedlings for both transgenic lines found numerous differentially expressed genes (DEGs) including transcription factors and hormone-related genes involved in different aspects of cell wall development. These DEGs imply that the observed hypocotyl growth retardation is a consequence of the concerted effect of regulatory factors and multiple cell-wall related genes, which are important for cell wall remodelling during rapid hypocotyl elongation. This is further supported by co-expression analysis through network-centric approach of differential network cluster analysis. This first transcriptome-wide study of expansin manipulation explains why the effect of expansin overexpression is greater than suppression and provides insights into the dynamic nature of molecular regulation during etiolation.
Fulltext Transcriptome data of Epinephelus fuscoguttatus infected by Vibrio vulnificus

Jazamuddin FM, Aizat WM, Goh HH, Low CF, Baharum SN

Data Brief, 2018 Feb;16:466-469.
PMID: 29255779 DOI: 10.1016/j.dib.2017.11.024

Vibriosis disease by Vibrio spp. greatly reduced productivity of aquaculture, such as brown-marbled grouper (Epinephelus fuscoguttatus), which is an economically important fish species in Malaysia. Preventive measures and immediate treatment are critical to reduce the mortality of E. fuscoguttatus from vibriosis. To investigate the molecular mechanisms associated with immune response and host-bacteria interaction, a transcriptomic analysis was performed to compare between healthy and Vibrio-infected groupers. This permits the discovery of immune-related genes, specifically the resistance genes upon infection. Herein, we provide the raw transcriptome data from Illumina HiSeq. 4000 that have been deposited into NCBI SRA database with the BioProject accession number PRJNA396437. A total of 493,403,076 raw sequences of 74.5 Gb were obtained. Trimming of the raw data produced 437,186,232 clean reads of ~58 Gb. These datasets will be useful to elucidate the defence mechanisms of E. fuscoguttatus against Vibrio vulnificus infection for future development of effective prevention and treatment of vibriosis.
Fulltext The effects of amino acids and fatty acids on the disease resistance of Epinephelus fuscoguttatus in response to Vibrio vulnificus infection

Nurdalila AA, Natnan ME, Baharum SN

3 Biotech, 2020 Dec;10(12):544.
PMID: 33240745 DOI: 10.1007/s13205-020-02543-4

Mass mortality resulting from bacterial infection poses a major problem in the grouper aquaculture industry. The purpose of this study was to profile the metabolites released in challenged fish and to reconstruct the metabolic pathways of brown marble grouper (Epinephelus fuscoguttatus) in response to Vibrio vulnificus infection. Metabolite profiles from control and challenged treatment groups after feeding were determined using gas chromatography-mass spectrometry (GC-MS). Forty metabolites were identified from the GC-MS analysis. These metabolites comprised of amino acids, fatty acids, organic acids and carbohydrates. The profiles showed the highest percent area (33.1%) for leucine from the amino acid class in infected fish compared to the control treatment group (12.3%). Regarding the fatty acid class, a higher percent area of the metabolite 8,11-eicosadienoic acid (27.04%) was observed in fish infected with V. vulnificus than in the control treatment group (22.5%). Meanwhile, in the carbohydrate class, glucose (47.0%) was the metabolite in the carbohydrate class present at highest percentage in the control treatment group compared to infected fish (30.0%). Our findings highlight the importance of a metabolic analysis for understanding the changes of metabolites in E. fuscoguttatus in response to bacterial infections.
Fulltext Streamlining Natural Products Biomanufacturing With Omics and Machine Learning Driven Microbial Engineering

Ramzi AB, Baharum SN, Bunawan H, Scrutton NS

Front Bioeng Biotechnol, 2020;8:608918.
PMID: 33409270 DOI: 10.3389/fbioe.2020.608918

Increasing demands for the supply of biopharmaceuticals have propelled the advancement of metabolic engineering and synthetic biology strategies for biomanufacturing of bioactive natural products. Using metabolically engineered microbes as the bioproduction hosts, a variety of natural products including terpenes, flavonoids, alkaloids, and cannabinoids have been synthesized through the construction and expression of known and newly found biosynthetic genes primarily from model and non-model plants. The employment of omics technology and machine learning (ML) platforms as high throughput analytical tools has been increasingly leveraged in promoting data-guided optimization of targeted biosynthetic pathways and enhancement of the microbial production capacity, thereby representing a critical debottlenecking approach in improving and streamlining natural products biomanufacturing. To this end, this mini review summarizes recent efforts that utilize omics platforms and ML tools in strain optimization and prototyping and discusses the beneficial uses of omics-enabled discovery of plant biosynthetic genes in the production of complex plant-based natural products by bioengineered microbes.
Fulltext Sequence and Phylogenetic Analysis of the First Complete Genome of Ricetungro spherical virus in Malaysia

Kannan M, Mohamad Saad M, Zainal Z, Kassim H, Ismail I, Talip N, et al.

Iran J Biotechnol, 2020 Oct;18(4):e2566.
PMID: 34056024 DOI: 10.30498/IJB.2020.2566

Background: Rice tungro disease (RTD) is a viral disease mainly affecting rice in Asia. RTD caused by Rice tungro bacilliform virus and Rice tungro spherical virus. To date, there are only 5 RTSV isolates have been reported.
Objectives: In this study, we aimed to report the complete nucleotide sequence of Malaysian isolate of Rice tungro spherical virus Seberang Perai (RTSV-SP) for the first time. RTSV-SP was characterized and its evolutionary relationship with previously reported Indian and Philippines isolates were elucidated.
Materials and Methods: RTSV-SP isolate was isolated from a recent outbreak in a paddy field in Seberang Perai zone of Malaysia. Its complete genome was amplified by RT-PCR, cloned and sequenced.
Results: Sequence analysis indicated that the genome of RTSV-SP consisted of 12,173 nucleotides (nt). Comparative analysis of 6 complete genome sequences using Clustal Omega showed that Seberang Perai isolate shared the highest nucleotide identity (96.04%) with Philippine-A isolate, except that the sORF-2 of RTSV-SP is shorter than RTSV Philippine-A by 27 amino acid residues. RTSV-SP found to cluster in Southeast Asia (SEA) group based on the whole genome sequence phylogenetic analysis using MEGA X software.
Conclusions: Phylogenetic classification of RTSV isolates based on the complete nucleotide sequences showed more distinctive clustering pattern with the addition of RTSV-SP whole genome to the available isolates. Present study described the isolation and molecular characterization of RTSV-SP.
Fulltext Seamless and orthogonal expression of genetic parts in polyhydroxyalkanoate (PHA)-producing bacterial chassis for plastic bio-upcycling applications

Minggu MM, Naseron NAH, Shaberi HSA, Muhammad NAN, Baharum SN, Ramzi AB

MethodsX, 2023 Dec;11:102434.
PMID: 37846354 DOI: 10.1016/j.mex.2023.102434

Polyhydroxyalkanoate (PHA)-producing bacteria represent a powerful synthetic biology chassis for waste bioconversion and bio-upcycling where PHAs can be produced as the final products. In this study, we present a seamless plasmid construction for orthogonal expression of recombinant PET hydrolase (PETase) in model PHA-producing bacteria P. putida and C. necator. To this end, this study described seamless cloning and expression methods utilizing SureVector (SV) system for generating pSV-Ortho-PHA (pSVOP) expression platform in bioengineered P. putida and C. necator. Genetic parts specifically Trc promoter, pBBR1 origin of replication, anchoring proteins and signal sequences were utilized for the transformation of pSVOP-based plasmid in electrocompetent cells and orthogonal expression of PETase in both P. putida and C. necator. Validation steps in confirming functional expression of PETase activity in corresponding PETase-expressing strains were also described to demonstrate seamless and detailed methods in establishing bioengineered P. putida and C. necator as whole-cell biocatalysts tailored for plastic bio-upcycling.•Seamless plasmid construction for orthogonal expression in PHA-producing bacteria.•Step-by-step guide for high-efficiency generation of electrotransformants of P. putida and C. necator.•Adaptable methods for rapid strain development (Design, Build, Test and Learn) for whole-cell biocatalysis.
Fulltext Sauropus androgynus (L.) Merr. Induced Bronchiolitis Obliterans: From Botanical Studies to Toxicology

Bunawan H, Bunawan SN, Baharum SN, Noor NM

Evid Based Complement Alternat Med, 2015;2015:714158.
PMID: 26413127 DOI: 10.1155/2015/714158

Sauropus androgynus L. Merr. is one of the most popular herbs in South Asia, Southeast Asia, and China where it was known as a slimming agent until two outbreaks of pulmonary dysfunction were reported in Taiwan and Japan in 1995 and 2005, respectively. Several studies described that the excessive consumption of Sauropus androgynus could cause drowsiness, constipation, and bronchiolitis obliterans and may lead to respiratory failure. Interestingly, this herb has been used in Malaysia and Indonesia in cooking and is commonly called the "multigreen" or "multivitamin" plant due to its high nutritive value and inexpensive source of dietary protein. The plant is widely used in traditional medicine for wound healing, inducing lactation, relief of urinary disorders, as an antidiabetic cure and also fever reduction. Besides these medicinal uses, the plant can also be used as colouring agent in food. This review will explore and compile the fragmented knowledge available on the botany, ethnobotany, chemical constitutes, pharmacological properties, and toxicological aspects of this plant. This comprehensive review will give readers the fundamental, comprehensive, and current knowledge regarding Sauropus androgynus L. Merr.
S5 Lipase: an organic solvent tolerant enzyme

Rahman RN, Baharum SN, Salleh AB, Basri M

J Microbiol, 2006 Dec;44(6):583-90.
PMID: 17205035

In this study, an organic solvent tolerant bacterial strain was isolated. This strain was identified as Pseudomonas sp. strain S5, and was shown to degrade BTEX (Benzene, Toluene, Ethyl-Benzene, and Xylene). Strain S5 generates an organic solvent-tolerant lipase in the late logarithmic phase of growth. Maximum lipase production was exhibited when peptone was utilized as the sole nitrogen source. Addition of any of the selected carbon sources to the medium resulted in a significant reduction of enzyme production. Lower lipase generation was noted when an inorganic nitrogen source was used as the sole nitrogen source. This bacterium hydrolyzed all tested triglycerides and the highest levels of production were observed when olive oil was used as a natural triglyceride. Basal medium containing Tween 60 enhanced lipase production to the most significant degree. The absence of magnesium ions (Mg2+) in the basal medium was also shown to stimulate lipase production. Meanwhile, an alkaline earth metal ion, Na+, was found to stimulate the production of S5 lipase.
Recent advancement of engineering microbial hosts for the biotechnological production of flavonoids

Shah FLA, Ramzi AB, Baharum SN, Noor NM, Goh HH, Leow TC, et al.

Mol Biol Rep, 2019 Dec;46(6):6647-6659.
PMID: 31535322 DOI: 10.1007/s11033-019-05066-1

Flavonoids are polyphenols that are important organic chemicals in plants. The health benefits of flavonoids that result in high commercial values make them attractive targets for large-scale production through bioengineering. Strategies such as engineering a flavonoid biosynthetic pathway in microbial hosts provide an alternative way to produce these beneficial compounds. Escherichia coli, Saccharomyces cerevisiae and Streptomyces sp. are among the expression systems used to produce recombinant products, as well as for the production of flavonoid compounds through various bioengineering approaches including clustered regularly interspaced short palindromic repeats (CRISPR)-based genome engineering and genetically encoded biosensors to detect flavonoid biosynthesis. In this study, we review the recent advances in engineering model microbial hosts as being the factory to produce targeted flavonoid compounds.
Fulltext Polygonumins A, a newly isolated compound from the stem of Polygonum minus Huds with potential medicinal activities

Ahmad R, Sahidin I, Taher M, Low C, Noor NM, Sillapachaiyaporn C, et al.

Sci Rep, 2018 03 09;8(1):4202.
PMID: 29523802 DOI: 10.1038/s41598-018-22485-5

Polygonumins A, a new compound, was isolated from the stem of Polygonum minus. Based on NMR results, the compound's structure is identical to that of vanicoside A, comprising four phenylpropanoid ester units and a sucrose unit. The structure differences were located at C-3″″'. The cytotoxic activity of polygonumins A was evaluated on several cancer cell lines by a cell viability assay using tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). The compound showed the highest antiproliferative (p
Fulltext Phenotypic subgrouping and multi-omics analyses reveal reduced diazepam-binding inhibitor (DBI) protein levels in autism spectrum disorder with severe language impairment

Pichitpunpong C, Thongkorn S, Kanlayaprasit S, Yuwattana W, Plaingam W, Sangsuthum S, et al.

PLoS One, 2019;14(3):e0214198.
PMID: 30921354 DOI: 10.1371/journal.pone.0214198

BACKGROUND: The mechanisms underlying autism spectrum disorder (ASD) remain unclear, and clinical biomarkers are not yet available for ASD. Differences in dysregulated proteins in ASD have shown little reproducibility, which is partly due to ASD heterogeneity. Recent studies have demonstrated that subgrouping ASD cases based on clinical phenotypes is useful for identifying candidate genes that are dysregulated in ASD subgroups. However, this strategy has not been employed in proteome profiling analyses to identify ASD biomarker proteins for specific subgroups.
METHODS: We therefore conducted a cluster analysis of the Autism Diagnostic Interview-Revised (ADI-R) scores from 85 individuals with ASD to predict subgroups and subsequently identified dysregulated genes by reanalyzing the transcriptome profiles of individuals with ASD and unaffected individuals. Proteome profiling of lymphoblastoid cell lines from these individuals was performed via 2D-gel electrophoresis, and then mass spectrometry. Disrupted proteins were identified and compared to the dysregulated transcripts and reported dysregulated proteins from previous proteome studies. Biological functions were predicted using the Ingenuity Pathway Analysis (IPA) program. Selected proteins were also analyzed by Western blotting.
RESULTS: The cluster analysis of ADI-R data revealed four ASD subgroups, including ASD with severe language impairment, and transcriptome profiling identified dysregulated genes in each subgroup. Screening via proteome analysis revealed 82 altered proteins in the ASD subgroup with severe language impairment. Eighteen of these proteins were further identified by nano-LC-MS/MS. Among these proteins, fourteen were predicted by IPA to be associated with neurological functions and inflammation. Among these proteins, diazepam-binding inhibitor (DBI) protein was confirmed by Western blot analysis to be expressed at significantly decreased levels in the ASD subgroup with severe language impairment, and the DBI expression levels were correlated with the scores of several ADI-R items.
CONCLUSIONS: By subgrouping individuals with ASD based on clinical phenotypes, and then performing an integrated transcriptome-proteome analysis, we identified DBI as a novel candidate protein for ASD with severe language impairment. The mechanisms of this protein and its potential use as an ASD biomarker warrant further study.
Fulltext Papaya Dieback in Malaysia: A Step Towards A New Insight of Disease Resistance

Bunawan H, Baharum SN

Iran J Biotechnol, 2015 Dec;13(4):1-2.
PMID: 28959302 DOI: 10.15171/ijb.1139
Fulltext Oleic acid as potential immunostimulant in metabolism pathways of hybrid grouper fingerlings (Epinephelus fuscoguttatus × Epinephelus lanceolatus) infected with Vibrio vulnificus

Natnan ME, Low CF, Chong CM, Bunawan H, Baharum SN

Sci Rep, 2023 Aug 08;13(1):12830.
PMID: 37553472 DOI: 10.1038/s41598-023-40096-7

Grouper culture has been expanding in Malaysia due to the huge demand locally and globally. However, due to infectious diseases such as vibriosis, the fish mortality rate increased, which has affected the production of grouper. Therefore, this study focuses on the metabolic profiling of surviving infected grouper fed with different formulations of fatty acid diets that acted as immunostimulants for the fish to achieve desirable growth and health performance. After a six-week feeding trial and one-week post-bacterial challenge, the surviving infected grouper was sampled for GC-MS analysis. For metabolite extraction, a methanol/chloroform/water (2:2:1.8) extraction method was applied to the immune organs (spleen and liver) of surviving infected grouper. The distribution patterns of metabolites between experimental groups were then analyzed using a metabolomics platform. A total of 50 and 81 metabolites were putatively identified from the spleen and liver samples, respectively. Our further analysis identified glycine, serine, and threonine metabolism, and alanine, aspartate and glutamate metabolism had the most impacted pathways, respectively, in spleen and liver samples from surviving infected grouper. The metabolites that were highly abundant in the spleen found in these pathways were glycine (20.9%), l-threonine (1.0%) and l-serine (0.8%). Meanwhile, in the liver l-glutamine (1.8%) and aspartic acid (0.6%) were found to be highly abundant. Interestingly, among the fish diet groups, grouper fed with oleic acid diet produced more metabolites with a higher percent area compared to the control diets. The results obtained from this study elucidate the use of oleic acid as an immunostimulant in fish feed formulation affects more various immune-related metabolites than other formulated feed diets for vibriosis infected grouper.
Fulltext Molecular systematics of Polygonum minus Huds. based on ITS sequences

Bunawan H, Choong CY, Md-Zain BM, Baharum SN, Noor NM

Int J Mol Sci, 2011;12(11):7626-34.
PMID: 22174621 DOI: 10.3390/ijms12117626

Plastid trnL-trnF and nuclear ribosomal ITS sequences were obtained from selected wild-type individuals of Polygonum minus Huds. in Peninsular Malaysia. The 380 bp trnL-trnF sequences of the Polygonum minus accessions were identical. Therefore, the trnL-trnF failed to distinguish between the Polygonum minus accessions. However, the divergence of ITS sequences (650 bp) among the Polygonum minus accessions was 1%, indicating that these accessions could be distinguished by the ITS sequences. A phylogenetic relationship based on the ITS sequences was inferred using neighbor-joining, maximum parsimony and Bayesian inference. All of the tree topologies indicated that Polygonum minus from Peninsular Malaysia is unique and different from the synonymous Persicaria minor (Huds.) Opiz and Polygonum kawagoeanum Makino.
Molecular cloning and in silico analysis of chalcone isomerase from Polygonum minus

Shah FLA, Baharum SN, Goh HH, Leow TC, Ramzi AB, Oslan SN, et al.

Mol Biol Rep, 2023 Jun;50(6):5283-5294.
PMID: 37148413 DOI: 10.1007/s11033-023-08417-1

BACKGROUND: Chalcone isomerase (CHI; EC 5.5.1.6) is one of the key enzymes in the flavonoid biosynthetic pathway that is responsible for the intramolecular cyclization of chalcones into specific 2S-flavanones.
METHODS AND RESULTS: In this study, the open reading frame (ORF) of CHI was successfully isolated from the cDNA of Polygonum minus at 711-bp long, encoding for 236 amino acid residues, with a predicted molecular weight of 25.4 kDa. Multiple sequence alignment and phylogenetic analysis revealed that the conserved residues (Thr50, Tyr108, Asn115, and Ser192) in the cleft of CHI enzyme group active site are present in PmCHI protein sequence and classified as type I. PmCHI comprises more hydrophobic residues without a signal peptide and transmembrane helices. The three-dimensional (3D) structure of PmCHI predicted through homology modeling was validated by Ramachandran plot and Verify3D, with values within the acceptable range of a good model. PmCHI was cloned into pET-28b(+) plasmid, expressed in Escherichia coli BL21(DE3) at 16 °C and partially purified.
CONCLUSION: These findings contribute to a deeper understanding of the PmCHI protein and its potential for further characterization of its functional properties in the flavonoid biosynthetic pathway.
Metabolomics: Challenges and Opportunities in Systems Biology Studies

Mediani A, Baharum SN

Methods Mol Biol, 2024;2745:77-90.
PMID: 38060180 DOI: 10.1007/978-1-0716-3577-3_5

Metabolomics can provide diagnostic, prognostic, and therapeutic biomarker profiles of individual patients because a large number of metabolites can be simultaneously measured in biological samples in an unbiased manner. Minor stimuli can result in substantial alterations, making it a valuable target for analysis. Due to the complexity and sensitivity of the metabolome, studies must be devised to maintain consistency, minimize subject-to-subject variation, and maximize information recovery. This effort has been aided by technological advances in experimental design, rodent models, and instrumentation. Proton Nuclear Magnetic Resonance (1H-NMR) spectroscopy of biofluids, such as plasma, urine, and faeces provide the opportunity to identify biomarker change patterns that reflect the physiological or pathological status of an individual patient. Metabolomics has the ultimate potential to be useful in a clinical context, where it could be used to predict treatment response and survival and for early disease diagnosis. During drug treatment, an individual's metabolic status could be monitored and used to predict deleterious effects. Therefore, metabolomics has the potential to improve disease diagnosis, treatment, and follow-up care. In this chapter, we demonstrate how a metabolomics study can be used to diagnose a disease by classifying patients as either healthy or pathological, while accounting for individual variation.

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