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LI Y, ZHOU D, CHEN X, ZHAO J, GAO C, QIU X, TANG Z, DENG N, ZHAO W, BIAN Y. [Determination of the derivatization reactivity between α/β-dicarbonyl compounds and standard citrullinated peptides based on matrix-assisted laser desorption ionization-time-of-flight mass spectrometry]. Se Pu 2024; 42:711-720. [PMID: 38966979 PMCID: PMC11224938 DOI: 10.3724/sp.j.1123.2024.02002] [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: 02/03/2024] [Indexed: 07/06/2024] Open
Abstract
Protein citrullination is an irreversible post-translational modification process regulated by peptidylarginine deiminases (PADs) in the presence of Ca2+. This process is closely related to the occurrence and development of autoimmune diseases, cancers, neurological disorders, cardiovascular and cerebrovascular diseases, and other major diseases. The analysis of protein citrullination by biomass spectrometry confronts great challenges owing to its low abundance, lack of affinity tags, small mass-to-charge ratio change, and susceptibility to isotopic and deamidation interferences. The methods commonly used to study the protein citrullination mainly involve the chemical derivatization of the urea group of the guanine side chain of the peptide to increase the mass-to-charge ratio difference of the citrullinated peptide. Affinity-enriched labels are then introduced to effectively improve the sensitivity and accuracy of protein citrullination by mass spectrometry. 2,3-Butanedione or phenylglyoxal compounds are often used as derivatization reagents to increase the mass-to-charge ratio difference of the citrullinated peptide, and the resulting derivatives have been observed to contain α-dicarbonyl structures. To date, however, no relevant studies on the reactivity of dicarbonyl compounds with citrullinated peptides have been reported. In this study, we determined whether six α-dicarbonyl and two β-dicarbonyl compounds undergo derivatization reactions with standard citrullinated peptides using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Among the α-dicarbonyl compounds, 2,3-butanedione and glyoxal reacted efficiently with several standard citrullinated peptides, but yielded a series of by-products. Phenylglyoxal, methylglyoxal, 1,2-cyclohexanedione, and 1,10-phenanthroline-5,6-dione also derivated efficiently with standard citrullinated peptides, generating a single derivative. Thus, a new derivatization method that could yield a single derivative was identified. Among the β-dicarbonyl compounds, 1,3-cyclohexanedione and 2,4-pentanedione successfully reacted with the standard citrullinated peptides, and generated a single derivative. However, their reaction efficiency was very low, indicating that the β-dicarbonyl compounds are unsuitable for the chemical derivatization of citrullinated peptides. The above results indicate that the α-dicarbonyl structure is necessary for realizing the efficient and specific chemical derivatization of citrullinated peptides. Moreover, the side chains of the α-dicarbonyl structure determine the structure of the derivatives, derivatization efficiency, and generation (or otherwise) of by-products. Therefore, the specific enrichment and precise identification of citrullinated peptides can be achieved by synthesizing α-dicarbonyl structured compounds containing affinity tags. The proposed method enables the identification of citrullinated proteins and their modified sites by MS, thereby providing a better understanding of the distribution of citrullinated proteins in different tissues. The findings will be beneficial for studies on the mechanism of action of citrullinated proteins in a variety of diseases.
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Guo P, Chu X, Wu C, Qiao T, Guan W, Zhou C, Wang T, Tian C, He G, Chen G. Peptide Stapling by Crosslinking Two Amines with α-Ketoaldehydes through Diverse Modified Glyoxal-Lysine Dimer Linkers. Angew Chem Int Ed Engl 2024; 63:e202318893. [PMID: 38376389 DOI: 10.1002/anie.202318893] [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: 12/08/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
α-Ketoaldehydes play versatile roles in the ubiquitous natural processes of protein glycation. However, leveraging the reactivity of α-ketoaldehydes for biomedical applications has been challenging. Previously, the reactivity of α-ketoaldehydes with guanidine has been harnessed to design probes for labeling Arg residues on proteins in an aqueous medium. Herein, a highly effective, broadly applicable, and operationally simple protocol for stapling native peptides by crosslinking two amino groups through diverse imidazolium linkers with various α-ketoaldehyde reagents is described. The use of hexafluoroisopropanol as a solvent facilitates rapid and clean reactions under mild conditions and enables unique selectivity for Lys over Arg. The naturally occurring GOLD/MOLD linkers have been expanded to encompass a wide range of modified glyoxal-lysine dimer (OLD) linkers. In a proof-of-concept trial, these modular stapling reactions enabled a convenient two-round strategy to streamline the structure-activity relationship (SAR) study of the wasp venom peptide anoplin, leading to enhanced biological activities.
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Affiliation(s)
- Pan Guo
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chengjin Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Tianjiao Qiao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Wenli Guan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Tao Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Changlin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
- Frontiers Science Center for New Organic Matter, Nankai University, Tianjin, 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
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3
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Pitter MR, Kryczek I, Zhang H, Nagarsheth N, Xia H, Wu Z, Tian Y, Okla K, Liao P, Wang W, Zhou J, Li G, Lin H, Vatan L, Grove S, Wei S, Li Y, Zou W. PAD4 controls tumor immunity via restraining the MHC class II machinery in macrophages. Cell Rep 2024; 43:113942. [PMID: 38489266 PMCID: PMC11022165 DOI: 10.1016/j.celrep.2024.113942] [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: 09/08/2023] [Revised: 01/18/2024] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
Tumor-associated macrophages (TAMs) shape tumor immunity and therapeutic efficacy. However, it is poorly understood whether and how post-translational modifications (PTMs) intrinsically affect the phenotype and function of TAMs. Here, we reveal that peptidylarginine deiminase 4 (PAD4) exhibits the highest expression among common PTM enzymes in TAMs and negatively correlates with the clinical response to immune checkpoint blockade. Genetic and pharmacological inhibition of PAD4 in macrophages prevents tumor progression in tumor-bearing mouse models, accompanied by an increase in macrophage major histocompatibility complex (MHC) class II expression and T cell effector function. Mechanistically, PAD4 citrullinates STAT1 at arginine 121, thereby promoting the interaction between STAT1 and protein inhibitor of activated STAT1 (PIAS1), and the loss of PAD4 abolishes this interaction, ablating the inhibitory role of PIAS1 in the expression of MHC class II machinery in macrophages and enhancing T cell activation. Thus, the PAD4-STAT1-PIAS1 axis is an immune restriction mechanism in macrophages and may serve as a cancer immunotherapy target.
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Affiliation(s)
- Michael R Pitter
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Graduate Program in Molecular and Cellular Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Hongjuan Zhang
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Nisha Nagarsheth
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Houjun Xia
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Zhenyu Wu
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yuzi Tian
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Karolina Okla
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Peng Liao
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Weichao Wang
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Jiajia Zhou
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Gaopeng Li
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Heng Lin
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Linda Vatan
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Sara Grove
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Shuang Wei
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Yongqing Li
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Weiping Zou
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Center of Excellence for Cancer Immunology and Immunotherapy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Graduate Programs in Immunology and Cancer Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
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Albano C, Biolatti M, Mazibrada J, Pasquero S, Gugliesi F, Lo Cigno I, Calati F, Bajetto G, Riva G, Griffante G, Landolfo S, Gariglio M, De Andrea M, Dell’Oste V. PAD-mediated citrullination is a novel candidate diagnostic marker and druggable target for HPV-associated cervical cancer. Front Cell Infect Microbiol 2024; 14:1359367. [PMID: 38529474 PMCID: PMC10961408 DOI: 10.3389/fcimb.2024.1359367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
Citrullination is an emerging post-translational modification catalyzed by peptidyl-arginine deiminases (PADs) that convert peptidyl-arginine into peptidyl-citrulline. In humans, the PAD family consists of five isozymes (PADs 1-4, 6) involved in multiple diseases, including cancer. Given that high-risk (hr) human papillomaviruses (HPVs) are the etiological agents of cervical cancer, in this study, we sought to determine whether PAD-mediated protein citrullination would play a functional role in the HPV-driven transformation of epithelial cells. Here we show that both total protein citrullination and PAD4 expression levels are significantly associated with cervical cancer progression. Specifically, epithelial immunostaining for PAD4 revealed an increasingly higher histoscore from low-grade (CIN1) to high-grade (CIN2, CIN3) cervical intraepithelial neoplasia, and invasive squamous cell carcinoma (SCC) lesions, raising the attractive possibility that PAD4 may be used as tumor staging markers. Furthermore, taking advantage of the epidermoid cervical cancer cell line CaSki, which harbors multiple copies of the integrated HPV16 genome, we show that the expression of E6 and E7 HPV oncoproteins is impaired by treatment with the pharmacological pan-PAD inhibitor BB-Cl-amidine. Consistently, p53 and p21, two targets of HPV oncoproteins, are upregulated by the PAD inhibitor, which undergoes cell growth arrest and apoptosis. Altogether, these findings highlight a novel mechanism by which hrHPVs alter host regulatory pathways involved in cell cycle and survival to gain viral fitness, raising the possibility that PADs may represent an attractive target for developing novel host-targeting antivirals effective in preventing cervical cancer progression.
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Affiliation(s)
- Camilla Albano
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Jasenka Mazibrada
- Department of Cellular Pathology, The Cotman Centre Norfolk and Norwich University Hospital, Norwich, United Kingdom
| | - Selina Pasquero
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Francesca Gugliesi
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Irene Lo Cigno
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Federica Calati
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Greta Bajetto
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease-CAAD, Novara, Italy
| | - Giuseppe Riva
- Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Gloria Griffante
- IIGM Foundation – Italian Institute for Genomic Medicine, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Marisa Gariglio
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Marco De Andrea
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
- Center for Translational Research on Autoimmune and Allergic Disease-CAAD, Novara, Italy
| | - Valentina Dell’Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
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5
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Wang B, Li Z, Shi Y, Zhu Z, Fields L, Shelef MA, Li L. Mass Spectrometry-Based Precise Identification of Citrullinated Histones via Limited Digestion and Biotin Derivative Tag Enrichment. Anal Chem 2024; 96:2309-2317. [PMID: 38285917 DOI: 10.1021/acs.analchem.3c02646] [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: 01/31/2024]
Abstract
Histone citrullination is an essential epigenetic post-translational modification (PTM) that affects many important physiological and pathological processes, but effective tools to study histone citrullination are greatly limited due to several challenges, including the small mass shift caused by this PTM and its low abundance in biological systems. Although previous studies have reported frequent occurrences of histone citrullination, these methods failed to provide a high-throughput and site-specific strategy to detect histone citrullination. Recently, we developed a biotin thiol tag that enabled precise identification of protein citrullination coupled with mass spectrometry. However, very few histone citrullination sites were identified, likely due to the highly basic nature of these proteins. In this study, we develop a novel method utilizing limited digestion and biotin derivative tag enrichment to facilitate direct in vivo identification of citrullination sites on histones. We achieve improved coverage of histone identification via partial enzymatic digestion and lysine block by dimethylation. With biotin tag-assisted chemical derivatization and enrichment, we also achieve precise annotation of histone citrullination sites with high confidence. We further compare different fragmentation methods and find that the electron-transfer-dissociation-based approach enables the most in-depth analysis and characterization. In total, we unambiguously identify 18 unique citrullination sites on histones in human astrocytoma U87 cells, including 15 citrullinated sites being detected for the first time. Some of these citrullination sites are observed to exhibit noticeable alterations in response to DNA damage, which demonstrates the superiority of our strategy in understanding the roles of histone citrullination in critical biological processes.
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Affiliation(s)
- Bin Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Zihui Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yatao Shi
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Zexin Zhu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Miriam A Shelef
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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6
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Ahmed FF, Podder A, Bulbul MF, Hossain MA, Hasan M, Sarkar MAR, Kim D. Investigating the Precise Identification of Citrullination Sites with High- Performance Score Metrics Using a Powerful Computation Predicting Tool. Comb Chem High Throughput Screen 2024; 27:1381-1393. [PMID: 37702240 DOI: 10.2174/1386207326666230912151932] [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: 05/01/2023] [Revised: 06/18/2023] [Accepted: 08/02/2023] [Indexed: 09/14/2023]
Abstract
BACKGROUND To elucidate the detailed mechanisms of citrullination at the molecular level and design drugs applicable to major human diseases, predicting protein citrullination sites (PCSs) is essential. Using experimental approaches to predict PCSs is time-consuming and costly. However, there is a limited scope of the current PCS predictors. In particular, most predictors are commonly used for PCS prediction and have limited performance scores. OBJECTIVE This work aims to provide an improved sophisticated predictor of citrullination sites using a benchmark dataset in a machine learning platform. METHODS This study presents a reliable citrullination site predictor based on a benchmark dataset containing a 1:1 ratio of positive and negative samples. We classified citrullination sites using the Composition of the K-Spaced Amino Acid Pairs (CKSAAP) and Support Vector Machine (SVM). RESULTS We developed PCS predictors using integrated machine-learning methods that produced the highest average scores. Using 10-fold cross-validation on test datasets, the True Positive Rate (TPR) was 98.34%, the True Negative Rate (TNR) was 99.44%, the accuracy was 98.89%, the Mathew Correlation Coefficient (MCC) was 98.21%, the Area Under the ROC Curve (AUC) was 0.999, and the partial Area Under the ROC Curve (pAUC) was 0.1968. CONCLUSION According to overall performance, our developed predictor has a significantly higher implementation in comparison with the current tools on the same benchmark dataset. Moreover, it showed better performance metrics on both test and training datasets. Our developed predictor is promising and can be implemented as a complementary technique for identifying fast and precise citrullination sites.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Anamika Podder
- Department of Mathematics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Farhad Bulbul
- Department of Mathematics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Department of Computer Science & Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam, Pohang 37673, Korea
| | - Md Amzad Hossain
- Department of Electrical and Electronic Engineering, Jashore University of Science and Technology, Jashore -7408, Bangladesh
| | - Mahedi Hasan
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Daijin Kim
- Department of Computer Science & Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam, Pohang 37673, Korea
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7
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Yang C, Hu Z, Wang L, Fang L, Wang X, Li Q, Xu L, Wang J, Liu C, Lin N. Porphyromonas gingivalis with collagen immunization induces ACPA-positive rheumatoid arthritis in C3H mice. Clin Immunol 2024; 258:109859. [PMID: 38065368 DOI: 10.1016/j.clim.2023.109859] [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: 08/21/2023] [Revised: 11/06/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023]
Abstract
The pathogenic anti-citrullinated protein antibodies (ACPA) are thought to play a vital role in the initiation and immune maintenance of rheumatoid arthritis (RA). However, it is noteworthy that ACPA is not a salient characteristic of any conventional RA animal model. Porphyromonas gingivalis (Pg) is the first microorganism identified to induce citrullination and a target of autoantibodies in early rheumatoid arthritis (RA). Thus, we employed C3H mice with specific MHC types and combined Pg infection with collagen immunity to develop an animal model of ACPA-positive RA. The resulting model exhibited citrullination characteristics, as well as pathological and immune cell changes. 1) Mice showed a significant increase in ACPA levels, and various organs and tissues exhibited elevated levels of citrullinated protein. 2) The mice experienced heightened pain, inflammation, and bone destruction. 3) The spleen and lymph nodes of the mice showed a significant increase in the proportion of Tfh-GCB cell subpopulations responsible for regulating autoantibody production. In conclusion, the C3H mouse model of Pg infection with collagen immunity demonstrated significant alterations in ACPA levels, citrullinated protein expression, and immune cell subpopulations, which could be a crucial factor leading to increased pain, inflammation, and bone destruction.
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Affiliation(s)
- Chao Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhixing Hu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lili Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luochangting Fang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoxiao Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qun Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Liting Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jialin Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chunfang Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Na Lin
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
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8
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Pasquero S, Gugliesi F, Biolatti M, Dell’Oste V, Albano C, Bajetto G, Griffante G, Trifirò L, Brugo B, Raviola S, Lacarbonara D, Yang Q, Sudeshna S, Barasa L, Haniff H, Thompson PR, Landolfo S, De Andrea M. Citrullination profile analysis reveals peptidylarginine deaminase 3 as an HSV-1 target to dampen the activity of candidate antiviral restriction factors. PLoS Pathog 2023; 19:e1011849. [PMID: 38055760 PMCID: PMC10727434 DOI: 10.1371/journal.ppat.1011849] [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: 07/14/2023] [Revised: 12/18/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) is a neurotropic virus that remains latent in neuronal cell bodies but reactivates throughout an individual's life, causing severe adverse reactions, such as herpes simplex encephalitis (HSE). Recently, it has also been implicated in the etiology of Alzheimer's disease (AD). The absence of an effective vaccine and the emergence of numerous drug-resistant variants have called for the development of new antiviral agents that can tackle HSV-1 infection. Host-targeting antivirals (HTAs) have recently emerged as promising antiviral compounds that act on host-cell factors essential for viral replication. Here we show that a new class of HTAs targeting peptidylarginine deiminases (PADs), a family of calcium-dependent enzymes catalyzing protein citrullination, exhibits a marked inhibitory activity against HSV-1. Furthermore, we show that HSV-1 infection leads to enhanced protein citrullination through transcriptional activation of three PAD isoforms: PAD2, PAD3, and PAD4. Interestingly, PAD3-depletion by specific drugs or siRNAs dramatically inhibits HSV-1 replication. Finally, an analysis of the citrullinome reveals significant changes in the deimination levels of both cellular and viral proteins, with the interferon (IFN)-inducible proteins IFIT1 and IFIT2 being among the most heavily deiminated ones. As genetic depletion of IFIT1 and IFIT2 strongly enhances HSV-1 growth, we propose that viral-induced citrullination of IFIT1 and 2 is a highly efficient HSV-1 evasion mechanism from host antiviral resistance. Overall, our findings point to a crucial role of citrullination in subverting cellular responses to viral infection and demonstrate that PAD inhibitors efficiently suppress HSV-1 infection in vitro, which may provide the rationale for their repurposing as HSV-1 antiviral drugs.
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Affiliation(s)
- Selina Pasquero
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
| | - Francesca Gugliesi
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
| | - Valentina Dell’Oste
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
| | - Camilla Albano
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
| | - Greta Bajetto
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
- CAAD Center for Translational Research on Autoimmune and Allergic Disease, University of Piemonte Orientale, Novara Medical School, Novara, Italy
| | - Gloria Griffante
- Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Linda Trifirò
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
| | - Bianca Brugo
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
| | - Stefano Raviola
- CAAD Center for Translational Research on Autoimmune and Allergic Disease, University of Piemonte Orientale, Novara Medical School, Novara, Italy
- Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Davide Lacarbonara
- CAAD Center for Translational Research on Autoimmune and Allergic Disease, University of Piemonte Orientale, Novara Medical School, Novara, Italy
- Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Qiao Yang
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, P.R. China
| | - Sen Sudeshna
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, United States of America
| | - Leonard Barasa
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, United States of America
| | - Hafeez Haniff
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, United States of America
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, United States of America
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
| | - Marco De Andrea
- Department of Public Health and Pediatric Sciences, University of Turin – Medical School, Turin, Italy
- CAAD Center for Translational Research on Autoimmune and Allergic Disease, University of Piemonte Orientale, Novara Medical School, Novara, Italy
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9
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Rebak AS, Hendriks IA, Nielsen ML. Characterizing citrullination by mass spectrometry-based proteomics. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220237. [PMID: 37778389 PMCID: PMC10542455 DOI: 10.1098/rstb.2022.0237] [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: 03/15/2023] [Accepted: 05/25/2023] [Indexed: 10/03/2023] Open
Abstract
Citrullination is an important post-translational modification (PTM) of arginine, known to play a role in autoimmune disorders, innate immunity response and maintenance of stem cell potency. However, citrullination remains poorly characterized and not as comprehensively understood compared to other PTMs, such as phosphorylation and ubiquitylation. High-resolution mass spectrometry (MS)-based proteomics offers a valuable approach for studying citrullination in an unbiased manner, allowing confident identification of citrullination modification sites and distinction from deamidation events on asparagine and glutamine. MS efforts have already provided valuable insights into peptidyl arginine deaminase targeting along with site-specific information of citrullination in for example synovial fluids derived from rheumatoid arthritis patients. Still, there is unrealized potential for the wider citrullination field by applying MS-based mass spectrometry approaches for proteome-wide investigations. Here we will outline contemporary methods and current challenges for studying citrullination by MS, and discuss how the development of neoteric citrullination-specific proteomics approaches still may improve our understanding of citrullination networks. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- A. S. Rebak
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - I. A. Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - M. L. Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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10
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Williams JPC, Walport LJ. PADI6: What we know about the elusive fifth member of the peptidyl arginine deiminase family. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220242. [PMID: 37778376 PMCID: PMC10542454 DOI: 10.1098/rstb.2022.0242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/05/2023] [Indexed: 10/03/2023] Open
Abstract
Peptidyl arginine deiminase 6 (PADI6) is a maternal factor that is vital for early embryonic development. Deletion and mutations of its encoding gene in female mice or women lead to early embryonic developmental arrest, female infertility, maternal imprinting defects and hyperproliferation of the trophoblast. PADI6 is the fifth and least well-characterized member of the peptidyl arginine deiminases (PADIs), which catalyse the post-translational conversion of arginine to citrulline. It is less conserved than the other PADIs, and currently has no reported catalytic activity. While there are many suggested functions of PADI6 in the early mouse embryo, including in embryonic genome activation, cytoplasmic lattice formation, maternal mRNA and ribosome regulation, and organelle distribution, the molecular mechanisms of its function remain unknown. In this review, we discuss what is known about the function of PADI6 and highlight key outstanding questions that must be answered if we are to understand the crucial role it plays in early embryo development and female fertility. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
| | - Louise J. Walport
- Imperial College of Science Technology and Medicine, London, W12 0BZ, UK
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11
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Barasa L, Thompson PR. Protein citrullination: inhibition, identification and insertion. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220240. [PMID: 37778377 PMCID: PMC10542963 DOI: 10.1098/rstb.2022.0240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/26/2023] [Indexed: 10/03/2023] Open
Abstract
Protein citrullination is a post-translational modification (PTM) that is catalysed by the protein arginine deiminase (PAD) family of enzymes. This PTM involves the transformation of an arginine residue into citrulline. Protein citrullination is associated with several physiological processes, including the epigenetic regulation of gene expression, neutrophil extracellular trap formation and DNA damage-induced apoptosis. Aberrant protein citrullination is relevant to several autoimmune and neurodegenerative diseases and certain forms of cancer. PAD inhibitors have shown remarkable efficacy in a range of diseases including rheumatoid arthritis (RA), lupus, atherosclerosis and ulcerative colitis. In RA, anti-citrullinated protein antibodies can be detected prior to disease onset and are thus a valuable diagnostic tool for RA. Notably, citrullinated proteins may serve more generally as biomarkers of specific disease states; however, the identification of citrullinated protein residues remains challenging owing to the small 1 Da mass change that occurs upon citrullination. Herein, we highlight the progress made so far in the development of pan-PAD and isozyme selective inhibitors as well as the identification of citrullinated proteins and the site-specific incorporation of citrulline into proteins. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Leonard Barasa
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Paul R. Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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12
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Wang B, Fields L, Li L. Recent advances in characterization of citrullination and its implication in human disease research: From method development to network integration. Proteomics 2023; 23:e2200286. [PMID: 36546832 PMCID: PMC10285031 DOI: 10.1002/pmic.202200286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Post-translational modifications (PTM) of proteins increase the functional diversity of the proteome and have been implicated in the pathogenesis of numerous diseases. The most widely understood modifications include phosphorylation, methylation, acetylation, O-linked/N-linked glycosylation, and ubiquitination, all of which have been extensively studied and documented. Citrullination is a historically less explored, yet increasingly studied, protein PTM which has profound effects on protein conformation and protein-protein interactions. Dysregulation of protein citrullination has been associated with disease development and progression. Identification and characterization of citrullinated proteins is highly challenging, complicated by the low cellular abundance of citrullinated proteins, making it difficult to identify and quantify the extent of citrullination in samples, coupled with challenges associated with development of mass spectrometry (MS)-based methods, as the corresponding mass shift is relatively small, +0.984 Da, and identical to the mass shift of deamidation. The focus of this review is to discuss recent advancements of citrullination-specific MS approaches and integration of the potential methodology for improved citrullination identification and characterization. In addition, the association of citrullination in disease networks is also highlighted.
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Affiliation(s)
- Bin Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
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13
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Kim HJ, Shin HR, Yoon H, Park MS, Kim BG, Moon JI, Kim WJ, Park SG, Kim KT, Kim HN, Choi JY, Ryoo HM. Peptidylarginine deiminase 2 plays a key role in osteogenesis by enhancing RUNX2 stability through citrullination. Cell Death Dis 2023; 14:576. [PMID: 37648716 PMCID: PMC10468518 DOI: 10.1038/s41419-023-06101-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Peptidylarginine deiminase (PADI) 2 catalyzes the post-translational conversion of peptidyl-arginine to peptidyl-citrulline in a process called citrullination. However, the precise functions of PADI2 in bone formation and homeostasis remain unknown. In this study, our objective was to elucidate the function and regulatory mechanisms of PADI2 in bone formation employing global and osteoblast-specific Padi2 knockout mice. Our findings demonstrate that Padi2 deficiency leads to the loss of bone mass and results in a cleidocranial dysplasia (CCD) phenotype with delayed calvarial ossification and clavicular hypoplasia, due to impaired osteoblast differentiation. Mechanistically, Padi2 depletion significantly reduces RUNX2 levels, as PADI2-dependent stabilization of RUNX2 protected it from ubiquitin-proteasomal degradation. Furthermore, we discovered that PADI2 binds to RUNX2 and citrullinates it, and identified ten PADI2-induced citrullination sites on RUNX2 through high-resolution LC-MS/MS analysis. Among these ten citrullination sites, the R381 mutation in mouse RUNX2 isoform 1 considerably reduces RUNX2 levels, underscoring the critical role of citrullination at this residue in maintaining RUNX2 protein stability. In conclusion, these results indicate that PADI2 plays a distinct role in bone formation and osteoblast differentiation by safeguarding RUNX2 against proteasomal degradation. In addition, we demonstrate that the loss-of-function of PADI2 is associated with CCD, thereby providing a new target for the treatment of bone diseases.
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Affiliation(s)
- Hyun-Jung Kim
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Hye-Rim Shin
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Heein Yoon
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Min-Sang Park
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, South Korea
| | - Jae-I Moon
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Woo-Jin Kim
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Seung Gwa Park
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Ki-Tae Kim
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Ha-Neui Kim
- Center for Musculoskeletal Disease Research and Center for Osteoporosis and Metabolic Bone Diseases, Department of Internal Medicine, Division of Endocrinology and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Je-Yong Choi
- Department of Biochemistry and Cell Biology, Cell and Matrix Research Institute, BK21 Plus KNU Biomedical Convergence Program, Skeletal Disease Analysis Center, Korea Mouse Phenotyping Center, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Hyun-Mo Ryoo
- Department of Molecular Genetics and Dental Pharmacology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea.
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14
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Beygmoradi A, Homaei A, Hemmati R, Fernandes P. Recombinant protein expression: Challenges in production and folding related matters. Int J Biol Macromol 2023; 233:123407. [PMID: 36708896 DOI: 10.1016/j.ijbiomac.2023.123407] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
Protein folding is a biophysical process by which proteins reach a specific three-dimensional structure. The amino acid sequence of a polypeptide chain contains all the information needed to determine the final three-dimensional structure of a protein. When producing a recombinant protein, several problems can occur, including proteolysis, incorrect folding, formation of inclusion bodies, or protein aggregation, whereby the protein loses its natural structure. To overcome such limitations, several strategies have been developed to address each specific issue. Identification of proper protein refolding conditions can be challenging, and to tackle this high throughput screening for different recombinant protein folding conditions can prove a sound solution. Different approaches have emerged to tackle refolding issues. One particular approach to address folding issues involves molecular chaperones, highly conserved proteins that contribute to proper folding by shielding folding proteins from other proteins that could hinder the process. Proper protein folding is one of the main prerequisites for post-translational modifications. Incorrect folding, if not dealt with, can lead to a buildup of protein misfoldings that damage cells and cause widespread abnormalities. Said post-translational modifications, widespread in eukaryotes, are critical for protein structure, function and biological activity. Incorrect post-translational protein modifications may lead to individual consequences or aggregation of therapeutic proteins. In this review article, we have tried to examine some key aspects of recombinant protein expression. Accordingly, the relevance of these proteins is highlighted, major problems related to the production of recombinant protein and to refolding issues are pinpointed and suggested solutions are presented. An overview of post-translational modification, their biological significance and methods of identification are also provided. Overall, the work is expected to illustrate challenges in recombinant protein expression.
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Affiliation(s)
- Azadeh Beygmoradi
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
| | - Roohullah Hemmati
- Department of Biology, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Pedro Fernandes
- DREAMS and Faculdade de Engenharia, Universidade Lusófona de Humanidades e Tecnologias, Av. Campo Grande 376, 1749-024 Lisboa, Portugal; iBB-Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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15
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Brulet JW, Ciancone AM, Yuan K, Hsu K. Advances in Activity‐Based Protein Profiling of Functional Tyrosines in Proteomes. Isr J Chem 2023. [DOI: 10.1002/ijch.202300001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Jeffrey W. Brulet
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Anthony M. Ciancone
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Kun Yuan
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Ku‐Lung Hsu
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
- Department of Pharmacology University of Virginia School of Medicine Charlottesville Virginia 22908 United States
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia 22908 United States
- University of Virginia Cancer Center University of Virginia Charlottesville VA 22903 USA
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16
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Binder V, Chruścicka-Smaga B, Bergum B, Jaisson S, Gillery P, Sivertsen J, Hervig T, Kaminska M, Tilvawala R, Nemmara VV, Thompson PR, Potempa J, Marti HP, Mydel P. Carbamylation of Integrin α IIb β 3: The Mechanistic Link to Platelet Dysfunction in ESKD. J Am Soc Nephrol 2022; 33:1841-1856. [PMID: 36038265 PMCID: PMC9528322 DOI: 10.1681/asn.2022010013] [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: 01/04/2022] [Accepted: 06/05/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Bleeding diatheses, common among patients with ESKD, can lead to serious complications, particularly during invasive procedures. Chronic urea overload significantly increases cyanate concentrations in patients with ESKD, leading to carbamylation, an irreversible modification of proteins and peptides. METHODS To investigate carbamylation as a potential mechanistic link between uremia and platelet dysfunction in ESKD, we used liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) to quantify total homocitrulline, and biotin-conjugated phenylglyoxal labeling and Western blot to detect carbamylated integrin α IIb β 3 (a receptor required for platelet aggregation). Flow cytometry was used to study activation of isolated platelets and platelet-rich plasma. In a transient transfection system, we tested activity and fibrinogen binding of different mutated forms of the receptor. We assessed platelet adhesion and aggregation in microplate assays. RESULTS Carbamylation inhibited platelet activation, adhesion, and aggregation. Patients on hemodialysis exhibited significantly reduced activation of α IIb β 3 compared with healthy controls. We found significant carbamylation of both subunits of α IIb β 3 on platelets from patients receiving hemodialysis versus only minor modification in controls. In the transient transfection system, modification of lysine 185 in the β 3 subunit was associated with loss of receptor activity and fibrinogen binding. Supplementation of free amino acids, which was shown to protect plasma proteins from carbamylation-induced damage in patients on hemodialysis, prevented loss of α IIb β 3 activity in vitro. CONCLUSIONS Carbamylation of α IIb β 3-specifically modification of the K185 residue-might represent a mechanistic link between uremia and dysfunctional primary hemostasis in patients on hemodialysis. The observation that free amino acids prevented the carbamylation-induced loss of α IIb β 3 activity suggests amino acid administration during dialysis may help to normalize platelet function.
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Affiliation(s)
- Veronika Binder
- Broegelmann Research Laboratory, University of Bergen, Bergen, Norway
| | | | - Brith Bergum
- Broegelmann Research Laboratory, University of Bergen, Bergen, Norway
| | - Stéphane Jaisson
- Laboratory of Biochemistry and Molecular Biology, Unité Mixte de Recherche (UMR) Centre National de la Recherche Scientifique (CNRS) 7369, University of Reims Champagne-Ardenne, Reims, France
| | - Philippe Gillery
- Laboratory of Biochemistry and Molecular Biology, Unité Mixte de Recherche (UMR) Centre National de la Recherche Scientifique (CNRS) 7369, University of Reims Champagne-Ardenne, Reims, France
| | - Joar Sivertsen
- Department of Immunology and Transfusion Medicine, Haukeland University Hospital, Bergen, Norway
| | - Tor Hervig
- Broegelmann Research Laboratory, University of Bergen, Bergen, Norway
- Department of Immunology and Transfusion Medicine, Haukeland University Hospital, Bergen, Norway
| | - Marta Kaminska
- Broegelmann Research Laboratory, University of Bergen, Bergen, Norway
| | - Ronak Tilvawala
- Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Venkatesh V. Nemmara
- Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Paul R. Thompson
- Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jan Potempa
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Piotr Mydel
- Broegelmann Research Laboratory, University of Bergen, Bergen, Norway
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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17
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Zhao H, Shan A, Liang Y, Wu H, He Y, Chen H, Zeng J, Gu J, Song JP, Qiu H, Zhang J. Boron-Assisted Selective Citrulline Modification under Mild Conditions. Org Lett 2022; 24:6351-6355. [PMID: 35997298 DOI: 10.1021/acs.orglett.2c02722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein citrullination is one type of protein post-translational modification. Previous methods entail the use of a strongly acidic condition (pH <1), which impedes its exploration under physiological and pathological conditions. Here, we developed a biocompatible method based on o-boron-assisted citrulline modification. We demonstrated that this method enables selective and mainly irreversible modification of citrulline residues under neutral conditions. We expect that it will provide a valuable tool for the study of protein citrullination.
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Affiliation(s)
- Hailong Zhao
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Aidong Shan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yunshi Liang
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Haiting Wu
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Yiting He
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Huihong Chen
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jiaxin Zeng
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Jiangyong Gu
- Research Centre for Integrative Medicine, School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jian-Ping Song
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Hong Qiu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Zhang
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
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18
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Emenike B, Nwajiobi O, Raj M. Covalent Chemical Tools for Profiling Post-Translational Modifications. Front Chem 2022; 10:868773. [PMID: 35860626 PMCID: PMC9289218 DOI: 10.3389/fchem.2022.868773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
Nature increases the functional diversity of the proteome through posttranslational modifications (PTMs); a process that involves the proteolytic processing or catalytic attachment of diverse functional groups onto proteins. These modifications modulate a host of biological activities and responses. Consequently, anomalous PTMs often correlate to a host of diseases, hence there is a need to detect these transformations, both qualitatively and quantitatively. One technique that has gained traction is the use of robust chemical strategies to label different PTMs. By utilizing the intrinsic chemical reactivity of the different chemical groups on the target amino acid residues, this strategy can facilitate the delineation of the overarching and inclusionary roles of these different modifications. Herein, we will discuss the current state of the art in post-translational modification analysis, with a direct focus on covalent chemical methods used for detecting them.
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19
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Shih CT, Kuo BH, Tsai CY, Tseng MC, Shie JJ. Dibenzocyclooctendiones (DBCDOs): Arginine-Selective Chemical Labeling Reagents Obtained through Benzilic Acid Rearrangement. Org Lett 2022; 24:4694-4698. [PMID: 35727008 DOI: 10.1021/acs.orglett.2c01970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We demonstrate that dibenzocyclooctendiones (DBCDOs) are efficient chemical reagents for the site-specific labeling of arginine-containing biomolecules. Unlike the commonly used probes, DBCDOs undergo an irreversible ring-contracted rearrangement with the guanidinium group on arginine residues under mild reaction conditions. The regioselective dual-labeled arginine residues were obtained in a one-pot reaction with our tested substrates. The efficiency of DBCDOs reactions and their ease of synthesis make DBCDOs an attractive choice for the site-selective bioconjugation of arginine.
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Affiliation(s)
- Cheng-Ting Shih
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Bo-Hong Kuo
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Yi Tsai
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
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20
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Sarnik J, Makowska J. Citrullination good or bad guy? Immunobiology 2022; 227:152233. [DOI: 10.1016/j.imbio.2022.152233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 04/11/2022] [Accepted: 05/21/2022] [Indexed: 11/16/2022]
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21
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Chen Y, Weng L, Liu W, Deng C, Xuan J, Ma Y, Li C, Jiang J, Chen J, Ge S. Characterization of Monoclonal Antibodies Recognizing Citrulline-Modified Residues. Front Immunol 2022; 13:849779. [PMID: 35359951 PMCID: PMC8961739 DOI: 10.3389/fimmu.2022.849779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundCitrullination is a post-translational protein modification linked to the occurrence and development of a variety of diseases. The detection of citrullinated proteins is predominately based on antibody detection although currently available reagents demonstrate detection bias according to the environmental context of the citrullinated residues. This study aimed to develop improved antibody reagents capable of detecting citrullinated residues in proteins in an unbiased manner.MethodsBALB/c mice were sequentially immunized using citrulline conjugates with different carrier proteins, and specific monoclonal antibodies (mAbs) identified by primary screening using citrulline-conjugated proteins unrelated to the immunogen. Secondary screening was performed to identify mAbs whose reactivity could be specifically blocked by free citrulline, followed by identification and performance assessment.ResultsTwo mAbs, 22F1 and 30G2, specifically recognizing a single citrulline residue were screened from 22 mAbs reacting with citrulline conjugates. Compared with commercially available anti-citrulline antibodies (AB6464, AB100932 and MABN328), 22F1 and 30G2 demonstrated significantly higher reactivity as well as a broader detection spectrum against different citrullinated proteins. 22F1 and 30G2 also had higher specificity than commercial antibodies and overall better applicability to a range of different immunoassays.ConclusionTwo mAbs specifically recognizing a single citrulline residue were successfully produced, each possessing good specificity against different citrullinated proteins. The improved utility of these reagents is expected to make a strong contribution to protein citrullination-related research.
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Affiliation(s)
- Yaqiong Chen
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Lin Weng
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Wei Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China
| | - Chenxi Deng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China
| | - Jinxiu Xuan
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yuan Ma
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Cao Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China
| | - Jinlu Jiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China
| | - Juan Chen
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- *Correspondence: Juan Chen, ; Shengxiang Ge,
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China
- *Correspondence: Juan Chen, ; Shengxiang Ge,
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22
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Abstract
Natural products have traditionally been a fruitful source of chemical matter that has been developed into novel therapeutics. Actinomycetes and several other bacterial taxa are especially gifted in biosynthesizing natural products. However, many decades of intense bioactivity-based screening led to a large rediscovery problem, rendering industrial natural product discovery pipelines uneconomical. Numerous methods for circumventing the rediscovery problem have been developed, among them various chemistry-focused strategies, including reactivity-based screening. Emerging from the field of chemical proteomics, reactivity-based screening relies on a reactive probe that chemoselectively modifies a functional group of interest in the context of a complex biological sample. Reactivity-based probes for several distinct functional groups have been deployed to discover new polyketide and peptidic natural products. This chapter describes the protocols to conduct a reactivity-based screening campaign, including bacteria cultivation and screening of cellular extracts with phenylglyoxal-, tetrazine-, thiol-, and aminooxy-functionalized probes, which respectively target primary uriedo, electron-rich olefins, Michael acceptors, and reactive carbonyls. In addition, a recent case study is presented that employs reactivity-based screening as a component of a forward genetics screen to identify a previously unknown peptidyl arginine deiminase. We anticipate that these methods will be useful for those interested in discovering natural products that evade detection by traditional, bioassay-guided methods and others who wish to rapidly connect metabolic chemotype with genotype.
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Affiliation(s)
- Lonnie A. Harris
- Department of Chemistry, University of Illinois, Urbana, IL, United States
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois, Urbana, IL, United States,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States,Department of Microbiology, University of Illinois, Urbana, IL, United States,Corresponding Author: 600 S. Mathews Avenue, Roger Adams Laboratory, Rm. 361, University of Illinois, Urbana, IL 61801, 217-333-1345,
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23
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Grant J, Kimmel BR, Szymczak LC, Roll J, Mrksich M. Characterizing Enzyme Cooperativity with Imaging SAMDI-MS. Chemistry 2021; 28:e202103807. [PMID: 34890480 DOI: 10.1002/chem.202103807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Indexed: 11/11/2022]
Abstract
This paper describes a method that combines a microfluidic device and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI) mass spectrometry to calculate the cooperativity in binding of calcium ions to peptidylarginine deiminase type 2 (PAD2). This example uses only 120 µL of enzyme solution and three fluidic inputs. This microfluidic device incorporates a self-assembled monolayer that is functionalized with a peptide substrate for PAD2. The enzyme and different concentrations of calcium ions are flowed through each of eight channels, where the position along the channel corresponds to reaction time and position across the channel corresponds to the concentration of Ca2+. Imaging SAMDI (iSAMDI) is then used to determine the yield for the enzyme reaction at each 200 µm pixel on the monolayer, providing a time course for the reactions. Analysis of the peptide conversion as a function of position and time gives the degree of cooperativity (n) and the concentration of ligand required for half maximal activity (K0.5) for the Ca2+ - dependent activation of PAD2. This work establishes a high-throughput and label-free method for studying enzyme-ligand binding interactions and widens the applicability of microfluidics and matrix-assisted laser desorption/ionization mass spectrometry (MALDI) imaging mass spectrometry.
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Affiliation(s)
| | - Blaise R Kimmel
- Northwestern University, Chemical and Biological Engineering, UNITED STATES
| | | | - Juliet Roll
- Northwestern University, Biomedical Engineering, UNITED STATES
| | - Milan Mrksich
- Northwestern University, Department of Chemistry, 2145 Sheridan Road, 60208, Evanston, UNITED STATES
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24
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Maurais AJ, Salinger AJ, Tobin M, Shaffer SA, Weerapana E, Thompson PR. A Streamlined Data Analysis Pipeline for the Identification of Sites of Citrullination. Biochemistry 2021; 60:2902-2914. [PMID: 34491035 DOI: 10.1021/acs.biochem.1c00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Citrullination is an enzyme-catalyzed post-translational modification (PTM) that is essential for a host of biological processes, including gene regulation, programmed cell death, and organ development. While this PTM is required for normal cellular functions, aberrant citrullination is a hallmark of autoimmune disorders as well as cancer. Although aberrant citrullination is linked to human pathology, the exact role of citrullination in disease remains poorly characterized, in part because of the challenges associated with identifying the specific arginine residues that are citrullinated. Tandem mass spectrometry is the most precise method for uncovering sites of citrullination; however, due to the small mass shift (+0.984 Da) that results from citrullination, current database search algorithms commonly misannotate spectra, leading to a high number of false-positive assignments. To address this challenge, we developed an automated workflow to rigorously and rapidly mine proteomic data to unambiguously identify the sites of citrullination from complex peptide mixtures. The crux of this streamlined workflow is the ionFinder software program, which classifies citrullination sites with high confidence on the basis of the presence of diagnostic fragment ions. These diagnostic ions include the neutral loss of isocyanic acid, which is a dissociative event that is unique to citrulline residues. Using the ionFinder program, we have mapped the sites of autocitrullination on purified protein arginine deiminases (PAD1-4) and mapped the global citrullinome in a PAD2-overexpressing cell line. The ionFinder algorithm is a highly versatile, user-friendly, and open-source program that is agnostic to the type of instrument and mode of fragmentation that are used.
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Affiliation(s)
- Aaron J Maurais
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Ari J Salinger
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States.,Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Micaela Tobin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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25
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Griffante G, Gugliesi F, Pasquero S, Dell'Oste V, Biolatti M, Salinger AJ, Mondal S, Thompson PR, Weerapana E, Lebbink RJ, Soppe JA, Stamminger T, Girault V, Pichlmair A, Oroszlán G, Coen DM, De Andrea M, Landolfo S. Human cytomegalovirus-induced host protein citrullination is crucial for viral replication. Nat Commun 2021; 12:3910. [PMID: 34162877 PMCID: PMC8222335 DOI: 10.1038/s41467-021-24178-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/29/2021] [Indexed: 11/18/2022] Open
Abstract
Citrullination is the conversion of arginine-to-citrulline by protein arginine deiminases (PADs), whose dysregulation is implicated in the pathogenesis of various types of cancers and autoimmune diseases. Consistent with the ability of human cytomegalovirus (HCMV) to induce post-translational modifications of cellular proteins to gain a survival advantage, we show that HCMV infection of primary human fibroblasts triggers PAD-mediated citrullination of several host proteins, and that this activity promotes viral fitness. Citrullinome analysis reveals significant changes in deimination levels of both cellular and viral proteins, with interferon (IFN)-inducible protein IFIT1 being among the most heavily deiminated one. As genetic depletion of IFIT1 strongly enhances HCMV growth, and in vitro IFIT1 citrullination impairs its ability to bind to 5’-ppp-RNA, we propose that viral-induced IFIT1 citrullination is a mechanism of HCMV evasion from host antiviral resistance. Overall, our findings point to a crucial role of citrullination in subverting cellular responses to viral infection. Citrullination is a posttranslational modification of arginines. Here, the authors show that HCMV infection increases citrullination of host and virus proteins to promote infection and that citrullinated interferon-inducible protein IFIT1 is impaired in RNA binding, as a potential mechanism of evasion.
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Affiliation(s)
- Gloria Griffante
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy.,Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Francesca Gugliesi
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Selina Pasquero
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Valentina Dell'Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Ari J Salinger
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA.,Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Santanu Mondal
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | | | - Robert J Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jasper A Soppe
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Virginie Girault
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Gábor Oroszlán
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Donald M Coen
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Marco De Andrea
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy. .,CAAD Center for Translational Research on Autoimmune and Allergic Disease, University of Piemonte Orientale, Novara, Italy.
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy.
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26
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Zhu D, Zhang Y, Wang S. Histone citrullination: a new target for tumors. Mol Cancer 2021; 20:90. [PMID: 34116679 PMCID: PMC8192683 DOI: 10.1186/s12943-021-01373-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/13/2021] [Indexed: 01/08/2023] Open
Abstract
As the main protein components of chromatin, histones play central roles in gene regulation as spools of winding DNA. Histones are subject to various modifications, including phosphorylation, acetylation, glycosylation, methylation, ubiquitination and citrullination, which affect gene transcription. Histone citrullination, a posttranscriptional modification catalyzed by peptidyl arginine deiminase (PAD) enzymes, is involved in human carcinogenesis. In this study, we highlighted the functions of histone citrullination in physiological regulation and tumors. Additionally, because histone citrullination involves forming neutrophil extracellular traps (NETs), the relationship between NETs and tumors was illustrated. Finally, the clinical application of histone citrullination and PAD inhibitors was discussed.
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Affiliation(s)
- Dongwei Zhu
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212013, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yue Zhang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212013, China.
| | - Shengjun Wang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212013, China. .,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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27
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Yang ML, Sodré FMC, Mamula MJ, Overbergh L. Citrullination and PAD Enzyme Biology in Type 1 Diabetes - Regulators of Inflammation, Autoimmunity, and Pathology. Front Immunol 2021; 12:678953. [PMID: 34140951 PMCID: PMC8204103 DOI: 10.3389/fimmu.2021.678953] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023] Open
Abstract
The generation of post-translational modifications (PTMs) in human proteins is a physiological process leading to structural and immunologic variety in proteins, with potentially altered biological functions. PTMs often arise through normal responses to cellular stress, including general oxidative changes in the tissue microenvironment and intracellular stress to the endoplasmic reticulum or immune-mediated inflammatory stresses. Many studies have now illustrated the presence of 'neoepitopes' consisting of PTM self-proteins that induce robust autoimmune responses. These pathways of inflammatory neoepitope generation are commonly observed in many autoimmune diseases including systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and type 1 diabetes (T1D), among others. This review will focus on one specific PTM to self-proteins known as citrullination. Citrullination is mediated by calcium-dependent peptidylarginine deiminase (PAD) enzymes, which catalyze deimination, the conversion of arginine into the non-classical amino acid citrulline. PADs and citrullinated peptides have been associated with different autoimmune diseases, notably with a prominent role in the diagnosis and pathology of rheumatoid arthritis. More recently, an important role for PADs and citrullinated self-proteins has emerged in T1D. In this review we will provide a comprehensive overview on the pathogenic role for PADs and citrullination in inflammation and autoimmunity, with specific focus on evidence for their role in T1D. The general role of PADs in epigenetic and transcriptional processes, as well as their crucial role in histone citrullination, neutrophil biology and neutrophil extracellular trap (NET) formation will be discussed. The latter is important in view of increasing evidence for a role of neutrophils and NETosis in the pathogenesis of T1D. Further, we will discuss the underlying processes leading to citrullination, the genetic susceptibility factors for increased recognition of citrullinated epitopes by T1D HLA-susceptibility types and provide an overview of reported autoreactive responses against citrullinated epitopes, both of T cells and autoantibodies in T1D patients. Finally, we will discuss recent observations obtained in NOD mice, pointing to prevention of diabetes development through PAD inhibition, and the potential role of PAD inhibitors as novel therapeutic strategy in autoimmunity and in T1D in particular.
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Affiliation(s)
- Mei-Ling Yang
- Section of Rheumatology, Allergy and Clinical Immunology, Department of Internal Medicine, Yale University, New Haven, CT, United States
| | - Fernanda M C Sodré
- Department of Chronic Diseases, Metabolism and Ageing, Laboratory of Clinical and Experimental Endocrinology (CEE), KU Leuven, Leuven, Belgium
| | - Mark J Mamula
- Section of Rheumatology, Allergy and Clinical Immunology, Department of Internal Medicine, Yale University, New Haven, CT, United States
| | - Lut Overbergh
- Department of Chronic Diseases, Metabolism and Ageing, Laboratory of Clinical and Experimental Endocrinology (CEE), KU Leuven, Leuven, Belgium
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28
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Borne AL, Brulet JW, Yuan K, Hsu KL. Development and biological applications of sulfur-triazole exchange (SuTEx) chemistry. RSC Chem Biol 2021; 2:322-337. [PMID: 34095850 PMCID: PMC8174820 DOI: 10.1039/d0cb00180e] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/05/2021] [Indexed: 12/27/2022] Open
Abstract
Sulfur electrophiles constitute an important class of covalent small molecules that have found widespread applications in synthetic chemistry and chemical biology. Various electrophilic scaffolds, including sulfonyl fluorides and arylfluorosulfates as recent examples, have been applied for protein bioconjugation to probe ligand sites amenable for chemical proteomics and drug discovery. In this review, we describe the development of sulfonyl-triazoles as a new class of electrophiles for sulfur-triazole exchange (SuTEx) chemistry. SuTEx achieves covalent reaction with protein sites through irreversible modification of a residue with an adduct group (AG) upon departure of a leaving group (LG). A principal differentiator of SuTEx from other chemotypes is the selection of a triazole heterocycle as the LG, which introduces additional capabilities for tuning the sulfur electrophile. We describe the opportunities afforded by modifications to the LG and AG alone or in tandem to facilitate nucleophilic substitution reactions at the SO2 center in cell lysates and live cells. As a result of these features, SuTEx serves as an efficient platform for developing chemical probes with tunable bioactivity to study novel nucleophilic sites on established and poorly annotated protein targets. Here, we highlight a suite of biological applications for the SuTEx electrophile and discuss future goals for this enabling covalent chemistry.
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Affiliation(s)
- Adam L. Borne
- Department of Pharmacology, University of Virginia School of MedicineCharlottesvilleVirginia 22908USA
| | - Jeffrey W. Brulet
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
| | - Kun Yuan
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
| | - Ku-Lung Hsu
- Department of Pharmacology, University of Virginia School of MedicineCharlottesvilleVirginia 22908USA
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
- University of Virginia Cancer Center, University of VirginiaCharlottesvilleVA 22903USA
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleVirginia 22908USA
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29
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Mondal S, Thompson PR. Chemical biology of protein citrullination by the protein A arginine deiminases. Curr Opin Chem Biol 2021; 63:19-27. [PMID: 33676233 DOI: 10.1016/j.cbpa.2021.01.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/19/2021] [Accepted: 01/31/2021] [Indexed: 12/25/2022]
Abstract
Citrullination is a post-translational modification (PTM) that converts peptidyl-arginine into peptidyl-citrulline; citrullination is catalyzed by the protein arginine deiminases (PADs). This PTM is associated with several physiological processes, including the epigenetic regulation of gene expression, neutrophil extracellular trap formation, and DNA-damage induced apoptosis. Notably, aberrant protein citrullination is relevant to several autoimmune and neurodegenerative diseases and certain forms of cancer. As such, the PADs are promising therapeutic targets. In this review, we discuss recent advances in the development of PAD inhibitors and activity-based probes, the development and use of citrulline-specific probes in chemoproteomic applications, and methods to site-specifically incorporate citrulline into proteins.
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Affiliation(s)
- Santanu Mondal
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, MA, 01605, USA; Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, MA, 01605, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, MA, 01605, USA; Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, MA, 01605, USA.
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30
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Huang T, Hosseinibarkooie S, Borne AL, Granade ME, Brulet JW, Harris TE, Ferris HA, Hsu KL. Chemoproteomic profiling of kinases in live cells using electrophilic sulfonyl triazole probes. Chem Sci 2021; 12:3295-3307. [PMID: 34164099 PMCID: PMC8179411 DOI: 10.1039/d0sc06623k] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/08/2021] [Indexed: 12/23/2022] Open
Abstract
Sulfonyl-triazoles are a new class of electrophiles that mediate covalent reaction with tyrosine residues on proteins through sulfur-triazole exchange (SuTEx) chemistry. Recent studies demonstrate the broad utility and tunability of SuTEx chemistry for chemical proteomics and protein ligand discovery. Here, we present a strategy for mapping protein interaction networks of structurally complex binding elements using functionalized SuTEx probes. We show that the triazole leaving group (LG) can serve as a releasable linker for embedding hydrophobic fragments to direct molecular recognition while permitting efficient proteome-wide identification of binding sites in live cells. We synthesized a series of SuTEx probes functionalized with a lipid kinase fragment binder for discovery of ligandable tyrosines residing in catalytic and regulatory domains of protein and metabolic kinases in live cells. We performed competition studies with kinase inhibitors and substrates to demonstrate that probe binding is occurring in an activity-dependent manner. Our functional studies led to discovery of probe-modified sites within the C2 domain that were important for downregulation of protein kinase C-alpha in response to phorbol ester activation. Our proof of concept studies highlight the triazole LG of SuTEx probes as a traceless linker for locating protein binding sites targeted by complex recognition elements in live cells.
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Affiliation(s)
- Tao Huang
- Department of Chemistry, University of Virginia McCormick Road, P.O. Box 400319 Charlottesville Virginia 22904 USA +1-434-297-4864
| | | | - Adam L Borne
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
| | - Mitchell E Granade
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
| | - Jeffrey W Brulet
- Department of Chemistry, University of Virginia McCormick Road, P.O. Box 400319 Charlottesville Virginia 22904 USA +1-434-297-4864
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
| | - Heather A Ferris
- Department of Medicine, University of Virginia School of Medicine Charlottesville Virginia 22903 USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia McCormick Road, P.O. Box 400319 Charlottesville Virginia 22904 USA +1-434-297-4864
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
- University of Virginia Cancer Center, University of Virginia Charlottesville VA 22903 USA
- Department of Molecular Physiology and Biological Physics, University of Virginia Charlottesville Virginia 22908 USA
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31
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Site-specific incorporation of citrulline into proteins in mammalian cells. Nat Commun 2021; 12:45. [PMID: 33398026 PMCID: PMC7782748 DOI: 10.1038/s41467-020-20279-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/20/2020] [Indexed: 12/02/2022] Open
Abstract
Citrullination is a post-translational modification (PTM) of arginine that is crucial for several physiological processes, including gene regulation and neutrophil extracellular trap formation. Despite recent advances, studies of protein citrullination remain challenging due to the difficulty of accessing proteins homogeneously citrullinated at a specific site. Herein, we report a technology that enables the site-specific incorporation of citrulline (Cit) into proteins in mammalian cells. This approach exploits an engineered E. coli-derived leucyl tRNA synthetase-tRNA pair that incorporates a photocaged-citrulline (SM60) into proteins in response to a nonsense codon. Subsequently, SM60 is readily converted to Cit with light in vitro and in living cells. To demonstrate the utility of the method, we biochemically characterize the effect of incorporating Cit at two known autocitrullination sites in Protein Arginine Deiminase 4 (PAD4, R372 and R374) and show that the R372Cit and R374Cit mutants are 181- and 9-fold less active than the wild-type enzyme. This technology possesses the potential to decipher the biology of citrullination. Citrullination of arginine is crucial for several physiological processes. Here the authors report the site-specific incorporation of citrulline into proteins in mammalian cells using an engineered tRNA synthetase/tRNA pair and a photocaged-citrulline.
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32
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Dragoni G, De Hertogh G, Vermeire S. The Role of Citrullination in Inflammatory Bowel Disease: A Neglected Player in Triggering Inflammation and Fibrosis? Inflamm Bowel Dis 2021; 27:134-144. [PMID: 32426830 DOI: 10.1093/ibd/izaa095] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Indexed: 02/07/2023]
Abstract
Citrullination is a posttranslational modification of proteins mediated by a specific family of enzymes called peptidylarginine deiminases (PAD). Dysregulation of these enzymes is involved in the etiology of various diseases, from cancer to autoimmune disorders. In inflammatory bowel disease (IBD), data for a role of citrullination in the disease process are starting to accumulate at different experimental levels including gene expression analyses, RNA, and protein quantifications. Most data have been generated in ulcerative colitis, but data in Crohn disease are lacking so far. In addition, the citrullination of histones is the fundamental process promoting inflammation through the formation of neutrophil extracellular traps (NETs). Interestingly, NETs have also been shown to activate fibroblasts into myofibroblasts in fibrotic interstitial lung disease. Therefore, citrullination merits more thorough study in the bowel to determine its role in driving disease complications such as fibrosis. In this review we describe the process of citrullination and the different players in this pathway, the role of citrullination in autoimmunity with a special focus on IBD, the emerging role for citrullination and NETs in triggering fibrosis, and, finally, how this process could be therapeutically targeted.
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Affiliation(s)
- Gabriele Dragoni
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders, Leuven, Belgium.,Gastroenterology Research Unit, Department of Experimental and Clinical Biomedical Sciences Mario Serio, University of Florence, Florence, Italy.,Department of Medical Biotechnologies, University of Siena, Italy
| | - Gert De Hertogh
- KU Leuven, Department of Imaging and Pathology, Translational Cell & Tissue Research, Leuven, Belgium
| | - Séverine Vermeire
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
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33
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Harris LA, Saint-Vincent PMB, Guo X, Hudson GA, DiCaprio AJ, Zhu L, Mitchell DA. Reactivity-Based Screening for Citrulline-Containing Natural Products Reveals a Family of Bacterial Peptidyl Arginine Deiminases. ACS Chem Biol 2020; 15:3167-3175. [PMID: 33249828 DOI: 10.1021/acschembio.0c00685] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products defined by a genetically encoded precursor peptide that is processed by associated biosynthetic enzymes to form the mature product. Lasso peptides are a class of RiPP defined by an isopeptide linkage between the N-terminal amine and an internal Asp/Glu residue with the C-terminal sequence threaded through the macrocycle. This unique lariat topology, which typically provides considerable stability toward heat and proteases, has stimulated interest in lasso peptides as potential therapeutics. Post-translational modifications beyond the class-defining, threaded macrolactam have been reported, including one example of Arg deimination to yield citrulline (Cit). Although a Cit-containing lasso peptide (i.e., citrulassin) was serendipitously discovered during a genome-guided campaign, the gene(s) responsible for Arg deimination has remained unknown. Herein, we describe the use of reactivity-based screening to discriminate bacterial strains that produce Arg- versus Cit-bearing citrulassins, yielding 13 new lasso peptide variants. Partial phylogenetic profiling identified a distally encoded peptidyl arginine deiminase (PAD) gene ubiquitous to the Cit-containing variants. Absence of this gene correlated strongly with lasso peptide variants only containing Arg (i.e., des-citrulassin). Heterologous expression of the PAD gene in a des-citrulassin producer resulted in the production of the deiminated analog, confirming PAD involvement in Arg deimination. The PADs were then bioinformatically surveyed to provide a deeper understanding of their taxonomic distribution and genomic contexts and to facilitate future studies that will evaluate any additional biochemical roles for the superfamily.
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34
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Briot J, Simon M, Méchin MC. Deimination, Intermediate Filaments and Associated Proteins. Int J Mol Sci 2020; 21:E8746. [PMID: 33228136 PMCID: PMC7699402 DOI: 10.3390/ijms21228746] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Deimination (or citrullination) is a post-translational modification catalyzed by a calcium-dependent enzyme family of five peptidylarginine deiminases (PADs). Deimination is involved in physiological processes (cell differentiation, embryogenesis, innate and adaptive immunity, etc.) and in autoimmune diseases (rheumatoid arthritis, multiple sclerosis and lupus), cancers and neurodegenerative diseases. Intermediate filaments (IF) and associated proteins (IFAP) are major substrates of PADs. Here, we focus on the effects of deimination on the polymerization and solubility properties of IF proteins and on the proteolysis and cross-linking of IFAP, to finally expose some features of interest and some limitations of citrullinomes.
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Affiliation(s)
| | | | - Marie-Claire Méchin
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université Toulouse III Paul Sabatier, Université Fédérale de Toulouse Midi-Pyrénées, U1056, 31059 Toulouse, France; (J.B.); (M.S.)
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35
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Neutrophils as a Novel Target of Modified Low-Density Lipoproteins and an Accelerator of Cardiovascular Diseases. Int J Mol Sci 2020; 21:ijms21218312. [PMID: 33167592 PMCID: PMC7664187 DOI: 10.3390/ijms21218312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022] Open
Abstract
Neutrophil extracellular traps (NETs) significantly contribute to various pathophysiological conditions, including cardiovascular diseases. NET formation in the vasculature exhibits inflammatory and thrombogenic activities on the endothelium. NETs are induced by various stimulants such as exogenous damage-associated molecular patterns (DAMPs). Oxidatively modified low-density lipoprotein (oxLDL) has been physiologically defined as a subpopulation of LDL that comprises various oxidative modifications in the protein components and oxidized lipids, which could act as DAMPs. oxLDL has been recognized as a crucial initiator and accelerator of atherosclerosis through foam cell formation by macrophages; however, recent studies have demonstrated that oxLDL stimulates neutrophils to induce NET formation and enhance NET-mediated inflammatory responses in vascular endothelial cells, thereby suggesting that oxLDL may be involved in cardiovascular diseases through neutrophil activation. As NETs comprise myeloperoxidase and proteases, they have the potential to mediate oxidative modification of LDL. This review summarizes recent updates on the analysis of NETs, their implications for cardiovascular diseases, and prospects for a possible link between NET formation and oxidative modification of lipoproteins.
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36
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Huh S, Hwang D, Kim MS. Statistical Modeling for Enhancing the Discovery Power of Citrullination from Tandem Mass Spectrometry Data. Anal Chem 2020; 92:12975-12986. [PMID: 32876429 DOI: 10.1021/acs.analchem.0c01687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Citrullination is a post-translational modification implicated in various human diseases including rheumatoid arthritis, Alzheimer's disease, multiple sclerosis, and cancers. Due to a relatively low concentration of citrullinated proteins in the total proteome, confident identification of citrullinated proteome is challenging in mass spectrometry (MS)-based proteomic analysis. From these MS-based analyses, MS features that characterize citrullination, such as immonium ions (IMs) and neutral losses (NLs), called diagnostic ions, have been reported. However, there has been a lack of systematic approaches to comprehensively search for diagnostic ions and no statistical methods for the identification of citrullinated proteome based on these diagnostic ions. Here, we present a systematic approach to identify diagnostic IMs, internal ions (INTs), and NLs for citrullination from tandem mass (MS/MS) spectra. Diagnostic INTs mainly consisted of internal fragment ions for di- and tripeptides that contained two and three amino acids with at least one citrullinated arginine, respectively. A statistical logistic regression model was built for a confident assessment of citrullinated peptides that database searches identified (true positives) and prediction of citrullinated peptides that database searches failed to identify (false negatives) using the diagnostic IMs, INTs, and NLs. Applications of our model to complex global proteome data sets demonstrated the increased accuracy in the identification of citrullinated peptides, thereby enhancing the size and functional interpretation of citrullinated proteomes.
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Affiliation(s)
- Sunghyun Huh
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul 88026, Republic of Korea
| | - Min-Sik Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
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Chen H, Zhao H, Xiang L, Wu H, Liang Y, Huang XA, Zhang J. Aldol sensor-inspired fluorescent probes for measuring protein citrullination. Org Biomol Chem 2020; 18:5120-5124. [PMID: 32598414 DOI: 10.1039/c9ob02737h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein citrullination is an important posttranslational modification on an arginine residue. However, high quality fluorescent probes for measuring the citrullination level and capturing citrullinated proteins are quite limited. Inspired by the similarity between acid-promoted citrulline-labeling reaction and aldol reaction, here we present "turn-on" and "turn-off" fluorescent probes for measuring citrulline levels based on the scaffold of aldol sensors. Further application of the modified probe showed great potential to simultaneously monitor and capture citrullinated peptides.
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Affiliation(s)
- Huihong Chen
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
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38
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Brulet JW, Borne AL, Yuan K, Libby AH, Hsu KL. Liganding Functional Tyrosine Sites on Proteins Using Sulfur-Triazole Exchange Chemistry. J Am Chem Soc 2020; 142:8270-8280. [PMID: 32329615 DOI: 10.1021/jacs.0c00648] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tuning reactivity of sulfur electrophiles is key for advancing click chemistry and chemical probe discovery. To date, activation of the sulfur electrophile for protein modification has been ascribed principally to stabilization of a fluoride leaving group (LG) in covalent reactions of sulfonyl fluorides and arylfluorosulfates. We recently introduced sulfur-triazole exchange (SuTEx) chemistry to demonstrate the triazole as an effective LG for activating nucleophilic substitution reactions on tyrosine sites of proteins. Here, we probed tunability of SuTEx for fragment-based ligand discovery by modifying the adduct group (AG) and LG with functional groups of differing electron-donating and -withdrawing properties. We discovered the sulfur electrophile is highly sensitive to the position of modification (AG versus LG), which enabled both coarse and fine adjustments in solution and proteome activity. We applied these reactivity principles to identify a large fraction of tyrosine sites (∼30%) on proteins (∼44%) that can be liganded across >1500 probe-modified sites quantified by chemical proteomics. Our proteomic studies identified noncatalytic tyrosine and phosphotyrosine sites that can be liganded by SuTEx fragments with site specificity in lysates and live cells to disrupt protein function. Collectively, we describe SuTEx as a versatile covalent chemistry with broad applications for chemical proteomics and protein ligand discovery.
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Affiliation(s)
- Jeffrey W Brulet
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Adam L Borne
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Kun Yuan
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Adam H Libby
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,University of Virginia Cancer Center, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States.,University of Virginia Cancer Center, University of Virginia, Charlottesville, Virginia 22903, United States.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
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39
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Fert-Bober J, Darrah E, Andrade F. Insights into the study and origin of the citrullinome in rheumatoid arthritis. Immunol Rev 2019; 294:133-147. [PMID: 31876028 DOI: 10.1111/imr.12834] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/08/2019] [Indexed: 12/11/2022]
Abstract
The presence of autoantibodies and autoreactive T cells to citrullinated proteins and citrullinating enzymes in patients with rheumatoid arthritis (RA), together with the accumulation of citrullinated proteins in rheumatoid joints, provides substantial evidence that dysregulated citrullination is a hallmark feature of RA. However, understanding mechanisms that dysregulate citrullination in RA has important challenges. Citrullination is a normal process in immune and non-immune cells, which is likely activated by different conditions (eg, inflammation) with no pathogenic consequences. In a complex inflammatory environment such as the RA joint, unique strategies are therefore required to dissect specific mechanisms involved in the abnormal production of citrullinated proteins. Here, we will review current models of citrullination in RA and discuss critical components that, in our view, are relevant to understanding the accumulation of citrullinated proteins in the RA joint, collectively referred to as the RA citrullinome. In particular, we will focus on potential caveats in the study of citrullination in RA and will highlight methods to precisely detect citrullinated proteins in complex biological samples, which is a confirmatory approach to mechanistically link the RA citrullinome with unique pathogenic pathways in RA.
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Affiliation(s)
- Justyna Fert-Bober
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Erika Darrah
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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Abstract
Arylglyoxals are important synthons that have been used in the construction of a diverse spectrum of compounds. The use of multicomponent approaches in organic synthesis due to its environmentally friendly nature is a step forward towards sustainability. This review will offer the reader insightful perspectives on the use of arylglyoxals for the synthesis of various heterocyclic compounds like pyrroles, pyrazoles, furans, imidazoles, indoles, oxazoles, pyridines, quinazolines, pyrans, etc using multicomponent approach.
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Affiliation(s)
- Ankita Chaudhary
- Department of Chemistry, Maitreyi College, University of Delhi, New Delhi, India
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41
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Gill AD, Hickey BL, Wang S, Xue M, Zhong W, Hooley RJ. Sensing of citrulline modifications in histone peptides by deep cavitand hosts. Chem Commun (Camb) 2019; 55:13259-13262. [PMID: 31621759 DOI: 10.1039/c9cc07002h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Arrayed cavitand:fluorophore sensor complexes can selectively sense small citrulline modifications at arginine residues on post-translationally modified peptides. The sensor can differentiate between different numbers of citrulline modifications, and a simple two-fluorophore, 6-component array can effect cross-reactive discrimination between single modifications in aqueous solution.
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Affiliation(s)
- Adam D Gill
- Department of Biochemistry and Molecular Biology, University of California-Riverside, Riverside, CA 92521, USA.
| | - Briana L Hickey
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA
| | - Siwen Wang
- Environmental Toxicology Program, University of California-Riverside, Riverside, CA 92521, USA
| | - Min Xue
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA and Environmental Toxicology Program, University of California-Riverside, Riverside, CA 92521, USA
| | - Wenwan Zhong
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA and Environmental Toxicology Program, University of California-Riverside, Riverside, CA 92521, USA
| | - Richard J Hooley
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA and Department of Biochemistry and Molecular Biology, University of California-Riverside, Riverside, CA 92521, USA.
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Citrullination facilitates cross-reactivity of rheumatoid factor with non-IgG1 Fc epitopes in rheumatoid arthritis. Sci Rep 2019; 9:12068. [PMID: 31427662 PMCID: PMC6700074 DOI: 10.1038/s41598-019-48176-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/16/2019] [Indexed: 11/16/2022] Open
Abstract
Rheumatoid factor (RF) and anti-citrullinated protein antibodies (ACPAs) are the two most prevalent autoantibodies in rheumatoid arthritis (RA), and are thought to have distinct autoantigen targets. Whilst RF targets the Fc region of antibodies, ACPAs target a far broader spectrum of citrullinated peptides. Here we demonstrate significant sequence and structural homology between proposed RF target epitopes in IgG1 Fc and the ACPA target fibrinogen. Two of the three homologous sequences were susceptible to citrullination, and this modification, which occurs extensively in RA, permitted significant cross-reactivity of RF+ patient sera with fibrinogen in both western blots and ELISAs. Crucially, this reactivity was specific to RF as it was absent in RF− patient and healthy control sera, and could be inhibited by pre-incubation with IgG1 Fc. These studies establish fibrinogen as a common target for both RF and ACPAs, and suggest a new mechanism in RF-mediated autoimmune diseases wherein RF may act as a precursor from which the ACPA response evolves.
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43
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Fert-Bober J, Venkatraman V, Hunter CL, Liu R, Crowgey EL, Pandey R, Holewinski RJ, Stotland A, Berman BP, Van Eyk JE. Mapping Citrullinated Sites in Multiple Organs of Mice Using Hypercitrullinated Library. J Proteome Res 2019; 18:2270-2278. [PMID: 30990720 PMCID: PMC10363406 DOI: 10.1021/acs.jproteome.9b00118] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein citrullination (or deimination), an irreversible post-translational modification, has been implicated in several physiological and pathological processes, including gene expression regulation, apoptosis, rheumatoid arthritis, and Alzheimer's disease. Several research studies have been carried out on citrullination under many conditions. However, until now, challenges in sample preparation and data analysis have made it difficult to confidently identify a citrullinated protein and assign the citrullinated site. To overcome these limitations, we generated a mouse hyper-citrullinated spectral library and set up coordinates to confidently identify and validate citrullinated sites. Using this workflow, we detect a four-fold increase in citrullinated proteome coverage across six mouse organs compared with the current state-of-the art techniques. Our data reveal that the subcellular distribution of citrullinated proteins is tissue-type-dependent and that citrullinated targets are involved in fundamental physiological processes, including the metabolic process. These data represent the first report of a hyper-citrullinated library for the mouse and serve as a central resource for exploring the role of citrullination in this organism.
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Affiliation(s)
- Justyna Fert-Bober
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Vidya Venkatraman
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | | | - Ruining Liu
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Erin L. Crowgey
- Nemours Biomedical Research, Nemours - Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803, United States
| | - Rakhi Pandey
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Ronald J. Holewinski
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandr Stotland
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Benjamin P. Berman
- Bioinformatics and Computational Biology Research Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E. Van Eyk
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
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Kunieda K, Kawaguchi M, Ieda N, Nakagawa H. Development of a highly sensitive fluorescence probe for peptidyl arginine deiminase (PAD) activity. Bioorg Med Chem Lett 2019; 29:923-928. [PMID: 30773431 DOI: 10.1016/j.bmcl.2019.01.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/21/2019] [Accepted: 01/24/2019] [Indexed: 10/27/2022]
Abstract
Peptidyl arginine deiminases (PADs) catalyze the post-translational deimination of arginine residues to citrulline residues. Aberrant levels of PAD activity are associated with various diseases, such as rheumatoid arthritis, Alzheimer's disease, and multiple sclerosis, so there is a need for simple and convenient high-throughput screening systems to discover PAD inhibitors as candidate therapeutic agents. Here, we report a highly sensitive off/on-type fluorescence probe for PAD activity based on the donor-excited photoinduced electron transfer (d-PeT) mechanism, utilizing the specific cycloaddition reaction between the benzil group of the probe and the ureido group of the PAD product, citrulline, under acidic conditions. We synthesized and functionally evaluated a series of probes bearing substituents on the benzil phenyl group, and found that 4MEBz-FluME could successfully detect citrulline with higher sensitivity and broader dynamic range than our previously reported fluorescence probe, FGME. Moreover, we succeeded in establishing multiple assay systems for PAD subtypes activities, including PAD2 and PAD4, with 4MeBz-FluME thanks to its high sensitivity. We expect that our fluorescence probes will become a powerful tool for discovering PAD inhibitors of several subtypes. Thus, it should be suitable for high-throughput screening of chemical libraries for inhibitors of PADs.
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Affiliation(s)
- Kazuki Kunieda
- Graduate School of Pharmaceutical Science, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, Japan
| | - Mitsuyasu Kawaguchi
- Graduate School of Pharmaceutical Science, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, Japan
| | - Naoya Ieda
- Graduate School of Pharmaceutical Science, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, Japan
| | - Hidehiko Nakagawa
- Graduate School of Pharmaceutical Science, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, Japan.
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45
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Mondal S, Thompson PR. Protein Arginine Deiminases (PADs): Biochemistry and Chemical Biology of Protein Citrullination. Acc Chem Res 2019; 52:818-832. [PMID: 30844238 DOI: 10.1021/acs.accounts.9b00024] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proteins are well-known to undergo a variety of post-translational modifications (PTMs). One such PTM is citrullination, an arginine modification that is catalyzed by a group of hydrolases called protein arginine deiminases (PADs). Hundreds of proteins are known to be citrullinated and hypercitrullination is associated with autoimmune diseases including rheumatoid arthritis (RA), lupus, ulcerative colitis (UC), Alzheimer's disease, multiple sclerosis (MS), and certain cancers. In this Account, we summarize our efforts to understand the structure and mechanism of the PADs and to develop small molecule chemical probes of protein citrullination. PAD activity is highly regulated by calcium. Structural studies with PAD2 revealed that calcium-binding occurs in a stepwise fashion and induces a series of dramatic conformational changes to form a catalytically competent active site. These studies also identified the presence of a calcium-switch that controls the overall calcium-dependence and a gatekeeper residue that shields the active site in the absence of calcium. Using biochemical and site-directed mutagenesis studies, we identified the key residues (two aspartates, a cysteine, and a histidine) responsible for catalysis and proposed a general mechanism of citrullination. Although all PADs follow this mechanism, substrate binding to the thiolate or thiol form of the enzyme varies for different isozymes. Substrate-specificity studies revealed that PADs 1-4 prefer peptidyl-arginine over free arginine and certain citrullination sites on a peptide substrate. Using high-throughput screening and activity-based protein profiling (ABPP), we identified several reversible (streptomycin, minocycline, and chlorotetracycline) and irreversible (streptonigrin, NSC 95397) PAD-inhibitors. Screening of a DNA-encoded library and lead-optimization led to the development of GSK199 and GSK484 as highly potent PAD4-selective inhibitors. Furthermore, use of an electrophilic, cysteine-targeted haloacetamidine warhead to mimic the guanidinium group in arginine afforded several mechanism-based pan-PAD-inhibitors including Cl-amidine and BB-Cl-amidine. These compounds are highly efficacious in various animal models, including those mimicking RA, UC, and lupus. Structure-activity relationships identified numerous covalent PAD-inhibitors with different bioavailability, in vivo stability, and isozyme-selectivity (PAD1-selective: D-Cl-amidine; PAD2-selective: compounds 16-20; PAD3-selective: Cl4-amidine; and PAD4-selective: TDFA). Finally, this Account describes the development of PAD-targeted and citrulline-specific chemical probes. While PAD-targeted probes were utilized for identifying off-targets and developing high-throughput inhibitor screening platforms, citrulline-specific probes enabled the proteomic identification of novel diagnostic biomarkers of hypercitrullination-related autoimmune diseases.
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Affiliation(s)
- Santanu Mondal
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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46
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Tilvawala R, Thompson PR. Peptidyl arginine deiminases: detection and functional analysis of protein citrullination. Curr Opin Struct Biol 2019; 59:205-215. [PMID: 30833201 DOI: 10.1016/j.sbi.2019.01.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 11/29/2022]
Abstract
Citrullination is a post-translational modification of arginine that is catalyzed by the protein arginine deiminases (PADs). Abnormal citrullination is observed in many autoimmune diseases and cancers. Anti-citrullinated protein antibodies (ACPA) are hallmarks of RA and used as diagnostic markers for disease diagnosis. Even though citrullination is associated with many different pathologies, its role remains unclear due to the challenges associated with the detection of citrullinated proteins since the mass change is only 0.984 Da. Moreover, the functional effects of protein citrullination remain mostly unknown. Herein, we discuss a brief overview of PAD structure and function, recent advances in the detection of citrullinated proteins in complex biological systems and the functional consequences of protein citrullination.
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Affiliation(s)
- Ronak Tilvawala
- Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States
| | - Paul R Thompson
- Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States.
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O'Neil LJ, Kaplan MJ. Neutrophils in Rheumatoid Arthritis: Breaking Immune Tolerance and Fueling Disease. Trends Mol Med 2019; 25:215-227. [PMID: 30709614 DOI: 10.1016/j.molmed.2018.12.008] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/15/2022]
Abstract
Rheumatoid arthritis (RA), a common autoimmune disease, is characterized by a highly coordinated inflammatory response that involves innate and adaptive immunity. One of the hallmarks of RA is an immune response directed at citrullinated peptides that are specifically targeted by anticitrullinated protein antibodies (ACPAs). Among the various mechanisms by which neutrophils may promote immune dysregulation in RA, their ability to extrude neutrophil extracellular traps has recently been implicated in the development of ACPAs. In the synovium, neutrophils interact with resident fibroblast-like synoviocytes to endow them with antigen-presenting cell capabilities and an inflammatory phenotype. Further understanding how neutrophils modulate autoimmunity and tissue damage in RA may lead to the development of novel effective therapies.
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Affiliation(s)
- Liam J O'Neil
- Systemic Autoimmunity Branch, Intramural Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, Intramural Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
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Song S, Yu Y. Progression on Citrullination of Proteins in Gastrointestinal Cancers. Front Oncol 2019; 9:15. [PMID: 30740359 PMCID: PMC6357933 DOI: 10.3389/fonc.2019.00015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/04/2019] [Indexed: 01/02/2023] Open
Abstract
The citrullination modification (Cit) of proteins has received increasing attention in recent years. This kind of protein modification was first discovered in autoimmune diseases such as rheumatoid arthritis. The citrullination modification process is catalyzed by the peptidyl arginine deiminases (PADIs) family. A well-known citrullination of histone involves the key mechanism of neutrophil extracellular traps (NETs) of inflammation in the peripheral blood. Further studies revealed that citrullination modification of proteins also involves in carcinogenesis in human being. Citrullinated proteins disturbed the stability of proteins and caused DNA damages. There is increasing evidence that citrullinated proteins can be used as potential targets for cancer diagnosis or treatment. This review introduces the concept of citrullination modification of proteins, substrate proteins, examining methods and biological significances.
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Affiliation(s)
- Shuzheng Song
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai, China
| | - Yingyan Yu
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai, China
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Nemmara VV, Tilvawala R, Salinger AJ, Miller L, Nguyen SH, Weerapana E, Thompson PR. Citrullination Inactivates Nicotinamide- N-methyltransferase. ACS Chem Biol 2018; 13:2663-2672. [PMID: 30044909 DOI: 10.1021/acschembio.8b00578] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nicotinamide- N-methyltransferase (NNMT) catalyzes the irreversible methylation of nicotinamide (NAM) to form N-methyl nicotinamide using S-adenosyl methionine as a methyl donor. NNMT is implicated in several chronic disease conditions, including cancers, kidney disease, cardiovascular disease, and Parkinson's disease. Although phosphorylation of NNMT in gastric tumors is reported, the functional effects of this post-translational modification has not been investigated. We previously reported that citrullination of NNMT by Protein Arginine Deiminases abolished its methyltransferase activity. Herein, we investigate the mechanism of inactivation. Using tandem mass spectrometry, we identified three sites of citrullination in NNMT. With this information in hand, we used a combination of site-directed mutagenesis, kinetics, and circular dichoism experiments to demonstrate that citrullination of R132 leads to a structural perturbation that ultimately promotes NNMT inactivation.
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Affiliation(s)
- Venkatesh V. Nemmara
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ronak Tilvawala
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ari J. Salinger
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Lacey Miller
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Son Hong Nguyen
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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Grant J, Modica JA, Roll J, Perkovich P, Mrksich M. An Immobilized Enzyme Reactor for Spatiotemporal Control over Reaction Products. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800923. [PMID: 29971942 DOI: 10.1002/smll.201800923] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/07/2018] [Indexed: 05/19/2023]
Abstract
This paper describes a microfluidic chip wherein the position and order of two immobilized enzymes affects the type and quantity of reaction products in the flowing fluid. Assembly of the chip is based on a self-assembled monolayer presenting two orthogonal covalent capture ligands that immobilize their respective fusion enzyme. A thiol-tagged substrate is flowed over a region presenting the first enzyme-which generates a product that is efficiently transferred to the second enzyme-and the second enzyme's product binds to an adjacent thiol capture site on the chip. The amount of the three possible reaction products is quantified directly on the chip using self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry, revealing that the same microsystem can be spatiotemporally arranged to produce different products depending on the device design. This work allows for optimizing multistep biochemical transformations in favor of a desired product using a facile reaction and analytical format.
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Affiliation(s)
- Jennifer Grant
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Justin A Modica
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Juliet Roll
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Paul Perkovich
- Department of Chemical & Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
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