Regulation studies of phaC(C1 and C2) genes in Pseudomonas sp. USM 4-55

Among the various biodegradable plastics available, polyhydroxyalkanoates (PHAs) attract a lot of attention because these polymers are produced by bacteria and have thermoplastic properties. They are biodegradable, biocompatible, moisture resistant, versatile, have long shelf life and are made from renewable source materials (Pouton et al., 1996)

Biosynthetic production of human growth hormone gene in methylotrophic yeast, Pichia pastoris

Human growth hormone (hGH) is secreted from the anterior pituitary gland and exerts a wide variety of functions such as, IGF-1 production, protein synthesis, glucose metabolism, lipolysis, lipogenesis, and cell proliferation/differentiation (Isaksson et al., 1985; Press, 1988; Thorner and Vance, 1988; Strobl and Thomas, 1994)

Cloning and characterization of polyhydroxyalkanoate (PHA) genes from Pseudomonas sp. isolated from Antarctica

Pseudomonas strains accumulate mediumchain-length poly(R)-3-hydroxyalkanoate (PHA) as carbon and energy source under conditions of limiting nutrients in the presence of an excess of carbon source (Fidler et al., 1992)

Pengenalpastian dan profil pengekspresan gen biosintesis asid amino yis psikrofil, Glaciozyma antarctica

Mekanisme pengambilan dan penghasilan asid amino bagi mikroorganisma psikrofil yang bermandiri dan berpoliferasi pada persekitaran sejuk melampau masih belum difahami sepenuhnya. Objektif kajian ini ialah untuk mengenal pasti gen yang terlibat dalam penjanaan asid amino bagi yis psikrofil, Glaciozyma antarctica serta menentukan pengekspresan gen tersebut semasa kehadiran dan kekurangan asid amino dalam medium pertumbuhan. Pengenalpastian gen telah dilakukan melalui penjanaan penanda jujukan terekspres (ESTs) daripada dua perpustakaan cDNA yang dibina daripada sel yang dikultur dalam medium pertumbuhan kompleks dan medium pertumbuhan minimum tanpa asid amino. Sebanyak 3552 klon cDNA daripada setiap perpustakaan dipilih secara rawak untuk dijujuk menghasilkan 1492 transkrip unik (medium kompleks) dan 1928 transkrip unik (medium minimum). Analisis pemadanan telah mengenl pasti gen mengekod protein yang terlibat di dalam pengambilan asid amino bebas, biosintesis asid amino serta gen yang terlibat dengan kitar semula asid amino berdasarkan tapak jalan yang digunakan oleh yis model, Saccharomyces cerevisiae. Analisis pengekspresan gen menggunakan kaedah RT-qPCR menunjukkan pengekspresan gen mengekod protein yang terlibat di dalam pengambilan asid amino bebas iaitu permease adalah tinggi pada medium kompleks manakala pengekspresan kebanyakan gen mengekod protein yang terlibat dalam kitar semula dan biosintesis asid amino adalah tinggi di dalam medium minimum. Kesimpulannya, gen yang terlibat dalam penjanaan dan pengambilan asid amino bagi mikroorganisma psikrofil adalah terpulihara seperti mikroorganisma mesofil dan pengekspresan gen-gen ini adalah diaruh oleh kehadiran atau ketiadaan asid amino bebas pada persekitaran

Identification and expression profiles of amino acid biosynthesis genes from psychrophilic yeast, glaciozyma antarctica

The mechanism of amino acid uptake and synthesis in the psychrophilic microorganism lives and proliferate in the extreme low-temperature environment is still not well understood. The aim of this study was to identify genes involved in amino acid generation for psychrophilic yeast, Glaciozyma antarctica and to determine their expression profiles when cells grow in media rich in amino acids or with limited amount of amino acids. The identification of genes was carried out by generating expressed sequence tags (EST) from two cDNA libraries generated from cells grown in complex growth medium and minimal growth medium without amino acids. A total of 3552 cDNA clones from each library was randomly picked and sequenced, generating 1492 unique transcripts (complex medium) and 1928 unique transcripts (minimal medium). Homology analyses have identified genes encoding proteins required for free amino acid uptake, biosynthesis of amino acids and recycling of amino acids based on the pathway used in the model yeast, Saccharomyces cerevisiae. Gene expression analysis by RT-qPCR showed that genes required for free amino acid uptake showed a higher expression profile in the complex medium, whereas the expression of most genes encode for proteins essential for biosynthesis and recycling of amino acids are higher in the minimal medium. In summary, genes that are involved in the generation and the uptake of amino acids for psychrophilic microorganism are conserved as in their mesophilic counterparts and the expression of these genes are regulated in the presence or absent of free amino acids in the surrounding

An approach towards the prediction of protein tertiary structures: molecular modeling perspectives

Impressive advances in genomic sequencing technologies are flooding us with the complete genetic blueprints of human, rat, mouse, chimpanzee and various microorganisms at an extremely rapid pace. As these DNA sequences continue to accumulate, the challenge to determine the function of each gene is paramount. These functions are determined by their unique three-dimensional (3D) structures as a result of protein folding. Protein folding can be defined as the process in which proteins spontaneously arrange their linear sequence of amino acids into native 3D structures that will allow them to function properly. Thus, elucidation of the 3D structure of a protein is vital in understanding its function. However, it is not known how the newly synthesized polypeptide chains fold into a protein with specific function. It was not until 1973 that Anfinsen [1] postulated that all the information needed for a protein to correctly fold into its native structure is encoded solely in its amino acid sequence and that the native state of the protein is the conformation with the lowest energy. Consequently, this important principle has brought immense interests among the scientists to investigate how proteins fold into their native structures and eventually determine the correct functional fold for the proteins. The two most mature and conventional experimental techniques to solve the structure of a protein are the X-ray crystallography and Nuclear Magnetic Resonance (NMR). John Kendrew and Max Perutz shared the Nobel Prize in 1962 for their pioneering achievement in solving the atomic level structure of the protein myoglobin and hemoglobin, respectively, using X-ray diffraction. Since then, many protein structures were solved and various roles of proteins in living cells were known. Despite the accuracy and the advances of these experimental techniques, such methods are very costly and it may take months to years for solving one structure. The current number of 3D protein structures is very small compared to the number of protein sequences, creating a huge gap between them. It has become more pressing with the growth of genome sequencing projects providing protein sequences for which structural information is not available. As this gap is expected to keep on growing with the ongoing genome projects, the experimental techniques certainly cannot be expected to keep pace with the rapid flow of the sequences. This has caused an urgent need to accurately predict the 3D structure of proteins from the linear chain of amino acid sequence using other methods especially computational work that relies heavily on theoretical studies. However, despite decades of active research and the impressive advances [2,3,4,5], computational protein structure prediction and protein folding remain one of the most important unsolved problems in structural biology today [6,7,8]

Phylogeny and Characterization of Three nifH-Homologous Genes from Paenibacillus azotofixans

In this paper, we report the cloning and characterization of three Paenibacillus azotofixans DNA regions containing genes involved in nitrogen fixation. Sequencing analysis revealed the presence of nifB1H1D1K1 gene organization in the 4,607-bp SacI DNA fragment. This is the first report of linkage of a nifB open reading frame upstream of the structural nif genes. The second (nifB2H2) and third (nifH3) nif homologues are confined within the 6,350-bp HindIII and 2,840-bp EcoRI DNA fragments, respectively. Phylogenetic analysis demonstrated that NifH1 and NifH2 form a monophyletic group among cyanobacterial NifH proteins. NifH3, on the other hand, clusters among NifH proteins of the highly divergent methanogenic archaea