Unravelling the adaptation strategies employed by Glaciozyma antarctica PI12 on Antarctic sea ice

Biochemical and in silico structural characterization of a cold-active arginase from the psychrophilic yeast, Glaciozyma antarctica PI12

Glaciozyma antarctica PI12 is a psychrophilic yeast isolated from Antarctica. In this work, we describe the heterologous production, biochemical properties and in silico structure analysis of an arginase from this yeast (GaArg). GaArg is a metalloenzyme that catalyses the hydrolysis of L-arginine to L-ornithine and urea. The cDNA of GaArg was reversed transcribed, cloned, expressed and purified as a recombinant protein in Escherichia coli. The purified protein was active against L-arginine as its substrate in a reaction at 20 °C, pH 9. At 10-35 °C and pH 7-9, the catalytic activity of the protein was still present around 50%. Mn2+, Ni2+, Co2+ and K+ were able to enhance the enzyme activity more than two-fold, while GaArg is most sensitive to SDS, EDTA and DTT. The predicted structure model of GaArg showed a very similar overall fold with other known arginases. GaArg possesses predominantly smaller and uncharged amino acids, fewer salt bridges, hydrogen bonds and hydrophobic interactions compared to the other counterparts. GaArg is the first reported arginase that is cold-active, facilitated by unique structural characteristics for its adaptation of catalytic functions at low-temperature environments. The structure and function of cold-active GaArg provide insights into the potentiality of new applications in various biotechnology and pharmaceutical industries.

The Unusual Dominance of the Yeast Genus Glaciozyma in the Deeper Layer in an Antarctic Permafrost Core (Adélie Cove, Northern Victoria Land) Is Driven by Elemental Composition

Rock glaciers are relatively common in Antarctic permafrost areas and could be considered postglacial cryogenic landforms. Although the extensive presence of rock glaciers, their chemical–physical and biotic composition remain scarce. Chemical–physical parameters and fungal community (by sequencing the ITS2 rDNA, Illumina MiSeq) parameters of a permafrost core were studied. The permafrost core, reaching a depth of 6.10 m, was divided into five units based on ice content. The five units (U1–U5) of the permafrost core exhibited several significant (p < 0.05) differences in terms of chemical and physical characteristics, and significant (p < 0.05) higher values of Ca, K, Li, Mg, Mn, S, and Sr were found in U5. Yeasts dominated on filamentous fungi in all the units of the permafrost core; additionally, Ascomycota was the prevalent phylum among filamentous forms, while Basidiomycota was the dominant phylum among yeasts. Surprisingly, in U5 the amplicon sequence variants (ASVs) assigned to the yeast genus Glaciozyma represented about two-thirds of the total reads. This result may be considered extremely rare in Antarctic yeast diversity, especially in permafrost habitats. Based on of the chemical–physical composition of the units, the dominance of Glaciozyma in the deepest unit was correlated with the elemental composition of the core.

The Effects of Different Doses of ROCK Inhibitor, Antifreeze Protein III, and Boron Added to Semen Extender on Semen Freezeability of Ankara Bucks

In the presented study, the effects of ROCK inhibitor Y-27632, antifreeze protein III, and boron at two different doses were investigated on the spermatological parameters of Ankara buck semen after freeze−thawing. Ejaculates were collected from bucks using an electroejaculator during the breeding season. The ejaculates that showed appropriate characteristics were pooled and used in the dilution and freezing of semen. The extender groups were formed by adding two different doses of three different additives (ROCK inhibitor Y-27632, 5 and 20 µM; antifreeze protein III, 1 and 4 µg/mL; boron, 0.25 and 1 mM) to the control extender. The semen was diluted with the different extenders at 35−37 °C and loaded into straws. Sperm samples frozen in liquid nitrogen vapors, following equilibration, were stored in liquid nitrogen. It was observed that extender supplementation improved post-thaw motility of Ankara buck semen after freeze−thawing. Differences were significant (p < 0.01) for 5 and 10 µM doses of ROCK inhibitor (71.82% and 74.04 % motility), as well as for 0.25 and 1 mM doses of boron (76.36% and 72.08% motility), compared to the control group (66.15% motility). With respect to the evaluation of acrosomal integrity and mitochondrial activity after freeze−thawing, although supplementation provided protection at all doses, the efficacy was not statistically significant (p > 0.05). It was observed that DNA damage was improved by antifreeze protein III at 1 µg/mL (1.23% ± 0.23%) and by boron at all doses (0.25 mM: 1.83% and 1 mM: 1.18%) compared to the control group (3.37%) (p < 0.01), following the thawing process. In the present study, it was determined that some additives added to the extender provided significant improvements in buck spermatozoa motility and DNA damage after thawing.

Review Update on the Life Cycle, Plant–Microbe Interaction, Genomics, Detection and Control Strategies of the Oil Palm Pathogen Ganoderma boninense

Plant pathogens are key threats to agriculture and global food security, causing various crop diseases that lead to massive economic losses. Palm oil is a commodity export of economic importance in Southeast Asia, especially in Malaysia and Indonesia. However, the sustainability of oil palm plantations and production is threatened by basal stem rot (BSR), a devastating disease predominantly caused by the fungus Ganoderma boninense Pat. In Malaysia, infected trees have been reported in nearly 60% of plantation areas, and economic losses are estimated to reach up to ~USD500 million a year. This review covers the current knowledge of the mechanisms utilized by G. boninense during infection and the methods used in the disease management to reduce BSR, including cultural practices, chemical treatments and antagonistic microorganism manipulations. Newer developments arising from multi-omics technologies such as whole-genome sequencing (WGS) and RNA sequencing (RNA-Seq) are also reviewed. Future directions are proposed to increase the understanding of G. boninense invasion mechanisms against oil palm. It is hoped that this review can contribute towards an improved disease management and a sustainable oil palm production in this region.

Cold Adaptation Strategies and the Potential of Psychrophilic Enzymes from the Antarctic Yeast, Glaciozyma antarctica PI12

Psychrophilic organisms possess several adaptive strategies which allow them to sustain life at low temperatures between −20 to 20 °C. Studies on Antarctic psychrophiles are interesting due to the multiple stressors that exist on the permanently cold continent. These organisms produce, among other peculiarities, cold-active enzymes which not only have tremendous biotechnological potential but are valuable models for fundamental research into protein structure and function. Recent innovations in omics technologies such as genomics, transcriptomics, proteomics and metabolomics have contributed a remarkable perspective of the molecular basis underpinning the mechanisms of cold adaptation. This review critically discusses similar and different strategies of cold adaptation in the obligate psychrophilic yeast, Glaciozyma antarctica PI12 at the molecular (genome structure, proteins and enzymes, gene expression) and physiological (antifreeze proteins, membrane fluidity, stress-related proteins) levels. Our extensive studies on G. antarctica have revealed significant insights towards the innate capacity of- and the adaptation strategies employed by this psychrophilic yeast for life in the persistent cold. Furthermore, several cold-active enzymes and proteins with biotechnological potential are also discussed.

Diversity, Ecological Role and Biotechnological Potential of Antarctic Marine Fungi

The Antarctic Ocean is one of the most remote and inaccessible environments on our planet and hosts potentially high biodiversity, being largely unexplored and undescribed. Fungi have key functions and unique physiological and morphological adaptations even in extreme conditions, from shallow habitats to deep-sea sediments. Here, we summarized information on diversity, the ecological role, and biotechnological potential of marine fungi in the coldest biome on Earth. This review also discloses the importance of boosting research on Antarctic fungi as hidden treasures of biodiversity and bioactive molecules to better understand their role in marine ecosystem functioning and their applications in different biotechnological fields.

Oil Bioremediation in the Marine Environment of Antarctica: A Review and Bibliometric Keyword Cluster Analysis

Bioremediation of hydrocarbons has received much attention in recent decades, particularly relating to fuel and other oils. While of great relevance globally, there has recently been increasing interest in hydrocarbon bioremediation in the marine environments of Antarctica. To provide an objective assessment of the research interest in this field we used VOSviewer software to analyze publication data obtained from the ScienceDirect database covering the period 1970 to the present, but with a primary focus on the years 2000–2020. A bibliometric analysis of the database allowed identification of the co-occurrence of keywords. There was an increasing trend over time for publications relating to oil bioremediation in maritime Antarctica, including both studies on marine bioremediation and of the metabolic pathways of hydrocarbon degradation. Studies of marine anaerobic degradation remain under-represented compared to those of aerobic degradation. Emerging keywords in recent years included bioprospecting, metagenomic, bioindicator, and giving insight into changing research foci, such as increasing attention to microbial diversity. The study of microbial genomes using metagenomic approaches or whole genome studies is increasing rapidly and is likely to drive emerging fields in future, including rapid expansion of bioprospecting in diverse fields of biotechnology.

Structural and functional characterisation of a cold-active yet heat-tolerant dehydroquinase from Glaciozyma antarctica PI12

Dehydroquinase or 3-dehydroquinate dehydratase (DHQD) reversibly cleaves 3-dehydroquinate to form 3-dehydroshikimate. Here, we describe the functional and structural features of a cold active type II 3-dehydroquinate dehydratase from the psychrophilic yeast, Glaciozyma antarctica PI12 (GaDHQD). Functional studies showed that the enzyme was active at low temperatures (10-30 °C), but displayed maximal activity at 40 °C. Yet the enzyme was stable over a wide range of temperatures (10-70 °C) and between pH 6.0-10.0 with an optimum pH of 8.0. Interestingly, the enzyme was highly thermo-tolerant, denaturing only at approximately 84 °C. Three-dimensional structure analyses showed that the G. antarctica dehydroquinase (GaDHQD) possesses psychrophilic features in comparison with its mesophilic and thermophilic counterparts such as higher numbers of non-polar residues on the surface, lower numbers of arginine and higher numbers of glycine-residues with lower numbers of hydrophobic interactions. On the other hand, GaDHQD shares some traits (i.e. total number of hydrogen bonds, number of proline residues and overall folding) with its mesophilic and thermophilic counterparts. Combined, these features contribute synergistically towards the enzyme's ability to function at both low and high temperatures.

TMT-Based Quantitative Proteomics Analysis of the Fish-Borne Spoiler Shewanella putrefaciens Subjected to Cold Stress Using LC-MS/MS

Shewanella putrefaciens is a specific spoilage bacterium for fish during cold storage. To better understand the molecular mechanisms of cold stress adaptation of S. putrefaciens, tandem mass tag- (TMT-) based quantitative proteomic analysis was performed to detect the effects of cold stress on protein expression profiles in S. putrefaciens which had been cultivated at 4°C and 30°C, respectively. A total of 266670 peptide spectrum matching numbers were quantified proteins after data analysis. Of the 2292 proteins quantitatively analyzed, a total of 274 were found to be differentially expressed (DE) under cold stress compared with the nonstress control. By integrating the results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, 9 common KEGG terms were found notable for the cold-responsive proteins. Generally, the DE proteins involved in carbohydrate, amino acid, and fatty acid biosynthesis and metabolism were significantly upregulated, leading to a specific energy conservation survival mode. The DE proteins related to DNA repair, transcription, and translation were upregulated, implicating change of gene expression and more protein biosynthesis needed in response to cold stress.

The properties, biotechnologies, and applications of antifreeze proteins

By natural selection, organisms evolve different solutions to cope with extremely cold weather. The emergence of an antifreeze protein gene is one of the most momentous solutions. Antifreeze proteins possess an importantly functional ability for organisms to survive in cold environments and are widely found in various cold-tolerant species. In this review, we summarize the origin of antifreeze proteins, describe the diversity of their species-specific properties and functions, and highlight the related biotechnology on the basis of both laboratory tests and bioinformatics analysis. The most recent advances in the applications of antifreeze proteins are also discussed. We expect that this systematic review will contribute to the comprehensive knowledge of antifreeze proteins to readers.