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Singer A, Ramos A, Keating AE. Elaboration of the Homer1 recognition landscape reveals incomplete divergence of paralogous EVH1 domains. Protein Sci 2024; 33:e5094. [PMID: 38989636 DOI: 10.1002/pro.5094] [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: 02/26/2024] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 07/12/2024]
Abstract
Short sequences that mediate interactions with modular binding domains are ubiquitous throughout eukaryotic proteomes. Networks of short linear motifs (SLiMs) and their corresponding binding domains orchestrate many cellular processes, and the low mutational barrier to evolving novel interactions provides a way for biological systems to rapidly sample selectable phenotypes. Mapping SLiM binding specificity and the rules that govern SLiM evolution is fundamental to uncovering the pathways regulated by these networks and developing the tools to manipulate them. We used high-throughput screening of the human proteome to identify sequences that bind to the Enabled/VASP homology 1 (EVH1) domain of the postsynaptic density scaffolding protein Homer1. This expanded our understanding of the determinants of Homer EVH1 binding preferences and defined a new motif that can facilitate the discovery of additional Homer-mediated interactions. Interestingly, the Homer1 EVH1 domain preferentially binds to sequences containing an N-terminally overlapping motif that is bound by the paralogous family of Ena/VASP actin polymerases, and many of these sequences can bind to EVH1 domains from both protein families. We provide evidence from orthologous EVH1 domains in pre-metazoan organisms that the overlap in human Ena/VASP and Homer binding preferences corresponds to an incomplete divergence from a common Ena/VASP ancestor. Given this overlap in binding profiles, promiscuous sequences that can be recognized by both families either achieve specificity through extrinsic regulatory strategies or may provide functional benefits via multi-specificity. This may explain why these paralogs incompletely diverged despite the accessibility of further diverged isoforms.
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Affiliation(s)
- Avinoam Singer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alejandra Ramos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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2
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Singer A, Ramos A, Keating AE. Elaboration of the Homer1 Recognition Landscape Reveals Incomplete Divergence of Paralogous EVH1 Domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576863. [PMID: 38645240 PMCID: PMC11030225 DOI: 10.1101/2024.01.23.576863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Short sequences that mediate interactions with modular binding domains are ubiquitous throughout eukaryotic proteomes. Networks of Short Linear Motifs (SLiMs) and their corresponding binding domains orchestrate many cellular processes, and the low mutational barrier to evolving novel interactions provides a way for biological systems to rapidly sample selectable phenotypes. Mapping SLiM binding specificity and the rules that govern SLiM evolution is fundamental to uncovering the pathways regulated by these networks and developing the tools to manipulate them. We used high-throughput screening of the human proteome to identify sequences that bind to the Enabled/VASP homology 1 (EVH1) domain of the postsynaptic density scaffolding protein Homer1. In doing so, we expanded current understanding of the determinants of Homer EVH1 binding preferences and defined a new motif that can facilitate the discovery of additional Homer-mediated interactions. Interestingly, the Homer1 EVH1 domain preferentially binds to sequences containing an N-terminally overlapping motif that is bound by the paralogous family of Ena/VASP actin polymerases, and many of these sequences can bind to EVH1 domains from both protein families. We provide evidence from orthologous EVH1 domains in pre-metazoan organisms that the overlap in human Ena/VASP and Homer binding preferences corresponds to an incomplete divergence from a common Ena/VASP ancestor. Given this overlap in binding profiles, promiscuous sequences that can be recognized by both families either achieve specificity through extrinsic regulatory strategies or may provide functional benefits via multi-specificity. This may explain why these paralogs incompletely diverged despite the accessibility of further diverged isoforms.
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Affiliation(s)
- Avinoam Singer
- MIT Department of Biology, Cambridge, Massachusetts, USA
| | | | - Amy E. Keating
- MIT Department of Biology, Cambridge, Massachusetts, USA
- MIT Department of Biological Engineering, Cambridge, Massachusetts, USA
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
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3
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Lee CY, Hubrich D, Varga JK, Schäfer C, Welzel M, Schumbera E, Djokic M, Strom JM, Schönfeld J, Geist JL, Polat F, Gibson TJ, Keller Valsecchi CI, Kumar M, Schueler-Furman O, Luck K. Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation. Mol Syst Biol 2024; 20:75-97. [PMID: 38225382 PMCID: PMC10883280 DOI: 10.1038/s44320-023-00005-6] [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: 08/03/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
Structural resolution of protein interactions enables mechanistic and functional studies as well as interpretation of disease variants. However, structural data is still missing for most protein interactions because we lack computational and experimental tools at scale. This is particularly true for interactions mediated by short linear motifs occurring in disordered regions of proteins. We find that AlphaFold-Multimer predicts with high sensitivity but limited specificity structures of domain-motif interactions when using small protein fragments as input. Sensitivity decreased substantially when using long protein fragments or full length proteins. We delineated a protein fragmentation strategy particularly suited for the prediction of domain-motif interfaces and applied it to interactions between human proteins associated with neurodevelopmental disorders. This enabled the prediction of highly confident and likely disease-related novel interfaces, which we further experimentally corroborated for FBXO23-STX1B, STX1B-VAMP2, ESRRG-PSMC5, PEX3-PEX19, PEX3-PEX16, and SNRPB-GIGYF1 providing novel molecular insights for diverse biological processes. Our work highlights exciting perspectives, but also reveals clear limitations and the need for future developments to maximize the power of Alphafold-Multimer for interface predictions.
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Affiliation(s)
- Chop Yan Lee
- Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany
| | - Dalmira Hubrich
- Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany
| | - Julia K Varga
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | | | - Mareen Welzel
- Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany
| | - Eric Schumbera
- Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany
- Computational Biology and Data Mining Group Biozentrum I, 55128, Mainz, Germany
| | - Milena Djokic
- Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany
| | - Joelle M Strom
- Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany
| | - Jonas Schönfeld
- Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany
| | - Johanna L Geist
- Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany
| | - Feyza Polat
- Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69117, Germany
| | | | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69117, Germany
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel.
| | - Katja Luck
- Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany.
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4
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Allio R, Delsuc F, Belkhir K, Douzery EJP, Ranwez V, Scornavacca C. OrthoMaM v12: a database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics. Nucleic Acids Res 2024; 52:D529-D535. [PMID: 37843103 PMCID: PMC10767847 DOI: 10.1093/nar/gkad834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023] Open
Abstract
To date, the databases built to gather information on gene orthology do not provide end-users with descriptors of the molecular evolution information and phylogenetic pattern of these orthologues. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of coding sequences in mammalian genomes. OrthoMaM version 12 includes 15,868 alignments of orthologous coding sequences (CDS) from the 190 complete mammalian genomes currently available. All annotations and 1-to-1 orthology assignments are based on NCBI. Orthologous CDS can be mined for potential informative markers at the different taxonomic levels of the mammalian tree. To this end, several evolutionary descriptors of DNA sequences are provided for querying purposes (e.g. base composition and relative substitution rate). The graphical web interface allows the user to easily browse and sort the results of combined queries. The corresponding multiple sequence alignments and ML trees, inferred using state-of-the art approaches, are available for download both at the nucleotide and amino acid levels. OrthoMaM v12 can be used by researchers interested either in reconstructing the phylogenetic relationships of mammalian taxa or in understanding the evolutionary dynamics of coding sequences in their genomes. OrthoMaM is available for browsing, querying and complete or filtered download at https://orthomam.mbb.cnrs.fr/.
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Affiliation(s)
- Rémi Allio
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Univ. Montpellier, Montpellier, 34988, France
- ISEM, Univ. Montpellier, CNRS, IRD, Montpellier, 34095, France
| | - Frédéric Delsuc
- ISEM, Univ. Montpellier, CNRS, IRD, Montpellier, 34095, France
| | - Khalid Belkhir
- ISEM, Univ. Montpellier, CNRS, IRD, Montpellier, 34095, France
| | | | - Vincent Ranwez
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, 34398, France
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Skinnider MA, Akinlaja MO, Foster LJ. Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry. Nat Commun 2023; 14:8365. [PMID: 38102123 PMCID: PMC10724252 DOI: 10.1038/s41467-023-44139-5] [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: 06/24/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
We present CFdb, a harmonized resource of interaction proteomics data from 411 co-fractionation mass spectrometry (CF-MS) datasets spanning 21,703 fractions. Meta-analysis of this resource charts protein abundance, phosphorylation, and interactions throughout the tree of life, including a reference map of the human interactome. We show how large-scale CF-MS data can enhance analyses of individual CF-MS datasets, and exemplify this strategy by mapping the honey bee interactome.
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Affiliation(s)
- Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA
| | - Mopelola O Akinlaja
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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Mathews DH, Casadio R, Sternberg MJE. Computational Resources for Molecular Biology 2023. J Mol Biol 2023:168160. [PMID: 37244569 DOI: 10.1016/j.jmb.2023.168160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
| | - Rita Casadio
- Biocomputing Group, FABIT-University of Bologna, Bologna I-40126, Italy.
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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Chaltel-Lima L, Domínguez F, Domínguez-Ramírez L, Cortes-Hernandez P. The Role of the Estrogen-Related Receptor Alpha (ERRa) in Hypoxia and Its Implications for Cancer Metabolism. Int J Mol Sci 2023; 24:ijms24097983. [PMID: 37175690 PMCID: PMC10178695 DOI: 10.3390/ijms24097983] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Under low oxygen conditions (hypoxia), cells activate survival mechanisms including metabolic changes and angiogenesis, which are regulated by HIF-1. The estrogen-related receptor alpha (ERRα) is a transcription factor with important roles in the regulation of cellular metabolism that is overexpressed in hypoxia, suggesting that it plays a role in cell survival in this condition. This review enumerates and analyses the recent evidence that points to the role of ERRα as a regulator of hypoxic genes, both in cooperation with HIF-1 and through HIF-1- independent mechanisms, in invertebrate and vertebrate models and in physiological and pathological scenarios. ERRα's functions during hypoxia include two mechanisms: (1) direct ERRα/HIF-1 interaction, which enhances HIF-1's transcriptional activity; and (2) transcriptional activation by ERRα of genes that are classical HIF-1 targets, such as VEGF or glycolytic enzymes. ERRα is thus gaining recognition for its prominent role in the hypoxia response, both in the presence and absence of HIF-1. In some models, ERRα prepares cells for hypoxia, with important clinical/therapeutic implications.
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Affiliation(s)
- Leslie Chaltel-Lima
- Segal Cancer Center, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
| | - Fabiola Domínguez
- Centro de Investigación Biomédica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Atlixco 74360, Mexico
| | - Lenin Domínguez-Ramírez
- Centro de Investigación Biomédica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Atlixco 74360, Mexico
| | - Paulina Cortes-Hernandez
- Centro de Investigación Biomédica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Atlixco 74360, Mexico
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