1
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Sendker FL, Lo YK, Heimerl T, Bohn S, Persson LJ, Mais CN, Sadowska W, Paczia N, Nußbaum E, Del Carmen Sánchez Olmos M, Forchhammer K, Schindler D, Erb TJ, Benesch JLP, Marklund EG, Bange G, Schuller JM, Hochberg GKA. Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature 2024; 628:894-900. [PMID: 38600380 PMCID: PMC11041685 DOI: 10.1038/s41586-024-07287-2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Fractals are patterns that are self-similar across multiple length-scales1. Macroscopic fractals are common in nature2-4; however, so far, molecular assembly into fractals is restricted to synthetic systems5-12. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.
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Affiliation(s)
- Franziska L Sendker
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yat Kei Lo
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Stefan Bohn
- Cryo-EM Platform and Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Louise J Persson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - Wiktoria Sadowska
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Nicole Paczia
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eva Nußbaum
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | | | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | - Daniel Schindler
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- MaxGENESYS Biofoundry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan M Schuller
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
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2
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Dornes A, Mais CN, Bange G. Structure of the GDP-bound state of the SRP GTPase FlhF. Acta Crystallogr F Struct Biol Commun 2024; 80:53-58. [PMID: 38376823 PMCID: PMC10910532 DOI: 10.1107/s2053230x24000979] [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: 12/15/2023] [Accepted: 01/27/2024] [Indexed: 02/21/2024] Open
Abstract
The GTPase FlhF, a signal recognition particle (SRP)-type enzyme, is pivotal for spatial-numerical control and bacterial flagella assembly across diverse species, including pathogens. This study presents the X-ray structure of FlhF in its GDP-bound state at a resolution of 2.28 Å. The structure exhibits the classical N- and G-domain fold, consistent with related SRP GTPases such as Ffh and FtsY. Comparative analysis with GTP-loaded FlhF elucidates the conformational changes associated with GTP hydrolysis. These topological reconfigurations are similarly evident in Ffh and FtsY, and play a pivotal role in regulating the functions of these hydrolases.
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Affiliation(s)
- Anita Dornes
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, University of Marburg, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany
| | - Christopher-Nils Mais
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, University of Marburg, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, University of Marburg, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany
- Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany
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3
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Eilers K, Hoong Yam JK, Liu X, Goh YF, To KN, Paracuellos P, Morton R, Brizuela J, Hui Yong AM, Givskov M, Freibert SA, Bange G, Rice SA, Steinchen W, Filloux A. The dual GGDEF/EAL domain enzyme PA0285 is a Pseudomonas species housekeeping phosphodiesterase regulating early attachment and biofilm architecture. J Biol Chem 2024; 300:105659. [PMID: 38237678 PMCID: PMC10874727 DOI: 10.1016/j.jbc.2024.105659] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/23/2023] [Accepted: 01/04/2024] [Indexed: 02/15/2024] Open
Abstract
Bacterial lifestyles depend on conditions encountered during colonization. The transition between planktonic and biofilm growth is dependent on the intracellular second messenger c-di-GMP. High c-di-GMP levels driven by diguanylate cyclases (DGCs) activity favor biofilm formation, while low levels were maintained by phosphodiesterases (PDE) encourage planktonic lifestyle. The activity of these enzymes can be modulated by stimuli-sensing domains such as Per-ARNT-Sim (PAS). In Pseudomonas aeruginosa, more than 40 PDE/DGC are involved in c-di-GMP homeostasis, including 16 dual proteins possessing both canonical DGC and PDE motifs, that is, GGDEF and EAL, respectively. It was reported that deletion of the EAL/GGDEF dual enzyme PA0285, one of five c-di-GMP-related enzymes conserved across all Pseudomonas species, impacts biofilms. PA0285 is anchored in the membrane and carries two PAS domains. Here, we confirm that its role is conserved in various P. aeruginosa strains and in Pseudomonas putida. Deletion of PA0285 impacts the early stage of colonization, and RNA-seq analysis suggests that expression of cupA fimbrial genes is involved. We demonstrate that the C-terminal portion of PA0285 encompassing the GGDEF and EAL domains binds GTP and c-di-GMP, respectively, but only exhibits PDE activity in vitro. However, both GGDEF and EAL domains are important for PA0285 PDE activity in vivo. Complementation of the PA0285 mutant strain with a copy of the gene encoding the C-terminal GGDEF/EAL portion in trans was not as effective as complementation with the full-length gene. This suggests the N-terminal transmembrane and PAS domains influence the PDE activity in vivo, through modulating the protein conformation.
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Affiliation(s)
- Kira Eilers
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Yu Fen Goh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Ka-Ning To
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Patricia Paracuellos
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Richard Morton
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Jaime Brizuela
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Adeline Mei Hui Yong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Sven-Andreas Freibert
- Philipps University Marburg, Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Gert Bange
- Philipps University Marburg, Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Microbiomes for One Systems Health and Agriculture and Food, CSIRO, Westmead, New South Wales, Australia
| | - Wieland Steinchen
- Philipps University Marburg, Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
| | - Alain Filloux
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.
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Bittner E, Stehlik T, Lam J, Dimitrov L, Heimerl T, Schöck I, Harberding J, Dornes A, Heymons N, Bange G, Schuldiner M, Zalckvar E, Bölker M, Schekman R, Freitag J. Proteins that carry dual targeting signals can act as tethers between peroxisomes and partner organelles. PLoS Biol 2024; 22:e3002508. [PMID: 38377076 PMCID: PMC10906886 DOI: 10.1371/journal.pbio.3002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/01/2024] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Peroxisomes are organelles with crucial functions in oxidative metabolism. To correctly target to peroxisomes, proteins require specialized targeting signals. A mystery in the field is the sorting of proteins that carry a targeting signal for peroxisomes and as well as for other organelles, such as mitochondria or the endoplasmic reticulum (ER). Exploring several of these proteins in fungal model systems, we observed that they can act as tethers bridging organelles together to create contact sites. We show that in Saccharomyces cerevisiae this mode of tethering involves the peroxisome import machinery, the ER-mitochondria encounter structure (ERMES) at mitochondria and the guided entry of tail-anchored proteins (GET) pathway at the ER. Our findings introduce a previously unexplored concept of how dual affinity proteins can regulate organelle attachment and communication.
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Affiliation(s)
- Elena Bittner
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thorsten Stehlik
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jason Lam
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Lazar Dimitrov
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Thomas Heimerl
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Isabelle Schöck
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jannik Harberding
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Anita Dornes
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Nikola Heymons
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Bölker
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Randy Schekman
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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5
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Jakob S, Steinchen W, Hanßmann J, Rosum J, Langenfeld K, Osorio-Valeriano M, Steube N, Giammarinaro PI, Hochberg GKA, Glatter T, Bange G, Diepold A, Thanbichler M. The virulence regulator VirB from Shigella flexneri uses a CTP-dependent switch mechanism to activate gene expression. Nat Commun 2024; 15:318. [PMID: 38182620 PMCID: PMC10770331 DOI: 10.1038/s41467-023-44509-z] [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: 06/02/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024] Open
Abstract
The transcriptional antisilencer VirB acts as a master regulator of virulence gene expression in the human pathogen Shigella flexneri. It binds DNA sequences (virS) upstream of VirB-dependent promoters and counteracts their silencing by the nucleoid-organizing protein H-NS. However, its precise mode of action remains unclear. Notably, VirB is not a classical transcription factor but related to ParB-type DNA-partitioning proteins, which have recently been recognized as DNA-sliding clamps using CTP binding and hydrolysis to control their DNA entry gate. Here, we show that VirB binds CTP, embraces DNA in a clamp-like fashion upon its CTP-dependent loading at virS sites and slides laterally on DNA after clamp closure. Mutations that prevent CTP-binding block VirB loading in vitro and abolish the formation of VirB nucleoprotein complexes as well as virulence gene expression in vivo. Thus, VirB represents a CTP-dependent molecular switch that uses a loading-and-sliding mechanism to control transcription during bacterial pathogenesis.
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Affiliation(s)
- Sara Jakob
- Department of Biology, University of Marburg, Marburg, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Juri Hanßmann
- Department of Biology, University of Marburg, Marburg, Germany
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julia Rosum
- Department of Biology, University of Marburg, Marburg, Germany
| | - Katja Langenfeld
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, Marburg, Germany
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Niklas Steube
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Pietro I Giammarinaro
- Department of Chemistry, University of Marburg, Marburg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Georg K A Hochberg
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Mass Spectrometry and Proteomics Facility, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gert Bange
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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6
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Joiner JD, Steinchen W, Mozer N, Kronenberger T, Bange G, Poso A, Wagner S, Hartmann MD. HilE represses the activity of the Salmonella virulence regulator HilD via a mechanism distinct from that of intestinal long-chain fatty acids. J Biol Chem 2023; 299:105387. [PMID: 37890783 PMCID: PMC10696396 DOI: 10.1016/j.jbc.2023.105387] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The expression of virulence factors essential for the invasion of host cells by Salmonella enterica is tightly controlled by a network of transcription regulators. The AraC/XylS transcription factor HilD is the main integration point of environmental signals into this regulatory network, with many factors affecting HilD activity. Long-chain fatty acids, which are highly abundant throughout the host intestine, directly bind to and repress HilD, acting as environmental cues to coordinate virulence gene expression. The regulatory protein HilE also negatively regulates HilD activity, through a protein-protein interaction. Both of these regulators inhibit HilD dimerization, preventing HilD from binding to target DNA. We investigated the structural basis of these mechanisms of HilD repression. Long-chain fatty acids bind to a conserved pocket in HilD, in a comparable manner to that reported for other AraC/XylS regulators, whereas HilE forms a stable heterodimer with HilD by binding to the HilD dimerization interface. Our results highlight two distinct, mutually exclusive mechanisms by which HilD activity is repressed, which could be exploited for the development of new antivirulence leads.
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Affiliation(s)
- Joe D Joiner
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany; Department of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Nick Mozer
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, Germany; Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland; Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany
| | - Gert Bange
- Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany; Department of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Antti Poso
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, Germany; Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Samuel Wagner
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany; Partner-site Tübingen, German Center for Infection Research (DZIF), Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
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7
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Kohm K, Jalomo-Khayrova E, Krüger A, Basu S, Steinchen W, Bange G, Frunzke J, Hertel R, Commichau F, Czech L. Structural and functional characterization of MrpR, the master repressor of the Bacillus subtilis prophage SPβ. Nucleic Acids Res 2023; 51:9452-9474. [PMID: 37602373 PMCID: PMC10516654 DOI: 10.1093/nar/gkad675] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
Prophages control their lifestyle to either be maintained within the host genome or enter the lytic cycle. Bacillus subtilis contains the SPβ prophage whose lysogenic state depends on the MrpR (YopR) protein, a key component of the lysis-lysogeny decision system. Using a historic B. subtilis strain harboring the heat-sensitive SPβ c2 mutant, we demonstrate that the lytic cycle of SPβ c2 can be induced by heat due to a single nucleotide exchange in the mrpR gene, rendering the encoded MrpRG136E protein temperature-sensitive. Structural characterization revealed that MrpR is a DNA-binding protein resembling the overall fold of tyrosine recombinases. MrpR has lost its recombinase function and the G136E exchange impairs its higher-order structure and DNA binding activity. Genome-wide profiling of MrpR binding revealed its association with the previously identified SPbeta repeated element (SPBRE) in the SPβ genome. MrpR functions as a master repressor of SPβ that binds to this conserved element to maintain lysogeny. The heat-inducible excision of the SPβ c2 mutant remains reliant on the serine recombinase SprA. A suppressor mutant analysis identified a previously unknown component of the lysis-lysogeny management system that is crucial for the induction of the lytic cycle of SPβ.
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Affiliation(s)
- Katharina Kohm
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Ekaterina Jalomo-Khayrova
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
| | - Aileen Krüger
- Institute of Bio- and Geosciences, iBG-1: Biotechnology, FZ Jülich, Germany
| | - Syamantak Basu
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, iBG-1: Biotechnology, FZ Jülich, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Laura Czech
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
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8
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Weiland P, Dempwolff F, Steinchen W, Freibert S, Tian H, Glatter T, Martin R, Thomma BPHJ, Bange G, Altegoer F. Structural and functional analysis of the cerato-platanin-like protein Cpl1 suggests diverging functions in smut fungi. Mol Plant Pathol 2023; 24:768-787. [PMID: 37171083 PMCID: PMC10257043 DOI: 10.1111/mpp.13349] [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] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/28/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Plant-pathogenic fungi are causative agents of the majority of plant diseases and can lead to severe crop loss in infected populations. Fungal colonization is achieved by combining different strategies, such as avoiding and counteracting the plant immune system and manipulating the host metabolome. Of major importance are virulence factors secreted by fungi, which fulfil diverse functions to support the infection process. Most of these proteins are highly specialized, with structural and biochemical information often absent. Here, we present the atomic structures of the cerato-platanin-like protein Cpl1 from Ustilago maydis and its homologue Uvi2 from Ustilago hordei. Both proteins adopt a double-Ψβ-barrel architecture reminiscent of cerato-platanin proteins, a class so far not described in smut fungi. Our structure-function analysis shows that Cpl1 binds to soluble chitin fragments via two extended grooves at the dimer interface of the two monomer molecules. This carbohydrate-binding mode has not been observed previously and expands the repertoire of chitin-binding proteins. Cpl1 localizes to the cell wall of U. maydis and might synergize with cell wall-degrading and decorating proteins during maize infection. The architecture of Cpl1 harbouring four surface-exposed loop regions supports the idea that it might play a role in the spatial coordination of these proteins. While deletion of cpl1 has only mild effects on the virulence of U. maydis, a recent study showed that deletion of uvi2 strongly impairs U. hordei virulence. Our structural comparison between Cpl1 and Uvi2 reveals sequence variations in the loop regions that might explain a diverging function.
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Affiliation(s)
- Paul Weiland
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Felix Dempwolff
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Sven‐Andreas Freibert
- Center for Synthetic Microbiology (SYNMIKRO), Institute of CytobiologyPhilipps‐University MarburgMarburgGermany
- Protein Biochemistry and Spectroscopy Core Facility, Institute of CytobiologyPhilipps‐University MarburgMarburgGermany
| | - Hui Tian
- Institute for Plant SciencesUniversity of CologneCologneGermany
| | - Timo Glatter
- Max‐Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Roman Martin
- Faculty of Mathematics and Computer SciencePhilipps‐University MarburgMarburgGermany
| | - Bart P. H. J. Thomma
- Institute for Plant SciencesUniversity of CologneCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
- Max‐Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
- Max‐Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Institute of MicrobiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
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9
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Fischer S, Trinh VT, Simon C, Weber LM, Forné I, Nist A, Bange G, Abendroth F, Stiewe T, Steinchen W, Liefke R, Vázquez O. Peptide-mediated inhibition of the transcriptional regulator Elongin BC induces apoptosis in cancer cells. Cell Chem Biol 2023:S2451-9456(23)00155-1. [PMID: 37354906 DOI: 10.1016/j.chembiol.2023.05.012] [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: 12/01/2022] [Revised: 04/12/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Inhibition of protein-protein interactions (PPIs) via designed peptides is an effective strategy to perturb their biological functions. The Elongin BC heterodimer (ELOB/C) binds to a BC-box motif and is essential for cancer cell growth. Here, we report a peptide that mimics the high-affinity BC-box of the PRC2-associated protein EPOP. This peptide tightly binds to the ELOB/C dimer (kD = 0.46 ± 0.02 nM) and blocks the association of ELOB/C with its interaction partners, both in vitro and in the cellular environment. Cancer cells treated with our peptide inhibitor showed decreased cell viability, increased apoptosis, and perturbed gene expression. Therefore, our work proposes that blocking the BC-box-binding pocket of ELOB/C is a feasible strategy to impair its function and inhibit cancer cell growth. Our peptide inhibitor promises novel mechanistic insights into the biological function of the ELOB/C dimer and offers a starting point for therapeutics linked to ELOB/C dysfunction.
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Affiliation(s)
- Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), University of Marburg, 35043 Marburg, Germany
| | - Van Tuan Trinh
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany
| | - Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), University of Marburg, 35043 Marburg, Germany
| | - Lisa M Weber
- Institute of Molecular Biology and Tumor Research (IMT), University of Marburg, 35043 Marburg, Germany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, 82152 Martinsried, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), University of Marburg, 35043 Marburg, Germany
| | - Gert Bange
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, 35043 Marburg, Germany
| | - Frank Abendroth
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), University of Marburg, 35043 Marburg, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, 35043 Marburg, Germany
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), University of Marburg, 35043 Marburg, Germany; Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, 35043 Marburg, Germany.
| | - Olalla Vázquez
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, 35043 Marburg, Germany.
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10
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Brückner S, Müller F, Schadowski L, Kalle T, Weber S, Marino EC, Kutscher B, Möller AM, Adler S, Begerow D, Steinchen W, Bange G, Narberhaus F. (p)ppGpp and moonlighting RNases influence the first step of lipopolysaccharide biosynthesis in Escherichia coli. Microlife 2023; 4:uqad031. [PMID: 37426605 PMCID: PMC10326835 DOI: 10.1093/femsml/uqad031] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/12/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023]
Abstract
The outer membrane (OM) protects Gram-negative bacteria from harsh environmental conditions and provides intrinsic resistance to many antimicrobial compounds. The asymmetric OM is characterized by phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet. Previous reports suggested an involvement of the signaling nucleotide ppGpp in cell envelope homeostasis in Escherichia coli. Here, we investigated the effect of ppGpp on OM biosynthesis. We found that ppGpp inhibits the activity of LpxA, the first enzyme of LPS biosynthesis, in a fluorometric in vitro assay. Moreover, overproduction of LpxA resulted in elongated cells and shedding of outer membrane vesicles (OMVs) with altered LPS content. These effects were markedly stronger in a ppGpp-deficient background. We further show that RnhB, an RNase H isoenzyme, binds ppGpp, interacts with LpxA, and modulates its activity. Overall, our study uncovered new regulatory players in the early steps of LPS biosynthesis, an essential process with many implications in the physiology and susceptibility to antibiotics of Gram-negative commensals and pathogens.
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Affiliation(s)
- Simon Brückner
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Fabian Müller
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Laura Schadowski
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Tyll Kalle
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Sophia Weber
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Emily C Marino
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Blanka Kutscher
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Anna-Maria Möller
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Sabine Adler
- Evolution of Plants and Fungi, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Dominik Begerow
- Evolution of Plants and Fungi, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
- Organismische Botanik und Mykologie, Institut für Planzenwissenschaften und Mikrobiologie, Fachbereich Biologie, Universität Hamburg,Ohnhorststrasse 18, Hamburg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Strasse 14, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Strasse 14, Marburg, Germany
| | - Franz Narberhaus
- Corresponding author. Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Universitätsstrasse 150, NDEF 06/784, 44780 Bochum, Germany. Tel: +492343223100; Fax: +492343214620; E-mail:
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11
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Zegarra V, Mais CN, Freitag J, Bange G. The mysterious diadenosine tetraphosphate (AP4A). Microlife 2023; 4:uqad016. [PMID: 37223742 PMCID: PMC10148737 DOI: 10.1093/femsml/uqad016] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/15/2023] [Accepted: 04/21/2023] [Indexed: 05/25/2023]
Abstract
Dinucleoside polyphosphates, a class of nucleotides found amongst all the Trees of Life, have been gathering a lot of attention in the past decades due to their putative role as cellular alarmones. In particular, diadenosine tetraphosphate (AP4A) has been widely studied in bacteria facing various environmental challenges and has been proposed to be important for ensuring cellular survivability through harsh conditions. Here, we discuss the current understanding of AP4A synthesis and degradation, protein targets, their molecular structure where possible, and insights into the molecular mechanisms of AP4A action and its physiological consequences. Lastly, we will briefly touch on what is known with regards to AP4A beyond the bacterial kingdom, given its increasing appearance in the eukaryotic world. Altogether, the notion that AP4A is a conserved second messenger in organisms ranging from bacteria to humans and is able to signal and modulate cellular stress regulation seems promising.
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Affiliation(s)
- Victor Zegarra
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Christopher-Nils Mais
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Johannes Freitag
- Department of Biology, Philipps University Marburg, Marburg 35043, Germany
| | - Gert Bange
- Corresponding author. Karl-von-Frisch Strasse 14, 35043 Marburg, Germany. E-mail:
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12
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Steube N, Moldenhauer M, Weiland P, Saman D, Kilb A, Ramírez Rojas AA, Garg SG, Schindler D, Graumann PL, Benesch JLP, Bange G, Friedrich T, Hochberg GKA. Fortuitously compatible protein surfaces primed allosteric control in cyanobacterial photoprotection. Nat Ecol Evol 2023; 7:756-767. [PMID: 37012377 PMCID: PMC10172135 DOI: 10.1038/s41559-023-02018-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/21/2023] [Indexed: 04/05/2023]
Abstract
Highly specific interactions between proteins are a fundamental prerequisite for life, but how they evolve remains an unsolved problem. In particular, interactions between initially unrelated proteins require that they evolve matching surfaces. It is unclear whether such surface compatibilities can only be built by selection in small incremental steps, or whether they can also emerge fortuitously. Here, we used molecular phylogenetics, ancestral sequence reconstruction and biophysical characterization of resurrected proteins to retrace the evolution of an allosteric interaction between two proteins that act in the cyanobacterial photoprotection system. We show that this interaction between the orange carotenoid protein (OCP) and its unrelated regulator, the fluorescence recovery protein (FRP), evolved when a precursor of FRP was horizontally acquired by cyanobacteria. FRP's precursors could already interact with and regulate OCP even before these proteins first encountered each other in an ancestral cyanobacterium. The OCP-FRP interaction exploits an ancient dimer interface in OCP, which also predates the recruitment of FRP into the photoprotection system. Together, our work shows how evolution can fashion complex regulatory systems easily out of pre-existing components.
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Affiliation(s)
- Niklas Steube
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Marcus Moldenhauer
- Institute of Chemistry PC14, Technische Universität Berlin, Berlin, Germany
| | - Paul Weiland
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Dominik Saman
- Department of Chemistry, Oxford University, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford University, Oxford, UK
| | - Alexandra Kilb
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | | | - Sriram G Garg
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Peter L Graumann
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Justin L P Benesch
- Department of Chemistry, Oxford University, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford University, Oxford, UK
| | - Gert Bange
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Thomas Friedrich
- Institute of Chemistry PC14, Technische Universität Berlin, Berlin, Germany.
| | - Georg K A Hochberg
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Department of Chemistry, University of Marburg, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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13
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Wątor E, Wilk P, Biela A, Rawski M, Zak KM, Steinchen W, Bange G, Glatt S, Grudnik P. Cryo-EM structure of human eIF5A-DHS complex reveals the molecular basis of hypusination-associated neurodegenerative disorders. Nat Commun 2023; 14:1698. [PMID: 36973244 PMCID: PMC10042821 DOI: 10.1038/s41467-023-37305-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Hypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The initial step of hypusination, the formation of deoxyhypusine, is catalyzed by deoxyhypusine synthase (DHS), however, the molecular details of the DHS-mediated reaction remained elusive. Recently, patient-derived variants of DHS and eIF5A have been linked to rare neurodevelopmental disorders. Here, we present the cryo-EM structure of the human eIF5A-DHS complex at 2.8 Å resolution and a crystal structure of DHS trapped in the key reaction transition state. Furthermore, we show that disease-associated DHS variants influence the complex formation and hypusination efficiency. Hence, our work dissects the molecular details of the deoxyhypusine synthesis reaction and reveals how clinically-relevant mutations affect this crucial cellular process.
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Affiliation(s)
- Elżbieta Wątor
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Piotr Wilk
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Biela
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Michał Rawski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Krzysztof M Zak
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Wieland Steinchen
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Gert Bange
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Molecular Physiology of Microbes, Marburg, Germany
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Przemysław Grudnik
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
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14
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Abstract
Nucleotides are at the heart of the most essential biological processes in the cell, be it as key protagonists in the dogma of molecular biology or by regulating multiple metabolic pathways. The dynamic nature of nucleotides, the cross talk between them, and their constant feedback to and from the cell's metabolic state position them as a hallmark of adaption toward environmental and growth challenges. It has become increasingly clear how the activity of RNA polymerase, the synthesis and maintenance of tRNAs, mRNA translation at all stages, and the biogenesis and assembly of ribosomes are fine-tuned by the pools of intracellular nucleotides. With all aspects composing protein synthesis involved, the ribosome emerges as the molecular hub in which many of these nucleotides encounter each other and regulate the state of the cell. In this review, we aim to highlight intracellular nucleotides in bacteria as dynamic characters permanently cross talking with each other and ultimately regulating protein synthesis at various stages in which the ribosome is mainly the principal character.
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Affiliation(s)
- Lorenzo Eugenio Leiva
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Victor Zegarra
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
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15
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Shearer HL, Loi VV, Weiland P, Bange G, Altegoer F, Hampton MB, Antelmann H, Dickerhof N. MerA functions as a hypothiocyanous acid reductase and defense mechanism in Staphylococcus aureus. Mol Microbiol 2023; 119:456-470. [PMID: 36779383 DOI: 10.1111/mmi.15035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 08/24/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/14/2023]
Abstract
The major pathogen Staphylococcus aureus has to cope with host-derived oxidative stress to cause infections in humans. Here, we report that S. aureus tolerates high concentrations of hypothiocyanous acid (HOSCN), a key antimicrobial oxidant produced in the respiratory tract. We discovered that the flavoprotein disulfide reductase (FDR) MerA protects S. aureus from this oxidant by functioning as a HOSCN reductase, with its deletion sensitizing bacteria to HOSCN. Crystal structures of homodimeric MerA (2.4 Å) with a Cys43 -Cys48 intramolecular disulfide, and reduced MerACys43 S (1.6 Å) showed the FAD cofactor close to the active site, supporting that MerA functions as a group I FDR. MerA is controlled by the redox-sensitive repressor HypR, which we show to be oxidized to intermolecular disulfides under HOSCN stress, resulting in its inactivation and derepression of merA transcription to promote HOSCN tolerance. Our study highlights the HOSCN tolerance of S. aureus and characterizes the structure and function of MerA as a major HOSCN defense mechanism. Crippling the capacity to respond to HOSCN may be a novel strategy for treating S. aureus infections.
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Affiliation(s)
- Heather L Shearer
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Vu V Loi
- Freie Universität Berlin, Institute of Biology-Microbiology, Berlin, Germany
| | - Paul Weiland
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Center for Tumor Biology and Immunology, Department of Medicine, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Institute of Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Haike Antelmann
- Freie Universität Berlin, Institute of Biology-Microbiology, Berlin, Germany
| | - Nina Dickerhof
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
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16
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Klemm P, Christ M, Altegoer F, Freitag J, Bange G, Lechner M. Evolutionary reconstruction, nomenclature and functional meta-analysis of the Kiwellin protein family. Front Plant Sci 2022; 13:1034708. [PMID: 36618657 PMCID: PMC9813671 DOI: 10.3389/fpls.2022.1034708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Crop diseases caused by pathogens critically affect global food security and plant ecology. Pathogens are well adapted to their host plants and have developed sophisticated mechanisms allowing successful colonization. Plants in turn have taken measures to counteract pathogen attacks resulting in an evolutionary arms race. Recent studies provided mechanistic insights into how two plant Kiwellin proteins from Zea mays mitigate the activity of the chorismate mutase Cmu1, a virulence factor secreted by the fungal pathogen Ustilago maydis during maize infection. Formerly identified as human allergens in kiwifruit, the biological function of Kiwellins is apparently linked to plant defense. We combined the analysis of proteome data with structural predictions to obtain a holistic overview of the Kiwellin protein family, that is subdivided into proteins with and without a N-terminal kissper domain. We found that Kiwellins are evolutionarily conserved in various plant species. At median five Kiwellin paralogs are encoded in each plant genome. Structural predictions revealed that Barwin-like proteins and Kiwellins cannot be discriminated purely at the sequence level. Our data shows that Kiwellins emerged in land plants (embryophyta) and are not present in fungi as suggested earlier. They evolved via three major duplication events that lead to clearly distinguishable subfamilies. We introduce a systematic Kiwellin nomenclature based on a detailed evolutionary reconstruction of this protein family. A meta-analysis of publicly available transcriptome data demonstrated that Kiwellins can be differentially regulated upon the interaction of plants with pathogens but also with symbionts. Furthermore, significant differences in Kiwellin expression levels dependent on tissues and cultivars were observed. In summary, our study sheds light on the evolution and regulation of a large protein family and provides a framework for a more detailed understanding of the molecular functions of Kiwellins.
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Affiliation(s)
- Paul Klemm
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Marvin Christ
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- Institute of Microbiology, Heinrich Heine University Dusseldorf, Düsseldorf, Germany
| | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Molecular Physiology of Microbes, Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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17
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Shi YM, Crames JJ, Czech L, Bozhüyük KAJ, Shi YN, Hirschmann M, Lamberth S, Claus P, Paczia N, Rückert C, Kalinowski J, Bange G, Bode HB. Genome Mining Enabled by Biosynthetic Characterization Uncovers a Class of Benzoxazolinate-Containing Natural Products in Diverse Bacteria. Angew Chem Int Ed Engl 2022; 61:e202206106. [PMID: 36198080 PMCID: PMC10098953 DOI: 10.1002/anie.202206106] [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: 04/26/2022] [Indexed: 11/18/2022]
Abstract
Benzoxazolinate is a rare bis-heterocyclic moiety that interacts with proteins and DNA and confers extraordinary bioactivities on natural products, such as C-1027. However, the biosynthetic gene responsible for the key cyclization step of benzoxazolinate remains unclear. Herein, we show a putative acyl AMP-ligase responsible for the last cyclization step. We used the enzyme as a probe for genome mining and discovered that the orphan benzobactin gene cluster in entomopathogenic bacteria prevails across Proteobacteria and Firmicutes. It turns out that Pseudomonas chlororaphis produces various benzobactins, whose biosynthesis is highlighted by a synergistic effect of two unclustered genes encoding enzymes on boosting benzobactin production; the formation of non-proteinogenic 2-hydroxymethylserine by a serine hydroxymethyltransferase; and the types I and II NRPS architecture for structural diversity. Our findings reveal the biosynthetic potential of a widespread benzobactin gene cluster.
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Affiliation(s)
- Yi-Ming Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jan J Crames
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Laura Czech
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Kenan A J Bozhüyük
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Yan-Ni Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Merle Hirschmann
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Stefanie Lamberth
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Peter Claus
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615, Bielefeld, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany.,Chemical Biology, Department of Chemistry, Philipps University of Marburg, 35043, Marburg, Germany
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18
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Herbel SM, Moyon L, Christ M, Elsayed EM, Caffrey BE, Malmsheimer S, Grin I, Hoffmann K, Surmann K, Blankenburg S, Jung AL, Herkt CE, Borsò M, Bozdag B, Imhof A, Becker A, Wagner S, Bange G, Völker U, Bertrams W, Marsico A, Schmeck B. Screening for eukaryotic motifs in Legionella pneumophila reveals Smh1 as bacterial deacetylase of host histones. Virulence 2022; 13:2042-2058. [PMID: 36411449 PMCID: PMC9704406 DOI: 10.1080/21505594.2022.2149973] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Legionella pneumophila (L.p.) is a bacterial pathogen which is a common causative agent of pneumonia. In humans, it infects alveolar macrophages and transfers hundreds of virulence factors that interfere with cellular signalling pathways and the transcriptomic landscape to sustain its own replication. By this interaction, it has acquired eukaryote-like protein motifs by gene transfer events that partake in the pathogenicity of Legionella. In a computational screening approach for eukaryotic motifs in the transcriptome of Legionella, we identified the L.p. strain Corby protein ABQ55614 as putative histone-deacetylase and named it "suppressing modifier of histones 1" (Smh1). During infection, Smh1 is translocated from the Legionella vacuole into the host cytosol. When expressed in human macrophage THP-1 cells, Smh1 was localized predominantly in the nucleus, leading to broad histone H3 and H4 deacetylation, blunted expression of a large number of genes (e.g. IL-1β and IL-8), and fostered intracellular bacterial replication. L.p. with a Smh1 knockdown grew normally in media but showed a slight growth defect inside the host cell. Furthermore, Smh1 showed a very potent histone deacetylation activity in vitro, e.g. at H3K14, that could be inhibited by targeted mutation of the putative catalytic center inferred by analogy with eukaryotic HDAC8, and with the deacetylase inhibitor trichostatin A. In summary, Smh1 displays functional homology with class I/II type HDACs. We identified Smh1 as a new Legionella virulence factor with a eukaryote-like histone-deacetylase activity that moderates host gene expression and might pave the way for further histone modifications.IMPORTANCELegionella pneumophila (L.p.) is a prominent bacterial pathogen, which is a common causative agent of pneumonia. In order to survive inside the host cell, the human macrophage, it profoundly interacts with host cell processes to advance its own replication. In this study, we identify a bacterial factor, Smh1, with yet unknown function as a host histone deacetylase. The activity of this factor in the host cell leads to attenuated gene expression and increased intracellular bacterial replication.
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Affiliation(s)
- Stefanie M. Herbel
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Lambert Moyon
- Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marvin Christ
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Eslam M. Elsayed
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany,Department of Biology, Philipps-Universität Marburg, Marburg, Germany,Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Brian E. Caffrey
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Silke Malmsheimer
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Iwan Grin
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Kerstin Hoffmann
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Kristin Surmann
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Sascha Blankenburg
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Anna Lena Jung
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Christina E. Herkt
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Marco Borsò
- Zentrallabor für Proteinanalytik, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Planegg-Martinsried
| | - Beyza Bozdag
- Zentrallabor für Proteinanalytik, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Planegg-Martinsried
| | - Axel Imhof
- Zentrallabor für Proteinanalytik, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Planegg-Martinsried
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany,Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Samuel Wagner
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany,German Center for Infection Research (DZIF), Partner-site Tübingen, Tübingen, Germany
| | - Gert Bange
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Wilhelm Bertrams
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany,Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, Philipps-University, Member of the German Center for Lung Research (DZL), Marburg, Germany,Institute for Lung Health (ILH), Justus-Liebig-University, Giessen, Germany,Member of the German Center for Infectious Disease Research (DZIF), Marburg, Germany,CONTACT Bernd Schmeck
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19
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Stoll J, Zegarra V, Bange G, Graumann PL. Single-molecule dynamics suggest that ribosomes assemble at sites of translation in Bacillus subtilis. Front Microbiol 2022; 13:999176. [PMID: 36406443 PMCID: PMC9670183 DOI: 10.3389/fmicb.2022.999176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 04/07/2024] Open
Abstract
Eukaryotic cells transcribe ribosomal RNA and largely assemble ribosomes in a structure called the nucleolus, where chromosomal regions containing rRNA operons are clustered. In bacteria, many rRNA operons cluster close to the origin regions that are positioned on the outer borders of nucleoids, close to polar areas, where translating 70S ribosomes are located. Because outer regions of the nucleoids contain the highest accumulation of RNA polymerase, it has been hypothesized that bacteria contain "nucleolus-like" structures. However, ribosome subunits freely diffuse through the entire cells, and could thus be assembled and matured throughout the non-compartmentalized cell. By tracking single molecules of two GTPases that play an essential role in ribosomal folding and processing in Bacillus subtilis, we show that this process takes place at sites of translation, i.e., predominantly at the cell poles. Induction of the stringent response led to a change in the population of GTPases assumed to be active in maturation, but did not abolish nucleoid occlusion of ribosomes or of GTPases. Our findings strongly support the idea of the conceptualization of nucleolus-like structures in bacteria, i.e., rRNA synthesis, ribosomal protein synthesis and subunit assembly occurring in close proximity at the cell poles, facilitating the efficiency of ribosome maturation even under conditions of transient nutrient deprivation.
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Affiliation(s)
| | | | | | - Peter L. Graumann
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
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20
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Shi YM, Crames JJ, Czech L, Bozhüyük KAJ, Shi YN, Hirschmann M, Lamberth S, Claus P, Paczia N, Rückert C, Kalinowski J, Bange G, Bode HB. Genome Mining Enabled by Biosynthetic Characterization Uncovers a Class of Benzoxazolinate‐Containing Natural Products in Diverse Bacteria. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yi-Ming Shi
- Max Planck Institute for Terrestrial Microbiology: Max-Planck-Institut fur terrestrische Mikrobiologie Natural Products in Organismic Interactions Karl-von-Frisch-Strasse 10 35043 Marburg GERMANY
| | - Jan J. Crames
- Max Planck Institute for Terrestrial Microbiology: Max-Planck-Institut fur terrestrische Mikrobiologie Natural Products in Organismic Interactions GERMANY
| | - Laura Czech
- University of Marburg: Philipps-Universitat Marburg Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry GERMANY
| | - Kenan A. J. Bozhüyük
- Max Planck Institute for Terrestrial Microbiology: Max-Planck-Institut fur terrestrische Mikrobiologie Natural Products in Organismic Interactions GERMANY
| | - Yan-Ni Shi
- Max Planck Institute for Terrestrial Microbiology: Max-Planck-Institut fur terrestrische Mikrobiologie Natural Products in Organismic Interactions GERMANY
| | - Merle Hirschmann
- Goethe-Universitat Frankfurt am Main Molecular Biotechnology, Department of Biosciences GERMANY
| | - Stefanie Lamberth
- Goethe-Universitat Frankfurt am Main Molecular Biotechnology, Department of Biosciences GERMANY
| | - Peter Claus
- Max Planck Institute for Terrestrial Microbiology: Max-Planck-Institut fur terrestrische Mikrobiologie Core Facility for Metabolomics and Small Molecule Mass Spectrometry GERMANY
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology: Max-Planck-Institut fur terrestrische Mikrobiologie Core Facility for Metabolomics and Small Molecule Mass Spectrometry GERMANY
| | - Christian Rückert
- Universität Bielefeld: Universitat Bielefeld Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec) GERMANY
| | - Jörn Kalinowski
- Universität Bielefeld: Universitat Bielefeld Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec) GERMANY
| | - Gert Bange
- University of Marburg: Philipps-Universitat Marburg Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry GERMANY
| | - Helge B Bode
- Max Planck Institute for Terrestrial Microbiology: Max-Planck-Institut fur terrestrische Mikrobiologie Department of Naturalproducts in organismic interactions Karl-von-Frisch-Str. 10 35043 Marburg GERMANY
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21
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Mühlenhoff U, Weiler BD, Nadler F, Millar R, Kothe I, Freibert SA, Altegoer F, Bange G, Lill R. The iron-sulfur cluster assembly (ISC) protein Iba57 executes a tetrahydrofolate-independent function in mitochondrial [4Fe-4S] protein maturation. J Biol Chem 2022; 298:102465. [PMID: 36075292 PMCID: PMC9551070 DOI: 10.1016/j.jbc.2022.102465] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 10/25/2022] Open
Abstract
Mitochondria harbor the bacteria-inherited iron-sulfur cluster assembly (ISC) machinery to generate [2Fe-2S] and [4Fe-4S] proteins. In yeast, assembly of [4Fe-4S] proteins specifically involves the ISC proteins Isa1, Isa2, Iba57, Bol3, and Nfu1. Functional defects in their human equivalents cause the multiple mitochondrial dysfunction syndromes (MMDS), severe disorders with a broad clinical spectrum. The bacterial Iba57 ancestor YgfZ was described to require tetrahydrofolate (THF) for its function in the maturation of selected [4Fe-4S] proteins. Both YgfZ and Iba57 are structurally related to an enzyme family catalyzing THF-dependent one-carbon transfer reactions including GcvT of the glycine cleavage system. On this basis, a universally conserved folate requirement in ISC-dependent [4Fe-4S] protein biogenesis was proposed. To test this idea for mitochondrial Iba57, we performed genetic and biochemical studies in S. cerevisiae, and we solved the crystal structure of Iba57 from the thermophilic fungus Chaetomium thermophilum. We provide three lines of evidence for the THF independence of the Iba57-catalyzed [4Fe-4S] protein assembly pathway. First, yeast mutants lacking folate show no defect in mitochondrial [4Fe-4S] protein maturation. Second, the 3D structure of Iba57 lacks many of the side chain contacts to THF as defined in GcvT, and the THF binding pocket is constricted. Third, mutations in conserved Iba57 residues that are essential for THF-dependent catalysis in GcvT do not impair Iba57 function in vivo, in contrast to an exchange of the invariant, surface-exposed cysteine residue. We conclude that mitochondrial Iba57, despite structural similarities to both YgfZ and THF-binding proteins, does not utilize folate for its function.
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Affiliation(s)
- Ulrich Mühlenhoff
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany.
| | - Benjamin Dennis Weiler
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany
| | - Franziska Nadler
- Present address: University Medical Center Göttingen, Department of Cellular Biochemistry Humboldtallee 23, 37073 Göttingen, Germany
| | - Robert Millar
- Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Present address: Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Isabell Kothe
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany
| | - Sven-Andreas Freibert
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany
| | - Florian Altegoer
- Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Fachbereich Chemie, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Present address: Heinrich-Heine Universität Du¨sseldorf, Institut für Mikrobiologie, Universitätsstraße 1, 40225 Du¨sseldorf, Germany
| | - Gert Bange
- Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Fachbereich Chemie, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany.
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22
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Giammarinaro PI, Young MKM, Steinchen W, Mais CN, Hochberg G, Yang J, Stevenson DM, Amador-Noguez D, Paulus A, Wang JD, Bange G. Diadenosine tetraphosphate regulates biosynthesis of GTP in Bacillus subtilis. Nat Microbiol 2022; 7:1442-1452. [PMID: 35953658 PMCID: PMC10439310 DOI: 10.1038/s41564-022-01193-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Diadenosine tetraphosphate (Ap4A) is a putative second messenger molecule that is conserved from bacteria to humans. Nevertheless, its physiological role and the underlying molecular mechanisms are poorly characterized. We investigated the molecular mechanism by which Ap4A regulates inosine-5'-monophosphate dehydrogenase (IMPDH, a key branching point enzyme for the biosynthesis of adenosine or guanosine nucleotides) in Bacillus subtilis. We solved the crystal structure of BsIMPDH bound to Ap4A at a resolution of 2.45 Å to show that Ap4A binds to the interface between two IMPDH subunits, acting as the glue that switches active IMPDH tetramers into less active octamers. Guided by these insights, we engineered mutant strains of B. subtilis that bypass Ap4A-dependent IMPDH regulation without perturbing intracellular Ap4A pools themselves. We used metabolomics, which suggests that these mutants have a dysregulated purine, and in particular GTP, metabolome and phenotypic analysis, which shows increased sensitivity of B. subtilis IMPDH mutant strains to heat compared with wild-type strains. Our study identifies a central role for IMPDH in remodelling metabolism and heat resistance, and provides evidence that Ap4A can function as an alarmone.
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Affiliation(s)
- Pietro I Giammarinaro
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Megan K M Young
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Wieland Steinchen
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Christopher-Nils Mais
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Georg Hochberg
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jin Yang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Anja Paulus
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Gert Bange
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany.
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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23
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Rick T, Kreiling V, Höing A, Fiedler S, Glatter T, Steinchen W, Hochberg G, Bähre H, Seifert R, Bange G, Knauer SK, Graumann PL, Thormann KM. GGDEF domain as spatial on-switch for a phosphodiesterase by interaction with landmark protein HubP. NPJ Biofilms Microbiomes 2022; 8:35. [PMID: 35501424 PMCID: PMC9061725 DOI: 10.1038/s41522-022-00297-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractIn bacteria, the monopolar localization of enzymes and protein complexes can result in a bimodal distribution of enzyme activity between the dividing cells and heterogeneity of cellular behaviors. In Shewanella putrefaciens, the multidomain hybrid diguanylate cyclase/phosphodiesterase PdeB, which degrades the secondary messenger c-di-GMP, is located at the flagellated cell pole. Here, we show that direct interaction between the inactive diguanylate cyclase (GGDEF) domain of PdeB and the FimV domain of the polar landmark protein HubP is crucial for full function of PdeB as a phosphodiesterase. Thus, the GGDEF domain serves as a spatially controlled on-switch that effectively restricts PdeBs activity to the flagellated cell pole. PdeB regulates abundance and activity of at least two crucial surface-interaction factors, the BpfA surface-adhesion protein and the MSHA type IV pilus. The heterogeneity in c-di-GMP concentrations, generated by differences in abundance and timing of polar appearance of PdeB, orchestrates the population behavior with respect to cell-surface interaction and environmental spreading.
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24
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Schwarz P, Nikolskiy I, Bidaud AL, Sommer F, Bange G, Dannaoui E. In Vitro Synergy of Isavuconazole Combined With Colistin Against Common Candida Species. Front Cell Infect Microbiol 2022; 12:892893. [PMID: 35573795 PMCID: PMC9100415 DOI: 10.3389/fcimb.2022.892893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/09/2022] [Accepted: 03/31/2022] [Indexed: 12/16/2022] Open
Abstract
Interactions of isavuconazole and colistin were evaluated against 57 common Candida strains belonging to the species Candida albicans (n = 10), Candida glabrata (n = 10), Candida kefyr (n = 8), Candida krusei (n = 10), Candida parapsilosis (n = 9), and Candida tropicalis (n = 10) by a broth microdilution checkerboard technique based on the European Committee on Antimicrobial Susceptibility Testing (EUCAST) reference methodology for antifungal susceptibility testing. Results were analyzed with the fractional inhibitory concentration index and by the response surface analysis. Interpretation by the fractional inhibitory concentration index showed synergy for 50%, 80%, 90%, and 90% of the C. kefyr, C. krusei, C. glabrata, and C. tropicalis strains, respectively. Combination of isavuconazole with colistin against C. albicans and C. parapsilosis exhibited only indifference for 100% and 90% of the strains, respectively. The results were confirmed by response surface analysis for all species except for C. glabrata, for which an indifferent interaction was found for the majority of strains. Antagonistic interaction was never seen regardless of the interpretation model was used.
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Affiliation(s)
- Patrick Schwarz
- Department of Internal Medicine, Respiratory and Critical Care Medicine, University Hospital Marburg, Marburg, Germany
- Center for Invasive Mycoses and Antifungals, Faculty of Medicine, Philipps University Marburg, Marburg, Germany
| | - Ilya Nikolskiy
- Center for Invasive Mycoses and Antifungals, Faculty of Medicine, Philipps University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Anne-Laure Bidaud
- Unité de Parasitologie-Mycologie, Hôpital Européen Georges-Pompidou, Paris, France
| | - Frank Sommer
- Department of Microbiology, University Hospital Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps University Marburg, Marburg, Germany
- Max Planck Fellow Group, Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eric Dannaoui
- Unité de Parasitologie-Mycologie, Hôpital Européen Georges-Pompidou, Paris, France
- Dynamyc Research Group (EA 7380), Faculté de Médecine de Créteil, Université Paris-Est-Créteil-Val-de-Marne, Créteil, France
- Faculté de Médecine, Université de Paris, Paris, France
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25
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Bremer E, Hoffmann T, Dempwolff F, Bedrunka P, Bange G. The many faces of the unusual biofilm activator RemA. Bioessays 2022; 44:e2200009. [PMID: 35289951 DOI: 10.1002/bies.202200009] [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: 01/11/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/08/2022]
Abstract
Biofilms can be viewed as tissue-like structures in which microorganisms are organized in a spatial and functional sophisticated manner. Biofilm formation requires the orchestration of a highly integrated network of regulatory proteins to establish cell differentiation and production of a complex extracellular matrix. Here, we discuss the role of the essential Bacillus subtilis biofilm activator RemA. Despite intense research on biofilms, RemA is a largely underappreciated regulatory protein. RemA forms donut-shaped octamers with the potential to assemble into dimeric superstructures. The presumed DNA-binding mode suggests that RemA organizes its target DNA into nucleosome-like structures, which are the basis for its role as transcriptional activator. We discuss how RemA affects gene expression in the context of biofilm formation, and its regulatory interplay with established components of the biofilm regulatory network, such as SinR, SinI, SlrR, and SlrA. We emphasize the additional role of RemA played in nitrogen metabolism and osmotic-stress adjustment.
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Affiliation(s)
- Erhard Bremer
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Felix Dempwolff
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Patricia Bedrunka
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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26
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Albert L, Nagpal J, Steinchen W, Zhang L, Werel L, Djokovic N, Ruzic D, Hoffarth M, Xu J, Kaspareit J, Abendroth F, Royant A, Bange G, Nikolic K, Ryu S, Dou Y, Essen LO, Vázquez O. Bistable Photoswitch Allows in Vivo Control of Hematopoiesis. ACS Cent Sci 2022; 8:57-66. [PMID: 35106373 PMCID: PMC8796299 DOI: 10.1021/acscentsci.1c00434] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 05/09/2023]
Abstract
Optical control has enabled functional modulation in cell culture with unparalleled spatiotemporal resolution. However, current tools for in vivo manipulation are scarce. Here, we design and implement a genuine on-off optochemical probe capable of achieving hematopoietic control in zebrafish. Our photopharmacological approach first developed conformationally strained visible light photoswitches (CS-VIPs) as inhibitors of the histone methyltransferase MLL1 (KMT2A). In blood homeostasis MLL1 plays a crucial yet controversial role. CS-VIP 8 optimally fulfils the requirements of a true bistable functional system in vivo under visible-light irradiation, and with unprecedented stability. These properties are exemplified via hematopoiesis photoinhibition with a single isomer in zebrafish. The present interdisciplinary study uncovers the mechanism of action of CS-VIPs. Upon WDR5 binding, CS-VIP 8 causes MLL1 release with concomitant allosteric rearrangements in the WDR5/RbBP5 interface. Since our tool provides on-demand reversible control without genetic intervention or continuous irradiation, it will foster hematopathology and epigenetic investigations. Furthermore, our workflow will enable exquisite photocontrol over other targets inhibited by macrocycles.
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Affiliation(s)
- Lea Albert
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
| | - Jatin Nagpal
- APC Microbiome
Ireland, University College Cork, Cork, Ireland
| | - Wieland Steinchen
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
- Center
for Synthetic Microbiology (SYNMIKRO), University
of Marburg, 35037 Marburg, Germany
| | - Lei Zhang
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
| | - Laura Werel
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
| | - Nemanja Djokovic
- Department
of Pharmaceutical Chemistry, University
of Belgrade, 11000 Belgrade, Serbia
| | - Dusan Ruzic
- Department
of Pharmaceutical Chemistry, University
of Belgrade, 11000 Belgrade, Serbia
| | - Malte Hoffarth
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
| | - Jing Xu
- Department
of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Johanna Kaspareit
- University
Medical Center, Johannes Gutenberg University Mainz, 55122 Mainz, Germany
| | - Frank Abendroth
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
| | - Antoine Royant
- Univ.
Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
- European
Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Gert Bange
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
- Center
for Synthetic Microbiology (SYNMIKRO), University
of Marburg, 35037 Marburg, Germany
| | - Katarina Nikolic
- Department
of Pharmaceutical Chemistry, University
of Belgrade, 11000 Belgrade, Serbia
| | - Soojin Ryu
- University
Medical Center, Johannes Gutenberg University Mainz, 55122 Mainz, Germany
- College
of Medicine and Health, University of Exeter, Exeter EX4 4PY, U.K.
- Living
Systems Institute, University of Exeter, Exeter EX4 QD, U.K.
| | - Yali Dou
- Norris
Comprehensive Cancer Center, University
of Southern California, Los Angeles, California 90007, United States
| | - Lars-Oliver Essen
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
- Center
for Synthetic Microbiology (SYNMIKRO), University
of Marburg, 35037 Marburg, Germany
| | - Olalla Vázquez
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
- Center
for Synthetic Microbiology (SYNMIKRO), University
of Marburg, 35037 Marburg, Germany
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27
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Osorio-Valeriano M, Altegoer F, Das CK, Steinchen W, Panis G, Connolley L, Giacomelli G, Feddersen H, Corrales-Guerrero L, Giammarinaro PI, Hanßmann J, Bramkamp M, Viollier PH, Murray S, Schäfer LV, Bange G, Thanbichler M. The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes. Mol Cell 2021; 81:3992-4007.e10. [PMID: 34562373 DOI: 10.1016/j.molcel.2021.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 05/19/2021] [Revised: 07/27/2021] [Accepted: 08/31/2021] [Indexed: 01/29/2023]
Abstract
ParB-like CTPases mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centromere of target DNA molecules and spread laterally to form large nucleoprotein complexes serving as docking points for the DNA segregation machinery. Here, we solve crystal structures of ParB in the pre- and post-hydrolysis state and illuminate the catalytic mechanism of nucleotide hydrolysis. Moreover, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. The study of CTPase-deficient ParB variants reveals that CTP hydrolysis serves to limit the sliding time of ParB clamps and thus drives the establishment of a well-defined ParB diffusion gradient across the centromere whose dynamics are critical for DNA segregation. These findings clarify the role of the ParB CTPase cycle in partition complex assembly and function and thus advance our understanding of this prototypic CTP-dependent molecular switch.
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Affiliation(s)
- Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Florian Altegoer
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Lara Connolley
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Giacomo Giacomelli
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Helge Feddersen
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | | | - Pietro I Giammarinaro
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Juri Hanßmann
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Marc Bramkamp
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Seán Murray
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany.
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28
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Kaspar F, Seeger M, Westarp S, Köllmann C, Lehmann AP, Pausch P, Kemper S, Neubauer P, Bange G, Schallmey A, Werz DB, Kurreck A. Diversification of 4′-Methylated Nucleosides by Nucleoside Phosphorylases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Felix Kaspar
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13349 Berlin, Germany
| | - Margarita Seeger
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13349 Berlin, Germany
| | - Christoph Köllmann
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Anna P. Lehmann
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Patrick Pausch
- Center for Synthetic Microbiology (SYNMIKRO) & Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse 6, C07, 35043 Marburg, Germany
| | - Sebastian Kemper
- Institute for Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse 6, C07, 35043 Marburg, Germany
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Daniel B. Werz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13349 Berlin, Germany
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29
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Bange G, Brodersen DE, Liuzzi A, Steinchen W. Two P or Not Two P: Understanding Regulation by the Bacterial Second Messengers (p)ppGpp. Annu Rev Microbiol 2021; 75:383-406. [PMID: 34343020 DOI: 10.1146/annurev-micro-042621-122343] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Under stressful growth conditions and nutrient starvation, bacteria adapt by synthesizing signaling molecules that profoundly reprogram cellular physiology. At the onset of this process, called the stringent response, members of the RelA/SpoT homolog (RSH) protein superfamily are activated by specific stress stimuli to produce several hyperphosphorylated forms of guanine nucleotides, commonly referred to as (p)ppGpp. Some bifunctional RSH enzymes also harbor domains that allow for degradation of (p)ppGpp by hydrolysis. (p)ppGpp synthesis or hydrolysis may further be executed by single-domain alarmone synthetases or hydrolases, respectively. The downstream effects of (p)ppGpp rely mainly on direct interaction with specific intracellular effectors, which are widely used throughout most cellular processes. The growing number of identified (p)ppGpp targets allows us to deduce both common features of and differences between gram-negative and gram-positive bacteria. In this review, we give an overview of (p)ppGpp metabolism with a focus on the functional and structural aspects of the enzymes involved and discuss recent findings on alarmone-regulated cellular effectors. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gert Bange
- SYNMIKRO Research Center, Philipps-University Marburg, 35043 Marburg, Germany; .,Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Centre for Bacterial Stress Response and Persistence, Aarhus University, 8000 Aarhus C, Denmark
| | - Anastasia Liuzzi
- Department of Molecular Biology and Genetics, Centre for Bacterial Stress Response and Persistence, Aarhus University, 8000 Aarhus C, Denmark
| | - Wieland Steinchen
- SYNMIKRO Research Center, Philipps-University Marburg, 35043 Marburg, Germany; .,Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
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30
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Pecina A, Schwan M, Blagotinsek V, Rick T, Klüber P, Leonhard T, Bange G, Thormann KM. Corrigendum: The Stand-Alone PilZ-Domain Protein MotL Specifically Regulates the Activity of the Secondary Lateral Flagellar System in Shewanella putrefaciens. Front Microbiol 2021; 12:726192. [PMID: 34335556 PMCID: PMC8322970 DOI: 10.3389/fmicb.2021.726192] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/28/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
- Anna Pecina
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Meike Schwan
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Vitan Blagotinsek
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Tim Rick
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Patrick Klüber
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Tabea Leonhard
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Gert Bange
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
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31
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Feyh R, Waeber NB, Prinz S, Giammarinaro PI, Bange G, Hochberg G, Hartmann RK, Altegoer F. Structure and mechanistic features of the prokaryotic minimal RNase P. eLife 2021; 10:70160. [PMID: 34180399 PMCID: PMC8266387 DOI: 10.7554/elife.70160] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 05/07/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022] Open
Abstract
Endonucleolytic removal of 5'-leader sequences from tRNA precursor transcripts (pre-tRNAs) by ribonuclease P (RNase P) is essential for protein synthesis. Beyond RNA-based RNase P enzymes, protein-only versions of the enzyme exert this function in various eukarya (there termed PRORPs) and in some bacteria (Aquifex aeolicus and close relatives); both enzyme types belong to distinct subgroups of the PIN domain metallonuclease superfamily. Homologs of Aquifex RNase P (HARPs) are also expressed in some other bacteria and many archaea, where they coexist with RNA-based RNase P and do not represent the main RNase P activity. Here, we solved the structure of the bacterial HARP from Halorhodospira halophila by cryo-electron microscopy, revealing a novel screw-like dodecameric assembly. Biochemical experiments demonstrate that oligomerization is required for RNase P activity of HARPs. We propose that the tRNA substrate binds to an extended spike-helix (SH) domain that protrudes from the screw-like assembly to position the 5'-end in close proximity to the active site of the neighboring dimer. The structure suggests that eukaryotic PRORPs and prokaryotic HARPs recognize the same structural elements of pre-tRNAs (tRNA elbow region and cleavage site). Our analysis thus delivers the structural and mechanistic basis for pre-tRNA processing by the prokaryotic HARP system.
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Affiliation(s)
- Rebecca Feyh
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Nadine B Waeber
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Simone Prinz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Pietro Ivan Giammarinaro
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg Hochberg
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
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32
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Hermann L, Mais CN, Czech L, Smits SHJ, Bange G, Bremer E. The ups and downs of ectoine: structural enzymology of a major microbial stress protectant and versatile nutrient. Biol Chem 2021; 401:1443-1468. [PMID: 32755967 DOI: 10.1515/hsz-2020-0223] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 06/18/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
Ectoine and its derivative 5-hydroxyectoine are compatible solutes and chemical chaperones widely synthesized by Bacteria and some Archaea as cytoprotectants during osmotic stress and high- or low-growth temperature extremes. The function-preserving attributes of ectoines led to numerous biotechnological and biomedical applications and fostered the development of an industrial scale production process. Synthesis of ectoines requires the expenditure of considerable energetic and biosynthetic resources. Hence, microorganisms have developed ways to exploit ectoines as nutrients when they are no longer needed as stress protectants. Here, we summarize our current knowledge on the phylogenomic distribution of ectoine producing and consuming microorganisms. We emphasize the structural enzymology of the pathways underlying ectoine biosynthesis and consumption, an understanding that has been achieved only recently. The synthesis and degradation pathways critically differ in the isomeric form of the key metabolite N-acetyldiaminobutyric acid (ADABA). γ-ADABA serves as preferred substrate for the ectoine synthase, while the α-ADABA isomer is produced by the ectoine hydrolase as an intermediate in catabolism. It can serve as internal inducer for the genetic control of ectoine catabolic genes via the GabR/MocR-type regulator EnuR. Our review highlights the importance of structural enzymology to inspire the mechanistic understanding of metabolic networks at the biological scale.
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Affiliation(s)
- Lucas Hermann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Karl-von Frisch Str. 10, D-35043 Marburg, Germany
| | - Christopher-Nils Mais
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Laura Czech
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
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33
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Bange G, Bedrunka P. Physiology of guanosine-based second messenger signaling in Bacillus subtilis. Biol Chem 2021; 401:1307-1322. [PMID: 32881708 DOI: 10.1515/hsz-2020-0241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/22/2020] [Indexed: 12/19/2022]
Abstract
The guanosine-based second messengers (p)ppGpp and c-di-GMP are key players of the physiological regulation of the Gram-positive model organism Bacillus subtilis. Their regulatory spectrum ranges from key metabolic processes over motility to biofilm formation. Here we review our mechanistic knowledge on their synthesis and degradation in response to environmental and stress signals as well as what is known on their cellular effectors and targets. Moreover, we discuss open questions and our gaps in knowledge on these two important second messengers.
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Affiliation(s)
- Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse 6, C07, Marburg, D-35043,Germany
| | - Patricia Bedrunka
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse 6, C07, Marburg, D-35043,Germany
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34
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Abstract
A main function of bacterial metabolism is to supply biomass building blocks and energy for growth. This seems to imply that metabolism is idle in non-growing bacteria. But how relevant is metabolism for the physiology of non-growing bacteria and how active is their metabolism? Here, we reviewed literature describing metabolism of non-growing bacteria in their natural environment, as well as in biotechnological and medical applications. We found that metabolism does play an important role during dormancy and that especially the demand for ATP determines metabolic activity of non-growing bacteria.
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Affiliation(s)
- Martin Lempp
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany.,SYNMIKRO Research Center, D-35043 Marburg, Germany
| | - Paul Lubrano
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany.,SYNMIKRO Research Center, D-35043 Marburg, Germany
| | - Gert Bange
- SYNMIKRO Research Center, D-35043 Marburg, Germany.,Department of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse 6, C07, D-35032 Marburg, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany.,SYNMIKRO Research Center, D-35043 Marburg, Germany
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35
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Pecina A, Schwan M, Blagotinsek V, Rick T, Klüber P, Leonhard T, Bange G, Thormann KM. The Stand-Alone PilZ-Domain Protein MotL Specifically Regulates the Activity of the Secondary Lateral Flagellar System in Shewanella putrefaciens. Front Microbiol 2021; 12:668892. [PMID: 34140945 PMCID: PMC8203827 DOI: 10.3389/fmicb.2021.668892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 02/17/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
A number of bacterial species control the function of the flagellar motor in response to the levels of the secondary messenger c-di-GMP, which is often mediated by c-di-GMP-binding proteins that act as molecular brakes or clutches to slow the motor rotation. The gammaproteobacterium Shewanella putrefaciens possesses two distinct flagellar systems, the primary single polar flagellum and a secondary system with one to five lateral flagellar filaments. Here, we identified a protein, MotL, which specifically regulates the activity of the lateral, but not the polar, flagellar motors in response to the c-di-GMP levels. MotL only consists of a single PilZ domain binding c-di-GMP, which is crucial for its function. Deletion and overproduction analyses revealed that MotL slows down the lateral flagella at elevated levels of c-di-GMP, and may speed up the lateral flagellar-mediated movement at low c-di-GMP concentrations. In vitro interaction studies hint at an interaction of MotL with the C-ring of the lateral flagellar motors. This study shows a differential c-di-GMP-dependent regulation of the two flagellar systems in a single species, and implicates that PilZ domain-only proteins can also act as molecular regulators to control the flagella-mediated motility in bacteria.
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Affiliation(s)
- Anna Pecina
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Meike Schwan
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Vitan Blagotinsek
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Tim Rick
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Patrick Klüber
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Tabea Leonhard
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Gert Bange
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
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36
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Pausch P, Abdelshahid M, Steinchen W, Schäfer H, Gratani FL, Freibert SA, Wolz C, Turgay K, Wilson DN, Bange G. Structural Basis for Regulation of the Opposing (p)ppGpp Synthetase and Hydrolase within the Stringent Response Orchestrator Rel. Cell Rep 2021; 32:108157. [PMID: 32937119 DOI: 10.1016/j.celrep.2020.108157] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022] Open
Abstract
The stringent response enables metabolic adaptation of bacteria under stress conditions and is governed by RelA/SpoT Homolog (RSH)-type enzymes. Long RSH-type enzymes encompass an N-terminal domain (NTD) harboring the second messenger nucleotide (p)ppGpp hydrolase and synthetase activity and a stress-perceiving and regulatory C-terminal domain (CTD). CTD-mediated binding of Rel to stalled ribosomes boosts (p)ppGpp synthesis. However, how the opposing activities of the NTD are controlled in the absence of stress was poorly understood. Here, we demonstrate on the RSH-type protein Rel that the critical regulative elements reside within the TGS (ThrRS, GTPase, and SpoT) subdomain of the CTD, which associates to and represses the synthetase to concomitantly allow for activation of the hydrolase. Furthermore, we show that Rel forms homodimers, which appear to control the interaction with deacylated-tRNA, but not the enzymatic activity of Rel. Collectively, our study provides a detailed molecular view into the mechanism of stringent response repression in the absence of stress.
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Affiliation(s)
- Patrick Pausch
- Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Strasse, C07, Philipps-University Marburg, 35043 Marburg, Germany
| | - Maha Abdelshahid
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Strasse, C07, Philipps-University Marburg, 35043 Marburg, Germany
| | - Heinrich Schäfer
- Leibniz University of Hannover, Institute for Microbiology & Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117 Berlin, Germany
| | - Fabio Lino Gratani
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Sven-Andreas Freibert
- Center for Synthetic Microbiology & Institute for Cytobiology and Cytopathology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Kürşad Turgay
- Leibniz University of Hannover, Institute for Microbiology & Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117 Berlin, Germany.
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| | - Gert Bange
- Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Strasse, C07, Philipps-University Marburg, 35043 Marburg, Germany.
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37
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Mayer B, Schwan M, Oviedo-Bocanegra LM, Bange G, Thormann KM, Graumann PL. Dynamics of Bacterial Signal Recognition Particle at a Single Molecule Level. Front Microbiol 2021; 12:663747. [PMID: 33995327 PMCID: PMC8120034 DOI: 10.3389/fmicb.2021.663747] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 02/03/2021] [Accepted: 03/18/2021] [Indexed: 11/21/2022] Open
Abstract
We have studied the localization and dynamics of bacterial Ffh, part of the SRP complex, its receptor FtsY, and of ribosomes in the Gamma-proteobacterium Shewanella putrefaciens. Using structured illumination microscopy, we show that ribosomes show a pronounced accumulation at the cell poles, whereas SRP and FtsY are distributed at distinct sites along the cell membrane, but they are not accumulated at the poles. Single molecule dynamics can be explained by assuming that all three proteins/complexes move as three distinguishable mobility fractions: a low mobility/static fraction may be engaged in translation, medium-fast diffusing fractions may be transition states, and high mobility populations likely represent freely diffusing molecules/complexes. Diffusion constants suggest that SRP and FtsY move together with slow-mobile ribosomes. Inhibition of transcription leads to loss of static molecules and reduction of medium-mobile fractions, in favor of freely diffusing subunits, while inhibition of translation appears to stall the medium mobile fractions. Depletion of FtsY leads to aggregation of Ffh, but not to loss of the medium mobile fraction, indicating that Ffh/SRP can bind to ribosomes independently from FtsY. Heat maps visualizing the three distinct diffusive populations show that while static molecules are mostly clustered at the cell membrane, diffusive molecules are localized throughout the cytosol. The medium fast populations show an intermediate pattern of preferential localization, suggesting that SRP/FtsY/ribosome transition states may form within the cytosol to finally find a translocon.
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Affiliation(s)
- Benjamin Mayer
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Meike Schwan
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Luis M. Oviedo-Bocanegra
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Kai M. Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Peter L. Graumann
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
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38
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Potrykus K, Cashel M, Bange G. Editorial: (p)ppGpp and Its Homologs: Enzymatic and Mechanistic Diversity Among the Microbes. Front Microbiol 2021; 12:658282. [PMID: 33841386 PMCID: PMC8026867 DOI: 10.3389/fmicb.2021.658282] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Michael Cashel
- Intramural Program, Eunice Kennedy Shriver Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Gert Bange
- Department of Chemistry, Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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39
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Steinchen W, Ahmad S, Valentini M, Eilers K, Majkini M, Altegoer F, Lechner M, Filloux A, Whitney JC, Bange G. Dual role of a (p)ppGpp- and (p)ppApp-degrading enzyme in biofilm formation and interbacterial antagonism. Mol Microbiol 2021; 115:1339-1356. [PMID: 33448498 DOI: 10.1111/mmi.14684] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022]
Abstract
The guanosine nucleotide-based second messengers ppGpp and pppGpp (collectively: (p)ppGpp) enable adaptation of microorganisms to environmental changes and stress conditions. In contrast, the closely related adenosine nucleotides (p)ppApp are involved in type VI secretion system (T6SS)-mediated killing during bacterial competition. Long RelA-SpoT Homolog (RSH) enzymes regulate synthesis and degradation of (p)ppGpp (and potentially also (p)ppApp) through their synthetase and hydrolase domains, respectively. Small alarmone hydrolases (SAH) that consist of only a hydrolase domain are found in a variety of bacterial species, including the opportunistic human pathogen Pseudomonas aeruginosa. Here, we present the structure and mechanism of P. aeruginosa SAH showing that the enzyme promiscuously hydrolyses (p)ppGpp and (p)ppApp in a strictly manganese-dependent manner. While being dispensable for P. aeruginosa growth or swimming, swarming, and twitching motilities, its enzymatic activity is required for biofilm formation. Moreover, (p)ppApp-degradation by SAH provides protection against the T6SS (p)ppApp synthetase effector Tas1, suggesting that SAH enzymes can also serve as defense proteins during interbacterial competition.
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Affiliation(s)
- Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Shehryar Ahmad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Martina Valentini
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Kira Eilers
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Mohamad Majkini
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
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40
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Hook JC, Blagotinsek V, Pané-Farré J, Mrusek D, Altegoer F, Dornes A, Schwan M, Schier L, Thormann KM, Bange G. A Proline-Rich Element in the Type III Secretion Protein FlhB Contributes to Flagellar Biogenesis in the Beta- and Gamma-Proteobacteria. Front Microbiol 2020; 11:564161. [PMID: 33384667 PMCID: PMC7771051 DOI: 10.3389/fmicb.2020.564161] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/26/2020] [Indexed: 11/24/2022] Open
Abstract
Flagella are bacterial organelles of locomotion. Their biogenesis is highly coordinated in time and space and relies on a specialized flagellar type III secretion system (fT3SS) required for the assembly of the extracellular hook, rod, and filament parts of this complex motor device. The fT3SS protein FlhB switches secretion substrate specificity once the growing hook reaches its determined length. Here we present the crystal structure of the cytoplasmic domain of the transmembrane protein FlhB. The structure visualizes a so-far unseen proline-rich region (PRR) at the very C-terminus of the protein. Strains lacking the PRR show a decrease in flagellation as determined by hook- and filament staining, indicating a role of the PRR during assembly of the hook and filament structures. Phylogenetic analysis shows that the PRR is a primary feature of FlhB proteins of flagellated beta- and gamma-proteobacteria. Taken together, our study adds another layer of complexity and organismic diversity to the process of flagella biogenesis.
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Affiliation(s)
- John C Hook
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Vitan Blagotinsek
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Jan Pané-Farré
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Devid Mrusek
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Anita Dornes
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Meike Schwan
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Lukas Schier
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Gert Bange
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
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41
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Weng TH, Steinchen W, Beatrix B, Berninghausen O, Becker T, Bange G, Cheng J, Beckmann R. Architecture of the active post-translational Sec translocon. EMBO J 2020; 40:e105643. [PMID: 33305433 PMCID: PMC7849165 DOI: 10.15252/embj.2020105643] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 05/18/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 01/19/2023] Open
Abstract
In eukaryotes, most secretory and membrane proteins are targeted by an N‐terminal signal sequence to the endoplasmic reticulum, where the trimeric Sec61 complex serves as protein‐conducting channel (PCC). In the post‐translational mode, fully synthesized proteins are recognized by a specialized channel additionally containing the Sec62, Sec63, Sec71, and Sec72 subunits. Recent structures of this Sec complex in the idle state revealed the overall architecture in a pre‐opened state. Here, we present a cryo‐EM structure of the yeast Sec complex bound to a substrate, and a crystal structure of the Sec62 cytosolic domain. The signal sequence is inserted into the lateral gate of Sec61α similar to previous structures, yet, with the gate adopting an even more open conformation. The signal sequence is flanked by two Sec62 transmembrane helices, the cytoplasmic N‐terminal domain of Sec62 is more rigidly positioned, and the plug domain is relocated. We crystallized the Sec62 domain and mapped its interaction with the C‐terminus of Sec63. Together, we obtained a near‐complete and integrated model of the active Sec complex.
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Affiliation(s)
- Tsai-Hsuan Weng
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Wieland Steinchen
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Birgitta Beatrix
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Otto Berninghausen
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Thomas Becker
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Gert Bange
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Jingdong Cheng
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
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42
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Braun V, Brötz-Oesterhelt H, Mueller JW, Aichane K, Lassak J, Mais N, Bange G, Kruck D, Sander J, Shvarev D, Schipper K, McIntosh M, Kretz J. Journal Club. ACTA ACUST UNITED AC 2020; 26:646-651. [PMID: 33078046 PMCID: PMC7556609 DOI: 10.1007/s12268-020-1461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Volkmar Braun
- Max-Planck-Institut für Entwicklungsbiologie, Spemannstraße 35, D-72076 Tübingen, Deutschland
| | - Heike Brötz-Oesterhelt
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Universität Tübingen, Auf der Morgenstelle 28/E7, D-72076 Tübingen, Deutschland
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research (IMSR) and Centre for Endocrinology, Diabetes and Metabolism (CEDAM), IBR Tower, University of Birmingham, Birmingham, B15 2TT UK
| | - Khadija Aichane
- Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, D-30625 Hannover, Deutschland
| | - Jürgen Lassak
- Biozentrum Department Biologie I, Mikrobiologie, LMU München, Großhaderner Straße 2-4, Planegg-Martinsried, D-82152 München, Deutschland
| | - Nils Mais
- LOEWE Zentrum für synthetische Mikrobiologie (SYNMIKRO), Hans-Meerwein-Straße, D-35043 Marburg, Deutschland
| | - Gert Bange
- LOEWE Zentrum für synthetische Mikrobiologie (SYNMIKRO), Hans-Meerwein-Straße, D-35043 Marburg, Deutschland
| | - Daniela Kruck
- Medizinische Hochschule Hannover, Institut für Neurophysiologie, Carl-Neuberg-Straße 1, D-30625 Hannover, Deutschland
| | | | - Dmitry Shvarev
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, D-60438 Frankfurt a. M., Deutschland
| | - Kerstin Schipper
- Institut für Mikrobiologie, Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Deutschland
| | - Matthew McIntosh
- Institut für Mikrobiologie und Molekularbiologie, Universität Gießen, Heinrich-Buff-Ring 26-32, D-35392 Gießen, Deutschland
| | - Jonas Kretz
- Institut für Mikrobiologie und Molekularbiologie, Universität Gießen, Heinrich-Buff-Ring 26-32, D-35392 Gießen, Deutschland
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43
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Corrales-Guerrero L, He B, Refes Y, Panis G, Bange G, Viollier PH, Steinchen W, Thanbichler M. Molecular architecture of the DNA-binding sites of the P-loop ATPases MipZ and ParA from Caulobacter crescentus. Nucleic Acids Res 2020; 48:4769-4779. [PMID: 32232335 PMCID: PMC7229837 DOI: 10.1093/nar/gkaa192] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/18/2020] [Accepted: 03/17/2020] [Indexed: 12/21/2022] Open
Abstract
The spatiotemporal regulation of chromosome segregation and cell division in Caulobacter crescentus is mediated by two different P-loop ATPases, ParA and MipZ. Both of these proteins form dynamic concentration gradients that control the positioning of regulatory targets within the cell. Their proper localization depends on their nucleotide-dependent cycling between a monomeric and a dimeric state and on the ability of the dimeric species to associate with the nucleoid. In this study, we use a combination of genetic screening, biochemical analysis and hydrogen/deuterium exchange mass spectrometry to comprehensively map the residues mediating the interactions of MipZ and ParA with DNA. We show that MipZ has non-specific DNA-binding activity that relies on an array of positively charged and hydrophobic residues lining both sides of the dimer interface. Extending our analysis to ParA, we find that the MipZ and ParA DNA-binding sites differ markedly in composition, although their relative positions on the dimer surface and their mode of DNA binding are conserved. In line with previous experimental work, bioinformatic analysis suggests that the same principles may apply to other members of the P-loop ATPase family. P-loop ATPases thus share common mechanistic features, although their functions have diverged considerably during the course of evolution.
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Affiliation(s)
| | - Binbin He
- Department of Biology, University of Marburg, D-35043 Marburg, Germany
| | - Yacine Refes
- Department of Biology, University of Marburg, D-35043 Marburg, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Gert Bange
- Center for Synthetic Microbiology, D-35043 Marburg, Germany.,Department of Chemistry, University of Marburg, D-35043 Marburg, Germany
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Wieland Steinchen
- Center for Synthetic Microbiology, D-35043 Marburg, Germany.,Department of Chemistry, University of Marburg, D-35043 Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, D-35043 Marburg, Germany.,Center for Synthetic Microbiology, D-35043 Marburg, Germany.,Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
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44
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Abstract
When bacteria experience growth-limiting environmental conditions, the synthesis of the hyperphosphorylated guanosine derivatives (p)ppGpp is induced by enzymes of the RelA/SpoT homology (RSH)-type protein family. High levels of (p)ppGpp induce a process called "stringent response", a major cellular reprogramming during which ribosomal RNA (rRNA) and transfer RNA (tRNA) synthesis is downregulated, stress-related genes upregulated, messenger RNA (mRNA) stability and translation altered, and allocation of scarce resources optimized. The (p)ppGpp-mediated stringent response is thus often regarded as an all-or-nothing paradigm induced by stress. Over the past decades, several binding partners of (p)ppGpp have been uncovered displaying dissociation constants from below one micromolar to more than one millimolar and thus coincide with the accepted intracellular concentrations of (p)ppGpp under non-stringent (basal levels) and stringent conditions. This suggests that the ability of (p)ppGpp to modulate target proteins or processes would be better characterized as an unceasing continuum over a concentration range instead of being an abrupt switch of biochemical processes under specific conditions. We analyzed the reported binding affinities of (p)ppGpp targets and depicted a scheme for prioritization of modulation by (p)ppGpp. In this ranking, many enzymes of e.g., nucleotide metabolism are among the first targets to be affected by rising (p)ppGpp while more fundamental processes such as DNA replication are among the last. This preference should be part of (p)ppGpp's "magic" in the adaptation of microorganisms while still maintaining their potential for outgrowth once a stressful condition is overcome.
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Affiliation(s)
- Wieland Steinchen
- Department of Chemistry, Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | | | - Gert Bange
- Department of Chemistry, Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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45
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Mais CN, Hermann L, Altegoer F, Seubert A, Richter AA, Wernersbach I, Czech L, Bremer E, Bange G. Degradation of the microbial stress protectants and chemical chaperones ectoine and hydroxyectoine by a bacterial hydrolase-deacetylase complex. J Biol Chem 2020; 295:9087-9104. [PMID: 32404365 PMCID: PMC7335791 DOI: 10.1074/jbc.ra120.012722] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
When faced with increased osmolarity in the environment, many bacterial cells accumulate the compatible solute ectoine and its derivative 5-hydroxyectoine. Both compounds are not only potent osmostress protectants, but also serve as effective chemical chaperones stabilizing protein functionality. Ectoines are energy-rich nitrogen and carbon sources that have an ecological impact that shapes microbial communities. Although the biochemistry of ectoine and 5-hydroxyectoine biosynthesis is well understood, our understanding of their catabolism is only rudimentary. Here, we combined biochemical and structural approaches to unravel the core of ectoine and 5-hydroxy-ectoine catabolisms. We show that a conserved enzyme bimodule consisting of the EutD ectoine/5-hydroxyectoine hydrolase and the EutE deacetylase degrades both ectoines. We determined the high-resolution crystal structures of both enzymes, derived from the salt-tolerant bacteria Ruegeria pomeroyi and Halomonas elongata These structures, either in their apo-forms or in forms capturing substrates or intermediates, provided detailed insights into the catalytic cores of the EutD and EutE enzymes. The combined biochemical and structural results indicate that the EutD homodimer opens the pyrimidine ring of ectoine through an unusual covalent intermediate, N-α-2 acetyl-l-2,4-diaminobutyrate (α-ADABA). We found that α-ADABA is then deacetylated by the zinc-dependent EutE monomer into diaminobutyric acid (DABA), which is further catabolized to l-aspartate. We observed that the EutD-EutE bimodule synthesizes exclusively the α-, but not the γ-isomers of ADABA or hydroxy-ADABA. Of note, α-ADABA is known to induce the MocR/GabR-type repressor EnuR, which controls the expression of many ectoine catabolic genes clusters. We conclude that hydroxy-α-ADABA might serve a similar function.
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Affiliation(s)
- Christopher-Nils Mais
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Lucas Hermann
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany
| | - Florian Altegoer
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Andreas Seubert
- Philipps-University Marburg, Faculty of Chemistry, Marburg, Germany
| | - Alexandra A Richter
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany
| | - Isa Wernersbach
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Laura Czech
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany
| | - Erhard Bremer
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany.
| | - Gert Bange
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany.
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46
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Wehrmann M, Elsayed EM, Köbbing S, Bendz L, Lepak A, Schwabe J, Wierckx N, Bange G, Klebensberger J. Engineered PQQ-Dependent Alcohol Dehydrogenase for the Oxidation of 5-(Hydroxymethyl)furoic Acid. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01789] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Matthias Wehrmann
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Eslam M. Elsayed
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, 44519 Zagazig, Egypt
| | - Sebastian Köbbing
- Institute of Applied Microbiology-iAMB, RWTH Aachen University, 52074 Aachen, Germany
| | - Laura Bendz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Alexander Lepak
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Johannes Schwabe
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology-iAMB, RWTH Aachen University, 52074 Aachen, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gert Bange
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
| | - Janosch Klebensberger
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
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47
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Osorio-Valeriano M, Altegoer F, Steinchen W, Urban S, Liu Y, Bange G, Thanbichler M. ParB-type DNA Segregation Proteins Are CTP-Dependent Molecular Switches. Cell 2020; 179:1512-1524.e15. [PMID: 31835030 DOI: 10.1016/j.cell.2019.11.015] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/22/2019] [Accepted: 11/12/2019] [Indexed: 11/24/2022]
Abstract
During cell division, newly replicated DNA is actively segregated to the daughter cells. In most bacteria, this process involves the DNA-binding protein ParB, which condenses the centromeric regions of sister DNA molecules into kinetochore-like structures that recruit the DNA partition ATPase ParA and the prokaroytic SMC/condensin complex. Here, we report the crystal structure of a ParB-like protein (PadC) that emerges to tightly bind the ribonucleotide CTP. The CTP-binding pocket of PadC is conserved in ParB and composed of signature motifs known to be essential for ParB function. We find that ParB indeed interacts with CTP and requires nucleotide binding for DNA condensation in vivo. We further show that CTP-binding modulates the affinity of ParB for centromeric parS sites, whereas parS recognition stimulates its CTPase activity. ParB proteins thus emerge as a new class of CTP-dependent molecular switches that act in concert with ATPases and GTPases to control fundamental cellular functions.
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Affiliation(s)
- Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Florian Altegoer
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Svenja Urban
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Ying Liu
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Gert Bange
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany.
| | - Martin Thanbichler
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany.
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Mazzantini D, Fonnesu R, Celandroni F, Calvigioni M, Vecchione A, Mrusek D, Bange G, Ghelardi E. GTP-Dependent FlhF Homodimer Supports Secretion of a Hemolysin in Bacillus cereus. Front Microbiol 2020; 11:879. [PMID: 32435240 PMCID: PMC7218170 DOI: 10.3389/fmicb.2020.00879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 02/28/2020] [Accepted: 04/15/2020] [Indexed: 01/09/2023] Open
Abstract
The multidomain (B-NG) protein FlhF, a flagellar biogenesis regulator in several bacteria, is the third paralog of the signal recognition particle (SRP)-GTPases Ffh and FtsY, which are known to drive protein-delivery to the plasma membrane. Previously, we showed that FlhF is required for Bacillus cereus pathogenicity in an insect model of infection, being essential for physiological peritrichous flagellation, for motility, and for the secretion of virulence proteins. Among these proteins, we found that the L2 component of hemolysin BL, one of the most powerful toxins B. cereus produces, was drastically reduced by the FlhF depletion. Herein, we demonstrate that B. cereus FlhF forms GTP-dependent homodimers in vivo since the replacement of residues critical for their GTP-dependent homodimerization alters this ability. The protein directly or indirectly controls flagellation by affecting flagellin-gene transcription and its overproduction leads to a hyperflagellated phenotype. On the other hand, FlhF does not affect the expression of the L2-encoding gene (hblC), but physically binds L2 when in its homodimeric form, recruiting the protein to the plasma membrane for secretion. We additionally show that FlhF overproduction increases L2 secretion and that the FlhF/L2 interaction requires the NG domain of FlhF. Our findings demonstrate the peculiar behavior of B. cereus FlhF, which is required for the correct flagellar pattern and acts as SRP-GTPase in the secretion of a bacterial toxin subunit.
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Affiliation(s)
- Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Rossella Fonnesu
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marco Calvigioni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Alessandra Vecchione
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Devid Mrusek
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps University, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps University, Marburg, Germany
| | - Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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Altegoer F, Weiland P, Giammarinaro PI, Freibert SA, Binnebesel L, Han X, Lepak A, Kahmann R, Lechner M, Bange G. The two paralogous kiwellin proteins KWL1 and KWL1-b from maize are structurally related and have overlapping functions in plant defense. J Biol Chem 2020; 295:7816-7825. [PMID: 32350112 DOI: 10.1074/jbc.ra119.012207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 12/09/2019] [Revised: 04/23/2020] [Indexed: 12/17/2022] Open
Abstract
Many plant-pathogenic bacteria and fungi deploy effector proteins that down-regulate plant defense responses and reprogram plant metabolism for colonization and survival in planta Kiwellin (KWL) proteins are a widespread family of plant-defense proteins that target these microbial effectors. The KWL1 protein from maize (corn, Zea mays) specifically inhibits the enzymatic activity of the secreted chorismate mutase Cmu1, a virulence-promoting effector of the smut fungus Ustilago maydis. In addition to KWL1, 19 additional KWL paralogs have been identified in maize. Here, we investigated the structure and mechanism of the closest KWL1 homolog, KWL1-b (ZEAMA_GRMZM2G305329). We solved the Cmu1-KWL1-b complex to 2.75 Å resolution, revealing a highly symmetric Cmu1-KWL1-b heterotetramer in which each KWL1-b monomer interacts with a monomer of the Cmu1 homodimer. The structure also revealed that the overall architecture of the heterotetramer is highly similar to that of the previously reported Cmu1-KWL1 complex. We found that upon U. maydis infection of Z. mays, KWL1-b is expressed at significantly lower levels than KWL1 and exhibits differential tissue-specific expression patterns. We also show that KWL1-b inhibits Cmu1 activity similarly to KWL1. We conclude that KWL1 and KWL1-b are part of a redundant defense system that tissue-specifically targets Cmu1. This notion was supported by the observation that both KWL proteins are carbohydrate-binding proteins with distinct and likely tissue-related specificities. Moreover, binding by Cmu1 modulated the carbohydrate-binding properties of both KWLs. These findings indicate that KWL proteins are part of a spatiotemporally coordinated, plant-wide defense response comprising proteins with overlapping activities.
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Affiliation(s)
- Florian Altegoer
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Paul Weiland
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Pietro Ivan Giammarinaro
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Sven-Andreas Freibert
- Institute for Cytobiology and Cytopathology, Philipps-University Marburg, Marburg, Germany
| | - Lynn Binnebesel
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Xiaowei Han
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Alexander Lepak
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Marcus Lechner
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
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50
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Schäfer H, Beckert B, Frese CK, Steinchen W, Nuss AM, Beckstette M, Hantke I, Driller K, Sudzinová P, Krásný L, Kaever V, Dersch P, Bange G, Wilson DN, Turgay K. The alarmones (p)ppGpp are part of the heat shock response of Bacillus subtilis. PLoS Genet 2020; 16:e1008275. [PMID: 32176689 PMCID: PMC7098656 DOI: 10.1371/journal.pgen.1008275] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 03/26/2020] [Accepted: 02/26/2020] [Indexed: 11/24/2022] Open
Abstract
Bacillus subtilis cells are well suited to study how bacteria sense and adapt to proteotoxic stress such as heat, since temperature fluctuations are a major challenge to soil-dwelling bacteria. Here, we show that the alarmones (p)ppGpp, well known second messengers of nutrient starvation, are also involved in the heat stress response as well as the development of thermo-resistance. Upon heat-shock, intracellular levels of (p)ppGpp rise in a rapid but transient manner. The heat-induced (p)ppGpp is primarily produced by the ribosome-associated alarmone synthetase Rel, while the small alarmone synthetases RelP and RelQ seem not to be involved. Furthermore, our study shows that the generated (p)ppGpp pulse primarily acts at the level of translation, and only specific genes are regulated at the transcriptional level. These include the down-regulation of some translation-related genes and the up-regulation of hpf, encoding the ribosome-protecting hibernation-promoting factor. In addition, the alarmones appear to interact with the activity of the stress transcription factor Spx during heat stress. Taken together, our study suggests that (p)ppGpp modulates the translational capacity at elevated temperatures and thereby allows B. subtilis cells to respond to proteotoxic stress, not only by raising the cellular repair capacity, but also by decreasing translation to concurrently reduce the protein load on the cellular protein quality control system.
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Affiliation(s)
- Heinrich Schäfer
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Wieland Steinchen
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Marburg, Germany
| | - Aaron M. Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ingo Hantke
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | | | - Petra Sudzinová
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Libor Krásný
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Volkhard Kaever
- Hannover Medical School, Research Core Unit Metabolomics, Hannover, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Infectiology, University of Münster, Münster, Germany
| | - Gert Bange
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Marburg, Germany
| | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Kürşad Turgay
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
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