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Zheng P, Yang H, Zhang H, Shen C, Sun H. Influence of hydrological parameters on hydroxylated tetraether lipids in a deep Lake Fuxian, China: Implications for their use as environmental proxies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165022. [PMID: 37348708 DOI: 10.1016/j.scitotenv.2023.165022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/22/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023]
Abstract
Hydroxylated isoprenoid glycerol dialkyl glycerol tetraethers (OH-GDGTs) have shown their potential in environmental reconstructions. However, the unclear underlying mechanism challenges their application. To elucidate the effects of water parameters on OH-GDGT-derived indices and understand their environmental implications, we investigated the core OH-GDGTs of suspended particulate matter (SPM) from water columns in a year cycle and surface sediments at different water depths along a nearshore-offshore transect in Lake Fuxian, a deep and large lake in southwestern China. OH-GDGTs were primarily found in the hypolimnion and were produced in situ by Group I.1a Thaumarchaeota. The relative abundance of OH-GDGTs (%OH-GDGTs) and ring indices (RI-OH and RI-OH') in the hypolimnion were significantly influenced by dissolved oxygen (DO) and pH, particularly DO, which regulated the inverse physiological functions of the hydroxyl and cyclopentane moieties of archaea. %OH-GDGTs values in SPM were positively correlated with DO and negatively correlated with pH levels, while RI-OH values exhibited an inverse relationship with DO and positive correlation with pH levels. OH-GDGTs in surface sediments appeared to be homologous to that of water columns, indicating that their inferred proxies could be regulated by the configuration of water parameters. The sedimentary %OH-GDGTs values increased as the RI-OH values decreased with water depth along the transect from the lakeshore to the lake center, suggesting their potential as lake-level proxies.
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Affiliation(s)
- Pingbo Zheng
- Yunnan Key Laboratory of Plateau Geographical Processes and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, China
| | - Huan Yang
- Hubei Key Laboratory of Critical Zone Evolution, School of Geography and Information Engineering, China University of Geosciences, Wuhan 430078, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Caiming Shen
- Yunnan Key Laboratory of Plateau Geographical Processes and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, China
| | - Huiling Sun
- Yunnan Key Laboratory of Plateau Geographical Processes and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, China.
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Finkel PL, Carrizo D, Parro V, Sánchez-García L. An Overview of Lipid Biomarkers in Terrestrial Extreme Environments with Relevance for Mars Exploration. ASTROBIOLOGY 2023; 23:563-604. [PMID: 36880883 PMCID: PMC10150655 DOI: 10.1089/ast.2022.0083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lipid molecules are organic compounds, insoluble in water, and based on carbon-carbon chains that form an integral part of biological cell membranes. As such, lipids are ubiquitous in life on Earth, which is why they are considered useful biomarkers for life detection in terrestrial environments. These molecules display effective membrane-forming properties even under geochemically hostile conditions that challenge most of microbial life, which grants lipids a universal biomarker character suitable for life detection beyond Earth, where a putative biological membrane would also be required. What discriminates lipids from nucleic acids or proteins is their capacity to retain diagnostic information about their biological source in their recalcitrant hydrocarbon skeletons for thousands of millions of years, which is indispensable in the field of astrobiology given the time span that the geological ages of planetary bodies encompass. This work gathers studies that have employed lipid biomarker approaches for paleoenvironmental surveys and life detection purposes in terrestrial environments with extreme conditions: hydrothermal, hyperarid, hypersaline, and highly acidic, among others; all of which are analogous to current or past conditions on Mars. Although some of the compounds discussed in this review may be abiotically synthesized, we focus on those with a biological origin, namely lipid biomarkers. Therefore, along with appropriate complementary techniques such as bulk and compound-specific stable carbon isotope analysis, this work recapitulates and reevaluates the potential of lipid biomarkers as an additional, powerful tool to interrogate whether there is life on Mars, or if there ever was.
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Affiliation(s)
- Pablo L Finkel
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
- Department of Physics and Mathematics and Department of Automatics, University of Alcalá, Madrid, Spain
| | | | - Victor Parro
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
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Li X, Ye M, Wang Y, Qiu M, Fu T, Zhang J, Zhou B, Lu S. How Parkinson's disease-related mutations disrupt the dimerization of WD40 domain in LRRK2: a comparative molecular dynamics simulation study. Phys Chem Chem Phys 2021; 22:20421-20433. [PMID: 32914822 DOI: 10.1039/d0cp03171b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The multidomain kinase enzyme leucine-rich-repeat kinase 2 (LRRK2), activated through a homodimerization manner, has been identified as an important pathogenic factor in Parkinson's disease (PD), the second most common neurodegenerative disease wordwide. The Trp-Asp-40 (WD40) domain, located in the C-terminal LRRK2, harbours one of the most frequent PD-related variants, G2385R. However, the detailed dynamics of WD40 during LRRK2 dimerization and the underlying mechanism through which the pathogenic mutations disrupt the formation of the WD40 dimer have remained elusive. Here, microsecond-scale molecular dynamics simulations were employed to provide a mechanistic view underlying the WD40 dimerization and unveil the structural basis by which the interface-based mutations G2385R, H2391D and R2394E compromise the corresponding process. The simulation results identified important residues, D2351, R2394, E2395, R2413, and R2443, involved in establishing the complex binding network along the dimerization interface, which was significantly weakened in the presence of interfacial mutations. A "sag-bulge" model was proposed to explain the unfavorable dimer formation in the mutant systems. In addition, mutations altered the community configuration in the wild-type system in which inter-monomeric interplay is prominent, leading to the destabilization of the WD40 dimer under mutation.
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Affiliation(s)
- Xinyi Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.
| | - Mingyu Ye
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.
| | - Yue Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.
| | - Ming Qiu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.
| | - Tingting Fu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.
| | - Bin Zhou
- Department of Emergency, Changhai Hospital, Affiliated to Navy Military Medical University, Shanghai, 200433, China.
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.
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Pirkhezranian Z, Tahmoorespur M, Monhemi H, Sekhavati MH. Computational Peptide Engineering Approach for Selection the Best Engendered Camel Lactoferrin-Derive Peptide with Potency to Interact with DNA. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-10012-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Li J, Wu G, Fu Q, Ge H, Liu S, Li X, Cheng B. Exploring the influence of conserved lysine69 on the catalytic activity of the helicobacter pylori shikimate dehydrogenase: A combined QM/MM and MD simulations. Comput Biol Chem 2019; 83:107098. [DOI: 10.1016/j.compbiolchem.2019.107098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 08/04/2019] [Indexed: 12/29/2022]
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Moradi S, Nowroozi A, Shahlaei M. Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study. RSC Adv 2019; 9:4644-4658. [PMID: 35520151 PMCID: PMC9060685 DOI: 10.1039/c8ra08441f] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/12/2019] [Accepted: 01/16/2019] [Indexed: 12/20/2022] Open
Abstract
In recent years, a massive increase has been observed in the number of published articles describing accurate and reliable molecular dynamics simulations of lipid bilayers. This is due to several reasons, including the development of fast and efficient methods for treating long-range electrostatic interactions, significant progress in computer hardware, progress in atomistic simulation algorithms and the development of well-validated empirical molecular mechanical force fields. Although molecular dynamics is an effective approach for investigating different aspects of lipid bilayers, to the best of our knowledge, there is no review in the literature that explains the different analyses that can be carried out with membrane simulation. This review gives an overview about the some of the most important possible analyses, technical challenges, and existing protocols that can be performed on the biological membrane by molecular dynamics simulation. The reviewed analyses include the degree of membrane disruption, average area per lipid, probability distributions for the area per lipid molecule, membrane thickness, membrane area compressibility, lateral diffusion, rotational diffusion, order parameters, head group tilt, electron density profile, mass density profile, electrostatic potential profile, ordering of vicinity waters, number of hydrogen bonds, and radial distribution function.
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Affiliation(s)
- Sajad Moradi
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences Kermanshah Iran
| | - Amin Nowroozi
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Kermanshah University of Medical Sciences Kermanshah Iran
| | - Mohsen Shahlaei
- Medical Biology Research Center, Kermanshah University of Medical Sciences Kermanshah Iran
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Marquês JT, Marinho HS, de Almeida RF. Sphingolipid hydroxylation in mammals, yeast and plants – An integrated view. Prog Lipid Res 2018; 71:18-42. [DOI: 10.1016/j.plipres.2018.05.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/11/2018] [Accepted: 05/04/2018] [Indexed: 02/07/2023]
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Elling FJ, Könneke M, Nicol GW, Stieglmeier M, Bayer B, Spieck E, de la Torre JR, Becker KW, Thomm M, Prosser JI, Herndl GJ, Schleper C, Hinrichs KU. Chemotaxonomic characterisation of the thaumarchaeal lipidome. Environ Microbiol 2017; 19:2681-2700. [PMID: 28419726 DOI: 10.1111/1462-2920.13759] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/28/2022]
Abstract
Thaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the phylum Thaumarchaeota. Here, we comprehensively describe the core and intact polar lipid (IPL) inventory of ten ammonia-oxidising thaumarchaeal cultures representing all four characterized phylogenetic clades. IPLs of these thaumarchaeal strains are generally similar and consist of membrane-spanning, glycerol dibiphytanyl glycerol tetraethers with monoglycosyl, diglycosyl, phosphohexose and hexose-phosphohexose headgroups. However, the relative abundances of these IPLs and their core lipid compositions differ systematically between the phylogenetic subgroups, indicating high potential for chemotaxonomic distinction of thaumarchaeal clades. Comparative lipidomic analyses of 19 euryarchaeal and crenarchaeal strains suggested that the lipid methoxy archaeol is synthesized exclusively by Thaumarchaeota and may thus represent a diagnostic lipid biomarker for this phylum. The unprecedented diversity of the thaumarchaeal lipidome with 118 different lipids suggests that membrane lipid composition and adaptation mechanisms in Thaumarchaeota are more complex than previously thought and include unique lipids with as yet unresolved properties.
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Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany.,Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134, Ecully, France
| | | | - Barbara Bayer
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria
| | - Eva Spieck
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, 22609, Germany
| | - José R de la Torre
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Regensburg, 93053, Germany
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Gerhard J Herndl
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Texel, The Netherlands
| | | | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
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