1
|
Silberberg JM, Ketter S, Böhm PJN, Jordan K, Wittenberg M, Grass J, Hänelt I. KdpD is a tandem serine histidine kinase that controls K + pump KdpFABC transcriptionally and post-translationally. Nat Commun 2024; 15:3223. [PMID: 38622146 PMCID: PMC11018627 DOI: 10.1038/s41467-024-47526-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Two-component systems, consisting of a histidine kinase and a response regulator, serve signal transduction in bacteria, often regulating transcription in response to environmental stimuli. Here, we identify a tandem serine histidine kinase function for KdpD, previously described as a histidine kinase of the KdpDE two-component system, which controls production of the potassium pump KdpFABC. We show that KdpD additionally mediates an inhibitory serine phosphorylation of KdpFABC at high potassium levels, using not its C-terminal histidine kinase domain but an N-terminal atypical serine kinase domain. Sequence analysis of KdpDs from different species highlights that some KdpDs are much shorter than others. We show that, while Escherichia coli KdpD's atypical serine kinase domain responds directly to potassium levels, a shorter version from Deinococcus geothermalis is controlled by second messenger cyclic di-AMP. Our findings add to the growing functional diversity of sensor kinases while simultaneously expanding the framework for regulatory mechanisms in bacterial potassium homeostasis.
Collapse
Affiliation(s)
- Jakob M Silberberg
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Sophie Ketter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Paul J N Böhm
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Kristin Jordan
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Marcel Wittenberg
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Julia Grass
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Inga Hänelt
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany.
| |
Collapse
|
2
|
Ansell TB, Song W, Coupland CE, Carrique L, Corey RA, Duncan AL, Cassidy CK, Geurts MMG, Rasmussen T, Ward AB, Siebold C, Stansfeld PJ, Sansom MSP. LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins. Nat Commun 2023; 14:7774. [PMID: 38012131 PMCID: PMC10682427 DOI: 10.1038/s41467-023-43392-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) enables the determination of membrane protein structures in native-like environments. Characterising how membrane proteins interact with the surrounding membrane lipid environment is assisted by resolution of lipid-like densities visible in cryo-EM maps. Nevertheless, establishing the molecular identity of putative lipid and/or detergent densities remains challenging. Here we present LipIDens, a pipeline for molecular dynamics (MD) simulation-assisted interpretation of lipid and lipid-like densities in cryo-EM structures. The pipeline integrates the implementation and analysis of multi-scale MD simulations for identification, ranking and refinement of lipid binding poses which superpose onto cryo-EM map densities. Thus, LipIDens enables direct integration of experimental and computational structural approaches to facilitate the interpretation of lipid-like cryo-EM densities and to reveal the molecular identities of protein-lipid interactions within a bilayer environment. We demonstrate this by application of our open-source LipIDens code to ten diverse membrane protein structures which exhibit lipid-like densities.
Collapse
Affiliation(s)
- T Bertie Ansell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- MSD R&D Innovation Centre, 120 Moorgate, London, EC2M 6UR, UK
| | - Claire E Coupland
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Loic Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Chemistry, Aarhus University, Lagelsandsgade 140, 8000, Aarhus C, Denmark
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Maxwell M G Geurts
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tim Rasmussen
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, Haus D15, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| |
Collapse
|
3
|
Palmgren M. P-type ATPases: Many more enigmas left to solve. J Biol Chem 2023; 299:105352. [PMID: 37838176 PMCID: PMC10654040 DOI: 10.1016/j.jbc.2023.105352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023] Open
Abstract
P-type ATPases constitute a large ancient super-family of primary active pumps that have diverse substrate specificities ranging from H+ to phospholipids. The significance of these enzymes in biology cannot be overstated. They are structurally related, and their catalytic cycles alternate between high- and low-affinity conformations that are induced by phosphorylation and dephosphorylation of a conserved aspartate residue. In the year 1988, all P-type sequences available by then were analyzed and five major families, P1 to P5, were identified. Since then, a large body of knowledge has accumulated concerning the structure, function, and physiological roles of members of these families, but only one additional family, P6 ATPases, has been identified. However, much is still left to be learned. For each family a few remaining enigmas are presented, with the intention that they will stimulate interest in continued research in the field. The review is by no way comprehensive and merely presents personal views with a focus on evolution.
Collapse
Affiliation(s)
- Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.
| |
Collapse
|
4
|
Galles GD, Infield DT, Clark CJ, Hemshorn ML, Manikandan S, Fazan F, Rasouli A, Tajkhorshid E, Galpin JD, Cooley RB, Mehl RA, Ahern CA. Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells. Nat Commun 2023; 14:59. [PMID: 36599844 PMCID: PMC9813137 DOI: 10.1038/s41467-022-35761-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
The aromatic side-chains of phenylalanine, tyrosine, and tryptophan interact with their environments via both hydrophobic and electrostatic interactions. Determining the extent to which these contribute to protein function and stability is not possible with conventional mutagenesis. Serial fluorination of a given aromatic is a validated method in vitro and in silico to specifically alter electrostatic characteristics, but this approach is restricted to a select few experimental systems. Here, we report a group of pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs (tRNA/RS pairs) that enable the site-specific encoding of a varied spectrum of fluorinated phenylalanine amino acids in E. coli and mammalian (HEK 293T) cells. By allowing the cross-kingdom expression of proteins bearing these unnatural amino acids at biochemical scale, these tools may potentially enable the study of biological mechanisms which utilize aromatic interactions in structural and cellular contexts.
Collapse
Affiliation(s)
- Grace D Galles
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Colin J Clark
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Marcus L Hemshorn
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Shivani Manikandan
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Frederico Fazan
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Ali Rasouli
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Richard B Cooley
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Ryan A Mehl
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA.
| |
Collapse
|
5
|
Thangaratnarajah C, Rheinberger J, Paulino C. Cryo-EM studies of membrane proteins at 200 keV. Curr Opin Struct Biol 2022; 76:102440. [PMID: 36029606 DOI: 10.1016/j.sbi.2022.102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/03/2022]
Abstract
Single-particle cryogenic electron-microscopy (cryo-EM) has emerged as a powerful technique for the structural characterisation of membrane proteins, especially for targets previously thought to be intractable. Taking advantage of the latest hard- and software developments, high-resolution three-dimensional (3D) reconstructions of membrane proteins by cryo-EM has become routine, with 300-kV transmission electron microscopes (TEMs) being the current standard. The use of 200-kV cryo-TEMs is gaining increasingly prominence, showing the capabilities of reaching better than 2 Å resolution for soluble proteins and better than 3 Å resolution for membrane proteins. Here, we highlight the challenges working with membrane proteins and the impact of cryo-EM, and review the technical and practical benefits, achievements and limitations of imaging at lower electron acceleration voltages.
Collapse
Affiliation(s)
- Chancievan Thangaratnarajah
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
| | - Jan Rheinberger
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands. https://twitter.com/rheinbergerj
| | - Cristina Paulino
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
| |
Collapse
|