1
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Baes R, Grünberger F, Pyr dit Ruys S, Couturier M, De Keulenaer S, Skevin S, Van Nieuwerburgh F, Vertommen D, Grohmann D, Ferreira-Cerca S, Peeters E. Transcriptional and translational dynamics underlying heat shock response in the thermophilic crenarchaeon Sulfolobus acidocaldarius. mBio 2023; 14:e0359322. [PMID: 37642423 PMCID: PMC10653856 DOI: 10.1128/mbio.03593-22] [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: 12/24/2022] [Accepted: 06/29/2023] [Indexed: 08/31/2023] Open
Abstract
IMPORTANCE Heat shock response is the ability to respond adequately to sudden temperature increases that could be harmful for cellular survival and fitness. It is crucial for microorganisms living in volcanic hot springs that are characterized by high temperatures and large temperature fluctuations. In this study, we investigated how S. acidocaldarius, which grows optimally at 75°C, responds to heat shock by altering its gene expression and protein production processes. We shed light on which cellular processes are affected by heat shock and propose a hypothesis on underlying regulatory mechanisms. This work is not only relevant for the organism's lifestyle, but also with regard to its evolutionary status. Indeed, S. acidocaldarius belongs to the archaea, an ancient group of microbes that is more closely related to eukaryotes than to bacteria. Our study thus also contributes to a better understanding of the early evolution of heat shock response.
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Affiliation(s)
- Rani Baes
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Felix Grünberger
- Institute of Microbiology and Archaea Centre, Universität Regensburg, Regensburg, Germany
| | | | - Mohea Couturier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sarah De Keulenaer
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sonja Skevin
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | | | - Didier Vertommen
- Institut de Duve, Université Catholique de Louvain, Brussels, Belgium
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, Universität Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Cellular Biochemistry of Microorganisms, Biochemie III, Universität Regensburg, Regensburg, Germany
- Laboratoire de Biologie Structurale de la Cellule (BIOC), UMR 7654 -CNRS, Ecole polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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2
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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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3
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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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4
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Zhang J, Li T, Hong Z, Ma C, Fang X, Zheng F, Teng W, Zhang C, Si T. Biosynthesis of Hybrid Neutral Lipids with Archaeal and Eukaryotic Characteristics in Engineered Saccharomyces cerevisiae. Angew Chem Int Ed Engl 2023; 62:e202214344. [PMID: 36424352 DOI: 10.1002/anie.202214344] [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: 09/29/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/26/2022]
Abstract
Discovery of the Asgard superphylum of archaea provides new evidence supporting the two-domain model of life: eukaryotes originated from an Asgard-related archaeon that engulfed a bacterial endosymbiont. However, how eukaryotes acquired bacterial-like membrane lipids with a sn-glycerol-3-phosphate (G3P) backbone instead of the archaeal-like sn-glycerol-1-phosphate (G1P) backbone remains unknown. In this study, we reconstituted archaeal lipid production in Saccharomyces cerevisiae by expressing unsaturated archaeol-synthesizing enzymes. Using Golden Gate cloning for pathway assembly, modular gene replacement was performed, revealing the potential biosynthesis of both G1P- and G3P-based unsaturated archaeol by uncultured Asgard archaea. Unexpectedly, hybrid neutral lipids containing both archaeal isoprenoids and eukaryotic fatty acids were observed in recombinant S. cerevisiae. The ability of yeast and archaeal diacylglycerol acyltransferases to synthesize such hybrid lipids was demonstrated.
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Affiliation(s)
- Jianzhi Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 XueYuan Avenue, Xili, NanShan District, Shenzhen, 518055, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1088 Xueyuan Avenue, Xili, NanShan District, Shenzhen, 518055, China
| | - Tuo Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 XueYuan Avenue, Xili, NanShan District, Shenzhen, 518055, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1088 Xueyuan Avenue, Xili, NanShan District, Shenzhen, 518055, China
| | - Zhilai Hong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 XueYuan Avenue, Xili, NanShan District, Shenzhen, 518055, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1088 Xueyuan Avenue, Xili, NanShan District, Shenzhen, 518055, China
| | - Chenfei Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 XueYuan Avenue, Xili, NanShan District, Shenzhen, 518055, China
| | - Xiaoting Fang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 XueYuan Avenue, Xili, NanShan District, Shenzhen, 518055, China
| | - Fengfeng Zheng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Avenue, Xili, NanShan District, Shenzhen, 518055, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1088 Xueyuan Avenue, Xili, NanShan District, Shenzhen, 518055, China
| | - Wenkai Teng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Avenue, Xili, NanShan District, Shenzhen, 518055, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1088 Xueyuan Avenue, Xili, NanShan District, Shenzhen, 518055, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Avenue, Xili, NanShan District, Shenzhen, 518055, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1088 Xueyuan Avenue, Xili, NanShan District, Shenzhen, 518055, China
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 XueYuan Avenue, Xili, NanShan District, Shenzhen, 518055, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1088 Xueyuan Avenue, Xili, NanShan District, Shenzhen, 518055, China
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5
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de Kok NAW, Driessen AJM. The catalytic and structural basis of archaeal glycerophospholipid biosynthesis. Extremophiles 2022; 26:29. [PMID: 35976526 PMCID: PMC9385802 DOI: 10.1007/s00792-022-01277-w] [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: 03/21/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the “lipid-divide”. The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.
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Affiliation(s)
- Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
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6
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Structural insights into a spindle-shaped archaeal virus with a sevenfold symmetrical tail. Proc Natl Acad Sci U S A 2022; 119:e2119439119. [PMID: 35895681 PMCID: PMC9351363 DOI: 10.1073/pnas.2119439119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Archaeal viruses with a spindle-shaped virion are abundant and widespread in extremely diverse environments. However, efforts to obtain the high-resolution structure of a spindle-shaped virus have been unsuccessful. Here, we present the structure of SSV19, a spindle-shaped virus infecting the hyperthermophilic archaeon Sulfolobus sp. E11-6. Our near-atomic structure reveals an unusual sevenfold symmetrical virus tail consisting of the tailspike, nozzle, and adaptor proteins. The spindle-shaped capsid shell is formed by seven left-handed helical strands, constructed of the hydrophobic major capsid protein, emanating from the highly glycosylated tail assembly. Sliding between adjacent strands is responsible for the variation of a virion in size. Ultrathin sections of the SSV19-infected cells show that SSV19 virions adsorb to the host cell membrane through the tail after penetrating the S-layer. The tailspike harbors a putative endo-mannanase domain, which shares structural similarity to a Bacteroides thetaiotaomicro endo-mannanase. Molecules of glycerol dibiphytanyl glycerol tetraether lipid were observed in hydrophobic clefts between the tail and the capsid shell. The nozzle protein resembles the stem and clip domains of the portals of herpesviruses and bacteriophages, implying an evolutionary relationship among the archaeal, bacterial, and eukaryotic viruses.
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7
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Tourte M, Coffinet S, Wörmer L, Lipp JS, Hinrichs KU, Oger PM. The Exploration of the Thermococcus barophilus Lipidome Reveals the Widest Variety of Phosphoglycolipids in Thermococcales. Front Microbiol 2022; 13:869479. [PMID: 35865931 PMCID: PMC9294538 DOI: 10.3389/fmicb.2022.869479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
One of the most distinctive characteristics of archaea is their unique lipids. While the general nature of archaeal lipids has been linked to their tolerance to extreme conditions, little is known about the diversity of lipidic structures archaea are able to synthesize, which hinders the elucidation of the physicochemical properties of their cell membrane. In an effort to widen the known lipid repertoire of the piezophilic and hyperthermophilic model archaeon Thermococcus barophilus, we comprehensively characterized its intact polar lipid (IPL), core lipid (CL), and polar head group compositions using a combination of cutting-edge liquid chromatography and mass spectrometric ionization systems. We tentatively identified 82 different IPLs based on five distinct CLs and 10 polar head group derivatives of phosphatidylhexoses, including compounds reported here for the first time, e.g., di-N-acetylhexosamine phosphatidylhexose-bearing lipids. Despite having extended the knowledge on the lipidome, our results also indicate that the majority of T. barophilus lipids remain inaccessible to current analytical procedures and that improvements in lipid extraction and analysis are still required. This expanded yet incomplete lipidome nonetheless opens new avenues for understanding the physiology, physicochemical properties, and organization of the membrane in this archaeon as well as other archaea.
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Affiliation(s)
- Maxime Tourte
- Univ. Lyon, Univ. Lyon 1, CNRS, UMR 5240, Villeurbanne, France
- Univ. Lyon, INSA Lyon, CNRS, UMR 5240, Villeurbanne, France
| | - Sarah Coffinet
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Lars Wörmer
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Julius S. Lipp
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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8
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Zeng Z, Chen Y, Pinilla-Redondo R, Shah SA, Zhao F, Wang C, Hu Z, Wu C, Zhang C, Whitaker RJ, She Q, Han W. A short prokaryotic Argonaute activates membrane effector to confer antiviral defense. Cell Host Microbe 2022; 30:930-943.e6. [PMID: 35594868 DOI: 10.1016/j.chom.2022.04.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/25/2022] [Accepted: 04/26/2022] [Indexed: 11/03/2022]
Abstract
Argonaute (Ago) proteins are widespread nucleic-acid-guided enzymes that recognize targets through complementary base pairing. Although, in eukaryotes, Agos are involved in RNA silencing, the functions of prokaryotic Agos (pAgos) remain largely unknown. In particular, a clade of truncated and catalytically inactive pAgos (short pAgos) lacks characterization. Here, we reveal that a short pAgo protein in the archaeon Sulfolobus islandicus, together with its two genetically associated proteins, Aga1 and Aga2, provide robust antiviral protection via abortive infection. Aga2 is a toxic transmembrane effector that binds anionic phospholipids via a basic pocket, resulting in membrane depolarization and cell killing. Ago and Aga1 form a stable complex that exhibits nucleic-acid-directed nucleic-acid-recognition ability and directly interacts with Aga2, pointing to an immune sensing mechanism. Together, our results highlight the cooperation between pAgos and their widespread associated proteins, suggesting an uncharted diversity of pAgo-derived immune systems.
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Affiliation(s)
- Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Fen Zhao
- Hubei Hongshan Laboratory, 430070 Wuhan, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070 Wuhan, China
| | - Chen Wang
- Hubei Hongshan Laboratory, 430070 Wuhan, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zeyu Hu
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Chang Wu
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Rachel J Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, 266237 Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China.
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9
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Tourte M, Schaeffer P, Grossi V, Oger PM. Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids. Environ Microbiol 2022; 24:2029-2046. [PMID: 35106897 DOI: 10.1111/1462-2920.15923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022]
Abstract
Microbes preserve membrane functionality under fluctuating environmental conditions by modulating their membrane lipid composition. Although several studies have documented membrane adaptations in Archaea, the influence of most biotic and abiotic factors on archaeal lipid compositions remains underexplored. Here, we studied the influence of temperature, pH, salinity, the presence/absence of elemental sulfur, the carbon source, and the genetic background on the lipid core composition of the hyperthermophilic neutrophilic marine archaeon Pyrococcus furiosus. Every growth parameter tested affected the lipid core composition to some extent, the carbon source and the genetic background having the greatest influence. Surprisingly, P. furiosus appeared to only marginally rely on the two major responses implemented by Archaea, i.e., the regulation of the ratio of diether to tetraether lipids and that of the number of cyclopentane rings in tetraethers. Instead, this species increased the ratio of glycerol monoalkyl glycerol tetraethers (GMGT, aka. H-shaped tetraethers) to glycerol dialkyl glycerol tetrathers (GDGT) in response to decreasing temperature and pH and increasing salinity, thus providing for the first time evidence of adaptive functions for GMGT. Besides P. furiosus, numerous other species synthesize significant proportions of GMGT, which suggests that this unprecedented adaptive strategy might be common in Archaea. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Maxime Tourte
- Univ Lyon, Univ. Lyon 1, CNRS, UMR 5240, F-69622, Villeurbanne, France.,Univ Lyon, INSA Lyon, CNRS, UMR 5240, F-69621, Villeurbanne, France
| | | | - Vincent Grossi
- Univ Lyon, Univ. Lyon 1, CNRS, ENSL, UJM, UMR 5276 LGL-TPE, F-69622, Villeurbanne, France
| | - Philippe M Oger
- Univ Lyon, INSA Lyon, CNRS, UMR 5240, F-69621, Villeurbanne, France
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10
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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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11
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de Kok NAW, Exterkate M, Andringa RLH, Minnaard AJ, Driessen AJM. A versatile method to separate complex lipid mixtures using 1-butanol as eluent in a reverse-phase UHPLC-ESI-MS system. Chem Phys Lipids 2021; 240:105125. [PMID: 34453926 DOI: 10.1016/j.chemphyslip.2021.105125] [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: 04/13/2021] [Revised: 07/07/2021] [Accepted: 08/20/2021] [Indexed: 10/20/2022]
Abstract
Simple, robust and versatile LC-MS based methods add to the rapid assessment of the lipidome of biological cells. Here we present a versatile RP-UHPLC-MS method using 1-butanol as the eluent, specifically designed to separate different highly hydrophobic lipids. This method is capable of separating different lipid classes of glycerophospholipid standards, in addition to phospholipids of the same class with a different acyl chain composition. The versatility of this method was demonstrated through analysis of lipid extracts of the bacterium Escherichia coli and the archaeon Sulfolobus acidocaldarius. In contrast to 2-propanol-based methods, the 1-butanol-based mobile phase is capable of eluting highly hydrophobic analytes such as cardiolipins, tetraether lipids and mycolic acids during the gradient instead of the isocratic purge phase, resulting in an enhanced separation of cardiolipins and extending the analytical range for RPLC.
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Affiliation(s)
- Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.
| | - Marten Exterkate
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.
| | - Ruben L H Andringa
- Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands.
| | - Adriaan J Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands.
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.
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12
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Tourte M, Schaeffer P, Grossi V, Oger PM. Acid Hydrolysis for the Extraction of Archaeal Core Lipids and HPLC-MS Analysis. Bio Protoc 2021; 11:e4118. [PMID: 34541037 DOI: 10.21769/bioprotoc.4118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 11/02/2022] Open
Abstract
Lipid membranes are essential cellular elements as they provide cellular integrity and selective permeability under a broad range of environmental settings upon cell growth. In particular, Archaea are commonly recognized for their tolerance to extreme conditions, which is now widely accepted to stem from the unique structure of their lipids. While enhancing the stability of the archaeal cell membrane, the exceptional properties of archaeal lipids also hinder their extraction using regular procedures initially developed for bacterial and eukaryotic lipids. The protocol described here circumvents these issues by directly hydrolyzing the polar head group(s) of archaeal lipids and extracting the resulting core lipids. Although leading to a loss of information on the nature of polar heads, this procedure allows the quantitative extraction of core lipids for most types of archaeal cells in an efficient, reproducible, and rapid manner.
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Affiliation(s)
- Maxime Tourte
- Univ Lyon, INSA Lyon, CNRS, UMR 5240, F-69621, Villeurbanne, France
| | | | - Vincent Grossi
- Univ Lyon, Univ. Lyon 1, ENSL, CNRS, UMR 5276 LGL-TPE, F-69622 Villeurbanne, France
| | - Philippe M Oger
- Univ Lyon, INSA Lyon, CNRS, UMR 5240, F-69621, Villeurbanne, France
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13
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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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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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15
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Hu C, Wang C, He L, Han X. Novel strategies for enhancing shotgun lipidomics for comprehensive analysis of cellular lipidomes. Trends Analyt Chem 2019; 120:115330. [PMID: 32647401 PMCID: PMC7344273 DOI: 10.1016/j.trac.2018.11.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Shotgun lipidomics is one of the most powerful tools in analysis of cellular lipidomes in lipidomics, which directly analyzes lipids from lipid extracts of diverse biological samples with high accuracy/precision. However, despite its great advances in high throughput analysis of cellular lipidomes, low coverage of poorly ionized lipids, especially those species in very low abundance, and some types of isomers within complex lipid extracts by shotgun lipidomics remains a huge challenge. In the past few years, many strategies have been developed to enhance shotgun lipidomics for comprehensive analysis of lipid species. Chemical derivatization represents one of the most attractive and effective strategies, already receiving considerable attention. This review focuses on novel advanced derivatization strategies for enhancing shotgun lipidomics. It is anticipated that with the development of enhanced strategies, shotgun lipidomics can make greater contributions to biological and biomedical research.
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Affiliation(s)
- Changfeng Hu
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
| | - Chunyan Wang
- Barshop Institute for Longevity and Aging Research, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Lijiao He
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
| | - Xianlin Han
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
- Barshop Institute for Longevity and Aging Research, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Department of Medicine – Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
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Řezanka T, Kolouchová I, Gharwalová L, Palyzová A, Sigler K. Lipidomic Analysis: From Archaea to Mammals. Lipids 2018; 53:5-25. [PMID: 29446847 DOI: 10.1002/lipd.12001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 09/19/2017] [Accepted: 10/06/2017] [Indexed: 12/29/2022]
Abstract
Lipids are among the most important organic compounds found in all living cells, from primitive archaebacteria to flowering plants or mammalian cells. They form part of cell walls and constitute cell storage material. Their biosynthesis and metabolism play key roles in faraway topics such as biofuel production (third-generation biofuels produced by microorganisms, e.g. algae) and human diseases such as adrenoleukodystrophy, Zellweger syndrome, or Refsum disease. Current lipidomic analysis requires fast and accurate processing of samples and especially their characterization. Because the number of possible lipids and, more specifically, molecular species of lipids is of the order of hundreds to thousands, it is necessary to process huge amounts of data in a short time. There are two basic approaches to lipidomic analysis: shotgun and liquid chromatography-mass spectometry. Both methods have their pros and cons. This review deals with lipidomics not according to the type of ionization or the lipid classes analyzed but according to the types of samples (organisms) under study. Thus, it is divided into lipidomic analysis of archaebacteria, bacteria, yeast, fungi, algae, plants, and animals.
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Affiliation(s)
- Tomáš Řezanka
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague, 142 20, Czech Republic
| | - Irena Kolouchová
- Department of Biotechnology, University of Chemical Technology Prague, Technická 5, Prague, 166 28, Czech Republic
| | - Lucia Gharwalová
- Department of Biotechnology, University of Chemical Technology Prague, Technická 5, Prague, 166 28, Czech Republic
| | - Andrea Palyzová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague, 142 20, Czech Republic
| | - Karel Sigler
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague, 142 20, Czech Republic
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17
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Wang M, Wang C, Han X. Selection of internal standards for accurate quantification of complex lipid species in biological extracts by electrospray ionization mass spectrometry-What, how and why? MASS SPECTROMETRY REVIEWS 2017; 36:693-714. [PMID: 26773411 PMCID: PMC4947032 DOI: 10.1002/mas.21492] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/28/2015] [Indexed: 05/20/2023]
Abstract
Lipidomics is rapidly expanding because of the great facilitation of recent advances in, and novel applications of, electrospray ionization mass spectrometry techniques. The greatest demands have been for successful quantification of lipid classes, subclasses, and individual molecular species in biological samples at acceptable accuracy. This review addresses the selection of internal standards in different methods for accurate quantification of individual lipid species. The principles of quantification with electrospray ionization mass spectrometry are first discussed to recognize the essentials for quantification. The basics of different lipidomics approaches are overviewed to understand the variables that need to be considered for accurate quantification. The factors that affect accurate quantification are extensively discussed, and the solutions to resolve these factors are proposed-largely through addition of internal standards. Finally, selection of internal standards for different methods is discussed in detail to address the issues of what, how, and why related to internal standards. We believe that thorough discussion of the topics related to internal standards should aid in quantitative analysis of lipid classes, subclasses, and individual molecular species and should have big impacts on advances in lipidomics. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:693-714, 2017.
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Affiliation(s)
- Miao Wang
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827 USA
| | - Chunyan Wang
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827 USA
| | - Xianlin Han
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827 USA
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
- To whom correspondence should be addressed: Xianlin Han, Ph.D., Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, Florida 32827, USA, Telephone: (407) 745-2139, Fax: (407) 745-2016,
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18
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Jurowski K, Kochan K, Walczak J, Barańska M, Piekoszewski W, Buszewski B. Analytical Techniques in Lipidomics: State of the Art. Crit Rev Anal Chem 2017; 47:418-437. [PMID: 28340309 DOI: 10.1080/10408347.2017.1310613] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Current studies related to lipid identification and determination, or lipidomics in biological samples, are one of the most important issues in modern bioanalytical chemistry. There are many articles dedicated to specific analytical strategies used in lipidomics in various kinds of biological samples. However, in such literature, there is a lack of articles dedicated to a comprehensive review of the actual analytical methodologies used in lipidomics. The aim of this article is to characterize the lipidomics methods used in modern bioanalysis according to the methodological point of view: (1) chromatography/separation methods, (2) spectroscopic methods and (3) mass spectrometry and also hyphenated methods. In the first part, we discussed thin layer chromatography (TLC), high-pressure liquid chromatography (HPLC), gas chromatography (GC) and capillary electrophoresis (CE). The second part includes spectroscopic techniques such as Raman spectroscopy (RS), Fourier transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance (NMR). The third part is a synthetic review of mass spectrometry, matrix-assisted laser desorption/ionization (MALDI), hyphenated methods, which include liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS) and also multidimensional techniques. Other aspects are the possibilities of the application of the described methods in lipidomics studies. Due to the fact that the exploration of new methods of lipidomics analysis and their applications in clinical and medical studies are still challenging for researchers working in life science, we hope that this review article will be very useful for readers.
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Affiliation(s)
- Kamil Jurowski
- a Kraków Higher School of Health Promotion , Krakow , Poland
| | - Kamila Kochan
- b Jagiellonian Centre for Experimental Therapeutics (JCET) , Jagiellonian University in Cracow , Cracow , Poland.,c Centre for Biospectroscopy and School of Chemistry , Monash University , Clayton , Victoria , Australia
| | - Justyna Walczak
- d Department of Environmental Chemistry and Bioanalytics , Faculty of Chemistry, Nicolaus Copernicus University , Torun , Poland
| | - Małgorzata Barańska
- b Jagiellonian Centre for Experimental Therapeutics (JCET) , Jagiellonian University in Cracow , Cracow , Poland.,e Department of Chemical Physics, Faculty of Chemistry , Jagiellonian University in Cracow , Cracow , Poland
| | - Wojciech Piekoszewski
- f Department of Analytical Chemistry, Faculty of Chemistry , Jagiellonian University in Cracow , Cracow , Poland.,g School of Biomedicine , Far Eastern Federal University , Vladivostok , Russia
| | - Bogusław Buszewski
- d Department of Environmental Chemistry and Bioanalytics , Faculty of Chemistry, Nicolaus Copernicus University , Torun , Poland
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Triebl A, Hartler J, Trötzmüller M, C Köfeler H. Lipidomics: Prospects from a technological perspective. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:740-746. [PMID: 28341148 DOI: 10.1016/j.bbalip.2017.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/16/2022]
Abstract
Over the last two decades, lipidomics has evolved into an 'omics' technology pari passu with benchmarking 'omics' technologies, such as genomics or proteomics. The driving force behind this development was a constant advance in mass spectrometry and related technologies. The aim of this opinion article is to give the interested reader a concise but still comprehensive overview about the technological state of the art in lipidomics, current challenges and perspectives for future development. As such, this article guides through the whole workflow of lipidomics, from sampling to data analysis. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.
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Affiliation(s)
- Alexander Triebl
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Jürgen Hartler
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria; Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Martin Trötzmüller
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Harald C Köfeler
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
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20
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Ghaste M, Mistrik R, Shulaev V. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics. Int J Mol Sci 2016; 17:ijms17060816. [PMID: 27231903 PMCID: PMC4926350 DOI: 10.3390/ijms17060816] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 02/02/2023] Open
Abstract
Metabolomics, along with other "omics" approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data.
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Affiliation(s)
- Manoj Ghaste
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
| | | | - Vladimir Shulaev
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
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21
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Jensen SM, Christensen CJ, Petersen JM, Treusch AH, Brandl M. Liposomes containing lipids from Sulfolobus islandicus withstand intestinal bile salts: An approach for oral drug delivery? Int J Pharm 2015; 493:63-9. [DOI: 10.1016/j.ijpharm.2015.07.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/08/2015] [Accepted: 07/09/2015] [Indexed: 12/16/2022]
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22
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Jensen SM, Neesgaard VL, Skjoldbjerg SLN, Brandl M, Ejsing CS, Treusch AH. The Effects of Temperature and Growth Phase on the Lipidomes of Sulfolobus islandicus and Sulfolobus tokodaii. Life (Basel) 2015; 5:1539-66. [PMID: 26308060 PMCID: PMC4598652 DOI: 10.3390/life5031539] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/02/2015] [Accepted: 08/14/2015] [Indexed: 12/18/2022] Open
Abstract
The functionality of the plasma membrane is essential for all organisms. Adaption to high growth temperatures imposes challenges and Bacteria, Eukarya, and Archaea have developed several mechanisms to cope with these. Hyperthermophilic archaea have earlier been shown to synthesize tetraether membrane lipids with an increased number of cyclopentane moieties at higher growth temperatures. Here we used shotgun lipidomics to study this effect as well as the influence of growth phase on the lipidomes of Sulfolobus islandicus and Sulfolobus tokodaii for the first time. Both species were cultivated at three different temperatures, with samples withdrawn during lag, exponential, and stationary phases. Three abundant tetraether lipid classes and one diether lipid class were monitored. Beside the expected increase in the number of cyclopentane moieties with higher temperature in both archaea, we observed previously unreported changes in the average cyclization of the membrane lipids throughout growth. The average number of cyclopentane moieties showed a significant dip in exponential phase, an observation that might help to resolve the currently debated biosynthesis pathway of tetraether lipids.
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Affiliation(s)
- Sara Munk Jensen
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense 5230, Denmark.
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark.
| | - Vinnie Lund Neesgaard
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense 5230, Denmark.
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark.
| | - Sandra Landbo Nedergaard Skjoldbjerg
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense 5230, Denmark.
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark.
| | - Martin Brandl
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark.
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense 5230, Denmark.
| | - Alexander H Treusch
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense 5230, Denmark.
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Wörmer L, Lipp JS, Hinrichs KU. Comprehensive Analysis of Microbial Lipids in Environmental Samples Through HPLC-MS Protocols. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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