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Lytje K, Pedersen JS. Validation of electron-microscopy maps using solution small-angle X-ray scattering. Acta Crystallogr D Struct Biol 2024; 80:493-505. [PMID: 38935344 PMCID: PMC11220840 DOI: 10.1107/s2059798324005497] [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: 04/24/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
The determination of the atomic resolution structure of biomacromolecules is essential for understanding details of their function. Traditionally, such a structure determination has been performed with crystallographic or nuclear resonance methods, but during the last decade, cryogenic transmission electron microscopy (cryo-TEM) has become an equally important tool. As the blotting and flash-freezing of the samples can induce conformational changes, external validation tools are required to ensure that the vitrified samples are representative of the solution. Although many validation tools have already been developed, most of them rely on fully resolved atomic models, which prevents early screening of the cryo-TEM maps. Here, a novel and automated method for performing such a validation utilizing small-angle X-ray scattering measurements, publicly available through the new software package AUSAXS, is introduced and implemented. The method has been tested on both simulated and experimental data, where it was shown to work remarkably well as a validation tool. The method provides a dummy atomic model derived from the EM map which best represents the solution structure.
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Affiliation(s)
- Kristian Lytje
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityGustav Wieds Vej 148000AarhusDenmark
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityGustav Wieds Vej 148000AarhusDenmark
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Lin JD, Stogios PJ, Abe KT, Wang A, MacPherson J, Skarina T, Gingras AC, Savchenko A, Ensminger AW. Functional diversification despite structural congruence in the HipBST toxin-antitoxin system of Legionella pneumophila. mBio 2023; 14:e0151023. [PMID: 37819088 PMCID: PMC10653801 DOI: 10.1128/mbio.01510-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Toxin-antitoxin (TA) systems are parasitic genetic elements found in almost all bacterial genomes. They are exchanged horizontally between cells and are typically poorly conserved across closely related strains and species. Here, we report the characterization of a tripartite TA system in the bacterial pathogen Legionella pneumophila that is highly conserved across Legionella species genomes. This system (denoted HipBSTLp) is a distant homolog of the recently discovered split-HipA system in Escherichia coli (HipBSTEc). We present bioinformatic, molecular, and structural analyses of the divergence between these two systems and the functionality of this newly described TA system family. Furthermore, we provide evidence to refute previous claims that the toxin in this system (HipTLp) possesses bifunctionality as an L. pneumophila virulence protein. Overall, this work expands our understanding of the split-HipA system architecture and illustrates the potential for undiscovered biology in these abundant genetic elements.
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Affiliation(s)
- Jordan D. Lin
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kento T. Abe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Avril Wang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John MacPherson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Calgary, Calgary, Alberta, Canada
| | - Alexander W. Ensminger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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