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Cui HL, Hou J, Amoozegar MA, Dyall-Smith ML, de la Haba RR, Minegishi H, Montalvo-Rodriguez R, Oren A, Sanchez-Porro C, Ventosa A, Vreeland RH. Proposed minimal standards for description of new taxa of the class Halobacteria. Int J Syst Evol Microbiol 2024; 74:006290. [PMID: 38456846 PMCID: PMC10999741 DOI: 10.1099/ijsem.0.006290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/24/2024] [Indexed: 03/09/2024] Open
Abstract
Halophilic archaea of the class Halobacteria are the most salt-requiring prokaryotes within the domain Archaea. In 1997, minimal standards for the description of new taxa in the order Halobacteriales were proposed. From then on, the taxonomy of the class Halobacteria provides an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods were implemented. The last decades have witnessed a rapid expansion of the number of described taxa within the class Halobacteria coinciding with the era of genome sequencing development. The current members of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria propose these revisions to the recommended minimal standards and encourage the use of advanced technologies in the taxonomic description of members of the Halobacteria. Most previously required and some recommended minimal standards for the description of new taxa in the class Halobacteria were retained in the present revision, but changes have been proposed in line with the new methodologies. In addition to the 16S rRNA gene, the rpoB' gene is an important molecular marker for the identification of members of the Halobacteria. Phylogenomic analysis based on concatenated conserved, single-copy marker genes is required to infer the taxonomic status of new taxa. The overall genome relatedness indexes have proven to be determinative in the classification of the taxa within the class Halobacteria. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values should be calculated for rigorous comparison among close relatives.
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Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Mohammad Ali Amoozegar
- Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran 14178-64411, Iran
| | - Mike L. Dyall-Smith
- Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, 3010, Australia
| | - Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Hiroaki Minegishi
- Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University, Kawagoe, Japan
| | | | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Cristina Sanchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Russell H. Vreeland
- Eastern Shore Microbes, 15397 Merry Cat Lane, Post Office Box 216, Belle Haven, VA 23306, USA
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Feng S, Wang R, Pastor RW, Klauda JB, Im W. Location and Conformational Ensemble of Menaquinone and Menaquinol, and Protein-Lipid Modulations in Archaeal Membranes. J Phys Chem B 2021; 125:4714-4725. [PMID: 33913729 PMCID: PMC8379905 DOI: 10.1021/acs.jpcb.1c01930] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Halobacteria, a type of archaea in high salt environments, have phytanyl ether phospholipid membranes containing up to 50% menaquinone. It is not understood why a high concentration of menaquinone is required and how it influences membrane properties. In this study, menaquinone-8 headgroup and torsion parameters of isoprenoid tail are optimized in the CHARMM36 force field. Molecular dynamics simulations of archaeal bilayers containing 0 to 50% menaquinone characterize the distribution of menaquinone-8 and menaquinol-8, as well as their effects on mechanical properties and permeability. Menaquinone-8 segregates to the membrane midplane above concentrations of 10%, favoring an extended conformation in a fluid state. Menaquinone-8 increases the bilayer thickness but does not significantly alter the area compressibility modulus and lipid chain ordering. Counterintuitively, menaquinone-8 increases water permeability because it lowers the free energy barrier in the midplane. The thickness increase due to menaquinone-8 may help halobacteria ameliorate hyper-osmotic pressure by increasing the membrane bending constant. Simulations of the archaeal membranes with archaerhodopsin-3 show that the local membrane surface adjusts to accommodate the thick membranes. Overall, this study delineates the biophysical landscape of 50% menaquinone in the archaeal bilayer, demonstrates the mixing of menaquinone and menaquinol, and provides atomistic details about menaquinone configurations.
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Affiliation(s)
- Shasha Feng
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Ruixing Wang
- Department of Chemistry and Biochemistry, Chemistry Program, University of Maryland, College Park, Maryland 20742, USA
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, Biophysics Program, University of Maryland, College Park, Maryland 20742, USA
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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Kellermann MY, Yoshinaga MY, Valentine RC, Wörmer L, Valentine DL. Important roles for membrane lipids in haloarchaeal bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2940-2956. [PMID: 27565574 DOI: 10.1016/j.bbamem.2016.08.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 08/11/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
Abstract
Recent advances in lipidomic analysis in combination with various physiological experiments set the stage for deciphering the structure-function of haloarchaeal membrane lipids. Here we focused primarily on changes in lipid composition of Haloferax volcanii, but also performed a comparative analysis with four other haloarchaeal species (Halobacterium salinarum, Halorubrum lacusprofundi, Halorubrum sodomense and Haloplanus natans) all representing distinctive cell morphologies and behaviors (i.e., rod shape vs. pleomorphic behavior). Common to all five haloarchaea, our data reveal an extraordinary high level of menaquinone, reaching up to 72% of the total lipids. This ubiquity suggests that menaquinones may function beyond their ordinary role as electron and proton transporter, acting simultaneously as ion permeability barriers and as powerful shield against oxidative stress. In addition, we aimed at understanding the role of cations interacting with the characteristic negatively charged surface of haloarchaeal membranes. We propose for instance that by bridging the negative charges of adjacent anionic phospholipids, Mg2+ acts as surrogate for cardiolipin, a molecule that is known to control curvature stress of membranes. This study further provides a bioenergetic perspective as to how haloarchaea evolved following oxygenation of Earth's atmosphere. The success of the aerobic lifestyle of haloarchaea includes multiple membrane-based strategies that successfully balance the need for a robust bilayer structure with the need for high rates of electron transport - collectively representing the molecular basis to inhabit hypersaline water bodies around the planet.
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Affiliation(s)
- Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
| | - Marcos Y Yoshinaga
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Leobener Strasse, D-28359 Bremen, Germany
| | | | - Lars Wörmer
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Leobener Strasse, D-28359 Bremen, Germany
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
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Yoshinaga MY, Kellermann MY, Valentine DL, Valentine RC. Phospholipids and glycolipids mediate proton containment and circulation along the surface of energy-transducing membranes. Prog Lipid Res 2016; 64:1-15. [PMID: 27448687 DOI: 10.1016/j.plipres.2016.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 05/29/2016] [Accepted: 07/13/2016] [Indexed: 01/06/2023]
Abstract
Proton bioenergetics provides the energy for growth and survival of most organisms in the biosphere ranging from unicellular marine phytoplankton to humans. Chloroplasts harvest light and generate a proton electrochemical gradient (proton motive force) that drives the production of ATP needed for carbon dioxide fixation and plant growth. Mitochondria, bacteria and archaea generate proton motive force to energize growth and other physiologies. Energy transducing membranes are at the heart of proton bioenergetics and are responsible for catalyzing the conversion of energy held in high-energy electrons→electron transport chain→proton motive force→ATP. Whereas the electron transport chain is understood in great detail there are major gaps in understanding mechanisms of proton transfer or circulation during proton bioenergetics. This paper is built on the proposition that phospho- and glyco-glycerolipids form proton transport circuitry at the membrane's surface. By this proposition, an emergent membrane property, termed the hyducton, confines active/unbound protons or hydronium ions to a region of low volume close to the membrane surface. In turn, a von Grotthuß mechanism rapidly moves proton substrate in accordance with nano-electrochemical poles on the membrane surface created by powerful proton pumps such as ATP synthase.
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Affiliation(s)
- Marcos Y Yoshinaga
- University of Bremen, MARUM - Center for Marine and Environmental Sciences, Germany.
| | - Matthias Y Kellermann
- University of California Santa Barbara - Department of Earth Science and Marine Science Institute, USA
| | - David L Valentine
- University of California Santa Barbara - Department of Earth Science and Marine Science Institute, USA
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Shimoshige H, Yamada T, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Usami R. Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt. Int J Syst Evol Microbiol 2013; 63:861-866. [DOI: 10.1099/ijs.0.037432-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaea, strains MGY-184T and MGY-205, were isolated from sea salt produced in Japan and rock salt imported from Bolivia, respectively. Both strains were pleomorphic, non-motile, Gram-negative and required more than 5 % (w/v) NaCl for growth, with optimum at 9–12 %, in the presence of 2 % (w/v) MgCl2 . 6H2O. In the presence of 18 % (w/v) MgCl2 . 6H2O, however, both strains showed growth even at 1.0 % (w/v) NaCl. Both strains possessed two 16S rRNA genes (rrnA and rrnB), and they revealed closest similarity to
Halobaculum gomorrense
JCM 9908T, the single species with a validly published name of the genus
Halobaculum
, with similarity of 97.8 %. The rrnA and rrnB genes of both strains were 100 % similar. The rrnA genes were 97.6 % similar to the rrnB genes in both strains. DNA G+C contents of strains MGY-184T and MGY-205 were 67.0 and 67.4 mol%, respectively. Polar lipid analysis revealed that the two strains contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester derived from C20C20 archaeol. The DNA–DNA hybridization value between the two strains was 70 % and both strains showed low levels of DNA–DNA relatedness (48–50 %) with
Halobaculum gomorrense
JCM 9908T. Physiological and biochemical characteristics allowed differentiation of strains MGY-184T and MGY-205 from
Halobaculum gomorrense
JCM 9908T. Therefore, strains MGY-184T and MGY-205 represent a novel species of the genus
Halobaculum
, for which the name Halobaculum magnesiiphilum sp. nov. is proposed; the type strain is MGY-184T ( = JCM 17821T = KCTC 4100T).
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Affiliation(s)
- Hirokazu Shimoshige
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Tomoaki Yamada
- Department of Biological Applied Chemistry, Graduate School of Engineering, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Hiroaki Minegishi
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Akinobu Echigo
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Masahiro Kamekura
- Halophiles Research Institute, 677-1 Shimizu, Noda, Chiba 278-0043, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ron Usami
- Graduate School of Interdisciplinary New Science, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
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Oren A. Life in Magnesium- and Calcium-Rich Hypersaline Environments: Salt Stress by Chaotropic Ions. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Lopez-Cortes A, Ochoa J. The biological significance of Halobacteria on nucleation and sodium chloride crystal growth. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0167-2991(99)80384-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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8
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In vitro spontaneous reorganization of Haloferax volcanii envelope material into geometrical forms. Arch Microbiol 1993. [DOI: 10.1007/bf00249132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Affiliation(s)
- P Messner
- Zentrum für Ultrastrukturforschung, Universität für Bodenkultur, Wien, Austria
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10
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Nature of the salt dependence of the envelope of a Dead Sea archaebacterium, Haloferax volcanii. Arch Microbiol 1991. [DOI: 10.1007/bf00249115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Rosenshine I, Tchelet R, Mevarech M. The mechanism of DNA transfer in the mating system of an archaebacterium. Science 1989; 245:1387-9. [PMID: 2818746 DOI: 10.1126/science.2818746] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The genetic transfer system in the extremely halophilic archaebacterium Halobacterium volcanii is the only archaebacterial mating system known. The mechanism of genetic transfer of this archaebacterium was studied by using the immobile plasmids pHV2 and pHV11 as cytoplasmic markers. It was found that the cytoplasms of the parental types do not mix during the mating process, that each parental type can serve both as a donor and as a recipient, and that cytoplasmic bridges, with dimensions of up to 2 micrometers long and 0.1 micrometer in diameter, were formed between the parental types. These bridges appear to be used for the transfer of DNA from one cell to another. If so, this archaebacterial mating system is different from both eubacterial conjugation and eukaryotic sexual cell fusion.
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Affiliation(s)
- I Rosenshine
- Department of Microbiology, Tel Aviv University, Ramat Aviv, Israel
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13
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Kessel M, Buhle EL, Cohen S, Aebi U. The cell wall structure of a magnesium-dependent halobacterium, Halobacterium volcanii CD-2, from the Dead Sea. JOURNAL OF ULTRASTRUCTURE AND MOLECULAR STRUCTURE RESEARCH 1988; 100:94-106. [PMID: 3209861 DOI: 10.1016/0889-1605(88)90062-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cell wall preparations from the magnesium-dependent halophilic bacterium, Halobacterium volcanii, were studied by high-resolution electron microscopy complemented with image analysis and processing. For ultrastructural studies, specimens were prepared by a variety of methods, including negative staining, and metal shadowing after air-drying, freeze-drying, or freeze-fracturing and etching. All methods revealed the cell wall to be composed of a near-hexagonal lattice of unit cells having a center-to-center spacing of 15.5 nm. While negatively stained samples yielded two types variably revealed the unit cell to be composed of six protomers surrounding a central mass depression. This low-resolution unit cell morphology appears very similar to that of other bacterial cell wall S-layers studied to date.
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Affiliation(s)
- M Kessel
- Department of Cell Biology and Anatomy, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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16
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Muriana FJG, Rodulfo JD, Alvarez-Ossorio MC, Relimpio AM. Influence of cations on the viability ofHalobacterium mediter-ranei cells. J Basic Microbiol 1988. [DOI: 10.1002/jobm.3620280711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Imhoff JF. Survival strategies of microorganisms in extreme saline environments. ADVANCES IN SPACE RESEARCH : THE OFFICIAL JOURNAL OF THE COMMITTEE ON SPACE RESEARCH (COSPAR) 1986; 6:299-306. [PMID: 11537834 DOI: 10.1016/0273-1177(86)90098-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Halophilic representatives are found in all main lines of evolutionary descendence of microbes: in archaebacteria, Gram-negative and Gram-positive eubacteria, and also in eucaryotes. In principle all halophilic microorganisms have to adapt their surface and membrane structures to their highly ionic environments. Concerning their intracellular compartment two different strategies have been developed: Inorganic ions are largely excluded in some microorganisms while such ions are actively accumulated in others. In particular the second group of organisms has to adapt the whole metabolic machinery to the highly ionic conditions of several molar salts, whereas in the first group only the outer surface of the cytoplasmic membrane and the extracytoplasmic structures are in contact with high concentrations of inorgainic ions. In this latter group, a variety of organic solutes is accumulated in response to increases of the salinity of the environment.
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Affiliation(s)
- J F Imhoff
- Institut fur Mikrobiologie der Universitat Bonn, FRG
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