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Gonzalez-Ordenes F, Cea PA, Fuentes-Ugarte N, Muñoz SM, Zamora RA, Leonardo D, Garratt RC, Castro-Fernandez V, Guixé V. ADP-Dependent Kinases From the Archaeal Order Methanosarcinales Adapt to Salt by a Non-canonical Evolutionarily Conserved Strategy. Front Microbiol 2018; 9:1305. [PMID: 29997580 PMCID: PMC6028617 DOI: 10.3389/fmicb.2018.01305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/29/2018] [Indexed: 11/13/2022] Open
Abstract
Halophilic organisms inhabit hypersaline environments where the extreme ionic conditions and osmotic pressure have driven the evolution of molecular adaptation mechanisms. Understanding such mechanisms is limited by the common difficulties encountered in cultivating such organisms. Within the Euryarchaeota, for example, only the Halobacteria and the order Methanosarcinales include readily cultivable halophilic species. Furthermore, only the former have been extensively studied in terms of their component proteins. Here, in order to redress this imbalance, we investigate the halophilic adaptation of glycolytic enzymes from the ADP-dependent phosphofructokinase/glucokinase family (ADP-PFK/GK) derived from organisms of the order Methanosarcinales. Structural analysis of proteins from non-halophilic and halophilic Methanosarcinales shows an almost identical composition and distribution of amino acids on both the surface and within the core. However, these differ from those observed in Halobacteria or Eukarya. Proteins from Methanosarcinales display a remarkable increase in surface lysine content and have no reduction to the hydrophobic core, contrary to the features ubiquitously observed in Halobacteria and which are thought to be the main features responsible for their halophilic properties. Biochemical characterization of recombinant ADP-PFK/GK from M. evestigatum (halophilic) and M. mazei (non-halophilic) shows the activity of both these extant enzymes to be only moderately inhibited by salt. Nonetheless, its activity over time is notoriously stabilized by salt. Furthermore, glycine betaine has a protective effect against KCl inhibition and enhances the thermal stability of both enzymes. The resurrection of the last common ancestor of ADP-PFK/GK from Methanosarcinales shows that the ancestral enzyme displays an extremely high salt tolerance and thermal stability. Structure determination of the ancestral protein reveals unique traits such as an increase in the Lys and Glu content at the protein surface and yet no reduction to the volume of the hydrophobic core. Our results suggest that the halophilic character is an ancient trait in the evolution of this protein family and that proteins from Methanosarcinales have adapted to highly saline environments by a non-canonical strategy, different from that currently proposed for Halobacteria. These results open up new avenues for the search and development of novel salt tolerant biocatalysts.
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Affiliation(s)
- Felipe Gonzalez-Ordenes
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo A Cea
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Nicolás Fuentes-Ugarte
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sebastián M Muñoz
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ricardo A Zamora
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Diego Leonardo
- São Carlos Institute of Physics, University of São Paulo at São Carlos, São Paulo, Brazil
| | - Richard C Garratt
- São Carlos Institute of Physics, University of São Paulo at São Carlos, São Paulo, Brazil
| | - Victor Castro-Fernandez
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Victoria Guixé
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Yakimov MM, Giuliano L, Crisafi E, Chernikova TN, Timmis KN, Golyshin PN. Microbial community of a saline mud volcano at San Biagio-Belpasso, Mt. Etna (Italy). Environ Microbiol 2002; 4:249-56. [PMID: 12030850 DOI: 10.1046/j.1462-2920.2002.00293.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In San Biagio of Belpasso, approximately 20 km south of Mt. Etna, in the area of contact between volcanic and sedimentary formations, a number of small (3- 60 cm in diameter) active mud eruptions discharge CO2-rich gases, mud and NaCl brines. They can be described as mini-volcanoes owing to their typical conic shapes and continuously bubbling peak craters. Samples were collected from the active peak craters at a depth of 20 cm and DNA was immediately extracted and amplified with universal 16S rRNA gene-specific primers, followed by cloning procedure. A total of 140 bacterial clones obtained were screened and clustered by restriction fragment length polymorphism (RFLP) analysis. The pool of 16S rRNA sequences representing each RFLP cluster was subjected to phylogenetic analysis. All of the 33 sequences analysed were affiliated with the kingdom of Eubacteria; 28 sequences (77% of all clones) affiliated with the Proteobacteria, two sequences (19% of all clones) were affiliated with Actinobacteria and three sequences (4% of all clones) were affiliated with the Flexibacter-Cytophaga-Bacteroides division. The data obtained suggest that the microorganisms phylogenetically affiliated to autotrophic methane oxidizers and heterotrophic hydrocarbon degraders belonging to the gamma-subclass of Proteobacteria are major constituents of the microbial communities of the saline volcanic muds. Overall, the composition of the microbial community of the San Biagio mud volcano resembles the compositions of marine microbial communities, which might indicate that wind-blown seawater vapour acted as an inoculum for microbial community described in present work.
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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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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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Koga Y, Nishihara M, Morii H, Akagawa-Matsushita M. Ether polar lipids of methanogenic bacteria: structures, comparative aspects, and biosyntheses. Microbiol Rev 1993; 57:164-82. [PMID: 8464404 PMCID: PMC372904 DOI: 10.1128/mr.57.1.164-182.1993] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Complete structures of nearly 40 ether polar lipids from seven species of methanogens have been elucidated during the past 10 years. Three kinds of variations of core lipids, macrocyclic archaeol and two hydroxyarchaeols, were identified, in addition to the usual archaeol and caldarchaeol (for the nomenclature of archaeal [archaebacterial] ether lipids, see the text). Polar head groups of methanogen phospholipids include ethanolamine, serine, inositol, N-acetylglucosamine, dimethyl- and trimethylaminopentanetetrol, and glucosaminylinositol. Glucose is the sole hexose moiety of glycolipids in most methanogens, and galactose and mannose have been found in a few species. Methanogen lipids are characterized by their diversity in phosphate-containing polar head groups and core lipids, which in turn can be used for chemotaxonomy of methanogens. This was shown by preliminary simplified analyses of lipid component residues. Core lipid analysis by high-pressure liquid chromatography provides a method of determining the methanogenic biomass in natural samples. There has been significant progress in the biosynthetic studies of methanogen lipids in recent years. In vivo incorporation experiments have led to delineation of the outline of the synthetic route of the diphytanylglycerol ether core. The mechanisms of biosynthesis of tetraether lipids and various polar lipids, and cell-free systems of either lipid synthesis, however, remain to be elucidated. The significance and the origin of archaeal ether lipids is discussed in terms of the lipid composition of bacteria living in a wide variety of environments, the oxygen requirement for biosynthesis of hydrocarbon chains, and the physicochemical properties and functions of lipids as membrane constituents.
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Affiliation(s)
- Y Koga
- Department of Chemistry, University of Occupational and Environmental Health, Kitakyushu, Japan
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Woese CR. Introduction The archaea: Their history and significance. THE BIOCHEMISTRY OF ARCHAEA (ARCHAEBACTERIA) 1993. [DOI: 10.1016/s0167-7306(08)60248-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
The small subunit rRNA sequence of twenty archaea, members of the Methanomicrobiales, permits a detailed phylogenetic tree to be inferred for the group. The tree confirms earlier studies, based on far fewer sequences, in showing the group to be divided into two major clusters, temporarily designated the "methanosarcina" group and the "methanogenium" group. The tree also defines phylogenetic relationships within these two groups, which in some cases do not agree with the phylogenetic relationships implied by current taxonomic names--a problem most acute for the genus Methanogenium and its relatives. The present phylogenetic characterization provides the basis for a consistent taxonomic restructuring of this major methanogenic taxon.
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Affiliation(s)
- P Rouvière
- Department of Microbiology, University of Illinois, Urbana 61801, USA
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Gutell RR, Schnare MN, Gray MW. A compilation of large subunit (23S- and 23S-like) ribosomal RNA structures. Nucleic Acids Res 1992; 20 Suppl:2095-109. [PMID: 1375996 PMCID: PMC333986 DOI: 10.1093/nar/20.suppl.2095] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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