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Sieg J, Sandmeier CC, Lieske J, Meents A, Lemmen C, Streit WR, Rarey M. Analyzing structural features of proteins from deep-sea organisms. Proteins 2022; 90:1521-1537. [PMID: 35313380 DOI: 10.1002/prot.26337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 12/31/2022]
Abstract
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 deep-sea 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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Affiliation(s)
- Jochen Sieg
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
| | | | - Julia Lieske
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | | | - Wolfgang R Streit
- Universität Hamburg, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
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Trimethylamine N-Oxide (TMAO) and Trimethylamine (TMA) Determinations of Two Hadal Amphipods. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10040454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Hadal trenches are a unique habitat with high hydrostatic pressure, low temperature and scarce food supplies. Amphipods are the dominant scavenging metazoan species in this ecosystem. Trimethylamine (TMA) and trimethylamine oxide (TMAO) have been shown to play important roles in regulating osmotic pressure in mammals, hadal dwellers and even microbes. However, the distributions of TMAO and TMA concentrations of hadal animals among different tissues have not been reported so far. Here, the TMAO and TMA contents of eight tissues of two hadal amphipods, Hirondellea gigas and Alicella gigantea from the Mariana Trench and the New Britain Trench, were detected by using the ultrahigh performance liquid chromatography–mass spectrometry (UPLC-MS/MS) method. Compared with the shallow water Decapoda, Penaeus vannamei, the hadal amphipods possessed significantly higher TMAO concentrations and a similar level of TMA in all the detected tissues. A higher level of TMAO was detected in the external organs (such as the eye and exoskeleton) for both of the two hadal amphipods, which indicated that the TMAO concentration was not evenly distributed, although the same hydrostatic pressure existed in the outer and internal organs. Moreover, a strong positive correlation was found between the concentrations of TMAO and TMA in the two hadal amphipods. In addition, evolutionary analysis regarding FMO3, the enzyme to convert TMA into TMAO, was also conducted. Three positive selected sites in the conserved region and two specific mutation sites in two conserved motifs were found in the A. gigantea FMO3 gene. Combined together, this study supports the important role of TMAO for the environmental adaptability of hadal amphipods and speculates on the molecular evolution and protein structure of FMO3 in hadal species.
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Wang K, Shen Y, Yang Y, Gan X, Liu G, Hu K, Li Y, Gao Z, Zhu L, Yan G, He L, Shan X, Yang L, Lu S, Zeng H, Pan X, Liu C, Yuan Y, Feng C, Xu W, Zhu C, Xiao W, Dong Y, Wang W, Qiu Q, He S. Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation. Nat Ecol Evol 2019; 3:823-833. [PMID: 30988486 DOI: 10.1038/s41559-019-0864-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 03/06/2019] [Indexed: 12/30/2022]
Abstract
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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Affiliation(s)
- Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Yanjun Shen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiaoni Gan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guichun Liu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Kuang Hu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yongxin Li
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Zhaoming Gao
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Li Zhu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guoyong Yan
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Lisheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xiujuan Shan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao, China
| | - Liandong Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Suxiang Lu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Honghui Zeng
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiangyu Pan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chang Liu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yuan Yuan
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Chenguang Feng
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Wenjie Xu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Chenglong Zhu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Wuhan Xiao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yang Dong
- Biological Big Data College, Yunnan Agricultural University, Kunming, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China. .,Qingdao Research Institute, Northwestern Polytechnical University, Qingdao, China. .,Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
| | - Qiang Qiu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China. .,State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China. .,Qingdao Research Institute, Northwestern Polytechnical University, Qingdao, China.
| | - Shunping He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China. .,Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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Chakravorty D, Khan MF, Patra S. Multifactorial level of extremostability of proteins: can they be exploited for protein engineering? Extremophiles 2017; 21:419-444. [PMID: 28283770 DOI: 10.1007/s00792-016-0908-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022]
Abstract
Research on extremostable proteins has seen immense growth in the past decade owing to their industrial importance. Basic research of attributes related to extreme-stability requires further exploration. Modern mechanistic approaches to engineer such proteins in vitro will have more impact in industrial biotechnology economy. Developing a priori knowledge about the mechanism behind extreme-stability will nurture better understanding of pathways leading to protein molecular evolution and folding. This review is a vivid compilation about all classes of extremostable proteins and the attributes that lead to myriad of adaptations divulged after an extensive study of 6495 articles belonging to extremostable proteins. Along with detailing on the rationale behind extreme-stability of proteins, emphasis has been put on modern approaches that have been utilized to render proteins extremostable by protein engineering. It was understood that each protein shows different approaches to extreme-stability governed by minute differences in their biophysical properties and the milieu in which they exist. Any general rule has not yet been drawn regarding adaptive mechanisms in extreme environments. This review was further instrumental to understand the drawback of the available 14 stabilizing mutation prediction algorithms. Thus, this review lays the foundation to further explore the biophysical pleiotropy of extreme-stable proteins to deduce a global prediction model for predicting the effect of mutations on protein stability.
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Affiliation(s)
- Debamitra Chakravorty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Mohd Faheem Khan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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