1
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Zhou J, Dong L. Structural insights linking H-bridging of archaeal GDGTs to high temperature. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:174120. [PMID: 38901598 DOI: 10.1016/j.scitotenv.2024.174120] [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: 03/22/2024] [Revised: 06/07/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
Isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs), characteristic membrane lipids of archaea, are widely used in ecological and geochemical studies, especially for paleoenvironmental reconstruction. Glycerol monoalkyl glycerol tetraethers (GMGTs, also known as H-GDGTs), a unique variant of GDGTs, have covalent bonds linking the two alkyl chains. Despite some studies suggesting a link between GMGTs and high temperatures, the reliability and mechanisms remain unclear. Using molecular dynamics simulations, we elucidated the mechanism connecting GMGTs to high temperatures. Our findings show that H-bridging linkages reduce the distance between alkyl chains, leading to thicker and denser membranes with lower fluidity and permeability. The diffusion coefficient of GMGTs decreased by approximately 35 % compared to GDGTs, indicating their role as a archaeal high-temperature adaptation. This study provides a mechanistic basis for using archaeal GMGTs in geochemical studies and enhances confidence in their use for paleotemperature reconstruction.
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Affiliation(s)
- Jiaming Zhou
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; and School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Liang Dong
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; and School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China.
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2
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Rahn HP, Sun J, Li Z, Waymouth RM, Levy R, Wender PA. Isoprenoid CARTs: In Vitro and In Vivo mRNA Delivery by Charge-Altering Releasable Transporters Functionalized with Archaea-inspired Branched Lipids. Biomacromolecules 2024; 25:4305-4316. [PMID: 38814265 DOI: 10.1021/acs.biomac.4c00373] [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: 05/31/2024]
Abstract
The delivery of oligonucleotides across biological barriers is a challenge of unsurpassed significance at the interface of materials science and medicine, with emerging clinical utility in prophylactic and therapeutic vaccinations, immunotherapies, genome editing, and cell rejuvenation. Here, we address the role of readily available branched lipids in the design, synthesis, and evaluation of isoprenoid charge-altering releasable transporters (CARTs), a pH-responsive oligomeric nanoparticle delivery system for RNA. Systematic variation of the lipid block reveals an emergent relationship between the lipid block and the neutralization kinetics of the polycationic block. Unexpectedly, iA21A11, a CART with the smallest lipid side chain, isoamyl-, was identified as the lead isoprenoid CART for the in vitro transfection of immortalized lymphoblastic cell lines. When administered intramuscularly in a murine model, iA21A11-mRNA complexes induce higher protein expression levels than our previous lead CART, ONA. Isoprenoid CARTs represent a new delivery platform for RNA vaccines and other polyanion-based therapeutics.
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Affiliation(s)
- Harrison P Rahn
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jiuzhi Sun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Zhijian Li
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Robert M Waymouth
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ronald Levy
- Stanford Cancer Institute, Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, United States
| | - Paul A Wender
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
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3
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Yoshida R, Motoyama K, Ito T, Hemmi H. Effects of producing high levels of hyperthermophile-specific C 25,C 25-archaeal membrane lipids in Escherichia coli. Biochem Biophys Res Commun 2024; 729:150349. [PMID: 38972140 DOI: 10.1016/j.bbrc.2024.150349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/09/2024]
Abstract
A hyperthermophilic archaeon, Aeropyrum pernix, synthesizes C25,C25-archaeal membrane lipids, or extended archaeal membrane lipids, which contain two C25 isoprenoid chains that are linked to glycerol-1-phosphate via ether bonds and are longer than the usual C20,C20-archaeal membrane lipids. The C25,C25-archaeal membrane lipids are believed to allow the archaeon to survive under harsh conditions, because they are able to form lipid membranes that are impermeable at temperatures approaching the boiling point. The effect that C25,C25-archaeal membrane lipids exert on living cells, however, remains unproven along with an explanation for why the hyperthermophilic archaeon synthesizes these specific lipids instead of the more common C20,C20-archaeal lipids or double-headed tetraether lipids. To shed light on the effects that these hyperthermophile-specific membrane lipids exert on living cells, we have constructed an E. coli strain that produces C25,C25-archaeal membrane lipids. However, a resultant low level of productivity would not allow us to assess the effects of their production in E. coli cells. Herein, we report an enhancement of the productivity of C25,C25-archaeal membrane lipids in engineered E. coli strains via the introduction of metabolic pathways such as an artificial isoprenol utilization pathway where the precursors of isoprenoids are synthesized via a two-step phosphorylation of prenol and isoprenol supplemented to a growth medium. In the strain with the highest titer, a major component of C25,C25-archaeal membrane lipids reached ∼11 % of total lipids of E. coli. It is noteworthy that the high production of the extended archaeal lipids did not significantly affect the growth of the bacterial cells. The permeability of the cell membrane of the strain became slightly lower in the presence of the exogenous membrane lipids with longer hydrocarbon chains, which demonstrated the possibility to enhance bacterial cell membranes by the hyperthermophile-specific lipids, along with the surprising robustness of the E. coli cell membrane.
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Affiliation(s)
- Ryo Yoshida
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 460-8601, Japan
| | - Kento Motoyama
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 460-8601, Japan
| | - Tomokazu Ito
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 460-8601, Japan
| | - Hisashi Hemmi
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 460-8601, Japan.
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4
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Reeder BJ, Svistunenko DA, Wilson MT. Hell's Gate Globin-I from Methylacidiphilum infernorum Displays a Unique Temperature-Independent pH Sensing Mechanism Utililized a Lipid-Induced Conformational Change. Int J Mol Sci 2024; 25:6794. [PMID: 38928500 PMCID: PMC11203436 DOI: 10.3390/ijms25126794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/05/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Hell's Gate globin-I (HGb-I) is a thermally stable globin from the aerobic methanotroph Methylacidiphilium infernorum. Here we report that HGb-I interacts with lipids stoichiometrically to induce structural changes in the heme pocket, changing the heme iron distal ligation coordination from hexacoordinate to pentacoordinate. Such changes in heme geometry have only been previously reported for cytochrome c and cytoglobin, linked to apoptosis regulation and enhanced lipid peroxidation activity, respectively. However, unlike cytoglobin and cytochrome c, the heme iron of HGb-I is altered by lipids in ferrous as well as ferric oxidation states. The apparent affinity for lipids in this thermally stable globin is highly pH-dependent but essentially temperature-independent within the range of 20-60 °C. We propose a mechanism to explain these observations, in which lipid binding and stability of the distal endogenous ligand are juxtaposed as a function of temperature. Additionally, we propose that these coupled equilibria may constitute a mechanism through which this acidophilic thermophile senses the pH of its environment.
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Affiliation(s)
- Brandon J. Reeder
- School of Biological Sciences, University of Essex, Wivenhoe Park Colchester, Essex CO4 3SQ, UK; (D.A.S.); (M.T.W.)
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5
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Rhim JH, Zhou A, Amenabar MJ, Boyer GM, Elling FJ, Weber Y, Pearson A, Boyd ES, Leavitt WD. Mode of carbon and energy metabolism shifts lipid composition in the thermoacidophile Acidianus. Appl Environ Microbiol 2024; 90:e0136923. [PMID: 38236067 PMCID: PMC10880624 DOI: 10.1128/aem.01369-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/01/2023] [Indexed: 01/19/2024] Open
Abstract
The degree of cyclization, or ring index (RI), in archaeal glycerol dibiphytanyl glycerol tetraether (GDGT) lipids was long thought to reflect homeoviscous adaptation to temperature. However, more recent experiments show that other factors (e.g., pH, growth phase, and energy flux) can also affect membrane composition. The main objective of this study was to investigate the effect of carbon and energy metabolism on membrane cyclization. To do so, we cultivated Acidianus sp. DS80, a metabolically flexible and thermoacidophilic archaeon, on different electron donor, acceptor, and carbon source combinations (S0/Fe3+/CO2, H2/Fe3+/CO2, H2/S0/CO2, or H2/S0/glucose). We show that differences in energy and carbon metabolism can result in over a full unit of change in RI in the thermoacidophile Acidianus sp. DS80. The patterns in RI correlated with the normalized electron transfer rate between the electron donor and acceptor and did not always align with thermodynamic predictions of energy yield. In light of this, we discuss other factors that may affect the kinetics of cellular energy metabolism: electron transfer chain (ETC) efficiency, location of ETC reaction components (cytoplasmic vs. extracellular), and the physical state of electron donors and acceptors (gas vs. solid). Furthermore, the assimilation of a more reduced form of carbon during heterotrophy appears to decrease the demand for reducing equivalents during lipid biosynthesis, resulting in lower RI. Together, these results point to the fundamental role of the cellular energy state in dictating GDGT cyclization, with those cells experiencing greater energy limitation synthesizing more cyclized GDGTs.IMPORTANCESome archaea make unique membrane-spanning lipids with different numbers of five- or six-membered rings in the core structure, which modulate membrane fluidity and permeability. Changes in membrane core lipid composition reflect the fundamental adaptation strategies of archaea in response to stress, but multiple environmental and physiological factors may affect the needs for membrane fluidity and permeability. In this study, we tested how Acidianus sp. DS80 changed its core lipid composition when grown with different electron donor/acceptor pairs. We show that changes in energy and carbon metabolisms significantly affected the relative abundance of rings in the core lipids of DS80. These observations highlight the need to better constrain metabolic parameters, in addition to environmental factors, which may influence changes in membrane physiology in Archaea. Such consideration would be particularly important for studying archaeal lipids from habitats that experience frequent environmental fluctuations and/or where metabolically diverse archaea thrive.
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Affiliation(s)
- Jeemin H. Rhim
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Alice Zhou
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Maximiliano J. Amenabar
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Grayson M. Boyer
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Felix J. Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- Leibniz-Laboratory for Radiometric Dating and Isotope Research, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Yuki Weber
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Eric S. Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
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6
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Wang W, Lei J, Li M, Zhang X, Xiang X, Wang H, Lu X, Ma L, Liu X, Tuovinen OH. Archaea are better adapted to antimony stress than their bacterial counterparts in Xikuangshan groundwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166999. [PMID: 37714340 DOI: 10.1016/j.scitotenv.2023.166999] [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: 06/26/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 09/17/2023]
Abstract
Archaea are important ecological components of microbial communities in various environments, but are currently poorly investigated in antimony (Sb) contaminated groundwater particularly on their ecological differences in comparison with bacteria. To address this issue, groundwater samples were collected from Xikuangshan aquifer along an Sb gradient and subjected to 16S rRNA gene amplicon sequencing and bioinformatic analysis. The results demonstrated that bacterial communities were more susceptibly affected by elevated Sb concentration than their archaeal counterparts, and the positive stimulation of Sb concentration on bacterial diversity coincided with the intermediate disturbance hypothesis. Overall, the balance of environmental variables (Sb, pH, and EC), competitive interactions, and stochastic events jointly regulated bacterial and archaeal communities. Linear fitting analysis revealed that Sb significantly drove the deterministic process (heterogeneous selection) of bacterial communities, whereas stochastic process (dispersal limitation) contributed more to archaeal community assembly. In contract, the assembly of Sb-resistant bacteria and archaea was dominated by the stochastic process (undominated), which implied the important role of diversification and drift instead of selection. Compared with Sb-resistant microorganisms, bacterial and archaeal communities showed lower niche width, which may result from the constraints of Sb concentration and competitive interaction. Moreover, Sb-resistant archaea had a higher niche than that of Sb-resistant bacteria via investing on flexible metabolic pathways such as organic metabolism, ammonia oxidation; and carbon fixation to enhance their competitiveness. Our results offered new insights into the ecological adaptation mechanisms of bacteria and archaea in Sb-contaminated groundwater.
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Affiliation(s)
- Weiqi Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Jingwen Lei
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Min Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xinyue Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; College of Life Science, Shangrao Normal University, Shangrao 334000, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaoyan Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus 43210, USA
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7
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Blum LN, Colman DR, Eloe-Fadrosh EA, Kellom M, Boyd ES, Zhaxybayeva O, Leavitt WD. Distribution and abundance of tetraether lipid cyclization genes in terrestrial hot springs reflect pH. Environ Microbiol 2023; 25:1644-1658. [PMID: 37032561 DOI: 10.1111/1462-2920.16375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/15/2023] [Indexed: 04/11/2023]
Abstract
Many Archaea produce membrane-spanning lipids that enable life in extreme environments. These isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs) may contain up to eight cyclopentyl and one cyclohexyl ring, where higher degrees of cyclization are associated with more acidic, hotter or energy-limited conditions. Recently, the genes encoding GDGT ring synthases, grsAB, were identified in two Sulfolobaceae; however, the distribution and abundance of grs homologs across environments inhabited by these and related organisms remain a mystery. To address this, we examined the distribution of grs homologs in relation to environmental temperature and pH, from thermal springs across Earth, where sequences derive from metagenomes, metatranscriptomes, single-cell and cultivar genomes. The abundance of grs homologs shows a strong negative correlation to pH, but a weak positive correlation to temperature. Archaeal genomes and metagenome-assembled genomes (MAGs) that carry two or more grs copies are more abundant in low pH springs. We also find grs in 12 archaeal classes, with the most representatives in Thermoproteia, followed by MAGs of the uncultured Korarchaeia, Bathyarchaeia and Hadarchaeia, while several Nitrososphaeria encodes >3 copies. Our findings highlight the key role of grs-catalysed lipid cyclization in archaeal diversification across hot and acidic environments.
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Affiliation(s)
- Laura N Blum
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | | | - Matthew Kellom
- Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
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8
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LoRicco JG, Hoffmann I, Caliò A, Peters J. The membrane regulator squalane increases membrane rigidity under high hydrostatic pressure in archaeal membrane mimics. SOFT MATTER 2023; 19:6280-6286. [PMID: 37553974 DOI: 10.1039/d3sm00352c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Apolar lipids within the membranes of archaea are thought to play a role in membrane regulation. In this work we explore the effect of the apolar lipid squalane on the dynamics of a model archaeal-like membrane, under pressure, using neutron spin echo spectroscopy. To the best of our knowledge, this is the first report on membrane dynamics at high pressure using NSE spectroscopy. Increasing pressure leads to an increase in membrane rigidity, in agreement with other techniques. The presence of squalane in the membrane results in a stiffer membrane supporting its role as a membrane regulator.
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Affiliation(s)
| | | | - Antonino Caliò
- Université de Lyon, INSA Lyon, CNRS, MAP UMR 5240, Villeurbanne, France
| | - Judith Peters
- Institut Laue-Langevin, Grenoble, France.
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
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9
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Chiu BK, Waldbauer J, Elling FJ, Mete ÖZ, Zhang L, Pearson A, Eggleston EM, Leavitt WD. Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Front Microbiol 2023; 14:1219779. [PMID: 37649629 PMCID: PMC10465181 DOI: 10.3389/fmicb.2023.1219779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors such as temperature, pH, and energy availability shifts. However, archaeal expression patterns that correspond with changes in GDGT composition are less understood. Here we characterize the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A using growth rates, core GDGT lipid profiles, transcriptomics and proteomics. We show that both stressors result in impaired growth, lower average GDGT cyclization, and differences in gene and protein expression. Transcription data revealed differential expression of the GDGT ring synthase grsB in response to both acid stress and cold stress. Although the GDGT ring synthase encoded by grsB forms highly cyclized GDGTs with ≥5 ring moieties, S. islandicus grsB upregulation under acidic pH conditions did not correspond with increased abundances of highly cyclized GDGTs. Our observations highlight the inability to predict GDGT changes from transcription data alone. Broader analysis of transcriptomic data revealed that S. islandicus differentially expresses many of the same transcripts in response to both acid and cold stress. These included upregulation of several biosynthetic pathways and downregulation of oxidative phosphorylation and motility. Transcript responses specific to either of the two stressors tested here included upregulation of genes related to proton pumping and molecular turnover in acid stress conditions and upregulation of transposases in cold stress conditions. Overall, our study provides a comprehensive understanding of the GDGT modifications and differential expression characteristic of the acid stress and cold stress responses in S. islandicus.
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Affiliation(s)
- Beverly K. Chiu
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Felix J. Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
- Leibniz-Laboratory for Radiometric Dating and Isotope Research, Kiel University, Kiel, Germany
| | - Öykü Z. Mete
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Lichun Zhang
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Erin M. Eggleston
- Department of Biology, Middlebury College, Middlebury, VT, United States
| | - William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Chemistry, Dartmouth College, Hanover, NH, United States
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10
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Řezanka T, Kyselová L, Murphy DJ. Archaeal lipids. Prog Lipid Res 2023; 91:101237. [PMID: 37236370 DOI: 10.1016/j.plipres.2023.101237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.
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Affiliation(s)
- Tomáš Řezanka
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Lucie Kyselová
- Research Institute of Brewing and Malting, Lípová 511, 120 44 Prague, Czech Republic
| | - Denis J Murphy
- School of Applied Sciences, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
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11
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Ruiz J, LoRicco JG, Soulère L, Castell MS, Grélard A, Kauffmann B, Dufourc EJ, Demé B, Popowycz F, Peters J. Membrane plasticity induced by myo-inositol derived archaeal lipids: chemical synthesis and biophysical characterization. Phys Chem Chem Phys 2023. [PMID: 37305972 DOI: 10.1039/d3cp01646c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Archaeal membrane lipids have specific structures that allow Archaea to withstand extreme conditions of temperature and pressure. In order to understand the molecular parameters that govern such resistance, the synthesis of 1,2-di-O-phytanyl-sn-glycero-3-phosphoinositol (DoPhPI), an archaeal lipid derived from myo-inositol, is reported. Benzyl protected myo-inositol was first prepared and then transformed to phosphodiester derivatives using a phosphoramidite based-coupling reaction with archaeol. Aqueous dispersions of DoPhPI alone or mixed with DoPhPC can be extruded and form small unilamellar vesicles, as detected by DLS. Neutron, SAXS, and solid-state NMR demonstrated that the water dispersions could form a lamellar phase at room temperature that then evolves into cubic and hexagonal phases with increasing temperature. Phytanyl chains were also found to impart remarkable and nearly constant dynamics to the bilayer over wide temperature ranges. All these new properties of archaeal lipids are proposed as providers of plasticity and thus means for the archaeal membrane to resist extreme conditions.
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Affiliation(s)
- Johal Ruiz
- Univ Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, UMR 5246, CNRS, ICBMS, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Bât. E. Lederer, 1 Rue Victor Grignard, F-69622 Villeurbanne, France
| | | | - Laurent Soulère
- Univ Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, UMR 5246, CNRS, ICBMS, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Bât. E. Lederer, 1 Rue Victor Grignard, F-69622 Villeurbanne, France
| | | | - Axelle Grélard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
- Institut Européen de Chimie et Biologie, CNRS, Université de Bordeaux, INSERM, UAR3033, France
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie, CNRS, Université de Bordeaux, INSERM, UAR3033, France
| | - Erick J Dufourc
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
- Institut Européen de Chimie et Biologie, CNRS, Université de Bordeaux, INSERM, UAR3033, France
| | - Bruno Demé
- Institut Laue-Langevin, 38000 Grenoble, France.
| | - Florence Popowycz
- Univ Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, UMR 5246, CNRS, ICBMS, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Bât. E. Lederer, 1 Rue Victor Grignard, F-69622 Villeurbanne, France
| | - Judith Peters
- Institut Laue-Langevin, 38000 Grenoble, France.
- Univ. Grenoble Alpes, LiPhy, CNRS, 38000 Grenoble, France
- Institut Universitaire de France, France
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12
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Mohammadpour H, Cardin M, Carraro L, Fasolato L, Cardazzo B. Characterization of the archaeal community in foods: The neglected part of the food microbiota. Int J Food Microbiol 2023; 401:110275. [PMID: 37295268 DOI: 10.1016/j.ijfoodmicro.2023.110275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/30/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
Despite the large number of studies conducted on archaea associated with extreme environments, the archaeal community composition in food products is still poorly known. Here, we investigated a new insight into exploring the archaeal community in several food matrices, with a particular focus on determining whether living archaea were present. A total of 71 samples of milk, cheese and its derived brine, honey, hamburger, clam, and trout were analyzed by high-throughput 16S rRNA sequencing. Archaea were detected in all the samples, ranging from 0.62 % of microbial communities in trout to 37.71 % in brine. Methanogens dominated 47.28 % of the archaeal communities, except for brine, which was dominated by halophilic taxa affiliated with the genus Haloquadratum (52.45 %). Clams were found to be a food with high richness and diversity of archaea and were targeted for culturing living archaea under different incubation time and temperature conditions. A subset of 16 communities derived from culture-dependent and culture-independent communities were assessed. Among the homogenates and living archaeal communities, the predominant taxa were distributed in the genera Nitrosopumilus (47.61 %) and Halorussus (78.78 %), respectively. A comparison of the 28 total taxa obtained by culture-dependent and culture-independent methods enabled their categorization into different groups, including detectable (8 out of 28), cultivable (8 out of 28), and detectable-cultivable (12 out of 28) taxa. Furthermore, using the culture method, the majority (14 out of 20) of living taxa grew at lower temperatures of 22 and 4 °C during long-term incubation, and few taxa (2 out of 20) were found at 37 °C during the initial days of incubation. Our results demonstrated the distribution of archaea in all analyzed food matrices, which opens new perspectives to expand our knowledge on archaea in foods and their beneficial and detrimental effects.
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Affiliation(s)
- Hooriyeh Mohammadpour
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| | - Marco Cardin
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy.
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
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13
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Jin Z, Vighi A, Dong Y, Bureau JA, Ignea C. Engineering membrane architecture for biotechnological applications. Biotechnol Adv 2023; 64:108118. [PMID: 36773706 DOI: 10.1016/j.biotechadv.2023.108118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Cellular membranes, predominantly described as a dynamic bilayer, are composed of different lipids, transmembrane proteins, and carbohydrates. Most research on biological membranes focuses on the identification, characterization, and mechanistic aspects of their different components. These studies provide a fundamental understanding of membrane structure, function, and dynamics, establishing a basis for the development of membrane engineering strategies. To date, approaches in this field concentrate on membrane adaptation to harsh conditions during industrial fermentation, which can be caused by temperature, osmotic, or organic solvent stress. With advances in the field of metabolic engineering and synthetic biology, recent breakthroughs include proof of concept microbial production of essential medicines, such as cannabinoids and vinblastine. However, long pathways, low yields, and host adaptation continue to pose challenges to the efficient scale up production of many important compounds. The lipid bilayer is profoundly linked to the activity of heterologous membrane-bound enzymes and transport of metabolites. Therefore, strategies for improving enzyme performance, facilitating pathway reconstruction, and enabling storage of products to increase the yields directly involve cellular membranes. At the forefront of membrane engineering research are re-emerging approaches in lipid research and synthetic biology that manipulate membrane size and composition and target lipid profiles across species. This review summarizes engineering strategies applied to cellular membranes and discusses the challenges and future perspectives, particularly with regards to their applications in host engineering and bioproduction.
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Affiliation(s)
- Zimo Jin
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Asia Vighi
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | | | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada.
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14
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Romero EL, Morilla MJ. Ether lipids from archaeas in nano-drug delivery and vaccination. Int J Pharm 2023; 634:122632. [PMID: 36690132 DOI: 10.1016/j.ijpharm.2023.122632] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/26/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
Archaea are microorganisms more closely related to eukaryotes than bacteria. Almost 50 years after being defined as a new domain of life on earth, new species continue to be discovered and their phylogeny organized. The study of the relationship between their genetics and metabolism and some of their extreme habitats has even positioned them as a model of extraterrestrial life forms. Archaea, however, are deeply connected to the life of our planet: they can be found in arid, acidic, warm areas; on most of the earth's surface, which is cold (below 5 °C), playing a prominent role in the cycles of organic materials on a global scale and they are even part of our microbiota. The constituent materials of these microorganisms differ radically from those produced by eukaryotes and bacteria, and the nanoparticles that can be manufactured using their ether lipids as building blocks exhibit unique properties that are of interest in nanomedicine. Here, we present for the first time a complete overview of the pre-clinical applications of nanomedicines based on ether archaea lipids, focused on drug delivery and adjuvancy over the last 25 years, along with a discussion on their pros, cons and their future industrial implementation.
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Affiliation(s)
- Eder Lilia Romero
- Nanomedicines Research and Development Centre (NARD), Science and Technology Department, National University of Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, Argentina.
| | - Maria Jose Morilla
- Nanomedicines Research and Development Centre (NARD), Science and Technology Department, National University of Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, Argentina
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15
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Yang W, Chen H, Chen Y, Chen A, Feng X, Zhao B, Zheng F, Fang H, Zhang C, Zeng Z. Thermophilic archaeon orchestrates temporal expression of GDGT ring synthases in response to temperature and acidity stress. Environ Microbiol 2023; 25:575-587. [PMID: 36495168 DOI: 10.1111/1462-2920.16301] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022]
Abstract
Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are unique archaeal membrane-spanning lipids with 0-8 cyclopentane rings on the biphytanyl chains. The cyclization pattern of GDGTs is affected by many environmental factors, such as temperature and pH, but the underlying molecular mechanism remains elusive. Here, we find that the expression regulation of GDGT ring synthase genes grsA and grsB in thermophilic archaeon Sulfolobus acidocaldarius is temperature- and pH-dependent. Moreover, the presence of functional GrsA protein, or more likely its products cyclic GDGTs rather than the accumulation of GrsA protein itself, is required to induce grsB expression, resulting in temporal regulation of grsA and grsB expression. Our findings establish a molecular model of GDGT cyclization regulated by environment factors in a thermophilic ecosystem, which could be also relevant to that in mesophilic marine archaea. Our study will help better understand the biological basis for GDGT-based paleoclimate proxies. Archaea inhabit a wide range of terrestrial and marine environments. In response to environment fluctuations, archaea modulate their unique membrane GDGTs lipid composition with different strategies, in particular GDGTs cyclization significantly alters membrane permeability. However, the regulation details of archaeal GDGTs cyclization in response to different environmental factor changes remain unknown. We demonstrated, for the first time, thermophilic archaea orchestrate the temporal expression of GDGT ring synthases, leading to delicate control of GDGTs cyclization to respond environmental temperature and acidity stress. Our study provides insight into the regulation of archaea membrane plasticity, and the survival strategy of archaea in fluctuating environments.
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Affiliation(s)
- Wei Yang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Huahui Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yufei Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Aiping Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xi Feng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Bo Zhao
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Fengfeng Zheng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Hongwei Fang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Zhirui Zeng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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16
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Oliva R, Winter R. Harnessing Pressure-Axis Experiments to Explore Volume Fluctuations, Conformational Substates, and Solvation of Biomolecular Systems. J Phys Chem Lett 2022; 13:12099-12115. [PMID: 36546666 DOI: 10.1021/acs.jpclett.2c03186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Intrinsic thermodynamic fluctuations within biomolecules are crucial for their function, and flexibility is one of the strategies that evolution has developed to adapt to extreme environments. In this regard, pressure perturbation is an important tool for mechanistically exploring the causes and effects of volume fluctuations in biomolecules and biomolecular assemblies, their role in biomolecular interactions and reactions, and how they are affected by the solvent properties. High hydrostatic pressure is also a key parameter in the context of deep-sea and subsurface biology and the study of the origin and physical limits of life. We discuss the role of pressure-axis experiments in revealing intrinsic structural fluctuations as well as high-energy conformational substates of proteins and other biomolecular systems that are important for their function and provide some illustrative examples. We show that the structural and dynamic information obtained from such pressure-axis studies improves our understanding of biomolecular function, disease, biological evolution, and adaptation.
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Affiliation(s)
- Rosario Oliva
- Department of Chemistry and Chemical Biology, Physical Chemistry I, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 6, Dortmund44227, Germany
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126Naples, Italy
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Physical Chemistry I, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 6, Dortmund44227, Germany
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17
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Haldar S. Delving into Membrane Heterogeneity Utilizing Fluorescence Lifetime Distribution Analysis. J Membr Biol 2022; 255:553-561. [PMID: 35486159 DOI: 10.1007/s00232-022-00235-z] [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: 02/28/2022] [Accepted: 03/29/2022] [Indexed: 12/12/2022]
Abstract
Lipid bilayer membranes are indispensable parts of cellular architecture. One of the integral properties of bilayer membranes is the environmental heterogeneity over a wide range of spatiotemporal scales. The environmental heterogeneity is a manifestation of the dynamic and compositional anisotropy in the plane of the membrane as well as along the bilayer normal. Fluorescence lifetime distribution analysis provides a spectroscopic tool to quantitatively characterize such heterogeneities. The review discusses recent applications of fluorescence lifetime distribution analysis utilizing the maximum entropy method to characterize horizontal and vertical heterogeneities in membranes.
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Affiliation(s)
- Sourav Haldar
- Division of Virus Research and Therapeutics, CSIR- Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India.
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18
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Sánchez-Andrea I, van der Graaf CM, Hornung B, Bale NJ, Jarzembowska M, Sousa DZ, Rijpstra WIC, Sinninghe Damsté JS, Stams AJM. Acetate Degradation at Low pH by the Moderately Acidophilic Sulfate Reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov. Front Microbiol 2022; 13:816605. [PMID: 35391737 PMCID: PMC8982180 DOI: 10.3389/fmicb.2022.816605] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/31/2022] [Indexed: 11/19/2022] Open
Abstract
In acid drainage environments, biosulfidogenesis by sulfate-reducing bacteria (SRB) attenuates the extreme conditions by enabling the precipitation of metals as their sulfides, and the neutralization of acidity through proton consumption. So far, only a handful of moderately acidophilic SRB species have been described, most of which are merely acidotolerant. Here, a novel species within a novel genus of moderately acidophilic SRB is described, Acididesulfobacillus acetoxydans gen. nov. sp. nov. strain INE, able to grow at pH 3.8. Bioreactor studies with strain INE at optimum (5.0) and low (3.9) pH for growth showed that strain INE alkalinized its environment, and that this was more pronounced at lower pH. These studies also showed the capacity of strain INE to completely oxidize organic acids to CO2, which is uncommon among acidophilic SRB. Since organic acids are mainly in their protonated form at low pH, which increases their toxicity, their complete oxidation may be an acid stress resistance mechanism. Comparative proteogenomic and membrane lipid analysis further indicated that the presence of saturated ether-bound lipids in the membrane, and their relative increase at lower pH, was a protection mechanism against acid stress. Interestingly, other canonical acid stress resistance mechanisms, such as a Donnan potential and increased active charge transport, did not appear to be active.
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Affiliation(s)
- Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- *Correspondence: Irene Sánchez-Andrea,
| | | | - Bastian Hornung
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Monika Jarzembowska
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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19
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Law KP, He W, Tao J, Zhang C. A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry. Front Microbiol 2021; 12:735878. [PMID: 34925256 PMCID: PMC8674956 DOI: 10.3389/fmicb.2021.735878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.
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Affiliation(s)
- Kai P Law
- Southern University of Science and Technology, SUSTech Academy for Advanced Interdisciplinary Studies, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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20
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Kriegler S, Paulisch TO, Wegner T, Glorius F, Winter R. Bipolar Imidazolium-Based Lipid Analogues for Artificial Archaeosomes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11996-12006. [PMID: 34619962 DOI: 10.1021/acs.langmuir.1c01565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Archaeal lipids have harvested biomedical and biotechnological interest because of their ability to form membranes with low permeability and enhanced temperature and pressure stability. Because of problems in isolating archaeal lipids, chemical synthesis appears to be a suitable means of producing model lipids that mimic the biological counterparts. Here, we introduce a new concept: we synthesized bipolar alkylated imidazolium salts of different chain lengths (BIm10-32) and studied their structure and lyotropic phase behavior. Furthermore, mixtures of the bolalipid analogues with phospholipid model biomembranes of diverse complexity were studied. DSC, fluorescence and FTIR spectroscopy, confocal fluorescence microscopy, DLS, SAXS, and TEM were used to reveal changes in lipid phase behavior, fluidity, the lipid's conformational order, and membrane morphology over a wide range of temperatures and for selected pressures. It could be shown that the long-chain BImN32 can form monolayer sheets. Integrated in phospholipid membranes, it reveals a fluidizing effect. Here, the two polar head groups, connected by a long alkyl chain, enable the integration into the bilayer. Interestingly, addition of BImN32 to fluid DPPC liposomes increased the lipid packing markedly, rendering the membrane system more stable at higher temperatures. The membrane system is also stable against compression as indicated by the high-pressure stability of the system, mimicking an archaeal lipid-like behavior. BImN32 incorporation into raft-like anionic model biomembranes led to marked changes in lateral membrane organization, topology, and fusogenicity of the membrane. Overall, it was found that long-chain imidazolium-based bolalipid analogues can help adjust membrane's biophysical properties, while the imidazolium headgroup provides the ability for crucial electrostatic interaction for vesicle fusion or selective interaction with membrane-related signaling molecules and polypeptides in a synthetically tractable manner. The results obtained may help to develop new approaches for rational design of extremophilic bolalipid-based liposomes for various applications, including delivery of drugs and vaccines.
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Affiliation(s)
- Simon Kriegler
- Department of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Otto Hahn Str. 4a, D-44221 Dortmund, Germany
| | - Tiffany O Paulisch
- Institute of Organic Chemistry, University of Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Tristan Wegner
- Institute of Organic Chemistry, University of Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Frank Glorius
- Institute of Organic Chemistry, University of Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Otto Hahn Str. 4a, D-44221 Dortmund, Germany
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21
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Ferraz L, Sauer M, Sousa MJ, Branduardi P. The Plasma Membrane at the Cornerstone Between Flexibility and Adaptability: Implications for Saccharomyces cerevisiae as a Cell Factory. Front Microbiol 2021; 12:715891. [PMID: 34434179 PMCID: PMC8381377 DOI: 10.3389/fmicb.2021.715891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
In the last decade, microbial-based biotechnological processes are paving the way toward sustainability as they implemented the use of renewable feedstocks. Nonetheless, the viability and competitiveness of these processes are often limited due to harsh conditions such as: the presence of feedstock-derived inhibitors including weak acids, non-uniform nature of the substrates, osmotic pressure, high temperature, extreme pH. These factors are detrimental for microbial cell factories as a whole, but more specifically the impact on the cell’s membrane is often overlooked. The plasma membrane is a complex system involved in major biological processes, including establishing and maintaining transmembrane gradients, controlling uptake and secretion, intercellular and intracellular communication, cell to cell recognition and cell’s physical protection. Therefore, when designing strategies for the development of versatile, robust and efficient cell factories ready to tackle the harshness of industrial processes while delivering high values of yield, titer and productivity, the plasma membrane has to be considered. Plasma membrane composition comprises diverse macromolecules and it is not constant, as cells adapt it according to the surrounding environment. Remarkably, membrane-specific traits are emerging properties of the system and therefore it is not trivial to predict which membrane composition is advantageous under certain conditions. This review includes an overview of membrane engineering strategies applied to Saccharomyces cerevisiae to enhance its fitness under industrially relevant conditions as well as strategies to increase microbial production of the metabolites of interest.
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Affiliation(s)
- Luís Ferraz
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria João Sousa
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
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22
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Falk ID, Gál B, Bhattacharya A, Wei JH, Welander PV, Boxer SG, Burns NZ. Enantioselective Total Synthesis of the Archaeal Lipid Parallel GDGT‐0 (Isocaldarchaeol)**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Isaac D. Falk
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Bálint Gál
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | | | - Jeremy H. Wei
- Department of Earth System Science Stanford University Stanford CA 94305 USA
| | - Paula V. Welander
- Department of Earth System Science Stanford University Stanford CA 94305 USA
| | - Steven G. Boxer
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Noah Z. Burns
- Department of Chemistry Stanford University Stanford CA 94305 USA
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23
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Holzheimer M, Sinninghe Damsté JS, Schouten S, Havenith RWA, Cunha AV, Minnaard AJ. Total Synthesis of the Alleged Structure of Crenarchaeol Enables Structure Revision**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mira Holzheimer
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Jaap S. Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research Department of Marine Microbiology and Biogeochemistry PO Box 59 1790 AB Den Burg The Netherlands
- Faculty of Geosciences Department of Earth Sciences Utrecht University PO Box 80.021 3508 TA Utrecht The Netherlands
| | - Stefan Schouten
- NIOZ Royal Netherlands Institute for Sea Research Department of Marine Microbiology and Biogeochemistry PO Box 59 1790 AB Den Burg The Netherlands
- Faculty of Geosciences Department of Earth Sciences Utrecht University PO Box 80.021 3508 TA Utrecht The Netherlands
| | - Remco W. A. Havenith
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
- Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- Ghent Quantum Chemistry Group Department of Chemistry Ghent University Krijgslaan 281 (S3) 9000 Gent Belgium
| | - Ana V. Cunha
- Eenheid Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 1050 Brussels Belgium
| | - Adriaan J. Minnaard
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
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24
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Holzheimer M, Sinninghe Damsté JS, Schouten S, Havenith RWA, Cunha AV, Minnaard AJ. Total Synthesis of the Alleged Structure of Crenarchaeol Enables Structure Revision*. Angew Chem Int Ed Engl 2021; 60:17504-17513. [PMID: 34114718 PMCID: PMC8361987 DOI: 10.1002/anie.202105384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Indexed: 12/31/2022]
Abstract
Crenarchaeol is a glycerol dialkyl glycerol tetraether lipid produced exclusively in Archaea of the phylum Thaumarchaeota. This membrane‐spanning lipid is undoubtedly the structurally most sophisticated of all known archaeal lipids and an iconic molecule in organic geochemistry. The 66‐membered macrocycle possesses a unique chemical structure featuring 22 mostly remote stereocenters, and a cyclohexane ring connected by a single bond to a cyclopentane ring. Herein we report the first total synthesis of the proposed structure of crenarchaeol. Comparison with natural crenarchaeol allowed us to propose a revised structure of crenarchaeol, wherein one of the 22 stereocenters is inverted.
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Affiliation(s)
- Mira Holzheimer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, PO Box 59, 1790 AB, Den Burg, The Netherlands.,Faculty of Geosciences, Department of Earth Sciences, Utrecht University, PO Box 80.021, 3508, TA, Utrecht, The Netherlands
| | - Stefan Schouten
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, PO Box 59, 1790 AB, Den Burg, The Netherlands.,Faculty of Geosciences, Department of Earth Sciences, Utrecht University, PO Box 80.021, 3508, TA, Utrecht, The Netherlands
| | - Remco W A Havenith
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.,Ghent Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan 281 (S3), 9000, Gent, Belgium
| | - Ana V Cunha
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Brussels, Belgium
| | - Adriaan J Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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25
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Falk ID, Gál B, Bhattacharya A, Wei JH, Welander PV, Boxer SG, Burns NZ. Enantioselective Total Synthesis of the Archaeal Lipid Parallel GDGT-0 (Isocaldarchaeol)*. Angew Chem Int Ed Engl 2021; 60:17491-17496. [PMID: 33930240 DOI: 10.1002/anie.202104051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Indexed: 12/13/2022]
Abstract
Archaeal glycerol dibiphytanyl glycerol tetraethers (GDGT) are some of the most unusual membrane lipids identified in nature. These amphiphiles are the major constituents of the membranes of numerous Archaea, some of which are extremophilic organisms. Due to their unique structures, there has been significant interest in studying both the biophysical properties and the biosynthesis of these molecules. However, these studies have thus far been hampered by limited access to chemically pure samples. Herein, we report a concise and stereoselective synthesis of the archaeal tetraether lipid parallel GDGT-0 and the synthesis and self-assembly of derivatives bearing different polar groups.
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Affiliation(s)
- Isaac D Falk
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Bálint Gál
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | | | - Jeremy H Wei
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Paula V Welander
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Noah Z Burns
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
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26
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Salvador-Castell M, Golub M, Erwin N, Demé B, Brooks NJ, Winter R, Peters J, Oger PM. Characterisation of a synthetic Archeal membrane reveals a possible new adaptation route to extreme conditions. Commun Biol 2021; 4:653. [PMID: 34079059 PMCID: PMC8172549 DOI: 10.1038/s42003-021-02178-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
It has been proposed that adaptation to high temperature involved the synthesis of monolayer-forming ether phospholipids. Recently, a novel membrane architecture was proposed to explain the membrane stability in polyextremophiles unable to synthesize such lipids, in which apolar polyisoprenoids populate the bilayer midplane and modify its physico-chemistry, extending its stability domain. Here, we have studied the effect of the apolar polyisoprenoid squalane on a model membrane analogue using neutron diffraction, SAXS and fluorescence spectroscopy. We show that squalane resides inside the bilayer midplane, extends its stability domain, reduces its permeability to protons but increases that of water, and induces a negative curvature in the membrane, allowing the transition to novel non-lamellar phases. This membrane architecture can be transposed to early membranes and could help explain their emergence and temperature tolerance if life originated near hydrothermal vents. Transposed to the archaeal bilayer, this membrane architecture could explain the tolerance to high temperature in hyperthermophiles which grow at temperatures over 100 °C while having a membrane bilayer. The induction of a negative curvature to the membrane could also facilitate crucial cell functions that require high bending membranes.
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Affiliation(s)
| | - Maksym Golub
- Université Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue Langevin, Grenoble, France
| | - Nelli Erwin
- Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Dortmund, Germany
| | - Bruno Demé
- Institut Laue Langevin, Grenoble, France
| | | | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Dortmund, Germany
| | - Judith Peters
- Université Grenoble Alpes, CNRS, LiPhy, Grenoble, France.
- Institut Laue Langevin, Grenoble, France.
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27
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Rasouli A, Jamali Y, Tajkhorshid E, Bavi O, Pishkenari HN. Mechanical properties of ester- and ether-DPhPC bilayers: A molecular dynamics study. J Mech Behav Biomed Mater 2021; 117:104386. [PMID: 33588213 PMCID: PMC8009841 DOI: 10.1016/j.jmbbm.2021.104386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 01/03/2021] [Accepted: 02/04/2021] [Indexed: 10/22/2022]
Abstract
In addition to its biological importance, DPhPC lipid bilayers are widely used in droplet bilayers, study of integral membrane proteins, drug delivery systems as well as patch-clamp electrophysiology of ion channels, yet their mechanical properties are not fully measured. Herein, we examined the effect of the ether linkage on the mechanical properties of ester- and ether-DPhPC lipid bilayers using all-atom molecular dynamics simulation. The values of area per lipid, thickness, intrinsic lateral pressure profile, order parameter, and elasticity moduli were estimated using various computational frameworks and were compared with available experimental values. Overall, a good agreement was observed between the two. The global properties of the two lipid bilayers are vastly different, with ether bilayer being stiffer, less ordered, and thicker than ester bilayer. Moreover, ether linkage decreased the area per lipid in the ether lipid bilayer. Our computational framework and output demonstrate how ether modification changes the mechano-chemical properties of DPhPC bilayers.
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Affiliation(s)
- Ali Rasouli
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, And Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yousef Jamali
- School of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, And Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, Iran.
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28
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Moosmann B, Schindeldecker M, Hajieva P. Cysteine, glutathione and a new genetic code: biochemical adaptations of the primordial cells that spread into open water and survived biospheric oxygenation. Biol Chem 2021; 401:213-231. [PMID: 31318686 DOI: 10.1515/hsz-2019-0232] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022]
Abstract
Life most likely developed under hyperthermic and anaerobic conditions in close vicinity to a stable geochemical source of energy. Epitomizing this conception, the first cells may have arisen in submarine hydrothermal vents in the middle of a gradient established by the hot and alkaline hydrothermal fluid and the cooler and more acidic water of the ocean. To enable their escape from this energy-providing gradient layer, the early cells must have overcome a whole series of obstacles. Beyond the loss of their energy source, the early cells had to adapt to a loss of external iron-sulfur catalysis as well as to a formidable temperature drop. The developed solutions to these two problems seem to have followed the principle of maximum parsimony: Cysteine was introduced into the genetic code to anchor iron-sulfur clusters, and fatty acid unsaturation was installed to maintain lipid bilayer viscosity. Unfortunately, both solutions turned out to be detrimental when the biosphere became more oxidizing after the evolution of oxygenic photosynthesis. To render cysteine thiol groups and fatty acid unsaturation compatible with life under oxygen, numerous counter-adaptations were required including the advent of glutathione and the addition of the four latest amino acids (methionine, tyrosine, tryptophan, selenocysteine) to the genetic code. In view of the continued diversification of derived antioxidant mechanisms, it appears that modern life still struggles with the initially developed strategies to escape from its hydrothermal birthplace. Only archaea may have found a more durable solution by entirely exchanging their lipid bilayer components and rigorously restricting cysteine usage.
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Affiliation(s)
- Bernd Moosmann
- Evolutionary Biochemistry and Redox Medicine, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Mario Schindeldecker
- Evolutionary Biochemistry and Redox Medicine, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Parvana Hajieva
- Cellular Adaptation Group, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
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29
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Cobban A, Zhang Y, Zhou A, Weber Y, Elling FJ, Pearson A, Leavitt WD. Multiple environmental parameters impact lipid cyclization in Sulfolobus acidocaldarius. Environ Microbiol 2021; 22:4046-4056. [PMID: 32783317 DOI: 10.1111/1462-2920.15194] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/09/2020] [Indexed: 01/19/2023]
Abstract
Adaptation of lipid membrane composition is an important component of archaeal homeostatic response. Historically, the number of cyclopentyl and cyclohexyl rings in the glycerol dibiphytanyl glycerol tetraether (GDGT) Archaeal lipids has been linked to variation in environmental temperature. However, recent work with GDGT-making archaea highlight the roles of other factors, such as pH or energy availability, in influencing the degree of GDGT cyclization. To better understand the role of multiple variables in a consistent experimental framework and organism, we cultivated the model Crenarchaeon Sulfolobus acidocaldarius DSM639 at different combinations of temperature, pH, oxygen flux, or agitation speed. We quantified responses in growth rate, biomass yield, and core lipid compositions, specifically the degree of core GDGT cyclization. The degree of GDGT cyclization correlated with growth rate under most conditions. The results suggest the degree of cyclization in archaeal lipids records a universal response to energy availability at the cellular level, both in thermoacidophiles, and in other recent findings in the mesoneutrophilic Thaumarchaea. Although we isolated the effects of key individual parameters, there remains a need for multi-factor experiments (e.g., pH + temperature + redox) in order to more robustly establish a framework to better understand homeostatic membrane responses.
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Affiliation(s)
- Alec Cobban
- Department of Earth Sciences, Dartmouth College, Hanover, NH, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Yujiao Zhang
- Department of Earth Sciences, Dartmouth College, Hanover, NH, 03755, USA.,State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Alice Zhou
- Department of Earth Sciences, Dartmouth College, Hanover, NH, 03755, USA.,Department of Earth Science, University of Michigan, Ann Arbor, MI, USA
| | - Yuki Weber
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA.,Greenlight Biosciences Inc., Medford, MA, USA
| | - Felix J Elling
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Ann Pearson
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA.,Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA
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30
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Misuraca L, Demé B, Oger P, Peters J. Alkanes increase the stability of early life membrane models under extreme pressure and temperature conditions. Commun Chem 2021; 4:24. [PMID: 36697785 PMCID: PMC9814696 DOI: 10.1038/s42004-021-00467-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/14/2021] [Indexed: 01/31/2023] Open
Abstract
Terrestrial life appeared on our planet within a time window of [4.4-3.5] billion years ago. During that time, it is suggested that the first proto-cellular forms developed in the surrounding of deep-sea hydrothermal vents, oceanic crust fractures that are still present nowadays. However, these environments are characterized by extreme temperature and pressure conditions that question the early membrane compartment's capability to endure a stable structural state. Recent studies proposed an adaptive strategy employed by present-day extremophiles: the use of apolar molecules as structural membrane components in order to tune the bilayer dynamic response when needed. Here we extend this hypothesis on early life protomembrane models, using linear and branched alkanes as apolar stabilizing molecules of prebiotic relevance. The structural ordering and chain dynamics of these systems have been investigated as a function of temperature and pressure. We found that both types of alkanes studied, even the simplest linear ones, impact highly the multilamellar vesicle ordering and chain dynamics. Our data show that alkane-enriched membranes have a lower multilamellar vesicle swelling induced by the temperature increase and are significantly less affected by pressure variation as compared to alkane-free samples, suggesting a possible survival strategy for the first living forms.
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Affiliation(s)
- Loreto Misuraca
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France ,grid.156520.50000 0004 0647 2236Institut Laue - Langevin, Grenoble, France
| | - Bruno Demé
- grid.156520.50000 0004 0647 2236Institut Laue - Langevin, Grenoble, France
| | - Philippe Oger
- grid.7849.20000 0001 2150 7757Univ Lyon, INSA Lyon, CNRS UMR5240, Villeurbanne, France
| | - Judith Peters
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France ,grid.156520.50000 0004 0647 2236Institut Laue - Langevin, Grenoble, France
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31
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LoRicco JG, Salvador-Castell M, Demé B, Peters J, Oger PM. Apolar Polyisoprenoids Located in the Midplane of the Bilayer Regulate the Response of an Archaeal-Like Membrane to High Temperature and Pressure. Front Chem 2020; 8:594039. [PMID: 33282836 PMCID: PMC7689154 DOI: 10.3389/fchem.2020.594039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/13/2020] [Indexed: 01/02/2023] Open
Abstract
Archaea are known to inhabit some of the most extreme environments on Earth. The ability of archaea possessing membrane bilayers to adapt to high temperature (>85°C) and high pressure (>1,000 bar) environments is proposed to be due to the presence of apolar polyisoprenoids at the midplane of the bilayer. In this work, we study the response of this novel membrane architecture to both high temperature and high hydrostatic pressure using neutron diffraction. A mixture of two diether, phytanyl chain lipids (DoPhPC and DoPhPE) and squalane was used to model this novel architecture. Diffraction data indicate that at high temperatures a stable coexistence of fluid lamellar phases exists within the membrane and that stable coexistence of these phases is also possible at high pressure. Increasing the amount of squalane in the membrane regulates the phase separation with respect to both temperature and pressure, and also leads to an increase in the lamellar repeat spacing. The ability of squalane to regulate the ultrastructure of an archaea-like membrane at high pressure and temperature supports the hypothesis that archaea can use apolar lipids as an adaptive mechanism to extreme conditions.
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Affiliation(s)
| | | | - Bruno Demé
- Department of Large Scale Structures, Institut Laue-Langevin, Grenoble, France
| | - Judith Peters
- Department of Large Scale Structures, Institut Laue-Langevin, Grenoble, France
- Department of Spectroscopy, Université Grenoble Alpes, LiPhy, Grenoble, France
| | - Philippe M. Oger
- Univ Lyon, INSA de Lyon, CNRS, MAP UMR 5240, Villeurbanne, France
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32
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The Cell Membrane of Sulfolobus spp.-Homeoviscous Adaption and Biotechnological Applications. Int J Mol Sci 2020; 21:ijms21113935. [PMID: 32486295 PMCID: PMC7312580 DOI: 10.3390/ijms21113935] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
The microbial cell membrane is affected by physicochemical parameters, such as temperature and pH, but also by the specific growth rate of the host organism. Homeoviscous adaption describes the process of maintaining membrane fluidity and permeability throughout these environmental changes. Archaea, and thereby, Sulfolobus spp. exhibit a unique lipid composition of ether lipids, which are altered in regard to the ratio of diether to tetraether lipids, number of cyclopentane rings and type of head groups, as a coping mechanism against environmental changes. The main biotechnological application of the membrane lipids of Sulfolobus spp. are so called archaeosomes. Archaeosomes are liposomes which are fully or partly generated from archaeal lipids and harbor the potential to be used as drug delivery systems for vaccines, proteins, peptides and nucleic acids. This review summarizes the influence of environmental parameters on the cell membrane of Sulfolobus spp. and the biotechnological applications of their membrane lipids.
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33
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Batishchev OV, Alekseeva AS, Tretiakova DS, Galimzyanov TR, Chernyadyev AY, Onishchenko NR, Volynsky PE, Boldyrev IA. Cyclopentane rings in hydrophobic chains of a phospholipid enhance the bilayer stability to electric breakdown. SOFT MATTER 2020; 16:3216-3223. [PMID: 32161934 DOI: 10.1039/c9sm02001b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Archaeal lipids ensure unprecedented stability of archaea membranes in extreme environments. Here, we incorporate a characteristic structural feature of an archaeal lipid, the cyclopentane ring, into hydrocarbon chains of a short-chain (C12) phosphatidylcholine to explore whether the insertion would allow such a lipid (1,2-di-(3-(3-hexylcyclopentyl)-propanoate)-sn-glycero-3-phosphatidylcholine, diC12cp-PC) to form stable bilayers at room temperature. According to fluorescence-based assays, in water diC12cp-PC formed liquid-crystalline bilayers at room temperature. Liposomes produced from diC12cp-PC retained calcein for over a week when stored at +4 °C. diC12cp-PC could also form model bilayer lipid membranes that were by an order of magnitude more stable to electrical breakdown than egg PC membranes. Molecular dynamics simulation showed that the cyclopentane fragment fixes five carbon atoms (or four C-C bonds), which is compensated by the higher mobility of the rest of the chain. This was found to be the reason for the remarkable stability of the diC12cp-PC bilayer: restricted conformational mobility of a chain segment increases the membrane bending modulus (compared to a normal hydrocarbon chain of the same length). Here, higher stiffness practically does not affect the line tension of a membrane pore edge. Rather it makes it more difficult for diC12cp-PC to rearrange in order to line the edge of a hydrophilic pore; therefore, fewer pores are formed.
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Affiliation(s)
- Oleg V Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Anna S Alekseeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Daria S Tretiakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Timur R Galimzyanov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia and National University of Science and Technology MISiS, Moscow, 119049, Russia
| | - Andrey Yu Chernyadyev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Natalia R Onishchenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Pavel E Volynsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Ivan A Boldyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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34
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Quehenberger J, Pittenauer E, Allmaier G, Spadiut O. The influence of the specific growth rate on the lipid composition of Sulfolobus acidocaldarius. Extremophiles 2020; 24:413-420. [PMID: 32200441 PMCID: PMC7174258 DOI: 10.1007/s00792-020-01165-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/09/2020] [Indexed: 12/22/2022]
Abstract
Archaeal lipids are constituted of two isoprenoid chains connected via ether bonds to glycerol in the sn-2, 3 position. Due to these unique properties archaeal lipids are significantly more stable against high temperature, low pH, oxidation and enzymatic degradation than conventional lipids. Additionally, in members of the phylum Crenarchaeota condensation of two (monopolar) archaeal diether lipids to a single (bipolar) tetraether lipid as well as formation of cyclopentane rings in the isoprenoid core strongly reduce permeability of the crenarchaeal membranes. In this work we show that the Crenarchaeum Sulfolobus acidocaldarius changes its lipid composition as reaction to a shift in growth rate caused by nutrient limitation. We thereby identified a novel influencing factor for the lipid composition of S. acidocaldarius and were able to determine the effect of this factor on the lipid composition by using MALDI-MS for the semi-quantification of an archaeal lipidome: a shift in the specific growth rate during a controlled continuous cultivation of S. acidocaldarius from 0.011 to 0.035 h−1 led to a change in the ratio of diether to tetraether lipids from 1:3 to 1:5 and a decrease of the average number of cyclopentane rings from 5.1 to 4.6.
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Affiliation(s)
- Julian Quehenberger
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Ernst Pittenauer
- Research Group for Mass Spectrometric Bio and Polymer Analytics, Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Günter Allmaier
- Research Group for Mass Spectrometric Bio and Polymer Analytics, Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
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35
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Mineev KS, Volynsky PE, Galimzyanov TR, Tretiakova DS, Bobrov MY, Alekseeva AS, Boldyrev IA. Archaeal cyclopentane fragment in a surfactant's hydrophobic tail decreases the Krafft point. SOFT MATTER 2020; 16:1333-1341. [PMID: 31934706 DOI: 10.1039/c9sm02000d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Archaea are prokaryotic microorganisms famous for their ability to adapt to extreme environments, including low and high temperatures. Archaeal lipids often are macrocycles with two polar heads and a hydrophobic core that contains methyl groups and in-line cycles. Here we present the design of novel general-purpose surfactants that have inherited features of archaeal lipids. These are C12 and C14 carboxylic acids containing in-line cyclopentanes. The cyclopentanes disturb the chain packing, which results in remarkable expansion of the operational range of the surfactant into the low-temperature region. We report synthesis and properties of these novel archaea-like surfactants and details of their chain packing derived from thermodynamics model predictions, molecular dynamics simulations, and experimental data on CMC and Krafft points.
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Affiliation(s)
- Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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36
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Zhou A, Weber Y, Chiu BK, Elling FJ, Cobban AB, Pearson A, Leavitt WD. Energy flux controls tetraether lipid cyclization in Sulfolobus acidocaldarius. Environ Microbiol 2019; 22:343-353. [PMID: 31696620 DOI: 10.1111/1462-2920.14851] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/16/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022]
Abstract
Microorganisms regulate the composition of their membranes in response to environmental cues. Many Archaea maintain the fluidity and permeability of their membranes by adjusting the number of cyclic moieties within the cores of their glycerol dibiphytanyl glycerol tetraether (GDGT) lipids. Cyclized GDGTs increase membrane packing and stability, which has been shown to help cells survive shifts in temperature and pH. However, the extent of this cyclization also varies with growth phase and electron acceptor or donor limitation. These observations indicate a relationship between energy metabolism and membrane composition. Here we show that the average degree of GDGT cyclization increases with doubling time in continuous cultures of the thermoacidophile Sulfolobus acidocaldarius (DSM 639). This is consistent with the behavior of a mesoneutrophile, Nitrosopumilus maritimus SCM1. Together, these results demonstrate that archaeal GDGT distributions can shift in response to electron donor flux and energy availability, independent of pH or temperature. Paleoenvironmental reconstructions based on GDGTs thus capture the energy available to microbes, which encompasses fluctuations in temperature and pH, as well as electron donor and acceptor availability. The ability of Archaea to adjust membrane composition and packing may be an important strategy that enables survival during episodes of energy stress.
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Affiliation(s)
- Alice Zhou
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
| | - Yuki Weber
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, Massachusetts, 02318, USA
| | - Beverly K Chiu
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
| | - Felix J Elling
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, Massachusetts, 02318, USA
| | - Alec B Cobban
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
| | - Ann Pearson
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, Massachusetts, 02318, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA.,Department of Chemistry, Dartmouth College, Hanover, New Hampshire, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
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Salvador-Castell M, Golub M, Martinez N, Ollivier J, Peters J, Oger P. The first study on the impact of osmolytes in whole cells of high temperature-adapted microorganisms. SOFT MATTER 2019; 15:8381-8391. [PMID: 31613294 DOI: 10.1039/c9sm01196j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The hyperthermophilic piezophile, Thermococcus barophilus displays a strong stress response characterized by the accumulation of the organic osmolyte, mannosylglycerate during growth under sub-optimal pressure conditions (0.1 MPa). Taking advantage of this known effect, the impact of osmolytes in piezophiles in an otherwise identical cellular context was investigated, by comparing T. barophilus cells grown under low or optimal pressures (40 MPa). Using neutron scattering techniques, we studied the molecular dynamics of live cells of T. barophilus at different pressures and temperatures. We show that in the presence of osmolytes, cells present a higher diffusion coefficient of hydration water and an increase of bulk water motions at a high temperature. In the absence of osmolytes, the T. barophilus cellular dynamics is more responsive to high temperature and high hydrostatic pressure. These results therefore give clear evidence for a protecting effect of osmolytes on proteins.
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Salvador-Castell M, Tourte M, Oger PM. In Search for the Membrane Regulators of Archaea. Int J Mol Sci 2019; 20:E4434. [PMID: 31505830 PMCID: PMC6770870 DOI: 10.3390/ijms20184434] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 11/23/2022] Open
Abstract
Membrane regulators such as sterols and hopanoids play a major role in the physiological and physicochemical adaptation of the different plasmic membranes in Eukarya and Bacteria. They are key to the functionalization and the spatialization of the membrane, and therefore indispensable for the cell cycle. No archaeon has been found to be able to synthesize sterols or hopanoids to date. They also lack homologs of the genes responsible for the synthesis of these membrane regulators. Due to their divergent membrane lipid composition, the question whether archaea require membrane regulators, and if so, what is their nature, remains open. In this review, we review evidence for the existence of membrane regulators in Archaea, and propose tentative location and biological functions. It is likely that no membrane regulator is shared by all archaea, but that they may use different polyterpenes, such as carotenoids, polyprenols, quinones and apolar polyisoprenoids, in response to specific stressors or physiological needs.
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Affiliation(s)
- Marta Salvador-Castell
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
| | - Maxime Tourte
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
| | - Philippe M Oger
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
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39
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Guan Z, Delago A, Nußbaum P, Meyer BH, Albers SV, Eichler J. Gene deletions leading to a reduction in the number of cyclopentane rings in Sulfolobus acidocaldarius tetraether lipids. FEMS Microbiol Lett 2019; 365:4675213. [PMID: 29211845 DOI: 10.1093/femsle/fnx250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/24/2017] [Indexed: 11/14/2022] Open
Abstract
The cell membrane of (hyper)thermophilic archaea, including the thermoacidophile Sulfolobus acidocaldarius, incorporates dibiphytanylglycerol tetraether lipids. The hydrophobic cores of such tetraether lipids can include up to eight cyclopentane rings. Presently, nothing is known of the biosynthesis of these rings. In this study, a series of S. acidocaldarius mutants deleted of genes currently annotated as encoding proteins involved in sugar/polysaccharide processing were generated and their glycolipids were considered. Whereas the glycerol-dialkyl-glycerol tetraether core of a S. acidocaldarius tetraether glycolipid considered here mostly includes four cyclopentane rings, in cells where the Saci_0421 or Saci_1201 genes had been deleted, species containing zero, two or four cyclopentane rings were observed. At the same time, in cells lacking Saci_0201, Saci_0275, Saci_1101, Saci_1249 or Saci_1706, lipids containing mostly four cyclopentane rings were detected. Although Saci_0421 and Saci_1201 are not found in proximity to other genes putatively involved in lipid biosynthesis, homologs of these sequences exist in other Archaea containing cyclopentane-containing tetraether lipids. Thus, Saci_0421 and Saci_1201 represent the first proteins described that somehow contribute to the appearance of cyclopentane rings in the core moiety of the S. acidocaldarius glycolipid considered here.
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Affiliation(s)
- Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Antonia Delago
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva 84105, Israel
| | - Phillip Nußbaum
- Molecular Biology of Archaea, Institute for Biology II-Microbiology, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
| | - Benjamin H Meyer
- Molecular Biology of Archaea, Institute for Biology II-Microbiology, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute for Biology II-Microbiology, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva 84105, Israel
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40
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Winter R. Interrogating the Structural Dynamics and Energetics of Biomolecular Systems with Pressure Modulation. Annu Rev Biophys 2019; 48:441-463. [DOI: 10.1146/annurev-biophys-052118-115601] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High hydrostatic pressure affects the structure, dynamics, and stability of biomolecular systems and is a key parameter in the context of the exploration of the origin and the physical limits of life. This review lays out the conceptual framework for exploring the conformational fluctuations, dynamical properties, and activity of biomolecular systems using pressure perturbation. Complementary pressure-jump relaxation studies are useful tools to study the kinetics and mechanisms of biomolecular phase transitions and structural transformations, such as membrane fusion or protein and nucleic acid folding. Finally, the advantages of using pressure to explore biomolecular assemblies and modulate enzymatic reactions are discussed.
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Affiliation(s)
- Roland Winter
- Faculty of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44227 Dortmund, Germany
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41
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Halococcoides cellulosivorans gen. nov., sp. nov., an extremely halophilic cellulose-utilizing haloarchaeon from hypersaline lakes. Int J Syst Evol Microbiol 2019; 69:1327-1335. [DOI: 10.1099/ijsem.0.003312] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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42
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Woodcock EM, Girvan P, Eckert J, Lopez-Duarte I, Kubánková M, van Loon JJWA, Brooks NJ, Kuimova MK. Measuring Intracellular Viscosity in Conditions of Hypergravity. Biophys J 2019; 116:1984-1993. [PMID: 31053255 DOI: 10.1016/j.bpj.2019.03.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/28/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022] Open
Abstract
Gravity-sensitive cellular responses are regularly observed in both specialized and nonspecialized cells. One potential mechanism for this sensitivity is a changing viscosity of the intracellular organelles. Here, we report a novel, to our knowledge, viscosity-sensitive molecular rotor based on mesosubstituted boron-dipyrrin used to investigate the response of viscosity of cellular membranes to hypergravity conditions created at the large diameter centrifuge at the European Space Agency Technology Centre. Mouse osteoblastic (MC3T3-E1) and endothelial (human umbilical vein endothelial cell) cell lines were tested, and an increase in viscosity was found with increasing hypergravity loading. This response is thought to be primarily biologically driven, with the potential for a small, instantaneous physical mechanism also contributing to the observed effect. This work provides the first, to our knowledge, quantitative data for cellular viscosity changes under hypergravity, up to 15 × g.
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Affiliation(s)
- Emma M Woodcock
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom; Institute of Chemical Biology, Imperial College London, South Kensington, London, United Kingdom
| | - Paul Girvan
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom; Institute of Chemical Biology, Imperial College London, South Kensington, London, United Kingdom
| | - Julia Eckert
- Department of Physics, School of Science, Technische Universität Dresden, Dresden, Germany; European Space Agency Technology Centre, TEC-MMG LIS Lab, Noordwijk, the Netherlands
| | - Ismael Lopez-Duarte
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Markéta Kubánková
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Jack J W A van Loon
- European Space Agency Technology Centre, TEC-MMG LIS Lab, Noordwijk, the Netherlands; Department of Oral and Maxillofacial Surgery/Oral Pathology, Dutch Experiment Support Centre, Academic Centre for Dentistry Amsterdam, VU University Medical Centre, Amsterdam, the Netherlands
| | - Nicholas J Brooks
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom; Institute of Chemical Biology, Imperial College London, South Kensington, London, United Kingdom.
| | - Marina K Kuimova
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom; Institute of Chemical Biology, Imperial College London, South Kensington, London, United Kingdom.
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43
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Xu R, Dehghan A, Shi AC, Zhou J. Elastic property of membranes self-assembled from diblock and triblock copolymers. Chem Phys Lipids 2019; 221:83-92. [PMID: 30926383 DOI: 10.1016/j.chemphyslip.2019.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/23/2019] [Accepted: 03/25/2019] [Indexed: 01/31/2023]
Abstract
The elastic property of membranes self-assembled from AB diblock and ABA triblock copolymers, as coarse-grained model of lipids and the bolalipids, are studied using the self-consistent field theory (SCFT). Specifically, solutions of the SCFT equations, corresponding to membranes in different geometries (planar, cylindrical, spherical, and pore) have been obtained for a model system composed of amphiphilic AB diblock copolymers and ABA triblock copolymers dissolved in A homopolymers. The free energy of the membranes with different geometries is then used to extract the bending modulus, Gaussian modulus, and line tension of the membranes. The results reveal that the bending modulus of the triblock membrane is greater than that of the diblock membrane. Furthermore, the Gaussian modulus and line tension of the triblock membrane indicate that the triblock membranes have higher pore formation energy than that of the diblock membranes. The equilibrium bridging and looping fractions of the triblock copolymers are also obtained. Implications of the theoretical results on the elastic properties of biologically equivalent lipid bilayers and the bolalipid membranes are discussed.
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Affiliation(s)
- Rui Xu
- Department of Physics & Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4M1, Canada
| | - Ashkan Dehghan
- Department of Physics & Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4M1, Canada
| | - An-Chang Shi
- Department of Physics & Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4M1, Canada.
| | - Jiajia Zhou
- Center of Soft Matter Physics and its Applications, Beihang University, Beijing 100191, China; School of Chemistry, Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beihang University, Beijing 100191, China; Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China.
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44
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Bale NJ, Sorokin DY, Hopmans EC, Koenen M, Rijpstra WIC, Villanueva L, Wienk H, Sinninghe Damsté JS. New Insights Into the Polar Lipid Composition of Extremely Halo(alkali)philic Euryarchaea From Hypersaline Lakes. Front Microbiol 2019; 10:377. [PMID: 30930858 PMCID: PMC6423904 DOI: 10.3389/fmicb.2019.00377] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/13/2019] [Indexed: 12/14/2022] Open
Abstract
We analyzed the polar membrane lipids of 13 strains of halo(alkali)philic euryarchaea from hypersaline lakes. Nine belong to the class Halobacteria, representing two functional groups: aerobic polysaccharide utilizers and sulfur-respiring anaerobes. The other four strains represent halo(alkali)philic methanogens from the class Methanomicrobia and a recently discovered class Methanonatronarchaeia. A wide range of polar lipids were detected across the 13 strains including dialkyl glycerol diethers (archaeols), membrane-spanning glycerol tetraethers and diether-based cardiolipins. The archaeols contained a range of core lipid structures, including combinations of C20 and C25 isoprenoidal alkyl chains, unsaturations, and hydroxy moieties. Several diether lipids were novel, including: (a) a phosphatidylglycerolhexose (PG-Gly) headgroup, (b) a N,N,N-trimethyl aminopentanetetrol (APT)-like lipid with a methoxy group in place of a hydroxy group on the pentanetetrol, (c) a series of polar lipids with a headgroup with elemental composition of either C12H25NO13S or C12H25NO16S2, and (d) novel cardiolipins containing a putative phosphatidylglycerolphosphate glycerophosphate (PGPGP) polar moiety. We found that the lipid distribution of the 13 strains could be generally separated into two groups, the methanogens (group) and the Halobacteria (class) based on the presence of specific core lipids. Within the methanogens, adaption to a high or more moderate salt concentration resulted in different ratios of glycerol dialkyl glycerol tetraethers (GDGTs) to archaeol. The methanogen Methanosalsum natronophilum AME2T had the most complex diether lipid composition of any of the 13 strains, including hydroxy archaeol and macrocyclic archaeol which we surmise is an order-specific membrane adaption. The zwitterionic headgroups APT and APT-Me were detected only in the Methanomicrobiales member Methanocalculus alkaliphilus AMF2T which also contained the highest level of unsaturated lipids. Only alkaliphilic members of the Natrialbales order contained PGPGP cardiolipins and the PG-Gly headgroup. The four analyzed neutrophilic members of the Halobacteria were characterized by the presence of sulfur-containing headgroups and glycolipids. The presence of cardiolipins with one or more i-C25 alkyl chains, generally termed extended archaeol (EXT-AR), in one of the Methanonatronarchaeia strains was unexpected as only one other order of methanogenic archaea has been reported to produce EXT-AR. We examined this further by looking into the genomic potential of various archaea to produce EXT-AR.
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Affiliation(s)
- Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Dimitry Y. Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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45
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Startek JB, Boonen B, Talavera K, Meseguer V. TRP Channels as Sensors of Chemically-Induced Changes in Cell Membrane Mechanical Properties. Int J Mol Sci 2019; 20:E371. [PMID: 30654572 PMCID: PMC6359677 DOI: 10.3390/ijms20020371] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/19/2022] Open
Abstract
Transient Receptor Potential ion channels (TRPs) have been described as polymodal sensors, being responsible for transducing a wide variety of stimuli, and being involved in sensory functions such as chemosensation, thermosensation, mechanosensation, and photosensation. Mechanical and chemical stresses exerted on the membrane can be transduced by specialized proteins into meaningful intracellular biochemical signaling, resulting in physiological changes. Of particular interest are compounds that can change the local physical properties of the membrane, thereby affecting nearby proteins, such as TRP channels, which are highly sensitive to the membrane environment. In this review, we provide an overview of the current knowledge of TRP channel activation as a result of changes in the membrane properties induced by amphipathic structural lipidic components such as cholesterol and diacylglycerol, and by exogenous amphipathic bacterial endotoxins.
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Affiliation(s)
- Justyna B Startek
- Laboratory of Ion Channel Research, Department of Cellular and Molecular Medicine, KU Leuven; VIB Center for Brain & Disease Research, Herestraat 49, Campus Gasthuisberg O&N1 bus 802, 3000 Leuven, Belgium.
| | - Brett Boonen
- Laboratory of Ion Channel Research, Department of Cellular and Molecular Medicine, KU Leuven; VIB Center for Brain & Disease Research, Herestraat 49, Campus Gasthuisberg O&N1 bus 802, 3000 Leuven, Belgium.
| | - Karel Talavera
- Laboratory of Ion Channel Research, Department of Cellular and Molecular Medicine, KU Leuven; VIB Center for Brain & Disease Research, Herestraat 49, Campus Gasthuisberg O&N1 bus 802, 3000 Leuven, Belgium.
| | - Victor Meseguer
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández y CSIC, E-03550 Alicante , Spain.
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46
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Youssefian S, Rahbar N, Van Dessel S. Thermal conductivity and rectification in asymmetric archaeal lipid membranes. J Chem Phys 2018; 148:174901. [DOI: 10.1063/1.5018589] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Sina Youssefian
- Department of Civil, Environmental and Architectural Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
| | - Nima Rahbar
- Department of Civil, Environmental and Architectural Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
| | - Steven Van Dessel
- Department of Civil, Environmental and Architectural Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
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47
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Youssefian S, Rahbar N, Lambert CR, Van Dessel S. Variation of thermal conductivity of DPPC lipid bilayer membranes around the phase transition temperature. J R Soc Interface 2018; 14:rsif.2017.0127. [PMID: 28539484 PMCID: PMC5454301 DOI: 10.1098/rsif.2017.0127] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/26/2017] [Indexed: 01/28/2023] Open
Abstract
Given their amphiphilic nature and chemical structure, phospholipids exhibit a strong thermotropic and lyotropic phase behaviour in an aqueous environment. Around the phase transition temperature, phospholipids transform from a gel-like state to a fluid crystalline structure. In this transition, many key characteristics of the lipid bilayers such as structure and thermal properties alter. In this study, we employed atomistic simulation techniques to study the structure and underlying mechanisms of heat transfer in dipalmitoylphosphatidylcholine (DPPC) lipid bilayers around the fluid–gel phase transformation. To investigate this phenomenon, we performed non-equilibrium molecular dynamics simulations for a range of different temperature gradients. The results show that the thermal properties of the DPPC bilayer are highly dependent on the temperature gradient. Higher temperature gradients cause an increase in the thermal conductivity of the DPPC lipid bilayer. We also found that the thermal conductivity of DPPC is lowest at the transition temperature whereby one lipid leaflet is in the gel phase and the other is in the liquid crystalline phase. This is essentially related to a growth in thermal resistance between the two leaflets of lipid at the transition temperature. These results provide significant new insights into developing new thermal insulation for engineering applications.
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Affiliation(s)
- Sina Youssefian
- Civil and Environmental Engineering Department, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Nima Rahbar
- Civil and Environmental Engineering Department, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Christopher R Lambert
- Chemistry and Biochemistry Department, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Steven Van Dessel
- Civil and Environmental Engineering Department, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
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48
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Dymond MK. Mammalian phospholipid homeostasis: evidence that membrane curvature elastic stress drives homeoviscous adaptation in vivo. J R Soc Interface 2017; 13:rsif.2016.0228. [PMID: 27534697 DOI: 10.1098/rsif.2016.0228] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/25/2016] [Indexed: 12/23/2022] Open
Abstract
Several theories of phospholipid homeostasis have postulated that cells regulate the molecular composition of their bilayer membranes, such that a common biophysical membrane parameter is under homeostatic control. Two commonly cited theories are the intrinsic curvature hypothesis, which states that cells control membrane curvature elastic stress, and the theory of homeoviscous adaptation, which postulates cells control acyl chain packing order (membrane order). In this paper, we present evidence from data-driven modelling studies that these two theories correlate in vivo. We estimate the curvature elastic stress of mammalian cells to be 4-7 × 10(-12) N, a value high enough to suggest that in mammalian cells the preservation of membrane order arises through a mechanism where membrane curvature elastic stress is controlled. These results emerge from analysing the molecular contribution of individual phospholipids to both membrane order and curvature elastic stress in nearly 500 cellular compositionally diverse lipidomes. Our model suggests that the de novo synthesis of lipids is the dominant mechanism by which cells control curvature elastic stress and hence membrane order in vivo These results also suggest that cells can increase membrane curvature elastic stress disproportionately to membrane order by incorporating polyunsaturated fatty acids into lipids.
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Affiliation(s)
- Marcus K Dymond
- Division of Chemistry, School of Pharmacy and Biological Sciences, University of Brighton, Brighton BN2 4GL, UK
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49
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Baker JA, Wong WC, Eisenhaber B, Warwicker J, Eisenhaber F. Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule". BMC Biol 2017; 15:66. [PMID: 28738801 PMCID: PMC5525207 DOI: 10.1186/s12915-017-0404-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/07/2017] [Indexed: 11/25/2022] Open
Abstract
Background Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane’s hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein’s biological functions. Results With statistics derived from a large body of protein sequences, we demonstrate that, in addition to the positive charge preference at the cytoplasmic inside (positive-inside rule), negatively charged residues preferentially occur or are even enriched at the non-cytoplasmic flank or, at least, they are suppressed at the cytoplasmic flank (negative-not-inside/negative-outside (NNI/NO) rule). As negative residues are generally rare within or near TMHs, the statistical significance is sensitive with regard to details of TMH alignment and residue frequency normalisation and also to dataset size; therefore, this trend was obscured in previous work. We observe variations amongst taxa as well as for organelles along the secretory pathway. The effect is most pronounced for TMHs from single-pass transmembrane (bitopic) proteins compared to those with multiple TMHs (polytopic proteins) and especially for the class of simple TMHs that evolved for the sole role as membrane anchors. Conclusions The charged-residue flank bias is only one of the TMH sequence features with a role in the anchorage mechanisms, others apparently being the leucine intra-helix propensity skew towards the cytoplasmic side, tryptophan flanking as well as the cysteine and tyrosine inside preference. These observations will stimulate new prediction methods for TMHs and protein topology from a sequence as well as new engineering designs for artificial membrane proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0404-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James Alexander Baker
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore.,School of Chemistry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK
| | - Wing-Cheong Wong
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore
| | - Jim Warwicker
- School of Chemistry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore. .,School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore.
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50
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Singh A, Krishnan KP, Prabaharan D, Sinha RK. Lipid membrane modulation and pigmentation: A cryoprotection mechanism in Arctic pigmented bacteria. J Basic Microbiol 2017; 57:770-780. [DOI: 10.1002/jobm.201700182] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/31/2017] [Accepted: 06/06/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Archana Singh
- National Centre for Antarctic and Ocean Research; Headland Sada; Vasco-da-Gama Goa India
| | - Kottekattu P. Krishnan
- National Centre for Antarctic and Ocean Research; Headland Sada; Vasco-da-Gama Goa India
| | - Dharmar Prabaharan
- National Facility for Marine Cyanobacteria; Bharathidasan University; Tiruchirappalli Tamil Nadu India
| | - Rupesh K. Sinha
- National Centre for Antarctic and Ocean Research; Headland Sada; Vasco-da-Gama Goa India
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