Comparative Analysis of Barophily-Related Amino Acid Content in Protein Domains of<i>Pyrococcus abyssi</i>and<i>Pyrococcus furiosus</i>

Yafremava, Liudmila S.; Giulio, Massimo Di; Caetano‐Anollés, Gustavo

doi:10.1155/2013/680436

Cited by 7 publications

(3 citation statements)

References 39 publications

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“…These changes in the gene's protein-coding and regulatory sequences may help the MHS increase intracellular TMAO levels to enhance protein stability. Structural adaptations of proteins to deep-sea conditions may include changes in amino acid substitution patterns and protein structure that counteract the effects of pressure on protein function 41,42 . To characterize these adaptations, we compared the MHS with other species with respect to the amino acid composition and substitution of all coding genes together ( Supplementary Fig.…”

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confidence: 99%

Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation

et al. 2019

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It is largely unknown how living organisms—especially vertebrates—survive and thrive in the coldness, darkness and high pressures of the hadal zone. Here, we describe the unique morphology and genome of Pseudoliparis swirei—a recently described snailfish species living below a depth of 6,000 m in the Mariana Trench. Unlike closely related shallow sea species, P. swirei has transparent, unpigmented skin and scales, thin and incompletely ossified bones, an inflated stomach and a non-closed skull. Phylogenetic analyses show that P. swirei diverged from a close relative living near the sea surface about 20 million years ago and has abundant genetic diversity. Genomic analyses reveal that: (1) the bone Gla protein (bglap) gene has a frameshift mutation that may cause early termination of cartilage calcification; (2) cell membrane fluidity and transport protein activity in P. swirei may have been enhanced by changes in protein sequences and gene expansion; and (3) the stability of its proteins may have been increased by critical mutations in the trimethylamine N-oxide-synthesizing enzyme and hsp90 chaperone protein. Our results provide insights into the morphological, physiological and molecular evolution of hadal vertebrates.

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confidence: 99%

Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation

et al. 2019

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“…Proteomic comparative analysis of P. furiosus and P. abyssi shows that Asp and Arg are the only two amino acids that can be designated preferentially barophilic, although previous studies designated five (Arg, Ser, Val, Asp, and Gly). On the other hand, only three amino acids (Asn, Lys, and Thr) display a clear preference for nonbarophily [103].…”

Section: Piezophilesmentioning

confidence: 97%

Evolution, Metabolism and Molecular Mechanisms Underlying Extreme Adaptation of Euryarchaeota and Its Biotechnological Potential

Castro‐Fernández¹,

Zamora²,

Herrera-Morandé³

et al. 2017

Archaea - New Biocatalysts, Novel Pharmaceuticals and Various Biotechnological Applications

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Archaeal organisms harbor many unique genotypic and phenotypic properties, testifying their peculiar evolutionary status. Thus, the so-called extremophiles must be adequately adapted to cope with many extreme environments with regard to metabolic processes, biological functions, genomes, and transcriptomes to overcome the challenges of life. This chapter will illustrate recent progress in the research on extremophiles from the phylum Euryarchaeota and compile their evolutive history, metabolic strategies, lipid composition, the structural adaptations of their enzymes to temperature, salinity, and pH and their biotechnological applications. Archaeal organisms have evolved to deal with one or more extreme conditions, and over the evolution, they have accumulated changes in order to optimize protein structure and enzyme activity. The structural basis of these adaptations resulted in the construction of a vast repertoire of macromolecules with particular features not found in other organisms. This repertoire can be explored as an inexhaustible source of biological molecules for industrial or biotechnological applications. We hope that the information compiled herein will open new research lines that will shed light on various aspects of these extremophilic microorganisms. In addition, this information will be a valuable resource for future studies looking for archaeal enzymes with particular properties.

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“…Currently, not many studies are taking a data-driven perspective to compare characteristics of proteins of piezophiles or deep-sea organisms with their homologs from other environments. Of the existing studies most are comparing amino acid preferences in the proteom based on genome data 16,[27][28][29][30][31] while analysis of protein structures on a larger scale are becoming available only recently. 32 Consequently, it becomes interesting to assess the state of experimental protein structures from deep-sea organisms currently available and comprehensively analyze their features regarding adaptations.…”

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confidence: 99%

Analyzing structural features of proteins from deep‐sea organisms

et al. 2022

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Protein adaptations to extreme environmental conditions are drivers in biotechnological process optimization and essential to unravel the molecular limits of life. Most proteins with such desirable adaptations are found in extremophilic organisms inhabiting extreme environments. The deep sea is such an environment and a promising resource that poses multiple extremes on its inhabitants. Conditions like high hydrostatic pressure and high or low temperature are prevalent and many deep-sea organisms tolerate multiple of these extremes. While molecular adaptations to high temperature are comparatively good described, adaptations to other extremes like high pressure are not well-understood yet. To fully unravel the molecular mechanisms of individual adaptations it is probably necessary to disentangle multifactorial adaptations. In this study, we evaluate differences of protein structures from deepsea organisms and their respective related proteins from nondeep-sea organisms. We created a data collection of 1281 experimental protein structures from 25 deep-sea organisms and paired them with orthologous proteins. We exhaustively evaluate differences between the protein pairs with machine learning and Shapley values to determine characteristic differences in sequence and structure. The results show a reasonable discrimination of deep-sea and nondeep-sea proteins from which we distinguish correlations previously attributed to thermal stability from other signals potentially describing adaptions to high pressure. While some distinct correlations can be observed the overall picture appears intricate.

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Comparative Analysis of Barophily-Related Amino Acid Content in Protein Domains ofPyrococcus abyssiandPyrococcus furiosus

Cited by 7 publications

References 39 publications

Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation

Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation

Evolution, Metabolism and Molecular Mechanisms Underlying Extreme Adaptation of Euryarchaeota and Its Biotechnological Potential

Analyzing structural features of proteins from deep‐sea organisms

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