Browsing by Author "Suhaila Sulaiman"
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Publication Deciphering The Pan-Genome Of Ganoderma sp. To Depict Potential Genomic Components That Contribute To Ganoderma Boninense Pathogenicity(Malaysian Society of Applied Biology, 2018) ;Suhaila Sulaiman ;Nur Syamimi Yusoff ;Tan Joon SheongLee Yang PingThe soil-borne fungus, Ganoderma boninense is notorious as the cause of basal stem rot (BSR) disease in oil palm that results in severe economic losses. Due to insufficient functional information of its genome, mechanism underlying the infection is still enigmatic. Despite the constraint, here we report the pan-genome of eight draft genomes of Ganoderma sp. that delineated into 35,121 orthologous genes (OGs), consisting 4,898 genes in core genome and 30,223 genes in accessory genome, whilst the latter encompasses of 1,905 species-specific genes. Further genome-wide comparative analysis discovers 607 genes in pathogenic fungi G. boninense but not in its related non-pathogenic Ganoderma sp., suggesting their potential role in G. boninense pathogenicity towards its host. By implementing various bioinformatics tools and public databases, the incorporated functional enrichment of the candidate genes leads to inference of their role during host-pathogen interaction. This enables us to narrow down the entire gene catalogue in Ganoderma sp. for experimental verification in the laboratory. It is undeniable that the harnessing of Ganoderma sp. pan-genome data will conform to a more structured downstream analysis in understanding the role of G. boninense as the key agent of BSR in oil palm. - Some of the metrics are blocked by yourconsent settings
Publication Draft Genome Assembly Dataset Of The Basidiomycete Pathogenic Fungus, Ganoderma Boninense(Elsevier, 2020) ;Suhaila Sulaiman ;Nur Qistina Othman ;Joon Sheong TanYang Ping LeeGanoderma boninense is a soil-borne Basidiomycete pathogenic fungus that eminent as the key causal of devastating disease in oil palm, named basal stem rot. Being a threat to sustainable palm oil production, it is essential to comprehend the fundamental view of this fungus. However, there is gap of information due to its limited number of genome sequence that is available for this pathogenic fungus. This implies the hitches in performing biological research to unravel the mechanism underlying the pathogen attack in oil palm. Therefore, here we report a dataset of draft genome of G. boninense that was sequenced using Illumina Hiseq 2000. The raw reads were deposited into NCBI database (SRX7136614 and SRX7136615) and can be accessed via Bioproject accession number PRJNA503786. - Some of the metrics are blocked by yourconsent settings
Publication Effect of Pichia pastoris host strain on the properties of recombinant Aspergillus niger endoglucanase, EglB(Malaysian Society for Microbiology, 2018) ;Shazilah Kamaruddin ;Nor Muhammad Mahadi ;Rosli Md Illias ;Osman Hassan ;Suhaila Sulaiman ;William Broughton ;Izwan Bharudin ;Farah Diba Abu BakarAbdul Munir Abdul MuradAims: The methylotrophic yeast Pichia pastoris is widely used to express foreign proteins fused to secretion signals. As the effect of the expression host on the final protein product is unclear, we compared the properties of an endoglucanase (eglB of Aspergillus niger) expressed in two different P. pastoris strains. Methodology and results: Full-length cDNA encoding endoglucanase of A. niger strain ATCC10574 was isolated and expressed in P. pastoris X33 (the methanol utilisation plus phenotype, Mut+) and P. pastoris GS115 (slow methanol utilisation, MutS). EglB-GS115 showed the highest activity and stability at 60 °C while EglB-X33 was most active at 50 °C. EglB-X33 was active towards other substrates such as arabinogalactan, guar gum and locust bean gum besides its specific substrate, carboxymethyl cellulose (CMC). However, EglB-GS115 was only active on CMC. The affinity of EglB-X33 towards CMC (Km = 7.5 mg.mL-1 and specific activity 658 U.mg-1) was higher than that of EglB-GS115 (Km = 11.57 mg.mL-1, specific activity 144 U.mg-1). Conclusion, significance and impact of study: Although eglB was cloned in the same expression vector (pPICZαC), two different characteristics of enzymes were recovered from the supernatant of the different hosts. Thus, expression of recombinant enzyme in different P. pastoris strains greatly affects the physical structure and biochemical properties of the enzyme. Keywords: cellulase, endoglucanase, glycosylation, methanol utilisation phenotype, recombinant enzyme - Some of the metrics are blocked by yourconsent settings
Publication Genome-wide Comparative Analysis In Discovering Potential Evolved Hypothetical Genes In Infected Oil Palm(Malaysian Society of Applied Biology, 2018) ;Suhaila Sulaiman ;Nur Syamimi YusoffLee Yang PingBased on the genome annotation, oil palm genes can have either known or unknown functions. Hypothetical genes or unknown genes constitute averagely 24.40% from three gene model versions of oil palm (Elaeis guineensis Jacq.). The conventional method to prove their existence is labourious and limited, thus by bioinformatics analysis of genomic and transcriptomicdata, the potential role of hypothetical genes can be scrutinised comprehensively. In this study, the annotated hypotheticalgenes are reanalysed using sequence-based and transcriptomic data analysis to investigate their presence, differential expression and potential horizontal gene transfer (HGT) event with distantly related organisms in infected oil palm. In total 610 sequences still remain as hypothetical whilst others showed similarities with known genes which are not considered as hypothetical anymore. From the 610 genes, 92 are conserved in model plants and non-Plantae and eight genes are potential candidates of HGT events in oil palm with changes of expression during Ganoderma boninense infection. A transferred gene usually possess critical function, thus the presence of true hypothetical genes should not be ignored since it can be served as potential biomarkers of desired traits in oil palm. - Some of the metrics are blocked by yourconsent settings
Publication The Glaciozyma Antarctica Genome Reveals An Array Of Systems That Provide Sustained Responses Towards Temperature Variations In A Persistently Cold Habitat(Public Library of Science (PLOS), 2018) ;Mohd Firdaus-Raih ;Noor Haza Fazlin Hashim ;Izwan Bharudin ;Mohd Faizal Abu Bakar ;Kie Kyon Huang ;Halimah Alias ;Bernard K. B. Lee ;Mohd Noor Mat Isa ;Shuhaila Mat-Sharani ;Suhaila Sulaiman ;Lih Jinq Tay ;Radziah Zolkefli ;Yusuf Muhammad Noor ;Douglas Sie Nguong Law ;Siti Hamidah Abdul Rahman ;Rosli Md-Illias ;Farah Diba Abu Bakar ;Nazalan Najimudin ;Abdul Munir Abdul MuradNor Muhammad MahadiExtremely low temperatures present various challenges to life that include ice formation and effects on metabolic capacity. Psyhcrophilic microorganisms typically have an array of mechanisms to enable survival in cold temperatures. In this study, we sequenced and analysed the genome of a psychrophilic yeast isolated in the Antarctic region, Glaciozyma antarctica. The genome annotation identified 7857 protein coding sequences. From the genome sequence analysis we were able to identify genes that encoded for proteins known to be associated with cold survival, in addition to annotating genes that are unique to G. antarctica. For genes that are known to be involved in cold adaptation such as anti-freeze proteins (AFPs), our gene expression analysis revealed that they were differentially transcribed over time and in response to different temperatures. This indicated the presence of an array of adaptation systems that can respond to a changing but persistent cold environment. We were also able to validate the activity of all the AFPs annotated where the recombinant AFPs demonstrated anti-freeze capacity. This work is an important foundation for further collective exploration into psychrophilic microbiology where among other potential, the genes unique to this species may represent a pool of novel mechanisms for cold survival. - Some of the metrics are blocked by yourconsent settings
Publication Identification Of sRNA Mediated Responses To Nutrient Depletion In Burkholderia Pseudomallei(Nature Research, 2017) ;Hirzahida Mohd-Padil ;Nadzirah Damiri ;Suhaila Sulaiman ;Shiao-Fei Chai ;Sheila NathanMohd Firdaus-RaihThe Burkholderia genus includes many species that are known to survive in diverse environmental conditions including low nutrient environments. One species, Burkholderia pseudomallei is a versatile pathogen that can survive in a wide range of hosts and environmental conditions. In this study, we investigated how a nutrient depleted growth environment evokes sRNA mediated responses by B. pseudomallei. Computationally predicted B. pseudomallei D286 sRNAs were mapped to RNA-sequencing data for cultures grown under two conditions: (1) BHIB as a nutrient rich media reference environment and (2) M9 media as a nutrient depleted stress environment. The sRNAs were further selected to identify potentially cis-encoded systems by investigating their possible interactions with their flanking genes. The mappings of predicted sRNA genes and interactions analysis to their flanking genes identified 12 sRNA candidates that may possibly have cis-acting regulatory roles that are associated to a nutrient depleted growth environment. Our approach can be used for identifying novel sRNA genes and their possible role as cis-mediated regulatory systems. - Some of the metrics are blocked by yourconsent settings
Publication Molecular cloning, expression and characterisation of Afp4, an antifreeze protein from Glaciozyma antarctica(SpringerLink, 2014) ;Noor Haza Fazlin Hashim ;Suhaila Sulaiman ;Farah Diba Abu Bakar ;Rosli Md Illias ;Hidehisa Kawahara ;Nazalan Najimudin ;Nor Muhammad MahadiAbdul Munir Abdul MuradAntifreeze proteins (AFPs) are proteins with affinity towards ice and contribute to the survival of psychrophiles in subzero environment. Limited studies have been conducted on how AFPs from psychrophilic yeasts interact with ice. In this study, we describe the functional properties of an antifreeze protein from a psychrophilic Antarctic yeast, Glaciozyma antarctica. A cDNA encoding the antifreeze protein, AFP4, from G. antarctica PI12 was amplified from the mRNA extracted from cells grown at 4 °C. Sequence characterisation of Afp4 showed high similarity to fungal AFPs from Leucosporidium sp. AY30, LeIBP (93 %). The 786-bp cDNA encodes a 261-amino-acid protein with a theoretical pI of 4.4. Attempts to produce the recombinant Afp4 in Escherichia coli resulted in the formation of inclusion bodies (IB). The IB were subsequently denatured and refolded by dilution. Gel filtration confirmed that the refolded recombinant Afp4 is monomeric with molecular mass of ~25 kDa. Thermal hysteresis (TH) and recrystallisation inhibition assays confirmed the function of Afp4 as an antifreeze protein. In the presence of Afp4, ice crystals were modified into hexagonal shapes with TH values of 0.08 °C and smaller ice grains were observed compared with solutions without AFP. Structural analyses via homology modelling showed that Afp4 folds into β-helices with three distinct faces: a, b and c. Superimposition analyses predicted the b-face as the ice-binding surface of Afp4, whereby the mechanism of interaction is driven by hydrophobic interactions and the flatness of surface. This study may contribute towards an understanding of AFPs from psychrophilic yeasts. - Some of the metrics are blocked by yourconsent settings
Publication Transcriptomic Data Of Mature Oil Palm Basal Trunk Tissue Infected With Ganoderma Boninense(Elsevier, 2019) ;Nur Qistina Othman ;Suhaila Sulaiman ;Yang Ping LeeJoon Sheong TanTo date, Ganoderma boninense is known to be the causal agent of basal stem rot (BSR) disease in oil palm (Elaeis guineensis). This disease causes rotting in the roots, basal and upper stem of oil palm. Infection causes progressive destruction of the basal tissues at the oil palm trunk and internal dry rotting, particularly at the intersection between the bole and trunk. Molecular responses of oil palm during infection are not well study although this information is crucial to strategize effective measures to control or eliminate BSR. Here we report three sets of transcriptome data from samples of near-rot section of basal stem tissue of oil palm tree infected with G. boninense (IPIT), healthy section of basal stem tissue of the same G. boninense infected palm (IPHT) and the healthy section of basal stem tissue of the healthy palm (HPHT). The raw reads were deposited into NCBI database and can be accessed via BioProject accession number PRJNA530030.