Mohd Firdaus Raih

NBBnet - The National Biotechnology and Bioinformatics Network: A Malaysian initiative towards a national infrastructure for bioinformatics

Bioinformatics is a necessary technology and tool, which current molecular biologists cannot do without in light of the genome data explosion and advent of fields such as genomics and proteomics. Yet, even with this in mind, there is still a limited pool of human resource to support and develop bioinformatics particularly in poorer developing nations. The highly multidisciplinary nature of this field can be an obstacle in converting just any molecular biologist into a proficient and capable bioinformaticist. Coupled with the high costs of software, hardware, technical maintenance and systems support; many developing and poor countries may not be able to fully realize their biotech potential either academically or economically due to the inability to fully utilize bioinformatics as a technology to support and co-develop with molecular biology oriented research programmes. Malaysia, a developing South East Asian nation took steps to counter these problems and develop an infrastructure for bioinformatics to support nationally important biotech research agendas, particularly government initiatives in genomics and proteomics, with the setting up of NBBnet - The National Biotechnology and Bioinformatics network. We further propose the setting up of similar models in other developing countries, an endeavour which we are willing to share our experiences and resources. We hope that these networks may in the future evolve into a super network of national or regional networks on biotechnology and bioinformatics.

Draft Genome Sequence of Erwinia mallotivora BT-MARDI, Causative Agent of Papaya Dieback Disease

ABSTRACT Erwinia mallotivora was isolated from papaya trees infected with dieback disease, which were planted at the Malaysian Agricultural Research and Development Institute (MARDI), Malaysia. Here, we report a draft genome sequence of E. mallotivora BT-MARDI, which offers an important source of information for understanding pathogen and host interaction during papaya dieback development.

A comparative genomic analysis of the alkalitolerant soil bacterium Bacillus lehensis G1

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.

ProLysED: An integrated database and meta-server of bacterial protease systems

UNLABELLED Bacterial proteases are an important group of enzymes that have very diverse biochemical and cellular functions. Proteases from prokaryotic sources also have a wide range of uses, either in medicine as pathogenic factors or in industry and therapeutics. ProLysED (Prokaryotic Lysis Enzymes Database), our meta-server integrated database of bacterial proteases, is a useful, albeit very niche, resource. The features include protease classification browsing and searching, organism-specific protease browsing, molecular information and visualisation of protease structures from the Protein Data Bank (PDB) as well as predicted protease structures. AVAILABILITY ProLysED is integrated into the ProLysES (Prokaryotic Lysis Enzymes Site) website at http://genome.ukm.my/prolyses/. Access to the ProLysED database is free for academic users upon registration.

EMASGRID: an NBBnet grid initiative for a bioinformatics and computational biology servicesinfrastructure in malaysia

The plethora of bioinformatics tools currently available to the biologist, and the diversity of problems that these applications were designed to solve, has necessitated a look at providing a single environment which can serve as an interface to these many applications. At the same time, this environment should also be able to function as an infrastructure resource with adequate computational capacity to solve the data volume which is currently available from numerous genomics projects. We discuss the setting up of a national level infrastructure initiative which utilizes grid computing technology to serve geographically distributed users in Malaysia. This infrastructure was designed to provide access to high performance computational resources made available by Sun Microsystems Sun Grid Engine (SGE) using different interfaces which access a pipeline of bioinformatics software. The underlying computer system, such as operating systems and high performance computing applications, were bypassed with the creation of an application layer of bioinformatics tools (BioGrappler) or by accessing the compute resources by the Grid Engine Portal (BioBox).

Structure prediction of Fe(II) 2-oxoglutarate dioxygenase from a psychrophilic yeast Glaciozyma antarctica PI12

A cDNA encoding Fe(II) 2-oxoglutarate (2OG) dependent dioxygenases was isolated from psychrophilic yeast, Glaciozyma antarctica PI12. We have successfully amplified 1,029 bp cDNA sequence that encodes 342 amino acid with predicted molecular weight 38 kDa. The prediction protein was analysed using various bioinformatics tools to explore the properties of the protein. Based on a BLAST search analysis, the Fe2OX amino acid sequence showed 61% identity to the sequence of oxoglutarate/iron-dependent oxygenase from Rhodosporidium toruloides NP11. SignalP prediction showed that the Fe2OX protein contains no putative signal peptide, which suggests that this enzyme most probably localised intracellularly.The structure of Fe2OX was predicted by homology modelling using MODELLER9v11. The model with the lowest objective function was selected from hundred models generated using MODELLER9v11. Analysis of the structure revealed the longer loop at Fe2OX from G.antarctica that might be responsible for the flexibility of the structure, which contributes to its adaptation to low temperatures. Fe2OX hold a highly conserved Fe(II) binding HXD/E…H triad motif. The binding site for 2-oxoglutarate was found conserved for Arg280 among reported studies, however the Phe268 was found to be different in Fe2OX.

A predicted structure of the cytochrome c oxidase from Burkholderia pseudomallei

Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen. The enzyme belongs to the haem-copper-containing oxidases superfamily. A recombinant plasmid carrying a 2.0 kb insert from a Burkholderia pseudomallei genomic library was subjected to automated DNA sequencing utilizing a primer walking strategy. Analysis of the 2002 bp insert revealed a 1536 bp open reading frame predicted to encode a putative cytochrome c oxidase. Further analysis using sequence alignments and tertiary structure analysis tools demonstrated that the hypothetical B. pseudomallei cytochrome c oxidase is similar to cytochrome c oxidases from other organisms such as Thermus thermophilus (36% protein sequence identity), Paracoccus denitrificans and bovine heart mitochondrial, the latter two which crystal structures available. The deduced 512 residue protein sequence includes the six canonical histidine residues involved in binding the low spin heme B and the binuclear center Cu B /hemeA. The predicted tertiary structure of the hypothetical protein is consistent with previous models of electron transfer for cytochrome c oxidase.

Pencirian molekul glikogen sintase kinase-3 dari Eimeria tenella

Penemuan sasaran dadah antikoksidia baharu merupakan antara usaha yang diperlukan untuk mengawal penyakit koksidiosis ayam yang disebabkan oleh spesies Eimeria. Dalam kajian ini, serpihan yang mengekodkan glikogen sintase kinase-3 (GSK-3) Eimeria tenella putatif telah diamplifikasi daripada cDNA E. tenella. Hasil pemadanan homologi menunjukkan jujukan GSK-3 E. tenella yang terjana mempunyai padanan yang tinggi dengan jujukan GSK-3 organisma lain. Domain terpulihara GSK-3 dan residu yang penting untuk aktiviti GSK-3 juga diramalkan hadir dalam jujukan GSK-3 E. tenella. Analisis struktur sekunder serta pemodelan homologi menunjukkan pembahagian struktur protein kepada domain bebenang beta pada hujung N dan domain heliks alfa pada hujung C, yang merupakan ciri enzim GSK-3. Kesemua hasil analisis ini menyokong bahawa jujukan yang dikaji mengekodkan protein GSK-3 dalam E. tenella. Walaupun darjah keterpuliharaan adalah tinggi, namun terdapat perbezaan yang bermakna diperhatikan antara GSK-3 E. tenella dan perumahnya. Residu Ser 9 yang dilaporkan penting untuk perencatan aktiviti GSK-3 didapati tidak terpulihara dalam GSK-3 E. tenella. Memandangkan Ser 9 merupakan tapak pemfosfatan bagi GSK-3β dalam haiwan vertebrata, ketiadaan residu ini dalam jujukan GSK-3 E. tenella mencadangkan bahawa pengawalaturan GSK-3 E. tenella melibatkan tapak pemfosfatan dan mekanisme yang berbeza. Tambahan pula, hasil analisis filogenetik menunjukkan bahawa GSK-3 E. tenella mempunyai pertalian yang rapat dengan protein GSK-3 tumbuh-tumbuhan. Analisis superposisi GSK-3 E. tenella dengan GSK-3β Homo sapiens pula menunjukkan bahawa perencat GSK-3 mampu berinteraksi dengan protein GSK-3 E. tenella. Keputusan kajian ini mencadangkan bahawa GSK-3 E. tenella mempunyai potensi untuk diperkembangkan sebagai sasaran dadah antikoksidia.