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Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2024; 43:857-887. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
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Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
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2
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Roark RS, Habib R, Gorman J, Li H, Connell AJ, Bonsignori M, Guo Y, Hogarty MP, Olia AS, Sowers K, Zhang B, Bibollet-Ruche F, Callaghan S, Carey JW, Cerutti G, Harris DR, He W, Lewis E, Liu T, Mason RD, Park Y, Rando JM, Singh A, Wolff J, Lei QP, Louder MK, Doria-Rose NA, Andrabi R, Saunders KO, Seaman MS, Haynes BF, Kulp DW, Mascola JR, Roederer M, Sheng Z, Hahn BH, Shaw GM, Kwong PD, Shapiro L. HIV-1 neutralizing antibodies in SHIV-infected macaques recapitulate structurally divergent modes of human V2 apex recognition with a single D gene. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598384. [PMID: 38903070 PMCID: PMC11188099 DOI: 10.1101/2024.06.11.598384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Broadly neutralizing antibodies targeting the V2 apex of the HIV-1 envelope trimer are among the most common specificities elicited in HIV-1-infected humans and simian-human immunodeficiency virus (SHIV)-infected macaques. To gain insight into the prevalent induction of these antibodies, we isolated and characterized 11 V2 apex-directed neutralizing antibody lineages from SHIV-infected rhesus macaques. Remarkably, all SHIV-induced V2 apex lineages were derived from reading frame two of the rhesus DH3-15*01 gene. Cryo-EM structures of envelope trimers in complex with antibodies from nine rhesus lineages revealed modes of recognition that mimicked three canonical human V2 apex-recognition modes. Notably, amino acids encoded by DH3-15*01 played divergent structural roles, inserting into a hole at the trimer apex, H-bonding to an exposed strand, or forming part of a loop scaffold. Overall, we identify a DH3-15*01-signature for rhesus V2 apex broadly neutralizing antibodies and show that highly selected genetic elements can play multiple roles in antigen recognition. Highlights Isolated 11 V2 apex-targeted HIV-neutralizing lineages from 10 SHIV-infected Indian-origin rhesus macaquesCryo-EM structures of Fab-Env complexes for nine rhesus lineages reveal modes of recognition that mimic three modes of human V2 apex antibody recognitionAll SHIV-elicited V2 apex lineages, including two others previously published, derive from the same DH3-15*01 gene utilizing reading frame twoThe DH3-15*01 gene in reading frame two provides a necessary, but not sufficient, signature for V2 apex-directed broadly neutralizing antibodiesStructural roles played by DH3-15*01-encoded amino acids differed substantially in different lineages, even for those with the same recognition modePropose that the anionic, aromatic, and extended character of DH3-15*01 in reading frame two provides a selective advantage for V2 apex recognition compared to B cells derived from other D genes in the naïve rhesus repertoireDemonstrate that highly selected genetic elements can play multiple roles in antigen recognition, providing a structural means to enhance recognition diversity.
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3
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Chen X, van de Sande JW, Ritmejeris J, Wen C, Brinkerhoff H, Laszlo AH, Albada B, Dekker C. Resolving sulfation PTMs on a plant peptide hormone using nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593138. [PMID: 38765996 PMCID: PMC11100766 DOI: 10.1101/2024.05.08.593138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Peptide phytohormones are decorated with post-translational modifications (PTMs) that are crucial for receptor recognition. Tyrosine sulfation on these hormones is essential for plant growth and development1. Measuring the occurrence and position of sulfotyrosine is, however, compromised by major technical challenges during isolation and detection2. We recently introduced a nanopore peptide sequencing method that sensitively detects PTMs at the single-molecule level3. By translocating PTM variants of the plant pentapeptide hormone phytosulfokine (PSK) through a nanopore, we here demonstrate accurate identification of sulfation and phosphorylation on the two tyrosine residues of PSK. Sulfation can be clearly detected and distinguished (>90%) from phosphorylation on the same residue. Moreover, the presence or absence of PTMs on the two close-by tyrosine residues can be accurately determined (>96% accuracy). Our findings demonstrate the extraordinary sensitivity of nanopore protein measurements, providing a new tool for identifying sulfation on peptide phytohormones and promising wider applications to identify protein PTMs.
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Affiliation(s)
- Xiuqi Chen
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
- These authors contributed equally
| | - Jasper W. van de Sande
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, the Netherlands
- These authors contributed equally
| | - Justas Ritmejeris
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
- These authors contributed equally
| | - Chenyu Wen
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | | | - Andrew H. Laszlo
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
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4
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D’Antona AM, Lee JM, Zhang M, Friedman C, He T, Mosyak L, Bennett E, Lin L, Silverman M, Cometa F, Meade C, Hageman T, Sousa E, Cohen J, Marquette K, Ferguson D, Zhong X. Tyrosine Sulfation at Antibody Light Chain CDR-1 Increases Binding Affinity and Neutralization Potency to Interleukine-4. Int J Mol Sci 2024; 25:1931. [PMID: 38339208 PMCID: PMC10855961 DOI: 10.3390/ijms25031931] [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: 12/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Structure and function of therapeutic antibodies can be modulated by a variety of post-translational modifications (PTM). Tyrosine (Tyr) sulfation is a type of negatively charged PTM that occurs during protein trafficking through the Golgi. In this study, we discovered that an anti-interleukin (IL)-4 human IgG1, produced by transiently transfected HEK293 cells, contained a fraction of unusual negatively charged species. Interestingly, the isolated acidic species exhibited a two-fold higher affinity to IL-4 and a nearly four-fold higher potency compared to the main species. Mass spectrometry (MS) showed the isolated acidic species possessed an +80-Dalton from the expected mass, suggesting an occurrence of Tyr sulfation. Consistent with this hypothesis, we show the ability to control the acidic species during transient expression with the addition of Tyr sulfation inhibitor sodium chlorate or, conversely, enriched the acidic species from 30% to 92% of the total antibody protein when the IL-4 IgG was co-transfected with tyrosylprotein sulfotransferase genes. Further MS and mutagenesis analysis identified a Tyr residue at the light chain complementarity-determining region-1 (CDRL-1), which was sulfated specifically. These results together have demonstrated for the first time that Tyr sulfation at CDRL-1 could modulate antibody binding affinity and potency to a human immune cytokine.
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Affiliation(s)
- Aaron M. D’Antona
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Julie M. Lee
- Translational Clinical Sciences, Pfizer Discovery & Early Development, 610 Main Street, Cambridge, MA 02139, USA
| | - Melvin Zhang
- Inflammation and Immunology Research Unit, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA
| | - Clarence Friedman
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Tao He
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Lidia Mosyak
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Eric Bennett
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Laura Lin
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Maddison Silverman
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Funi Cometa
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Caryl Meade
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Tyler Hageman
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Eric Sousa
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Justin Cohen
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Kimberly Marquette
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Darren Ferguson
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Xiaotian Zhong
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
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5
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Kweon HK, Kong AT, Hersberger KE, Huang S, Nesvizhskii AI, Wang Y, Hakansson K, Andrews PC. Sulfoproteomics Workflow with Precursor Ion Accurate Mass Shift Analysis Reveals Novel Tyrosine Sulfoproteins in the Golgi. J Proteome Res 2024; 23:71-83. [PMID: 38112105 PMCID: PMC11218929 DOI: 10.1021/acs.jproteome.3c00323] [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] [Indexed: 12/20/2023]
Abstract
Tyrosine sulfation in the Golgi of secreted and membrane proteins is an important post-translational modification (PTM). However, its labile nature has limited analysis by mass spectrometry (MS), a major reason why no sulfoproteome studies have been previously reported. Here, we show that a phosphoproteomics experimental workflow, which includes serial enrichment followed by high resolution, high mass accuracy MS, and tandem MS (MS/MS) analysis, enables sulfopeptide coenrichment and identification via accurate precursor ion mass shift open MSFragger database search. This approach, supported by manual validation, allows the confident identification of sulfotyrosine-containing peptides in the presence of high levels of phosphorylated peptides, thus enabling these two sterically and ionically similar isobaric PTMs to be distinguished and annotated in a single proteomic analysis. We applied this approach to isolated interphase and mitotic rat liver Golgi membranes and identified 67 tyrosine sulfopeptides, corresponding to 26 different proteins. This work discovered 23 new sulfoproteins with functions related to, for example, Ca2+-binding, glycan biosynthesis, and exocytosis. In addition, we report the first preliminary evidence for crosstalk between sulfation and phosphorylation in the Golgi, with implications for functional control.
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Affiliation(s)
- Hye Kyong Kweon
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, United States
| | - Andy T Kong
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109-5602, United States
| | - Katherine E Hersberger
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Shijiao Huang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109-5602, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109-2218, United States
| | - Yanzhuang Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
| | - Kristina Hakansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Philip C Andrews
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109-2218, United States
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6
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Daly L, Byrne DP, Perkins S, Brownridge PJ, McDonnell E, Jones AR, Eyers PA, Eyers CE. Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides. J Proteome Res 2023; 22:3754-3772. [PMID: 37939282 PMCID: PMC10696596 DOI: 10.1021/acs.jproteome.3c00425] [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: 07/14/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Protein tyrosine sulfation (sY) is a post-translational modification (PTM) catalyzed by Golgi-resident tyrosyl protein sulfo transferases (TPSTs). Information on sY in humans is currently limited to ∼50 proteins, with only a handful having verified sites of sulfation. As such, the contribution of sulfation to the regulation of biological processes remains poorly defined. Mass spectrometry (MS)-based proteomics is the method of choice for PTM analysis but has yet to be applied for systematic investigation of the "sulfome", primarily due to issues associated with discrimination of sY-containing from phosphotyrosine (pY)-containing peptides. In this study, we developed an MS-based workflow for sY-peptide characterization, incorporating optimized Zr4+ immobilized metal-ion affinity chromatography (IMAC) and TiO2 enrichment strategies. Extensive characterization of a panel of sY- and pY-peptides using an array of fragmentation regimes (CID, HCD, EThcD, ETciD, UVPD) highlighted differences in the generation of site-determining product ions and allowed us to develop a strategy for differentiating sulfated peptides from nominally isobaric phosphopeptides based on low collision energy-induced neutral loss. Application of our "sulfomics" workflow to a HEK-293 cell extracellular secretome facilitated identification of 21 new sulfotyrosine-containing proteins, several of which we validate enzymatically, and reveals new interplay between enzymes relevant to both protein and glycan sulfation.
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Affiliation(s)
- Leonard
A. Daly
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Dominic P. Byrne
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Simon Perkins
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Philip J. Brownridge
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Euan McDonnell
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Andrew R. Jones
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Patrick A. Eyers
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Claire E. Eyers
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
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7
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Hasegawa Y, Tonsho S, Nakazawa T, Kainuma T, Kagasaki K, Sakurai S, Kitagawa K, Asada S. ADY tripeptide is a minimum sequence for Tyrosylprotein sulfotransferases 1 and 2 substrate recognition. Biochem Biophys Res Commun 2023; 676:73-77. [PMID: 37490834 DOI: 10.1016/j.bbrc.2023.07.026] [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: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/27/2023]
Abstract
Tyrosylprotein sulfotransferases (TPSTs) catalyze the transfer of a sulphonate moiety from 3'-Phosphoadenosine 5'-Phosphosulfate (PAPS) to the hydroxyl group of a tyrosine residue in substrate proteins. The positively charged substrate binding region of TPST homodimer interacts with acidic residues located in N-terminal region from the sulfated tyrosine in substrates. However, the sequence pattern in TPST substrate recognition remains unclear. Therefore, we aimed to determine the minimum recognition chain length required for tyrosine sulfation. We prepared His-tagged polypeptide, His-TPST143-370 and His-TPST243-377, form 43-370 of TPST1 and 43-377 of TPST2. Next, we prepared a series of synthesized ADYAE peptides and used a combination of reverse phase high-performance liquid chromatography (RP-HPLC) and mass spectrometric analysis to show that the tripeptide amino acid sequence, ADY, was sulfated by TPST1 and TPST2. Furthermore, we found that the acidic residue, located two residues C-terminal region from the tyrosine residue, may be involved in the TPST-induced sulfation regulation. The results in our study propose that proteins with the ADY sequence may be useful for searching the novel TPST tyrosine sulfated substrates.
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Affiliation(s)
- Yuta Hasegawa
- Laboratory of Bioorganic and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Medical and Life Sciences, 265-1 Higashijima, Akiha-ku, Niigata, 956-8603, Japan
| | - Sayaka Tonsho
- Laboratory of Bioorganic and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Medical and Life Sciences, 265-1 Higashijima, Akiha-ku, Niigata, 956-8603, Japan
| | - Taiyo Nakazawa
- Laboratory of Bioorganic and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Medical and Life Sciences, 265-1 Higashijima, Akiha-ku, Niigata, 956-8603, Japan
| | - Tadashi Kainuma
- Laboratory of Bioorganic and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Medical and Life Sciences, 265-1 Higashijima, Akiha-ku, Niigata, 956-8603, Japan
| | - Kaori Kagasaki
- Laboratory of Bioorganic and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Medical and Life Sciences, 265-1 Higashijima, Akiha-ku, Niigata, 956-8603, Japan
| | - Shota Sakurai
- Laboratory of Bioorganic and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Medical and Life Sciences, 265-1 Higashijima, Akiha-ku, Niigata, 956-8603, Japan
| | - Kouki Kitagawa
- Laboratory of Bioorganic and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Medical and Life Sciences, 265-1 Higashijima, Akiha-ku, Niigata, 956-8603, Japan
| | - Shinichi Asada
- Laboratory of Bioorganic and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Medical and Life Sciences, 265-1 Higashijima, Akiha-ku, Niigata, 956-8603, Japan.
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8
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Daly LA, Clarke CJ, Po A, Oswald SO, Eyers CE. Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond. Chem Commun (Camb) 2023; 59:11484-11499. [PMID: 37681662 PMCID: PMC10521633 DOI: 10.1039/d3cc02909c] [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: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
Post-translational modifications (PTMs) are ubiquitous and key to regulating protein function. Understanding the dynamics of individual PTMs and their biological roles requires robust characterisation. Mass spectrometry (MS) is the method of choice for the identification and quantification of protein modifications. This article focusses on the MS-based analysis of those covalent modifications that induce a mass shift of +80 Da, notably phosphorylation and sulfation, given the challenges associated with their discrimination and pinpointing the sites of modification on a polypeptide chain. Phosphorylation in particular is highly abundant, dynamic and can occur on numerous residues to invoke specific functions, hence robust characterisation is crucial to understanding biological relevance. Showcasing our work in the context of other developments in the field, we highlight approaches for enrichment and site localisation of phosphorylated (canonical and non-canonical) and sulfated peptides, as well as modification analysis in the context of intact proteins (top down proteomics) to explore combinatorial roles. Finally, we discuss the application of native ion-mobility MS to explore the effect of these PTMs on protein structure and ligand binding.
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Affiliation(s)
- Leonard A Daly
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Christopher J Clarke
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Allen Po
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Sally O Oswald
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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9
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Liu C, Liu X, Zhou M, Xia C, Lyu Y, Peng Q, Soni C, Zhou Z, Su Q, Wu Y, Weerapana E, Gao J, Chatterjee A, Cheng L, Jia N. Fluorosulfate as a Latent Sulfate in Peptides and Proteins. J Am Chem Soc 2023; 145:20189-20195. [PMID: 37647087 PMCID: PMC10623540 DOI: 10.1021/jacs.3c07937] [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] [Indexed: 09/01/2023]
Abstract
Sulfation widely exists in the eukaryotic proteome. However, understanding the biological functions of sulfation in peptides and proteins has been hampered by the lack of methods to control its spatial or temporal distribution in the proteome. Herein, we report that fluorosulfate can serve as a latent precursor of sulfate in peptides and proteins, which can be efficiently converted to sulfate by hydroxamic acid reagents under physiologically relevant conditions. Photocaging the hydroxamic acid reagents further allowed for the light-controlled activation of functional sulfopeptides. This work provides a valuable tool for probing the functional roles of sulfation in peptides and proteins.
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Affiliation(s)
- Chao Liu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Xueyi Liu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Mi Zhou
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Chaoshuang Xia
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Yuhan Lyu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Qianni Peng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Chintan Soni
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Zefeng Zhou
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Qiwen Su
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Yujia Wu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Lin Cheng
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Niu Jia
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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10
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Wang J, Wang C, Wang T, Zhang S, Yan K, Yang G, Wu C, Zheng C, Huang J. Tyrosylprotein sulfotransferase suppresses ABA signaling via sulfation of SnRK2.2/2.3/2.6. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1846-1851. [PMID: 37052306 DOI: 10.1111/jipb.13493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/07/2023] [Indexed: 05/17/2023]
Abstract
Phytohormone abscisic acid (ABA) plays vital roles in stress tolerance, while long-term overactivation of ABA signaling suppresses plant growth and development. However, the braking mechanism of ABA responses is not clear. Protein tyrosine sulfation catalyzed by tyrosylprotein sulfotransferase (TPST) is a critical post-translational modification. Through genetic screening, we identified a tpst mutant in Arabidopsis that was hypersensitive to ABA. In-depth analysis revealed that TPST could interact with and sulfate SnRK2.2/2.3/2.6, which accelerated their degradation and weakened the ABA signaling. Taken together, these findings uncovered a novel mechanism of desensitizing ABA responses via protein sulfation.
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Affiliation(s)
- Jun Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
- Department of Food Science and Engineering, Shandong Agriculture and Engineering University, Jinan, 250100, China
| | - Chunyan Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Tianrun Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
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11
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Yu W, Zhou R, Li N, Lei ZC, Guo D, Peng F, Li Y, Bai X, Feng S, Wang Y, He J, Yin S, Zeng X, He L, Gao Y, Li M, Guo YR, Liu K, Wang Y. Histone tyrosine sulfation by SULT1B1 regulates H4R3me2a and gene transcription. Nat Chem Biol 2023; 19:855-864. [PMID: 36805701 DOI: 10.1038/s41589-023-01267-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 01/16/2023] [Indexed: 02/22/2023]
Abstract
Tyrosine sulfation is a common posttranslational modification in mammals. To date, it has been thought to be limited to secreted and transmembrane proteins, but little is known about tyrosine sulfation on nuclear proteins. Here we report that SULT1B1 is a histone sulfotransferase that can sulfate the tyrosine 99 residue of nascent histone H3 in cytosol. The sulfated histone H3 can be transported into the nucleus and majorly deposited in the promoter regions of genes in chromatin. While the H3Y99 residue is buried inside octameric nucleosome, dynamically regulated subnucleosomal structures provide chromatin-H3Y99sulf the opportunity of being recognized and bound by PRMT1, which deposits H4R3me2a in chromatin. Disruption of H3Y99sulf reduces PRMT1 binding to chromatin, H4R3me2a level and gene transcription. These findings reveal the mechanisms underlying H3Y99 sulfation and its cross-talk with H4R3me2a to regulate gene transcription. This study extends the spectrum of tyrosine sulfation on nuclear proteins and the repertoire of histone modifications regulating chromatin functions.
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Affiliation(s)
- Weixing Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Runxin Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhi-Chao Lei
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dingyuan Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Peng
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xue Bai
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Shan Feng
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yu Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie He
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sibi Yin
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao Zeng
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Leya He
- Department of Gastrointestinal Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Gao
- Institute of Precision Medicine, Jining Medical University, Jining, China
| | - Mingchang Li
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yusong R Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China.
| | - Yugang Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China.
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12
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Niu W, Guo J. Co-translational Installation of Posttranslational Modifications by Non-canonical Amino Acid Mutagenesis. Chembiochem 2023; 24:e202300039. [PMID: 36853967 PMCID: PMC10202221 DOI: 10.1002/cbic.202300039] [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: 01/18/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/02/2023]
Abstract
Protein posttranslational modifications (PTMs) play critical roles in regulating cellular activities. Here we provide a survey of genetic code expansion (GCE) methods that were applied in the co-translational installation and studies of PTMs through noncanonical amino acid (ncAA) mutagenesis. We begin by reviewing types of PTM that have been installed by GCE with a focus on modifications of tyrosine, serine, threonine, lysine, and arginine residues. We also discuss examples of applying these methods in biological studies. Finally, we end the piece with a short discussion on the challenges and the opportunities of the field.
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Affiliation(s)
- Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, N-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
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13
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Harel O, Jbara M. Chemical Synthesis of Bioactive Proteins. Angew Chem Int Ed Engl 2023; 62:e202217716. [PMID: 36661212 DOI: 10.1002/anie.202217716] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/21/2023]
Abstract
Nature has developed a plethora of protein machinery to operate and maintain nearly every task of cellular life. These processes are tightly regulated via post-expression modifications-transformations that modulate intracellular protein synthesis, folding, and activation. Methods to prepare homogeneously and precisely modified proteins are essential to probe their function and design new bioactive modalities. Synthetic chemistry has contributed remarkably to protein science by allowing the preparation of novel biomacromolecules that are often challenging or impractical to prepare via common biological means. The ability to chemically build and precisely modify proteins has enabled the production of new molecules with novel physicochemical properties and programmed activity for biomedical research, diagnostic, and therapeutic applications. This minireview summarizes recent developments in chemical protein synthesis to produce bioactive proteins, with emphasis on novel analogs with promising in vitro and in vivo activity.
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Affiliation(s)
- Omer Harel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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14
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Fedoreyeva LI. Molecular Mechanisms of Regulation of Root Development by Plant Peptides. PLANTS (BASEL, SWITZERLAND) 2023; 12:1320. [PMID: 36987008 PMCID: PMC10053774 DOI: 10.3390/plants12061320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/14/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Peptides perform many functions, participating in the regulation of cell differentiation, regulating plant growth and development, and also involved in the response to stress factors and in antimicrobial defense. Peptides are an important class biomolecules for intercellular communication and in the transmission of various signals. The intercellular communication system based on the ligand-receptor bond is one of the most important molecular bases for creating complex multicellular organisms. Peptide-mediated intercellular communication plays a critical role in the coordination and determination of cellular functions in plants. The intercellular communication system based on the receptor-ligand is one of the most important molecular foundations for creating complex multicellular organisms. Peptide-mediated intercellular communication plays a critical role in the coordination and determination of cellular functions in plants. The identification of peptide hormones, their interaction with receptors, and the molecular mechanisms of peptide functioning are important for understanding the mechanisms of both intercellular communications and for regulating plant development. In this review, we drew attention to some peptides involved in the regulation of root development, which implement this regulation by the mechanism of a negative feedback loop.
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Affiliation(s)
- Larisa I Fedoreyeva
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia
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15
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Vamva E, Ozog S, Leaman DP, Yu-Hong Cheng R, Irons NJ, Ott A, Stoffers C, Khan I, Goebrecht GK, Gardner MR, Farzan M, Rawlings DJ, Zwick MB, James RG, Torbett BE. A lentiviral vector B cell gene therapy platform for the delivery of the anti-HIV-1 eCD4-Ig-knob-in-hole-reversed immunoadhesin. Mol Ther Methods Clin Dev 2023; 28:366-384. [PMID: 36879849 PMCID: PMC9984920 DOI: 10.1016/j.omtm.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
Barriers to effective gene therapy for many diseases include the number of modified target cells required to achieve therapeutic outcomes and host immune responses to expressed therapeutic proteins. As long-lived cells specialized for protein secretion, antibody-secreting B cells are an attractive target for foreign protein expression in blood and tissue. To neutralize HIV-1, we developed a lentiviral vector (LV) gene therapy platform for delivery of the anti-HIV-1 immunoadhesin, eCD4-Ig, to B cells. The EμB29 enhancer/promoter in the LV limited gene expression in non-B cell lineages. By engineering a knob-in-hole-reversed (KiHR) modification in the CH3-Fc eCD4-Ig domain, we reduced interactions between eCD4-Ig and endogenous B cell immunoglobulin G proteins, which improved HIV-1 neutralization potency. Unlike previous approaches in non-lymphoid cells, eCD4-Ig-KiHR produced in B cells promoted HIV-1 neutralizing protection without requiring exogenous TPST2, a tyrosine sulfation enzyme required for eCD4-Ig-KiHR function. This finding indicated that B cell machinery is well suited to produce therapeutic proteins. Lastly, to overcome the inefficient transduction efficiency associated with VSV-G LV delivery to primary B cells, an optimized measles pseudotyped LV packaging methodology achieved up to 75% transduction efficiency. Overall, our findings support the utility of B cell gene therapy platforms for therapeutic protein delivery.
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Affiliation(s)
- Eirini Vamva
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Stosh Ozog
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Daniel P. Leaman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene Yu-Hong Cheng
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Nicholas J. Irons
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Andee Ott
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Claire Stoffers
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Iram Khan
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
| | | | - Matthew R. Gardner
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael Farzan
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, FL, USA
| | - David J. Rawlings
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael B. Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Richard G. James
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA, USA
| | - Bruce E. Torbett
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
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16
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He X, Chen Y, Guo J, Niu W. Site-Specific Incorporation of Sulfotyrosine into Proteins in Mammalian Cells. Methods Mol Biol 2023; 2676:233-243. [PMID: 37277637 DOI: 10.1007/978-1-0716-3251-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Protein tyrosine O-sulfation (PTS) plays a crucial role in numerous extracellular protein-protein interactions. It is involved in diverse physiological processes and the development of human diseases, including AIDS and cancer. To facilitate the study of PTS in live mammalian cells, an approach for the site-specific synthesis of tyrosine-sulfated proteins (sulfoproteins) was developed. This approach takes advantage of an evolved Escherichia coli tyrosyl-tRNA synthetase to genetically encode sulfotyrosine (sTyr) into any proteins of interest (POI) in response to a UAG stop codon. Here, we give a step-by-step account of the incorporation of sTyr in HEK293T cells using the enhanced green fluorescent protein as an example. This method can be widely applied to incorporating sTyr into any POI to investigate the biological functions of PTS in mammalian cells.
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Affiliation(s)
- Xinyuan He
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Yan Chen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA.
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA.
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17
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Waldrop SP, Niu W, Guo J. Engineering of SH2 Domains for the Recognition of Protein Tyrosine O-Sulfation Sites. Methods Mol Biol 2023; 2705:293-305. [PMID: 37668981 DOI: 10.1007/978-1-0716-3393-9_16] [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] [Indexed: 09/06/2023]
Abstract
Protein engineering has brought advances to industrial processes, biomaterials, nanotechnology, biosensors, and biomedical applications. This chapter will focus on the engineering of Src Homology 2 domains (SH2) to act as an antibody mimetic for the recognition of sulfotyrosine-containing peptides or proteins. In comparison to anti-sulfotyrosine antibodies, SH2 mutants have much smaller size and can be heterologously expressed and purified in large quantity at low cost. This chapter will describe the use of phage display to identify a sulfotyrosine-binding SH2 mutant and the subsequent enrichment of sulfotyrosine-containing peptides in complex biological samples.
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Affiliation(s)
- Sean Paul Waldrop
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA.
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18
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Zhong X, D’Antona AM. A potential antibody repertoire diversification mechanism through tyrosine sulfation for biotherapeutics engineering and production. Front Immunol 2022; 13:1072702. [PMID: 36569848 PMCID: PMC9774471 DOI: 10.3389/fimmu.2022.1072702] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
The diversity of three hypervariable loops in antibody heavy chain and light chain, termed the complementarity-determining regions (CDRs), defines antibody's binding affinity and specificity owing to the direct contact between the CDRs and antigens. These CDR regions typically contain tyrosine (Tyr) residues that are known to engage in both nonpolar and pi stacking interaction with antigens through their complementary aromatic ring side chains. Nearly two decades ago, sulfotyrosine residue (sTyr), a negatively charged Tyr formed by Golgi-localized membrane-bound tyrosylprotein sulfotransferases during protein trafficking, were also found in the CDR regions and shown to play an important role in modulating antibody-antigen interaction. This breakthrough finding demonstrated that antibody repertoire could be further diversified through post-translational modifications, in addition to the conventional genetic recombination. This review article summarizes the current advances in the understanding of the Tyr-sulfation modification mechanism and its application in potentiating protein-protein interaction for antibody engineering and production. Challenges and opportunities are also discussed.
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19
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Computationally guided conversion of the specificity of E-selectin to mimic that of Siglec-8. Proc Natl Acad Sci U S A 2022; 119:e2117743119. [PMID: 36191232 PMCID: PMC9564326 DOI: 10.1073/pnas.2117743119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sulfated glycans have been found to be associated with various diseases and therefore have significant potential in molecular pathology as biomarkers. Although lectins are useful reagents for detecting glycans, there is a paucity of sulfate-recognizing lectins, and those that exist, such as from Maackia amurensis, display mixed specificities. Recombinant lectin engineering offers an emerging tool for creating novel glycan recognition by altering and/or enhancing endogenous specificities. The present study demonstrated the use of computational approaches in the engineering of a mutated form of E-selectin that displayed highly specific recognition of 6'-sulfo-sialyl Lewis X (6'-sulfo-sLex), with negligible binding to its endogenous nonsulfated ligand, sLex. This new specificity mimics that of the unrelated protein Siglec-8, for which 6'-sulfo-sLex is its preferred ligand. Molecular dynamics simulations and energy calculations predicted that two point mutations (E92A/E107A) would be required to stabilize binding to the sulfated oligosaccharide with E-selectin. In addition to eliminating putative repulsions between the negatively charged side chains and the sulfate moiety, the mutations also abolished favorable interactions with the endogenous ligand. Glycan microarray screening of the recombinantly expressed proteins confirmed the predicted specificity change but also identified the introduction of unexpected affinity for the unfucosylated form of 6'-sulfo-sLex (6'-sulfo-sLacNAc). Three key requirements were demonstrated in this case for engineering specificity for sulfated oligosaccharide: 1) removal of unfavorable interactions with the 6'-sulfate, 2) introduction of favorable interactions for the sulfate, and 3) removal of favorable interactions with the endogenous ligand.
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20
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Lima MA, Rudd TR, Fernig DG, Yates EA. Phosphorylation and sulfation share a common biosynthetic pathway, but extend biochemical and evolutionary diversity of biological macromolecules in distinct ways. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022; 19:20220391. [PMID: 35919982 PMCID: PMC9346353 DOI: 10.1098/rsif.2022.0391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphate and sulfate groups are integral to energy metabolism and introduce negative charges into biological macromolecules. One purpose of such modifications is to elicit precise binding/activation of protein partners. The physico-chemical properties of the two groups, while superficially similar, differ in one important respect—the valency of the central (phosphorus or sulfur) atom. This dictates the distinct properties of their respective esters, di-esters and hence their charges, interactions with metal ions and their solubility. These, in turn, determine the contrasting roles for which each group has evolved in biological systems. Biosynthetic links exist between the two modifications; the sulfate donor 3′-phosphoadenosine-5′-phosphosulfate being formed from adenosine triphosphate (ATP) and adenosine phosphosulfate, while the latter is generated from sulfate anions and ATP. Furthermore, phosphorylation, by a xylosyl kinase (Fam20B, glycosaminoglycan xylosylkinase) of the xylose residue of the tetrasaccharide linker region that connects nascent glycosaminoglycan (GAG) chains to their parent proteoglycans, substantially accelerates their biosynthesis. Following observations that GAG chains can enter the cell nucleus, it is hypothesized that sulfated GAGs could influence events in the nucleus, which would complete a feedback loop uniting the complementary anionic modifications of phosphorylation and sulfation through complex, inter-connected signalling networks and warrants further exploration.
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Affiliation(s)
- M A Lima
- Centre for Glycosciences, Keele University, Keele ST5 5BG, UK.,School of Life Sciences, Keele University, Keele ST5 5BG, UK
| | - T R Rudd
- Analytical and Biological Science Department, National Institute of Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar EN6 3QG, UK.,Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - D G Fernig
- Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - E A Yates
- School of Life Sciences, Keele University, Keele ST5 5BG, UK.,Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
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21
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Pedersen LC, Yi M, Pedersen LG, Kaminski AM. From Steroid and Drug Metabolism to Glycobiology, Using Sulfotransferase Structures to Understand and Tailor Function. Drug Metab Dispos 2022; 50:1027-1041. [PMID: 35197313 PMCID: PMC10753775 DOI: 10.1124/dmd.121.000478] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/06/2021] [Indexed: 11/22/2022] Open
Abstract
Sulfotransferases are ubiquitous enzymes that transfer a sulfo group from the universal cofactor donor 3'-phosphoadenosine 5'-phosphosulfate to a broad range of acceptor substrates. In humans, the cytosolic sulfotransferases are involved in the sulfation of endogenous compounds such as steroids, neurotransmitters, hormones, and bile acids as well as xenobiotics including drugs, toxins, and environmental chemicals. The Golgi associated membrane-bound sulfotransferases are involved in post-translational modification of macromolecules from glycosaminoglycans to proteins. The sulfation of small molecules can have profound biologic effects on the functionality of the acceptor, including activation, deactivation, or enhanced metabolism and elimination. Sulfation of macromolecules has been shown to regulate a number of physiologic and pathophysiological pathways by enhancing binding affinity to regulatory proteins or binding partners. Over the last 25 years, crystal structures of these enzymes have provided a wealth of information on the mechanisms of this process and the specificity of these enzymes. This review will focus on the general commonalities of the sulfotransferases, from enzyme structure to catalytic mechanism as well as providing examples into how structural information is being used to either design drugs that inhibit sulfotransferases or to modify the enzymes to improve drug synthesis. SIGNIFICANCE STATEMENT: This manuscript honors Dr. Masahiko Negishi's contribution to the understanding of sulfotransferase mechanism, specificity, and roles in biology by analyzing the crystal structures that have been solved over the last 25 years.
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Affiliation(s)
- Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - MyeongJin Yi
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - Lee G Pedersen
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - Andrea M Kaminski
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
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22
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Stewart V, Ronald PC. Sulfotyrosine residues: interaction specificity determinants for extracellular protein-protein interactions. J Biol Chem 2022; 298:102232. [PMID: 35798140 PMCID: PMC9372746 DOI: 10.1016/j.jbc.2022.102232] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Tyrosine sulfation, a post-translational modification, can determine and often enhance protein–protein interaction specificity. Sulfotyrosyl residues (sTyrs) are formed by the enzyme tyrosyl-protein sulfotransferase during protein maturation in the Golgi apparatus and most often occur singly or as a cluster within a six-residue span. With both negative charge and aromatic character, sTyr facilitates numerous atomic contacts as visualized in binding interface structural models, thus there is no discernible binding site consensus. Found exclusively in secreted proteins, in this review, we discuss the four broad sequence contexts in which sTyr has been observed: first, a solitary sTyr has been shown to be critical for diverse high-affinity interactions, such as between peptide hormones and their receptors, in both plants and animals. Second, sTyr clusters within structurally flexible anionic segments are essential for a variety of cellular processes, including coreceptor binding to the HIV-1 envelope spike protein during virus entry, chemokine interactions with receptors, and leukocyte rolling cell adhesion. Third, a subcategory of sTyr clusters is found in conserved acidic sequences termed hirudin-like motifs that enable proteins to interact with thrombin; consequently, many proven and potential therapeutic proteins derived from blood-consuming invertebrates depend on sTyrs for their activity. Finally, several proteins that interact with collagen or similar proteins contain one or more sTyrs within an acidic residue array. Refined methods to direct sTyr incorporation in peptides synthesized both in vitro and in vivo, together with continued advances in mass spectrometry and affinity detection, promise to accelerate discoveries of sTyr occurrence and function.
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Affiliation(s)
- Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, USA.
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, USA; Genome Center, University of California, Davis, USA.
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23
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Zhao D, Li C, Jiang H, Yin Y, Zhou C, Huang H, Qi Y, Li L. Engineering of Src Homology 2 Domain Leading to Sulfotyrosine Recognition With a High Affinity by Integrating a Distinctive Selection Theme and Next-Generation Sequencing. Front Microbiol 2022; 13:901558. [PMID: 35722314 PMCID: PMC9204161 DOI: 10.3389/fmicb.2022.901558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Tyrosine sulfation plays a vital role in various biochemical reactions. Although sulfated tyrosine (sTyr) has a similar structure to phosphotyrosine (pTyr), the number of available sTyr sites is significantly less than that of pTyr sites, mainly because of the lack of effective sTyr probes. A few sTyr binders were identified on the basis of structural similarity by engineering the pTyr-binding pocket of an Src Homology 2 (SH2) domain through phage selections against sTyr peptides. Nevertheless, they still interact with pTyr peptides with comparable affinity. This study aims to identify sTyr superbinders using the SH2 domain as a template. We created a distinctive phage selection scheme that separately covered selections against sTyr and pTyr peptides, followed by next-generation sequencing (NGS). After selections, phage pools showed strong enzyme-linked immunosorbent assay (ELISA) signal intensities for both modified peptides, indicating that the variants evolved with a high affinity for these peptides, which causes difficulty in identifying sTyr-specific binders. In contrast, NGS data from selected pools showed significant differences, suggesting the enrichment of sTyr-specific variants during selections. Accordingly, we obtained the sTyr features based on NGS data analysis and prioritized a few potential sTyr binders. The variant SH2-4 showed a stronger affinity for sTyr than pTyr and was superior to previous sTyr binders as measured by the Biolayer Interferometry assay. In summary, we described the strategy of integrating NGS data mining with a novel selection scheme to identify sTyr superbinders.
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Affiliation(s)
- Dongping Zhao
- School of Basic Medicine, Qingdao University, Qingdao, China
- Department of Drug Discovery, Noventi Biopharmaceuticals Co., Ltd., Shanghai, China
| | - Chan Li
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Haoqiang Jiang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yuqing Yin
- Department of Drug Discovery, Noventi Biopharmaceuticals Co., Ltd., Shanghai, China
| | | | - Haiming Huang
- Department of Drug Discovery, Noventi Biopharmaceuticals Co., Ltd., Shanghai, China
| | - Yunkun Qi
- School of Pharmacy, Qingdao University, Qingdao, China
- *Correspondence: Yunkun Qi,
| | - Lei Li
- School of Basic Medicine, Qingdao University, Qingdao, China
- Lei Li,
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24
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He X, Guo J, Niu W. Studying Protein Tyrosine O-Sulfation in Mammalian Cells with Genetically Encoded Sulfotyrosine. Curr Protoc 2021; 1:e301. [PMID: 34767302 PMCID: PMC8597929 DOI: 10.1002/cpz1.301] [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] [Indexed: 06/13/2023]
Abstract
Protein tyrosine O-sulfation (PTS) is a post-translational modification (PTM) that occurs exclusively on secreted and membrane-bound proteins. It participates in a wide range of important biological processes and is involved in the development of many diseases. The biomedical importance of PTS can only be fully unveiled when the right chemical/biological tools are available. This article outlines the steps for using an engineered Escherichia coli tyrosyl-tRNA synthetase to genetically encode sulfotyrosine (sTyr) for biological investigations of PTS in mammalian cells. Two basic protocols are described to demonstrate this methodology, including the site-specific incorporation of sTyr into eGFP protein in HEK293T cells and the functional study of an sTyr-containing CXCR4 protein using a calcium mobilization assay. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Site-specific incorporation of sTyr into eGFP Basic Protocol 2: Functional study of site-specifically sulfated CXCR4.
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Affiliation(s)
- Xinyuan He
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln
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25
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Šmak P, Tvaroška I, Koča J. The catalytic reaction mechanism of tyrosylprotein sulfotransferase-1. Phys Chem Chem Phys 2021; 23:23850-23860. [PMID: 34647946 DOI: 10.1039/d1cp03718h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tyrosine sulfation alters the biological activity of many proteins involved in different physiological and pathophysiological conditions, such as non-specific immune reaction, response to inflammation and ischemia, targeting of leukocytes and stem cells, or the formation of cancer metastases. Tyrosine sulfation is catalyzed by the enzymes tyrosylprotein sulfotransferases (TPST). In this study, we used QM/MM Car-Parrinello metadynamics simulations together with QM/MM potential energy calculations to investigate the catalytic mechanism of isoform TPST-1. The structural changes along the reaction coordinate are analyzed and discussed. Furthermore, both the methods supported the SN2 type of catalytic mechanism. The reaction barrier obtained from CPMD metadynamics was 12.8 kcal mol-1, and the potential energy scan led to reaction barriers of 11.6 kcal mol-1 and 13.7 kcal mol-1 with the B3LYP and OPBE functional, respectively. The comparison of the two methods (metadynamics and potential energy scan) may be helpful for future mechanistic studies. The insight into the reaction mechanism of TPST-1 might help with the rational design of transition-state TPST inhibitors.
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Affiliation(s)
- Pavel Šmak
- National Center for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Igor Tvaroška
- National Center for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic.,Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Jaroslav Koča
- National Center for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
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26
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Dowman LJ, Agten SM, Ripoll-Rozada J, Calisto BM, Pereira PJB, Payne RJ. Synthesis and evaluation of peptidic thrombin inhibitors bearing acid-stable sulfotyrosine analogues. Chem Commun (Camb) 2021; 57:10923-10926. [PMID: 34596182 DOI: 10.1039/d1cc04742f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tyrosine sulfation is an important post-translational modification of peptides and proteins which underpins and modulates many protein-protein interactions. In order to overcome the inherent instability of the native modification, we report the synthesis of two sulfonate analogues and their incorporation into two thrombin-inhibiting sulfopeptides. The effective mimicry of these sulfonate analogues for native sulfotyrosine was validated in the context of their thrombin inhibitory activity and binding mode, as determined by X-ray crystallography.
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Affiliation(s)
- Luke J Dowman
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydne, NSW 2006, Australia
| | - Stijn M Agten
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Jorge Ripoll-Rozada
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | | | - Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydne, NSW 2006, Australia
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27
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Co-Injection of Sulfotyrosine Facilitates Retinal Uptake of Hyaluronic Acid Nanospheres Following Intravitreal Injection. Pharmaceutics 2021; 13:pharmaceutics13091510. [PMID: 34575586 PMCID: PMC8469555 DOI: 10.3390/pharmaceutics13091510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
Gene and drug delivery to the retina is a critical therapeutic goal. While the majority of inherited forms of retinal degeneration affect the outer retina, specifically the photoreceptors and retinal pigment epithelium, effective targeted delivery to this region requires invasive subretinal delivery. Our goal in this work was to evaluate two innovative approaches for increasing both the persistence of delivered nanospheres and their penetration into the outer retina while using the much less invasive intravitreal delivery method. We formulated novel hyaluronic acid nanospheres (HA-NS, 250 nm and 500 nm in diameter) conjugated to fluorescent reporters and delivered them intravitreally to the adult Balb/C mouse retina. They exhibited persistence in the vitreous and along the inner limiting membrane (ILM) for up to 30 days (longest timepoint examined) but little retinal penetration. We thus evaluated the ability of the small molecule, sulfotyrosine, to disrupt the ILM, and found that 3.2 µg/µL sulfotyrosine led to significant improvement in delivery to the outer retina following intravitreal injections without causing retinal inflammation, degeneration, or loss of function. Co-delivery of sulfotyrosine and HA-NS led to robust improvements in penetration of HA-NS into the retina and accumulation along the interface between the photoreceptors and the retinal pigment epithelium. These exciting findings suggest that sulfotyrosine and HA-NS may be an effective strategy for outer retinal targeting after intravitreal injection.
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28
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Fujita S. CASPARIAN STRIP INTEGRITY FACTOR (CIF) family peptides - regulator of plant extracellular barriers. Peptides 2021; 143:170599. [PMID: 34174383 DOI: 10.1016/j.peptides.2021.170599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/24/2021] [Accepted: 06/18/2021] [Indexed: 01/17/2023]
Abstract
In multicellular organisms, water and most of the small molecules, such as nutrients, toxic substances, and signaling compounds, move freely through extracellular spaces, depending on their biochemical nature. To restrict the simple diffusion of small molecules, multicellular organisms have evolved extracellular barriers across specific tissue layers, such as tight junctions in the animal epithelium. Similar extracellular barriers are also generated in plants through the accumulation of hydrophobic chemicals, such as lignin or cutin, although the detailed molecular mechanisms underlying this process remain elusive. Here, I summarize recent advances in extracellular barrier formation in plants by focusing mainly on CASPARIAN STRIP INTEGRITY FACTOR (CIF) family peptides, which trigger the spatially precise deposition of designated cell wall components, enabling plants to establish transcellular barrier networks correctly. The genome of Arabidopsis thaliana, a model plant species, harbors five CIF genes, which encode propeptides which are processed into small secreted peptides of 21-24 amino acids. Sulfation of tyrosine residues in CIF peptides ensures their full bioactivity and high-affinity binding to their receptors SCHENGEN3/GASSHO1 (SGN3/GSO1) and GSO2 in vitro. Additionally, in vivo analysis shows that physical restriction of CIF peptide diffusion and the subcellular localization of a signaling module and expression patterns of a peptide processing enzyme specify the location of signal activation. Thus, the CIF peptide family provides fascinating models for understanding mature peptide biogenesis and spatially limited signal activation with small diffusive molecules.
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Affiliation(s)
- Satoshi Fujita
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
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29
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Lawrie J, Waldrop S, Morozov A, Niu W, Guo J. Engineering of a Small Protein Scaffold To Recognize Sulfotyrosine with High Specificity. ACS Chem Biol 2021; 16:1508-1517. [PMID: 34251168 DOI: 10.1021/acschembio.1c00382] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein tyrosine O-sulfation is an essential post-translational modification required for effective biological processes such as hemostasis, inflammatory response, and visual phototransduction. Because of its unstable nature under mass spectrometry conditions and residing on low-abundance cell surface proteins, sulfated tyrosine (sulfotyrosine) residues are difficult to detect or analyze. Enrichment of sulfotyrosine-containing proteins (sulfoproteins) from complex biological samples are typically required before analysis. In this work, we seek to engineer the phosphotyrosine binding pocket of a Src Homology 2 (SH2) domain to act as an antisulfotyrosine antibody mimic. Using tailored selection schemes, several SH2 mutants are identified with high affinity and specificity to sulfotyrosine. Further molecular docking simulations highlight potential mechanisms supporting observed characteristics of these SH2 mutants. Utilities of the evolved SH2 mutants were demonstrated by the detection and enrichment of sulfoproteins.
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Affiliation(s)
- Justin Lawrie
- Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Sean Waldrop
- Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Anya Morozov
- Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
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30
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Shinohara H. Root meristem growth factor RGF, a sulfated peptide hormone in plants. Peptides 2021; 142:170556. [PMID: 33901628 DOI: 10.1016/j.peptides.2021.170556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022]
Abstract
In recent decades, small secreted peptides have been recognized as a new class of intercellular signaling phytohormones in plants. Tyrosine sulfation plays crucial roles in peptide hormone bioactivities in plants. The Arabidopsis tyrosylprotein sulfotransferase mutant tpst-1 causes severe abnormalities in the root tip due to deficiency in the biosynthesis of all functional tyrosine-sulfated peptides. Root meristem growth factor RGF, a sulfated peptide hormone specifically expressed in the root tip, was found to complement tpst-1 root defects. This review summarizes the history of the identification of RGF, the characteristics of RGF, the identification of RGF receptors, and the target of RGF. In brief, RGF is a 13 amino acid sulfated peptide. The RGF peptide mutant rgf1,2,3 exhibited a reduced size of the root apical meristem, indicating that RGF maintains cell proliferation activity in the root apical meristem. RGF receptors were identified by comprehensive binding analysis with a custom-made receptor expression library. The RGF receptor mutant rgfr1,2,3 showed a phenotype of reduced root length due to a reduction in the root apical meristem and was insensitive to RGF. The signaling cascade through RGF-RGF receptor pairs regulates the gradient formation of PLETHORA (PLT), which is known as the master regulator of root formation. In the peptide mutant rgf1,2,3 and receptor mutant rgfr1,2,3, the gradient of PLT proteins disappeared, indicating that RGF defines the PLT protein gradient to ensure robust root growth and root development. Recent studies of the downstream signaling of RGF-RGF receptor pairs are also described in this review.
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Affiliation(s)
- Hidefumi Shinohara
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan.
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31
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Liu R, Zhang Y, Kumar A, Huhn S, Hullinger L, Du Z. Modulating tyrosine sulfation of recombinant antibodies in CHO cell culture by host selection and sodium chlorate supplementation. Biotechnol J 2021; 16:e2100142. [PMID: 34081410 DOI: 10.1002/biot.202100142] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Tyrosine sulfation is a post-translational modification found on many surface receptors and plays an important role in cell-cell and cell-matrix interactions. However, tyrosine sulfation of therapeutic antibodies has only been reported very recently. Because of potential potency and immunogenicity concerns, tyrosine sulfation needs to be controlled during the manufacturing process. METHODS AND RESULTS In this study, we explored methods to modulate antibody tyrosine sulfation during cell line development and upstream production process. We found that tyrosine sulfation levels were significantly different in various Chinese hamster ovary (CHO) cell lines due to differential expression of genes in the sulfation pathway including tyrosylprotein sulfotransferase 2 (TPST2) and the sulfation substrate transporter SLC35B2. We also screened chemical inhibitors to reduce tyrosine sulfation in CHO culture and found that sodium chlorate could significantly inhibit tyrosine sulfation while having minimal impact on cell growth and antibody production. We further confirmed this finding in a standard fed-batch production assay. Sodium chlorate at 16 mM markedly inhibited tyrosine sulfation by more than 50% and had no significant impact on antibody titer or quality. CONCLUSION These data suggest that we can control tyrosine sulfation by selecting CHO cell lines based on the expression level of TPST2 and SLC35B2 or adding sodium chlorate in upstream production process.
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Affiliation(s)
- Ren Liu
- Process Cell Sciences, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Yixiao Zhang
- Process Cell Sciences, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Amit Kumar
- Process Cell Sciences, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Steven Huhn
- Process Cell Sciences, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Laurie Hullinger
- Process Cell Sciences, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Zhimei Du
- Process Cell Sciences, Merck & Co., Inc., Kenilworth, New Jersey, USA
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32
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Tost AS, Kristensen A, Olsen LI, Axelsen KB, Fuglsang AT. The PSY Peptide Family-Expression, Modification and Physiological Implications. Genes (Basel) 2021; 12:genes12020218. [PMID: 33540946 PMCID: PMC7913133 DOI: 10.3390/genes12020218] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023] Open
Abstract
Small post-translationally modified peptides are gaining increasing attention as important signaling molecules in plant development. In the family of plant peptides containing tyrosine sulfation (PSYs), only PSY1 has been characterized at the mature level as an 18-amino-acid peptide, carrying one sulfated tyrosine, and involved in cell elongation. This review presents seven additional homologs in Arabidopsis all sharing high conservation in the active peptide domain, and it shows that PSY peptides are found in all higher plants and mosses. It is proposed that all eight PSY homologs are post-translationally modified to carry a sulfated tyrosine and that subtilisin-like subtilases (SBTs) are involved in the processing of PSY propeptides. The PSY peptides show differential expression patterns indicating that they serve several distinct functions in plant development. PSY peptides seem to be at least partly regulated at the transcriptional level, as their expression is greatly influenced by developmental factors. Finally, a model including a receptor in addition to PSY1R is proposed.
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Affiliation(s)
- Amalie Scheel Tost
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (A.S.T.); (A.K.); (L.I.O.); or (K.B.A.)
| | - Astrid Kristensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (A.S.T.); (A.K.); (L.I.O.); or (K.B.A.)
| | - Lene Irene Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (A.S.T.); (A.K.); (L.I.O.); or (K.B.A.)
| | - Kristian Buhl Axelsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (A.S.T.); (A.K.); (L.I.O.); or (K.B.A.)
- SIB Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, CH-1211 Geneve, Switzerland
| | - Anja Thoe Fuglsang
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark; (A.S.T.); (A.K.); (L.I.O.); or (K.B.A.)
- Correspondence: ; Tel.: +45-35-33-25-86
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33
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Nair J, Maheshwari A. Epigenetics in Necrotizing Enterocolitis. Curr Pediatr Rev 2021; 17:172-184. [PMID: 33882811 DOI: 10.2174/1573396317666210421110608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/14/2021] [Accepted: 02/26/2021] [Indexed: 11/22/2022]
Abstract
Epigenetic alterations in our genetic material can lead to heritable changes in the risk, clinical manifestations, course, and outcomes of many diseases. Understanding these epigenetic mechanisms can help in identifying potential therapeutic targets. This is especially important in necrotizing enterocolitis (NEC), where prenatal as well as postnatal factors impact susceptibility to this devastating condition, but our therapeutic options are limited. Developmental factors affecting intestinal structure and function, our immune system, gut microbiome, and postnatal enteral nutrition are all thought to play a prominent role in this disease. In this manuscript, we have reviewed the epigenetic mechanisms involved in NEC. These include key developmental changes in DNA methylation in the immature intestine, the role of long non-coding RNA (lncRNA) in maintaining intestinal barrier function, epigenetic influences of prenatal inflammation on immunological pathways in NEC pathogenesis such as Toll-Like Receptor 4 (TLR4) and epigenetic changes associated with enteral feeding causing upregulation of pro-inflammatory genes. We have assimilated research findings from our own laboratory with an extensive review of the literature utilizing key terms in multiple databases, including PubMed, EMBASE, and Science Direct.
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Affiliation(s)
- Jayasree Nair
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Akhil Maheshwari
- Department of Pediatrics, Johns Hopkins University, Baltimore, MA, United States
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34
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Structure of the human sodium leak channel NALCN. Nature 2020; 587:313-318. [DOI: 10.1038/s41586-020-2570-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/02/2020] [Indexed: 01/17/2023]
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35
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Tvaroška I, Selvaraj C, Koča J. Selectins-The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules-A Review. Molecules 2020; 25:molecules25122835. [PMID: 32575485 PMCID: PMC7355470 DOI: 10.3390/molecules25122835] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/27/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Selectins belong to a group of adhesion molecules that fulfill an essential role in immune and inflammatory responses and tissue healing. Selectins are glycoproteins that decode the information carried by glycan structures, and non-covalent interactions of selectins with these glycan structures mediate biological processes. The sialylated and fucosylated tetrasaccharide sLex is an essential glycan recognized by selectins. Several glycosyltransferases are responsible for the biosynthesis of the sLex tetrasaccharide. Selectins are involved in a sequence of interactions of circulated leukocytes with endothelial cells in the blood called the adhesion cascade. Recently, it has become evident that cancer cells utilize a similar adhesion cascade to promote metastases. However, like Dr. Jekyll and Mr. Hyde’s two faces, selectins also contribute to tissue destruction during some infections and inflammatory diseases. The most prominent function of selectins is associated with the initial stage of the leukocyte adhesion cascade, in which selectin binding enables tethering and rolling. The first adhesive event occurs through specific non-covalent interactions between selectins and their ligands, with glycans functioning as an interface between leukocytes or cancer cells and the endothelium. Targeting these interactions remains a principal strategy aimed at developing new therapies for the treatment of immune and inflammatory disorders and cancer. In this review, we will survey the significant contributions to and the current status of the understanding of the structure of selectins and the role of selectins in various biological processes. The potential of selectins and their ligands as therapeutic targets in chronic and acute inflammatory diseases and cancer will also be discussed. We will emphasize the structural characteristic of selectins and the catalytic mechanisms of glycosyltransferases involved in the biosynthesis of glycan recognition determinants. Furthermore, recent achievements in the synthesis of selectin inhibitors will be reviewed with a focus on the various strategies used for the development of glycosyltransferase inhibitors, including substrate analog inhibitors and transition state analog inhibitors, which are based on knowledge of the catalytic mechanism.
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Affiliation(s)
- Igor Tvaroška
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovak Republic
- Correspondence: (I.T.); (J.K.); Tel.: +421-948-535-601 (I.T.); +420-731-682-606 (J.K.)
| | - Chandrabose Selvaraj
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Jaroslav Koča
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Correspondence: (I.T.); (J.K.); Tel.: +421-948-535-601 (I.T.); +420-731-682-606 (J.K.)
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Mutated Human P-Selectin Glycoprotein Ligand-1 and Viral Protein-1 of Enterovirus 71 Interactions on Au Nanoplasmonic Substrate for Specific Recognition by Surface-Enhanced Raman Spectroscopy. COATINGS 2020. [DOI: 10.3390/coatings10040403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein tyrosine sulfation is a common post-translational modification that stimulates intercellular or extracellular protein-protein interactions and is responsible for various important biological processes, including coagulation, inflammation, and virus infections. Recently, human P-selectin glycoprotein ligand-1 (PSGL-1) has been shown to serve as a functional receptor for enterovirus 71 (EV71). It has been proposed that the capsid viral protein VP1 of EV71 is directly involved in this specific interaction with sulfated or mutated PSGL-1. Surface-enhanced Raman spectroscopy (SERS) is used to distinguish PSGL-1 and VP1 interactions on an Au nanoporous substrate and identify specific VP1 interaction positions of tyrosine residue sites (46, 48, and 51). The three tyrosine sites in PSGL-1 were replaced by phenylalanine (F), as determined using SERS. A strong phenylalanine SERS signal was obtained in three regions of the mutated protein on the nanoporous substrate. The mutated protein positions at (51F) and (48F, 51F) produced a strong SERS peak at 1599–1666 cm−1, which could be related to a binding with the mutated protein and anti-sulfotyrosine interactions on the nanoporous substrate. A strong SERS effect of the mutated protein and VP1 interactions appeared at (48F), (51F), and (46F, 48F). In these positions, there was less interaction with VP1, as indicated by a strong phenylalanine signal from the mutated protein.
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Abstract
Gastric acid secretion (i) facilitates digestion of protein as well as absorption of micronutrients and certain medications, (ii) kills ingested microorganisms, including Helicobacter pylori, and (iii) prevents bacterial overgrowth and enteric infection. The principal regulators of acid secretion are the gastric peptides gastrin and somatostatin. Gastrin, the major hormonal stimulant for acid secretion, is synthesized in pyloric mucosal G cells as a 101-amino acid precursor (preprogastrin) that is processed to yield biologically active amidated gastrin-17 and gastrin-34. The C-terminal active site of gastrin (Trp-Met-Asp-Phe-NH2 ) binds to gastrin/CCK2 receptors on parietal and, more importantly, histamine-containing enterochromaffin-like (ECL) cells, located in oxyntic mucosa, to induce acid secretion. Histamine diffuses to the neighboring parietal cells where it binds to histamine H2 -receptors coupled to hydrochloric acid secretion. Gastrin is also a trophic hormone that maintains the integrity of gastric mucosa, induces proliferation of parietal and ECL cells, and is thought to play a role in carcinogenesis. Somatostatin, present in D cells of the gastric pyloric and oxyntic mucosa, is the main inhibitor of acid secretion, particularly during the interdigestive period. Somatostatin exerts a tonic paracrine restraint on gastrin secretion from G cells, histamine secretion from ECL cells, and acid secretion from parietal cells. Removal of this restraint, for example by activation of cholinergic neurons during ingestion of food, initiates and maximizes acid secretion. Knowledge regarding the structure and function of gastrin, somatostatin, and their respective receptors is providing novel avenues to better diagnose and manage acid-peptic disorders and certain cancers. Published 2020. Compr Physiol 10:197-228, 2020.
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Affiliation(s)
- Mitchell L Schubert
- Division of Gastroenterology, Department of Medicine, Virginia Commonwealth University Health System, Richmond, Virginia, USA.,Hunter Holmes McGuire Veterans Affairs Medical Center, Richmond, Virginia, USA
| | - Jens F Rehfeld
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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38
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Kaufmann C, Sauter M. Sulfated plant peptide hormones. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4267-4277. [PMID: 31231771 PMCID: PMC6698702 DOI: 10.1093/jxb/erz292] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/11/2019] [Indexed: 05/08/2023]
Abstract
Sulfated peptides are plant hormones that are active at nanomolar concentrations. The sulfation at one or more tyrosine residues is catalysed by tyrosylprotein sulfotransferase (TPST), which is encoded by a single-copy gene. The sulfate group is provided by the co-substrate 3´-phosphoadenosine 5´-phosphosulfate (PAPS), which links synthesis of sulfated signaling peptides to sulfur metabolism. The precursor proteins share a conserved DY-motif that is implicated in specifying tyrosine sulfation. Several sulfated peptides undergo additional modification such as hydroxylation of proline and glycosylation of hydroxyproline. The modifications render the secreted signaling molecules active and stable. Several sulfated signaling peptides have been shown to be perceived by leucine-rich repeat receptor-like kinases (LRR-RLKs) but have signaling pathways that, for the most part, are yet to be elucidated. Sulfated peptide hormones regulate growth and a wide variety of developmental processes, and intricately modulate immunity to pathogens. While basic research on sulfated peptides has made steady progress, their potential in agricultural and pharmaceutical applications has yet to be explored.
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Affiliation(s)
- Christine Kaufmann
- Plant Developmental Biology and Physiology, University of Kiel, Am Botanischen Garten, Kiel, Germany
- Correspondence:
| | - Margret Sauter
- Plant Developmental Biology and Physiology, University of Kiel, Am Botanischen Garten, Kiel, Germany
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39
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Amann T, Schmieder V, Faustrup Kildegaard H, Borth N, Andersen MR. Genetic engineering approaches to improve posttranslational modification of biopharmaceuticals in different production platforms. Biotechnol Bioeng 2019; 116:2778-2796. [PMID: 31237682 DOI: 10.1002/bit.27101] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/27/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022]
Abstract
The number of approved biopharmaceuticals, where product quality attributes remain of major importance, is increasing steadily. Within the available variety of expression hosts, the production of biopharmaceuticals faces diverse limitations with respect to posttranslational modifications (PTM), while different biopharmaceuticals demand different forms and specifications of PTMs for proper functionality. With the growing toolbox of genetic engineering technologies, it is now possible to address general as well as host- or biopharmaceutical-specific product quality obstacles. In this review, we present diverse expression systems derived from mammalians, bacteria, yeast, plants, and insects as well as available genetic engineering tools. We focus on genes for knockout/knockdown and overexpression for meaningful approaches to improve biopharmaceutical PTMs and discuss their applicability as well as future trends in the field.
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Affiliation(s)
- Thomas Amann
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valerie Schmieder
- acib GmbH-Austrian Centre of Industrial Biotechnology, Graz, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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40
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Barukab O, Khan YD, Khan SA, Chou KC. iSulfoTyr-PseAAC: Identify Tyrosine Sulfation Sites by Incorporating Statistical Moments via Chou's 5-steps Rule and Pseudo Components. Curr Genomics 2019; 20:306-320. [PMID: 32030089 PMCID: PMC6983959 DOI: 10.2174/1389202920666190819091609] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/04/2019] [Accepted: 08/06/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The amino acid residues, in protein, undergo post-translation modification (PTM) during protein synthesis, a process of chemical and physical change in an amino acid that in turn alters behavioral properties of proteins. Tyrosine sulfation is a ubiquitous posttranslational modification which is known to be associated with regulation of various biological functions and pathological pro-cesses. Thus its identification is necessary to understand its mechanism. Experimental determination through site-directed mutagenesis and high throughput mass spectrometry is a costly and time taking process, thus, the reliable computational model is required for identification of sulfotyrosine sites. METHODOLOGY In this paper, we present a computational model for the prediction of the sulfotyrosine sites named iSulfoTyr-PseAAC in which feature vectors are constructed using statistical moments of protein amino acid sequences and various position/composition relative features. These features are in-corporated into PseAAC. The model is validated by jackknife, cross-validation, self-consistency and in-dependent testing. RESULTS Accuracy determined through validation was 93.93% for jackknife test, 95.16% for cross-validation, 94.3% for self-consistency and 94.3% for independent testing. CONCLUSION The proposed model has better performance as compared to the existing predictors, how-ever, the accuracy can be improved further, in future, due to increasing number of sulfotyrosine sites in proteins.
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Affiliation(s)
| | | | - Sher Afzal Khan
- Address correspondence to this author at the Department of Information Technology, Faculty of Computing and Information Technology in Rabigh, King Abdulaziz University, P.O. Box 344, Rabigh, 21911, Saudi Arabia; and Department of Computer Sciences, Abdul Wali Khan University, Mardan, Pakistan; E-mail:
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41
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Semenyuk P, Muronetz V. Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications. Int J Mol Sci 2019; 20:E1252. [PMID: 30871103 PMCID: PMC6429204 DOI: 10.3390/ijms20051252] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/18/2022] Open
Abstract
Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for "generic" proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.
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Affiliation(s)
- Pavel Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Vladimir Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia.
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43
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Kershaw NM, Byrne DP, Parsons H, Berry NG, Fernig DG, Eyers PA, Cosstick R. Structure-based design of nucleoside-derived analogues as sulfotransferase inhibitors. RSC Adv 2019; 9:32165-32173. [PMID: 35530783 PMCID: PMC9072872 DOI: 10.1039/c9ra07567d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 10/03/2019] [Indexed: 12/12/2022] Open
Abstract
Regulated sulfation of biomolecules by sulfotransferases (STs) plays a role in many biological processes with implications for a number of disease areas. A structure-based approach and molecular docking were used to design a library of ST inhibitors.
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Affiliation(s)
- Neil M. Kershaw
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - Dominic P. Byrne
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
- UK
| | - Hollie Parsons
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - Neil G. Berry
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - David G. Fernig
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
- UK
| | - Patrick A. Eyers
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
- UK
| | - Richard Cosstick
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
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44
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New tools for evaluating protein tyrosine sulfation and carbohydrate sulfation. Biochem J 2018; 475:3035-3037. [PMID: 30291171 PMCID: PMC6173261 DOI: 10.1042/bcj20180480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/11/2018] [Accepted: 09/11/2018] [Indexed: 12/31/2022]
Abstract
Sulfation is a common modification of extracelluar glycans and tyrosine residues on proteins, which is important in many signalling pathways and interactions. Existing methods for studying sulfotransferases, the enzymes that catalyse sulfation, are cumbersome and low-throughput. Recent studies published in the Biochemical Journal have repurposed established biochemical assays from the kinase field and applied them to the characterisation of sulfotransferases. Biochemical screening of a library of kinase inhibitors revealed that compounds that target RAF kinases may also be repurposed to inhibit sulfotransferases. Together with the available structures of sulfotransferases, these studies open the door to the development of chemical tools to probe the biological functions of these important enzymes.
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45
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Christie AE, Stanhope ME, Gandler HI, Lameyer TJ, Pascual MG, Shea DN, Yu A, Dickinson PS, Hull JJ. Molecular characterization of putative neuropeptide, amine, diffusible gas and small molecule transmitter biosynthetic enzymes in the eyestalk ganglia of the American lobster, Homarus americanus. INVERTEBRATE NEUROSCIENCE 2018; 18:12. [PMID: 30276482 DOI: 10.1007/s10158-018-0216-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/21/2018] [Indexed: 02/03/2023]
Abstract
The American lobster, Homarus americanus, is a model for investigating the neuromodulatory control of physiology and behavior. Prior studies have shown that multiple classes of chemicals serve as locally released/circulating neuromodulators/neurotransmitters in this species. Interestingly, while many neuroactive compounds are known from Homarus, little work has focused on identifying/characterizing the enzymes responsible for their biosynthesis, despite the fact that these enzymes are key components for regulating neuromodulation/neurotransmission. Here, an eyestalk ganglia-specific transcriptome was mined for transcripts encoding enzymes involved in neuropeptide, amine, diffusible gas and small molecule transmitter biosynthesis. Using known Drosophila melanogaster proteins as templates, transcripts encoding putative Homarus homologs of peptide precursor processing (signal peptide peptidase, prohormone processing protease and carboxypeptidase) and immature peptide modifying (glutaminyl cyclase, tyrosylprotein sulfotransferase, protein disulfide isomerase, peptidylglycine-α-hydroxylating monooxygenase and peptidyl-α-hydroxyglycine-α-amidating lyase) enzymes were identified in the eyestalk assembly. Similarly, transcripts encoding full complements of the enzymes responsible for dopamine [tryptophan-phenylalanine hydroxylase (TPH), tyrosine hydroxylase and DOPA decarboxylase (DDC)], octopamine (TPH, tyrosine decarboxylase and tyramine β-hydroxylase), serotonin (TPH or tryptophan hydroxylase and DDC) and histamine (histidine decarboxylase) biosynthesis were identified from the eyestalk ganglia, as were those responsible for the generation of the gases nitric oxide (nitric oxide synthase) and carbon monoxide (heme oxygenase), and the small molecule transmitters acetylcholine (choline acetyltransferase), glutamate (glutaminase) and GABA (glutamic acid decarboxylase). The presence and identity of the transcriptome-derived transcripts were confirmed using RT-PCR. The data presented here provide a foundation for future gene-based studies of neuromodulatory control at the level of neurotransmitter/modulator biosynthesis in Homarus.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI, 96822, USA.
| | - Meredith E Stanhope
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA
| | - Helen I Gandler
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA
| | - Tess J Lameyer
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA
| | - Micah G Pascual
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI, 96822, USA
| | - Devlin N Shea
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA
| | - Andy Yu
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI, 96822, USA
| | - Patsy S Dickinson
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME, 04011, USA
| | - J Joe Hull
- Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ, 85138, USA
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Wang CC, Chen BH, Lu LY, Hung KS, Yang YS. Preparation of Tyrosylprotein Sulfotransferases for In Vitro One-Pot Enzymatic Synthesis of Sulfated Proteins/Peptides. ACS OMEGA 2018; 3:11633-11642. [PMID: 30320268 PMCID: PMC6173500 DOI: 10.1021/acsomega.7b01533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/13/2018] [Indexed: 06/08/2023]
Abstract
Protein tyrosine sulfation (PTS), catalyzed by membrane-anchored tyrosylprotein sulfotransferase (TPST), is one of the most common post-translational modifications of secretory and transmembrane proteins. PTS, a key modulator of extracellular protein-protein interactions, accounts for various important biological activities, namely, virus entry, inflammation, coagulation, and sterility. The preparation and characterization of TPST is fundamental for understanding the synthesis of tyrosine-sulfated proteins and for studying PTS in biology. A sulfated protein was prepared using a TPST-coupled protein sulfation system that involves the generation of the active sulfate 3'-phosphoadenosine-5'-phosphosulfate (PAPS) through either PAPS synthetase (PAPSS) or phenol sulfotransferase. The preparation of sulfated proteins was confirmed through radiometric or immunochemical assays. In this study, enzymatically active Drosophila melanogaster TPST (DmTPST) and human TPSTs (hTPST1 and hTPST2) were expressed in Escherichia coli BL21(DE3) host cells and purified to homogeneity in high yield. Our results revealed that recombinant DmTPST was particularly useful considering its catalytic efficiency and ease of preparation in large quantities. This study provides tools for high-efficiency, one-step synthesis of sulfated proteins and peptides that are useful for further deciphering the mechanisms, functions, and future applications of PTS.
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Affiliation(s)
- Chen-Chu Wang
- Department
of Biological Science and Technology, National
Chiao Tung University, No. 75, Po-Ai Street, Hsinchu 30050, Taiwan
| | - Bo-Han Chen
- Department
of Biological Science and Technology, National
Chiao Tung University, No. 75, Po-Ai Street, Hsinchu 30050, Taiwan
| | - Lu-Yi Lu
- Department
of Biological Science and Technology, National
Chiao Tung University, No. 75, Po-Ai Street, Hsinchu 30050, Taiwan
| | - Kuo-Sheng Hung
- Department
of Neurosurgery, Center of Excellence for Clinical Trial and Research, Taipei Medical University-Wan Fang Medical Center, No.111, Section 3, Hsing-Long Road, Taipei 11696, Taiwan
| | - Yuh-Shyong Yang
- Department
of Biological Science and Technology, National
Chiao Tung University, No. 75, Po-Ai Street, Hsinchu 30050, Taiwan
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47
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New tools for evaluating protein tyrosine sulfation: tyrosylprotein sulfotransferases (TPSTs) are novel targets for RAF protein kinase inhibitors. Biochem J 2018; 475:2435-2455. [PMID: 29934490 PMCID: PMC6094398 DOI: 10.1042/bcj20180266] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/14/2018] [Accepted: 06/21/2018] [Indexed: 12/11/2022]
Abstract
Protein tyrosine sulfation is a post-translational modification best known for regulating extracellular protein–protein interactions. Tyrosine sulfation is catalysed by two Golgi-resident enzymes termed tyrosylprotein sulfotransferases (TPSTs) 1 and 2, which transfer sulfate from the cofactor PAPS (3′-phosphoadenosine 5′-phosphosulfate) to a context-dependent tyrosine in a protein substrate. A lack of quantitative tyrosine sulfation assays has hampered the development of chemical biology approaches for the identification of small-molecule inhibitors of tyrosine sulfation. In the present paper, we describe the development of a non-radioactive mobility-based enzymatic assay for TPST1 and TPST2, through which the tyrosine sulfation of synthetic fluorescent peptides can be rapidly quantified. We exploit ligand binding and inhibitor screens to uncover a susceptibility of TPST1 and TPST2 to different classes of small molecules, including the anti-angiogenic compound suramin and the kinase inhibitor rottlerin. By screening the Published Kinase Inhibitor Set, we identified oxindole-based inhibitors of the Ser/Thr kinase RAF (rapidly accelerated fibrosarcoma) as low-micromolar inhibitors of TPST1 and TPST2. Interestingly, unrelated RAF inhibitors, exemplified by the dual BRAF/VEGFR2 inhibitor RAF265, were also TPST inhibitors in vitro. We propose that target-validated protein kinase inhibitors could be repurposed, or redesigned, as more-specific TPST inhibitors to help evaluate the sulfotyrosyl proteome. Finally, we speculate that mechanistic inhibition of cellular tyrosine sulfation might be relevant to some of the phenotypes observed in cells exposed to anionic TPST ligands and RAF protein kinase inhibitors.
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Schiza C, Korbakis D, Panteleli E, Jarvi K, Drabovich AP, Diamandis EP. Discovery of a Human Testis-specific Protein Complex TEX101-DPEP3 and Selection of Its Disrupting Antibodies. Mol Cell Proteomics 2018; 17:2480-2495. [PMID: 30097533 DOI: 10.1074/mcp.ra118.000749] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/11/2018] [Indexed: 01/01/2023] Open
Abstract
TEX101 is a testis-specific protein expressed exclusively in male germ cells and is a validated biomarker of male infertility. Studies in mice suggest that TEX101 is a cell-surface chaperone which regulates, through protein-protein interactions, the maturation of proteins involved in spermatozoa transit and oocyte binding. Male TEX101-null mice are sterile. Here, we identified by co-immunoprecipitation-mass spectrometry the interactome of human TEX101 in testicular tissues and spermatozoa. The testis-specific cell-surface dipeptidase 3 (DPEP3) emerged as the top hit. We further validated the TEX101-DPEP3 complex by using hybrid immunoassays. Combinations of antibodies recognizing different epitopes of TEX101 and DPEP3 facilitated development of a simple immunoassay to screen for disruptors of TEX101-DPEP3 complex. As a proof-of-a-concept, we demonstrated that anti-TEX101 antibody T4 disrupted the native TEX101-DPEP3 complex. Disrupting antibodies may be used to study the human TEX101-DPEP3 complex, and to develop modulators for male fertility.
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Affiliation(s)
- Christina Schiza
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Dimitrios Korbakis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Efstratia Panteleli
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Keith Jarvi
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Department of Surgery, Division of Urology, Mount Sinai Hospital, Toronto, Canada
| | - Andrei P Drabovich
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada.
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49
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Chen G, Zhang Y, Trinidad JC, Dann C. Distinguishing Sulfotyrosine Containing Peptides from their Phosphotyrosine Counterparts Using Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:455-462. [PMID: 29313205 DOI: 10.1007/s13361-017-1854-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 11/15/2017] [Accepted: 11/18/2017] [Indexed: 06/07/2023]
Abstract
Sulfotyrosine and phosphotyrosine are two post-translational modifications present in higher eukaryotes. A simple and direct mass spectrometry method to distinguish between these modifications is crucial to advance our understanding of the sulfoproteome. While sulfation and phosphorylation are nominally isobaric, the accurate mass of the sulfuryl moiety is 9.6 mDa less than the phosphoryl moiety. Based on this difference, we have used an Orbitrap Fusion Lumos mass spectrometer to characterize, resolve, and distinguish between sulfotyrosine and phosphotyrosine modifications using a set of model peptides. Multiple fragmentation techniques, namely HCD, CID, ETD, ETciD, and EThcD, have been used to compare the different fragmentation behaviors between peptides modified with these species. Sulfotyrosine undergoes neutral loss using HCD and CID, but the sulfuryl moiety is largely stable under ETD. In contrast, phosphotyrosine is stable during fragmentation using all these methods. This differential stability provides a mechanism to distinguish sulfopeptides from phosphopeptides. Based on the rigorous characterization presented herein, this work serves as a model for accurate identification of phosphotyrosine and, more challenging, sulfotyrosine, in complex proteomic samples. Graphical Abstract ᅟ.
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Affiliation(s)
- Guangming Chen
- Department of Chemistry and Interdisciplinary Graduate Program in Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Yixiang Zhang
- Department of Chemistry and Laboratory for Biological Mass Spectrometry, Indiana University, Bloomington, IN, 47405, USA
| | - Jonathan C Trinidad
- Department of Chemistry and Laboratory for Biological Mass Spectrometry, Indiana University, Bloomington, IN, 47405, USA.
| | - Charles Dann
- Department of Chemistry and Interdisciplinary Graduate Program in Biochemistry, Indiana University, Bloomington, IN, 47405, USA.
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Wang CC, Sivashanmugan K, Chen CK, Hong JR, Sung WI, Liao JD, Yang YS. Specific Unbinding Forces Between Mutated Human P-Selectin Glycoprotein Ligand-1 and Viral Protein-1 Measured Using Force Spectroscopy. J Phys Chem Lett 2017; 8:5290-5295. [PMID: 29016136 DOI: 10.1021/acs.jpclett.7b02373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Protein tyrosine sulfation (PTS) is a key modulator of extracellular protein-protein interaction (PPI), which regulates principal biological processes. For example, the capsid protein VP1 of enterovirus 71 (EV71) specifically interacts with sulfated P-selectin glycoprotein ligand-1 (PSGL-1) to facilitate virus invasion. Currently available methods cannot be used to directly observe PTS-induced PPI. In this study, atomic force microscopy was used to measure the interaction between sulfated or mutated PSGL-1 and VP1. We found that the binding strength increased by 6.7-fold following PTS treatment on PSGL-1 with a specific antisulfotyrosine antibody. Similar results were obtained when the antisulfotyrosine antibody was replaced with the VP1 protein of EV71; however, the interaction forces of VP1 were only approximately one-third of those of the antisulfotyrosine antibody. We also found that PTS on the tyrosine-51 residue of glutathione S-transferases fusion-PSGL-1 was mainly responsible for the PTS-induced PPI. Our results contribute to the fundamental understanding of PPI regulated through PTS.
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Affiliation(s)
- Chen-Chu Wang
- Department of Biological Science and Technology, National Chiao Tung University , Hsinchu, Taiwan 300
| | - Kundan Sivashanmugan
- Department of Materials Science and Engineering, National Cheng Kung University , Tainan, Taiwan 701
| | - Chung-Ku Chen
- Department of Materials Science and Engineering, National Cheng Kung University , Tainan, Taiwan 701
| | - Jian-Ren Hong
- Department of Biological Science and Technology, National Chiao Tung University , Hsinchu, Taiwan 300
| | - Wei-I Sung
- Department of Materials Science and Engineering, National Cheng Kung University , Tainan, Taiwan 701
| | - Jiunn-Der Liao
- Department of Materials Science and Engineering, National Cheng Kung University , Tainan, Taiwan 701
| | - Yuh-Shyong Yang
- Department of Biological Science and Technology, National Chiao Tung University , Hsinchu, Taiwan 300
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