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Buda DM, Szekeres E, Tudoran LB, Esclapez J, Banciu HL. Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T. BMC Microbiol 2023; 23:381. [PMID: 38049746 PMCID: PMC10694973 DOI: 10.1186/s12866-023-03133-z] [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: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND The extremely halophilic archaeon Haloferax (Hfx.) alexandrinus DSM 27206 T was previously documented for the ability to biosynthesize silver nanoparticles while mechanisms underlying its silver tolerance were overlooked. In the current study, we aimed to assess the transcriptional response of this haloarchaeon to varying concentrations of silver, seeking a comprehensive understanding of the molecular determinants underpinning its heavy metal tolerance. RESULTS The growth curves confirmed the capacity of Hfx. alexandrinus to surmount silver stress, while the SEM-EDS analysis illustrated the presence of silver nanoparticles in cultures exposed to 0.5 mM silver nitrate. The RNA-Seq based transcriptomic analysis of Hfx. alexandrinus cells exposed to 0.1, 0.25, and 0.5 mM silver nitrate revealed the differential expression of multiple sets of genes potentially employed in heavy-metal stress response, genes mostly related to metal transporters, basic metabolism, oxidative stress response and cellular motility. The RT-qPCR analysis of selected transcripts was conducted to verify and validate the generated RNA-Seq data. CONCLUSIONS Our results indicated that copA, encoding the copper ATPase, is essential for the survival of Hfx. alexandrinus cells in silver-containing saline media. The silver-exposed cultures underwent several metabolic adjustments that enabled the activation of enzymes involved in the oxidative stress response and impairment of the cellular movement capacity. To our knowledge, this study represents the first comprehensive analysis of gene expression in halophillic archaea facing increased levels of heavy metals.
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Grants
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- VIGRO-016 Vicerrectorado de Investigación y Transferencia de Conocimiento of the University of Alicante
- Ministry of Research, Innovation and Digitization, CNCS/CCCDI – UEFISCD
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Affiliation(s)
- Doriana Mădălina Buda
- Doctoral School of Integrative Biology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania.
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania.
| | - Edina Szekeres
- Institute of Biological Research Cluj, NIRDBS, Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Lucian Barbu Tudoran
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania
- National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Julia Esclapez
- Biochemistry and Molecular Biology and Soil and Agricultural Chemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Alicante, Spain
| | - Horia Leonard Banciu
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania.
- Emil G. Racoviță Institute, Babeș-Bolyai University, Cluj-Napoca, Romania.
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2
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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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3
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Cha G, Liu Y, Yang Q, Bai L, Cheng L, Fan W. Comparative Genomic Insights into Chemoreceptor Diversity and Habitat Adaptation of Archaea. Appl Environ Microbiol 2022; 88:e0157422. [PMID: 36314867 PMCID: PMC9680633 DOI: 10.1128/aem.01574-22] [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: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022] Open
Abstract
Diverse archaea, including many unknown species and phylogenetically deeply rooted taxa, survive in extreme environments. They play crucial roles in the global carbon cycle and element fluxes in many terrestrial, marine, saline, host-associated, hot-spring, and oilfield environments. There is little knowledge of the diversity of chemoreceptors that are presumably involved in their habitat adaptation. Thus, we have explored this diversity through phylogenetic and comparative genomic analyses of complete archaeal genomes. The results show that chemoreceptors are significantly richer in archaea of mild environments than in those of extreme environments, that specific ligand-binding domains of the chemoreceptors are strongly associated with specific habitats, and that the number of chemoreceptors correlates with genome size. The results indicate that the successful adaptation of archaea to specific habitats has been associated with the acquisition and maintenance of chemoreceptors, which may be crucial for their survival in these environments. IMPORTANCE 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. Here, we have explored this diversity through phylogenetic and comparative genomic analyses of complete archaeal genomes. Signaling sensing and adaptation processes are tightly related to the ligand-binding domain, and it is clear that evolution and natural selection in specialized niches under constant conditions have selected for smaller genome sizes. Taken together, our results extend the understanding of archaeal adaptations to different environments and emphasize the importance of ecological constraints in shaping their evolution.
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Affiliation(s)
- Guihong Cha
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Yugeng Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong, China
| | - Qing Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Liping Bai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Wei Fan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Gambelli L, Isupov MN, Conners R, McLaren M, Bellack A, Gold V, Rachel R, Daum B. An archaellum filament composed of two alternating subunits. Nat Commun 2022; 13:710. [PMID: 35132062 PMCID: PMC8821640 DOI: 10.1038/s41467-022-28337-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023] Open
Abstract
Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. In many species, several archaellin homologs are encoded in the same operon; however, previous structural studies indicated that archaellum filaments mainly consist of only one protein species. Here, we use electron cryo-microscopy to elucidate the structure of the archaellum from Methanocaldococcus villosus at 3.08 Å resolution. The filament is composed of two alternating archaellins, suggesting that the architecture and assembly of archaella is more complex than previously thought. Moreover, we identify structural elements that may contribute to the filament’s flexibility. The archaellum is a molecular machine used by archaea to swim, consisting of an intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. Here, the authors use electron cryo-microscopy to elucidate the structure of an archaellum, and find that the filament is composed of two alternating archaellins.
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Affiliation(s)
- Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, EX4 4QF, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Annett Bellack
- Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Vicki Gold
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Reinhard Rachel
- Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK. .,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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5
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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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6
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Tittes C, Schwarzer S, Quax TEF. Viral Hijack of Filamentous Surface Structures in Archaea and Bacteria. Viruses 2021; 13:v13020164. [PMID: 33499367 PMCID: PMC7911016 DOI: 10.3390/v13020164] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
The bacterial and archaeal cell surface is decorated with filamentous surface structures that are used for different functions, such as motility, DNA exchange and biofilm formation. Viruses hijack these structures and use them to ride to the cell surface for successful entry. In this review, we describe currently known mechanisms for viral attachment, translocation, and entry via filamentous surface structures. We describe the different mechanisms used to exploit various surface structures bacterial and archaeal viruses. This overview highlights the importance of filamentous structures at the cell surface for entry of prokaryotic viruses.
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7
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Pyatibratov MG, Syutkin AS, Quax TEF, Melnik TN, Papke RT, Gogarten JP, Kireev II, Surin AK, Beznosov SN, Galeva AV, Fedorov OV. Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum. Microbiologyopen 2020; 9:e1047. [PMID: 32352651 PMCID: PMC7349177 DOI: 10.1002/mbo3.1047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/23/2020] [Accepted: 03/28/2020] [Indexed: 12/24/2022] Open
Abstract
Halophilic archaea from the genus Halorubrum possess two extraordinarily diverged archaellin genes, flaB1 and flaB2. To clarify roles for each archaellin, we compared two natural Halorubrum lacusprofundi strains: One of them contains both archaellin genes, and the other has the flaB2 gene only. Both strains synthesize functional archaella; however, the strain, where both archaellins are present, is more motile. In addition, we expressed these archaellins in a Haloferax volcanii strain from which the endogenous archaellin genes were deleted. Three Hfx. volcanii strains expressing Hrr. lacusprofundi archaellins produced functional filaments consisting of only one (FlaB1 or FlaB2) or both (FlaB1/FlaB2) archaellins. All three strains were motile, although there were profound differences in the efficiency of motility. Both native and recombinant FlaB1/FlaB2 filaments have greater thermal stability and resistance to low salinity stress than single‐component filaments. Functional supercoiled Hrr. lacusprofundi archaella can be composed of either single archaellin: FlaB2 or FlaB1; however, the two divergent archaellin subunits provide additional stabilization to the archaellum structure and thus adaptation to a wider range of external conditions. Comparative genomic analysis suggests that the described combination of divergent archaellins is not restricted to Hrr. lacusprofundi, but is occurring also in organisms from other haloarchaeal genera.
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Affiliation(s)
- Mikhail G Pyatibratov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey S Syutkin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Tatjana N Melnik
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Igor I Kireev
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,State Research Center for Applied Microbiology & Biotechnology, Obolensk, Moscow Region, Russia
| | - Sergei N Beznosov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Anna V Galeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oleg V Fedorov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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