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Kennedy PH, Alborzian Deh Sheikh A, Balakar M, Jones AC, Olive ME, Hegde M, Matias MI, Pirete N, Burt R, Levy J, Little T, Hogan PG, Liu DR, Doench JG, Newton AC, Gottschalk RA, de Boer CG, Alarcón S, Newby GA, Myers SA. Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput. Nat Methods 2024; 21:1033-1043. [PMID: 38684783 DOI: 10.1038/s41592-024-02256-z] [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: 10/16/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024]
Abstract
Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here we describe the high-throughput, functional assessment of phosphorylation sites through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of PHLPP1, which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.
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Affiliation(s)
- Patrick H Kennedy
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Amin Alborzian Deh Sheikh
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Alexander C Jones
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, CA, USA
| | | | - Mudra Hegde
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria I Matias
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Natan Pirete
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajan Burt
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Tamia Little
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Patrick G Hogan
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Program in Immunology, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Rachel A Gottschalk
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carl G de Boer
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzie Alarcón
- La Jolla Institute for Immunology, La Jolla, CA, USA
- AUGenomics, San Diego, CA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA.
- Program in Immunology, University of California San Diego, San Diego, CA, USA.
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA.
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Kennedy PH, Deh Sheikh AA, Balakar M, Jones AC, Olive ME, Hegde M, Matias MI, Pirete N, Burt R, Levy J, Little T, Hogan PG, Liu DR, Doench JG, Newton AC, Gottschalk RA, de Boer C, Alarcón S, Newby G, Myers SA. Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566649. [PMID: 38014346 PMCID: PMC10680671 DOI: 10.1101/2023.11.11.566649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here, we describe "signaling-to-transcription network" mapping through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally-resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of the phosphatase PHLPP1 which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.
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Arbaciauskaite M, Pirhanov A, Ammermann E, Lei Y, Cho YK. Yeast biopanning against site-specific phosphorylations in tau. Protein Eng Des Sel 2023; 36:gzad005. [PMID: 37294629 PMCID: PMC10281017 DOI: 10.1093/protein/gzad005] [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: 01/30/2023] [Revised: 05/11/2023] [Accepted: 06/01/2023] [Indexed: 06/11/2023] Open
Abstract
The detection of site-specific phosphorylation in the microtubule-associated protein tau is emerging as a means to diagnose and monitor the progression of Alzheimer's Disease and other neurodegenerative diseases. However, there is a lack of phospho-specific monoclonal antibodies and limited validation of their binding specificity. Here, we report a novel approach using yeast biopanning against synthetic peptides containing site-specific phosphorylations. Using yeast cells displaying a previously validated phospho-tau (p-tau) single-chain variable region fragment (scFv), we show selective yeast cell binding based on single amino acid phosphorylation on the antigen. We identify conditions that allow phospho-specific biopanning using scFvs with a wide range of affinities (KD = 0.2 to 60 nM). Finally, we demonstrate the capability of screening large libraries by performing biopanning in 6-well plates. These results show that biopanning can effectively select yeast cells based on phospho-site specific antibody binding, opening doors for the facile identification of high-quality monoclonal antibodies.
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Affiliation(s)
- Monika Arbaciauskaite
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Azady Pirhanov
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Erik Ammermann
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Yu Lei
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Yong Ku Cho
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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Rieloff E, Skepö M. The Effect of Multisite Phosphorylation on the Conformational Properties of Intrinsically Disordered Proteins. Int J Mol Sci 2021; 22:11058. [PMID: 34681718 PMCID: PMC8541499 DOI: 10.3390/ijms222011058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 02/06/2023] Open
Abstract
Intrinsically disordered proteins are involved in many biological processes such as signaling, regulation, and recognition. A common strategy to regulate their function is through phosphorylation, as it can induce changes in conformation, dynamics, and interactions with binding partners. Although phosphorylated intrinsically disordered proteins have received increased attention in recent years, a full understanding of the conformational and structural implications of phosphorylation has not yet been achieved. Here, we present all-atom molecular dynamics simulations of five disordered peptides originated from tau, statherin, and β-casein, in both phosphorylated and non-phosphorylated state, to compare changes in global dimensions and structural elements, in an attempt to gain more insight into the controlling factors. The changes are in qualitative agreement with experimental data, and we observe that the net charge is not enough to predict the impact of phosphorylation on the global dimensions. Instead, the distribution of phosphorylated and positively charged residues throughout the sequence has great impact due to the formation of salt bridges. In statherin, a preference for arginine-phosphoserine interaction over arginine-tyrosine accounts for a global expansion, despite a local contraction of the phosphorylated region, which implies that also non-charged residues can influence the effect of phosphorylation.
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Affiliation(s)
- Ellen Rieloff
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden;
| | - Marie Skepö
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden;
- LINXS—Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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