Nor Muhammad Mahadi

Malaysia Genome Institute, Kuala Lumpor, Kuala Lumpur, Malaysia

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Publications (84)187.8 Total impact

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    ABSTRACT: Objectives To express and determine the hydrolytic activity of a cellobiohydrolase (TTCBH6B) from the thermophilic fungus Thielavia terrestris in Pichia pastoris. Results Ttcbh6B encodes a protein of 507 amino acid residues with a predicted molecular mass of 54 kDa. TTCBH6B contains a familial 6-glycosyl hydrolase catalytic domain and a type I carbohydrate-binding module. TTCBH6B was expressed and purified to homogeneity but the purified enzyme was inactive against Avicel. It could, however, digest Celluclast-treated Avicel producing cellobiose (0.27 μmol min−1 mg−1). To determine the substrate preferences of TTCBH6B, oligosaccharides of varying numbers of subunits were generated by acid hydrolysis of Avicel and fluorescently tagged. Peaks corresponding to oligosaccharides containing three to six glucose units were reduced to cellobiose after addition of TTCBH6B. Conclusion TTCBH6B is active against shorter oligosaccharides rather than polysaccharides.
    No preview · Article · Feb 2016 · Biotechnology Letters
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    ABSTRACT: A gene encoding a thermotolerant endo-1,4-β-mannanase belonging to glycosyl hydrolase family 5 (GH5) was isolated from the fungal strain Trichoderma virens UKM1 (manTV). The aim of this work was to heterologously express and characterize manTV for subsequent applications. The 1,329 bp β-mannanase gene was cloned and expressed in Pichia pastoris X33 yeast cells, and the recombinant mannanase (rMANTV) was expressed as a His6-tagged glycoprotein of approximately 65–70 kDa. The purified rMANTV showed a specific activity of 415.49 Umg−1 for 0.5% locust bean gum (LBG). This enzyme had a high optimum temperature, 70 °C, with stability from 20 °C to 65 °C. The rMANTV had its highest activity at pH 5, with a wide pH stability range of pH 3–9. It was relatively stable in the presence of several metal ions and chemical substances. In addition, rMANTV had Km values of 2.61 mgmL−1 and 1.49 mgmL−1 for LBG and Konjac glucomannan, respectively. Its catalytic efficiency (Kcat/Km) was 225.41 ± 20.14 mLmg−1 s−1 for LBG and 336.67 ± 27.39 mLmg−1 s−1 for Konjac glucomannan. The high temperature tolerance of this endo-1,4-β-mannanase makes it a good potential candidate for industrial applications.
    No preview · Article · Jan 2016 · Journal of Molecular Catalysis B Enzymatic
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    ABSTRACT: Background Protein microarrays have enormous potential as in vitro diagnostic tools stemming from the ability to miniaturize whilst generating maximum evaluation of diagnostically relevant information from minute amounts of sample. In this report, we present a method known as repeatable arrays of proteins using immobilized DNA microplates (RAPID-M) for high-throughput in situ protein microarray fabrication. The RAPID-M technology comprises of cell-free expression using immobilized DNA templates and in situ protein purification onto standard microarray slides. Results To demonstrate proof-of-concept, the repeatable protein arrays developed using our RAPID-M technology utilized green fluorescent protein (GFP) and a bacterial outer membrane protein (OmpA) as the proteins of interest for microarray fabrication. Cell-free expression of OmpA and GFP proteins using beads-immobilized DNA yielded protein bands with the expected molecular sizes of 27 and 30 kDa, respectively. We demonstrate that the beads-immobilized DNA remained stable for at least four cycles of cell-free expression. The OmpA and GFP proteins were still functional after in situ purification on the Ni–NTA microarray slide. Conclusion The RAPID-M platform for protein microarray fabrication of two different representative proteins was successfully developed.
    Full-text · Article · Nov 2015 · BMC Research Notes
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    ABSTRACT: Malto-oligosaccharide synthesis using maltogenic amylase often struggles with product re-hydrolyzation. The malto-oligosaccharide synthesis using a maltogenic amylase (MAG1) from Bacillus lehensis G1 was enhanced using a structure-guided protein engineering approach. Mutations decreased the hydrolysis activity of the enzyme and caused various modulations in its transglycosylation properties. W359F, Y377F and M375I mutations caused a reduction in steric interference, an alteration of subsite occupation and an increase in internal flexibility to accommodate longer donor/acceptor molecules for transglycosylation, resulting in an increase in the transglycosylation to hydrolysis ratio of up to 4.0-fold. The increase in active site hydrophobicity that was caused from the W359F and M375I mutations reduced the concentration of maltotriose required for use as a donor/acceptor for transglycosylation to 100 mM and 50 mM, respectively, compared to the 200 mM needed for wild-type. An improvement of the transglycosylation to hydrolysis ratio by 4.2-fold was also demonstrated in each of the mutants. Interestingly, a reduction of steric interference and hydrolysis suppression was caused by the Y377F mutation and introduced a synergistic effect to produce malto-oligosaccharides with a higher degree of polymerization than wild-type. These findings showed that modification of the active site structure imposed various effects on MAG1 activities during malto-oligosaccharide synthesis.
    Full-text · Article · Oct 2015 · PROCESS BIOCHEMISTRY
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    ABSTRACT: The gene encoding a cellobiohydrolase (CBH7B) of the thermophilic fungus Thielavia terrestris was identified, sub-cloned and expressed in Pichia pastoris. CBH7B encoded 455 amino acid residues with a molecular mass of 51.8 kD. Domain analysis indicated that CBH7B contains a family 7 glycosyl hydrolase catalytic core but lacks a carbohydrate-binding module (CBM). Purified CBH7B exhibited optimum catalytic activity at pH 5.0 and 55°C with methylumbelliferryl-cellobioside (MUC) as the substrate and retained 85% of its activity following 24 h incubation at 50°C. Despite the lack of activity towards microcrystalline substrates, this enzyme worked synergistically with the commercial enzyme cocktail Cellic® CTec2 to enhance saccharification by 39% when added to a reaction mixture containing 0.25% alkaline pretreated oil palm empty fruit bunch (OPEFB). Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy suggested a reduction of lignin and crystalline cellulose in OPEFB samples supplemented with CBH7B. Scanning electron microscopy (SEM) revealed greater destruction extent of OPEFB strands in samples supplemented with CBH7B as compared to the non-supplemented control. CBH7B therefore has the potential to complement commercial enzymes in hydrolyzing lignocellulosic biomass.
    Full-text · Article · Aug 2015 · Biotechnology and Applied Biochemistry
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    ABSTRACT: The synthesis of small RNA (sRNA) were extracted from Glaciozyma Antarctica PII2 (G. Antarctica) yeast using the Next-Generation Sequencing (NGS) technology. Statistical approach is used in this study to analyze sRNA from G. Antarctica in order to increase the production of this yeast given in biological conditions such as temperature, time and medium of growth. Hence, this study uses the analysis of variance (ANOVA) with F-test statistic (F ANOVA) and shrinkage F-test (F S) to analyze the NGS data in identifying factors affecting the differential expression level of genes from G. Antarctica. F ANOVA statistics are computed on a gene-by-gene basis from the residual sum of squares (SSE). Whereas F S-test refers to the shrinking of variance estimators from the variance estimators of the gene-by-gene (σ  g 2) F-value obtained from ANOVA. Then, the analysis results between F ANOVA-test and F S-test are compared in order to identify which statistical test is best in analyzing significantly differentially expressed gene based on accuracy value and area under the Receiver Operator Characteristics (ROC) curve. The statistical test with higher accuracy value and has a larger area under the ROC curve is the best statistical test. We found that both F ANOVA and F S tests show that the majority of genes that are significantly differentially expressed are most affected by the main effects temperature (A) and time (B) and the interaction effect between temperature and time (AB). As for the best test, we found that F S-test is the best statistical test compared to F
    Full-text · Article · Jun 2015 · Indian Journal of Science and Technology
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    ABSTRACT: Glaciozyma antarctica is a psychrophilic yeast isolated from the Antarctic sea ice. In this study, we performed a de novo characterisation of molecular chaperones from G. antarctica genome datasets. A total of 7857 genes that code for various types of proteins have been predicted from the G. antarctica genome sequence. From these genes, we identified 89 possible molecular chaperones that matched known molecular chaperones from other organisms available in various databases such as Uniprot, Gene Ontology, cpnDB and NCBI. For an in-depth analysis of molecular functions, we used homologous clustering to transfer knowledge from unknown to known functions using Cluster Analysis of Sequences (CLANS) bioinformatics software. The results reveal 12 major groups of chaperones that contribute to the cold-adaptation mechanism through their molecular function, biological processes and cellular components. The findings lay the foundation for future functional genomics studies on this organism and shed light on how lower eukaryotic cells respond to low temperature. © 2015, Malaysian Society of Applied Biology. All rights reserved.
    No preview · Article · Jan 2015
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    ABSTRACT: Glycoside hydrolases are enzymes that hydrolyse glycosidic bonds in carbohydrate chains to produce simple molecules. In fungi, glycoside hydrolases are important enzymes that hydrolyse complex carbohydrates into simple sugars that can subsequently be consumed for energy metabolism. Glaciozyma antarctica is a psychrophilic yeast isolated from sea ice in Antarctica. The G. antarctica genome has been completely sequenced, and a total of 7,857 genes have been predicted. The objective of the present study was to determine different classes of glycoside hydrolases from the G. antarctica genome and predict the localisation of these enzymes. Using genome mining, a total of 97 G. antarctica genes were predicted to encode glycoside hydrolases. The majority of the enzymes, including endoglucanases, xylanases, and chitinases, were identified from GH family 5 (12 genes), followed by GH family 45 (11 genes), GH family 10 (11 genes) and GH family 18 (9 genes). The secreted glycoside hydrolase enzymes were primarily endoglucanases from GH family 45, and these enzymes degrade celluloses in the cell walls of plants and algae. Extracellular glycoside hydrolases have been implicated as important in nutrient scavenging and organic decomposition in Antarctic sea ice. © 2015, Malaysian Society of Applied Biology. All rights reserved.
    No preview · Article · Jan 2015
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    ABSTRACT: To survive in extremely cold environments, psychrophilic microorganisms produce exopolysaccharides (EPS), which are carbohydrate polymers that constitute a substantial component of the extracellular polymers surrounding cells of these microorganisms. EPS can interfere with RNA extraction and decrease the purity of the RNA extracted from EPS producing microorganisms. In this work, six commercial RNA extraction kits and two published protocols for RNA extraction were evaluated for total RNA extraction from the psychrophilic yeast, Glaciozyma antarctica. All the protocols were optimised to obtain the highest quality of total RNA. The results show that all of the tested commercial kits and the tested conventional methods yielded RNA from G. antarctica, albeit with varying quality. The protocol that utilises TRIzolⓇ reagent was the most effective method for isolating total RNA from G. antarctica of which this protocol resulted in the highest RNA yield and purity compared to other methods. This method of RNA extraction produced RNA of sufficient quality for reverse transcriptase PCR (RT-PCR) to detect the expression of the G. antarctica delta 9-fatty acid desaturase gene as well as for the construction of a G. antarctica cDNA library. © 2014, Malaysian Society of Applied Biology. All rights reserved.
    Full-text · Article · Dec 2014 · Malaysian Applied Biology
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    Full-text · Dataset · Oct 2014
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    ABSTRACT: A maltogenic amylase (MAG1) from alkaliphilicBacillus lehensisG1 was cloned, expressed inEscherichia coli, purified and characterised for its hydrolysis and transglycosylation properties. The enzyme exhibited high stability at pH values from 7.0 to 10.0. The hydrolysis of b-cyclodextrin (b-CD) produced malto-oligosaccharides of various lengths. In addition to hydrolysis, MAG1 also demonstrated transglycosylation activity for the synthesis of longer malto-oligosaccharides. The thermodynamic equilibrium of the multiple reactions was shifted towards synthesis when the reaction conditions were optimised and the water activity was suppressed, which resulted in a yield of 38% transglycosylation products consisting of malto-oligosaccharides of various lengths. Thin layer chromatography and high-performance liquid chromatography analyses revealed the presence of malto-oligosaccharides with a higher degree of polymerisation than maltoheptaose, which has never been reported for other maltogenic amylases. The addition of organic solvents into the reaction further suppressed the water activity. The increase in the transglycosylation-to-hydrolysis ratio from 1.29 to 2.15 and the increased specificity toward maltopentaose production demonstrated the enhanced synthetic property of the enzyme. The high transglycosylation activity of maltogenic amylase offers a great advantage for synthesising malto-oligosaccharides and rare carbohydrates.
    Full-text · Article · Sep 2014 · PLoS ONE
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    ABSTRACT: Bacillus lehensis G1 is a Gram-positive, moderately alkalitolerant bacterium isolated from soil samples. B. lehensis produces cyclodextrin glucanotransferase (CGTase), an enzyme that has enabled the extensive use of cyclodextrin in foodstuffs, chemicals, and pharmaceuticals. The genome sequence of B. lehensis G1 consists of a single circular 3.99 Mb chromosome containing 4017 protein-coding sequences (CDSs), of which 2818 (70.15%) have assigned biological roles, 936 (23.30%) have conserved domains with unknown functions, and 263 (6.55%) have no match with any protein database. Bacillus clausii KSM-K16 was established as the closest relative to B. lehensis G1 based on gene content similarity and 16S rRNA phylogenetic analysis. A total of 2820 proteins from B. lehensis G1 were found to have orthologues in B. clausii, including sodium–proton antiporters, transport proteins, and proteins involved in ATP synthesis. A comparative analysis of these proteins and those in B. clausii and other alkaliphilic Bacillus species was carried out to investigate their contributions towards the alkalitolerance of the microorganism. The similarities and differences in alkalitolerance-related genes among alkalitolerant/alkaliphilic Bacillus species highlight the complex mechanism of pH homeostasis. The B. lehensis G1 genome was also mined for proteins and enzymes with potential viability for industrial and commercial purposes.
    Full-text · Article · Jul 2014 · Gene

  • No preview · Article · Jul 2014 · PLoS ONE
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    ABSTRACT: Antifreeze proteins (AFPs) are proteins with affinity towards ice and contribute to the survival of psy-chrophiles 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 pro-duce the recombinant Afp4 in Escherichia coli resulted in the formation of inclusion bodies (IB). The IB were subsequently denatured and refolded by dilution. Gel fil-tration 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 b-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.
    Full-text · Article · Jul 2014 · Polar Biology
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    ABSTRACT: Burkholderia pseudomallei is an opportunistic pathogen and the causative agent of melioidosis. It is able to adapt to harsh environments and can live intracellularly in its infected hosts. In this study, identification of transcriptional factors that associate with the β' subunit (RpoC) of RNA polymerase was performed. The N-terminal region of this subunit is known to trigger promoter melting when associated with a sigma factor. A pull-down assay using histidine-tagged B. pseudomallei RpoC N-terminal region as bait showed that a hypothetical protein BPSS1356 was one of the proteins bound. This hypothetical protein is conserved in all B. pseudomallei strains and present only in the Burkholderia genus. A BPSS1356 deletion mutant was generated to investigate its biological function. The mutant strain exhibited reduced biofilm formation and a lower cell density during the stationary phase of growth in LB medium. Electron microscopic analysis revealed that the ΔBPSS1356 mutant cells had a shrunken cytoplasm indicative of cell plasmolysis and a rougher surface when compared to the wild type. An RNA microarray result showed that a total of 63 genes were transcriptionally affected by the BPSS1356 deletion with fold change values of higher than 4. The expression of a group of genes encoding membrane located transporters was concurrently down-regulated in ΔBPSS1356 mutant. Amongst the affected genes, the putative ion transportation genes were the most severely suppressed. Deprivation of BPSS1356 also down-regulated the transcriptions of genes for the arginine deiminase system, glycerol metabolism, type III secretion system cluster 2, cytochrome bd oxidase and arsenic resistance. It is therefore obvious that BPSS1356 plays a multiple regulatory roles on many genes.
    Full-text · Article · Jun 2014 · PLoS ONE
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    ABSTRACT: A Pichia pastoris transformant carrying the cutinase cDNA of Glomerella cingulata was over-expressed in a 5 L bioreactor (2.0L working volume) under fed-batch conditions. Bioreactor experiments rely on varying selected parameters in repeated rounds of optimisation: here these included duration of induction, pH and temperature. Highest cell densities (320g.L(-1) wet cell weight) with a cutinase production of 3,800mg.L(-1) and an activity of 434 U.mL(-1) were achieved 24h after induction with methanol in basal salt medium (at pH 5 and 28°C). Characterisation of the cutinase showed that it was stable between pH 6 and pH 11, had an optimum pH of 8.0 and retained activity for 30min at 50°C (optimum temperature 25°C).The preferred substrates of G. cingulata cutinase were the medium- to long-chain ρ-nitrophenyl esters of ρ-nitrophenylcaprylate (C8), ρ-nitrophenyllaurate (C12) and ρ-nitrophenylmyristate (C14), with the highest catalytic efficiency, kcat/Km of 7.7±0.7mM(-1)s(-1) for ρ-nitrophenylcaprylate. Microscopic analyses showed that the G. cingulata cutinase was also capable of depolymerising the high molecular weight synthetic polyester, polyethylene terephthalate.
    Full-text · Article · Jun 2014 · Journal of Biotechnology
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    ABSTRACT: Bacillus lehensis G1 is a Gram-positive, moderately alkalitolerant bacterium isolated from soil samples. B. lehensis produces cyclodextrin glucanotransferase (CGTase), an enzyme that has enabled the extensive use of cyclodextrin in foodstuffs, chemicals, and pharmaceuticals. The genome sequence of B. lehensis G1 consists of a single circular 3.99Mb chromosome containing 4017 protein-coding sequences (CDSs), of which 2818 (70.15%) have assigned biological roles, 936 (23.30%) have conserved domains with unknown functions, and 263 (6.55%) have no match with any protein database. Bacillus clausii KSM-K16 was established as the closest relative to B. lehensis G1 based on gene content similarity and 16S rRNA phylogenetic analysis. A total of 2820 proteins from B. lehensis G1 were found to have orthologues in B. clausii, including sodium-proton antiporters, transport proteins, and proteins involved in ATP synthesis. A comparative analysis of these proteins and those in B. clausii and other alkaliphilic Bacillus species was carried out to investigate their contributions towards the alkalitolerance of the microorganism. The similarities and differences in alkalitolerance-related genes among alkalitolerant/alkaliphilic Bacillus species highlight the complex mechanism of pH homeostasis. The B. lehensis G1 genome was also mined for proteins and enzymes with potential viability for industrial and commercial purposes.
    Full-text · Article · May 2014 · Gene
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    ABSTRACT: Lactococcus lactis is the most studied mesophilic fermentative lactic acid bacterium. It is used extensively in the food industry and plays a pivotal role as a cell factory and also as vaccine delivery platforms. The proteome of the Malaysian isolated L. lactis M4 dairy strain, obtained from the milk of locally bred cows, was studied to elucidate the physiological changes occurring between the growth phases of this bacterium. In this study, ultraperformance liquid chromatography nanoflow electrospray ionization tandem mass spectrometry (UPLC- nano-ESI-MS(E)) approach was used for qualitative proteomic analysis. A total of 100 and 121 proteins were identified from the midexponential and early stationary growth phases, respectively, of the L. lactis strain M4. During the exponential phase, the most important reaction was the generation of sufficient energy, whereas, in the early stationary phase, the metabolic energy pathways decreased and the biosynthesis of proteins became more important. Thus, the metabolism of the cells shifted from energy production in the exponential phase to the synthesis of macromolecules in the stationary phase. The resultant proteomes are essential in providing an improved view of the cellular machinery of L. lactis during the transition of growth phases and hence provide insight into various biotechnological applications.
    Full-text · Article · Mar 2014
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    ABSTRACT: At least a quarter of any complete genome encodes for hypothetical proteins (HPs) which are largely non-similar to other known, well-characterized proteins. Predicting and solving their structures and functions is imperative to aid understanding of any given organism as a complete biological system. The present study highlights the primary effort to classify and cluster 1202 HPs of Bacillus lehensis G1 alkaliphile to serve as a platform to mine and select specific HP(s) to be studied further in greater detail. All HPs of B. lehensis G1 were grouped according to their predicted functions based on the presence of functional domains in their sequences. From the metal-binding group of HPs of the cluster, an HP termed Bleg1_2507 was discovered to contain a thioredoxin (Trx) domain and highly-conserved metal-binding ligands represented by Cys69, Cys73 and His159, similar to all prokaryotic and eukaryotic Sco proteins. The built 3D structure of Bleg1_2507 showed that it shared the betaalphabetaalphabetabeta core structure of Trx-like proteins as well as three flanking beta-sheets, a 310 -helix at the N-terminus and a hairpin structure unique to Sco proteins. Docking simulations provided an interesting view of Bleg1_2507 in association with its putative cytochrome c oxidase subunit II (COXII) redox partner, Bleg1_2337, where the latter can be seen to hold its partner in an embrace, facilitated by hydrophobic and ionic interactions between the proteins. Although Bleg1_2507 shares relatively low sequence identity (47%) to BsSco, interestingly, the predicted metal-binding residues of Bleg1_2507 i.e. Cys-69, Cys-73 and His-159 were located at flexible active loops similar to other Sco proteins across biological taxa. This highlights structural conservation of Sco despite their various functions in prokaryotes and eukaryotes. We propose that HP Bleg1_2507 is a Sco protein which is able to interact with COXII, its redox partner and therefore, may possess metallochaperone and redox functions similar to other documented bacterial Sco proteins. It is hoped that this scientific effort will help to spur the search for other physiologically relevant proteins among the so-called "orphan" proteins of any given organism.
    Full-text · Article · Mar 2014 · BMC Structural Biology
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    ABSTRACT: One of the prerequisites for the functional and structural characterisation of proteins is to obtain a sufficiently high amount of the protein sample. Recombinant protein expression systems are usually employed for the overproduction of proteins in cases where isolation from their native host is difficult. For each protein, a suitable expression system must be optimised to obtain the sample in a soluble, correctly folded conformation with high production yield. The recent discovery of psychrophilic yeasts and their potential in industrial applications have sparked interest in overexpression strategies for high-level expression of psychrophilic proteins. Here, we discuss some of the recent developments in the recombinant production of cold-adapted yeast proteins, particularly those from Glaciozyma antarctica PI12, in suitable heterologous hosts. Findings from our work, as well as from recent publications, are included.
    No preview · Chapter · Jan 2014

Publication Stats

434 Citations
187.80 Total Impact Points

Institutions

  • 2007-2015
    • Malaysia Genome Institute
      Kuala Lumpor, Kuala Lumpur, Malaysia
  • 2005-2015
    • National University of Malaysia
      • • Institute of Systems Biology (INBIOSIS)
      • • School of Biosciences and Biotechnology
      Putrajaya, Putrajaya, Malaysia
  • 2004
    • National Institute of Molecular Biology and Biotechnology
      Diliman, Central Luzon, Philippines