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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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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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Lloyd CT, Iwig DF, Wang B, Cossu M, Metcalf WW, Boal AK, Booker SJ. Discovery, structure, and mechanism of a tetraether lipid synthase. Nature 2022; 609:197-203. [PMID: 35882349 PMCID: PMC9433317 DOI: 10.1038/s41586-022-05120-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022]
Abstract
Archaea synthesize isoprenoid-based ether-linked membrane lipids, which enable them to withstand extreme environmental conditions, such as high temperatures, high salinity, and low or high pH values1–5. In some archaea, such as Methanocaldococcus jannaschii, these lipids are further modified by forming carbon–carbon bonds between the termini of two lipid tails within one glycerophospholipid to generate the macrocyclic archaeol or forming two carbon–carbon bonds between the termini of two lipid tails from two glycerophospholipids to generate the macrocycle glycerol dibiphytanyl glycerol tetraether (GDGT)1,2. GDGT contains two 40-carbon lipid chains (biphytanyl chains) that span both leaflets of the membrane, providing enhanced stability to extreme conditions. How these specialized lipids are formed has puzzled scientists for decades. The reaction necessitates the coupling of two completely inert sp3-hybridized carbon centres, which, to our knowledge, has not been observed in nature. Here we show that the gene product of mj0619 from M. jannaschii, which encodes a radical S-adenosylmethionine enzyme, is responsible for biphytanyl chain formation during synthesis of both the macrocyclic archaeol and GDGT membrane lipids6. Structures of the enzyme show the presence of four metallocofactors: three [Fe4S4] clusters and one mononuclear rubredoxin-like iron ion. In vitro mechanistic studies show that Csp3–Csp3 bond formation takes place on fully saturated archaeal lipid substrates and involves an intermediate bond between the substrate carbon and a sulfur of one of the [Fe4S4] clusters. Our results not only establish the biosynthetic route for tetraether formation but also improve the use of GDGT in GDGT-based paleoclimatology indices7–10. In Methanocaldococcus jannaschii, a radical S-adenosylmethionine enzyme catalyses the formation of the biphytanyl chain.
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Affiliation(s)
- Cody T Lloyd
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - David F Iwig
- The Howard Hughes Medical Institute, Pennsylvania State University, University. Park, PA, USA
| | - Bo Wang
- The Howard Hughes Medical Institute, Pennsylvania State University, University. Park, PA, USA
| | - Matteo Cossu
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - William W Metcalf
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Institute for Genomic Biology, University of Illinois Urbana- Champaign, Urbana, IL, USA
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. .,The Howard Hughes Medical Institute, Pennsylvania State University, University. Park, PA, USA.
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. .,The Howard Hughes Medical Institute, Pennsylvania State University, University. Park, PA, USA. .,Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
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Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids. Nat Commun 2022; 13:1545. [PMID: 35318330 PMCID: PMC8941075 DOI: 10.1038/s41467-022-29264-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/07/2022] [Indexed: 01/08/2023] Open
Abstract
Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are archaeal monolayer membrane lipids that can provide a competitive advantage in extreme environments. Here, we identify a radical SAM protein, tetraether synthase (Tes), that participates in the synthesis of GDGTs. Attempts to generate a tes-deleted mutant in Sulfolobus acidocaldarius were unsuccessful, suggesting that the gene is essential in this organism. Heterologous expression of tes homologues leads to production of GDGT and structurally related lipids in the methanogen Methanococcus maripaludis (which otherwise does not synthesize GDGTs and lacks a tes homolog, but produces a putative GDGT precursor, archaeol). Tes homologues are encoded in the genomes of many archaea, as well as in some bacteria, in which they might be involved in the synthesis of bacterial branched glycerol dialkyl glycerol tetraethers.
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Summons RE, Welander PV, Gold DA. Lipid biomarkers: molecular tools for illuminating the history of microbial life. Nat Rev Microbiol 2022; 20:174-185. [PMID: 34635851 DOI: 10.1038/s41579-021-00636-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 11/09/2022]
Abstract
Fossilized lipids preserved in sedimentary rocks offer singular insights into the Earth's palaeobiology. These 'biomarkers' encode information pertaining to the oxygenation of the atmosphere and oceans, transitions in ocean plankton, the greening of continents, mass extinctions and climate change. Historically, biomarker interpretations relied on inventories of lipids present in extant microorganisms and counterparts in natural environments. However, progress has been impeded because only a small fraction of the Earth's microorganisms can be cultured, many environmentally significant microorganisms from the past no longer exist and there are gaping holes in knowledge concerning lipid biosynthesis. The revolution in genomics and bioinformatics has provided new tools to expand our understanding of lipid biomarkers, their biosynthetic pathways and distributions in nature. In this Review, we explore how preserved organic molecules provide a unique perspective on the history of the Earth's microbial life. We discuss how advances in molecular biology have helped elucidate biomarker origins and afforded more robust interpretations of fossil lipids and how the rock record provides vital calibration points for molecular clocks. Such studies are open to further exploitation with the expansion of sequenced microbial genomes in accessible databases.
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Affiliation(s)
- Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Paula V Welander
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - David A Gold
- Department of Earth & Planetary Sciences, University of California Davis, Davis, CA, USA
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