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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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Zheng P, Yang H, Zhang H, Shen C, Sun H. Influence of hydrological parameters on hydroxylated tetraether lipids in a deep Lake Fuxian, China: Implications for their use as environmental proxies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165022. [PMID: 37348708 DOI: 10.1016/j.scitotenv.2023.165022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/22/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023]
Abstract
Hydroxylated isoprenoid glycerol dialkyl glycerol tetraethers (OH-GDGTs) have shown their potential in environmental reconstructions. However, the unclear underlying mechanism challenges their application. To elucidate the effects of water parameters on OH-GDGT-derived indices and understand their environmental implications, we investigated the core OH-GDGTs of suspended particulate matter (SPM) from water columns in a year cycle and surface sediments at different water depths along a nearshore-offshore transect in Lake Fuxian, a deep and large lake in southwestern China. OH-GDGTs were primarily found in the hypolimnion and were produced in situ by Group I.1a Thaumarchaeota. The relative abundance of OH-GDGTs (%OH-GDGTs) and ring indices (RI-OH and RI-OH') in the hypolimnion were significantly influenced by dissolved oxygen (DO) and pH, particularly DO, which regulated the inverse physiological functions of the hydroxyl and cyclopentane moieties of archaea. %OH-GDGTs values in SPM were positively correlated with DO and negatively correlated with pH levels, while RI-OH values exhibited an inverse relationship with DO and positive correlation with pH levels. OH-GDGTs in surface sediments appeared to be homologous to that of water columns, indicating that their inferred proxies could be regulated by the configuration of water parameters. The sedimentary %OH-GDGTs values increased as the RI-OH values decreased with water depth along the transect from the lakeshore to the lake center, suggesting their potential as lake-level proxies.
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Affiliation(s)
- Pingbo Zheng
- Yunnan Key Laboratory of Plateau Geographical Processes and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, China
| | - Huan Yang
- Hubei Key Laboratory of Critical Zone Evolution, School of Geography and Information Engineering, China University of Geosciences, Wuhan 430078, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Caiming Shen
- Yunnan Key Laboratory of Plateau Geographical Processes and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, China
| | - Huiling Sun
- Yunnan Key Laboratory of Plateau Geographical Processes and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, China.
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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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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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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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Physiological Characterization of Sulfolobus acidocaldarius in a Controlled Bioreactor Environment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18115532. [PMID: 34064179 PMCID: PMC8196767 DOI: 10.3390/ijerph18115532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 01/28/2023]
Abstract
The crenarchaeal model organism Sulfolobus acidocaldarius is typically cultivated in shake flasks. Although shake flasks represent the state-of-the-art for the cultivation of this microorganism, in these systems crucial process parameters, like pH or substrate availability, are only set initially, but cannot be controlled during the cultivation process. As a result, a thorough characterization of growth parameters under controlled conditions is still missing for S. acidocaldarius. In this study, we conducted chemostat cultivations at 75 °C using a growth medium containing L-glutamate and D-glucose as main carbon sources. Different pH values and dilution rates were applied with the goal to physiologically characterize the organism in a controlled bioreactor environment. Under these controlled conditions a pH optimum of 3.0 was determined. Washout of the cells occurred at a dilution rate of 0.097 h−1 and the optimal productivity of biomass was observed at a dilution rate of 0.062 h−1. While both carbon sources were taken up by S. acidocaldarius concomitantly, a 6.6-fold higher affinity for L-glutamate was shown. When exposed to suboptimal growth conditions, S. acidocaldarius reacted with a change in the respiratory behavior and an increased trehalose production rate in addition to a decreased growth rate.
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