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Wagner Mackenzie B, West AG, Waite DW, Lux CA, Douglas RG, Taylor MW, Biswas K. A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis. Front Cell Infect Microbiol 2020; 10:398. [PMID: 32850496 PMCID: PMC7423975 DOI: 10.3389/fcimb.2020.00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/29/2020] [Indexed: 01/07/2023] Open
Abstract
Human microbiome studies remain focused on bacteria, as they comprise the dominant component of the microbiota. Recent advances in sequencing technology and optimization of amplicon sequencing protocols have allowed the description of other members of the microbiome, including eukaryotes (fungi) and, most recently, archaea. There are no known human-associated archaeal pathogens. Their diversity and contribution to health and chronic respiratory diseases, such as chronic rhinosinusitis (CRS), are unknown. Patients with CRS suffer from long-term sinus infections, and while the microbiota is hypothesized to play a role in its pathogenesis, the exact mechanism is poorly understood. In this cross-sectional study, we applied a recently optimized protocol to describe the prevalence, diversity and abundance of archaea in swab samples from the middle meatus of 60 individuals with and without CRS. A nested PCR approach was used to amplify the archaeal 16S rRNA gene for sequencing, and bacterial and archaeal load (also based on 16S rRNA genes) were estimated using Droplet Digital™ PCR (ddPCR). A total of 16 archaeal amplicon sequence variants (ASVs) from the phyla Euryarchaeota and Thaumarchaeota were identified. Archaeal ASVs were detected in 7/60 individuals, independent of disease state, whereas bacterial ASVs were detected in 60/60. Bacteria were also significantly more abundant than archaea. The ddPCR method was more sensitive than amplicon sequencing at detecting archaeal DNA in samples. Phylogenetic trees were constructed to visualize the evolutionary relationships between archaeal ASVs, isolates and clones. ASVs were placed into phylogenetic clades containing an apparent paucity of human-associated reference sequences, revealing how little studied the human archaeome is. This is the largest study to date to examine the human respiratory-associated archaeome, and provides the first insights into the prevalence, diversity and abundance of archaea in the human sinuses.
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Affiliation(s)
| | - Annie G. West
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - David W. Waite
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Christian A. Lux
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Richard G. Douglas
- Department of Surgery, The University of Auckland, Auckland, New Zealand
| | - Michael W. Taylor
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kristi Biswas
- Department of Surgery, The University of Auckland, Auckland, New Zealand
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2
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Abstract
The cell wall of archaea, as of any other prokaryote, is surrounding the cell outside the cytoplasmic membrane and is mediating the interaction with the environment. In this regard, it can be involved in cell shape maintenance, protection against virus, heat, acidity or alkalinity. Throughout the formation of pore like structures, it can resemble a micro sieve and thereby enable or disable transport processes. In some cases, cell wall components can make up more than 10% of the whole cellular protein. So far, a great variety of different cell envelope structures and compounds have be found and described in detail. From all archaeal cell walls described so far, the most common structure is the S-layer. Other archaeal cell wall structures are pseudomurein, methanochondroitin, glutaminylglycan, sulfated heteropolysaccharides and protein sheaths and they are sometimes associated with additional proteins and protein complexes like the STABLE protease or the bindosome. Recent advances in electron microscopy also illustrated the presence of an outer(most) cellular membrane within several archaeal groups, comparable to the Gram-negative cell wall within bacteria. Each new cell wall structure that can be investigated in detail and that can be assigned with a specific function helps us to understand, how the earliest cells on earth might have looked like.
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Affiliation(s)
- Andreas Klingl
- Plant Development and Electron Microscopy, Department of Biology I, Biocenter LMU Munich, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany.
| | - Carolin Pickl
- Plant Development and Electron Microscopy, Department of Biology I, Biocenter LMU Munich, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jennifer Flechsler
- Plant Development and Electron Microscopy, Department of Biology I, Biocenter LMU Munich, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany
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3
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Goda S, Koga T, Yamashita K, Kuriura R, Ueda T. A novel carbohydrate-binding surface layer protein from the hyperthermophilic archaeon Pyrococcus horikoshii. Biosci Biotechnol Biochem 2018; 82:1327-1334. [PMID: 29629656 DOI: 10.1080/09168451.2018.1460571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In Archaea and Bacteria, surface layer (S-layer) proteins form the cell envelope and are involved in cell protection. In the present study, a putative S-layer protein was purified from the crude extract of Pyrococcus horikoshii using affinity chromatography. The S-layer gene was cloned and expressed in Escherichia coli. Isothermal titration calorimetry analyses showed that the S-layer protein bound N-acetylglucosamine and induced agglutination of the gram-positive bacterium Micrococcus lysodeikticus. The protein comprised a 21-mer structure, with a molecular mass of 1,340 kDa, as determined using small-angle X-ray scattering. This protein showed high thermal stability, with a midpoint of thermal denaturation of 79 °C in dynamic light scattering experiments. This is the first description of the carbohydrate-binding archaeal S-layer protein and its characteristics.
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Affiliation(s)
- Shuichiro Goda
- a Biomolecular Chemistry Laboratory, Graduate School of Engineering , Nagasaki University , Nagasaki , Japan
| | - Tomoyuki Koga
- a Biomolecular Chemistry Laboratory, Graduate School of Engineering , Nagasaki University , Nagasaki , Japan
| | - Kenichiro Yamashita
- a Biomolecular Chemistry Laboratory, Graduate School of Engineering , Nagasaki University , Nagasaki , Japan
| | - Ryo Kuriura
- a Biomolecular Chemistry Laboratory, Graduate School of Engineering , Nagasaki University , Nagasaki , Japan
| | - Toshifumi Ueda
- a Biomolecular Chemistry Laboratory, Graduate School of Engineering , Nagasaki University , Nagasaki , Japan
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4
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Bader M, Müller K, Foerstendorf H, Schmidt M, Simmons K, Swanson JS, Reed DT, Stumpf T, Cherkouk A. Comparative analysis of uranium bioassociation with halophilic bacteria and archaea. PLoS One 2018; 13:e0190953. [PMID: 29329319 PMCID: PMC5766140 DOI: 10.1371/journal.pone.0190953] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 12/23/2017] [Indexed: 11/18/2022] Open
Abstract
Rock salt represents a potential host rock formation for the final disposal of radioactive waste. The interactions between indigenous microorganisms and radionuclides, e.g. uranium, need to be investigated to better predict the influence of microorganisms on the safety assessment of the repository. Hence, the association process of uranium with two microorganisms isolated from rock salt was comparatively studied. Brachybacterium sp. G1, which was isolated from the German salt dome Gorleben, and Halobacterium noricense DSM15987T, were selected as examples of a moderately halophilic bacterium and an extremely halophilic archaeon, respectively. The microorganisms exhibited completely different association behaviors with uranium. While a pure biosorption process took place with Brachybacterium sp. G1 cells, a multistage association process occurred with the archaeon. In addition to batch experiments, in situ attenuated total reflection Fourier-transform infrared spectroscopy was applied to characterize the U(VI) interaction process. Biosorption was identified as the dominating process for Brachybacterium sp. G1 with this method. Carboxylic functionalities are the dominant interacting groups for the bacterium, whereas phosphoryl groups are also involved in U(VI) association by the archaeon H. noricense.
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Affiliation(s)
- Miriam Bader
- Helmholtz-Zentrum Dresden—Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - Katharina Müller
- Helmholtz-Zentrum Dresden—Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - Harald Foerstendorf
- Helmholtz-Zentrum Dresden—Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - Matthias Schmidt
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany
| | - Karen Simmons
- Los Alamos National Laboratory Carlsbad Operations, Repository Science and Operations, Carlsbad, New Mexico, United States of America
| | - Juliet S. Swanson
- Los Alamos National Laboratory Carlsbad Operations, Repository Science and Operations, Carlsbad, New Mexico, United States of America
| | - Donald T. Reed
- Los Alamos National Laboratory Carlsbad Operations, Repository Science and Operations, Carlsbad, New Mexico, United States of America
| | - Thorsten Stumpf
- Helmholtz-Zentrum Dresden—Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - Andrea Cherkouk
- Helmholtz-Zentrum Dresden—Rossendorf, Institute of Resource Ecology, Dresden, Germany
- * E-mail:
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5
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Microbial Diversity in Extreme Marine Habitats and Their Biomolecules. Microorganisms 2017; 5:microorganisms5020025. [PMID: 28509857 PMCID: PMC5488096 DOI: 10.3390/microorganisms5020025] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/02/2017] [Accepted: 05/11/2017] [Indexed: 11/17/2022] Open
Abstract
Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined. Thermophile, halophile, alkalophile, psychrophile, piezophile and polyextremophile microorganisms have been isolated from these marine environments; they proliferate thanks to adaptation strategies involving diverse cellular metabolic mechanisms. Therefore, a vast number of new biomolecules such as enzymes, polymers and osmolytes from the inhabitant microbial community of the sea have been studied, and there is a growing interest in the potential returns of several industrial production processes concerning the pharmaceutical, medical, environmental and food fields.
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6
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Bader M, Müller K, Foerstendorf H, Drobot B, Schmidt M, Musat N, Swanson JS, Reed DT, Stumpf T, Cherkouk A. Multistage bioassociation of uranium onto an extremely halophilic archaeon revealed by a unique combination of spectroscopic and microscopic techniques. JOURNAL OF HAZARDOUS MATERIALS 2017; 327:225-232. [PMID: 28081458 DOI: 10.1016/j.jhazmat.2016.12.053] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/09/2016] [Accepted: 12/26/2016] [Indexed: 06/06/2023]
Abstract
The interactions of two extremely halophilic archaea with uranium were investigated at high ionic strength as a function of time, pH and uranium concentration. Halobacterium noricense DSM-15987 and Halobacterium sp. putatively noricense, isolated from the Waste Isolation Pilot Plant repository, were used for these investigations. The kinetics of U(VI) bioassociation with both strains showed an atypical multistage behavior, meaning that after an initial phase of U(VI) sorption, an unexpected interim period of U(VI) release was observed, followed by a slow reassociation of uranium with the cells. By applying in situ attenuated total reflection Fourier-transform infrared spectroscopy, the involvement of phosphoryl and carboxylate groups in U(VI) complexation during the first biosorption phase was shown. Differences in cell morphology and uranium localization become visible at different stages of the bioassociation process, as shown with scanning electron microscopy in combination with energy dispersive X-ray spectroscopy. Our results demonstrate for the first time that association of uranium with the extremely halophilic archaeon is a multistage process, beginning with sorption and followed by another process, probably biomineralization.
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Affiliation(s)
- Miriam Bader
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Katharina Müller
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Harald Foerstendorf
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Björn Drobot
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Matthias Schmidt
- Helmholtz Centre for Environmental Research-UFZ, Department of Isotope Biogeochemistry, Permoserstraße 15, 04318 Leipzig, Germany
| | - Niculina Musat
- Helmholtz Centre for Environmental Research-UFZ, Department of Isotope Biogeochemistry, Permoserstraße 15, 04318 Leipzig, Germany
| | - Juliet S Swanson
- Los Alamos National Laboratory, Repository Science and Operations, 1400 University Drive, Carlsbad, NM, 88220, USA
| | - Donald T Reed
- Los Alamos National Laboratory, Repository Science and Operations, 1400 University Drive, Carlsbad, NM, 88220, USA
| | - Thorsten Stumpf
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Andrea Cherkouk
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany.
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7
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Liao Y, Williams TJ, Ye J, Charlesworth J, Burns BP, Poljak A, Raftery MJ, Cavicchioli R. Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi. Sci Rep 2016; 6:37454. [PMID: 27874045 PMCID: PMC5118699 DOI: 10.1038/srep37454] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/26/2016] [Indexed: 12/21/2022] Open
Abstract
Biofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures. Extracellular DNA was found to be critical to biofilms, with cell surface proteins and quorum sensing also implicated in biofilm formation. Quantitative proteomics was used to define pathways and cellular processes involved in forming biofilms; these included enhanced purine synthesis and specific cell surface proteins involved in DNA metabolism; post-translational modification of cell surface proteins; specific pathways of carbon metabolism involving acetyl-CoA; and specific responses to oxidative stress. The study provides a new level of understanding about the molecular mechanisms involved in biofilm formation of this important member of the Deep Lake community.
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Affiliation(s)
- Y Liao
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - T J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Ye
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia.,Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - B P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - A Poljak
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - M J Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - R Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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8
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An overview of siderophores for iron acquisition in microorganisms living in the extreme. Biometals 2016; 29:551-71. [PMID: 27457587 DOI: 10.1007/s10534-016-9949-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/08/2016] [Indexed: 12/11/2022]
Abstract
Siderophores are iron-chelating molecules produced by microbes when intracellular iron concentrations are low. Low iron triggers a cascade of gene activation, allowing the cell to survive due to the synthesis of important proteins involved in siderophore synthesis and transport. Generally, siderophores are classified by their functional groups as catecholates, hydroxamates and hydroxycarboxylates. Although other chemical structural modifications and functional groups can be found. The functional groups participate in the iron-chelating process when the ferri-siderophore complex is formed. Classified as acidophiles, alkaliphiles, halophiles, thermophiles, psychrophiles, piezophiles, extremophiles have particular iron requirements depending on the environmental conditions in where they grow. Most of the work done in siderophore production by extremophiles is based in siderophore concentration and/or genomic studies determining the presence of siderophore synthesis and transport genes. Siderophores produced by extremophiles are not well known and more work needs to be done to elucidate chemical structures and their role in microorganism survival and metal cycling in extreme environments.
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9
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The Confluence of Heavy Metal Biooxidation and Heavy Metal Resistance: Implications for Bioleaching by Extreme Thermoacidophiles. MINERALS 2015. [DOI: 10.3390/min5030397] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Perras AK, Daum B, Ziegler C, Takahashi LK, Ahmed M, Wanner G, Klingl A, Leitinger G, Kolb-Lenz D, Gribaldo S, Auerbach A, Mora M, Probst AJ, Bellack A, Moissl-Eichinger C. S-layers at second glance? Altiarchaeal grappling hooks (hami) resemble archaeal S-layer proteins in structure and sequence. Front Microbiol 2015; 6:543. [PMID: 26106369 PMCID: PMC4460559 DOI: 10.3389/fmicb.2015.00543] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/17/2015] [Indexed: 01/02/2023] Open
Abstract
The uncultivated “Candidatus Altiarchaeum hamiconexum” (formerly known as SM1 Euryarchaeon) carries highly specialized nano-grappling hooks (“hami”) on its cell surface. Until now little is known about the major protein forming these structured fibrous cell surface appendages, the genes involved or membrane anchoring of these filaments. These aspects were analyzed in depth in this study using environmental transcriptomics combined with imaging methods. Since a laboratory culture of this archaeon is not yet available, natural biofilm samples with high Ca. A. hamiconexum abundance were used for the entire analyses. The filamentous surface appendages spanned both membranes of the cell, which are composed of glycosyl-archaeol. The hami consisted of multiple copies of the same protein, the corresponding gene of which was identified via metagenome-mapped transcriptome analysis. The hamus subunit proteins, which are likely to self-assemble due to their predicted beta sheet topology, revealed no similiarity to known microbial flagella-, archaella-, fimbriae- or pili-proteins, but a high similarity to known S-layer proteins of the archaeal domain at their N-terminal region (44–47% identity). Our results provide new insights into the structure of the unique hami and their major protein and indicate their divergent evolution with S-layer proteins.
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Affiliation(s)
- Alexandra K Perras
- Department of Internal Medicine, Medical University of Graz Graz, Austria ; Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Bertram Daum
- Department of Structural Biology, Max Planck Institute of Biophysics Frankfurt, Germany
| | - Christine Ziegler
- Department of Biophysics, University of Regensburg Regensburg, Germany
| | - Lynelle K Takahashi
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Musahid Ahmed
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Gerhard Wanner
- Faculty of Biology, Ludwig-Maximilians-University of Munich Munich, Germany
| | - Andreas Klingl
- Faculty of Biology, Ludwig-Maximilians-University of Munich Munich, Germany
| | - Gerd Leitinger
- Research Unit Electron Microscopic Techniques, Institute of Cell Biology, Histology and Embryology, Medical University of Graz Graz, Austria
| | - Dagmar Kolb-Lenz
- Institute of Cell Biology, Histology and Embryology, Medical University of Graz Graz, Austria ; Core Facility Ultrastructure, Analysis, Center for Medical Research Institute, Medical University of Graz Graz, Austria
| | - Simonetta Gribaldo
- Unité Biologie Moléculaire du Gene chez les Extrêmophiles, Departément de Microbiologie, Institut Pasteur Paris, France
| | - Anna Auerbach
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Maximilian Mora
- Department of Internal Medicine, Medical University of Graz Graz, Austria
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley Berkeley, CA, USA
| | - Annett Bellack
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz Graz, Austria ; Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany ; BioTechMed-Graz Graz, Austria
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11
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Marine extremophiles: a source of hydrolases for biotechnological applications. Mar Drugs 2015; 13:1925-65. [PMID: 25854643 PMCID: PMC4413194 DOI: 10.3390/md13041925] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/22/2015] [Accepted: 03/25/2015] [Indexed: 12/26/2022] Open
Abstract
The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons. Extremozymes are adapted to work in harsh physical-chemical conditions and their use in various industrial applications such as the biofuel, pharmaceutical, fine chemicals and food industries has increased. The understanding of the specific factors that confer the ability to withstand extreme habitats on such enzymes has become a priority for their biotechnological use. The most studied marine extremophiles are prokaryotes and in this review, we present the most studied archaea and bacteria extremophiles and their hydrolases, and discuss their use for industrial applications.
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12
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Leon DR, Ytterberg AJ, Boontheung P, Kim U, Loo JA, Gunsalus RP, Ogorzalek Loo RR. Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1. Front Microbiol 2015; 6:149. [PMID: 25798134 PMCID: PMC4350412 DOI: 10.3389/fmicb.2015.00149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 02/09/2015] [Indexed: 12/11/2022] Open
Abstract
Proteomic tools identify constituents of complex mixtures, often delivering long lists of identified proteins. The high-throughput methods excel at matching tandem mass spectrometry data to spectra predicted from sequence databases. Unassigned mass spectra are ignored, but could, in principle, provide valuable information on unanticipated modifications and improve protein annotations while consuming limited quantities of material. Strategies to "mine" information from these discards are presented, along with discussion of features that, when present, provide strong support for modifications. In this study we mined LC-MS/MS datasets of proteolytically-digested concanavalin A pull down fractions from Methanosarcina mazei Gö1 cell lysates. Analyses identified 154 proteins. Many of the observed proteins displayed post-translationally modified forms, including O-formylated and methyl-esterified segments that appear biologically relevant (i.e., not artifacts of sample handling). Interesting cleavages and modifications (e.g., S-cyanylation and trimethylation) were observed near catalytic sites of methanogenesis enzymes. Of 31 Methanosarcina protein N-termini recovered by concanavalin A binding or from a previous study, only M. mazei S-layer protein MM1976 and its M. acetivorans C2A orthologue, MA0829, underwent signal peptide excision. Experimental results contrast with predictions from algorithms SignalP 3.0 and Exprot, which were found to over-predict the presence of signal peptides. Proteins MM0002, MM0716, MM1364, and MM1976 were found to be glycosylated, and employing chromatography tailored specifically for glycopeptides will likely reveal more. This study supplements limited, existing experimental datasets of mature archaeal N-termini, including presence or absence of signal peptides, translation initiation sites, and other processing. Methanosarcina surface and membrane proteins are richly modified.
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Affiliation(s)
- Deborah R Leon
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles, CA, USA
| | - A Jimmy Ytterberg
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles, CA, USA
| | - Pinmanee Boontheung
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles, CA, USA
| | - Unmi Kim
- Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles Los Angeles, CA, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles, CA, USA ; Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles Los Angeles, CA, USA ; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles Los Angeles, CA, USA
| | - Robert P Gunsalus
- Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles Los Angeles, CA, USA ; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles Los Angeles, CA, USA
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles Los Angeles, CA, USA ; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles Los Angeles, CA, USA
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13
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Giménez MI, Cerletti M, De Castro RE. Archaeal membrane-associated proteases: insights on Haloferax volcanii and other haloarchaea. Front Microbiol 2015; 6:39. [PMID: 25774151 PMCID: PMC4343526 DOI: 10.3389/fmicb.2015.00039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/12/2015] [Indexed: 11/17/2022] Open
Abstract
The function of membrane proteases range from general house-keeping to regulation of cellular processes. Although the biological role of these enzymes in archaea is poorly understood, some of them are implicated in the biogenesis of the archaeal cell envelope and surface structures. The membrane-bound ATP-dependent Lon protease is essential for cell viability and affects membrane carotenoid content in Haloferax volcanii. At least two different proteases are needed in this archaeon to accomplish the posttranslational modifications of the S-layer glycoprotein. The rhomboid protease RhoII is involved in the N-glycosylation of the S-layer protein with a sulfoquinovose-containing oligosaccharide while archaeosortase ArtA mediates the proteolytic processing coupled-lipid modification of this glycoprotein facilitating its attachment to the archaeal cell surface. Interestingly, two different signal peptidase I homologs exist in H. volcanii, Sec11a and Sec11b, which likely play distinct physiological roles. Type IV prepilin peptidase PibD processes flagellin/pilin precursors, being essential for the biogenesis and function of the archaellum and other cell surface structures in H. volcanii.
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Affiliation(s)
- María I Giménez
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas Mar del Plata, Argentina
| | - Micaela Cerletti
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas Mar del Plata, Argentina
| | - Rosana E De Castro
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas Mar del Plata, Argentina
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Kandiba L, Eichler J. Archaeal S-layer glycoproteins: post-translational modification in the face of extremes. Front Microbiol 2014; 5:661. [PMID: 25505464 PMCID: PMC4245038 DOI: 10.3389/fmicb.2014.00661] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/14/2014] [Indexed: 11/29/2022] Open
Abstract
Corresponding to the sole or basic component of the surface (S)-layer surrounding the archaeal cell in most known cases, S-layer glycoproteins are in direct contact with the harsh environments that characterize niches where Archaea can thrive. Accordingly, early work examining archaeal S-layer glycoproteins focused on identifying those properties that allow members of this group of proteins to maintain their structural integrity in the face of extremes of temperature, pH, and salinity, as well as other physical challenges. However, with expansion of the list of archaeal strains serving as model systems, as well as growth in the number of molecular tools available for the manipulation of these strains, studies on archaeal S-layer glycoproteins are currently more likely to consider the various post-translational modifications these polypeptides undergo. For instance, archaeal S-layer glycoproteins can undergo proteolytic cleavage, both N- and O-glycosylation, lipid-modification and oligomerization. In this mini-review, recent findings related to the post-translational modification of archaeal S-layer glycoproteins are considered.
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Affiliation(s)
- Lina Kandiba
- Department of Life Sciences, Ben Gurion University of the Negev , Beersheva, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev , Beersheva, Israel
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15
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Klingl A. S-layer and cytoplasmic membrane - exceptions from the typical archaeal cell wall with a focus on double membranes. Front Microbiol 2014; 5:624. [PMID: 25505452 PMCID: PMC4243693 DOI: 10.3389/fmicb.2014.00624] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 10/31/2014] [Indexed: 11/13/2022] Open
Abstract
The common idea of typical cell wall architecture in archaea consists of a pseudo-crystalline proteinaceous surface layer (S-layer), situated upon the cytoplasmic membrane. This is true for the majority of described archaea, hitherto. Within the crenarchaea, the S-layer often represents the only cell wall component, but there are various exceptions from this wall architecture. Beside (glycosylated) S-layers in (hyper)thermophilic cren- and euryarchaea as well as halophilic archaea, one can find a great variety of other cell wall structures like proteoglycan-like S-layers (Halobacteria), glutaminylglycan (Natronococci), methanochondroitin (Methanosarcina) or double layered cell walls with pseudomurein (Methanothermus and Methanopyrus). The presence of an outermost cellular membrane in the crenarchaeal species Ignicoccus hospitalis already gave indications for an outer membrane similar to Gram-negative bacteria. Although there is just limited data concerning their biochemistry and ultrastructure, recent studies on the euryarchaeal methanogen Methanomassiliicoccus luminyensis, cells of the ARMAN group, and the SM1 euryarchaeon delivered further examples for this exceptional cell envelope type consisting of two membranes.
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Affiliation(s)
- Andreas Klingl
- Plant Development, Department of Biology, Biocenter LMU Munich - Botany, Ludwig Maximilian University Munich Munich, Germany
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16
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Stieglmeier M, Klingl A, Alves RJE, Rittmann SKMR, Melcher M, Leisch N, Schleper C. Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota. Int J Syst Evol Microbiol 2014; 64:2738-2752. [PMID: 24907263 PMCID: PMC4129164 DOI: 10.1099/ijs.0.063172-0] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A mesophilic, neutrophilic and aerobic, ammonia-oxidizing archaeon, strain EN76(T), was isolated from garden soil in Vienna (Austria). Cells were irregular cocci with a diameter of 0.6-0.9 µm and possessed archaella and archaeal pili as cell appendages. Electron microscopy also indicated clearly discernible areas of high and low electron density, as well as tubule-like structures. Strain EN76(T) had an S-layer with p3 symmetry, so far only reported for members of the Sulfolobales. Crenarchaeol was the major core lipid. The organism gained energy by oxidizing ammonia to nitrite aerobically, thereby fixing CO2, but growth depended on the addition of small amounts of organic acids. The optimal growth temperature was 42 °C and the optimal pH was 7.5, with ammonium and pyruvate concentrations of 2.6 and 1 mM, respectively. The genome of strain EN76(T) had a DNA G+C content of 52.7 mol%. Phylogenetic analyses of 16S rRNA genes showed that strain EN76(T) is affiliated with the recently proposed phylum Thaumarchaeota, sharing 85% 16S rRNA gene sequence identity with the closest cultivated relative 'Candidatus Nitrosopumilus maritimus' SCM1, a marine ammonia-oxidizing archaeon, and a maximum of 81% 16S rRNA gene sequence identity with members of the phyla Crenarchaeota and Euryarchaeota and any of the other recently proposed phyla (e.g. 'Korarchaeota' and 'Aigarchaeota'). We propose the name Nitrososphaera viennensis gen. nov., sp. nov. to accommodate strain EN76(T). The type strain of Nitrososphaera viennensis is strain EN76(T) ( = DSM 26422(T) = JMC 19564(T)). Additionally, we propose the family Nitrososphaeraceae fam. nov., the order Nitrososphaerales ord. nov. and the class Nitrososphaeria classis nov.
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Affiliation(s)
- Michaela Stieglmeier
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstr. 14, 1090 Vienna, Austria
| | - Andreas Klingl
- Cell Biology and LOEWE Research Centre for Synthetic Microbiology (Synmikro), Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Ricardo J. E. Alves
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstr. 14, 1090 Vienna, Austria
| | - Simon K.-M. R. Rittmann
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstr. 14, 1090 Vienna, Austria
| | - Michael Melcher
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstr. 14, 1090 Vienna, Austria
| | - Nikolaus Leisch
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstr. 14, 1090 Vienna, Austria
| | - Christa Schleper
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstr. 14, 1090 Vienna, Austria
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17
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General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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19
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Sanapala SR, Kulkarni SS. Chemical synthesis of asparagine-linked archaeal N-glycan from Methanothermus fervidus. Chemistry 2014; 20:3578-83. [PMID: 24616211 DOI: 10.1002/chem.201304950] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/02/2014] [Indexed: 12/12/2022]
Abstract
Several N-linked glycoproteins have been identified in archaea and there is growing evidence that the N-glycan is involved in survival and functioning of archaea in extreme conditions. Chemical synthesis of the archaeal N-glycans represents a crucial step towards understanding the putative function of protein glycosylation in archaea. Herein the first total synthesis of the archaeal L-asparagine linked hexasaccharide from Methanothermus fervidus is reported using a highly convergent [3+3] glycosylation approach in high overall yields. The synthesis relies on efficient preparation of regioselectively protected thioglycoside building blocks for orthogonal glycosylations and late stage N-aspartylation.
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Affiliation(s)
- Someswara Rao Sanapala
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 (India)
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20
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Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea. ISME JOURNAL 2014; 8:1645-58. [PMID: 24553470 DOI: 10.1038/ismej.2014.18] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/29/2013] [Accepted: 01/17/2014] [Indexed: 11/08/2022]
Abstract
Deep Lake in Antarctica is a cold, hypersaline system where four types of haloarchaea representing distinct genera comprise >70% of the lake community: strain tADL ∼44%, strain DL31 ∼18%, Halorubrum lacusprofundi ∼10% and strain DL1 ∼0.3%. By performing comparative genomics, growth substrate assays, and analyses of distribution by lake depth, size partitioning and lake nutrient composition, we were able to infer important metabolic traits and ecophysiological characteristics of the four Antarctic haloarchaea that contribute to their hierarchical persistence and coexistence in Deep Lake. tADL is characterized by a capacity for motility via flagella (archaella) and gas vesicles, a highly saccharolytic metabolism, a preference for glycerol, and photoheterotrophic growth. In contrast, DL31 has a metabolism specialized in processing proteins and peptides, and appears to prefer an association with particulate organic matter, while lacking the genomic potential for motility. H. lacusprofundi is the least specialized, displaying a genomic potential for the utilization of diverse organic substrates. The least abundant species, DL1, is characterized by a preference for catabolism of amino acids, and is the only one species that lacks genes needed for glycerol degradation. Despite the four haloarchaea being distributed throughout the water column, our analyses describe a range of distinctive features, including preferences for substrates that are indicative of ecological niche partitioning. The individual characteristics could be responsible for shaping the composition of the haloarchaeal community throughout the lake by enabling selection of ecotypes and maintaining sympatric speciation.
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21
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Balonova L, Hernychova L, Bilkova Z. Bioanalytical tools for the discovery of eukaryotic glycoproteins applied to the analysis of bacterial glycoproteins. Expert Rev Proteomics 2014; 6:75-85. [DOI: 10.1586/14789450.6.1.75] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Orange F, Disnar JR, Gautret P, Westall F, Bienvenu N, Lottier N, Prieur D. Preservation and evolution of organic matter during experimental fossilisation of the hyperthermophilic archaea Methanocaldococcus jannaschii. ORIGINS LIFE EVOL B 2012; 42:587-609. [PMID: 23254852 DOI: 10.1007/s11084-012-9318-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/06/2012] [Indexed: 10/27/2022]
Abstract
Identification of the earliest traces of life is made difficult by the scarcity of the preserved microbial remains and by the alteration and potential contamination of the organic matter (OM) content of rocks. These factors can confuse interpretations of the biogenicity and syngenicity of fossilised structures and organic molecules found in ancient rocks. In order to improve our knowledge of the fossilisation processes and their effects at the molecular level, we made a preliminary study of the fate of OM during experimental fossilisation. Changes in the composition and quantity of amino acids, monosaccharides and fatty acids were followed with HPLC, GC and GC-MS analyses during 1 year of silicification of the hyperthermophilic Archaea Methanocaldococcus jannaschii. Although the cells themselves did not fossilise and the accompanying extracellular polymeric substances (EPS) did, our analyses showed that the OM initially present in both cells and EPS was uniformly preserved in the precipitated silica, with amino acids and fatty acids being the best preserved compounds. This study thus completes previous data obtained by electron microscopy investigations of simulated microbial fossilisation and can help better identification and interpretation of microbial biosignatures in both ancient rocks and in recent hydrothermal formations and sediments.
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Affiliation(s)
- François Orange
- Centre de Biophysique Moléculaire - UPR 4301, CNRS, Rue Charles Sadron, 45071, Orléans Cedex 2, France.
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23
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Lipid modification gives rise to two distinct Haloferax volcanii S-layer glycoprotein populations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012. [PMID: 23201543 DOI: 10.1016/j.bbamem.2012.11.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The S-layer glycoprotein is the sole component of the protein shell surrounding Haloferax volcanii cells. The deduced amino acid sequence of the S-layer glycoprotein predicts the presence of a C-terminal membrane-spanning domain. However, several earlier observations, including the ability of EDTA to selectively solubilize the protein, are inconsistent with the presence of a trans-membrane sequence. In the present report, sequential solubilization of the S-layer glycoprotein by EDTA and then with detergent revealed the existence of two distinct populations of the S-layer glycoprotein. Whereas both S-layer glycoprotein populations underwent signal peptide cleavage and N-glycosylation, base hydrolysis followed by mass spectrometry revealed that a lipid, likely archaetidic acid, modified only the EDTA-solubilized version of the protein. These observations are consistent with the S-layer glycoprotein being initially synthesized as an integral membrane protein and subsequently undergoing a processing event in which the extracellular portion of the protein is separated from the membrane-spanning domain and transferred to a waiting lipid moiety.
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24
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Cai L, Zhao D, Hou J, Wu J, Cai S, Dassarma P, Xiang H. Cellular and organellar membrane-associated proteins in haloarchaea: Perspectives on the physiological significance and biotechnological applications. SCIENCE CHINA-LIFE SCIENCES 2012; 55:404-14. [DOI: 10.1007/s11427-012-4321-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 04/15/2012] [Indexed: 11/24/2022]
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25
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Klein R, Rössler N, Iro M, Scholz H, Witte A. Haloarchaeal myovirus φCh1 harbours a phase variation system for the production of protein variants with distinct cell surface adhesion specificities. Mol Microbiol 2011; 83:137-50. [PMID: 22111759 DOI: 10.1111/j.1365-2958.2011.07921.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The φCh1 myovirus, which infects the haloalkaliphilic archaeon Natrialba magadii, contains an invertible region that comprises the convergent open reading frames (ORFs) 34 and 36, which code for the putative tail fibre proteins gp34 and gp36 respectively. The inversion leads to an exchange of the C-termini of these proteins, thereby creating different types of tail fibres. Gene expression experiments revealed that only ORF34 is transcribed, indicating that φCh1 produces tail fibre proteins exclusively from this particular ORF. Only one of the two types of tail fibres encoded by ORF34 is able to bind to Nab. magadii in vitro. This is reflected by the observation that during the early phases of the infection cycle, the lysogenic strain L11 carries its invertible region exclusively in the orientation that produces that specific type of tail fibre. Obviously, Nab. magadii can only be infected by viruses carrying this particular type of tail fibre. By mutational analysis, the binding domain of gp34 was localized to the C-terminal part of the protein, particularly to a galactose-binding domain. The involvement of galactose residues in cell adhesion was supported by the observation that the addition of α-D-galactose to purified gp34 or whole virions prevented their attachment to Nab. magadii.
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Affiliation(s)
- R Klein
- Children's Cancer Research Institute, Department of Molecular Microbiology, Vienna, Austria
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26
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Murein and pseudomurein cell wall binding domains of bacteria and archaea--a comparative view. Appl Microbiol Biotechnol 2011; 92:921-8. [PMID: 22012341 PMCID: PMC3210951 DOI: 10.1007/s00253-011-3637-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 09/29/2011] [Accepted: 10/07/2011] [Indexed: 02/02/2023]
Abstract
The cell wall, a major barrier protecting cells from their environment, is an essential compartment of both bacteria and archaea. It protects the organism from internal turgor pressure and gives a defined shape to the cell. The cell wall serves also as an anchoring surface for various proteins and acts as an adhesion platform for bacteriophages. The walls of bacteria and archaea are mostly composed of murein and pseudomurein, respectively. Cell wall binding domains play a crucial role in the non-covalent attachment of proteins to cell walls. Here, we give an overview of the similarities and differences in the biochemical and functional properties of the two major murein and pseudomurein cell wall binding domains, i.e., the Lysin Motif (LysM) domain (Pfam PF01476) and the pseudomurein binding (PMB) domain (Pfam PF09373) of bacteria and archaea, respectively.
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27
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Klevenhusen F, Meile L, Kreuzer M, Soliva CR. Effects of monolaurin on ruminal methanogens and selected bacterial species from cattle, as determined with the rumen simulation technique. Anaerobe 2011; 17:232-8. [PMID: 21787874 DOI: 10.1016/j.anaerobe.2011.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 06/02/2011] [Accepted: 07/05/2011] [Indexed: 11/30/2022]
Abstract
Before being able to implement effective ruminal methane mitigation strategies via feed supplementation, the assessment of side effects on ruminal fermentation and rumen microbial populations is indispensable. In this respect we investigated the effects of monolaurin, a methane-mitigating lipid, on methanogens and important carbohydrate-degrading bacteria present in ruminal fluid of dairy cattle in continuous culture employing the rumen simulation technique. In six experimental runs, each lasting for 10 days, four diets with different carbohydrate composition, based on hay, maize, wheat and a maize-wheat mixture, either remained non-supplemented or were supplemented with monolaurin and incubated in a ruminal-fluid buffer mixture. Incubation liquid samples from days 6 to 10 of incubation were analyzed with relative quantitative polymerase chain reaction (qPCR) of 16S rRNA genes to assess monolaurin-induced shifts in specific rumen microbial populations in relation to the corresponding non-supplemented diets. Monolaurin completely inhibited Fibrobacter succinogenes in all diets while the response of the other cellulolytic bacteria varied in dependence of the diet. Megasphaera elsdenii remained unaffected by monolaurin in the two diets containing maize, but was slightly stimulated by monolaurin with the wheat and largely with the hay diet. The supply of monolaurin suppressed Methanomicrobiales below the detection limit with all diets, whereas relative 16S rRNA gene copy numbers of Methanobacteriales increased by 7-fold with monolaurin in case of the hay diet. Total Archaea were decreased by up to over 90%, but this was significant only for the wheat containing diets. Thus, monolaurin exerted variable effects mediated by unknown mechanisms on important ruminal microbes involved in carbohydrate degradation, along with its suppression of methane formation. The applicability of monolaurin for methane mitigation in ruminants thus depends on the extent to which adverse effects on carbohydrate-degrading bacteria actually impair the supply of digested carbohydrates to the animal.
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28
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Analysis of the surface proteins of Acidithiobacillus ferrooxidans strain SP5/1 and the new, pyrite-oxidizing Acidithiobacillus isolate HV2/2, and their possible involvement in pyrite oxidation. Arch Microbiol 2011; 193:867-82. [PMID: 21698546 DOI: 10.1007/s00203-011-0720-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 05/05/2011] [Accepted: 05/07/2011] [Indexed: 10/18/2022]
Abstract
Two strains of rod-shaped, pyrite-oxidizing acidithiobacilli, their cell envelope structure and their interaction with pyrite were investigated in this study. Cells of both strains, Acidithiobacillus ferrooxidans strain SP5/1 and the moderately thermophilic Acidithiobacillus sp. strain HV2/2, were similar in size, with slight variations in length and diameter. Two kinds of cell appendages were observed: flagella and pili. Besides a typical Gram-negative cell architecture with inner and outer membrane, enclosing a periplasm, both strains were covered by a hitherto undescribed, regularly arranged 2-D protein crystal with p2-symmetry. In A. ferrooxidans, this protein forms a stripe-like structure on the surface. A similar surface pattern with almost identical lattice vectors was also seen on the cells of strain HV2/2. For the surface layer of both bacteria, a direct contact to pyrite crystals was observed in ultrathin sections, indicating that the S-layer is involved in maintaining this contact site. Observations on an S-layer-deficient strain show, however, that cell adhesion does not strictly depend on the presence of the S-layer and that this surface protein has an influence on cell shape. Furthermore, the presented data suggest the ability of the S-layer protein to complex Fe3+ ions, suggesting a role in the physiology of the microorganisms.
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29
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Reitz T, Merroun M, Rossberg A, Selenska-Pobell S. Interactions of Sulfolobus acidocaldarius with uranium. RADIOCHIM ACTA 2010. [DOI: 10.1524/ract.2010.1716] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
Interactions of the acidothermophilic archaeon Sulfolobus acidocaldarius DSM 639 with U(VI) were studied by using a combination of batch experiments, X-ray absorption spectroscopy (XAS), and time-resolved laser-induced fluorescence spectroscopy (TRLFS). We demonstrated that at pH 2 this archaeal strain possesses a low tolerance to U(VI) and that its growth is limited to a uranium concentration below 1.1 mM. At similarly high acidic conditions (pH 1.5 and 3.0), covering the physiological pH growth optimum of S. acidocaldarius, at which U(VI) is soluble and highly toxic, rapid accumulation of the radionuclide by the cells of the strain occurred. About half of the uranium binding capacity was reached by the strain after an incubation of five minutes and nearly total saturation of the binding sites was achieved after 30 min. Both, EXAFS- and TRLF-spectroscopic analyses showed that the accumulated U(VI) was complexed mainly through organic phosphate groups. The EXAFS measurements revealed that U(VI) is coordinated to the organic phosphate ligands of the archaeal cells in a monodentate binding mode with an average U–P bond distance of 3.60±0.02 Å.
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Affiliation(s)
| | - Mohamed Merroun
- Forschungszentrum Dresden-Rossendorf, Institute of Radiochemistry, Dresden, Deutschland
| | - Andre Rossberg
- Forschungszentrum Rossendorf, Institute of Radiochemistry, Dresden, Deutschland
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30
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Maita N, Nyirenda J, Igura M, Kamishikiryo J, Kohda D. Comparative structural biology of eubacterial and archaeal oligosaccharyltransferases. J Biol Chem 2010; 285:4941-50. [PMID: 20007322 PMCID: PMC2836098 DOI: 10.1074/jbc.m109.081752] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 11/18/2009] [Indexed: 11/06/2022] Open
Abstract
Oligosaccharyltransferase (OST) catalyzes the transfer of an oligosaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains. In the bacterium Campylobacter jejuni, a single-subunit membrane protein, PglB, catalyzes N-glycosylation. We report the 2.8 A resolution crystal structure of the C-terminal globular domain of PglB and its comparison with the previously determined structure from the archaeon Pyrococcus AglB. The two distantly related oligosaccharyltransferases share unexpected structural similarity beyond that expected from the sequence comparison. The common architecture of the putative catalytic sites revealed a new catalytic motif in PglB. Site-directed mutagenesis analyses confirmed the contribution of this motif to the catalytic function. Bacterial PglB and archaeal AglB constitute a protein family of the catalytic subunit of OST along with STT3 from eukaryotes. A structure-aided multiple sequence alignment of the STT3/PglB/AglB protein family revealed three types of OST catalytic centers. This novel classification will provide a useful framework for understanding the enzymatic properties of the OST enzymes from Eukarya, Archaea, and Bacteria.
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Affiliation(s)
- Nobuo Maita
- From the Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - James Nyirenda
- From the Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mayumi Igura
- From the Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Jun Kamishikiryo
- From the Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daisuke Kohda
- From the Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
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31
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Ferguson JT, Wenger CD, Metcalf WW, Kelleher NL. Top-down proteomics reveals novel protein forms expressed in Methanosarcina acetivorans. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1743-50. [PMID: 19577935 PMCID: PMC2832193 DOI: 10.1016/j.jasms.2009.05.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 04/29/2009] [Accepted: 05/23/2009] [Indexed: 05/12/2023]
Abstract
Using both automated nanospray and online liquid chromatography mass spectrometry LC-MS strategies, 99 proteins have been newly identified by top-down tandem mass spectrometry (MS/MS) in Methanosarcina acetivorans, the methanogen with the largest known genome [5.7 mega base pairs (Mb)] for an Archaeon. Because top-down MS/MS was used, 15 proteins were detected with mispredicted start sites along with an additional five from small open reading frames (SORFs). Beyond characterization of these more common discrepancies in genome annotation, one SORF resulted from a rare start codon (AUA) as the initiation site for translation of this protein. Also, a methylation on a 30S ribosomal protein (MA1259) was localized to Pro59-Val69, contrasting sharply from its homologue in Escherichia coli (rp S12) known to harbor an unusual beta-thiomethylated aspartic acid residue.
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Affiliation(s)
- Jonathan T Ferguson
- Department of Chemistry at University of Illinois at Urbana-Champaign, Urbana, Illinois 6180, USA
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Palmieri G, Cannio R, Fiume I, Rossi M, Pocsfalvi G. Outside the unusual cell wall of the hyperthermophilic archaeon Aeropyrum pernix K1. Mol Cell Proteomics 2009; 8:2570-81. [PMID: 19640852 DOI: 10.1074/mcp.m900012-mcp200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In contrast to the extensively studied eukaryal and bacterial protein secretion systems, comparatively less is known about how and which proteins cross the archaeal cell membrane. To identify secreted proteins of the hyperthermophilic archaeon Aeropyrum pernix K1 we used a proteomics approach to analyze the extracellular and cell surface protein fractions. The experimentally obtained data comprising 107 proteins were compared with the in silico predicted secretome. Because of the lack of signal peptide and cellular localization prediction tools specific for archaeal species, programs trained on eukaryotic and/or Gram-positive and Gram-negative bacterial signal peptide data sets were used. PSortB Gram-negative and Gram-positive analysis predicted 21 (1.2% of total ORFs) and 24 (1.4% of total ORFs) secreted proteins, respectively, from the entire A. pernix K1 proteome, 12 of which were experimentally identified in this work. Six additional proteins were predicted to follow non-classical secretion mechanisms using SecP algorithms. According to at least one of the two PSortB predictions, 48 proteins identified in the two fractions possess an unknown localization site. In addition, more than half of the proteins do not contain signal peptides recognized by current prediction programs. This suggests that known mechanisms only partly describe archaeal protein secretion. The most striking characteristic of the secretome was the high number of transport-related proteins identified from the ATP-binding cassette (ABC), tripartite ATP-independent periplasmic, ATPase, small conductance mechanosensitive ion channel (MscS), and dicarboxylate amino acid-cation symporter transporter families. In particular, identification of 21 solute-binding receptors of the ABC superfamily of the 24 predicted in silico confirms that ABC-mediated transport represents the most frequent strategy adopted by A. pernix for solute translocation across the cell membrane.
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Affiliation(s)
- Gianna Palmieri
- Institute of Protein Biochemistry-National Research Council, 80131 Naples, Italy
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Jones MB, Rosenberg JN, Betenbaugh MJ, Krag SS. Structure and synthesis of polyisoprenoids used in N-glycosylation across the three domains of life. Biochim Biophys Acta Gen Subj 2009; 1790:485-94. [PMID: 19348869 DOI: 10.1016/j.bbagen.2009.03.030] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 03/26/2009] [Accepted: 03/30/2009] [Indexed: 01/11/2023]
Abstract
N-linked protein glycosylation was originally thought to be specific to eukaryotes, but evidence of this post-translational modification has now been discovered across all domains of life: Eucarya, Bacteria, and Archaea. In all cases, the glycans are first assembled in a step-wise manner on a polyisoprenoid carrier lipid. At some stage of lipid-linked oligosaccharide synthesis, the glycan is flipped across a membrane. Subsequently, the completed glycan is transferred to specific asparagine residues on the protein of interest. Interestingly, though the N-glycosylation pathway seems to be conserved, the biosynthetic pathways of the polyisoprenoid carriers, the specific structures of the carriers, and the glycan residues added to the carriers vary widely. In this review we will elucidate how organisms in each basic domain of life synthesize the polyisoprenoids that they utilize for N-linked glycosylation and briefly discuss the subsequent modifications of the lipid to generate a lipid-linked oligosaccharide.
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Affiliation(s)
- Meredith B Jones
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Francoleon DR, Boontheung P, Yang Y, Kim U, Ytterberg AJ, Denny PA, Denny PC, Loo JA, Gunsalus RP, Ogorzalek Loo RR. S-layer, surface-accessible, and concanavalin A binding proteins of Methanosarcina acetivorans and Methanosarcina mazei. J Proteome Res 2009; 8:1972-82. [PMID: 19228054 PMCID: PMC2666069 DOI: 10.1021/pr800923e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The outermost cell envelope structure of many archaea and bacteria contains a proteinaceous lattice termed the surface layer or S-layer. It is typically composed of only one or two abundant, often posttranslationally modified proteins that self-assemble to form the highly organized arrays. Surprisingly, over 100 proteins were annotated to be S-layer components in the archaeal species Methanosarcina acetivorans C2A and Methanosarcina mazei Gö1, reflecting limitations of current predictions. An in vivo biotinylation methodology was devised to affinity tag surface-exposed proteins while overcoming unique challenges in working with these fragile organisms. Cells were adapted to growth under N2 fixing conditions, thus, minimizing free amines reactive to the NHS-label, and high pH media compatible with the acylation chemistry was used. A 3-phase separation procedure was employed to isolate intact, labeled cells from lysed-cell derived proteins. Streptavidin affinity enrichment followed by stringent wash conditions removed nonspecifically bound proteins. This methodology revealed S-layer proteins in M. acetivorans C2A and M. mazei Gö1 to be MA0829 and MM1976, respectively. Each was demonstrated to exist as multiple glycosylated forms using SDS-PAGE coupled with glycoprotein-specific staining, and by interaction with the lectin, Concanavalin A. A number of additional surface-exposed proteins and glycoproteins were identified and included all three subunits of the thermosome: the latter suggests that the chaperonin complex is both surface- and cytoplasmically localized. This approach provides an alternative strategy to study surface proteins in the archaea.
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Affiliation(s)
- Deborah R. Francoleon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Pinmanee Boontheung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Yanan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Unmi Kim
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
| | - A. Jimmy Ytterberg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Patricia A. Denny
- University of Southern California School of Dentistry, Los Angeles, CA 90089
| | - Paul C. Denny
- University of Southern California School of Dentistry, Los Angeles, CA 90089
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Robert P. Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
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Fendrihan S, Legat A, Pfaffenhuemer M, Gruber C, Weidler G, Gerbl F, Stan-Lotter H. Extremely halophilic archaea and the issue of long-term microbial survival. RE/VIEWS IN ENVIRONMENTAL SCIENCE AND BIO/TECHNOLOGY 2006; 5:203-218. [PMID: 21984879 PMCID: PMC3188376 DOI: 10.1007/s11157-006-0007-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Halophilic archaebacteria (haloarchaea) thrive in environments with salt concentrations approaching saturation, such as natural brines, the Dead Sea, alkaline salt lakes and marine solar salterns; they have also been isolated from rock salt of great geological age (195-250 million years). An overview of their taxonomy, including novel isolates from rock salt, is presented here; in addition, some of their unique characteristics and physiological adaptations to environments of low water activity are reviewed. The issue of extreme long-term microbial survival is considered and its implications for the search for extraterrestrial life. The development of detection methods for subterranean haloarchaea, which might also be applicable to samples from future missions to space, is presented.
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Affiliation(s)
- Sergiu Fendrihan
- Department of Microbiology, University of Salzburg, Billrothstr. 11, A-5020 Salzburg, Austria
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Claus H, Akça E, Debaerdemaeker T, Evrard C, Declercq JP, Harris JR, Schlott B, König H. Molecular organization of selected prokaryotic S-layer proteins. Can J Microbiol 2006; 51:731-43. [PMID: 16391651 DOI: 10.1139/w05-093] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Regular crystalline surface layers (S-layers) are widespread among prokaryotes and probably represent the earliest cell wall structures. S-layer genes have been found in approximately 400 different species of the prokaryotic domains bacteria and archaea. S-layers usually consist of a single (glyco-)protein species with molecular masses ranging from about 40 to 200 kDa that form lattices of oblique, tetragonal, or hexagonal architecture. The primary sequences of hyperthermophilic archaeal species exhibit some characteristic signatures. Further adaptations to their specific environments occur by various post-translational modifications, such as linkage of glycans, lipids, phosphate, and sulfate groups to the protein or by proteolytic processing. Specific domains direct the anchoring of the S-layer to the underlying cell wall components and transport across the cytoplasma membrane. In addition to their presumptive original role as protective coats in archaea and bacteria, they have adapted new functions, e.g., as molecular sieves, attachment sites for extracellular enzymes, and virulence factors.
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Affiliation(s)
- Harald Claus
- Institut für Mikrobiologie und Weinforschung, Johannes Gutenberg-Universität Mainz, Germany
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Ferrer M, Golyshina OV, Plou FJ, Timmis KN, Golyshin PN. A novel alpha-glucosidase from the acidophilic archaeon Ferroplasma acidiphilum strain Y with high transglycosylation activity and an unusual catalytic nucleophile. Biochem J 2006; 391:269-76. [PMID: 15954864 PMCID: PMC1276924 DOI: 10.1042/bj20050346] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ferroplasma acidiphilum strain Y (DSM 12658), a ferrous iron-oxidizing, acidophilic and mesophilic archaeon, was found to produce a membrane-bound alpha-glucosidase (alphaGluFa) showing no significant similarity to any of the known glycoside hydrolases classified in different families and having an unusual catalytic site consisting of a threonine and a histidine residue. The highest alpha-glucosidase activity was found at low pH, 2.4-3.5, and the substrate preference order was: sucrose>maltose>maltotriose >>maltotetraose>>malto-oligosaccharides from maltopentaose to maltoheptaose>>>soluble starch (kcat/K(m) was 293.0, 197.0, 18.8, 0.3 and 0.02 s(-1) x mM(-1) respectively). The enzyme was able to transfer glucosyl groups from maltose as donor, to produce exclusively maltotriose (up to 300 g/l). Chemical modification and electrospray ionization MS analysis of 5-fluoro-alpha-D-glucopyranosyl-enzyme derivatives, coupled with site-directed mutagenesis, strongly suggested that the putative catalytic nucleophile in this enzyme is Thr212. Iron was found to be essential for enzyme activity and integrity, and His390 was shown to be essential for iron binding. These results suggest that the metalloenzyme alphaGluFa is a new member of the glycosyl hydrolase family that uses a novel mechanism for sugar glycosylation and/or transglycosylation.
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Affiliation(s)
- Manuel Ferrer
- Department of Microbiology, German Research Centre for Biotechnology (GFB), Mascheroder Weg 1, 38124 Braunschweig, Germany.
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Merkl R. A comparative categorization of protein function encoded in bacterial or archeal genomic islands. J Mol Evol 2005; 62:1-14. [PMID: 16341468 DOI: 10.1007/s00239-004-0311-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Accepted: 06/14/2005] [Indexed: 01/11/2023]
Abstract
Genomes of prokaryotes harbor genomic islands (GIs), which are frequently acquired via horizontal gene transfer (HGT). Here I present an analysis of GIs with respect to gene-encoded functions. GIs were identified by statistical analysis of codon usage and clustering. Genes classified as putatively alien (pA) or putatively native (pN) were categorized according to the COG database. Among pA and pN genes, the distribution of COG functions and classes were studied for different groupings of prokaryotes. Groups were formed according to taxonomical relation or habitats. In all groups, genes related to class L (replication, recombination, and repair) were statistically significantly overrepresented in GIs. GIs of bacteria and archaea showed a distinct pattern of preferences. In archeal GIs, genes belonging to COG class M (cell wall/membrane/envelope biogenesis) or Q (secondary metabolites biosynthesis, transport, and catabolism) were more frequent. In bacterial GIs, genes of classes U (intracellular trafficking, secretion, and vesicular transport), N (cell motility), and V (defense mechanisms) were predominant. Underrepresentation was strongest for genes belonging to class J (translation, ribosomal structure, and biogenesis). Among single COG functions overrepresented in GIs were transferases and transporters. In both superkingdoms, HGT enhances genomic content by meeting demands that are independent of the studied habitats. These findings are in agreement with the complexity theory, which predicts the preferential import of operational genes. However, only specific subsets of operational genes were enriched in GIs. Modification of the cell envelope, cell motility, secretion, and protection of cellular DNA are major issues in HGT.
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Affiliation(s)
- Rainer Merkl
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany.
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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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Moissl C, Rachel R, Briegel A, Engelhardt H, Huber R. The unique structure of archaeal 'hami', highly complex cell appendages with nano-grappling hooks. Mol Microbiol 2005; 56:361-70. [PMID: 15813730 DOI: 10.1111/j.1365-2958.2005.04294.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Proteinaceous, hair-like appendages known as fimbriae or pili commonly extend from the surface of prokaryotic cells and serve important functions such as cell adhesion, biofilm formation, motility and DNA transfer. Here we show that a novel group of archaea from cold, sulphidic springs has developed cell surface appendages of an unexpectedly high complexity with a well-defined base-to-top organization. It represents a new class of filamentous cell appendages, for which the term 'hamus' is proposed. Each archaeal cell is surrounded by a halo of about 100 hami, which mediate strong adhesion of the cells to surfaces of different chemical composition. The hami are mainly composed of 120 kDa subunits and remained stable in a broad temperature and pH range (0-70 degrees C; 0.5-11.5). Electron microscopy and cryo-electron tomography revealed that the hamus filament possesses a helical basic structure. At periodic distances, three prickles emanate from the filament, giving it the character of industrially produced barbwire. At its distal end the hami carry a tripartite, barbed grappling hook (60 nm in diameter). The architecture of this molecular hook is reminiscent of man-made fishhooks, grapples and anchors. It appears that nature has developed a perfect mechanical nano-tool in the course of biological evolution, which also might prove useful in the field of nanobiotechnology.
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Affiliation(s)
- Christine Moissl
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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Voisin S, Houliston RS, Kelly J, Brisson JR, Watson D, Bardy SL, Jarrell KF, Logan SM. Identification and characterization of the unique N-linked glycan common to the flagellins and S-layer glycoprotein of Methanococcus voltae. J Biol Chem 2005; 280:16586-93. [PMID: 15723834 DOI: 10.1074/jbc.m500329200] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The flagellum of Methanococcus voltae is composed of four structural flagellin proteins FlaA, FlaB1, FlaB2, and FlaB3. These proteins possess a total of 15 potential N-linked sequons (NX(S/T)) and show a mass shift on an SDS-polyacrylamide gel indicating significant post-translational modification. We describe here the structural characterization of the flagellin glycan from M. voltae using mass spectrometry to examine the proteolytic digests of the flagellin proteins in combination with NMR analysis of the purified glycan using a sensitive, cryogenically cooled probe. Nano-liquid chromatography-tandem mass spectrometry analysis of the proteolytic digests of the flagellin proteins revealed that they are post-translationally modified with a novel N-linked trisaccharide of mass 779 Da that is composed of three sugar residues with masses of 318, 258, and 203 Da, respectively. In every instance the glycan is attached to the peptide through the asparagine residue of a typical N-linked sequon. The glycan modification has been observed on 14 of the 15 sequon sites present on the four flagellin structural proteins. The novel glycan structure elucidated by NMR analysis was shown to be a trisaccharide composed of beta-ManpNAcA6Thr-(1-4)-beta-Glc-pNAc3NAcA-(1-3)-beta-GlcpNAc linked to Asn. In addition, the same trisaccharide was identified on a tryptic peptide of the S-layer protein from this organism implicating a common N-linked glycosylation pathway.
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Affiliation(s)
- Sebastien Voisin
- Institute for Biological Sciences, National Research Council, Ottawa, Ontario K1A OR6, Canada
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Abstract
Extremophiles are organisms that can grow and thrive in harsh conditions, e.g., extremes of temperature, pH, salinity, radiation, pressure and oxygen tension. Thermophilic, halophilic and radiation-resistant organisms are all microbes, some of which are able to withstand multiple extremes. Psychrophiles, or cold-loving organisms, include not only microbes, but fish that live in polar waters and animals that can withstand freezing. Extremophiles are structurally adapted at a molecular level to withstand these conditions. Thermophiles have particularly stable proteins and cell membranes, psychrophiles have flexible cellular proteins and membranes and/or antifreeze proteins, salt-resistant halophiles contain compatible solutes or high concentrations of inorganic ions, and acidophiles and alkaliphiles are able to pump ions to keep their internal pH close to neutrality. Their interest to veterinary medicine resides in their capacity to be pathogenic, and as sources of enzymes and other molecules for diagnostic and pharmaceutical purposes. In particular, thermostable DNA polymerases are a mainstay of PCR-based diagnostics.
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Affiliation(s)
- Paul Messner
- Zentrum für NanoBiotechnologie, Universität für Bodenkultur Wien, A-1180 Vienna, Austria.
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