scholarly journals Systematic Affiliation and Genome Analysis of Subtercola vilae DB165T with Particular Emphasis on Cold Adaptation of an Isolate from a High-Altitude Cold Volcano Lake

2019 ◽  
Vol 7 (4) ◽  
pp. 107 ◽  
Author(s):  
Alvaro S. Villalobos ◽  
Jutta Wiese ◽  
Johannes F. Imhoff ◽  
Cristina Dorador ◽  
Alexander Keller ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Cold Shock ◽  
Extreme Environment ◽  
Crystal Formation ◽  
Ice Crystal ◽  
Cold Environments ◽  
Ice Binding ◽  
Shock Proteins ◽  
Harsh Conditions ◽  
Insight Into

Among the Microbacteriaceae the species of Subtercola and Agreia form closely associated clusters. Phylogenetic analysis demonstrated three major phylogenetic branches of these species. One of these branches contains the two psychrophilic species Subtercola frigoramans and Subtercola vilae, together with a larger number of isolates from various cold environments. Genomic evidence supports the separation of Agreia and Subtercola species. In order to gain insight into the ability of S. vilae to adapt to life in this extreme environment, we analyzed the genome with a particular focus on properties related to possible adaptation to a cold environment. General properties of the genome are presented, including carbon and energy metabolism, as well as secondary metabolite production. The repertoire of genes in the genome of S. vilae DB165T linked to adaptations to the harsh conditions found in Llullaillaco Volcano Lake includes several mechanisms to transcribe proteins under low temperatures, such as a high number of tRNAs and cold shock proteins. In addition, S. vilae DB165T is capable of producing a number of proteins to cope with oxidative stress, which is of particular relevance at low temperature environments, in which reactive oxygen species are more abundant. Most important, it obtains capacities to produce cryo-protectants, and to combat against ice crystal formation, it produces ice-binding proteins. Two new ice-binding proteins were identified which are unique to S. vilae DB165T. These results indicate that S. vilae has the capacity to employ different mechanisms to live under the extreme and cold conditions prevalent in Llullaillaco Volcano Lake.

scholarly journals Expression of Ice-Binding Proteins in Caenorhabditis elegans Improves the Survival Rate upon Cold Shock and during Freezing

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Masahiro Kuramochi ◽  
Chiaki Takanashi ◽  
Akari Yamauchi ◽  
Motomichi Doi ◽  
Kazuhiro Mio ◽  
...  
Keyword(s):  
Survival Rate ◽  
Caenorhabditis Elegans ◽  
Binding Proteins ◽  
Cold Shock ◽  
Ice Binding

scholarly journals An Ice-Binding Protein from an Antarctic Ascomycete Is Fine-Tuned to Bind to Specific Water Molecules Located in the Ice Prism Planes

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 759
Author(s):  
Akari Yamauchi ◽  
Tatsuya Arai ◽  
Hidemasa Kondo ◽  
Yuji C. Sasaki ◽  
Sakae Tsuda
Keyword(s):  
Water Molecules ◽  
Ice Crystal ◽  
Water Network ◽  
Cold Environments ◽  
Ice Binding ◽  
Defective Mutant ◽  
Ice Binding Protein ◽  
Function Relationship ◽  
Relationship Of ◽  
Ice Water

Many microbes that survive in cold environments are known to secrete ice-binding proteins (IBPs). The structure–function relationship of these proteins remains unclear. A microbial IBP denoted AnpIBP was recently isolated from a cold-adapted fungus, Antarctomyces psychrotrophicus. The present study identified an orbital illumination (prism ring) on a globular single ice crystal when soaked in a solution of fluorescent AnpIBP, suggesting that AnpIBP binds to specific water molecules located in the ice prism planes. In order to examine this unique ice-binding mechanism, we carried out X-ray structural analysis and mutational experiments. It appeared that AnpIBP is made of 6-ladder β-helices with a triangular cross section that accompanies an “ice-like” water network on the ice-binding site. The network, however, does not exist in a defective mutant. AnpIBP has a row of four unique hollows on the IBS, where the distance between the hollows (14.7 Å) is complementary to the oxygen atom spacing of the prism ring. These results suggest the structure of AnpIBP is fine-tuned to merge with the ice–water interface of an ice crystal through its polygonal water network and is then bound to a specific set of water molecules constructing the prism ring to effectively halt the growth of ice.

scholarly journals Ice-binding proteins that accumulate on different ice crystal planes produce distinct thermal hysteresis dynamics

2014 ◽  
Vol 11 (98) ◽  
pp. 20140526 ◽  
Author(s):  
Ran Drori ◽  
Yeliz Celik ◽  
Peter L. Davies ◽  
Ido Braslavsky
Keyword(s):  
Basal Plane ◽  
Binding Proteins ◽  
Thermal Hysteresis ◽  
Freezing Point ◽  
Ice Crystal ◽  
Ice Binding ◽  
Time Sensitivity ◽  
Custom Made ◽  
Order Of Magnitude ◽  
Accumulation Kinetics

Ice-binding proteins that aid the survival of freeze-avoiding, cold-adapted organisms by inhibiting the growth of endogenous ice crystals are called antifreeze proteins (AFPs). The binding of AFPs to ice causes a separation between the melting point and the freezing point of the ice crystal (thermal hysteresis, TH). TH produced by hyperactive AFPs is an order of magnitude higher than that produced by a typical fish AFP. The basis for this difference in activity remains unclear. Here, we have compared the time dependence of TH activity for both hyperactive and moderately active AFPs using a custom-made nanolitre osmometer and a novel microfluidics system. We found that the TH activities of hyperactive AFPs were time-dependent, and that the TH activity of a moderate AFP was almost insensitive to time. Fluorescence microscopy measurement revealed that despite their higher TH activity, hyperactive AFPs from two insects (moth and beetle) took far longer to accumulate on the ice surface than did a moderately active fish AFP. An ice-binding protein from a bacterium that functions as an ice adhesin rather than as an antifreeze had intermediate TH properties. Nevertheless, the accumulation of this ice adhesion protein and the two hyperactive AFPs on the basal plane of ice is distinct and extensive, but not detectable for moderately active AFPs. Basal ice plane binding is the distinguishing feature of antifreeze hyperactivity, which is not strictly needed in fish that require only approximately 1°C of TH. Here, we found a correlation between the accumulation kinetics of the hyperactive AFP at the basal plane and the time sensitivity of the measured TH.

Ice-binding proteins: a remarkable ice crystal regulator for frozen foods

2020 ◽  
pp. 1-14
Author(s):  
Xu Chen ◽  
Xiaodan Shi ◽  
Xixi Cai ◽  
Fujia Yang ◽  
Ling Li ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Ice Crystal ◽  
Frozen Foods ◽  
Ice Binding

scholarly journals Complete genome sequence of Arthrobacter sp. PAMC25564 and comparative genome analysis for elucidating the role of CAZymes in cold adaptation

2020 ◽  
Author(s):  
So-Ra Han ◽  
Byeollee Kim ◽  
Jong Hwa Jang ◽  
Hyun Park ◽  
Tae-Jin Oh
Keyword(s):  
Complete Genome ◽  
Cold Adaptation ◽  
Environmental Changes ◽  
Gc Content ◽  
Extreme Environment ◽  
Cold Environments ◽  
Carbohydrate Degradation ◽  
Survival Mechanisms ◽  
Insight Into

Abstract Background: The Arthrobacter group is a known isolate from cold areas, the species of which are highly likely to play diverse roles in low temperatures. However, their role and survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of sixteen strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that adapt and survive life in the cold environment.Results: The genome of Arthrobacter sp. PAMC25564 comprised 4,170,970 bp with 66.74 % GC content, a predicted genomic island, and 3,829 genes. This study provides an insight into the redundancy of CAZymes for potential cold adaptation and suggests that the isolate has glycogen, trehalose, and maltodextrin pathways associated to CAZyme genes. This strain can utilize polysaccharide or carbohydrate degradation as a source of energy. Moreover, this study provides a foundation on which to understand how the Arthrobacter strain produces energy in an extreme environment, and the genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how bacteria adapt and survive in such environments.Conclusions: We characterized the Arthrobacter sp. PAMC25564 complete genome and comparative analysis, provided an insight into the redundancy of CAZymes for potential cold adaptation. This provide a foundation to understand how Arthrobacter strain produces energy in an extreme environment, there are reports on the use of CAZymes in cold environments. Therefore, we suppose that this process has allowed Arthrobacter species to establish a symbiotic relationship with other bacteria in cold environments or live independently thanks to their capacity for adapting to environmental changes.

scholarly journals Basidiomycetous Yeast, Glaciozyma antarctica, Forming Frost-Columnar Colonies on Frozen Medium

2021 ◽  
Vol 9 (8) ◽  
pp. 1679
Author(s):  
Seiichi Fujiu ◽  
Masanobu Ito ◽  
Eriko Kobayashi ◽  
Yuichi Hanada ◽  
Midori Yoshida ◽  
...  
Keyword(s):  
Crystal Growth ◽  
Binding Proteins ◽  
East Antarctica ◽  
Basidiomycetous Yeast ◽  
Extracellular Polysaccharides ◽  
Unfrozen Water ◽  
Ice Crystal ◽  
Ice Binding

The basidiomycetous yeast, Glaciozyma antarctica, was isolated from various terrestrial materials collected from the Sôya coast, East Antarctica, and formed frost-columnar colonies on agar plates frozen at −1 °C. Thawed colonies were highly viscous, indicating that the yeast produced a large number of extracellular polysaccharides (EPS). G. antarctica was then cultured on frozen media containing red food coloring to observe the dynamics of solutes in unfrozen water; pigments accumulated in frozen yeast colonies, indicating that solutes were concentrated in unfrozen water of yeast colonies. Moreover, the yeast produced a small quantity of ice-binding proteins (IBPs) which inhibited ice crystal growth. Solutes in unfrozen water were considered to accumulate in the pore of frozen colonies. The extracellular IBPs may have held an unfrozen state of medium water after accumulation in the frost-columnar colony.

scholarly journals Predicted Cold Shock Proteins from the Extremophilic Bacterium Deinococcus maricopensis and Related Deinococcus Species

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Michael J. LaGier
Keyword(s):  
Cold Shock ◽  
Temperature Adaptation ◽  
Nucleic Acid Binding ◽  
Binding Motifs ◽  
Cold Shock Proteins ◽  
Cold Environments ◽  
Cold Shock Domain ◽  
Bioinformatic Approaches ◽  
Shock Proteins ◽  
Genome Information

While many studies have examined the mechanisms by which extremophilic Deinococci survive exposure to ionizing radiation, very few publications have characterized the cold shock adaptations of this group, despite many species being found in persistent cold environments and environments prone to significant daily temperature fluctuations. Bacterial cold shock proteins (Csps) are a family of conserved, RNA chaperone proteins that commonly play a role in cold temperature adaptation, including a downward shift in temperature (i.e., cold shock). The primary aim of this study was to test whether a representative, desert-dwelling Deinococcus, Deinococcus maricopensis, encodes Csps as part of its genome. Bioinformatic approaches were used to identify a Csp from D. maricopensis LB-34. The Csp, termed Dm-Csp1, contains sequence features of Csps including a conserved cold shock domain and nucleic acid binding motifs. A tertiary model of Dm-Csp1 revealed an anticipated Csp structure containing five anti-parallel beta-strands, and ligand prediction experiments identified N-terminally located residues capable of binding single-stranded nucleic acids. Putative Csps were identified from 100% of (27 of 27) Deinococci species for which genome information is available; and the Deinococci-encoded Csps identified contain a C-terminally located region that appears to be limited to members of the class Deinococci.

scholarly journals Ice-binding proteins and the applicability and limitations of the kinetic pinning model

2019 ◽  
Vol 377 (2146) ◽  
pp. 20180391 ◽  
Author(s):  
Michael Chasnitsky ◽  
Ido Braslavsky
Keyword(s):  
Binding Proteins ◽  
Thermal Hysteresis ◽  
Freezing Point ◽  
Ice Crystal ◽  
Water Ice ◽  
Ice Binding ◽  
Production Technologies ◽  
Seeding Time ◽  
Two Phases ◽  
Key Parameter

Ice-binding proteins (IBPs) are unique molecules that bind to and are active on the interface between two phases of water: ice and liquid water. This property allows them to affect ice growth in multiple ways: shaping ice crystals, suppressing the freezing point, inhibiting recrystallization and promoting nucleation. Advances in the protein's production technologies make these proteins promising agents for medical applications among others. Here, we focus on a special class of IBPs that suppress freezing by causing thermal hysteresis (TH): antifreeze proteins (AFPs). The kinetic pinning model describes the dynamics of a growing ice face with proteins binding to it, which eventually slow it down to a halt. We use the kinetic pinning model, with some adjustments made, to study the TH dependence on the solution's concentration of AFPs by fitting the model to published experimental data. We find this model describes the activity of (moderate) type III AFPs well, but is inadequate for the (hyperactive) Tenebrio molitor AFPs. We also find the engulfment resistance to be a key parameter, which depends on the protein's size. Finally, we explain intuitively how TH depends on the seeding time of the ice crystal in the protein solution. Using this insight, we explain the discrepancy in TH measurements between different assays. This article is part of the theme issue ‘The physics and chemistry of ice: scaffolding across scales, from the viability of life to the formation of planets’.

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