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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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2
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Yin X, Wu W, Maeke M, Richter-Heitmann T, Kulkarni AC, Oni OE, Wendt J, Elvert M, Friedrich MW. CO 2 conversion to methane and biomass in obligate methylotrophic methanogens in marine sediments. ISME JOURNAL 2019; 13:2107-2119. [PMID: 31040382 PMCID: PMC6775961 DOI: 10.1038/s41396-019-0425-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/04/2019] [Accepted: 04/13/2019] [Indexed: 11/24/2022]
Abstract
Methyl substrates are important compounds for methanogenesis in marine sediments but diversity and carbon utilization by methylotrophic methanogenic archaea have not been clarified. Here, we demonstrate that RNA-stable isotope probing (SIP) requires 13C-labeled bicarbonate as co-substrate for identification of methylotrophic methanogens in sediment samples of the Helgoland mud area, North Sea. Using lipid-SIP, we found that methylotrophic methanogens incorporate 60–86% of dissolved inorganic carbon (DIC) into lipids, and thus considerably more than what can be predicted from known metabolic pathways (~40% contribution). In slurry experiments amended with the marine methylotroph Methanococcoides methylutens, up to 12% of methane was produced from CO2, indicating that CO2-dependent methanogenesis is an alternative methanogenic pathway and suggesting that obligate methylotrophic methanogens grow in fact mixotrophically on methyl compounds and DIC. Although methane formation from methanol is the primary pathway of methanogenesis, the observed high DIC incorporation into lipids is likely linked to CO2-dependent methanogenesis, which was triggered when methane production rates were low. Since methylotrophic methanogenesis rates are much lower in marine sediments than under optimal conditions in pure culture, CO2 conversion to methane is an important but previously overlooked methanogenic process in sediments for methylotrophic methanogens.
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Affiliation(s)
- Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Weichao Wu
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,Department of Geosciences, University of Bremen, Bremen, Germany.,Department of Biogeochemistry of Agroecosystems, University of Goettingen, Goettingen, Germany
| | - Mara Maeke
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ajinkya C Kulkarni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Oluwatobi E Oni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, Bremen, Germany
| | - Jenny Wendt
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,Department of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,Department of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany. .,MARUM - Center for Marine Environmental Sciences, Bremen, Germany.
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3
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Functional annotation of operome from Methanothermobacter thermautotrophicus ΔH: An insight to metabolic gap filling. Int J Biol Macromol 2018; 123:350-362. [PMID: 30445075 DOI: 10.1016/j.ijbiomac.2018.11.100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/10/2018] [Accepted: 11/12/2018] [Indexed: 12/16/2022]
Abstract
Methanothermobacter thermautotrophicus ΔH (MTH) is a potential methanogen known to reduce CO2 with H2 for producing methane biofuel in thermophilic digesters. The genome of this organism contains ~50.5% conserved hypothetical proteins (HPs; operome) whose function is still not determined precisely. Here, we employed a combined bioinformatics approach to annotate a precise function to HPs and categorize them as enzymes, binding proteins, and transport proteins. Results of our study show that 315 (35.6%) HPs have exhibited well-defined functions contributing imperative roles in diverse cellular metabolism. Some of them are responsible for stress-response mechanisms and cell cycle, membrane transport, and regulatory processes. The genome-neighborhood analysis found five important gene clusters (dsr, ehb, kaiC, cmr, and gas) involving in the energetic metabolism and defense systems. MTH operome contains 223 enzymes with 15 metabolic subsystems, 15 cell cycle proteins, 17 transcriptional regulators and 33 binding proteins. Functional annotation of its operome is thus more fundamental to a profound understanding of the molecular and cellular machinery at systems-level.
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Ladevèze S, Laville E, Despres J, Mosoni P, Potocki-Véronèse G. Mannoside recognition and degradation by bacteria. Biol Rev Camb Philos Soc 2016; 92:1969-1990. [PMID: 27995767 DOI: 10.1111/brv.12316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/01/2016] [Accepted: 11/11/2016] [Indexed: 11/29/2022]
Abstract
Mannosides constitute a vast group of glycans widely distributed in nature. Produced by almost all organisms, these carbohydrates are involved in numerous cellular processes, such as cell structuration, protein maturation and signalling, mediation of protein-protein interactions and cell recognition. The ubiquitous presence of mannosides in the environment means they are a reliable source of carbon and energy for bacteria, which have developed complex strategies to harvest them. This review focuses on the various mannosides that can be found in nature and details their structure. It underlines their involvement in cellular interactions and finally describes the latest discoveries regarding the catalytic machinery and metabolic pathways that bacteria have developed to metabolize them.
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Affiliation(s)
- Simon Ladevèze
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France
| | - Elisabeth Laville
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France
| | - Jordane Despres
- INRA, UR454 Microbiologie, F-63122, Saint-Genès Champanelle, France
| | - Pascale Mosoni
- INRA, UR454 Microbiologie, F-63122, Saint-Genès Champanelle, France
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5
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Koga Y. From promiscuity to the lipid divide: on the evolution of distinct membranes in Archaea and Bacteria. J Mol Evol 2014; 78:234-42. [PMID: 24573438 DOI: 10.1007/s00239-014-9613-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
Abstract
The structural and biosynthetic features of archaeal phospholipids provide clues to the membrane lipid composition in the last universal common ancestor (LUCA) membranes. The evident similarity of the phospholipid biosynthetic pathways in Archaea and Bacteria suggests that one set of these biosynthetic enzymes would have worked on a wide range of lipids composed of enantiomeric glycerophosphate backbones linked with a variety of hydrocarbon chains. This notion was supported by the discovery of a wide range reactivity of enzymes belonging to the CDP-alcohol phosphatidyltransferase family. It is hypothesized that lipid promiscuity is generated from the prebiotic surface metabolism on pyrite proposed by Wächtershäuser. The significance of the phosphate groups on the intermediates of phospholipid biosynthesis and the extra anionic groups of a polar head group suggested the likely involvement of surface metabolism. Anionic groups are essential for surface metabolism. Since the early chemical evolution reactions are presumed to be non-specific, every combination of the available lipid component parts would be expected to be formed. The mixed lipid membranes present in LUCA were segregated and this led to the differentiation of Archaea and Bacteria, as described previously. The proper arrangement of membrane lipids was generated by the physicochemical drive arising from the promiscuity of the primordial membrane lipids.
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Affiliation(s)
- Yosuke Koga
- University of Occupational and Environmental Health, 9-14-20 Hinosato, Munakata, Fukuoka, 811-3425, Japan,
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6
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Gambacorta A, Gliozzi A, De Rosa M. Archaeal lipids and their biotechnological applications. World J Microbiol Biotechnol 2014; 11:115-31. [PMID: 24414415 DOI: 10.1007/bf00339140] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The lipids of Archaea, based on glycerol isopranoid ethers, can be used taxonomically to distinguish between phenotypic subgroups of the domain to delineate them clearly from all other organisms. This review is a general survey of the structural features of archaeal lipids and how they relate to survival in the harsh environments in which the Archaea live. The molecular organization of archaeal lipids in monolayers, artificial black membranes and vesicles and the unique properties and possible biotechnological applications of liposomes of the lipids are presented. The results with these liposomes are compared with similar data obtained with synthetic compounds which mimic the structure of archaeal lipids. Studies on computer simulation are also reported.
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7
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Tsai YH, Liu X, Seeberger PH. Chemical biology of glycosylphosphatidylinositol anchors. Angew Chem Int Ed Engl 2012; 51:11438-56. [PMID: 23086912 DOI: 10.1002/anie.201203912] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Indexed: 01/21/2023]
Abstract
Glycosylphosphatidylinositols (GPIs) are complex glycolipids that are covalently linked to the C-terminus of proteins as a posttranslational modification. They anchor the attached protein to the cell membrane and are essential for normal functioning of eukaryotic cells. GPI-anchored proteins are structurally and functionally diverse. Many GPIs have been structurally characterized but comprehension of their biological functions, beyond the simple physical anchoring, remains largely speculative. Work on functional elucidation at a molecular level is still limited. This Review focuses on the roles of GPI unraveled by using synthetic molecules and summarizes the structural diversity of GPIs, as well as their biological and chemical syntheses.
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Affiliation(s)
- Yu-Hsuan Tsai
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
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8
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Tsai YH, Liu X, Seeberger PH. Chemische Biologie der Glycosylphosphatidylinosit-Anker. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203912] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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da Costa MS, Albuquerque L, Nobre MF, Wait R. The Identification of Polar Lipids in Prokaryotes. METHODS IN MICROBIOLOGY 2011. [DOI: 10.1016/b978-0-12-387730-7.00007-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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10
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Michell RH. Inositol and its derivatives: Their evolution and functions. ACTA ACUST UNITED AC 2011; 51:84-90. [DOI: 10.1016/j.advenzreg.2010.10.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 10/20/2010] [Indexed: 12/27/2022]
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11
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Zavalova LL, Lazarev VN, Levitsky SA, Yudina TG, Baskova IP. Destabilase-lysozyme of medicinal leech. Multifunctionality of recombinant protein. BIOCHEMISTRY (MOSCOW) 2010; 75:1173-81. [PMID: 21077838 DOI: 10.1134/s0006297910090129] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Preparation and purification of a recombinant protein are described along with characteristics of its specific (for ε-(γ-Glu)-Lys and D-dimer substrates) and nonspecific (for L-γ-Glu-pNA) isopeptidase activities; the absence of peptidase function for α-(α-Glu)-Lys substrate is noted. It is shown that the protein exhibits muramidase (cell walls of Micrococcus lysodeikticus) and specific glycosidase activities. The latter was determined towards the fluorogenic substrate 4-methylumbelliferyl-tetra-N-acetyl-β-chitotetraoxide. Antimicrobial activity of recombinant destabilase-lysozyme protein (recDest-Lys) and its 11-membered amphipathic peptide was revealed towards cells of the strict anaerobic Archaean Methanosarcina barkeri, whose cell walls contain no murein. Possible mechanisms of the effect of recDest-Lys on these cells are discussed.
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Affiliation(s)
- L L Zavalova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 119997, Russia.
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12
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Sprott GD, Côté JP, Jarrell HC. Glycosidase-induced fusion of isoprenoid gentiobiosyl lipid membranes at acidic pH. Glycobiology 2008; 19:267-76. [PMID: 19029107 DOI: 10.1093/glycob/cwn129] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A difficulty in explaining the mechanism whereby archaeal lipid membrane vesicles (archaeosomes) deliver entrapped protein antigens to the MHC class I cytosolic pathway from phagolysosomes of antigen-presenting cells has been the observation that they tend not to fuse. Here, we determine that archaeosomes, composed of archaeal isoprenoid mixtures of glyco and phospholipids, can be highly fusogenic when exposed to the pH and enzymes found in late phagolysosomes. Fusions were strictly dependent on acidic pH and the presence of alpha- or beta-glucosidase. Resonance energy transfer (RET) assays demonstrated that fusion conditions induced lipid mixing of archaeosome lipids with self-unlabeled archaeosomes. Because PC/PG/cholesterol liposomes by themselves did not fuse, it was possible to unequivocally show a fusion of rhodamine-labeled liposomes with archaeosomes by fluorescence microscopy and to demonstrate lipid mixing between labeled liposomes and archaeosomes by the RET assay. Radiotracer and (1)H NMR studies revealed that glycolipids in fused archaeosomes were not degraded significantly by glucosidase treatment during fusion. Rather, the glucosidases dramatically induced small archaeosomes to rapidly and visually aggregate at pH 4.8, but not 6.8, thus bringing membranes together appropriately as a first step in the fusion process. (1)H NMR was used to demonstrate that conditions causing aggregation correlated with binding of glucosidase to the archaeosomes. Binding at acidic pH occurred by the electrostatic interaction of positively charged glucosidase with the anionic phospholipids, although the interaction also occurred with the gentiobiosyl lipids. The data indicate a mechanism of membrane-membrane fusion for archaeal glycolipid membranes induced by glycosidase and illustrate the importance for inclusion of glycolipids in compositions of vesicles designed to deliver protein antigens to the cytosol for MHC class I presentation.
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Affiliation(s)
- G Dennis Sprott
- Institute for Biological Sciences, National Research Council, 100 Sussex Drive, Ottawa, ON K1A OR6, Canada.
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13
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Oswal N, Sahni NS, Bhattacharya A, Komath SS, Muthuswami R. Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family. BMC Evol Biol 2008; 8:168. [PMID: 18522757 PMCID: PMC2446393 DOI: 10.1186/1471-2148-8-168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 06/04/2008] [Indexed: 11/10/2022] Open
Abstract
Background The first step of GPI anchor biosynthesis is catalyzed by PIG-A, an enzyme that transfers N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol. This protein is present in all eukaryotic organisms ranging from protozoa to higher mammals, as part of a larger complex of five to six 'accessory' proteins whose individual roles in the glycosyltransferase reaction are as yet unclear. The PIG-A gene has been shown to be an essential gene in various eukaryotes. In humans, mutations in the protein have been associated with paroxysomal noctural hemoglobuinuria. The corresponding PIG-A gene has also been recently identified in the genome of many archaeabacteria although genes of the accessory proteins have not been discovered in them. The present study explores the evolution of PIG-A and the phylogenetic relationship between this protein and other glycosyltransferases. Results In this paper we show that out of the twelve conserved motifs identified by us eleven are exclusively present in PIG-A and, therefore, can be used as markers to identify PIG-A from newly sequenced genomes. Three of these motifs are absent in the primitive eukaryote, G. lamblia. Sequence analyses show that seven of these conserved motifs are present in prokaryote and archaeal counterparts in rudimentary forms and can be used to differentiate PIG-A proteins from glycosyltransferases. Using partial least square regression analysis and data involving presence or absence of motifs in a range of PIG-A and glycosyltransferases we show that (i) PIG-A may have evolved from prokaryotic glycosyltransferases and lipopolysaccharide synthases, members of the GT4 family of glycosyltransferases and (ii) it is possible to uniquely classify PIG-A proteins versus glycosyltransferases. Conclusion Besides identifying unique motifs and showing that PIG-A protein from G. lamblia and some putative PIG-A proteins from archaebacteria are evolutionarily closer to glycosyltransferases, these studies provide a new method for identification and classification of PIG-A proteins.
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Affiliation(s)
- Nupur Oswal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110 067, India.
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15
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Koga Y, Morii H. Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations. Microbiol Mol Biol Rev 2007; 71:97-120. [PMID: 17347520 PMCID: PMC1847378 DOI: 10.1128/mmbr.00033-06] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This review deals with the in vitro biosynthesis of the characteristics of polar lipids in archaea along with preceding in vivo studies. Isoprenoid chains are synthesized through the classical mevalonate pathway, as in eucarya, with minor modifications in some archaeal species. Most enzymes involved in the pathway have been identified enzymatically and/or genomically. Three of the relevant enzymes are found in enzyme families different from the known enzymes. The order of reactions in the phospholipid synthesis pathway (glycerophosphate backbone formation, linking of glycerophosphate with two radyl chains, activation by CDP, and attachment of common polar head groups) is analogous to that of bacteria. sn-Glycerol-1-phosphate dehydrogenase is responsible for the formation of the sn-glycerol-1-phosphate backbone of phospholipids in all archaea. After the formation of two ether bonds, CDP-archaeol acts as a common precursor of various archaeal phospholipid syntheses. Various phospholipid-synthesizing enzymes from archaea and bacteria belong to the same large CDP-alcohol phosphatidyltransferase family. In short, the first halves of the phospholipid synthesis pathways play a role in synthesis of the characteristic structures of archaeal and bacterial phospholipids, respectively. In the second halves of the pathways, the polar head group-attaching reactions and enzymes are homologous in both domains. These are regarded as revealing the hybrid nature of phospholipid biosynthesis. Precells proposed by Wächtershäuser are differentiated into archaea and bacteria by spontaneous segregation of enantiomeric phospholipid membranes (with sn-glycerol-1-phosphate and sn-glycerol-3-phosphate backbones) and the fusion and fission of precells. Considering the nature of the phospholipid synthesis pathways, we here propose that common phospholipid polar head groups were present in precells before the differentiation into archaea and bacteria.
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Affiliation(s)
- Yosuke Koga
- Department of Chemistry, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan.
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Affiliation(s)
- Mary F Roberts
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
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Abstract
One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although archaeal proteins can undergo posttranslational modifications reminiscent of what their eucaryal and bacterial counterparts experience, examination of archaeal posttranslational modification often reveals aspects not previously observed in the other two domains of life. In some cases, posttranslational modification allows a protein to survive the extreme conditions often encountered by Archaea. The various posttranslational modifications experienced by archaeal proteins, the molecular steps leading to these modifications, and the role played by posttranslational modification in Archaea form the focus of this review.
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Affiliation(s)
- Jerry Eichler
- Dept. of Life Sciences, Ben Gurion University, P.O. Box 653, Beersheva 84105, Israel.
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Metzler DE, Metzler CM, Sauke DJ. Lipids, Membranes, and Cell Coats. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chen L, Zhou C, Yang H, Roberts MF. Inositol-1-phosphate synthase from Archaeoglobus fulgidus is a class II aldolase. Biochemistry 2000; 39:12415-23. [PMID: 11015222 DOI: 10.1021/bi001517q] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A gene putatively identified as the Archaeoglobus fulgidus inositol-1-phosphate synthase (IPS) gene was overexpressed to high level (about 30-40% of total soluble cellular proteins) in Escherichia coli. The recombinant protein was purified to homogeneity by heat treatment followed by two column chromatographic steps. The native enzyme was a tetramer of 168 +/- 4 kDa (subunit molecular mass of 44 kDa). At 90 degrees C the K(m) values for glucose-6-phosphate and NAD(+) were estimated as 0.12 +/- 0.04 mM and 5.1 +/- 0.9 microM, respectively. Use of (D)-[5-(13)C]glucose-6-phosphate as a substrate confirmed that the stereochemistry of the product of the IPS reaction was L-myo-inositol-1-phosphate. This archaeal enzyme, with the highest activity at its optimum growth temperature among all IPS reported (k(cat) = 9.6 +/- 0.4 s(-1) with an estimated activation energy of 69 kJ/mol), was extremely heat stable. However, the most unique feature of A. fulgidus IPS was that it absolutely required divalent metal ions for activity. Zn(2+) and Mn(2+) were the best activators with K(D) approximately 1 microM, while NH(4)(+) (a critical activator for all the other characterized IPS enzymes) had no effect on the enzyme. These properties suggested that this archaeal IPS was a class II aldolase. In support of this, stoichiometric reduction of NAD(+) to NADH could be followed spectrophotometrically when EDTA was present along with glucose-6-phosphate.
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Affiliation(s)
- L Chen
- Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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Morii H, Yagi H, Akutsu H, Nomura N, Sako Y, Koga Y. A novel phosphoglycolipid archaetidyl(glucosyl)inositol with two sesterterpanyl chains from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1436:426-36. [PMID: 9989273 DOI: 10.1016/s0005-2760(98)00157-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The structures of two novel polar lipids (AGI and AI) of an aerobic hyperthermophilic archaeon, Aeropyrum pernix, were elucidated. AGI and AI were the only two major lipids and accounted for 91 mol% and 9 mol%, respectively, of total polar lipids of this organism. The core lipid of A. pernix total lipids consisted solely of 2,3-di-O-sesterterpanyl-sn-glycerol (C25,25-archaeol). The molecular weights of the free acid forms of AGI and AI were shown by FAB-mass spectrometry to be 1196 and 1034, respectively. AI was completely hydrolyzed by phosphatidylinositol-specific phospholipase C, while AGI was not hydrolyzed at all under the same condition for the hydrolysis of AI. The molar ratio of phosphate, myo-inositol, and glucose in AGI was 1.0:0.97:0.95. The positions of linkages between myo-inositol and glucose, and between myo-inositol and phosphate in AGI were determined by NMR analyses of intact AGI and glucosylinositol prepared from AGI. Finally, it was concluded that the structures of AGI and AI were 2,3-di-O-sesterterpanyl-sn-glycerol-1-phospho-1'-(2'-O-alpha-D-glu cosyl)- myo-inositol (C25,25-archaetidyl(glucosyl)inositol) and 2,3-di-O-sesterterpanyl-sn-glycerol-1-phospho-myo-inositol (C25,25-archaetidylinositol), respectively. This is the first example that a core lipid of whole polar lipids is composed of only one species C25,25-archaeol in one organism and that glucosylinositol is found in a polar lipid as a polar head group.
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Affiliation(s)
- H Morii
- Department of Environmental Management, University of Occupational and Environmental Health, Kitakyushu, Japan.
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Asakawa S, Akagawa-Matsushita M, Morii H, Koga Y, Hayano K. Characterization of Methanosarcina mazeii TMA isolated from a paddy field soil. Curr Microbiol 1995. [DOI: 10.1007/bf00294631] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nishihara M, Koga Y. Two new phospholipids, hydroxyarchaetidylglycerol and hydroxyarchaetidylethanolamine, from the Archaea Methanosarcina barkeri. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1254:155-60. [PMID: 7827120 DOI: 10.1016/0005-2760(94)00178-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The structures of two new ether phospholipids of the methanogenic Archaea, Methanosarcina barkeri, were determined as hydroxyarchaetidylglycerol and hydroxyarchaetidylethanolamine by means of chemical, chromatographic and enzymatic analyses, and fast atom bombardment-mass spectrometry. These lipids are hydroxy diether analogs of phosphatidylglycerol and phosphatidylethanolamine, respectively, with beta-hydroxyarachaeol (2-O-(3'-hydroxy)phytanyl-3-O-phytanyl-sn-glycerol) as a core lipid. In addition, two other ether phospholipids, usual archaetidylglycerol and archaetidylethanolamine, were also identified in the organism. The stereochemical structure of the unalkylated glycerophosphate of hydroxyarchaetidylglycerol and archaetidylglycerol was determined as sn-glycerol-3-phosphate by use of sn-glycerol-3-phosphate dehydrogenase. The stereochemical configuration of the glycerophosphoglycerol backbone of these lipids was a mirror image of that of diacylphosphatidylglycerol from the organisms of the domains Bacteria and Eucarya, and it was shared with extremely halophilic Archaea. These four phospholipids, in addition to five lipids that had already been reported, accounted for 88% of the total polar lipids of this organism.
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Affiliation(s)
- M Nishihara
- Department of Chemistry, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
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Sprott GD, Ferrante G, Ekiel I. Tetraether lipids of Methanospirillum hungatei with head groups consisting of phospho-N,N-dimethylaminopentanetetrol, phospho-N,N,N-trimethylaminopentanetetrol, and carbohydrates. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1214:234-42. [PMID: 7918605 DOI: 10.1016/0005-2760(94)90069-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Acyclic, standard tetraether and diether lipids each account for about 50% of the total ether lipids found in Methanospirillum hungatei. Sixteen ether lipids were purified and defined according to relative weight percentage and staining reactions on thin-layer plates. Structures were elucidated for six previously uncharacterized tetraether lipids. Four of these lipids had as one head group either alpha-glcp-(1-2)-beta-gal(f)-, or beta-gal(f)-(1-6)-beta-gal(f)-, in glycosidic linkage to the first glycerol of the lipid backbone, and either a N,N-dimethyl-aminopentanetetrol or a N,N,N-trimethylaminopentanetetrol moiety in phosphodiester linkage to the second glycerol of the backbone. A fifth lipid was a tetraether structure novel in having carbohydrate moieties at both head group positions; namely alpha-glcp-(1-2)-gal(f)- and beta-gal(f)-. Two other lipids, a diether and a tetraether, had a single head group consisting of alpha-glcp-(1-2)-beta-gal(f)- modified by O-acetylation of the gal(f) residue at C-6. In addition to the seven new lipids described above, diether and tetraether analogs of phosphatidylglycerol were found.
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Affiliation(s)
- G D Sprott
- National Research Council of Canada, Institute for Biological Sciences, Ottawa, Ontario, Canada
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Koga Y, Akagawa-Matsushita M, Ohga M, Nishihara M. Taxonomic Significance of the Distribution of Component Parts of Polar Ether Lipids in Methanogens. Syst Appl Microbiol 1993. [DOI: 10.1016/s0723-2020(11)80264-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Structural data on archaebacterial lipids is presented with emphasis on the ether lipids of the methanogens. These ether lipids normally account for 80-95% of the membrane lipids with the remaining 5-20% of neutral squalenes and other isoprenoids. Genus-specific combinations of various lipid core structures found in methanogens include diether-tetraether, dietherhydroxydiether, or diether-macrocyclic diether-tetraether lipid moieties. Some species have only the standard diether core lipid, but none are known with predominantly tetraether lipids as found in certain sulfur-dependent archaebacteria. The relative proportions of these lipid cores are known to vary in relation to growth conditions in Methanococcus jannaschii and Methanobacterium thermoautotrophicum. Polar headgroups in glycosidic or phosphodiester linkage to the sn-1 or sn-1' carbons of glycerol consist of polyols, carbohydrates, and amino compounds. The available structural data indicate a close similarity among the polar lipids synthesized within the species of the same genus. Detection of lipid molecular ions by mass spectrometry of total polar lipid extracts is a promising technique to provide valuable comparative data. Since these lipid structures are stable within the extreme environments that many archaebacteria inhabit, there may be specific applications for their use in biotechnology.
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Affiliation(s)
- G D Sprott
- Institute of Biological Sciences, National Research Council, Ottawa, Canada
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