Genome sequences of two cold-adaptedCryobacterium spp. SO1 and SO2 from FildesPeninsula, Antarctica

Psychrophilic and psychrotrophic bacteria play important roles in nutrient cycling in cold environments. These bacteria are suitable as model organisms for studying cold-adaptation, and sources of cold-active enzymes and metabolites for industrial applications. Here, we report the genome sequences of two Cryobacterium sp. strains SO1 and SO2. Genes coding major proteins related to cold- or thermal-stress adaptations and those with industrial applications found in their genomes are described

Genome sequences of two cold-adaptedCryobacterium spp. SO1 and SO2 from FildesPeninsula, Antarctica

Psychrophilic and psychrotrophic bacteria play important roles in nutrient cycling in cold environments. These bacteria are suitable as model organisms for studying cold-adaptation, and sources of cold-active enzymes and metabolites for industrial applications. Here, we report the genome sequences of two Cryobacterium sp. strains SO1 and SO2. Genes coding major proteins related to cold- or thermal-stress adaptations and those with industrial applications found in their genomes are described

The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat

Extremely 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

The effects of gas phase on the protein conformation a molecular dynamics study on Eotaxin-3 Cytokine

In the current work, the structure of the enzyme CC chemokine eotaxin-3 (IG2S) was chosen as a case study to investigate the effects of gas phase on the protein conformation using molecular dynamics simulation. Generally, simulating proteins in the gas phase tend to suffer from various drawbacks, among which excessive numbers of proteinprotein hydrogen bonds. However, current results showed that the effects of gas phase simulation on IG2S did not amplify the protein-protein hydrogen bonds. It was also found that some of the hydrogen bonds which were crucial in maintaining the secondary structural elements were disrupted

Structure prediction on large protein using the combination of knowledge based and physics based approaches method validation on cholesterol esterase

The objective of this study was to predict the structure of a large protein using a combined approach of knowledge-based comparative modeling and physics-based Molecular Dynamics (MD) simulation applied to the enzyme cholesterol esterase. The core region of the enzyme was modelled using information from homologous known protein structures whereby leaving the end-terminal regions (the nonhomologous regions) to fold via MD simulation. Currently, there is yet a reported study where one begins with a knowledge-based model of the core region of a protein and allowing the remaining end terminal regions to fold via MD simulation. The method was categorized into three parts; ~ the development of the core region of the protein, the development of the complete protein structure and the MD refinement simulation. Three models were tested, CECRL-87, CETHG-45 and CEn~M-14, with each originating from different core regions developed at three different cutoff values of sequence identity; more than 70% (%id > 70%), less than 60% but more than 30% (30% < %id < 60%) and less than 20% (%id < 20%), respectively. The remaining residues were later added using MD simulation which then followed by 20 ns of MD refinement. It was shown that the use of different starting core regions did not significantly contribute towards correct structure predictions of large proteins. Furthermore, the use of restraint of the core region would only deteriorate the model as observed in CETHG-45

Estimation of Nitrogenase Enzyme Activities and Plant Growth of Legume and Non-legume Inoculated with Diazotrophic Bacteria

Biological Nitrogen Fixation (BNF) process benefits the agriculture sector especially for reducing cost of nitrogenfertilizer. In the process, the diazotrophs convert N2 into ammonia (NH3) which is useable by plants. The BNF process iscatalysed by nitrogenase enzyme that involved protons and electrons together with evolution of H2 therefore, theassessment of N2 fixation is also available via H2 production and electron allocation analysis. Thus, the aims of thisexperiment were to estimate the nitrogenase enzyme activities and observe the influence of diazothrophs on growth oflegume (soybean) and non legume (rice) plants. Host plants were inoculated with respective inocula; Bradyrhizobiumjaponicum (strain 532C) for soybean while Azospirillum brasilense (Sp7) and locally isolated diazotroph (isolate 5) forrice. At harvest, the plants were observed for plant growth parameters, H2 evolution, N2 fixation and electron allocationcoefficient (EAC) values. The experiment recorded N2 fixation activities of inoculated soybean plants at 141.2 μmol N2 h-1g-1 dry weight nodule, and the evolution of H2 at 144.4 μmol H2 h-1 g-1 dry weight nodule. The electron allocationcoefficient (EAC) of soybean was recorded at 0.982. For inoculated rice plants, none of the observations was successfully recorded. However, results for chlorophyll contents and plant dry weight of both plants inoculated with respective inocula were similar to the control treatments supplied with full nitrogen fertilization (+N). The experiment clearly showed that inoculation of diazotrophic bacteria could enhance growth of the host plants similar to plants treated with nitrogenous fertilizer due to efficient N2 fixation proces

Characterization and potential applications of a recombinant antifreeze protein from an antarctic yeast Glaciozyma antarctica produced in Pichia pastoris

Ice recrystallization during thawing post-cryopreservation results in extensive cellular damage and ultimately leads to cell death and reduced cell viability. Antifreeze proteins (AFPs) are a group of proteins that allow organisms to survive in subzero environments. These proteins have thermal hysteresis and ice recrystallization inhibitory activities. In this present study, we demonstrated the efficiency of a recombinant antifreeze protein from the Antarctic yeast, Glaciozyma antarctica, as a recrystallization inhibitor (RI) of ice growth and assessed its application as a cryopreservative of the fungal cutinase enzyme against freeze-thaw cycles. Recombinant Afp1 from G. antarctica, a psychrophilic yeast, has been produced in a methylotrophic yeast, Pichia pastoris, system that results in the expression of a hyper-glycoprotein (~55 kDa). Recombinant Afp1 exhibits antifreeze functions: thermal hysteresis (TH) and recrystallization inhibition where the highest TH values recorded for ~0.5°C at 10 mg/mL. The cryoprotective effects of Afp1 on purified recombinant cutinase showed that Afp1 can retain enzymatic activity up to ~20% when subjected to several cycles of freeze thawing. These findings indicate that Afp1 might act as a cryoprotective agent and thus, has great potential in biotechnology applications