1
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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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2
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Kropp C, Lipp J, Schmidt AL, Seisenberger C, Linde M, Hinrichs KU, Babinger P. Identification of acetylated diether lipids in halophilic Archaea. Microbiologyopen 2022; 11:e1299. [PMID: 35765181 PMCID: PMC9179154 DOI: 10.1002/mbo3.1299] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 11/10/2022] Open
Abstract
As a hallmark of Archaea, their cell membranes are comprised of ether lipids. However, Archaea-type ether lipids have recently been identified in Bacteria as well, with a somewhat different composition: In Bacillales, sn-glycerol 1-phosphate is etherified with one C35 isoprenoid chain, which is longer than the typical C20 chain in Archaea, and instead of a second isoprenoid chain, the product heptaprenylglyceryl phosphate becomes dephosphorylated and afterward diacetylated by the O-acetyltransferase YvoF. Interestingly, database searches have revealed YvoF homologs in Halobacteria (Archaea), too. Here, we demonstrate that YvoF from Haloferax volcanii can acetylate geranylgeranylglycerol in vitro. Additionally, we present the first-time identification of acetylated diether lipids in H. volcanii and Halobacterium salinarum by mass spectrometry. A variety of different acetylated lipids, namely acetylated archaeol, and acetylated archaetidylglycerol, were found, suggesting that halobacterial YvoF has a broad substrate range. We suppose that the acetyl group might serve to modify the polarity of the lipid headgroup, with still unknown biological effects.
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Affiliation(s)
- Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Julius Lipp
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Anna Lena Schmidt
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Christina Seisenberger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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3
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Kropp C, Bruckmann A, Babinger P. Controlling Enzymatic Activity by Modulating the Oligomerization State via Chemical Rescue and Optical Control. Chembiochem 2021; 23:e202100490. [PMID: 34633135 PMCID: PMC9298306 DOI: 10.1002/cbic.202100490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/08/2021] [Indexed: 12/22/2022]
Abstract
Selective switching of enzymatic activity has been a longstanding goal in synthetic biology. Drastic changes in activity upon mutational manipulation of the oligomerization state of enzymes have frequently been reported in the literature, but scarcely exploited for switching. Using geranylgeranylglyceryl phosphate synthase as a model, we demonstrate that catalytic activity can be efficiently controlled by exogenous modulation of the association state. We introduced a lysine‐to‐cysteine mutation, leading to the breakdown of the active hexamer into dimers with impaired catalytic efficiency. Addition of bromoethylamine chemically rescued the enzyme by restoring hexamerization and activity. As an alternative method, we incorporated the photosensitive unnatural amino acid o‐nitrobenzyl‐O‐tyrosine (ONBY) into the hexamerization interface. This again led to inactive dimers, but the hexameric state and activity could be recovered by UV‐light induced cleavage of ONBY. For both approaches, we obtained switching factors greater than 350‐fold, which compares favorably with previously reported activity changes that were caused by site‐directed mutagenesis.
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Affiliation(s)
- Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040, Regensburg, Germany
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4
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Villanueva L, von Meijenfeldt FAB, Westbye AB, Yadav S, Hopmans EC, Dutilh BE, Damsté JSS. Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids. THE ISME JOURNAL 2021; 15:168-182. [PMID: 32929208 PMCID: PMC7852524 DOI: 10.1038/s41396-020-00772-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/10/2020] [Accepted: 09/02/2020] [Indexed: 12/29/2022]
Abstract
Archaea synthesize membranes of isoprenoid lipids that are ether-linked to glycerol-1-phosphate (G1P), while Bacteria/Eukarya produce membranes consisting of fatty acids ester-bound to glycerol-3-phosphate (G3P). This dichotomy in membrane lipid composition (i.e., the 'lipid divide') is believed to have arisen after the Last Universal Common Ancestor (LUCA). A leading hypothesis is that LUCA possessed a heterochiral 'mixed archaeal/bacterial membrane'. However, no natural microbial representatives supporting this scenario have been shown to exist today. Here, we demonstrate that bacteria of the Fibrobacteres-Chlorobi-Bacteroidetes (FCB) group superphylum encode a putative archaeal pathway for ether-bound isoprenoid membrane lipids in addition to the bacterial fatty acid membrane pathway. Key genes were expressed in the environment and their recombinant expression in Escherichia coli resulted in the formation of a 'mixed archaeal/bacterial membrane'. Genomic evidence and biochemical assays suggest that the archaeal-like lipids of members of the FCB group could possess either a G1P or G3P stereochemistry. Our results support the existence of 'mixed membranes' in natural environments and their stability over a long period in evolutionary history, thereby bridging a once-thought fundamental divide in biology.
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Affiliation(s)
- Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands.
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands.
| | | | - Alexander B Westbye
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Subhash Yadav
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Ellen C Hopmans
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, 3584CH, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Utrecht, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
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5
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Kropp C, Straub K, Linde M, Babinger P. Hexamerization and thermostability emerged very early during geranylgeranylglyceryl phosphate synthase evolution. Protein Sci 2020; 30:583-596. [PMID: 33342010 PMCID: PMC7888582 DOI: 10.1002/pro.4016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
A large number of archaea live in hyperthermophilic environments. In consequence, their proteins need to adopt to these harsh conditions, including the enzymes that catalyze the synthesis of their membrane ether lipids. The enzyme that catalyzes the formation of the first ether bond in these lipids, geranylgeranylglyceryl phosphate synthase (GGGPS), exists as a hexamer in many hyperthermophilic archaea, and a recent study suggested that hexamerization serves for a fine‐tuning of the flexibility – stability trade‐off under hyperthermophilic conditions. We have recently reconstructed the sequences of ancestral group II GGGPS enzymes and now present a detailed biochemical characterization of nine of these predecessors, which allowed us to trace back the evolution of hexameric GGGPS and to draw conclusions about the properties of extant GGGPS branches that were not accessible to experiments up to now. Almost all ancestral GGGPS proteins formed hexamers, which demonstrates that hexamerization is even more widespread among the GGGPS family than previously assumed. Furthermore, all experimentally studied ancestral proteins showed high thermostability. Our results indicate that the hexameric oligomerization state and thermostability were present very early during the evolution of group II GGGPS, while the fine tuning of the flexibility – stability trade‐off developed very late, independent of the emergence of hexamerization.
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Affiliation(s)
- Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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6
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Yoshida R, Hemmi H. Construction of an artificial biosynthetic pathway for hyperextended archaeal membrane lipids in the bacterium Escherichia coli. Synth Biol (Oxf) 2020; 5:ysaa018. [PMID: 33263085 PMCID: PMC7680562 DOI: 10.1093/synbio/ysaa018] [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: 07/17/2020] [Revised: 09/08/2020] [Accepted: 09/16/2020] [Indexed: 11/12/2022] Open
Abstract
Archaea produce unique membrane lipids, which possess two fully saturated isoprenoid chains linked to the glycerol moiety via ether bonds. The isoprenoid chain length of archaeal membrane lipids is believed to be important for some archaea to thrive in extreme environments because the hyperthermophilic archaeon Aeropyrum pernix and some halophilic archaea synthesize extended C25,C25-archaeal diether-type membrane lipids, which have isoprenoid chains that are longer than those of typical C20,C20-diether lipids. Natural archaeal diether lipids possessing longer C30 or C35 isoprenoid chains, however, have yet to be isolated. In the present study, we attempted to synthesize such hyperextended archaeal membrane lipids. We investigated the substrate preference of the enzyme sn-2,3-(digeranylfarnesyl)glycerol-1-phosphate synthase from A. pernix, which catalyzes the transfer of the second C25 isoprenoid chain to the glycerol moiety in the biosynthetic pathway of C25,C25-archaeal membrane lipids. The enzyme was shown to accept sn-3-hexaprenylglycerol-1-phosphate, which has a C30 isoprenoid chain, as a prenyl acceptor substrate to synthesize sn-2-geranylfarnesyl-3-hexaprenylglycerol-1-phosphate, a supposed precursor for hyperextended C25,C30-archaeal membrane lipids. Furthermore, we constructed an artificial biosynthetic pathway by introducing 4 archaeal genes and 1 gene from Bacillus subtilis in the cells of Escherichia coli, which enabled the E. coli strain to produce hyperextended C25,C30-archaeal membrane lipids, which have never been reported so far.
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Affiliation(s)
- Ryo Yoshida
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Hisashi Hemmi
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
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7
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Blank PN, Barnett AA, Ronnebaum TA, Alderfer KE, Gillott BN, Christianson DW, Himmelberger JA. Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota. Acta Crystallogr D Struct Biol 2020; 76:542-557. [PMID: 32496216 PMCID: PMC7271946 DOI: 10.1107/s2059798320004878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 04/05/2020] [Indexed: 12/26/2022] Open
Abstract
Archaea are uniquely adapted to thrive in harsh environments, and one of these adaptations involves the archaeal membrane lipids, which are characterized by their isoprenoid alkyl chains connected via ether linkages to glycerol 1-phosphate. The membrane lipids of the thermophilic and acidophilic euryarchaeota Thermoplasma volcanium are exclusively glycerol dibiphytanyl glycerol tetraethers. The first committed step in the biosynthetic pathway of these archaeal lipids is the formation of the ether linkage between glycerol 1-phosphate and geranylgeranyl diphosphate, and is catalyzed by the enzyme geranylgeranylglyceryl phosphate synthase (GGGPS). The 1.72 Å resolution crystal structure of GGGPS from T. volcanium (TvGGGPS) in complex with glycerol and sulfate is reported here. The crystal structure reveals TvGGGPS to be a dimer, which is consistent with the absence of the aromatic anchor residue in helix α5a that is required for hexamerization in other GGGPS homologs; the hexameric quaternary structure in GGGPS is thought to provide thermostability. A phylogenetic analysis of the Euryarchaeota and a parallel ancestral state reconstruction investigated the relationship between optimal growth temperature and the ancestral sequences. The presence of an aromatic anchor residue is not explained by temperature as an ecological parameter. An examination of the active site of the TvGGGPS dimer revealed that it may be able to accommodate longer isoprenoid substrates, supporting an alternative pathway of isoprenoid membrane-lipid synthesis.
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Affiliation(s)
- P. N. Blank
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - A. A. Barnett
- Department of Biology, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
| | - T. A. Ronnebaum
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - K. E. Alderfer
- Department of Chemistry and Physics, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
| | - B. N. Gillott
- Department of Chemistry and Physics, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
| | - D. W. Christianson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - J. A. Himmelberger
- Department of Chemistry and Physics, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
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8
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Hanashima S, Yano Y, Murata M. Enantiomers of phospholipids and cholesterol: A key to decipher lipid‐lipid interplay in membrane. Chirality 2020; 32:282-298. [DOI: 10.1002/chir.23171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
| | - Yo Yano
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
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9
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Nemoto N, Miyazono KI, Tanokura M, Yamagishi A. Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with the substrate sn-glycerol 1-phosphate. Acta Crystallogr F Struct Biol Commun 2019; 75:470-479. [PMID: 31282866 PMCID: PMC6613444 DOI: 10.1107/s2053230x19007453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/22/2019] [Indexed: 01/17/2023] Open
Abstract
(S)-3-O-Geranylgeranylglyceryl phosphate synthase (GGGPS) catalyzes the initial ether-bond formation between sn-glycerol 1-phosphate (G1P) and geranylgeranyl pyrophosphate to synthesize (S)-3-O-geranylgeranylglyceryl phosphate in the production of an archaeal cell-membrane lipid molecule. Archaeal GGGPS proteins are divided into two groups (group I and group II). In this study, the crystal structure of the archaeal group II GGGPS from Thermoplasma acidophilum (TaGGGPS) was determined at 2.35 Å resolution. The structure of TaGGGPS showed that it has a TIM-barrel fold, the third helix of which is disordered (α3*), and that it forms a homodimer, although a pre-existing structure of an archaeal group II GGGPS (from Methanothermobacter thermautotrophicus) showed a hexameric form. The structure of TaGGGPS showed the precise G1P-recognition mechanism of an archaeal group II GGGPS. The structure of TaGGGPS and molecular-dynamics simulation analysis showed fluctuation of the β2-α2, α3* and α5a regions, which is predicted to be important for substrate uptake and/or product release by TaGGGPS.
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Affiliation(s)
- Naoki Nemoto
- Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
- Department of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Ken-ichi Miyazono
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaru Tanokura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akihiko Yamagishi
- Department of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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10
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Coleman GA, Pancost RD, Williams TA. Investigating the Origins of Membrane Phospholipid Biosynthesis Genes Using Outgroup-Free Rooting. Genome Biol Evol 2019; 11:883-898. [PMID: 30753429 PMCID: PMC6431249 DOI: 10.1093/gbe/evz034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 12/16/2022] Open
Abstract
One of the key differences between Bacteria and Archaea is their canonical membrane phospholipids, which are synthesized by distinct biosynthetic pathways with nonhomologous enzymes. This “lipid divide” has important implications for the early evolution of cells and the type of membrane phospholipids present in the last universal common ancestor. One of the main challenges in studies of membrane evolution is that the key biosynthetic genes are ancient and their evolutionary histories are poorly resolved. This poses major challenges for traditional rooting methods because the only available outgroups are distantly related. Here, we address this issue by using the best available substitution models for single-gene trees, by expanding our analyses to the diversity of uncultivated prokaryotes recently revealed by environmental genomics, and by using two complementary approaches to rooting that do not depend on outgroups. Consistent with some previous analyses, our rooted gene trees support extensive interdomain horizontal transfer of membrane phospholipid biosynthetic genes, primarily from Archaea to Bacteria. They also suggest that the capacity to make archaeal-type membrane phospholipids was already present in last universal common ancestor.
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Affiliation(s)
- Gareth A Coleman
- School of Biological Sciences, University of Bristol, United Kingdom
| | | | - Tom A Williams
- School of Biological Sciences, University of Bristol, United Kingdom
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11
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Straub K, Linde M, Kropp C, Blanquart S, Babinger P, Merkl R. Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase. Biol Chem 2019; 400:367-381. [PMID: 30763032 DOI: 10.1515/hsz-2018-0344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/07/2018] [Indexed: 11/15/2022]
Abstract
For evolutionary studies, but also for protein engineering, ancestral sequence reconstruction (ASR) has become an indispensable tool. The first step of every ASR protocol is the preparation of a representative sequence set containing at most a few hundred recent homologs whose composition determines decisively the outcome of a reconstruction. A common approach for sequence selection consists of several rounds of manual recompilation that is driven by embedded phylogenetic analyses of the varied sequence sets. For ASR of a geranylgeranylglyceryl phosphate synthase, we additionally utilized FitSS4ASR, which replaces this time-consuming protocol with an efficient and more rational approach. FitSS4ASR applies orthogonal filters to a set of homologs to eliminate outlier sequences and those bearing only a weak phylogenetic signal. To demonstrate the usefulness of FitSS4ASR, we determined experimentally the oligomerization state of eight predecessors, which is a delicate and taxon-specific property. Corresponding ancestors deduced in a manual approach and by means of FitSS4ASR had the same dimeric or hexameric conformation; this concordance testifies to the efficiency of FitSS4ASR for sequence selection. FitSS4ASR-based results of two other ASR experiments were added to the Supporting Information. Program and documentation are available at https://gitlab.bioinf.ur.de/hek61586/FitSS4ASR.
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Affiliation(s)
- Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Samuel Blanquart
- University of Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
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12
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Linde M, Heyn K, Merkl R, Sterner R, Babinger P. Hexamerization of Geranylgeranylglyceryl Phosphate Synthase Ensures Structural Integrity and Catalytic Activity at High Temperatures. Biochemistry 2018; 57:2335-2348. [DOI: 10.1021/acs.biochem.7b01284] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Mona Linde
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Kristina Heyn
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
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13
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Caforio A, Driessen AJM. Archaeal phospholipids: Structural properties and biosynthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1325-1339. [PMID: 28007654 DOI: 10.1016/j.bbalip.2016.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 01/06/2023]
Abstract
Phospholipids are major components of the cellular membranes present in all living organisms. They typically form a lipid bilayer that embroiders the cell or cellular organelles, constitute a barrier for ions and small solutes and form a matrix that supports the function of membrane proteins. The chemical composition of the membrane phospholipids present in the two prokaryotic domains Archaea and Bacteria are vastly different. Archaeal lipids are composed of highly-methylated isoprenoid chains that are ether-linked to a glycerol-1-phosphate backbone while bacterial phospholipids consist of straight fatty acids bound by ester bonds to the enantiomeric glycerol-3-phosphate backbone. The chemical structure of the archaeal lipids and their compositional diversity ensures the required stability at extreme environmental conditions as many archaea thrive at such conditions including high or low temperature, high salinity and extreme acidic or alkaline pH values. However, not all archaea are extremophiles, and the presence of ether-linked phospholipids is a phylogenetic marker that distinguishes Archaea from other life forms. During the past decade, our understanding of the biosynthesis of archaeal lipids has progressed resulting in the characterization of the main biosynthetic steps of the pathway including the reconstitution of lipid biosynthesis in vitro. Here we describe the chemical and physical properties of archaeal lipids and membranes derived thereof, summarize the existing knowledge about the enzymology of the archaeal lipid biosynthetic pathway and discuss evolutionary theories associated with the "Lipid Divide" that resulted in the differentiation of bacterial and archaeal organisms. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Antonella Caforio
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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14
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Villanueva L, Schouten S, Damsté JSS. Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’. Environ Microbiol 2016; 19:54-69. [DOI: 10.1111/1462-2920.13361] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ, Royal Netherlands Institute for Sea Research, and Utrecht UniversityP.O. Box 591790AB Den Burg Texel The Netherlands
| | - Stefan Schouten
- Department of Marine Microbiology and BiogeochemistryNIOZ, Royal Netherlands Institute for Sea Research, and Utrecht UniversityP.O. Box 591790AB Den Burg Texel The Netherlands
- Faculty of GeosciencesUtrecht UniversityP.O. Box 80.021Utrecht3508 TA The Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ, Royal Netherlands Institute for Sea Research, and Utrecht UniversityP.O. Box 591790AB Den Burg Texel The Netherlands
- Faculty of GeosciencesUtrecht UniversityP.O. Box 80.021Utrecht3508 TA The Netherlands
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15
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Linde M, Peterhoff D, Sterner R, Babinger P. Identification and Characterization of Heptaprenylglyceryl Phosphate Processing Enzymes in Bacillus subtilis. J Biol Chem 2016; 291:14861-70. [PMID: 27226549 DOI: 10.1074/jbc.m115.711994] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Indexed: 11/06/2022] Open
Abstract
In Archaea, ether lipids play an essential role as the main building blocks of the cellular membrane. Recently, ether lipids have also been discovered in the domain of Bacteria, and the key enzymes that catalyze their synthesis, glycerol-1-phosphate dehydrogenase and heptaprenylglyceryl phosphate synthase, have been described. In Bacillales, heptaprenylglyceryl phosphate does not become linked to a second polyprenyl moiety like ether lipids in Archaea but is dephosphorylated and acetylated. Here, we report on the enzymes that catalyze these reactions. We enriched the phosphatase activity from a B. subtilis cell extract and suppose that dephosphorylation is catalyzed by the phosphatase PhoB or by any other phosphatase in an unspecific manner. By screening a B. subtilis knock-out library for deficiency in acetylation, the yvoF gene product was identified to be the acetyltransferase. The acetyl-CoA-dependent enzyme YvoF is a close relative of maltose O-acetyltransferase (MAT). Its catalytic properties were analyzed and compared with MAT. YvoF and MAT partially overlap in substrate and product range in vitro, but MAT is not able to complement the yvoF knock-out in vivo.
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Affiliation(s)
- Mona Linde
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - David Peterhoff
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Reinhard Sterner
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Patrick Babinger
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
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16
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Abstract
In archaea, the membrane phospholipids consist of isoprenoid hydrocarbon chains that are ether-linked to a sn-glycerol1-phosphate backbone. This unique structure is believed to be vital for the adaptation of these micro-organisms to extreme environments, but it also reflects an evolutionary marker that distinguishes archaea from bacteria and eukaryotes. CDP-archaeol is the central precursor for polar head group attachment. We examined various bacterial enzymes involved in the attachment of L-serine and glycerol as polar head groups for their promiscuity in recognizing CDP-archaeol as a substrate. Using a combination of mutated bacterial and archaeal enzymes, archaetidylethanolamine (AE) and archaetidylglycerol (AG) could be produced in vitro using nine purified enzymes while starting from simple building blocks. The ether lipid pathway constituted by a set of archaeal and bacterial enzymes was introduced into Escherichia coli, which resulted in the biosynthesis of AE and AG. This is a further step in the reprogramming of E. coli for ether lipid biosynthesis.
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17
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Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL. Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1019-37. [PMID: 25900361 DOI: 10.1016/j.bbapap.2015.04.015] [Citation(s) in RCA: 558] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/30/2015] [Accepted: 04/14/2015] [Indexed: 11/19/2022]
Abstract
The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics and computational tools as well as experimental strategies for the prediction and assignment of functions (in vitro activities and in vivo physiological/metabolic roles) to uncharacterized enzymes discovered in genome projects. Protein sequence similarity networks (SSNs) are visually powerful tools for analyzing sequence relationships in protein families (H.J. Atkinson, J.H. Morris, T.E. Ferrin, and P.C. Babbitt, PLoS One 2009, 4, e4345). However, the members of the biological/biomedical community have not had access to the capability to generate SSNs for their "favorite" protein families. In this article we announce the EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool (http://efi.igb.illinois.edu/efi-est/) that is available without cost for the automated generation of SSNs by the community. The tool can create SSNs for the "closest neighbors" of a user-supplied protein sequence from the UniProt database (Option A) or of members of any user-supplied Pfam and/or InterPro family (Option B). We provide an introduction to SSNs, a description of EFI-EST, and a demonstration of the use of EFI-EST to explore sequence-function space in the OMP decarboxylase superfamily (PF00215). This article is designed as a tutorial that will allow members of the community to use the EFI-EST web tool for exploring sequence/function space in protein families.
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Affiliation(s)
- John A Gerlt
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA.
| | - Jason T Bouvier
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Daniel B Davidson
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Heidi J Imker
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Boris Sadkhin
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - David R Slater
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Katie L Whalen
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
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18
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Jain S, Caforio A, Driessen AJM. Biosynthesis of archaeal membrane ether lipids. Front Microbiol 2014; 5:641. [PMID: 25505460 PMCID: PMC4244643 DOI: 10.3389/fmicb.2014.00641] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/06/2014] [Indexed: 01/05/2023] Open
Abstract
A vital function of the cell membrane in all living organism is to maintain the membrane permeability barrier and fluidity. The composition of the phospholipid bilayer is distinct in archaea when compared to bacteria and eukarya. In archaea, isoprenoid hydrocarbon side chains are linked via an ether bond to the sn-glycerol-1-phosphate backbone. In bacteria and eukarya on the other hand, fatty acid side chains are linked via an ester bond to the sn-glycerol-3-phosphate backbone. The polar head groups are globally shared in the three domains of life. The unique membrane lipids of archaea have been implicated not only in the survival and adaptation of the organisms to extreme environments but also to form the basis of the membrane composition of the last universal common ancestor (LUCA). In nature, a diverse range of archaeal lipids is found, the most common are the diether (or archaeol) and the tetraether (or caldarchaeol) lipids that form a monolayer. Variations in chain length, cyclization and other modifications lead to diversification of these lipids. The biosynthesis of these lipids is not yet well understood however progress in the last decade has led to a comprehensive understanding of the biosynthesis of archaeol. This review describes the current knowledge of the biosynthetic pathway of archaeal ether lipids; insights on the stability and robustness of archaeal lipid membranes; and evolutionary aspects of the lipid divide and the LUCA. It examines recent advances made in the field of pathway reconstruction in bacteria.
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Affiliation(s)
- Samta Jain
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen Netherlands ; The Zernike Institute for Advanced Materials, University of Groningen, Groningen Netherlands
| | - Antonella Caforio
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen Netherlands ; The Zernike Institute for Advanced Materials, University of Groningen, Groningen Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen Netherlands ; The Zernike Institute for Advanced Materials, University of Groningen, Groningen Netherlands
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19
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Jain S, Caforio A, Fodran P, Lolkema JS, Minnaard AJ, Driessen AJM. Identification of CDP-archaeol synthase, a missing link of ether lipid biosynthesis in Archaea. ACTA ACUST UNITED AC 2014; 21:1392-1401. [PMID: 25219966 DOI: 10.1016/j.chembiol.2014.07.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/22/2014] [Accepted: 07/24/2014] [Indexed: 12/11/2022]
Abstract
Archaeal membrane lipid composition is distinct from Bacteria and Eukarya, consisting of isoprenoid chains etherified to the glycerol carbons. Biosynthesis of these lipids is poorly understood. Here we identify and characterize the archaeal membrane protein CDP-archaeol synthase (CarS) that catalyzes the transfer of the nucleotide to its specific archaeal lipid substrate, leading to the formation of a CDP-activated precursor (CDP-archaeol) to which polar head groups are attached. The discovery of CarS enabled reconstitution of the entire archaeal lipid biosynthesis pathway in vitro, starting from simple isoprenoid building blocks and using a set of five purified enzymes. The cell free synthetic strategy for archaeal lipids we describe opens opportunity for studies of archaeal lipid biochemistry. Additionally, insights into archaeal lipid biosynthesis reported here allow addressing the evolutionary hypothesis of the lipid divide between Archaea and Bacteria.
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Affiliation(s)
- Samta Jain
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands; Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Antonella Caforio
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands; Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Peter Fodran
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Juke S Lolkema
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands; Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Adriaan J Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands; Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, the Netherlands.
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