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Kacirani A, Uralcan B, Domingues TS, Haji-Akbari A. Effect of Pressure on the Conformational Landscape of Human γD-Crystallin from Replica Exchange Molecular Dynamics Simulations. J Phys Chem B 2024; 128:4931-4942. [PMID: 38685567 DOI: 10.1021/acs.jpcb.4c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Human γD-crystallin belongs to a crucial family of proteins known as crystallins located in the fiber cells of the human lens. Since crystallins do not undergo any turnover after birth, they need to possess remarkable thermodynamic stability. However, their sporadic misfolding and aggregation, triggered by environmental perturbations or genetic mutations, constitute the molecular basis of cataracts, which is the primary cause of blindness in the globe according to the World Health Organization. Here, we investigate the impact of high pressure on the conformational landscape of wild-type HγD-crystallin using replica exchange molecular dynamics simulations augmented with principal component analysis. We find pressure to have a modest impact on global measures of protein stability, such as root-mean-square displacement and radius of gyration. Upon projecting our trajectories along the first two principal components from principal component analysis, however, we observe the emergence of distinct free energy basins at high pressures. By screening local order parameters previously shown or hypothesized as markers of HγD-crystallin stability, we establish correlations between a tyrosine-tyrosine aromatic contact within the N-terminal domain and the protein's end-to-end distance with projections along the first and second principal components, respectively. Furthermore, we observe the simultaneous contraction of the hydrophobic core and its intrusion by water molecules. This exploration sheds light on the intricate responses of HγD-crystallin to elevated pressures, offering insights into potential mechanisms underlying its stability and susceptibility to environmental perturbations, crucial for understanding cataract formation.
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Affiliation(s)
- Arlind Kacirani
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, United States
| | - Betül Uralcan
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemical Engineering, Boğaziçi University, Istanbul 34342, Turkey
| | - Tiago S Domingues
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Graduate Program in Applied Mathematics, Yale University, New Haven, Connecticut 06520, United States
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
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2
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Wang Z, Niu Y, Zhao S, Tian Y, Yu K, Yamashita T, Youling X, Yuan C. Thermal stability of actin of silver carp (
Hypophthalmichthys molitrix
) harvested in summer and winter as affected by myosin complexation. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.17003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Zhuolin Wang
- United Graduate School of Agricultural Sciences Iwate University, Ueda 3‐18‐8, Morioka Iwate Japan
| | - Yabin Niu
- United Graduate School of Agricultural Sciences Iwate University, Ueda 3‐18‐8, Morioka Iwate Japan
| | | | - Yuanyong Tian
- College of Food Science and Technology Dalian Ocean University Dalian China
| | - Kefeng Yu
- Faculty of Agriculture Iwate University Iwate Japan
| | | | - Xiong Youling
- Department of Animal and Food Sciences University of Kentucky Lexington KY United States
| | - Chunhong Yuan
- Faculty of Agriculture Iwate University Iwate Japan
- Agri ‐ Innovation Center Iwate University Iwate Japan
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3
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Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques. Int J Mol Sci 2022; 23:ijms23105761. [PMID: 35628571 PMCID: PMC9144967 DOI: 10.3390/ijms23105761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/06/2023] Open
Abstract
Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of high pressure (>100 MPa = 1 kbar) in biology. Studies of high pressure can give insight into the volumetric aspects of various biological systems; this information cannot be obtained otherwise. High-pressure treatment is a potentially useful alternative method to heat-treatment in food science. Elevated pressure (up to 120 MPa) is present in the deep sea, which is a considerable part of the biosphere. From a basic scientific point of view, the application of the gamut of modern spectroscopic techniques provides information about the conformational changes of biomolecules, fluctuations, and flexibility. This paper reviews first the thermodynamic aspects of pressure science, the important parameters affecting the volume of a molecule. The technical aspects of high pressure production are briefly mentioned, and the most common high-pressure-compatible spectroscopic techniques are also discussed. The last part of this paper deals with the main biomolecules, lipids, proteins, and nucleic acids: how they are affected by pressure and what information can be gained about them using pressure. I I also briefly mention a few supramolecular structures such as viruses and bacteria. Finally, a subjective view of the most promising directions of high pressure bioscience is outlined.
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Molecular Responses to High Hydrostatic Pressure in Eukaryotes: Genetic Insights from Studies on Saccharomyces cerevisiae. BIOLOGY 2021; 10:biology10121305. [PMID: 34943220 PMCID: PMC8698847 DOI: 10.3390/biology10121305] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/27/2021] [Accepted: 12/06/2021] [Indexed: 01/19/2023]
Abstract
Simple Summary High hydrostatic pressure generally has an adverse effect on the biological systems of organisms inhabiting lands or shallow sea regions. Deep-sea piezophiles that prefer high hydrostatic pressure for growth have garnered considerable scientific attention. However, the underlying molecular mechanisms of their adaptation to high pressure remains unclear owing to the challenges of culturing and manipulating the genome of piezophiles. Humans also experience high hydrostatic pressure during exercise. A long-term stay in space can cause muscle weakness in astronauts. Thus, the human body indubitably senses mechanical stresses such as hydrostatic pressure and gravity. Nonetheless, the mechanisms underlying biological responses to high pressures are not clearly understood. This review summarizes the occurrence and significance of high-pressure effects in eukaryotic cells and how the cell responds to increasing pressure by particularly focusing on the physiology of S. cerevisiae at the molecular level. Abstract High hydrostatic pressure is common mechanical stress in nature and is also experienced by the human body. Organisms in the Challenger Deep of the Mariana Trench are habitually exposed to pressures up to 110 MPa. Human joints are intermittently exposed to hydrostatic pressures of 3–10 MPa. Pressures less than 50 MPa do not deform or kill the cells. However, high pressure can have various effects on the cell’s biological processes. Although Saccharomyces cerevisiae is not a deep-sea piezophile, it can be used to elucidate the molecular mechanism underlying the cell’s responses to high pressures by applying basic knowledge of the effects of pressure on industrial processes involving microorganisms. We have explored the genes associated with the growth of S. cerevisiae under high pressure by employing functional genomic strategies and transcriptomics analysis and indicated a strong association between high-pressure signaling and the cell’s response to nutrient availability. This review summarizes the occurrence and significance of high-pressure effects on complex metabolic and genetic networks in eukaryotic cells and how the cell responds to increasing pressure by particularly focusing on the physiology of S. cerevisiae at the molecular level. Mechanosensation in humans has also been discussed.
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Winnikoff JR, Haddock SHD, Budin I. Depth- and temperature-specific fatty acid adaptations in ctenophores from extreme habitats. J Exp Biol 2021; 224:jeb242800. [PMID: 34676421 PMCID: PMC8627573 DOI: 10.1242/jeb.242800] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/13/2021] [Indexed: 11/20/2022]
Abstract
Animals are known to regulate the composition of their cell membranes to maintain key biophysical properties in response to changes in temperature. For deep-sea marine organisms, high hydrostatic pressure represents an additional, yet much more poorly understood, perturbant of cell membrane structure. Previous studies in fish and marine microbes have reported correlations with temperature and depth of membrane-fluidizing lipid components, such as polyunsaturated fatty acids. Because little has been done to isolate the separate effects of temperature and pressure on the lipid pool, it is still not understood whether these two environmental factors elicit independent or overlapping biochemical adaptive responses. Here, we use the taxonomic and habitat diversity of the phylum Ctenophora to test whether distinct low-temperature and high-pressure signatures can be detected in fatty acid profiles. We measured the fatty acid composition of 105 individual ctenophores, representing 21 species, from deep and shallow Arctic, temperate, and tropical sampling locales (sea surface temperature, -2° to 28°C). In tropical and temperate regions, remotely operated submersibles (ROVs) enabled sampling down to 4000 m. We found that among specimens with body temperatures 7.5°C or colder, depth predicted fatty acid unsaturation levels. In contrast, in the upper 200 m of the water column, temperature predicted fatty acid chain lengths. Taken together, our findings suggest that lipid metabolism may be specialized with respect to multiple physical variables in diverse marine environments. Largely distinct modes of adaptation to depth and cold imply that polar marine invertebrates may not find a ready refugium from climate change in the deep.
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Affiliation(s)
- Jacob R. Winnikoff
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd., Moss Landing, CA 95039, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Steven H. D. Haddock
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd., Moss Landing, CA 95039, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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Silva AMM, Heeley DH. Existence in the actin world of a specialized slow skeletal muscle isoform. Comp Biochem Physiol B Biochem Mol Biol 2021; 254:110568. [PMID: 33545366 DOI: 10.1016/j.cbpb.2021.110568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 11/24/2022]
Affiliation(s)
- A Madhushika M Silva
- Department of Biochemistry, Memorial University, St. John's, Newfoundland A1B 3X9, Canada
| | - David H Heeley
- Department of Biochemistry, Memorial University, St. John's, Newfoundland A1B 3X9, Canada.
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Weber AAT, Hugall AF, O’Hara TD. Convergent Evolution and Structural Adaptation to the Deep Ocean in the Protein-Folding Chaperonin CCTα. Genome Biol Evol 2020; 12:1929-1942. [PMID: 32780796 PMCID: PMC7643608 DOI: 10.1093/gbe/evaa167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations; however, their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including chaperonin-containing TCP-1 subunit α (CCTα), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically corrected context and found that deep-sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα displays not only structural but also functional adaptations to deep-water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as a "cold-shock" protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, is a key metabolic deep-sea adaptation.
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Affiliation(s)
- Alexandra A -T Weber
- Sciences, Museums Victoria, Melbourne, Victoria, Australia
- Centre de Bretagne, REM/EEP, Ifremer, Laboratoire Environnement Profond, Plouzané, France
- Zoological Institute, University of Basel, Switzerland
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8
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Sung HL, Nesbitt DJ. High pressure single-molecule FRET studies of the lysine riboswitch: cationic and osmolytic effects on pressure induced denaturation. Phys Chem Chem Phys 2020; 22:15853-15866. [PMID: 32706360 DOI: 10.1039/d0cp01921f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Deep sea biology is known to thrive at pressures up to ≈1 kbar, which motivates fundamental biophysical studies of biomolecules under such extreme environments. In this work, the conformational equilibrium of the lysine riboswitch has been systematically investigated by single molecule FRET (smFRET) microscopy at pressures up to 1500 bar. The lysine riboswitch preferentially unfolds with increasing pressure, which signals an increase in free volume (ΔV0 > 0) upon folding of the biopolymer. Indeed, the effective lysine binding constant increases quasi-exponentially with pressure rise, which implies a significant weakening of the riboswitch-ligand interaction in a high-pressure environment. The effects of monovalent/divalent cations and osmolytes on folding are also explored to acquire additional insights into cellular mechanisms for adapting to high pressures. For example, we find that although Mg2+ greatly stabilizes folding of the lysine riboswitch (ΔΔG0 < 0), there is negligible impact on changes in free volume (ΔΔV0 ≈ 0) and thus any pressure induced denaturation effects. Conversely, osmolytes (commonly at high concentrations in deep sea marine species) such as the trimethylamine N-oxide (TMAO) significantly reduce free volumes (ΔΔV0 < 0) and thereby diminish pressure-induced denaturation. We speculate that, besides stabilizing RNA structure, enhanced levels of TMAO in cells might increase the dynamic range for competent riboswitch folding by suppressing the pressure-induced denaturation response. This in turn could offer biological advantage for vertical migration of deep-sea species, with impacts on food searching in a resource limited environment.
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Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA. and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA. and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and Department of Physics, University of Colorado, Boulder, CO 80309, USA
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9
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Yancey PH. Cellular responses in marine animals to hydrostatic pressure. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2020; 333:398-420. [DOI: 10.1002/jez.2354] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Paul H. Yancey
- Department of BiologyWhitman CollegeWalla Walla Washington
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10
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High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration. Sci Rep 2020; 10:2351. [PMID: 32047226 PMCID: PMC7012829 DOI: 10.1038/s41598-020-59172-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022] Open
Abstract
High pressure below 100 MPa interferes inter-molecular interactions without causing pressure denaturation of proteins. In Escherichia coli, the binding of the chemotaxis signaling protein CheY to the flagellar motor protein FliM induces reversal of the motor rotation. Using molecular dynamics (MD) simulations and parallel cascade selection MD (PaCS-MD), we show that high pressure increases the water density in the first hydration shell of CheY and considerably induces water penetration into the CheY-FliM interface. PaCS-MD enabled us to observe pressure-induced dissociation of the CheY-FliM complex at atomic resolution. Pressure dependence of binding free energy indicates that the increase of pressure from 0.1 to 100 MPa significantly weakens the binding. Using high-pressure microscopy, we observed that high hydrostatic pressure fixes the motor rotation to the counter-clockwise direction. In conclusion, the application of pressure enhances hydration of the proteins and weakens the binding of CheY to FliM, preventing reversal of the flagellar motor.
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11
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Lan Y, Sun J, Xu T, Chen C, Tian R, Qiu JW, Qian PY. De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish. BMC Genomics 2018; 19:394. [PMID: 29793428 PMCID: PMC5968573 DOI: 10.1186/s12864-018-4720-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/23/2018] [Indexed: 11/20/2022] Open
Abstract
Background High hydrostatic pressure and low temperatures make the deep sea a harsh environment for life forms. Actin organization and microtubules assembly, which are essential for intracellular transport and cell motility, can be disrupted by high hydrostatic pressure. High hydrostatic pressure can also damage DNA. Nucleic acids exposed to low temperatures can form secondary structures that hinder genetic information processing. To study how deep-sea creatures adapt to such a hostile environment, one of the most straightforward ways is to sequence and compare their genes with those of their shallow-water relatives. Results We captured an individual of the fish species Aldrovandia affinis, which is a typical deep-sea inhabitant, from the Okinawa Trough at a depth of 1550 m using a remotely operated vehicle (ROV). We sequenced its transcriptome and analyzed its molecular adaptation. We obtained 27,633 protein coding sequences using an Illumina platform and compared them with those of several shallow-water fish species. Analysis of 4918 single-copy orthologs identified 138 positively selected genes in A. affinis, including genes involved in microtubule regulation. Particularly, functional domains related to cold shock as well as DNA repair are exposed to positive selection pressure in both deep-sea fish and hadal amphipod. Conclusions Overall, we have identified a set of positively selected genes related to cytoskeleton structures, DNA repair and genetic information processing, which shed light on molecular adaptation to the deep sea. These results suggest that amino acid substitutions of these positively selected genes may contribute crucially to the adaptation of deep-sea animals. Additionally, we provide a high-quality transcriptome of a deep-sea fish for future deep-sea studies. Electronic supplementary material The online version of this article (10.1186/s12864-018-4720-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi Lan
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jin Sun
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Chong Chen
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Renmao Tian
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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Kumar A, Alam A, Tripathi D, Rani M, Khatoon H, Pandey S, Ehtesham NZ, Hasnain SE. Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome. Semin Cell Dev Biol 2018; 84:147-157. [PMID: 29331642 DOI: 10.1016/j.semcdb.2018.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/01/2017] [Accepted: 01/09/2018] [Indexed: 02/02/2023]
Abstract
The biological paradox about how extremophiles persist at extreme ecological conditions throws a fascinating picture of the enormous potential of a single cell to adapt to homeostatic conditions in order to propagate. Unicellular organisms face challenges from both environmental factors and the ecological niche provided by the host tissue. Although the existence of extremophiles and their physiological properties were known for a long time, availability of whole genome sequence has catapulted the study on mechanisms of adaptation and the underlying principles that have enabled these unique organisms to withstand evolutionary and environmental pressures. Comparative genomics has shown that extremophiles possess the unique set of genes and proteins that empower them with biochemical machinery necessary to thrive in extreme environments. The presence of these proteins safeguards the cell against a wide array of extreme conditions such as temperature, pressure, radiations, chemicals, drugs etc. An insight into these adaptive mechanisms in extremophiles may help us to devise strategies to alter the genes and proteins that may have therapeutic potential and commercial value. Here we present an overview of the various adaptations in extremophiles. We also try to explain how mycobacterium channelizes its proteome to survive in stress conditions posed by host immune system.
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Affiliation(s)
- Ashutosh Kumar
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Anwar Alam
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Deeksha Tripathi
- Department of Microbiology, Central University of Rajasthan, Bandar Sindri, Ajmer, Rajasthan, India
| | - Mamta Rani
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, India
| | - Hafeeza Khatoon
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Saurabh Pandey
- National Institute of Pathology, Safdarjang Hospital Campus, New Delhi, India
| | - Nasreen Z Ehtesham
- National Institute of Pathology, Safdarjang Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India; JH-Institute of Molecular Medicine, Hamdard Nagar, New Delhi, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India.
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13
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Lemaire B, Karchner SI, Goldstone JV, Lamb DC, Drazen JC, Rees JF, Hahn ME, Stegeman JJ. Molecular adaptation to high pressure in cytochrome P450 1A and aryl hydrocarbon receptor systems of the deep-sea fish Coryphaenoides armatus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:155-165. [PMID: 28694077 DOI: 10.1016/j.bbapap.2017.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 01/19/2023]
Abstract
Limited knowledge of the molecular evolution of deep-sea fish proteomes so far suggests that a few widespread residue substitutions in cytosolic proteins binding hydrophilic ligands contribute to resistance to the effects of high hydrostatic pressure (HP). Structure-function studies with additional protein systems, including membrane bound proteins, are essential to provide a more general picture of adaptation in these extremophiles. We explored molecular features of HP adaptation in proteins binding hydrophobic ligands, either in lipid bilayers (cytochrome P450 1A - CYP1A) or in the cytosol (the aryl hydrocarbon receptor - AHR), and their partners P450 oxidoreductase (POR) and AHR nuclear translocator (ARNT), respectively. Cloning studies identified the full-length coding sequence of AHR, CYP1A and POR, and a partial sequence of ARNT from Coryphaenoides armatus, an abyssal gadiform fish thriving down to 5000m depth. Inferred protein sequences were aligned with many non-deep-sea homologs to identify unique amino acid substitutions of possible relevance in HP adaptation. Positionally unique substitutions of various physicochemical properties were found in all four proteins, usually at sites of strong-to-absolute residue conservation. Some were in domains deemed important for protein-protein interaction or ligand binding. In addition, some involved removal or addition of beta-branched residues; local modifications of beta-branched residue patterns could be important to HP adaptation. In silico predictions further suggested that some unique substitutions might substantially modulate the flexibility of the polypeptide segment in which they are found. Repetitive motifs unique to the abyssal fish AHR were predicted to be rich in glycosylation sites, suggesting that post-translational changes could be involved in adaptation as well. Recombinant CYP1A and AHR showed functional properties (spectral characteristics, catalytic activity and ligand binding) that demonstrate proper folding at 1atm, indicating that they could be used as deep-sea fish protein models to further evaluate protein function under pressure. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone".
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Affiliation(s)
- Benjamin Lemaire
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02540, USA; Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02540, USA; Boston University Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
| | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02540, USA; Boston University Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
| | - David C Lamb
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02540, USA; Institute of Life Science, Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - Jeffrey C Drazen
- Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Jean François Rees
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02540, USA; Boston University Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02540, USA; Boston University Superfund Research Program, Boston University School of Public Health, Boston, MA, USA.
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14
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Lan Y, Sun J, Tian R, Bartlett DH, Li R, Wong YH, Zhang W, Qiu JW, Xu T, He LS, Tabata HG, Qian PY. Molecular adaptation in the world's deepest-living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas. Mol Ecol 2017; 26:3732-3743. [PMID: 28429829 DOI: 10.1111/mec.14149] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/30/2017] [Accepted: 04/05/2017] [Indexed: 12/17/2022]
Abstract
The Challenger Deep in the Mariana Trench is the deepest point in the oceans of our planet. Understanding how animals adapt to this harsh environment characterized by high hydrostatic pressure, food limitation, dark and cold is of great scientific interest. Of the animals dwelling in the Challenger Deep, amphipods have been captured using baited traps. In this study, we sequenced the transcriptome of the amphipod Hirondellea gigas collected at a depth of 10,929 m from the East Pond of the Challenger Deep. Assembly of these sequences resulted in 133,041 contigs and 22,046 translated proteins. Functional annotation of these contigs was made using the go and kegg databases. Comparison of these translated proteins with those of four shallow-water amphipods revealed 10,731 gene families, of which 5659 were single-copy orthologs. Base substitution analysis on these single-copy orthologs showed that 62 genes are positively selected in H. gigas, including genes related to β-alanine biosynthesis, energy metabolism and genetic information processing. For multiple-copy orthologous genes, gene family expansion analysis revealed that cold-inducible proteins (i.e., transcription factors II A and transcription elongation factor 1) as well as zinc finger domains are expanded in H. gigas. Overall, our results indicate that genetic adaptation to the hadal environment by H. gigas may be mediated by both gene family expansion and amino acid substitutions of specific proteins.
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Affiliation(s)
- Yi Lan
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Renmao Tian
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Douglas H Bartlett
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yue Him Wong
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Harry G Tabata
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
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15
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Zhang Y, Sun J, Chen C, Watanabe HK, Feng D, Zhang Y, Chiu JM, Qian PY, Qiu JW. Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species. Sci Rep 2017; 7:46205. [PMID: 28397791 PMCID: PMC5387418 DOI: 10.1038/srep46205] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 03/10/2017] [Indexed: 12/31/2022] Open
Abstract
Polynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids (Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid (Harmothoe imbricata). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes. Transcriptome assembly produced 98,806 to 225,709 contigs in the three species. There were more positively charged amino acids (i.e., histidine and arginine) and less negatively charged amino acids (i.e., aspartic acid and glutamic acid) in the deep-sea species. There were 120 genes showing clear evidence of positive selection. Among the 10% most highly expressed genes, there were more hemoglobin genes with high expression levels in both deep-sea species. The duplicated genes related to DNA recombination and metabolism, and gene expression were only enriched in deep-sea species. Deep-sea scale worms adopted two strategies of adaptation to hypoxia in the chemosynthesis-based habitats (i.e., rapid evolution of tetra-domain hemoglobin in Branchipolynoe or high expression of single-domain hemoglobin in Lepidonotopodium sp.).
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Affiliation(s)
- Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Jin Sun
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, P. R. China
| | - Chong Chen
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Hiromi K. Watanabe
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Dong Feng
- CAS Key Laboratory of Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, P. R. China
| | - Yu Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
| | - Jill M.Y. Chiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Pei-Yuan Qian
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, P. R. China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
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16
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Yancey PH, Siebenaller JF. Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms. ACTA ACUST UNITED AC 2016; 218:1880-96. [PMID: 26085665 DOI: 10.1242/jeb.114355] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Organisms experience a wide range of environmental factors such as temperature, salinity and hydrostatic pressure, which pose challenges to biochemical processes. Studies on adaptations to such factors have largely focused on macromolecules, especially intrinsic adaptations in protein structure and function. However, micromolecular cosolutes can act as cytoprotectants in the cellular milieu to affect biochemical function and they are now recognized as important extrinsic adaptations. These solutes, both inorganic and organic, have been best characterized as osmolytes, which accumulate to reduce osmotic water loss. Singly, and in combination, many cosolutes have properties beyond simple osmotic effects, e.g. altering the stability and function of proteins in the face of numerous stressors. A key example is the marine osmolyte trimethylamine oxide (TMAO), which appears to enhance water structure and is excluded from peptide backbones, favoring protein folding and stability and counteracting destabilizers like urea and temperature. Co-evolution of intrinsic and extrinsic adaptations is illustrated with high hydrostatic pressure in deep-living organisms. Cytosolic and membrane proteins and G-protein-coupled signal transduction in fishes under pressure show inhibited function and stability, while revealing a number of intrinsic adaptations in deep species. Yet, intrinsic adaptations are often incomplete, and those fishes accumulate TMAO linearly with depth, suggesting a role for TMAO as an extrinsic 'piezolyte' or pressure cosolute. Indeed, TMAO is able to counteract the inhibitory effects of pressure on the stability and function of many proteins. Other cosolutes are cytoprotective in other ways, such as via antioxidation. Such observations highlight the importance of considering the cellular milieu in biochemical and cellular adaptation.
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Affiliation(s)
- Paul H Yancey
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
| | - Joseph F Siebenaller
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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17
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Cario A, Mizgier A, Thiel A, Jebbar M, Oger PM. Restoration of the di-myo-inositol-phosphate pathway in the piezo-hyperthermophilic archaeon Thermococcus barophilus. Biochimie 2015; 118:286-93. [DOI: 10.1016/j.biochi.2015.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/13/2015] [Indexed: 12/16/2022]
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18
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Microbial diversity and adaptation to high hydrostatic pressure in deep-sea hydrothermal vents prokaryotes. Extremophiles 2015; 19:721-40. [DOI: 10.1007/s00792-015-0760-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022]
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19
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Rosin C, Estel K, Hälker J, Winter R. Combined effects of temperature, pressure, and co-solvents on the polymerization kinetics of actin. Chemphyschem 2015; 16:1379-85. [PMID: 25704394 DOI: 10.1002/cphc.201500083] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Indexed: 11/11/2022]
Abstract
In vivo studies have shown that the cytoskeleton of cells is very sensitive to changes in temperature and pressure. In particular, actin filaments get depolymerized when pressure is increased up to several hundred bars, conditions that are easily encountered in the deep sea. We quantitatively evaluate the effects of temperature, pressure, and osmolytes on the kinetics of the polymerization reaction of actin by high-pressure stopped-flow experiments in combination with fluorescence detection and an integrative stochastic simulation of the polymerization process. We show that the compatible osmolyte trimethylamine-N-oxide is not only able to compensate for the strongly retarding effect of chaotropic agents, such as urea, on actin polymerization, it is also able to largely offset the deteriorating effect of pressure on actin polymerization, thereby allowing biological cells to better cope with extreme environmental conditions.
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Affiliation(s)
- Christopher Rosin
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund (Germany)
| | - Kathrin Estel
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund (Germany)
| | - Jessica Hälker
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund (Germany)
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund (Germany).
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20
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Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation. Int J Genomics 2014; 2014:267482. [PMID: 25309900 PMCID: PMC4182897 DOI: 10.1155/2014/267482] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 07/19/2014] [Indexed: 11/29/2022] Open
Abstract
Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotations were performed by Newbler and InterPro/Pfam analyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against the NCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities between A. carbo and other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fish A. carbo first transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes.
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21
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Brown A, Thatje S. Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth. Biol Rev Camb Philos Soc 2014; 89:406-26. [PMID: 24118851 PMCID: PMC4158864 DOI: 10.1111/brv.12061] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 08/01/2013] [Accepted: 08/14/2013] [Indexed: 12/01/2022]
Abstract
Bathymetric biodiversity patterns of marine benthic invertebrates and demersal fishes have been identified in the extant fauna of the deep continental margins. Depth zonation is widespread and evident through a transition between shelf and slope fauna from the shelf break to 1000 m, and a transition between slope and abyssal fauna from 2000 to 3000 m; these transitions are characterised by high species turnover. A unimodal pattern of diversity with depth peaks between 1000 and 3000 m, despite the relatively low area represented by these depths. Zonation is thought to result from the colonisation of the deep sea by shallow-water organisms following multiple mass extinction events throughout the Phanerozoic. The effects of low temperature and high pressure act across hierarchical levels of biological organisation and appear sufficient to limit the distributions of such shallow-water species. Hydrostatic pressures of bathyal depths have consistently been identified experimentally as the maximum tolerated by shallow-water and upper bathyal benthic invertebrates at in situ temperatures, and adaptation appears required for passage to deeper water in both benthic invertebrates and demersal fishes. Together, this suggests that a hyperbaric and thermal physiological bottleneck at bathyal depths contributes to bathymetric zonation. The peak of the unimodal diversity-depth pattern typically occurs at these depths even though the area represented by these depths is relatively low. Although it is recognised that, over long evolutionary time scales, shallow-water diversity patterns are driven by speciation, little consideration has been given to the potential implications for species distribution patterns with depth. Molecular and morphological evidence indicates that cool bathyal waters are the primary site of adaptive radiation in the deep sea, and we hypothesise that bathymetric variation in speciation rates could drive the unimodal diversity-depth pattern over time. Thermal effects on metabolic-rate-dependent mutation and on generation times have been proposed to drive differences in speciation rates, which result in modern latitudinal biodiversity patterns over time. Clearly, this thermal mechanism alone cannot explain bathymetric patterns since temperature generally decreases with depth. We hypothesise that demonstrated physiological effects of high hydrostatic pressure and low temperature at bathyal depths, acting on shallow-water taxa invading the deep sea, may invoke a stress-evolution mechanism by increasing mutagenic activity in germ cells, by inactivating canalisation during embryonic or larval development, by releasing hidden variation or mutagenic activity, or by activating or releasing transposable elements in larvae or adults. In this scenario, increased variation at a physiological bottleneck at bathyal depths results in elevated speciation rate. Adaptation that increases tolerance to high hydrostatic pressure and low temperature allows colonisation of abyssal depths and reduces the stress-evolution response, consequently returning speciation of deeper taxa to the background rate. Over time this mechanism could contribute to the unimodal diversity-depth pattern.
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Affiliation(s)
- Alastair Brown
- Ocean and Earth Science, University of Southampton, National Oceanography Centre SouthamptonEuropean Way, Southampton, SO14 3ZH, U.K.
| | - Sven Thatje
- Ocean and Earth Science, University of Southampton, National Oceanography Centre SouthamptonEuropean Way, Southampton, SO14 3ZH, U.K.
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22
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Yancey PH, Gerringer ME, Drazen JC, Rowden AA, Jamieson A. Marine fish may be biochemically constrained from inhabiting the deepest ocean depths. Proc Natl Acad Sci U S A 2014; 111:4461-5. [PMID: 24591588 PMCID: PMC3970477 DOI: 10.1073/pnas.1322003111] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
No fish have been found in the deepest 25% of the ocean (8,400-11,000 m). This apparent absence has been attributed to hydrostatic pressure, although direct evidence is wanting because of the lack of deepest-living species to study. The common osmolyte trimethylamine N-oxide (TMAO) stabilizes proteins against pressure and increases with depth, going from 40 to 261 mmol/kg in teleost fishes from 0 to 4,850 m. TMAO accumulation with depth results in increasing internal osmolality (typically 350 mOsmol/kg in shallow species compared with seawater's 1,100 mOsmol/kg). Preliminary extrapolation of osmolalities of predicted isosmotic state at 8,000-8,500 m may indicate a possible physiological limit, as greater depths would require reversal of osmotic gradients and, thus, osmoregulatory systems. We tested this prediction by capturing five of the second-deepest known fish, the hadal snailfish (Notoliparis kermadecensis; Liparidae), from 7,000 m in the Kermadec Trench. We found their muscles to have a TMAO content of 386 ± 18 mmol/kg and osmolality of 991 ± 22 mOsmol/kg. These data fit previous extrapolations and, combined with new osmolalities from bathyal and abyssal fishes, predict isosmotic state at 8,200 m. This is previously unidentified evidence that biochemistry could constrain the depth of a large, complex taxonomic group.
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Affiliation(s)
- Paul H. Yancey
- Biology Department, Whitman College, Walla Walla, WA 99362
| | - Mackenzie E. Gerringer
- Biology Department, Whitman College, Walla Walla, WA 99362
- Department of Oceanography, University of Hawaii, Honolulu, HI 96822
| | - Jeffrey C. Drazen
- Department of Oceanography, University of Hawaii, Honolulu, HI 96822
| | - Ashley A. Rowden
- National Institute of Water and Atmospheric Research, Wellington 6021, New Zealand; and
| | - Alan Jamieson
- Oceanlab, Institute of Biological and Environmental Sciences, University of Aberdeen, Newburgh, Aberdeenshire AB41 6AA, United Kingdom
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23
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Wakai N, Takemura K, Morita T, Kitao A. Mechanism of deep-sea fish α-actin pressure tolerance investigated by molecular dynamics simulations. PLoS One 2014; 9:e85852. [PMID: 24465747 PMCID: PMC3896411 DOI: 10.1371/journal.pone.0085852] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 12/03/2013] [Indexed: 12/01/2022] Open
Abstract
The pressure tolerance of monomeric α-actin proteins from the deep-sea fish Coryphaenoides armatus and C. yaquinae was compared to that of non-deep-sea fish C. acrolepis, carp, and rabbit/human/chicken actins using molecular dynamics simulations at 0.1 and 60 MPa. The amino acid sequences of actins are highly conserved across a variety of species. The actins from C. armatus and C. yaquinae have the specific substitutions Q137K/V54A and Q137K/L67P, respectively, relative to C. acrolepis, and are pressure tolerant to depths of at least 6000 m. At high pressure, we observed significant changes in the salt bridge patterns in deep-sea fish actins, and these changes are expected to stabilize ATP binding and subdomain arrangement. Salt bridges between ATP and K137, formed in deep-sea fish actins, are expected to stabilize ATP binding even at high pressure. At high pressure, deep-sea fish actins also formed a greater total number of salt bridges than non-deep-sea fish actins owing to the formation of inter-helix/strand and inter-subdomain salt bridges. Free energy analysis suggests that deep-sea fish actins are stabilized to a greater degree by the conformational energy decrease associated with pressure effect.
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Affiliation(s)
- Nobuhiko Wakai
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Takemura
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Takami Morita
- Research Center for Fisheries Oceanography and Marine Ecosystem, National Research Institute of Fisheries Sciences, Fisheries Research Agency, Kanagawa, Japan
| | - Akio Kitao
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
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24
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Mercer RCC, Mudalige WAKA, Ige TO, Heeley DH. Vertebrate slow skeletal muscle actin - conservation, distribution and conformational flexibility. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1253-60. [PMID: 21722757 DOI: 10.1016/j.bbapap.2011.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Revised: 06/02/2011] [Accepted: 06/16/2011] [Indexed: 11/16/2022]
Abstract
The existence of a unique sarcomeric actin is demonstrated in teleosts that possess substantial amounts of slow skeletal muscle in the trunk. The slow skeletal isotype is conserved. There is one amino acid substitution between Atlantic herring slow skeletal actin and the equivalent in salmonids. Conversely, the intra-species variation is considerable; 13 substitutions between different herring skeletal isotypes (slow versus fast). The isomorphisms (non-conservative underlined: residues, 2, 3, 103, 155, 160, 165, 278, 281, 310, 329, 358, 360 and 363) are restricted to sub-domains 1 and 3 and include the substitution Asp-360 in 'slow' to Gln in 'fast' which results in an electrophoretic shift at alkaline pH. The musculature of the trunk facilitates the preparation of isoactins for biochemical study. Herring slow skeletal G-actin (Ca.ATP) is more susceptible to thermal, and urea, -induced denaturation and subtilisin cleavage than that in fast skeletal, but more stable than the counterpart in salmonids (one substitution, Gln354Ala) highlighting the critical nature of actin's carboxyl-terminal insert. Fluorescent spectra of G-actin isoforms containing the isomorphism Ser155Ala in complexation with 2'-deoxy 3' O-(N'-Methylanthraniloyl) ATP infer similar polarity of the nucleotide binding cleft. An electrophoretic survey detected two skeletal actins in some (smelt and mackerel) but not all teleosts. One skeletal muscle actin was detected in frog and bird.
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Affiliation(s)
- Robert C C Mercer
- Department of Biochemistry, Memorial University of Newfoundland, Newfoundland, Canada.
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25
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Nishiguchi Y, Abe F, Okada M. Different pressure resistance of lactate dehydrogenases from hagfish is dependent on habitat depth and caused by tetrameric structure dissociation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:137-141. [PMID: 20514503 DOI: 10.1007/s10126-010-9299-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 03/22/2010] [Indexed: 05/29/2023]
Abstract
The effects of high hydrostatic pressure on lactate dehydrogenase (LDH) activities from two species of hagfish were examined. LDH from Eptatretus okinoseanus, a deep-sea species, retained 67% of the original activity even at 100 MPa. LDH activity from Eptatretus burgeri, a shallow-sea species, was completely lost at 50 MPa but recovered to the original value at 0.1 MPa. The tetrameric structure of LDH-A(4) from E. okinoseanus did not change at 50 MPa. In contrast, almost all LDH tetramers from E. burgeri dissociated to dimers and monomers at 50 MPa but reverted to tetramers at 0.1 MPa. These results show that the dissociation of tetramers caused the inactivation of E. burgeri LDH. The difference depends on the number 6 and 10 amino acids. The mechanism of the slight, gradual inactivation of E. okinoseanus LDH at high pressure differs and is probably due to the metamorphosis of its inner structures.
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Affiliation(s)
- Yoshikazu Nishiguchi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, 274-8510, Japan.
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26
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Morita T. High-pressure adaptation of muscle proteins from deep-sea fishes, Coryphaenoides yaquinae and C. armatus. Ann N Y Acad Sci 2010; 1189:91-4. [PMID: 20233373 DOI: 10.1111/j.1749-6632.2009.05181.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The evolutionary adaptations of functional genes to life at high pressures are not well understood. To elucidate the mechanisms of protein adaptation to high pressures, we isolated two muscle protein-encoding cDNAs, alpha-actin and myosin heavy chain (MyHC), derived from skeletal muscles of two deep-sea fishes, Coryphaenoides yaquinae and C. armatus, and two non-deep-sea fishes, C. acrolepis and C. cinereus. The alpha-actins from two deep-sea fishes have three amino acid substitutions in comparison to those of non-deep-sea fishes. These substitutions enable the deep-sea fish actins to function even at 60 MPa. The MyHCs of the two deep-sea fishes have a proline residue in the loop-1 region and have a shorter loop-2 region than the non-deep-sea fishes. Additionally, the MyHCs of deep-sea fishes have biased amino acid substitutions at core positions within the coiled-coil structure of the rod region. The roles of these substitutions in the deep-sea fishes MyHCs, however, remain unclear.
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Affiliation(s)
- Takami Morita
- National Research Institute of Fisheries Science, Kanazawa-ku, Yokohama, Kanagawa, Japan.
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27
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Abstract
The manipulation of biological materials using elevated pressure is providing an ever-growing number of opportunities in both the applied and basic sciences. Manipulation of pressure is a useful parameter for enhancing food quality and shelf life; inactivating microbes, viruses, prions, and deleterious enzymes; affecting recombinant protein production; controlling DNA hybridization; and improving vaccine preparation. In biophysics and biochemistry, pressure is used as a tool to study intermediates in protein folding, enzyme kinetics, macromolecular interactions, amyloid fibrous protein aggregation, lipid structural changes, and to discern the role of solvation and void volumes in these processes. Biologists, including many microbiologists, examine the utility and basis of pressure inactivation of cells and cellular processes, and conversely seek to discover how deep-sea life has evolved a preference for high-pressure environments. This introduction and the papers that follow provide information on the nature and promise of the highly interdisciplinary field of high-pressure bioscience and biotechnology (HPBB).
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Affiliation(s)
- Douglas H Bartlett
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.
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28
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Structure and function of lactate dehydrogenase from hagfish. Mar Drugs 2010; 8:594-607. [PMID: 20411117 PMCID: PMC2857353 DOI: 10.3390/md8030594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 02/03/2010] [Accepted: 03/11/2010] [Indexed: 11/22/2022] Open
Abstract
The lactate dehydrogenases (LDHs) in hagfish have been estimated to be the prototype of those in higher vertebrates. The effects of high hydrostatic pressure from 0.1 to 100 MPa on LDH activities from three hagfishes were examined. The LDH activities of Eptatretus burgeri, living at 45–60 m, were completely lost at 5 MPa. In contrast, LDH-A and -B in Eptatretus okinoseanus maintained 70% of their activities even at 100 MPa. These results show that the deeper the habitat, the higher the tolerance to pressure. To elucidate the molecular mechanisms for adaptation to high pressure, we compared the amino acid sequences and three-dimensional structures of LDHs in these hagfish. There were differences in six amino acids (6, 10, 20, 156, 269, and 341). These amino acidresidues are likely to contribute to the stability of the E. okinoseanus LDH under high-pressure conditions. The amino acids responsible for the pressure tolerance of hagfish are the same in both human and hagfish LDHs, and one substitution that occurred as an adaptation during evolution is coincident with that observed in a human disease. Mutation of these amino acids can cause anomalies that may be implicated in the development of human diseases.
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Morita T. Comparative sequence analysis of myosin heavy chain proteins from congeneric shallow- and deep-living rattail fish (genus Coryphaenoides). ACTA ACUST UNITED AC 2008; 211:1362-7. [PMID: 18424669 DOI: 10.1242/jeb.017137] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The evolutionary adaptations of functional genes to life at high pressure are not well understood. To elucidate the mechanisms of protein adaptation to high pressure, we cloned the myosin heavy chain (MyHC) cDNA from skeletal muscle of two deep-sea fishes, Coryphaenoides yaquinae and C. armatus, and two non-deep-sea fishes, C. acrolepis and C. cinereus. The MyHCs of deep-sea fishes have a unique structure in two loop regions, loop-1 and loop-2, in comparison with those of non-deep-sea fishes. The loop-1 region of deep-sea fishes has a Pro residue and the loop-2 region, which is an actin-binding site, is shorter than the same region in non-deep-sea fishes. The amino acid substitution in the loop-1 region is expected to be mainly involved in ATPase activity, whereas the deletion in the loop-2 region affects the association of MyHC with actin filaments at high pressure. In addition, the MyHC of deep-sea fishes has biased amino acid substitutions at core positions in the coiled-coil structure of the rod region. These amino acid substitutions are likely to decrease the cavities in the coiled-coil structure and consequently make the structure more compact and unaffected by high pressure. Together, these results indicate that amino acid substitutions can adaptively alter the pressure sensitivity of a protein even if they do not directly influence core structure.
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Affiliation(s)
- Takami Morita
- National Research Institute of Fisheries Science, Fukuura 2-12-4, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan.
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Brindley AA, Pickersgill RW, Partridge JC, Dunstan DJ, Hunt DM, Warren MJ. Enzyme sequence and its relationship to hyperbaric stability of artificial and natural fish lactate dehydrogenases. PLoS One 2008; 3:e2042. [PMID: 18446214 PMCID: PMC2323112 DOI: 10.1371/journal.pone.0002042] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 03/11/2008] [Indexed: 11/18/2022] Open
Abstract
The cDNAs of lactate dehydrogenase b (LDH-b) from both deep-sea and shallow living fish species, Corphaenoides armatus and Gadus morhua respectively, have been isolated, sequenced and their encoded products overproduced as recombinant enzymes in E. coli. The proteins were characterised in terms of their kinetic and physical properties and their ability to withstand high pressures. Although the two proteins are very similar in terms of their primary structure, only 21 differences at the amino acid level exist between them, the enzyme from the deep-sea species has a significantly increased tolerance to pressure and a higher thermostability. It was possible to investigate whether the changes in the N-terminal or C-terminal regions played a greater role in barophilic adaptation by the construction of two chimeric enzymes by use of a common restriction site within the cDNAs. One of these hybrids was found to have even greater pressure stability than the recombinant enzyme from the deep-living fish species. It was possible to conclude that the major adaptive changes to pressure tolerance must be located in the N-terminal region of the protein. The types of changes that are found and their spatial location within the protein structure are discussed. An analysis of the kinetic parameters of the enzymes suggests that there is clearly a trade off between Km and kcat values, which likely reflects the necessity of the deep-sea enzyme to operate at low temperatures.
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Affiliation(s)
- Amanda A Brindley
- Department of Biosciences, University of Kent, Canterbury, Kent, United Kingdom.
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Song Z, Wang M, Wang X, Pan X, Liu W, Hao S, Zeng X. Nuclear actin is involved in the regulation of CSF1 gene transcription in a chromatin required, BRG1 independent manner. J Cell Biochem 2008; 102:403-11. [PMID: 17393431 DOI: 10.1002/jcb.21300] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Actin is an important protein in nucleus and has been implicated in transcription, however, the mechanism of its function in transcription is still not clear. In this article, we studied the role of actin in the regulation of human CSF1 gene transcription. Our results showed that nuclear actin stimulates the activity of CSF1 promoter, and the role in augmenting CSF1 gene transcription requires the formation of chromatin and Z-DNA structure. The ATP binding motifs of nuclear actin are essential for its function in regulating CSF1 gene transcription, and upon actin overexpression, there is an increase in the ATPase activity of nuclear proteins. Further investigation revealed that nuclear actin regulates CSF1 gene transcription in a BRG1 independent manner. Together, these original results have provided evidence for further understanding the mechanism of nuclear actin in regulating gene transcription.
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Affiliation(s)
- Zhaoxia Song
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
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Pressure-adaptive differences in lactate dehydrogenases of three hagfishes: Eptatretus burgeri, Paramyxine atami and Eptatretus okinoseanus. Extremophiles 2008; 12:477-80. [DOI: 10.1007/s00792-008-0140-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 12/26/2007] [Indexed: 10/22/2022]
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Piezotolerance of the cytoskeletal structure in cultured deep-sea fish cells using DNA transfection and protein introduction techniques. Cytotechnology 2007; 56:19-26. [PMID: 19002837 DOI: 10.1007/s10616-007-9099-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 09/19/2007] [Indexed: 10/22/2022] Open
Abstract
We used DNA transfection and protein introduction techniques to investigate the pressure tolerance of cytoskeletal structures in pectoral fin cells derived from the deep-sea fish Simenchelys parasiticus (habitat depth, 366-2,630 m). The deep-sea fish cells have G418 resistance. The cell number increased until day 6 of cultivation and all cells had died by day 35 when cultured in 35-mm Petri dishes in medium containing G418. Enhanced yellow fluorescent protein-tagged human beta-actin (EYFP-actin) was stably expressed by 1 in 100,000 deep-sea fish cells. Because almost none of the EYFP-actin was incorporated into actin filaments of the cells, we replaced the relatively large EYFP tag with a chemical fluorescent compound and succeeded in incorporating fluorescently labeled rabbit actins into the deep-sea fish actin filaments. Most of the filament structure in the cells with rabbit actin inserted underwent depolymerization when subjected to pressure of 100 MPa for 20 min, in contrast to control cells. There were no differences in the tubulin filament structure between control cells and deep-sea fish cells with fluorescein-labeled bovine tubulin inserted after the application of pressure ranging from 40 to 100 MPa for 20 min.
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Abstract
Salmonids utilize a unique, class II isoactin in slow skeletal muscle. This actin contains 12 replacements when compared with those from salmonid fast skeletal muscle, salmonid cardiac muscle and rabbit skeletal muscle. Substitutions are confined to subdomains 1 and 3, and most occur after residue 100. Depending on the pairing, the 'fast', 'cardiac' and rabbit actins share four, or fewer, substitutions. The two salmonid skeletal actins differ nonconservatively at six positions, residues 103, 155, 278, 281, 310 and 360, the latter involving a change in charge. The heterogeneity has altered the biochemical properties of the molecule. Slow skeletal muscle actin can be distinguished on the basis of mass, hydroxylamine cleavage and electrophoretic mobility at alkaline pH in the presence of 8 m urea. Further, compared with its counterpart in fast muscle, slow muscle actin displays lower activation of myosin in the presence of regulatory proteins, and weakened affinity for nucleotide. It is also less resistant to urea- and heat-induced denaturation. The midpoints of the change in far-UV ellipticity of G-actin versus temperature are approximately 45 degrees C ('slow' actin) and approximately 56 degrees C ('fast' actin). Similar melting temperatures are observed when thermal unfolding is monitored in the aromatic region, and is suggestive of differential stability within subdomain 1. The changes in nucleotide affinity and stability correlate with substitutions at the nucleotide binding cleft (residue 155), and in the C-terminal region, two parts of actin which are allosterically coupled. Actin is concluded to be a source of skeletal muscle plasticity.
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Samerotte AL, Drazen JC, Brand GL, Seibel BA, Yancey PH. Correlation of Trimethylamine Oxide and Habitat Depth within and among Species of Teleost Fish: An Analysis of Causation. Physiol Biochem Zool 2007; 80:197-208. [PMID: 17252516 DOI: 10.1086/510566] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2006] [Indexed: 11/03/2022]
Abstract
Most shallow-water teleosts have moderate levels of trimethylamine N-oxide (TMAO; approximately 50 mmol/kg wet mass), a common osmolyte in many other marine animals. Recently, muscle TMAO contents were found to increase linearly with depth in six families. In one hypothesis, this may be an adaptation to counteract the deleterious effects of pressure on protein function, which TMAO does in vitro. In another hypothesis, TMAO may be accumulated as a by-product of acylglycerol (AG) production, increasing with depth because of elevated lipid metabolisms known to occur in some deep-sea animals. Here we analyze muscle TMAO contents and total body AG (mainly triacyglycerol [TAG]) levels in 15 species of teleosts from a greater variety of depths than sampled previously, including eight individual species caught at two or more depths. Including data of previous studies (total of 17 species, nine families), there is an apparent sigmoidal increase in TMAO contents between 0- and 1.4-km depths, from about 40 to 150 mmol/kg. From 1.4 to 4.8 km, the increase appears to be linear (r2=0.91), rising to 261 mmol/kg at 4.8 km. The trend also occurred within species: in most cases in which a species was caught at two or more depths, TMAO was higher in the deeper-caught specimens (e.g., for Coryphaenoides armatus, TMAO was 173, 229, and 261 mmol/kg at 1.8, 4.1, and 4.8 km, respectively). TMAO contents not only were consistent within species at a given depth but also did not vary with season or over a wide range of body masses or TAG contents. Thus, no clear link between TMAO and lipid was found. However, TMAO contents might correlate with the rate (rather than content) of TAG production, which could not be quantified. Overall, the data strongly support the hypothesis that TMAO is adaptively regulated with depth in deep-sea teleosts. Whether lipid metabolism is the source of that TMAO is a question that remains to be tested fully.
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Koyama S, Kobayashi H, Inoue A, Miwa T, Aizawa M. Effects of the piezo-tolerance of cultured deep-sea eel cells on survival rates, cell proliferation, and cytoskeletal structures. Extremophiles 2005; 9:449-60. [PMID: 16082498 DOI: 10.1007/s00792-005-0462-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2005] [Accepted: 05/30/2005] [Indexed: 11/29/2022]
Abstract
We investigated the pressure tolerance of deep-sea eel (Simenchelys parasiticus; habitat depth, 366-2,630 m) cells, conger eel (Conger myriaster) cells, and mouse 3T3-L1 cells. Although there were no living mouse 3T3-L1 and conger eel cells after 130 MPa (0.1 MPa = 1 bar) hydrostatic pressurization for 20 min, all deep-sea eel cells remained alive after being subjected to pressures up to 150 MPa for 20 min. Pressurization at 40 MPa for 20 min induced disruption of actin and tubulin filaments with profound cell-shape changes in the mouse and conger eel cells. In the deep-sea eel cells, microtubules and some actin filaments were disrupted after being subjected to hydrostatic pressure of 100 MPa and greater for 20 min. Conger eel cells were sensitive to pressure and did not grow at 10 MPa. Mouse 3T3-L1 cells grew faster under pressure of 5 MPa than at atmospheric pressure and stopped growing at 18 MPa. Deep-sea eel cells were capable of growth in pressures up to 25 MPa and stopped growing at 30 MPa. Deep-sea eel cells required 4 h at 20 MPa to finish the M phase, which was approximately fourfold the time required under atmospheric conditions.
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Affiliation(s)
- Sumihiro Koyama
- Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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Ohmae E, Kubota K, Nakasone K, Kato C, Gekko K. Pressure-dependent Activity of Dihydrofolate Reductase from a Deep-sea BacteriumShewanella violaceaStrain DSS12. CHEM LETT 2004. [DOI: 10.1246/cl.2004.798] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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38
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Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2003.12.039] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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