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Stöckl R, Nißl L, Reichelt R, Rachel R, Grohmann D, Grünberger F. The transcriptional regulator EarA and intergenic terminator sequences modulate archaellation in Pyrococcus furiosus. Front Microbiol 2023; 14:1241399. [PMID: 38029142 PMCID: PMC10665913 DOI: 10.3389/fmicb.2023.1241399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The regulation of archaellation, the formation of archaeal-specific cell appendages called archaella, is crucial for the motility, adhesion, and survival of archaeal organisms. Although the heavily archaellated and highly motile Pyrococcus furiosus is a key model organism for understanding the production and function of archaella in Euryarchaea, the transcriptional regulation of archaellum assembly is so far unknown. Here we show that the transcription factor EarA is the master regulator of the archaellum (arl) operon transcription, which is further modulated by intergenic transcription termination signals. EarA deletion or overexpression strains demonstrate that EarA is essential for archaellation in P. furiosus and governs the degree of archaellation. Providing a single-molecule update on the transcriptional landscape of the arl operon in P. furiosus, we identify sequence motifs for EarA binding upstream of the arl operon and intergenic terminator sequences as critical elements for fine-tuning the expression of the multicistronic arl cluster. Furthermore, transcriptome re-analysis across different Thermococcales species demonstrated a heterogeneous production of major archaellins, suggesting a more diverse composition of archaella than previously recognized. Overall, our study provides novel insights into the transcriptional regulation of archaellation and highlights the essential role of EarA in Pyrococcus furiosus. These findings advance our understanding of the mechanisms governing archaellation and have implications for the functional diversity of archaella.
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Affiliation(s)
- Richard Stöckl
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Laura Nißl
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Reinhard Rachel
- Centre for Electron Microscopy, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
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2
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Chiu BK, Waldbauer J, Elling FJ, Mete ÖZ, Zhang L, Pearson A, Eggleston EM, Leavitt WD. Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Front Microbiol 2023; 14:1219779. [PMID: 37649629 PMCID: PMC10465181 DOI: 10.3389/fmicb.2023.1219779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors such as temperature, pH, and energy availability shifts. However, archaeal expression patterns that correspond with changes in GDGT composition are less understood. Here we characterize the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A using growth rates, core GDGT lipid profiles, transcriptomics and proteomics. We show that both stressors result in impaired growth, lower average GDGT cyclization, and differences in gene and protein expression. Transcription data revealed differential expression of the GDGT ring synthase grsB in response to both acid stress and cold stress. Although the GDGT ring synthase encoded by grsB forms highly cyclized GDGTs with ≥5 ring moieties, S. islandicus grsB upregulation under acidic pH conditions did not correspond with increased abundances of highly cyclized GDGTs. Our observations highlight the inability to predict GDGT changes from transcription data alone. Broader analysis of transcriptomic data revealed that S. islandicus differentially expresses many of the same transcripts in response to both acid and cold stress. These included upregulation of several biosynthetic pathways and downregulation of oxidative phosphorylation and motility. Transcript responses specific to either of the two stressors tested here included upregulation of genes related to proton pumping and molecular turnover in acid stress conditions and upregulation of transposases in cold stress conditions. Overall, our study provides a comprehensive understanding of the GDGT modifications and differential expression characteristic of the acid stress and cold stress responses in S. islandicus.
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Affiliation(s)
- Beverly K. Chiu
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Felix J. Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
- Leibniz-Laboratory for Radiometric Dating and Isotope Research, Kiel University, Kiel, Germany
| | - Öykü Z. Mete
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Lichun Zhang
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Erin M. Eggleston
- Department of Biology, Middlebury College, Middlebury, VT, United States
| | - William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Chemistry, Dartmouth College, Hanover, NH, United States
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3
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Lewis AM, Willard DJ, H. Manesh MJ, Sivabalasarma S, Albers SV, Kelly RM. Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin. mBio 2023; 14:e0005323. [PMID: 37036347 PMCID: PMC10127717 DOI: 10.1128/mbio.00053-23] [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: 01/09/2023] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
A type II VapB14 antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius through traditional toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC toxins are ribonucleases that are neutralized by their proteinaceous cognate type II VapB antitoxin. VapB antitoxins have a flexible tail at their C terminus that covers the toxin's active site, neutralizing its activity. VapB antitoxins also have a DNA-binding domain at their N terminus that allows them to autorepress not only their own promoters but also distal targets. VapB14 antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for type II antitoxins, which are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both upregulated in biofilm cells, supporting the role of the antitoxin in biofilm regulation. In several Sulfolobales species, including M. sedula, homologs of vapB14 and vapC14 are not colocalized. Strikingly, Sulfuracidifex tepidarius has an unpaired VapB14 homolog and lacks a cognate VapC14, illustrating the toxin-independent conservation of the VapB14 antitoxin. The findings here suggest that a stand-alone VapB-type antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior. IMPORTANCE Biofilms allow microbes to resist a multitude of stresses and stay proximate to vital nutrients. The mechanisms of entering and leaving a biofilm are highly regulated to ensure microbial survival, but are not yet well described in archaea. Here, a VapBC type II toxin-antitoxin system in the thermoacidophilic archaeon Sulfolobus acidocaldarius was shown to control biofilm dispersal through a multifaceted regulation of the archaeal motility structure, the archaellum. The VapC14 toxin degrades an RNA that causes an increase in archaella and swimming. The VapB14 antitoxin decreases archaella and biofilm dispersal by binding the VapC14 toxin and neutralizing its activity, while also repressing the archaellum genes. VapB14-like antitoxins are highly conserved across the Sulfolobales and respond similarly to biofilm growth. In fact, VapB14-like antitoxins are also found in other archaea, and even in bacteria, indicating an evolutionary pressure to maintain this protein and its role in biofilm formation.
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Affiliation(s)
- April M. Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Mohamad J. H. Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Shamphavi Sivabalasarma
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBBS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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4
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Rao A, de Kok NAW, Driessen AJM. Membrane Adaptations and Cellular Responses of Sulfolobus acidocaldarius to the Allylamine Terbinafine. Int J Mol Sci 2023; 24:ijms24087328. [PMID: 37108491 PMCID: PMC10138448 DOI: 10.3390/ijms24087328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Cellular membranes are essential for compartmentalization, maintenance of permeability, and fluidity in all three domains of life. Archaea belong to the third domain of life and have a distinct phospholipid composition. Membrane lipids of archaea are ether-linked molecules, specifically bilayer-forming dialkyl glycerol diethers (DGDs) and monolayer-forming glycerol dialkyl glycerol tetraethers (GDGTs). The antifungal allylamine terbinafine has been proposed as an inhibitor of GDGT biosynthesis in archaea based on radiolabel incorporation studies. The exact target(s) and mechanism of action of terbinafine in archaea remain elusive. Sulfolobus acidocaldarius is a strictly aerobic crenarchaeon thriving in a thermoacidophilic environment, and its membrane is dominated by GDGTs. Here, we comprehensively analyzed the lipidome and transcriptome of S. acidocaldarius in the presence of terbinafine. Depletion of GDGTs and the accompanying accumulation of DGDs upon treatment with terbinafine were growth phase-dependent. Additionally, a major shift in the saturation of caldariellaquinones was observed, which resulted in the accumulation of unsaturated molecules. Transcriptomic data indicated that terbinafine has a multitude of effects, including significant differential expression of genes in the respiratory complex, motility, cell envelope, fatty acid metabolism, and GDGT cyclization. Combined, these findings suggest that the response of S. acidocaldarius to terbinafine inhibition involves respiratory stress and the differential expression of genes involved in isoprenoid biosynthesis and saturation.
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Affiliation(s)
- Alka Rao
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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5
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Sivabalasarma S, de Sousa Machado JN, Albers SV, Jarrell KF. Archaella Isolation. Methods Mol Biol 2023; 2646:183-195. [PMID: 36842116 DOI: 10.1007/978-1-0716-3060-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Swimming archaea are propelled by a filamentous structure called the archaellum. The first step for the structural characterization of this filament is its isolation. Here we provide various methods that allow for the isolation of archaella filaments from well-studied archaeal model organisms. Archaella filaments have been successfully extracted from organisms belonging to different archaeal phyla, e.g., euryarchaeal methanogens such as Methanococcus voltae, and crenarchaeal hyperthermoacidophiles like Sulfolobus acidocaldarius. The filament isolation protocols that we provide in this chapter follow one of two strategies: either the filaments are sheared or extracted from whole cells by detergent extraction, prior to further final purification by centrifugation methods.
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Affiliation(s)
- Shamphavi Sivabalasarma
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - João N de Sousa Machado
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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6
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van Wolferen M, Pulschen AA, Baum B, Gribaldo S, Albers SV. The cell biology of archaea. Nat Microbiol 2022; 7:1744-1755. [PMID: 36253512 PMCID: PMC7613921 DOI: 10.1038/s41564-022-01215-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
The past decade has revealed the diversity and ubiquity of archaea in nature, with a growing number of studies highlighting their importance in ecology, biotechnology and even human health. Myriad lineages have been discovered, which expanded the phylogenetic breadth of archaea and revealed their central role in the evolutionary origins of eukaryotes. These discoveries, coupled with advances that enable the culturing and live imaging of archaeal cells under extreme environments, have underpinned a better understanding of their biology. In this Review we focus on the shape, internal organization and surface structures that are characteristic of archaeal cells as well as membrane remodelling, cell growth and division. We also highlight some of the technical challenges faced and discuss how new and improved technologies will help address many of the key unanswered questions.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Buzz Baum
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institute Pasteur, Paris, France.
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
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7
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Comparative Genomic Insights into Chemoreceptor Diversity and Habitat Adaptation of Archaea. Appl Environ Microbiol 2022; 88:e0157422. [DOI: 10.1128/aem.01574-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Archaea are capable of sensing and responding to environmental changes by several signal transduction systems with different mechanisms. Much attention is paid to model organisms with complex signaling networks to understand their composition and function, but general principles regarding how an archaeal species organizes its chemoreceptor diversity and habitat adaptation are poorly understood.
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8
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Mehler J, Behringer KI, Rollins RE, Pisarz F, Klingl A, Henle T, Heermann R, Becker NS, Hellwig M, Lassak J. Identification of Pseudomonas asiatica subsp. bavariensis str. JM1 as the first N ε -carboxy(m)ethyllysine degrading soil bacterium. Environ Microbiol 2022; 24:3229-3241. [PMID: 35621031 DOI: 10.1111/1462-2920.16079] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/03/2022]
Abstract
Thermal food processing leads to the formation of advanced glycation end products (AGE) such as Nε -carboxymethyllysine (CML). Accordingly, these non-canonical amino acids are an important part of the human diet. However, CML is only partially decomposed by our gut microbiota and up to 30% are excreted via feces and, hence, enter the environment. In frame of this study, we isolated a soil bacterium that can grow on CML as well as its higher homologue Nε -carboxyethyllysine (CEL) as sole source of carbon. Bioinformatic analyses upon whole genome sequencing revealed a subspecies of Pseudomonas asiatica, which we named 'bavariensis'. We performed a metabolite screening of P. asiatica subsp. bavariensis str. JM1 grown either on CML or CEL and identified N-carboxymethylaminopentanoic acid (CM-APA), and N-carboxyethylaminopentanoic acid (CE-APA), respectively. We further detected α-aminoadipate as intermediate in the metabolism of CML. These reaction products suggest two routes of degradation: While CEL seems to be predominantly processed from the α-C-atom, decomposition of CML can also be initiated with cleavage of the carboxymethyl group and under the release of acetate. Thus, our study provides novel insights into the metabolism of two important AGEs and how these are processed by environmental bacteria. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Judith Mehler
- Division of Microbiology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Kim Ina Behringer
- Technische Universität Braunschweig - Institute of Food Chemistry, Braunschweig, Germany
| | - Robert Ethan Rollins
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Friederike Pisarz
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andreas Klingl
- Division of Botany, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Thomas Henle
- Chair of Food Chemistry, Technische Universität Dresden, D-01062, Dresden, Germany
| | - Ralf Heermann
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Noémie S Becker
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Michael Hellwig
- Technische Universität Braunschweig - Institute of Food Chemistry, Braunschweig, Germany.,Chair of Special Food Chemistry, Technische Universität Dresden, D-01062, Dresden, Germany
| | - Jürgen Lassak
- Division of Microbiology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
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9
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Nuno de Sousa Machado J, Albers SV, Daum B. Towards Elucidating the Rotary Mechanism of the Archaellum Machinery. Front Microbiol 2022; 13:848597. [PMID: 35387068 PMCID: PMC8978795 DOI: 10.3389/fmicb.2022.848597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Motile archaea swim by means of a molecular machine called the archaellum. This structure consists of a filament attached to a membrane-embedded motor. The archaellum is found exclusively in members of the archaeal domain, but the core of its motor shares homology with the motor of type IV pili (T4P). Here, we provide an overview of the different components of the archaellum machinery and hypothetical models to explain how rotary motion of the filament is powered by the archaellum motor.
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Affiliation(s)
- João Nuno de Sousa Machado
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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10
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van Wolferen M, Albers SV. Progress and Challenges in Archaeal Cell Biology. Methods Mol Biol 2022; 2522:365-371. [PMID: 36125763 DOI: 10.1007/978-1-0716-2445-6_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the past decades there has been a growing interest in the domain of archaea. In this chapter we highlight the recent advances that have been made in studying the cell biology of archaea. We particularly focus on methods for genetic manipulation and imaging of different archaeal species and discuss the technical limitations at the often-extreme growth conditions. Several ongoing developments will help us overcoming these limitations, thereby facilitating future studies in the existing field of archaeal cell biology.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.
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11
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Patro M, van Wolferen M, Ye X, Albers SV, Quax TEF. Methods to Analyze Motility in Eury- and Crenarchaea. Methods Mol Biol 2022; 2522:373-385. [PMID: 36125764 DOI: 10.1007/978-1-0716-2445-6_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many archaea display swimming motility in liquid medium, which is empowered by the archaellum. Directional movement requires a functional archaellum and a sensing system, such as the chemotaxis system that is used by Euryarchaea. Two well-studied models are the euryarchaeon Haloferax volcanii and the crenarchaeon Sulfolobus acidocaldarius. In this chapter we describe two methods to analyze their swimming behavior and directional movement: (a) time-lapse microscopy under native temperatures and (b) spotting on semi-solid agar or gelrite plates. Whereas the first method allows for deep analysis of swimming behavior, the second method is suited for high throughput comparison of multiple strains.
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Affiliation(s)
- Megha Patro
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Marleen van Wolferen
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Xing Ye
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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12
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Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
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Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
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13
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Charles-Orszag A, Lord SJ, Mullins RD. High-Temperature Live-Cell Imaging of Cytokinesis, Cell Motility, and Cell-Cell Interactions in the Thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius. Front Microbiol 2021; 12:707124. [PMID: 34447359 PMCID: PMC8383144 DOI: 10.3389/fmicb.2021.707124] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Significant technical challenges have limited the study of extremophile cell biology. Here we describe a system for imaging samples at 75°C using high numerical aperture, oil-immersion lenses. With this system we observed and quantified the dynamics of cell division in the model thermoacidophilic crenarchaeon Sulfolobus acidocaldarius with unprecedented resolution. In addition, we observed previously undescribed dynamic cell shape changes, cell motility, and cell-cell interactions, shedding significant new light on the high-temperature lifestyle of this organism.
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Affiliation(s)
| | | | - R. Dyche Mullins
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, United States
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14
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de Sousa Machado JN, Vollmar L, Schimpf J, Chaudhury P, Kumariya R, van der Does C, Hugel T, Albers SV. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerization and interaction with ArlI, the motor ATPase of the archaellum. Mol Microbiol 2021; 116:943-956. [PMID: 34219289 DOI: 10.1111/mmi.14781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022]
Abstract
Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Since autophosphorylation and dephosphorylation of KaiC are central properties for the function of KaiC, we asked whether autophosphorylation is also a property of ArlH proteins. We observed that both ArlH from the euryarchaeon Pyrococcus furiosus (PfArlH) and from the crenarchaeon Sulfolobus acidocaldarius (SaArlH) have autophosphorylation activity. Using a combination of single-molecule fluorescence measurements and biochemical assays, we show that autophosphorylation of ArlH is closely linked to its oligomeric state when bound to hexameric ArlI. These experiments also strongly suggest that ArlH is a hexamer in its ArlI-bound state. Mutagenesis of the putative catalytic residue (Glu-57 in SaArlH) in ArlH results in a reduced autophosphorylation activity and abolished archaellation and motility in S. acidocaldarius, indicating that optimum phosphorylation activity of ArlH is essential for archaellation and motility.
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Affiliation(s)
- J Nuno de Sousa Machado
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Leonie Vollmar
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Julia Schimpf
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Paushali Chaudhury
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Rashmi Kumariya
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Chris van der Does
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
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15
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Jarrell KF, Albers SV, Machado JNDS. A comprehensive history of motility and Archaellation in Archaea. FEMS MICROBES 2021; 2:xtab002. [PMID: 37334237 PMCID: PMC10117864 DOI: 10.1093/femsmc/xtab002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/18/2021] [Indexed: 08/24/2023] Open
Abstract
Each of the three Domains of life, Eukarya, Bacteria and Archaea, have swimming structures that were all originally called flagella, despite the fact that none were evolutionarily related to either of the other two. Surprisingly, this was true even in the two prokaryotic Domains of Bacteria and Archaea. Beginning in the 1980s, evidence gradually accumulated that convincingly demonstrated that the motility organelle in Archaea was unrelated to that found in Bacteria, but surprisingly shared significant similarities to type IV pili. This information culminated in the proposal, in 2012, that the 'archaeal flagellum' be assigned a new name, the archaellum. In this review, we provide a historical overview on archaella and motility research in Archaea, beginning with the first simple observations of motile extreme halophilic archaea a century ago up to state-of-the-art cryo-tomography of the archaellum motor complex and filament observed today. In addition to structural and biochemical data which revealed the archaellum to be a type IV pilus-like structure repurposed as a rotating nanomachine (Beeby et al. 2020), we also review the initial discoveries and subsequent advances using a wide variety of approaches to reveal: complex regulatory events that lead to the assembly of the archaellum filaments (archaellation); the roles of the various archaellum proteins; key post-translational modifications of the archaellum structural subunits; evolutionary relationships; functions of archaella other than motility and the biotechnological potential of this fascinating structure. The progress made in understanding the structure and assembly of the archaellum is highlighted by comparing early models to what is known today.
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Affiliation(s)
- Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Sonja-Verena Albers
- Institute for Biology II- Microbiology, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, Freiburg 79104, Germany
| | - J Nuno de Sousa Machado
- Institute for Biology II- Microbiology, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, Freiburg 79104, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstraße 19A, 79104, Freiburg, Germany
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16
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de Sousa Machado JN, Vollmar L, Schimpf J, Chaudhury P, Kumariya R, van der Does C, Hugel T, Albers S. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerisation and interaction with ArlI, the motor ATPase of the archaellum.. [DOI: 10.1101/2021.03.19.436134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Similar to KaiC, ArlH exhibits autophosphorylation activity, which was observed for both ArlH of the euryarchaeonPyrococcus furiosus (PfArlH)and the crenarchaeonSulfolobus acidocaldarius(SaArlH). Using a combination of single molecule fluorescence measurements and biochemical assays, it is shown that autophosphorylation of ArlH is closely linked to the oligomeric state of ArlH bound to ArlI. These experiments also strongly suggest that ArlH is a hexamer in its functional ArlI bound state. Mutagenesis of the putative catalytic residue Glu-57 inSaArlH results in a reduced autophosphorylation activity and abolished archaellation and motility, suggesting that optimum phosphorylation activity of ArlH is essential for both archaellation and motility.
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17
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Ye X, van der Does C, Albers SV. SaUspA, the Universal Stress Protein of Sulfolobus acidocaldarius Stimulates the Activity of the PP2A Phosphatase and Is Involved in Growth at High Salinity. Front Microbiol 2020; 11:598821. [PMID: 33304342 PMCID: PMC7693658 DOI: 10.3389/fmicb.2020.598821] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/23/2020] [Indexed: 11/13/2022] Open
Abstract
In Sulfolobus acidocaldarius, the protein phosphatase PP2A plays important regulatory roles in many cellular processes, including cell growth, cell shape and synthesis of the archaellum. A conserved prokaryotic protein, designated as SaUspA, was identified as an interaction partner of the phosphatase PP2A. SaUspA belongs to the universal stress protein (USP) superfamily, members of which are found in bacteria, archaea, plants and invertebrates. Biochemical analysis showed that SaUspA is a homodimeric ATP-binding protein, which also in vitro binds to PP2A. SaUspA did not hydrolyze ATP, but stimulated the phosphatase activity of PP2A and might in this manner affect many other processes. Interestingly, binding of ATP further enhanced SaUspA's interaction with PP2A. In contrast to bacterial usp genes, environmental stress conditions including stationary phase, starvation stress, high salinity stress and UV stress did not stimulate expression of saUspA. Deletion of saUspA led to premature production of the archaellin FlaB in S. acidocaldarius although motility was not affected. The ΔsaUspA mutant showed a significant growth defect under high salinity stress and complementation of ATP-binding deficient mutant SaUspAG97A failed to restore this growth defect. Compared with the wild type strain, its growth or survival was not affected under heavy metal stress and UV stress. To date, this is the first study in which the physiological role of USP homologs in archaea have been reported.
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Affiliation(s)
- Xing Ye
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Chris van der Does
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
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18
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Li Z, Rodriguez‐Franco M, Albers S, Quax TEF. The switch complex ArlCDE connects the chemotaxis system and the archaellum. Mol Microbiol 2020; 114:468-479. [PMID: 32416640 PMCID: PMC7534055 DOI: 10.1111/mmi.14527] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022]
Abstract
Cells require a sensory system and a motility structure to achieve directed movement. Bacteria and archaea possess rotating filamentous motility structures that work in concert with the sensory chemotaxis system. This allows microorganisms to move along chemical gradients. The central response regulator protein CheY can bind to the motor of the motility structure, the flagellum in bacteria, and the archaellum in archaea. Both motility structures have a fundamentally different protein composition and structural organization. Yet, both systems receive input from the chemotaxis system. So far, it was unknown how the signal is transferred from the archaeal CheY to the archaellum motor to initiate motor switching. We applied a fluorescent microscopy approach in the model euryarchaeon Haloferax volcanii and shed light on the sequence order in which signals are transferred from the chemotaxis system to the archaellum. Our findings indicate that the euryarchaeal-specific ArlCDE are part of the archaellum motor and that they directly receive input from the chemotaxis system via the adaptor protein CheF. Hence, ArlCDE are an important feature of the archaellum of euryarchaea, are essential for signal transduction during chemotaxis and represent the archaeal switch complex.
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Affiliation(s)
- Zhengqun Li
- Molecular Biology of Archaea, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | | | - Sonja‐Verena Albers
- Molecular Biology of Archaea, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Tessa E. F. Quax
- Archaeal Virus–Host Interactions, Faculty of BiologyUniversity of FreiburgFreiburgGermany
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19
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Ye X, Vogt MS, van der Does C, Bildl W, Schulte U, Essen LO, Albers SV. The Phosphatase PP2A Interacts With ArnA and ArnB to Regulate the Oligomeric State and the Stability of the ArnA/B Complex. Front Microbiol 2020; 11:1849. [PMID: 32973695 PMCID: PMC7472852 DOI: 10.3389/fmicb.2020.01849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/15/2020] [Indexed: 12/30/2022] Open
Abstract
In the crenarchaeon Sulfolobus acidocaldarius, the archaellum, a type-IV pilus like motility structure, is synthesized in response to nutrient starvation. Synthesis of components of the archaellum is controlled by the archaellum regulatory network (arn). Protein phosphorylation plays an important role in this regulatory network since the deletion of several genes encoding protein kinases and the phosphatase PP2A affected cell motility. Several proteins in the archaellum regulatory network can be phosphorylated, however, details of how phosphorylation levels of different components affect archaellum synthesis are still unknown. To identify proteins interacting with the S. acidocaldarius phosphatases PTP and PP2A, co-immunoprecipitation assays coupled to mass spectrometry analysis were performed. Thirty minutes after growth in nutrient starvation medium, especially a conserved putative ATP/GTP binding protein (Saci_1281), a universal stress protein (Saci_0887) and the archaellum regulators ArnA and ArnB were identified as highly abundant interaction proteins of PP2A. The interaction between ArnA, ArnB, and PP2A was further studied. Previous studies showed that the Forkhead-associated domain containing ArnA interacts with von Willebrand type A domain containing ArnB, and that both proteins could be phosphorylated by the kinase ArnC in vitro. The ArnA/B heterodimer was reconstituted from the purified proteins. In complex with ArnA, phosphorylation of ArnB by the ArnC kinase was strongly stimulated and resulted in formation of (ArnA/B)2 and higher oligomeric complexes, while association and dephosphorylation by PP2A resulted in dissociation of these ArnA/B complexes.
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Affiliation(s)
- Xing Ye
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | | | - Chris van der Does
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Wolfgang Bildl
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Biological Signaling Studies(BIOSS), Freiburg, Germany.,Center for Integrative Signaling Studies (CIBSS), Freiburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, Marburg, Germany.,Loewe Center for Synthetic Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Center for Biological Signaling Studies(BIOSS), Freiburg, Germany
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20
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Wang P, Li LZ, Qin YL, Liang ZL, Li XT, Yin HQ, Liu LJ, Liu SJ, Jiang CY. Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera. Front Microbiol 2020; 11:1192. [PMID: 32655516 PMCID: PMC7325606 DOI: 10.3389/fmicb.2020.01192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/11/2020] [Indexed: 01/15/2023] Open
Abstract
Members of the genus Metallosphaera are widely found in sulfur-rich and metal-laden environments, but their physiological and ecological roles remain poorly understood. Here, we sequenced Metallosphaera tengchongensis Ric-A, a strain isolated from the Tengchong hot spring in Yunnan Province, China, and performed a comparative genome analysis with other Metallosphaera genomes. The genome of M. tengchongensis had an average nucleotide identity (ANI) of approximately 70% to that of Metallosphaera cuprina. Genes sqr, tth, sir, tqo, hdr, tst, soe, and sdo associated with sulfur oxidation, and gene clusters fox and cbs involved in iron oxidation existed in all Metallosphaera genomes. However, the adenosine-5'-phosphosulfate (APS) pathway was only detected in Metallosphaera sedula and Metallosphaera yellowstonensis, and several subunits of fox cluster were lost in M. cuprina. The complete 3-hydroxypropionate/4-hydroxybutyrate cycle and dicarboxylate/4-hydroxybutyrate cycle involved in carbon fixation were found in all Metallosphaera genomes. A large number of gene family gain events occurred in M. yellowstonensis and M. sedula, whereas gene family loss events occurred frequently in M. cuprina. Pervasive strong purifying selection was found acting on the gene families of Metallosphaera, of which transcription-related genes underwent the strongest purifying selection. In contrast, genes related to prophages, transposons, and defense mechanisms were under weaker purifying pressure. Taken together, this study expands knowledge of the genomic traits of Metallosphaera species and sheds light on their evolution.
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Affiliation(s)
- Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang Zhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Ya Ling Qin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zong Lin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiu Tong Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hua Qun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Li Jun Liu
- Department of Pathogen Biology, School of Basic Medical Science, Xi’an Medical University, Xi’an, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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21
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van der Kolk N, Wagner A, Wagner M, Waßmer B, Siebers B, Albers SV. Identification of XylR, the Activator of Arabinose/Xylose Inducible Regulon in Sulfolobus acidocaldarius and Its Application for Homologous Protein Expression. Front Microbiol 2020; 11:1066. [PMID: 32528450 PMCID: PMC7264815 DOI: 10.3389/fmicb.2020.01066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 04/29/2020] [Indexed: 11/13/2022] Open
Abstract
The thermophilic archaeon Sulfolobus acidocaldarius can use different carbon sources for growth, including the pentoses D-xylose and L-arabinose. In this study, we identified the activator XylR (saci_2116) responsible for the transcriptional regulation of the pentose transporter and pentose metabolizing genes in S. acidocaldarius. A xylR deletion mutant showed growth retardation on D-xylose/L-arabinose containing media and the lack of transcription of the respective ABC transporter. In contrast to so far used promoters for expression in S. acidocaldarius, the xylR responsive promoters have a very low background activity. Finally, two XylR dependent promoters next to the long-established maltose inducible promotor were used to construct a high-throughput expression vector system for S. acidocaldarius to efficiently clone and express proteins in S. acidocaldarius.
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Affiliation(s)
- Nienke van der Kolk
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
| | - Alexander Wagner
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany.,Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, Centre for Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Michaela Wagner
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany.,Biotechnologie, Hochschule Niederrhein, Krefeld, Germany
| | - Bianca Waßmer
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, Centre for Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
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22
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Beeby M, Ferreira JL, Tripp P, Albers SV, Mitchell DR. Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia. FEMS Microbiol Rev 2020; 44:253-304. [DOI: 10.1093/femsre/fuaa006] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Echoing the repeated convergent evolution of flight and vision in large eukaryotes, propulsive swimming motility has evolved independently in microbes in each of the three domains of life. Filamentous appendages – archaella in Archaea, flagella in Bacteria and cilia in Eukaryotes – wave, whip or rotate to propel microbes, overcoming diffusion and enabling colonization of new environments. The implementations of the three propulsive nanomachines are distinct, however: archaella and flagella rotate, while cilia beat or wave; flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force. These underlying differences reflect the tinkering required to evolve a molecular machine, in which pre-existing machines in the appropriate contexts were iteratively co-opted for new functions and whose origins are reflected in their resultant mechanisms. Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure. Here, we review the structure, assembly, mechanism and homologies of the three distinct solutions as a foundation to better understand how propulsive nanomachines evolved three times independently and to highlight principles of molecular evolution.
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Affiliation(s)
- Morgan Beeby
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Josie L Ferreira
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Patrick Tripp
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - David R Mitchell
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY 13210, USA
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23
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The structure of the periplasmic FlaG-FlaF complex and its essential role for archaellar swimming motility. Nat Microbiol 2019; 5:216-225. [PMID: 31844299 DOI: 10.1038/s41564-019-0622-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 10/23/2019] [Indexed: 11/08/2022]
Abstract
Motility structures are vital in all three domains of life. In Archaea, motility is mediated by the archaellum, a rotating type IV pilus-like structure that is a unique nanomachine for swimming motility in nature. Whereas periplasmic FlaF binds the surface layer (S-layer), the structure, assembly and roles of other periplasmic components remain enigmatic, limiting our knowledge of the archaellum's functional interactions. Here, we find that the periplasmic protein FlaG and the association with its paralogue FlaF are essential for archaellation and motility. Therefore, we determine the crystal structure of Sulfolobus acidocaldarius soluble FlaG (sFlaG), which reveals a β-sandwich fold resembling the S-layer-interacting FlaF soluble domain (sFlaF). Furthermore, we solve the sFlaG2-sFlaF2 co-crystal structure, define its heterotetrameric complex in solution by small-angle X-ray scattering and find that mutations that disrupt the complex abolish motility. Interestingly, the sFlaF and sFlaG of Pyrococcus furiosus form a globular complex, whereas sFlaG alone forms a filament, indicating that FlaF can regulate FlaG filament assembly. Strikingly, Sulfolobus cells that lack the S-layer component bound by FlaF assemble archaella but cannot swim. These collective results support a model where a FlaG filament capped by a FlaG-FlaF complex anchors the archaellum to the S-layer to allow motility.
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24
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Orell A, Tripp V, Aliaga-Tobar V, Albers SV, Maracaja-Coutinho V, Randau L. A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius. Nucleic Acids Res 2019. [PMID: 29529252 PMCID: PMC5961385 DOI: 10.1093/nar/gky144] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Non-coding RNAs (ncRNA) are involved in essential biological processes in all three domains of life. The regulatory potential of ncRNAs in Archaea is, however, not fully explored. In this study, RNA-seq analyses identified a set of 29 ncRNA transcripts in the hyperthermophilic archaeon Sulfolobus acidocaldarius that were differentially expressed in response to biofilm formation. The most abundant ncRNA of this set was found to be resistant to RNase R treatment (RNase R resistant RNA, RrrR(+)) due to duplex formation with a reverse complementary RNA (RrrR(−)). The deletion of the RrrR(+) gene resulted in significantly impaired biofilm formation, while its overproduction increased biofilm yield. RrrR(+) was found to act as an antisense RNA against the mRNA of a hypothetical membrane protein. The RrrR(+) transcript was shown to be stabilized by the presence of the RrrR(−) strand in S. acidocaldarius cell extracts. The accumulation of these RrrR duplexes correlates with an apparent absence of dsRNA degrading RNase III domains in archaeal proteins.
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Affiliation(s)
- Alvaro Orell
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg 35043, Germany.,Centro de Genómica y Bioinformática, Facultad de Ciencias, UniversidadMayor, Santiago, Chile
| | - Vanessa Tripp
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg 35043, Germany
| | - Victor Aliaga-Tobar
- 3Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación,Universidad Mayor, Santiago, Chile
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University Freiburg, Germany
| | - Vinicius Maracaja-Coutinho
- Centro de Genómica y Bioinformática, Facultad de Ciencias, UniversidadMayor, Santiago, Chile.,Departamento de Bioquímica y Biología Molecular,Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg 35043, Germany
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25
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De Corte D, Paredes G, Yokokawa T, Sintes E, Herndl GJ. Differential Response of Cafeteria roenbergensis to Different Bacterial and Archaeal Prey Characteristics. MICROBIAL ECOLOGY 2019; 78:1-5. [PMID: 30448922 DOI: 10.1007/s00248-018-1293-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
In the marine environment, the abundance of Bacteria and Archaea is either controlled bottom-up via nutrient availability or top-down via grazing. Heterotrophic nanoflagellates (HNF) are mainly responsible for prokaryotic grazing losses besides viral lysis. However, the grazing specificity of HNF on specific bacterial and archaeal taxa is under debate. Bacteria and Archaea might have different nutritive values and surface properties affecting the growth rates of HNF. In this study, we offered different bacterial and archaeal strains with different morphologic and physiologic characteristics to Cafeteria roenbergensis, one of the most abundant and ubiquitous species of HNF in the ocean. Two Nitrosopumilus maritimus-related strains isolated from the northern Adriatic Sea (Nitrosopumilus adriaticus, Nitrosopumilus piranensis), two Nitrosococcus strains, and two fast growing marine Bacteria (Pseudoalteromonas sp. and Marinobacter sp.) were fed to Cafeteria cultures. Cafeteria roenbergensis exhibited high growth rates when feeding on Pseudoalteromonas sp., Marinobacter sp., and Nitrosopumilus adriaticus, while the addition of the other strains resulted in minimal growth. Taken together, our data suggest that the differences in growth of Cafeteria roenbergensis associated to grazing on different thaumarchaeal and bacterial strains are likely due to the subtle metabolic, cell size, and physiological differences between different bacterial and thaumarchaeal taxa. Moreover, Nitrosopumilus adriaticus experienced a similar grazing pressure by Cafeteria roenbergensis as compared to the other strains, suggesting that other HNF may also prey on Archaea which might have important consequences on the global biogeochemical cycles.
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Affiliation(s)
- Daniele De Corte
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natushima 2-15, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Gabriela Paredes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Taichi Yokokawa
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natushima 2-15, Yokosuka, Kanagawa, 237-0061, Japan
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, PO Box 59, 1790 AB, Den Burg, The Netherlands
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26
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Zaretsky M, Darnell CL, Schmid AK, Eichler J. N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility. Front Microbiol 2019; 10:1367. [PMID: 31275283 PMCID: PMC6591318 DOI: 10.3389/fmicb.2019.01367] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022] Open
Abstract
Halobacterium salinarum are halophilic archaea that display directional swimming in response to various environmental signals, including light, chemicals and oxygen. In Hbt. salinarum, the building blocks (archaellins) of the archaeal swimming apparatus (the archaellum) are N-glycosylated. However, the physiological importance of archaellin N-glycosylation remains unclear. Here, a tetrasaccharide comprising a hexose and three hexuronic acids decorating the five archaellins was characterized by mass spectrometry. Such analysis failed to detect sulfation of the hexuronic acids, in contrast to earlier reports. To better understand the physiological significance of Hbt. salinarum archaellin N-glycosylation, a strain deleted of aglB, encoding the archaeal oligosaccharyltransferase, was generated. In this ΔaglB strain, archaella were not detected and only low levels of archaellins were released into the medium, in contrast to what occurs with the parent strain. Mass spectrometry analysis of the archaellins in ΔaglB cultures did not detect N-glycosylation. ΔaglB cells also showed a slight growth defect and were impaired for motility. Quantitative real-time PCR analysis revealed dramatically reduced transcript levels of archaellin-encoding genes in the mutant strain, suggesting that N-glycosylation is important for archaellin transcription, with downstream effects on archaellum assembly and function. Control of AglB-dependent post-translational modification of archaellins could thus reflect a previously unrecognized route for regulating Hbt. salinarum motility.
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Affiliation(s)
- Marianna Zaretsky
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheba, Israel
| | | | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC, United States.,Center for Genomics and Computational Biology, Duke University, Durham, NC, United States
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheba, Israel
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27
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Hoffmann L, Anders K, Bischof LF, Ye X, Reimann J, Khadouma S, Pham TK, van der Does C, Wright PC, Essen LO, Albers SV. Structure and interactions of the archaeal motility repression module ArnA–ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius. J Biol Chem 2019; 294:7460-7471. [PMID: 30902813 PMCID: PMC6509490 DOI: 10.1074/jbc.ra119.007709] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/20/2019] [Indexed: 11/06/2022] Open
Abstract
Phosphorylation-dependent interactions play crucial regulatory roles in all domains of life. Forkhead-associated (FHA) and von Willebrand type A (vWA) domains are involved in several phosphorylation-dependent processes of multiprotein complex assemblies. Although well-studied in eukaryotes and bacteria, the structural and functional contexts of these domains are not yet understood in Archaea. Here, we report the structural base for such an interacting pair of FHA and vWA domain-containing proteins, ArnA and ArnB, in the thermoacidophilic archaeon Sulfolobus acidocaldarius, where they act synergistically and negatively modulate motility. The structure of the FHA domain of ArnA at 1.75 Å resolution revealed that it belongs to the subclass of FHA domains, which recognizes double-pSer/pThr motifs. We also solved the 1.5 Å resolution crystal structure of the ArnB paralog vWA2, disclosing a complex topology comprising the vWA domain, a β-sandwich fold, and a C-terminal helix bundle. We further show that ArnA binds to the C terminus of ArnB, which harbors all the phosphorylation sites identified to date and is important for the function of ArnB in archaellum regulation. We also observed that expression levels of the archaellum components in response to changes in nutrient conditions are independent of changes in ArnA and ArnB levels and that a strong interaction between ArnA and ArnB observed during growth on rich medium sequentially diminishes after nutrient limitation. In summary, our findings unravel the structural features in ArnA and ArnB important for their interaction and functional archaellum expression and reveal how nutrient conditions affect this interaction.
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Affiliation(s)
- Lena Hoffmann
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Katrin Anders
- the Philipps University, Department of Chemistry, 35032 Marburg, Germany
| | - Lisa F Bischof
- From the Institute for Biology II, Molecular Biology of Archaea and
- the Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Xing Ye
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Julia Reimann
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Sunia Khadouma
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Trong K Pham
- the ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom, and
| | | | - Phillip C Wright
- the Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Lars-Oliver Essen
- the Philipps University, Department of Chemistry, 35032 Marburg, Germany,
- the LOEWE Center for Synthetic Microbiology, 35043 Marburg, Germany
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28
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Bischof LF, Haurat MF, Albers SV. Two membrane-bound transcription factors regulate expression of various type-IV-pili surface structures in Sulfolobus acidocaldarius. PeerJ 2019; 7:e6459. [PMID: 30828487 PMCID: PMC6396743 DOI: 10.7717/peerj.6459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/15/2019] [Indexed: 11/20/2022] Open
Abstract
In Archaea and Bacteria, gene expression is tightly regulated in response to environmental stimuli. In the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius nutrient limitation induces expression of the archaellum, the archaeal motility structure. This expression is orchestrated by a complex hierarchical network of positive and negative regulators-the archaellum regulatory network (arn). The membrane-bound one-component system ArnR and its paralog ArnR1 were recently described as main activators of archaellum expression in S. acidocaldarius. They regulate gene expression of the archaellum operon by targeting the promoter of flaB, encoding the archaellum filament protein. Here we describe a strategy for the isolation and biochemical characterization of these two archaellum regulators. Both regulators are capable of forming oligomers and are phosphorylated by the Ser/Thr kinase ArnC. Apart from binding to pflaB, ArnR but not ArnR1 bound to promoter sequences of aapF and upsX, which encode components of the archaeal adhesive pilus and UV-inducible pili system, demonstrating a regulatory connection between different surface appendages of S. acidocaldarius.
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Affiliation(s)
- Lisa Franziska Bischof
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Freiburg, Germany
| | - Maria Florencia Haurat
- Department of Molecular Microbiology, Washington University, School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
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29
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Bischof LF, Haurat MF, Hoffmann L, Albersmeier A, Wolf J, Neu A, Pham TK, Albaum SP, Jakobi T, Schouten S, Neumann-Schaal M, Wright PC, Kalinowski J, Siebers B, Albers SV. Early Response of Sulfolobus acidocaldarius to Nutrient Limitation. Front Microbiol 2019; 9:3201. [PMID: 30687244 PMCID: PMC6335949 DOI: 10.3389/fmicb.2018.03201] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/10/2018] [Indexed: 01/13/2023] Open
Abstract
In natural environments microorganisms encounter extreme changes in temperature, pH, osmolarities and nutrient availability. The stress response of many bacterial species has been described in detail, however, knowledge in Archaea is limited. Here, we describe the cellular response triggered by nutrient limitation in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. We measured changes in gene transcription and protein abundance upon nutrient depletion up to 4 h after initiation of nutrient depletion. Transcript levels of 1118 of 2223 protein coding genes and abundance of approximately 500 proteins with functions in almost all cellular processes were affected by nutrient depletion. Our study reveals a significant rerouting of the metabolism with respect to degradation of internal as well as extracellular-bound organic carbon and degradation of proteins. Moreover, changes in membrane lipid composition were observed in order to access alternative sources of energy and to maintain pH homeostasis. At transcript level, the cellular response to nutrient depletion in S. acidocaldarius seems to be controlled by the general transcription factors TFB2 and TFEβ. In addition, ribosome biogenesis is reduced, while an increased protein degradation is accompanied with a loss of protein quality control. This study provides first insights into the early cellular response of Sulfolobus to organic carbon and organic nitrogen depletion.
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Affiliation(s)
- Lisa F Bischof
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - M Florencia Haurat
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Andreas Albersmeier
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
| | - Astrid Neu
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Trong Khoa Pham
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Stefan P Albaum
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Jakobi
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Stefan Schouten
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research, Den Burg, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
| | - Phillip C Wright
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
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30
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Abstract
Microorganisms can move towards favorable growth conditions as a response to environmental stimuli. This process requires a motility structure and a system to direct the movement. For swimming motility, archaea employ a rotating filament, the archaellum. This archaea-specific structure is functionally equivalent, but structurally different, from the bacterial flagellum. To control the directionality of movement, some archaea make use of the chemotaxis system, which is used for the same purpose by bacteria. Over the past decades, chemotaxis has been studied in detail in several model bacteria. In contrast, archaeal chemotaxis is much less explored and largely restricted to analyses in halophilic archaea. In this review, we summarize the available information on archaeal taxis. We conclude that archaeal chemotaxis proteins function similarly as their bacterial counterparts. However, because the motility structures are fundamentally different, an archaea-specific docking mechanism is required, for which initial experimental data have only recently been obtained.
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31
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Syutkin AS, van Wolferen M, Surin AK, Albers SV, Pyatibratov MG, Fedorov OV, Quax TEF. Salt-dependent regulation of archaellins in Haloarcula marismortui. Microbiologyopen 2018; 8:e00718. [PMID: 30270530 PMCID: PMC6528647 DOI: 10.1002/mbo3.718] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/26/2022] Open
Abstract
Microorganisms require a motility structure to move towards optimal growth conditions. The motility structure from archaea, the archaellum, is fundamentally different from its bacterial counterpart, the flagellum, and is assembled in a similar fashion as type IV pili. The archaellum filament consists of thousands of copies of N‐terminally processed archaellin proteins. Several archaea, such as the euryarchaeon Haloarcula marismortui, encode multiple archaellins. Two archaellins of H. marismortui display differential stability under various ionic strengths. This suggests that these proteins behave as ecoparalogs and perform the same function under different environmental conditions. Here, we explored this intriguing system to study the differential regulation of these ecoparalogous archaellins by monitoring their transcription, translation, and assembly into filaments. The salt concentration of the growth medium induced differential expression of the two archaellins. In addition, this analysis indicated that archaellation in H. marismortui is majorly regulated on the level of secretion, by a still unknown mechanism. These findings indicate that in archaea, multiple encoded archaellins are not completely redundant, but in fact can display subtle functional differences, which enable cells to cope with varying environmental conditions.
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Affiliation(s)
- Alexey S Syutkin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Marleen van Wolferen
- Molecular Biology of Archaea, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Oleg V Fedorov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Tessa E F Quax
- Molecular Biology of Archaea, Faculty of Biology, University of Freiburg, Freiburg, Germany
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32
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Chaudhury P, van der Does C, Albers SV. Characterization of the ATPase FlaI of the motor complex of the Pyrococcus furiosus archaellum and its interactions between the ATP-binding protein FlaH. PeerJ 2018; 6:e4984. [PMID: 29938130 PMCID: PMC6011876 DOI: 10.7717/peerj.4984] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/25/2018] [Indexed: 01/09/2023] Open
Abstract
The archaellum, the rotating motility structure of archaea, is best studied in the crenarchaeon Sulfolobus acidocaldarius. To better understand how assembly and rotation of this structure is driven, two ATP-binding proteins, FlaI and FlaH of the motor complex of the archaellum of the euryarchaeon Pyrococcus furiosus, were overexpressed, purified and studied. Contrary to the FlaI ATPase of S. acidocaldarius, which only forms a hexamer after binding of nucleotides, FlaI of P. furiosus formed a hexamer in a nucleotide independent manner. In this hexamer only 2 of the ATP binding sites were available for binding of the fluorescent ATP-analog MANT-ATP, suggesting a twofold symmetry in the hexamer. P. furiosus FlaI showed a 250-fold higher ATPase activity than S. acidocaldarius FlaI. Interaction studies between the isolated N- and C-terminal domains of FlaI showed interactions between the N- and C-terminal domains and strong interactions between the N-terminal domains not previously observed for ATPases involved in archaellum assembly. These interactions played a role in oligomerization and activity, suggesting a conformational state of the hexamer not observed before. Further interaction studies show that the C-terminal domain of PfFlaI interacts with the nucleotide binding protein FlaH. This interaction stimulates the ATPase activity of FlaI optimally at a 1:1 stoichiometry, suggesting that hexameric PfFlaI interacts with hexameric PfFlaH. These data help to further understand the complex interactions that are required to energize the archaellar motor.
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Affiliation(s)
- Paushali Chaudhury
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Chris van der Does
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
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33
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Albers SV, Jarrell KF. The Archaellum: An Update on the Unique Archaeal Motility Structure. Trends Microbiol 2018; 26:351-362. [PMID: 29452953 DOI: 10.1016/j.tim.2018.01.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/08/2018] [Accepted: 01/19/2018] [Indexed: 11/24/2022]
Abstract
Each of the three domains of life exhibits a unique motility structure: while Bacteria use flagella, Eukarya employ cilia, and Archaea swim using archaella. Since the new name for the archaeal motility structure was proposed, in 2012, a significant amount of new data on the regulation of transcription of archaella operons, the structure and function of archaellum subunits, their interactions, and cryo-EM data on in situ archaellum complexes in whole cells have been obtained. These data support the notion that the archaellum is evolutionary and structurally unrelated to the flagellum, but instead is related to archaeal and bacterial type IV pili and emphasize that it is a motility structure unique to the Archaea.
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Affiliation(s)
- Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany.
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
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34
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Abstract
Motility is a central feature of many microorganisms and provides an efficient strategy to respond to environmental changes. Bacteria and archaea have developed fundamentally different rotary motors enabling their motility, termed flagellum and archaellum, respectively. Bacterial motility along chemical gradients, called chemotaxis, critically relies on the response regulator CheY, which, when phosphorylated, inverses the rotational direction of the flagellum via a switch complex at the base of the motor. The structural difference between archaellum and flagellum and the presence of functional CheY in archaea raises the question of how the CheY protein changed to allow communication with the archaeal motility machinery. Here we show that archaeal CheY shares the overall structure and mechanism of magnesium-dependent phosphorylation with its bacterial counterpart. However, bacterial and archaeal CheY differ in the electrostatic potential of the helix α4. The helix α4 is important in bacteria for interaction with the flagellar switch complex, a structure that is absent in archaea. We demonstrated that phosphorylation-dependent activation, and conserved residues in the archaeal CheY helix α4, are important for interaction with the archaeal-specific adaptor protein CheF. This forms a bridge between the chemotaxis system and the archaeal motility machinery. Conclusively, archaeal CheY proteins conserved the central mechanistic features between bacteria and archaea, but differ in the helix α4 to allow binding to an archaellum-specific interaction partner.
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35
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Sulfolobus acidocaldarius Transports Pentoses via a Carbohydrate Uptake Transporter 2 (CUT2)-Type ABC Transporter and Metabolizes Them through the Aldolase-Independent Weimberg Pathway. Appl Environ Microbiol 2018; 84:AEM.01273-17. [PMID: 29150511 DOI: 10.1128/aem.01273-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 11/12/2017] [Indexed: 12/15/2022] Open
Abstract
Sulfolobus spp. possess a great metabolic versatility and grow heterotrophically on various carbon sources, such as different sugars and peptides. Known sugar transporters in Archaea predominantly belong to ABC transport systems. Although several ABC transporters for sugar uptake have been characterized in the crenarchaeon Sulfolobus solfataricus, only one homologue of these transporters, the maltose/maltooligomer transporter, could be identified in the closely related Sulfolobus acidocaldarius Comparison of the transcriptome of S. acidocaldarius MW001 grown on peptides alone and peptides in the presence of d-xylose allowed for the identification of the ABC transporter for d-xylose and l-arabinose transport and the gaining of deeper insights into pentose catabolism under the respective growth conditions. The d-xylose/l-arabinose substrate binding protein (SBP) (Saci_2122) of the ABC transporter is unique in Archaea and shares more similarity to bacterial SBPs of the carbohydrate uptake transporter-2 (CUT2) family than to any characterized archaeal one. The identified pentose transporter is the first CUT2 family ABC transporter analyzed in the domain of Archaea Single-gene deletion mutants of the ABC transporter subunits exemplified the importance of the transport system for d-xylose and l-arabinose uptake. Next to the transporter operon, enzymes of the aldolase-independent pentose catabolism branch were found to be upregulated in N-Z-Amine and d-xylose medium. The α-ketoglutarate semialdehyde dehydrogenase (KGSADH; Saci_1938) seemed not to be essential for growth on pentoses. However, the deletion mutant of the 2-keto-3-deoxyarabinoate/xylonate dehydratase (KDXD [also known as KDAD]; Saci_1939) was no longer able to catabolize d-xylose or l-arabinose, suggesting the absence of the aldolase-dependent branch in S. acidocaldarius IMPORTANCE Thermoacidophilic microorganisms are emerging model organisms for biotechnological applications, as their optimal growth conditions resemble conditions used in certain biotechnologies such as industrial plant waste degradation. Because of its high genome stability, Sulfolobus acidocaldarius is especially suited as a platform organism for such applications. For use in (ligno)cellulose degradation, it was important to understand pentose uptake and metabolism in S. acidocaldarius This study revealed that only the aldolase-independent Weimberg pathway is required for growth of S. acidocaldarius MW001 on d-xylose and l-arabinose. Moreover, S. acidocaldarius employs a CUT2 ABC transporter for pentose uptake, which is more similar to bacterial than to archaeal ABC transporters. The identification of pentose-inducible promoters will expedite the metabolic engineering of S. acidocaldarius for its development into a platform organism for (ligno)cellulose degradation.
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36
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Chaudhury P, Quax TEF, Albers SV. Versatile cell surface structures of archaea. Mol Microbiol 2017; 107:298-311. [PMID: 29194812 DOI: 10.1111/mmi.13889] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
Abstract
Archaea are ubiquitously present in nature and colonize environments with broadly varying growth conditions. Several surface appendages support their colonization of new habitats. A hallmark of archaea seems to be the high abundance of type IV pili (T4P). However, some unique non T4 filaments are present in a number of archaeal species. Archaeal surface structures can mediate different processes such as cellular surface adhesion, DNA exchange, motility and biofilm formation and represent an initial attachment site for infecting viruses. In addition to the functionally characterized archaeal T4P, archaeal genomes encode a large number of T4P components that might form yet undiscovered surface structures with novel functions. In this review, we summarize recent advancement in structural and functional characterizations of known archaeal surface structures and highlight the diverse processes in which they play a role.
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Affiliation(s)
- Paushali Chaudhury
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Tessa E F Quax
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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37
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Peeters E, Boon M, Rollie C, Willaert RG, Voet M, White MF, Prangishvili D, Lavigne R, Quax TEF. DNA-Interacting Characteristics of the Archaeal Rudiviral Protein SIRV2_Gp1. Viruses 2017; 9:v9070190. [PMID: 28718834 PMCID: PMC5537682 DOI: 10.3390/v9070190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 12/02/2022] Open
Abstract
Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rod-shaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally characterize gp1, which is a SIRV2 gene with unknown function. The SIRV2_Gp1 protein is highly expressed during early stages of infection and it is the only protein that is encoded twice on the viral genome. It harbours a helix-turn-helix motif and was therefore hypothesized to bind DNA. The DNA-binding behavior of SIRV2_Gp1 was characterized with electrophoretic mobility shift assays and atomic force microscopy. We provide evidence that the protein interacts with DNA and that it forms large aggregates, thereby causing extreme condensation of the DNA. Furthermore, the N-terminal domain of the protein mediates toxicity to the viral host Sulfolobus. Our findings may lead to biotechnological applications, such as the development of a toxic peptide for the containment of pathogenic bacteria, and add to our understanding of the Rudiviral infection cycle.
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Affiliation(s)
- Eveline Peeters
- Research Group of Microbiology, Department of Bio-Engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
| | - Clare Rollie
- Biomedical Sciences Research Complex, University of St Andrews, Fife, North Haugh, St. Andrews KY16 9AJ, UK.
| | - Ronnie G Willaert
- Alliance Research Group VUB-UGhent NanoMicrobiology, IJRG VUB-EPFL, BioNanotechnology & NanoMedicine, Research Group Structural Biology Brussels, Department of Bio-Engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, Fife, North Haugh, St. Andrews KY16 9AJ, UK.
| | | | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
| | - Tessa E F Quax
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
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38
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Li L, Banerjee A, Bischof LF, Maklad HR, Hoffmann L, Henche AL, Veliz F, Bildl W, Schulte U, Orell A, Essen LO, Peeters E, Albers SV. Wing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius. Mol Microbiol 2017. [PMID: 28628237 DOI: 10.1111/mmi.13735] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In response to a variety of environmental cues, prokaryotes can switch between a motile and a sessile, biofilm-forming mode of growth. The regulatory mechanisms and signaling pathways underlying this switch are largely unknown in archaea but involve small winged helix-turn-helix DNA-binding proteins of the archaea-specific Lrs14 family. Here, we study the Lrs14 member AbfR1 of Sulfolobus acidocaldarius. Small-angle X-ray scattering data are presented, which are consistent with a model of dimeric AbfR1 in which dimerization occurs via an antiparallel coiled coil as suggested by homology modeling. Furthermore, solution structure data of AbfR1-DNA complexes suggest that upon binding DNA, AbfR1 induces deformations in the DNA. The wing residues tyrosine 84 and serine 87, which are phosphorylated in vivo, are crucial to establish stable protein-DNA contacts and their substitution with a negatively charged glutamate or aspartate residue inhibits formation of a nucleoprotein complex. Furthermore, mutation abrogates the cellular abundance and transcription regulatory function of AbfR1 and thus affects the resulting biofilm and motility phenotype of S. acidocaldarius. This work establishes a novel wHTH DNA-binding mode for Lrs14-like proteins and hints at an important role for protein phosphorylation as a signal transduction mechanism for the control of biofilm formation and motility in archaea.
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Affiliation(s)
- Lingling Li
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Ankan Banerjee
- Structural Biochemistry, Department of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Lisa Franziska Bischof
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, Freiburg, Germany
| | - Hassan Ramadan Maklad
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Anna-Lena Henche
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Fabian Veliz
- Molecular Microbiology of Extremophiles Group, Centre for Genomics and Bioinformatics, Faculty of Sciences, University Mayor, Santiago, Chile
| | - Wolfgang Bildl
- Institute of Physiology, University of Freiburg, Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, University of Freiburg, Freiburg, Germany.,Center for Biological Signaling Studies (BIOSS), Freiburg, Germany
| | - Alvaro Orell
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Molecular Microbiology of Extremophiles Group, Centre for Genomics and Bioinformatics, Faculty of Sciences, University Mayor, Santiago, Chile.,Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
| | - Lars-Oliver Essen
- Structural Biochemistry, Department of Chemistry, Philipps University of Marburg, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
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39
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Le TN, Wagner A, Albers SV. A conserved hexanucleotide motif is important in UV-inducible promoters in Sulfolobus acidocaldarius. MICROBIOLOGY-SGM 2017; 163:778-788. [PMID: 28463103 PMCID: PMC5817253 DOI: 10.1099/mic.0.000455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Upon DNA damage, Sulfolobales exhibit a global gene regulatory response resulting in the expression of DNA transfer and repair proteins and the repression of the cell division machinery. Because the archaeal DNA damage response is still poorly understood, we investigated the promoters of the highly induced ups operon. Ups pili are involved in cellular aggregation and DNA exchange between cells. With LacS reporter gene assays we identified a conserved, non-palindromic hexanucleotide motif upstream of the ups core promoter elements to be essential for promoter activity. Substitution of this cis regulatory motif in the ups promoters resulted in abolishment of cellular aggregation and reduced DNA transfer. By screening the Sulfolobus acidocaldarius genome we identified a total of 214 genes harbouring the hexanucleotide motif in their respective promoter regions. Many of these genes were previously found to be regulated upon UV light treatment. Given the fact that the identified motif is conserved among S. acidocaldarius and Sulfolobus tokodaii promoters, we speculate that a common regulatory mechanism is present in these two species in response to DNA-damaging conditions.
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Affiliation(s)
- Thuong Ngoc Le
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Alexander Wagner
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
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40
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Poweleit N, Ge P, Nguyen HH, Ogorzalek Loo RR, Gunsalus RP, Zhou ZH. CryoEM structure of the Methanospirillum hungatei archaellum reveals structural features distinct from the bacterial flagellum and type IV pilus. Nat Microbiol 2016; 2:16222. [PMID: 27922015 PMCID: PMC5695567 DOI: 10.1038/nmicrobiol.2016.222] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022]
Abstract
Archaea use flagella known as archaella-distinct both in protein composition and structure from bacterial flagella-to drive cell motility, but the structural basis of this function is unknown. Here, we report an atomic model of the archaella, based on the cryo electron microscopy (cryoEM) structure of the Methanospirillum hungatei archaellum at 3.4 Å resolution. Each archaellum contains ∼61,500 archaellin subunits organized into a curved helix with a diameter of 10 nm and average length of 10,000 nm. The tadpole-shaped archaellin monomer has two domains, a β-barrel domain and a long, mildly kinked α-helix tail. Our structure reveals multiple post-translational modifications to the archaella, including six O-linked glycans and an unusual N-linked modification. The extensive interactions among neighbouring archaellins explain how the long but thin archaellum maintains the structural integrity required for motility-driving rotation. These extensive inter-subunit interactions and the absence of a central pore in the archaellum distinguish it from both the bacterial flagellum and type IV pili.
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Affiliation(s)
- Nicole Poweleit
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
- Electron Imaging Center for Nanomachines, California Nano Systems Institute, UCLA, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Peng Ge
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
- Electron Imaging Center for Nanomachines, California Nano Systems Institute, UCLA, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Hong H. Nguyen
- Department of Chemistry and Biochemistry, UCLA, Los Angeles 90095, UCLA, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Rachel R. Ogorzalek Loo
- Department of Chemistry and Biochemistry, UCLA, Los Angeles 90095, UCLA, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Robert P. Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
- The UCLA-DOE Institute, UCLA, Los Angeles, California 90095, USA
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
- Electron Imaging Center for Nanomachines, California Nano Systems Institute, UCLA, Los Angeles (UCLA), Los Angeles, California 90095, USA
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41
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Haurat MF, Figueiredo AS, Hoffmann L, Li L, Herr K, J Wilson A, Beeby M, Schaber J, Albers SV. ArnS, a kinase involved in starvation-induced archaellum expression. Mol Microbiol 2016; 103:181-194. [PMID: 27731916 DOI: 10.1111/mmi.13550] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Organisms have evolved motility organelles that allow them to move to favourable habitats. Cells integrate environmental stimuli into intracellular signals to motility machineries to direct this migration. Many motility organelles are complex surface appendages that have evolved a tight, hierarchical regulation of expression. In the crenearchaeon Sulfolobus acidocaldarius, biosynthesis of the archaellum is regulated by regulatory network proteins that control expression of archaellum components in a phosphorylation-dependent manner. A major trigger for archaellum expression is nutrient starvation, but although some components are known, the regulatory cascade triggered by starvation is poorly understood. In this work, the starvation-induced Ser/Thr protein kinase ArnS (Saci_1181) which is located proximally to the archaellum operon was identified. Deletion of arnS results in reduced motility, though the archaellum is properly assembled. Therefore, our experimental and modelling results indicate that ArnS plays an essential role in the precisely controlled expression of archaellum components during starvation-induced motility in Sulfolobus acidocaldarius. Furthermore they combined in vivo experiments and mathematical models to describe for the first time in archaea the dynamics of key regulators of archaellum expression.
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Affiliation(s)
- M Florencia Haurat
- Molecular Biology of Archaea, Institute of Biology II University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
| | - Ana Sofia Figueiredo
- Institute for Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, Pfälzer Platz 2, Magdeburg, 39106, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute of Biology II University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
| | - Lingling Li
- Molecular Biology of Archaea, Institute of Biology II University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
| | - Katharina Herr
- Molecular Biology of Archaea, Institute of Biology II University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
| | - Amanda J Wilson
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Jörg Schaber
- Institute for Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, Pfälzer Platz 2, Magdeburg, 39106, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
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42
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Hoffmann L, Schummer A, Reimann J, Haurat MF, Wilson AJ, Beeby M, Warscheid B, Albers SV. Expanding the archaellum regulatory network - the eukaryotic protein kinases ArnC and ArnD influence motility of Sulfolobus acidocaldarius. Microbiologyopen 2016; 6. [PMID: 27771939 PMCID: PMC5300886 DOI: 10.1002/mbo3.414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/06/2016] [Accepted: 09/14/2016] [Indexed: 01/15/2023] Open
Abstract
Expression of the archaellum, the archaeal‐type IV pilus‐like rotating motility structure is upregulated under nutrient limitation. This is controlled by a network of regulators, called the archaellum regulatory network (arn). Several of the components of this network in Sulfolobus acidocaldarius can be phosphorylated, and the deletion of the phosphatase PP2A results in strongly increased motility during starvation, indicating a role for phosphorylation in the regulation of motility. Analysis of the motility of different protein kinase deletion strains revealed that deletion of saci_0965, saci_1181, and saci_1193 resulted in reduced motility, whereas the deletion of saci_1694 resulted in hypermotility. Here ArnC (Saci_1193) and ArnD (Saci_1694) are characterized. Purified ArnC and ArnD phosphorylate serine and threonine residues in the C‐terminus of the repressor ArnB. arnC is upregulated in starvation medium, whereas arnD is constitutively expressed. However, while differences in the expression and levels of flaB were observed in the ΔarnD strain during growth under rich conditions, under nutrient limiting conditions the ΔarnC and ΔarnD strains showed no large differences in the expression levels of the archaellum or of the studied regulators. This suggests that next to the regulation via the archaellum regulatory network additional regulatory mechanisms of expression and/or activity of the archaellum exist.
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Affiliation(s)
- Lena Hoffmann
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Andreas Schummer
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Julia Reimann
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Maria F Haurat
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Amanda J Wilson
- Department of Life Sciences, Imperial College of London, London, UK
| | - Morgan Beeby
- Department of Life Sciences, Imperial College of London, London, UK
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Sonja-V Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
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43
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Schäffer C, Messner P. Emerging facets of prokaryotic glycosylation. FEMS Microbiol Rev 2016; 41:49-91. [PMID: 27566466 DOI: 10.1093/femsre/fuw036] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/17/2016] [Accepted: 08/01/2016] [Indexed: 12/16/2022] Open
Abstract
Glycosylation of proteins is one of the most prevalent post-translational modifications occurring in nature, with a wide repertoire of biological implications. Pathways for the main types of this modification, the N- and O-glycosylation, can be found in all three domains of life-the Eukarya, Bacteria and Archaea-thereby following common principles, which are valid also for lipopolysaccharides, lipooligosaccharides and glycopolymers. Thus, studies on any glycoconjugate can unravel novel facets of the still incompletely understood fundamentals of protein N- and O-glycosylation. While it is estimated that more than two-thirds of all eukaryotic proteins would be glycosylated, no such estimate is available for prokaryotic glycoproteins, whose understanding is lagging behind, mainly due to the enormous variability of their glycan structures and variations in the underlying glycosylation processes. Combining glycan structural information with bioinformatic, genetic, biochemical and enzymatic data has opened up an avenue for in-depth analyses of glycosylation processes as a basis for glycoengineering endeavours. Here, the common themes of glycosylation are conceptualised for the major classes of prokaryotic (i.e. bacterial and archaeal) glycoconjugates, with a special focus on glycosylated cell-surface proteins. We describe the current knowledge of biosynthesis and importance of these glycoconjugates in selected pathogenic and beneficial microbes.
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Affiliation(s)
- Christina Schäffer
- Department of NanoBiotechnology, Institute of Biologically Inspired Materials, NanoGlycobiology unit, Universität für Bodenkultur Wien, A-1180 Vienna, Austria
| | - Paul Messner
- Department of NanoBiotechnology, Institute of Biologically Inspired Materials, NanoGlycobiology unit, Universität für Bodenkultur Wien, A-1180 Vienna, Austria
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44
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Esser D, Hoffmann L, Pham TK, Bräsen C, Qiu W, Wright PC, Albers SV, Siebers B. Protein phosphorylation and its role in archaeal signal transduction. FEMS Microbiol Rev 2016; 40:625-47. [PMID: 27476079 PMCID: PMC5007285 DOI: 10.1093/femsre/fuw020] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2016] [Indexed: 12/23/2022] Open
Abstract
Reversible protein phosphorylation is the main mechanism of signal transduction that enables cells to rapidly respond to environmental changes by controlling the functional properties of proteins in response to external stimuli. However, whereas signal transduction is well studied in Eukaryotes and Bacteria, the knowledge in Archaea is still rather scarce. Archaea are special with regard to protein phosphorylation, due to the fact that the two best studied phyla, the Euryarchaeota and Crenarchaeaota, seem to exhibit fundamental differences in regulatory systems. Euryarchaeota (e.g. halophiles, methanogens, thermophiles), like Bacteria and Eukaryotes, rely on bacterial-type two-component signal transduction systems (phosphorylation on His and Asp), as well as on the protein phosphorylation on Ser, Thr and Tyr by Hanks-type protein kinases. Instead, Crenarchaeota (e.g. acidophiles and (hyper)thermophiles) only depend on Hanks-type protein phosphorylation. In this review, the current knowledge of reversible protein phosphorylation in Archaea is presented. It combines results from identified phosphoproteins, biochemical characterization of protein kinases and protein phosphatases as well as target enzymes and first insights into archaeal signal transduction by biochemical, genetic and polyomic studies. The authors review the current knowledge about protein phosphorylation in Archaea and its impact on signaling in this organism group.
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Affiliation(s)
- Dominik Esser
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Trong Khoa Pham
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Wen Qiu
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Phillip C Wright
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, UK School of Chemical Engineering and Advanced Materials, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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45
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Meshcheryakov VA, Wolf M. Crystal structure of the flagellar accessory protein FlaH of Methanocaldococcus jannaschii suggests a regulatory role in archaeal flagellum assembly. Protein Sci 2016; 25:1147-55. [PMID: 27060465 DOI: 10.1002/pro.2932] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/30/2016] [Accepted: 03/30/2016] [Indexed: 11/11/2022]
Abstract
Archaeal flagella are unique structures that share functional similarity with bacterial flagella, but are structurally related to bacterial type IV pili. The flagellar accessory protein FlaH is one of the conserved components of the archaeal motility system. However, its function is not clearly understood. Here, we present the 2.2 Å resolution crystal structure of FlaH from the hyperthermophilic archaeon, Methanocaldococcus jannaschii. The protein has a characteristic RecA-like fold, which has been found previously both in archaea and bacteria. We show that FlaH binds to immobilized ATP-however, it lacks ATPase activity. Surface plasmon resonance analysis demonstrates that ATP affects the interaction between FlaH and the archaeal motor protein FlaI. In the presence of ATP, the FlaH-FlaI interaction becomes significantly weaker. A database search revealed similarity between FlaH and several DNA-binding proteins of the RecA superfamily. The closest structural homologs of FlaH are KaiC-like proteins, which are archaeal homologs of the circadian clock protein KaiC from cyanobacteria. We propose that one of the functions of FlaH may be the regulation of archaeal motor complex assembly.
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Affiliation(s)
- Vladimir A Meshcheryakov
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa 904-0495, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa 904-0495, Japan
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46
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Effects of growth conditions on archaellation and N-glycosylation in Methanococcus maripaludis. Microbiology (Reading) 2016; 162:339-350. [DOI: 10.1099/mic.0.000221] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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47
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Chaudhury P, Neiner T, D'Imprima E, Banerjee A, Reindl S, Ghosh A, Arvai AS, Mills DJ, van der Does C, Tainer JA, Vonck J, Albers SV. The nucleotide-dependent interaction of FlaH and FlaI is essential for assembly and function of the archaellum motor. Mol Microbiol 2015; 99:674-85. [PMID: 26508112 PMCID: PMC5019145 DOI: 10.1111/mmi.13260] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2015] [Indexed: 12/24/2022]
Abstract
The motor of the membrane-anchored archaeal motility structure, the archaellum, contains FlaX, FlaI and FlaH. FlaX forms a 30 nm ring structure that acts as a scaffold protein and was shown to interact with the bifunctional ATPase FlaI and FlaH. However, the structure and function of FlaH has been enigmatic. Here we present structural and functional analyses of isolated FlaH and archaellum motor subcomplexes. The FlaH crystal structure reveals a RecA/Rad51 family fold with an ATP bound on a conserved and exposed surface, which presumably forms an oligomerization interface. FlaH does not hydrolyze ATP in vitro, but ATP binding to FlaH is essential for its interaction with FlaI and for archaellum assembly. FlaH interacts with the C-terminus of FlaX, which was earlier shown to be essential for FlaX ring formation and to mediate interaction with FlaI. Electron microscopy reveals that FlaH assembles as a second ring inside the FlaX ring in vitro. Collectively these data reveal central structural mechanisms for FlaH interactions in mediating archaellar assembly: FlaH binding within the FlaX ring and nucleotide-regulated FlaH binding to FlaI form the archaellar basal body core.
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Affiliation(s)
- Paushali Chaudhury
- Molecular Biology of Archaea, University of Freiburg, Institute of Biology II, Schaenzlestr.1, 79104, Freiburg, Germany
| | - Tomasz Neiner
- Molecular Biology of Archaea, University of Freiburg, Institute of Biology II, Schaenzlestr.1, 79104, Freiburg, Germany
| | - Edoardo D'Imprima
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany
| | - Ankan Banerjee
- FB- Chemie-Biochemie, AG-Essen, Philipps Universität Marburg, Hans-Meerwein-Straße 4, 35039, Marburg, Germany
| | - Sophia Reindl
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Abhrajyoti Ghosh
- Molecular Biology of Archaea, University of Freiburg, Institute of Biology II, Schaenzlestr.1, 79104, Freiburg, Germany
| | - Andrew S Arvai
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany
| | - Chris van der Does
- Molecular Biology of Archaea, University of Freiburg, Institute of Biology II, Schaenzlestr.1, 79104, Freiburg, Germany
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, University of Freiburg, Institute of Biology II, Schaenzlestr.1, 79104, Freiburg, Germany
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Syutkin AS, Pyatibratov MG, Fedorov OV. Flagella of halophilic archaea: differences in supramolecular organization. BIOCHEMISTRY (MOSCOW) 2015; 79:1470-82. [PMID: 25749160 DOI: 10.1134/s0006297914130033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Archaeal flagella are similar functionally to bacterial flagella, but structurally they are completely different. Helical archaeal flagellar filaments are formed of protein subunits called flagellins (archaellins). Notwithstanding progress in studies of archaeal flagella achieved in recent years, many problems in this area are still unsolved. In this review, we analyze the formation of these supramolecular structures by the example of flagellar filaments of halophilic archaea. Recent data on the structure of the flagellar filaments demonstrate that their supramolecular organization differs considerably in different haloarchaeal species.
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Affiliation(s)
- A S Syutkin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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Chimileski S, Papke RT. Getting a hold on archaeal type IV pili: an expanding repertoire of cellular appendages implicates complex regulation and diverse functions. Front Microbiol 2015; 6:362. [PMID: 25999922 PMCID: PMC4419858 DOI: 10.3389/fmicb.2015.00362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/10/2015] [Indexed: 12/11/2022] Open
Affiliation(s)
- Scott Chimileski
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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FlaF Is a β-Sandwich Protein that Anchors the Archaellum in the Archaeal Cell Envelope by Binding the S-Layer Protein. Structure 2015; 23:863-872. [PMID: 25865246 PMCID: PMC4425475 DOI: 10.1016/j.str.2015.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 02/19/2015] [Accepted: 03/06/2015] [Indexed: 11/25/2022]
Abstract
Archaea employ the archaellum, a type IV pilus-like nanomachine, for swimming motility. In the crenarchaeon Sulfolobus acidocaldarius, the archaellum consists of seven proteins: FlaB/X/G/F/H/I/J. FlaF is conserved and essential for archaellum assembly but no FlaF structures exist. Here, we truncated the FlaF N terminus and solved 1.5-Å and 1.65-Å resolution crystal structures of this monotopic membrane protein. Structures revealed an N-terminal α-helix and an eight-strand β-sandwich, immunoglobulin-like fold with striking similarity to S-layer proteins. Crystal structures, X-ray scattering, and mutational analyses suggest dimer assembly is needed for in vivo function. The sole cell envelope component of S. acidocaldarius is a paracrystalline S-layer, and FlaF specifically bound to S-layer protein, suggesting that its interaction domain is located in the pseudoperiplasm with its N-terminal helix in the membrane. From these data, FlaF may act as the previously unknown archaellum stator protein that anchors the rotating archaellum to the archaeal cell envelope. This is the first structural and functional study of an archaellum stator component sFlaF is a β-sandwich, immunoglobulin-like dimeric protein FlaF resembles and binds to the S-layer protein FlaF exerts its function in the pseudoperiplasm
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