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Reddy KD, Rasool B, Akher FB, Kutlešić N, Pant S, Boudker O. Evolutionary analysis reveals the origin of sodium coupling in glutamate transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.03.569786. [PMID: 38106174 PMCID: PMC10723334 DOI: 10.1101/2023.12.03.569786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Secondary active membrane transporters harness the energy of ion gradients to concentrate their substrates. Homologous transporters evolved to couple transport to different ions in response to changing environments and needs. The bases of such diversification, and thus principles of ion coupling, are unexplored. Employing phylogenetics and ancestral protein reconstruction, we investigated sodium-coupled transport in prokaryotic glutamate transporters, a mechanism ubiquitous across life domains and critical to neurotransmitter recycling in humans. We found that the evolutionary transition from sodium-dependent to independent substrate binding to the transporter preceded changes in the coupling mechanism. Structural and functional experiments suggest that the transition entailed allosteric mutations, making sodium binding dispensable without affecting ion-binding sites. Allosteric tuning of transporters' energy landscapes might be a widespread route of their functional diversification.
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Affiliation(s)
- Krishna D. Reddy
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Burha Rasool
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Farideh Badichi Akher
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Nemanja Kutlešić
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Swati Pant
- Dept. of Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Olga Boudker
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
- Howard Hughes Medical Institute, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
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Ev LD, Poloni JDF, Damé-Teixeira N, Arthur RA, Corralo DJ, Henz SL, Do T, Maltz M, Parolo CCF. Hub genes and pathways related to caries-free dental biofilm: clinical metatranscriptomic study. Clin Oral Investig 2023; 27:7725-7735. [PMID: 37924358 DOI: 10.1007/s00784-023-05363-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
OBJECTIVE This study aimed to evaluate the microbial functional profile of biofilms related to caries-free (CF, n = 6) and caries-arrested (CI, n = 3) compared to caries-active (CA, n = 5) individuals. MATERIALS AND METHODS A metatranscriptomic was performed in supragingival biofilm from different clinical conditions related to caries or health. Total RNA was extracted and cDNAs were obtained and sequenced (Illumina HiSeq3000). Trimmed data (SortMeRNA) were submitted to the SqueezeMeta pipeline in the co-assembly mode for functional analysis and further differential gene expression analysis (DESeq2) and weighted gene co-expression network analysis (WCGNA) to explore and identify gene modules related to these clinical conditions. RESULTS A total of 5303 genes were found in the metatranscriptomic analysis. A co-expression network identified the most relevant modules strongly related to specific caries status. Correlation coefficients were calculated between the eigengene modules and the clinical conditions (CA, CI, and CF) discriminating multiple modules. CA and CI showed weak correlation coefficient strength across the modules, while the CF condition presented a very strong positive correlation coefficient (r = 0.9, p value = 4 × 10-9). Pearson's test was applied to further analyze the module membership and gene significance in CF conditions, and the most relevant were HSPA1s-K03283, Epr- K13277, and SLC1A-K05613. Gene Ontology (GO) shows important bioprocesses, such as two-component system, fructose and mannose metabolism, pentose and glucuronate interconversions, and flagellar assembly (p-adjust < 0.05). The ability to use different carbohydrates, integrate multiple signals, swarm, and bacteriocin production are significant metabolic advantages in the oral environment related to CF. CONCLUSIONS A distinct functional health profile could be found in CF, where co-occurring genes can act in different pathways at the same time. Genes HSPA1s, Epr, and SLC1A may be appointed as potential biomarkers for caries-free biofilms. CLINICAL RELEVANCE Potential biomarkers for caries-free biofilms could contribute to the knowledge of caries prevention and control.
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Affiliation(s)
- Laís Daniela Ev
- Department of Preventive and Social Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Joice de Faria Poloni
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, National Institute of Science and Technology - Forensic Science, Porto Alegre, Brazil
| | - Nailê Damé-Teixeira
- Department of Dentistry, Faculty of Health Sciences, University of Brasília, Brasília, DF, Brazil
| | - Rodrigo Alex Arthur
- Department of Preventive and Social Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Daniela Jorge Corralo
- Department of Dentistry, School of Dentistry, Passo Fundo University, Passo Fundo, RS, Brazil
| | - Sandra Liana Henz
- Department of Preventive and Social Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Thuy Do
- Division of Oral Biology, School of Dentistry, Faculty of Medicine & Health, University of Leeds, Leeds, UK
| | - Marisa Maltz
- Department of Preventive and Social Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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Huang Y, Reddy KD, Bracken C, Qiu B, Zhan W, Eliezer D, Boudker O. Environmentally Ultrasensitive Fluorine Probe to Resolve Protein Conformational Ensembles by 19F NMR and Cryo-EM. J Am Chem Soc 2023; 145:8583-8592. [PMID: 37023263 PMCID: PMC10119980 DOI: 10.1021/jacs.3c01003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Indexed: 04/08/2023]
Abstract
Limited chemical shift dispersion represents a significant barrier to studying multistate equilibria of large membrane proteins by 19F NMR. We describe a novel monofluoroethyl 19F probe that dramatically increases the chemical shift dispersion. The improved conformational sensitivity and line shape enable the detection of previously unresolved states in one-dimensional (1D) 19F NMR spectra of a 134 kDa membrane transporter. Changes in the populations of these states in response to ligand binding, mutations, and temperature correlate with population changes of distinct conformations in structural ensembles determined by single-particle cryo-electron microscopy (cryo-EM). Thus, 19F NMR can guide sample preparation to discover and visualize novel conformational states and facilitate image analysis and three-dimensional (3D) classification.
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Affiliation(s)
- Yun Huang
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Krishna D. Reddy
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Clay Bracken
- Department
of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Biao Qiu
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Wenhu Zhan
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - David Eliezer
- Department
of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Olga Boudker
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
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Eisner D. The Cranefield Awards 2022. J Gen Physiol 2023; 155:e202313385. [PMID: 36929935 PMCID: PMC10039667 DOI: 10.1085/jgp.202313385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Affiliation(s)
- David Eisner
- Division of Cardiovascular Sciences, University of Manchester, Manchester, UK
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Peter MF, Ruland JA, Depping P, Schneberger N, Severi E, Moecking J, Gatterdam K, Tindall S, Durand A, Heinz V, Siebrasse JP, Koenig PA, Geyer M, Ziegler C, Kubitscheck U, Thomas GH, Hagelueken G. Structural and mechanistic analysis of a tripartite ATP-independent periplasmic TRAP transporter. Nat Commun 2022; 13:4471. [PMID: 35927235 PMCID: PMC9352664 DOI: 10.1038/s41467-022-31907-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022] Open
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are found widely in bacteria and archaea and consist of three structural domains, a soluble substrate-binding protein (P-domain), and two transmembrane domains (Q- and M-domains). HiSiaPQM and its homologs are TRAP transporters for sialic acid and are essential for host colonization by pathogenic bacteria. Here, we reconstitute HiSiaQM into lipid nanodiscs and use cryo-EM to reveal the structure of a TRAP transporter. It is composed of 16 transmembrane helices that are unexpectedly structurally related to multimeric elevator-type transporters. The idiosyncratic Q-domain of TRAP transporters enables the formation of a monomeric elevator architecture. A model of the tripartite PQM complex is experimentally validated and reveals the coupling of the substrate-binding protein to the transporter domains. We use single-molecule total internal reflection fluorescence (TIRF) microscopy in solid-supported lipid bilayers and surface plasmon resonance to study the formation of the tripartite complex and to investigate the impact of interface mutants. Furthermore, we characterize high-affinity single variable domains on heavy chain (VHH) antibodies that bind to the periplasmic side of HiSiaQM and inhibit sialic acid uptake, providing insight into how TRAP transporter function might be inhibited in vivo.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Jan A Ruland
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Peer Depping
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
- Aston Centre for Membrane Proteins and Lipids Research, Aston St., B4 7ET, Birmingham, UK
| | - Niels Schneberger
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Emmanuele Severi
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
- Biosciences Institute, Newcastle University, Newcastle, NE2 4HH, UK
| | - Jonas Moecking
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Karl Gatterdam
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Sarah Tindall
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
| | - Alexandre Durand
- Institut de Génétique et de Biologie Molecule et Cellulaire, 1 Rue Laurent Fries, 67404, Illkirch Cedex, France
| | - Veronika Heinz
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Jan Peter Siebrasse
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Paul-Albert Koenig
- Core Facility Nanobodies, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Christine Ziegler
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Ulrich Kubitscheck
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
| | - Gregor Hagelueken
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
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