1
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Padalko A, Nair G, Sousa FL. Fusion/fission protein family identification in Archaea. mSystems 2024:e0094823. [PMID: 38700364 DOI: 10.1128/msystems.00948-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.
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Affiliation(s)
- Anastasiia Padalko
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Govind Nair
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Filipa L Sousa
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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2
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van Wolferen M, Ithurbide S, Santiago-Martínez MG, Charles-Orszag A. Editorial: Molecular Biology of Archaea - 2022. Front Microbiol 2024; 15:1393932. [PMID: 38655083 PMCID: PMC11035895 DOI: 10.3389/fmicb.2024.1393932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, Freiburg, Germany
| | - Solenne Ithurbide
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Michel Geovanni Santiago-Martínez
- The Microbial Ecophysiology Laboratory, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Arthur Charles-Orszag
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, United States
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3
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Blombach F, Sýkora M, Case J, Feng X, Baquero DP, Fouqueau T, Phung DK, Barker D, Krupovic M, She Q, Werner F. Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays. Nat Commun 2024; 15:1620. [PMID: 38388540 PMCID: PMC10883916 DOI: 10.1038/s41467-024-45728-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbour extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposons. Cbp1 recruits Cren7 forming together 'chimeric' chromatin-like structures at CRISPR arrays. We dissect Cbp1 function in vitro and in vivo and show that the third helix-turn-helix domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays.
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Affiliation(s)
- Fabian Blombach
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
| | - Michal Sýkora
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Jo Case
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Xu Feng
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute, Shandong University, Qingdao, 266237, PR China
| | - Diana P Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, F-75015, Paris, France
| | - Thomas Fouqueau
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Duy Khanh Phung
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Declan Barker
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, F-75015, Paris, France
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute, Shandong University, Qingdao, 266237, PR China
| | - Finn Werner
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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4
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Schiller H, Hong Y, Kouassi J, Rados T, Kwak J, DiLucido A, Safer D, Marchfelder A, Pfeiffer F, Bisson A, Schulze S, Pohlschroder M. Identification of structural and regulatory cell-shape determinants in Haloferax volcanii. Nat Commun 2024; 15:1414. [PMID: 38360755 PMCID: PMC10869688 DOI: 10.1038/s41467-024-45196-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Archaea play indispensable roles in global biogeochemical cycles, yet many crucial cellular processes, including cell-shape determination, are poorly understood. Haloferax volcanii, a model haloarchaeon, forms rods and disks, depending on growth conditions. Here, we used a combination of iterative proteomics, genetics, and live-cell imaging to identify mutants that only form rods or disks. We compared the proteomes of the mutants with wild-type cells across growth phases, thereby distinguishing between protein abundance changes specific to cell shape and those related to growth phases. The results identified a diverse set of proteins, including predicted transporters, transducers, signaling components, and transcriptional regulators, as important for cell-shape determination. Through phenotypic characterization of deletion strains, we established that rod-determining factor A (RdfA) and disk-determining factor A (DdfA) are required for the formation of rods and disks, respectively. We also identified structural proteins, including an actin homolog that plays a role in disk-shape morphogenesis, which we named volactin. Using live-cell imaging, we determined volactin's cellular localization and showed its dynamic polymerization and depolymerization. Our results provide insights into archaeal cell-shape determination, with possible implications for understanding the evolution of cell morphology regulation across domains.
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Affiliation(s)
- Heather Schiller
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Yirui Hong
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Joshua Kouassi
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Theopi Rados
- Brandeis University, Department of Biology, Waltham, MA, 02453, USA
| | - Jasmin Kwak
- Brandeis University, Department of Biology, Waltham, MA, 02453, USA
| | - Anthony DiLucido
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Daniel Safer
- University of Pennsylvania, Department of Physiology, Philadelphia, PA, 19104, USA
| | | | - Friedhelm Pfeiffer
- Biology II, Ulm University, 89069, Ulm, Germany
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Alexandre Bisson
- Brandeis University, Department of Biology, Waltham, MA, 02453, USA.
| | - Stefan Schulze
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA.
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, 14623, USA.
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5
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Tang SK, Zhi XY, Zhang Y, Makarova KS, Liu BB, Zheng GS, Zhang ZP, Zheng HJ, Wolf YI, Zhao YR, Jiang SH, Chen XM, Li EY, Zhang T, Chen PR, Feng YZ, Xiang MX, Lin ZQ, Shi JH, Chang C, Zhang X, Li R, Lou K, Wang Y, Chang L, Yin M, Yang LL, Gao HY, Zhang ZK, Tao TS, Guan TW, He FC, Lu YH, Cui HL, Koonin EV, Zhao GP, Xu P. Addendum: Cellular differentiation into hyphae and spores in halophilic archaea. Nat Commun 2024; 15:523. [PMID: 38302496 PMCID: PMC10834514 DOI: 10.1038/s41467-024-44821-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Affiliation(s)
- Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Bing-Bing Liu
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, China
| | - Guo-Song Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhen-Peng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 201203, China
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Yu-Rong Zhao
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Song-Hao Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Xi-Ming Chen
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - En-Yuan Li
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Pei-Ru Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Yu-Zhou Feng
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Ming-Xian Xiang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Zhi-Qian Lin
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Jia-Hui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Xue Zhang
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, China
| | - Rui Li
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Kai Lou
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Yun Wang
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Min Yin
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Ling-Ling Yang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Hui-Ying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Zhong-Kai Zhang
- Biotechnology and Genetic Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Tian-Shen Tao
- Department of Microbiology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China
| | - Tong-Wei Guan
- College of Food and Biological Engineering, Xihua University, Chengdu, 610039, China
| | - Fu-Chu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Yin-Hua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
| | - Guo-Ping Zhao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200032, China.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China.
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China.
- Department of Microbiology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China.
- Guizhou University, School of Medicine, Guiyang, 550025, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.
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6
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Gomes-Filho JV, Breuer R, Morales-Filloy HG, Pozhydaieva N, Borst A, Paczia N, Soppa J, Höfer K, Jäschke A, Randau L. Identification of NAD-RNA species and ADPR-RNA decapping in Archaea. Nat Commun 2023; 14:7597. [PMID: 37989750 PMCID: PMC10663502 DOI: 10.1038/s41467-023-43377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
NAD is a coenzyme central to metabolism that also serves as a 5'-terminal cap for bacterial and eukaryotic transcripts. Thermal degradation of NAD can generate nicotinamide and ADP-ribose (ADPR). Here, we use LC-MS/MS and NAD captureSeq to detect and identify NAD-RNAs in the thermophilic model archaeon Sulfolobus acidocaldarius and in the halophilic mesophile Haloferax volcanii. None of the four Nudix proteins of S. acidocaldarius catalyze NAD-RNA decapping in vitro, but one of the proteins (Saci_NudT5) promotes ADPR-RNA decapping. NAD-RNAs are converted into ADPR-RNAs, which we detect in S. acidocaldarius total RNA. Deletion of the gene encoding the 5'-3' exonuclease Saci-aCPSF2 leads to a 4.5-fold increase in NAD-RNA levels. We propose that the incorporation of NAD into RNA acts as a degradation marker for Saci-aCPSF2. In contrast, ADPR-RNA is processed by Saci_NudT5 into 5'-p-RNAs, providing another layer of regulation for RNA turnover in archaeal cells.
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Affiliation(s)
| | - Ruth Breuer
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | | | | | - Andreas Borst
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt am Main, Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt am Main, Germany
| | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- SYNMIKRO, Center for Synthetic Microbiology, Marburg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Lennart Randau
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany.
- SYNMIKRO, Center for Synthetic Microbiology, Marburg, Germany.
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7
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Tang SK, Zhi XY, Zhang Y, Makarova KS, Liu BB, Zheng GS, Zhang ZP, Zheng HJ, Wolf YI, Zhao YR, Jiang SH, Chen XM, Li EY, Zhang T, Chen PR, Feng YZ, Xiang MX, Lin ZQ, Shi JH, Chang C, Zhang X, Li R, Lou K, Wang Y, Chang L, Yin M, Yang LL, Gao HY, Zhang ZK, Tao TS, Guan TW, He FC, Lu YH, Cui HL, Koonin EV, Zhao GP, Xu P. Cellular differentiation into hyphae and spores in halophilic archaea. Nat Commun 2023; 14:1827. [PMID: 37005419 PMCID: PMC10067837 DOI: 10.1038/s41467-023-37389-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/14/2023] [Indexed: 04/04/2023] Open
Abstract
Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.
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Affiliation(s)
- Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Bing-Bing Liu
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, China
| | - Guo-Song Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhen-Peng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 201203, China
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Yu-Rong Zhao
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Song-Hao Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Xi-Ming Chen
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - En-Yuan Li
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Pei-Ru Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Yu-Zhou Feng
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Ming-Xian Xiang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Zhi-Qian Lin
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Jia-Hui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Xue Zhang
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, China
| | - Rui Li
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Kai Lou
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Yun Wang
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Min Yin
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Ling-Ling Yang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Hui-Ying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Zhong-Kai Zhang
- Biotechnology and Genetic Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Tian-Shen Tao
- Department of Microbiology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China
| | - Tong-Wei Guan
- College of Food and Biological Engineering, Xihua University, Chengdu, 610039, China
| | - Fu-Chu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Yin-Hua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
| | - Guo-Ping Zhao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200032, China.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China.
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China.
- Department of Microbiology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China.
- Guizhou University, School of Medicine, Guiyang, 550025, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.
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8
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Filée J, Becker HF, Mellottee L, Eddine RZ, Li Z, Yin W, Lambry JC, Liebl U, Myllykallio H. Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya. Nat Commun 2023; 14:838. [PMID: 36792581 DOI: 10.1038/s41467-023-36487-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.
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9
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Daugeron MC, Missoury S, Da Cunha V, Lazar N, Collinet B, van Tilbeurgh H, Basta T. A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea. Nat Commun 2023; 14:526. [PMID: 36720870 DOI: 10.1038/s41467-023-36210-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/20/2023] [Indexed: 02/02/2023] Open
Abstract
In Archaea and Eukaryotes, the synthesis of a universal tRNA modification, N6-threonyl-carbamoyl adenosine (t6A), is catalyzed by the KEOPS complex composed of Kae1, Bud32, Cgi121, and Pcc1. A fifth subunit, Gon7, is found only in Fungi and Metazoa. Here, we identify and characterize a fifth KEOPS subunit in Archaea. This protein, dubbed Pcc2, is a paralog of Pcc1 and is widely conserved in Archaea. Pcc1 and Pcc2 form a heterodimer in solution, and show modest sequence conservation but very high structural similarity. The five-subunit archaeal KEOPS does not form dimers but retains robust tRNA binding and t6A synthetic activity. Pcc2 can substitute for Pcc1 but the resulting KEOPS complex is inactive, suggesting a distinct function for the two paralogs. Comparative sequence and structure analyses point to a possible evolutionary link between archaeal Pcc2 and eukaryotic Gon7. Our work indicates that Pcc2 regulates the oligomeric state of the KEOPS complex, a feature that seems to be conserved from Archaea to Eukaryotes.
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10
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Pilotto S, Fouqueau T, Lukoyanova N, Sheppard C, Lucas-Staat S, Díaz-Santín LM, Matelska D, Prangishvili D, Cheung ACM, Werner F. Structural basis of RNA polymerase inhibition by viral and host factors. Nat Commun 2021; 12:5523. [PMID: 34535646 PMCID: PMC8448823 DOI: 10.1038/s41467-021-25666-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/19/2021] [Indexed: 12/26/2022] Open
Abstract
RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.
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Affiliation(s)
- Simona Pilotto
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK
| | - Thomas Fouqueau
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK
| | - Natalya Lukoyanova
- Institute for Structural and Molecular Biology, Birkbeck College, London, UK
| | - Carol Sheppard
- Section of Virology, Department of Infectious disease, Imperial College London, London, UK
| | | | | | - Dorota Matelska
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK
| | | | | | - Finn Werner
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK.
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11
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Abstract
Recruitment of RNA polymerase and initiation factors to the promoter is the only known target for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation are involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Saccharolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.
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Affiliation(s)
- Fabian Blombach
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Thomas Fouqueau
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Dorota Matelska
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Katherine Smollett
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Finn Werner
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK.
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12
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Pende N, Sogues A, Megrian D, Sartori-Rupp A, England P, Palabikyan H, Rittmann SKMR, Graña M, Wehenkel AM, Alzari PM, Gribaldo S. SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system. Nat Commun 2021; 12:3214. [PMID: 34088904 PMCID: PMC8178401 DOI: 10.1038/s41467-021-23099-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
Most archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.
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Affiliation(s)
- Nika Pende
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institut Pasteur, Paris, France
| | - Adrià Sogues
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France
| | - Daniela Megrian
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institut Pasteur, Paris, France
- École Doctorale Complexité du vivant, Sorbonne University, Paris, France
| | | | - Patrick England
- Plate-forme de biophysique moléculaire, C2RT-Institut Pasteur, CNRS, UMR 3528, Paris, France
| | - Hayk Palabikyan
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Wien, Austria
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Wien, Austria
| | - Martín Graña
- Bioinformatics Unit, Institut Pasteur of Montevideo, Montevideo, Uruguay
| | - Anne Marie Wehenkel
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France.
| | - Pedro M Alzari
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institut Pasteur, Paris, France.
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13
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Mauerhofer LM, Zwirtmayr S, Pappenreiter P, Bernacchi S, Seifert AH, Reischl B, Schmider T, Taubner RS, Paulik C, Rittmann SKMR. Hyperthermophilic methanogenic archaea act as high-pressure CH 4 cell factories. Commun Biol 2021; 4:289. [PMID: 33674723 PMCID: PMC7935968 DOI: 10.1038/s42003-021-01828-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH4) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH4 production kinetics at hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to systematically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH4 cell factories. Furthermore, our analysis revealed that high-performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyrα444 Glyα445 Tyrα446 in the alpha subunit of the methyl-coenzyme M reductase. Thus, high-pressure biological CH4 production in pure culture could provide a purposeful route for the transition to a carbon-neutral bioenergy sector.
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Affiliation(s)
- Lisa-Maria Mauerhofer
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
| | - Sara Zwirtmayr
- grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | - Patricia Pappenreiter
- grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | | | | | - Barbara Reischl
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria ,Krajete GmbH, Linz, Austria
| | - Tilman Schmider
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
| | - Ruth-Sophie Taubner
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria ,grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | - Christian Paulik
- grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | - Simon K.-M. R. Rittmann
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
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14
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Perez-Garcia P, Kobus S, Gertzen CGW, Hoeppner A, Holzscheck N, Strunk CH, Huber H, Jaeger KE, Gohlke H, Kovacic F, Smits SHJ, Streit WR, Chow J. A promiscuous ancestral enzyme´s structure unveils protein variable regions of the highly diverse metallo-β-lactamase family. Commun Biol 2021; 4:132. [PMID: 33514861 PMCID: PMC7846560 DOI: 10.1038/s42003-021-01671-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
The metallo-β-lactamase fold is an ancient protein structure present in numerous enzyme families responsible for diverse biological processes. The crystal structure of the hyperthermostable crenarchaeal enzyme Igni18 from Ignicoccus hospitalis was solved at 2.3 Å and could resemble a possible first archetype of a multifunctional metallo-β-lactamase. Ancestral enzymes at the evolutionary origin are believed to be promiscuous all-rounders. Consistently, Igni18´s activity can be cofactor-dependently directed from β-lactamase to lactonase, lipase, phosphodiesterase, phosphotriesterase or phospholipase. Its core-domain is highly conserved within metallo-β-lactamases from Bacteria, Archaea and Eukarya and gives insights into evolution and function of enzymes from this superfamily. Structural alignments with diverse metallo-β-lactamase-fold-containing enzymes allowed the identification of Protein Variable Regions accounting for modulation of activity, specificity and oligomerization patterns. Docking of different substrates within the active sites revealed the basis for the crucial cofactor dependency of this enzyme superfamily.
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Affiliation(s)
- Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Stefanie Kobus
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Christoph G W Gertzen
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Astrid Hoeppner
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Nicholas Holzscheck
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Christoph Heinrich Strunk
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
| | - Harald Huber
- Institute for Microbiology and Archaeal Center, Regensburg University, 93035, Regensburg, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany.
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15
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Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, Takano Y, Uematsu K, Ikuta T, Ito M, Matsui Y, Miyazaki M, Murata K, Saito Y, Sakai S, Song C, Tasumi E, Yamanaka Y, Yamaguchi T, Kamagata Y, Tamaki H, Takai K. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 2020; 577:519-525. [PMID: 31942073 PMCID: PMC7015854 DOI: 10.1038/s41586-019-1916-6] [Citation(s) in RCA: 313] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022]
Abstract
The origin of eukaryotes remains unclear1-4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E3) model.
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Affiliation(s)
- Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
| | - Nozomi Nakahara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yuki Morono
- Kochi Institute for Core Sample Research, X-star, JAMSTEC, Nankoku, Japan
| | - Miyuki Ogawara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshinori Takano
- Biogeochemistry Program, Research Institute for Marine Resources Utilization, JAMSTEC, Yokosuka, Japan
| | - Katsuyuki Uematsu
- Department of Marine and Earth Sciences, Marine Work Japan, Yokosuka, Japan
| | - Tetsuro Ikuta
- Research Institute for Global Change, JAMSTEC, Yokosuka, Japan
| | - Motoo Ito
- Kochi Institute for Core Sample Research, X-star, JAMSTEC, Nankoku, Japan
| | - Yohei Matsui
- Research Institute for Marine Resources Utilization, JAMSTEC, Yokosuka, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Yumi Saito
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Sanae Sakai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Chihong Song
- National Institute for Physiological Sciences, Okazaki, Japan
| | - Eiji Tasumi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yuko Yamanaka
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
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