CiteULike: Tag psychrophiles

Adaptation and acclimation of photosynthetic microorganisms to permanently cold environments

RM Morgan-Kiss — 2007-08-17T17:07:21-00:00

Microbiology and Molecular Biology Reviews, Vol. 70, No. 1. (2006), pp. 222-252.

Persistently cold environments constitute one of our world's largest ecosystems, and microorganisms dominate the biomass and metabolic activity in these extreme environments. The stress of low temperatures on life is exacerbated in organisms that rely on photoautrophic production of organic carbon and energy sources. Phototrophic organisms must coordinate temperature-independent reactions of light absorption and photochemistry with temperature-dependent processes of electron transport and utilization of energy sources through growth and metabolism. Despite this conundrum, phototrophic microorganisms thrive in all cold ecosystems described and (together with chemoautrophs) provide the base of autotrophic production in low-temperature food webs. Psychrophilic (organisms with a requirement for low growth temperatures) and psychrotolerant (organisms tolerant of low growth temperatures) photoautotrophs rely on low-temperature acclimative and adaptive strategies that have been described for other low-temperature-adapted heterotrophic organisms, such as cold-active proteins and maintenance of membrane fluidity. In addition, photoautrophic organisms possess other strategies to balance the absorption of light and the transduction of light energy to stored chemical energy products (NADPH and ATP) with downstream consumption of photosynthetically derived energy products at low temperatures. Lastly, differential adaptive and acclimative mechanisms exist in phototrophic microorganisms residing in low-temperature environments that are exposed to constant low-light environments versus high-light- and high-UV-exposed phototrophic assemblages. Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Cold-loving microbes, plants, and animals - fundamental and applied aspects

R Margesin — 2007-01-24T00:15:13-00:00

Naturwissenschaften, Vol. 94, No. 2. (February 2007), pp. 77-99.

Characterization of several Psychrobacter strains isolated from Antarctic environments and description of Psychrobacter luti sp. nov. and Psychrobacter fozii sp. nov.

Nuria Bozal — 2008-01-25T18:24:33-00:00

International Journal of Systematic and Evolutionary Microbiology, Vol. 53, No. 4. (1 July 2003), pp. 1093-1100.

Eleven psychrophilic bacteria isolated from Antarctic coastal marine environments were subjected to a polyphasic taxonomic study. The isolates were oxidase-positive, halotolerant, Gram-negative, non-motile coccobacilli with a strictly oxidative metabolism. The DNA G+C content ranged from 44 to 47 mol%. DNA-DNA hybridization experiments showed six homology groups, two of them related at the species level to the type strain of Psychrobacter immobilis, LMG 7203T (70-83 %). The highest DNA relatedness of two other groups to known Psychrobacter species was found to the type strain of Psychrobacter glacincola, LMG 21282T (51-57 %), and no significant similarity was found between Psychrobacter type strains and the last two groups. The predominant cellular fatty acids detected were typical of the genus Psychrobacter and included 18 : 1omega9c, 16 : 1omega7c and 17 : 1omega8c. 16S rRNA gene sequence analysis confirmed that the strains isolated belonged to the genus Psychrobacter. The results of the study assigned five isolates to P. immobilis, three isolates to P. glacincola and three isolates to novel Psychrobacter species. The names Psychrobacter luti sp. nov. (type strain NF11T=LMG 21276T= CECT 5885T) and Psychrobacter fozii sp. nov. (type strain NF23T=LMG 21280T =CECT 5889T) are proposed for these organisms. 10.1099/ijs.0.02457-0

Low-temperature extremophiles and their applications

R Cavicchioli — 2007-08-17T17:05:02-00:00

Curr. Opin. Biotechnol., Vol. 13, No. 3. (2002), pp. 253-261.

Psychrophilic (cold-adapted) organisms and their products have potential applications in a broad range of industrial, agricultural and medical processes. In order for growth to occur in low-temperature environments, all cellular components must adapt to the cold. This fact, in combination with the diversity of Archaea, Bacteria and Eucarya isolated from cold environments, highlights the breadth and type of biological products and processes that might be exploited for biotechnology. Relative to this undisputed potential, psychrophiles and their products are under-utilised in biotechnology; however, recent advances, particularly with cold-active enzymes, herald rapid growth for this burgeoning field.

Cold adapted enzymes.

AO Smalås — 2007-03-16T14:41:25-00:00

Biotechnol Annu Rev, Vol. 6 (2000), pp. 1-57.

The number of reports on enzymes from cold adapted organisms has increased significantly over the past years, and reveals that adaptive strategies for functioning at low temperature varies among enzymes. However, the high catalytic efficiency at low temperature seems, for the majority of cold active enzymes, to be accompanied by a reduced thermal stability. Increased molecular flexibility to compensate for the low working temperature, is therefore still the most dominating theory for cold adaptation, although there also seem to be other adaptive strategies. The number of experimentally determined 3D structures of enzymes possessing cold adaptation features is still limited, and restricts a structural rationalization for cold activity. The present summary of structural characteristics, based on comparative studies on crystal structures (7), homology models (7), and amino acid sequences (24), reveals that there are no common structural feature that can account for the low stability, increased catalytic efficiency, and proposed molecular flexibility. Analysis of structural features that are thought to be important for stability (e.g. intra-molecular hydrogen bonds and ion-pairs, proline-, methionine-, glycine-, or arginine content, surface hydrophilicity, helix stability, core packing), indicates that each cold adapted enzyme or enzyme system use different small selections of structural adjustments for gaining increased molecular flexibility that in turn give rise to increased catalytic efficiency and reduced stability. Nevertheless, there seem to be a clear correlation between cold adaptation and reduced number of interactions between structural domains or subunits. Cold active enzymes also seem, to a large extent, to increase their catalytic activity by optimizing the electrostatics at and around the active site.

Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins

Saelensminde — 2007-08-25T01:32:38-00:00

Extremophiles, Vol. 11, No. 4. (July 2007), pp. 585-596.

PGTdb: a database providing growth temperatures of prokaryotes.

SL Huang — 2007-03-16T14:54:22-00:00

Bioinformatics, Vol. 20, No. 2. (22 January 2004), pp. 276-278.

Included in Prokaryotic Growth Temperature database (PGTdb) are a total of 1334 temperature data from 1072 prokaryotic organisms, Bacteria and Archaea: PGTdb integrates microbial growth temperature data from literature survey with their nucleotide/protein sequence and protein structure data from related databases. A direct correlation is observed between the average growth temperature of an organism and the melting temperature of proteins from the organism. Therefore, this database is useful not only for microbiologists to obtain cultivation condition, but also for biochemists and structure biologists to study the correlation between protein sequences/structures and their thermostability. In addition, the taxonomy and ribosomal RNA sequence(s) of an organism are linked through NCBI Taxonomy and the Ribosomal RNA Operon Copy Number Database umdb, respectively. PGTdb is the only integrated database on the Internet to provide the growth temperature data of the prokaryotes and the combined information of their nucleotide/protein sequences, protein structures, taxonomy and phylogeny. AVAILABILITY: http://pgtdb.csie.ncu.edu.tw

Life at low temperatures: is disorder the driving force?

Feller — 2007-03-18T18:46:13-00:00

Extremophiles, Vol. 11, No. 2. (March 2007), pp. 211-216.

Psychrophilic enzymes: hot topics in cold adaptation.

G Feller — 2006-10-13T16:52:57-00:00

Nat Rev Microbiol, Vol. 1, No. 3. (December 2003), pp. 200-208.

More than three-quarters of the Earth's surface is occupied by cold ecosystems, including the ocean depths, and polar and alpine regions. These permanently cold environments have been successfully colonized by a class of extremophilic microorganisms that are known as psychrophiles (which literally means cold-loving). The ability to thrive at temperatures that are close to, or below, the freezing point of water requires a vast array of adaptations to maintain the metabolic rates and sustained growth compatible with life in these severe environmental conditions.

Some like it cold: biocatalysis at low temperatures.

D Georlette — 2007-03-16T14:44:47-00:00

FEMS Microbiol Rev, Vol. 28, No. 1. (February 2004), pp. 25-42.

In the last few years, increased attention has been focused on a class of organisms called psychrophiles. These organisms, hosts of permanently cold habitats, often display metabolic fluxes more or less comparable to those exhibited by mesophilic organisms at moderate temperatures. Psychrophiles have evolved by producing, among other peculiarities, "cold-adapted" enzymes which have the properties to cope with the reduction of chemical reaction rates induced by low temperatures. Thermal compensation in these enzymes is reached, in most cases, through a high catalytic efficiency associated, however, with a low thermal stability. Thanks to recent advances provided by X-ray crystallography, structure modelling, protein engineering and biophysical studies, the adaptation strategies are beginning to be understood. The emerging picture suggests that psychrophilic enzymes are characterized by an improved flexibility of the structural components involved in the catalytic cycle, whereas other protein regions, if not implicated in catalysis, may be even more rigid than their mesophilic counterparts. Due to their attractive properties, i.e., a high specific activity and a low thermal stability, these enzymes constitute a tremendous potential for fundamental research and biotechnological applications.

Increased flexibility as a strategy for cold adaptation: a comparative molecular dynamics study of cold- and warm-active uracil DNA glycosylase.

M Olufsen — 2008-02-20T14:39:15-00:00

J Biol Chem, Vol. 280, No. 18. (6 May 2005), pp. 18042-18048.

Uracil DNA glycosylase (UDG) is a DNA repair enzyme in the base excision repair pathway and removes uracil from the DNA strand. Atlantic cod UDG (cUDG), which is a cold-adapted enzyme, has been found to be up to 10 times more catalytically active in the temperature range 15-37 degrees C as compared with the warm-active human counterpart. The increased catalytic activity of cold-adapted enzymes as compared with their mesophilic homologues are partly believed to be caused by an increase in the structural flexibility. However, no direct experimental evidence supports the proposal of increased flexibility of cold-adapted enzymes. We have used molecular dynamics simulations to gain insight into the structural flexibility of UDG. The results from these simulations show that an important loop involved in DNA recognition (the Leu(272) loop) is the most flexible part of the cUDG structure and that the human counterpart has much lower flexibility in the Leu(272) loop. The flexibility in this loop correlates well with the experimental k(cat)/K(m) values. Thus, the data presented here add strong support to the idea that flexibility plays a central role in adaptation to cold environments.

Psychrophiles and polar regions.

JW Deming — 2007-03-16T14:43:11-00:00

Curr Opin Microbiol, Vol. 5, No. 3. (June 2002), pp. 301-309.

Most reviews of microbial life in cold environments begin with a lament of how little is known about the psychrophilic (cold-loving) inhabitants or their specific adaptations to the cold. This situation is changing, as research becomes better focused by new molecular genetic (and other) approaches, by awareness of accelerated environmental change in polar regions, and by strong interest in the habitability of frozen environments elsewhere in the solar system. This review highlights recent discoveries in molecular adaptation, biodiversity and microbial dynamics in the cold, along with the concept of eutectophiles, organisms living at the critical interface inherent to the phase change of water to ice.

Hydrogen bonds and salt bridges across protein-protein interfaces.

D Xu — 2007-05-18T14:24:35-00:00

Protein Eng, Vol. 10, No. 9. (September 1997), pp. 999-1012.

To understand further, and to utilize, the interactions across protein-protein interfaces, we carried out an analysis of the hydrogen bonds and of the salt bridges in a collection of 319 non-redundant protein-protein interfaces derived from high-quality X-ray structures. We found that the geometry of the hydrogen bonds across protein interfaces is generally less optimal and has a wider distribution than typically observed within the chains. This difference originates from the more hydrophilic side chains buried in the binding interface than in the folded monomer interior. Protein folding differs from protein binding. Whereas in folding practically all degrees of freedom are available to the chain to attain its optimal configuration, this is not the case for rigid binding, where the protein molecules are already folded, with only six degrees of translational and rotational freedom available to the chains to achieve their most favorable bound configuration. These constraints enforce many polar/charged residues buried in the interface to form weak hydrogen bonds with protein atoms, rather than strongly hydrogen bonding to the solvent. Since interfacial hydrogen bonds are weaker than the intra-chain ones to compete with the binding of water, more water molecules are involved in bridging hydrogen bond networks across the protein interface than in the protein interior. Interfacial water molecules both mediate non-complementary donor-donor or acceptor-acceptor pairs, and connect non-optimally oriented donor-acceptor pairs. These differences between the interfacial hydrogen bonding patterns and the intra-chain ones further substantiate the notion that protein complexes formed by rigid binding may be far away from the global minimum conformations. Moreover, we summarize the pattern of charge complementarity and of the conservation of hydrogen bond network across binding interfaces. We further illustrate the utility of this study in understanding the specificity of protein-protein associations, and hence in docking prediction and molecular (inhibitor) design.

Cold-adapted enzymes.

KS Siddiqui — 2007-02-05T21:22:32-00:00

Annu Rev Biochem, Vol. 75 (2006), pp. 403-433.

By far the largest proportion of the Earth's biosphere is comprised of organisms that thrive in cold environments (psychrophiles). Their ability to proliferate in the cold is predicated on a capacity to synthesize cold-adapted enzymes. These enzymes have evolved a range of structural features that confer a high level of flexibility compared to thermostable homologs. High flexibility, particularly around the active site, is translated into low-activation enthalpy, low-substrate affinity, and high specific activity at low temperatures. High flexibility is also accompanied by a trade-off in stability, resulting in heat lability and, in the few cases studied, cold lability. This review addresses the structure, function, and stability of cold-adapted enzymes, highlighting the challenges for immediate and future consideration. Because of the unique properties of cold-adapted enzymes, they are not only an important focus in extremophile biology, but also represent a valuable model for fundamental research into protein folding and catalysis.

Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii.

NF Saunders — 2007-02-06T16:51:44-00:00

Genome Res, Vol. 13, No. 7. (July 2003), pp. 1580-1588.

We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15 degrees -98 degrees C) were used to generate 1111 modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gln, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60 degrees C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles.

The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses.

BA Methé — 2006-10-17T12:31:57-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 31. (2 August 2005), pp. 10913-10918.

The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein homology from bacteria representing a range of optimal growth temperatures suggests changes to proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition.