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Dai R, Yang M, Zhao J, Liu X, Zhou Y, Kang L, Zhang W, Lyu L, Yuan S, Liu Z. The extracellular β-glucosidase BGL2 has two variants with different molecular sizes and hydrolytic activities in the stipe or pilei of Coprinopsis cinerea. MICROBIOLOGY-SGM 2021; 167. [PMID: 34788214 DOI: 10.1099/mic.0.001100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two variants of extracellular β-glucosidase (BGL2) were purified from the stipe and pilei of Coprinopsis cinerea. In the stipe, BGL2 was a monomeric protein with an apparent molecular mass of approximately 220 kDa, representing a mature full-length peptide of BGL2. However, in the pilei, the apparent molecular mass of BGL2 was only approximately 120 kDa, consisting of the 60 kDa N-terminal fragment and 55 kDa C-terminal fragment. The hydrolytic activities of BGL2 purified from the pilei were higher than those of BGL2 purified from the stipe. No mRNA splice variants of bgl2 were detected. Therefore, the different variants of BGL2 in the stipe and pilei were not formed by differential RNA splicing. Furthermore, in vitro experiments showed that full-length BGL2 could be cleaved by endogenous proteases from pilei or commercial trypsin at a similar site to form an oligomeric protein consisting of the N-terminal fragment and C-terminal fragment similar to BGL2 from pilei. The hydrolytic activity of BGL2 increased after cleavage by those proteases in vitro. We conclude that the 120 kDa variant of BGL2 in the pilei of C. cinerea is formed by posttranslational proteolytic cleavage. Posttranslational proteolytic cleavage is an efficient way to regulate the activity of BGL2 to adapt to the needs of different physiological functions in the elongation stipe and expansion pilei of C. cinerea.
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Affiliation(s)
- Rujuan Dai
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, PR China
| | - Mingmei Yang
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, PR China
| | - Jing Zhao
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, PR China
| | - Xiao Liu
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, PR China
| | - Yajun Zhou
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, PR China
| | - Liqin Kang
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, PR China
| | - Wenming Zhang
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, PR China
| | - Linna Lyu
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, PR China
| | - Sheng Yuan
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, PR China
| | - Zhonghua Liu
- Jiangsu Key Laboratory for Microbes and Microbial Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, PR China
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52
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Pablos I, Machado Y, de Jesus HCR, Mohamud Y, Kappelhoff R, Lindskog C, Vlok M, Bell PA, Butler GS, Grin PM, Cao QT, Nguyen JP, Solis N, Abbina S, Rut W, Vederas JC, Szekely L, Szakos A, Drag M, Kizhakkedathu JN, Mossman K, Hirota JA, Jan E, Luo H, Banerjee A, Overall CM. Mechanistic insights into COVID-19 by global analysis of the SARS-CoV-2 3CL pro substrate degradome. Cell Rep 2021; 37:109892. [PMID: 34672947 PMCID: PMC8501228 DOI: 10.1016/j.celrep.2021.109892] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 12/27/2022] Open
Abstract
The main viral protease (3CLpro) is indispensable for SARS-CoV-2 replication. We delineate the human protein substrate landscape of 3CLpro by TAILS substrate-targeted N-terminomics. We identify more than 100 substrates in human lung and kidney cells supported by analyses of SARS-CoV-2-infected cells. Enzyme kinetics and molecular docking simulations of 3CLpro engaging substrates reveal how noncanonical cleavage sites, which diverge from SARS-CoV, guide substrate specificity. Cleaving the interactors of essential effector proteins, effectively stranding them from their binding partners, amplifies the consequences of proteolysis. We show that 3CLpro targets the Hippo pathway, including inactivation of MAP4K5, and key effectors of transcription, mRNA processing, and translation. We demonstrate that Spike glycoprotein directly binds galectin-8, with galectin-8 cleavage disengaging CALCOCO2/NDP52 to decouple antiviral-autophagy. Indeed, in post-mortem COVID-19 lung samples, NDP52 rarely colocalizes with galectin-8, unlike in healthy lungs. The 3CLpro substrate degradome establishes a foundational substrate atlas to accelerate exploration of SARS-CoV-2 pathology and drug design.
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Affiliation(s)
- Isabel Pablos
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yoan Machado
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Hugo C Ramos de Jesus
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yasir Mohamud
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Cecilia Lindskog
- Department of Immunology Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Marli Vlok
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Peter A Bell
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Georgina S Butler
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Peter M Grin
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Quynh T Cao
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Jenny P Nguyen
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Nestor Solis
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Srinivas Abbina
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; The School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Laszlo Szekely
- Department of Pathology and Cytology, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Attila Szakos
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Laboratories, 141 86 Stockholm, Sweden
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; The School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jeremy A Hirota
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada; Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Honglin Luo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Arinjay Banerjee
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Christopher M Overall
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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53
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Lee S, Ju S, Kim SJ, Choi JO, Kim K, Kim D, Jeon ES, Lee C. tipNrich: A Tip-Based N-Terminal Proteome Enrichment Method. Anal Chem 2021; 93:14088-14098. [PMID: 34615347 DOI: 10.1021/acs.analchem.1c01722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mass spectrometry-based analysis of protein post-translational modifications requires large amounts of sample, complicating the analysis of samples with limited amounts of proteins such as clinical biopsies. Here, we present a tip-based N-terminal analysis method, tipNrich. The entire procedure is processed in a single pipette tip to minimize sample loss, which is so highly optimized to analyze small amounts of proteins, even femtomole-scale of a single protein. With tipNrich, we investigated various single proteins purified from different organisms using a low-resolution mass spectrometer and identified several N-terminal peptides with different Nt-modifications such as ragged N-termini. Furthermore, we applied matrix-assisted laser desorption ionization time-of-flight mass spectrometry to our method for shortening the analysis time. Moreover, we showed that our method could be utilized in disease diagnosis as exemplified by the characterization of wild-type transthyretin amyloidosis patients compared to the healthy individuals based on N-terminome profiling. In summary, tipNrich will satisfy the need of identifying N-terminal peptides even with highly scarce amounts of proteins and of having faster processing time to check the quality of protein products or to characterize N-terminal proteoform-related diseases.
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Affiliation(s)
- Seonjeong Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Seok Jin Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 02792, Korea.,Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 02792, Korea
| | - Jin-Oh Choi
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 02792, Korea
| | - Kihyun Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 02792, Korea
| | - Darae Kim
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 02792, Korea
| | - Eun-Seok Jeon
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 02792, Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
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54
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Koudelka T, Winkels K, Kaleja P, Tholey A. Shedding light on both ends: An update on analytical approaches for N- and C-terminomics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119137. [PMID: 34626679 DOI: 10.1016/j.bbamcr.2021.119137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/27/2021] [Accepted: 09/06/2021] [Indexed: 02/04/2023]
Abstract
Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a limited substrate pool. This irreversible posttranslational modification modulates the fate and activity of many proteins, making proteolytic processing a master switch in the regulation of e.g., the immune system, apoptosis and cancer progression. N- and C-terminomics, the identification of protein termini, has become indispensable in elucidating protease substrates and therefore protease function. Further, terminomics has the potential to identify yet unknown proteoforms, e.g. formed by alternative splicing or the recently discovered alternative ORFs. Different strategies and workflows have been developed that achieve higher sensitivity, a greater depth of coverage or higher throughput. In this review, we summarize recent developments in both N- and C-terminomics and include the potential of top-down proteomics which inherently delivers information on both ends of analytes in a single analysis.
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Affiliation(s)
- Tomas Koudelka
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Konrad Winkels
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Patrick Kaleja
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
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55
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Abstract
The human skin is our outermost layer and serves as a protective barrier against external insults. Advances in next generation sequencing have enabled the discoveries of a rich and diverse community of microbes - bacteria, fungi and viruses that are residents of this surface. The genomes of these microbes also revealed the presence of many secretory enzymes. In particular, proteases which are hydrolytic enzymes capable of protein cleavage and degradation are of special interest in the skin environment which is enriched in proteins and lipids. In this minireview, we will focus on the roles of these skin-relevant microbial secreted proteases, both in terms of their widely studied roles as pathogenic agents in tissue invasion and host immune inactivation, and their recently discovered roles in inter-microbial interactions and modulation of virulence factors. From these studies, it has become apparent that while microbial proteases are capable of a wide range of functions, their expression is tightly regulated and highly responsive to the environments the microbes are in. With the introduction of new biochemical and bioinformatics tools to study protease functions, it will be important to understand the roles played by skin microbial secretory proteases in cutaneous health, especially the less studied commensal microbes with an emphasis on contextual relevance.
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56
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Abstract
All living organisms depend on tightly regulated cellular networks to control biological functions. Proteolysis is an important irreversible post-translational modification that regulates most, if not all, cellular processes. Proteases are a large family of enzymes that perform hydrolysis of protein substrates, leading to protein activation or degradation. The 473 known and 90 putative human proteases are divided into 5 main mechanistic groups: metalloproteases, serine proteases, cysteine proteases, threonine proteases, and aspartic acid proteases. Proteases are fundamental to all biological systems, and when dysregulated they profoundly influence disease progression. Inhibiting proteases has led to effective therapies for viral infections, cardiovascular disorders, and blood coagulation just to name a few. Between 5 and 10% of all pharmaceutical targets are proteases, despite limited knowledge about their biological roles. More than 50% of all human proteases have no known substrates. We present here a comprehensive list of all current known human proteases. We also present current and novel biochemical tools to characterize protease functions in vitro, in vivo, and ex vivo. These tools make it achievable to define both beneficial and detrimental activities of proteases in health and disease.
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Affiliation(s)
- Longxiang Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kimberly Main
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Henry Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
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57
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Egorikhina MN, Semenycheva LL, Chasova VO, Bronnikova II, Rubtsova YP, Zakharychev EA, Aleynik DY. Changes in the Molecular Characteristics of Bovine and Marine Collagen in the Presence of Proteolytic Enzymes as a Stage Used in Scaffold Formation. Mar Drugs 2021; 19:502. [PMID: 34564164 PMCID: PMC8470260 DOI: 10.3390/md19090502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/25/2021] [Accepted: 08/31/2021] [Indexed: 12/16/2022] Open
Abstract
Biopolymers, in particular collagen and fibrinogen, are the leading materials for use in tissue engineering. When developing technology for scaffold formation, it is important to understand the properties of the source materials as well as the mechanisms that determine the formation of the scaffold structures. Both factors influence the properties of scaffolds to a great extent. Our present work aimed to identify the features of the molecular characteristics of collagens of different species origin and the changes they undergo during the enzymatic hydrolysis used for the process of scaffold formation. For this study, we used the methods of gel-penetrating chromatography, dynamic light scattering, reading IR spectra, and scanning electron microscopy. It was found that cod collagen (CC) and bovine collagen (BC) have different initial molecular weight parameters, and that, during hydrolysis, the majority of either type of protein is hydrolyzed by the proteolytic enzymes within the first minute. The differently sourced collagen samples were also hydrolyzed with the formation of two low molecular fractions: Mw ~ 10 kDa and ~20 kDa. In the case of CC, the microstructure of the final scaffolds contained denser, closely spaced fibrillar areas, while the BC-sourced scaffolds had narrow, short fibrils composed of unbound fibers of hydrolyzed collagen in their structure.
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Affiliation(s)
- Marfa N. Egorikhina
- Federal State Budgetary Educational Institution of Higher Education, Privolzhsky Research Medical University, the Ministry of Health of the Russian Federation (FSBEI HE PRMU MOH), Minin and Pozharsky Square 10/1, 603950 Nizhny Novgorod, Russia; (I.I.B.); (Y.P.R.); (D.Y.A.)
| | - Ludmila L. Semenycheva
- Faculty of Chemistry, Lobachevsky State University of Nizhny Novgorod, pr. Gagarina 23, 603950 Nizhny Novgorod, Russia; (L.L.S.); (V.O.C.); (E.A.Z.)
| | - Victoria O. Chasova
- Faculty of Chemistry, Lobachevsky State University of Nizhny Novgorod, pr. Gagarina 23, 603950 Nizhny Novgorod, Russia; (L.L.S.); (V.O.C.); (E.A.Z.)
| | - Irina I. Bronnikova
- Federal State Budgetary Educational Institution of Higher Education, Privolzhsky Research Medical University, the Ministry of Health of the Russian Federation (FSBEI HE PRMU MOH), Minin and Pozharsky Square 10/1, 603950 Nizhny Novgorod, Russia; (I.I.B.); (Y.P.R.); (D.Y.A.)
| | - Yulia P. Rubtsova
- Federal State Budgetary Educational Institution of Higher Education, Privolzhsky Research Medical University, the Ministry of Health of the Russian Federation (FSBEI HE PRMU MOH), Minin and Pozharsky Square 10/1, 603950 Nizhny Novgorod, Russia; (I.I.B.); (Y.P.R.); (D.Y.A.)
| | - Evgeniy A. Zakharychev
- Faculty of Chemistry, Lobachevsky State University of Nizhny Novgorod, pr. Gagarina 23, 603950 Nizhny Novgorod, Russia; (L.L.S.); (V.O.C.); (E.A.Z.)
| | - Diana Ya. Aleynik
- Federal State Budgetary Educational Institution of Higher Education, Privolzhsky Research Medical University, the Ministry of Health of the Russian Federation (FSBEI HE PRMU MOH), Minin and Pozharsky Square 10/1, 603950 Nizhny Novgorod, Russia; (I.I.B.); (Y.P.R.); (D.Y.A.)
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58
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Khoruddin NA, Noorizhab MN, Teh LK, Mohd Yusof FZ, Salleh MZ. Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays. Sci Rep 2021; 11:16158. [PMID: 34373545 PMCID: PMC8352870 DOI: 10.1038/s41598-021-95618-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most common genetic variations for various complex human diseases, including cancers. Genome-wide association studies (GWAS) have identified numerous SNPs that increase cancer risks, such as breast cancer, colorectal cancer, and leukemia. These SNPs were cataloged for scientific use. However, GWAS are often conducted on certain populations in which the Orang Asli and Malays were not included. Therefore, we have developed a bioinformatic pipeline to mine the whole-genome sequence databases of the Orang Asli and Malays to determine the presence of pathogenic SNPs that might increase the risks of cancers among them. Five different in silico tools, SIFT, PROVEAN, Poly-Phen-2, Condel, and PANTHER, were used to predict and assess the functional impacts of the SNPs. Out of the 80 cancer-related nsSNPs from the GWAS dataset, 52 nsSNPs were found among the Orang Asli and Malays. They were further analyzed using the bioinformatic pipeline to identify the pathogenic variants. Three nsSNPs; rs1126809 (TYR), rs10936600 (LRRC34), and rs757978 (FARP2), were found as the most damaging cancer pathogenic variants. These mutations alter the protein interface and change the allosteric sites of the respective proteins. As TYR, LRRC34, and FARP2 genes play important roles in numerous cellular processes such as cell proliferation, differentiation, growth, and cell survival; therefore, any impairment on the protein function could be involved in the development of cancer. rs1126809, rs10936600, and rs757978 are the important pathogenic variants that increase the risks of cancers among the Orang Asli and Malays. The roles and impacts of these variants in cancers will require further investigations using in vitro cancer models.
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Affiliation(s)
- Nurul Ain Khoruddin
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam Campus, Selangor, Malaysia
| | - Mohd NurFakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
| | - Farida Zuraina Mohd Yusof
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam Campus, Selangor, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia.
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia.
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59
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Kaminska M, Bruyat P, Malgorn C, Doladilhe M, Cassar‐Lajeunesse E, Fruchart Gaillard C, De Souza M, Beau F, Thai R, Correia I, Galat A, Georgiadis D, Lequin O, Dive V, Bregant S, Devel L. Ligand‐Directed Modification of Active Matrix Metalloproteases: Activity‐based Probes with no Photolabile Group. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Monika Kaminska
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Pierrick Bruyat
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Carole Malgorn
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Marion Doladilhe
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Evelyne Cassar‐Lajeunesse
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Carole Fruchart Gaillard
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Mélissa De Souza
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Fabrice Beau
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Robert Thai
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Isabelle Correia
- CNRS, Laboratoire des Biomolécules, LBM Sorbonne Université Ecole Normale Supérieure PSL University 75005 Paris France
| | - Andrzej Galat
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Dimitris Georgiadis
- Department of Chemistry Laboratory of Organic Chemistry University of Athens Panepistimiopolis Zografou 15771 Athens Greece
| | - Olivier Lequin
- CNRS, Laboratoire des Biomolécules, LBM Sorbonne Université Ecole Normale Supérieure PSL University 75005 Paris France
| | - Vincent Dive
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Sarah Bregant
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
| | - Laurent Devel
- Université Paris-Saclay CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS 91191 Gif-sur-Yvette France
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Mintoo M, Chakravarty A, Tilvawala R. N-Terminomics Strategies for Protease Substrates Profiling. Molecules 2021; 26:molecules26154699. [PMID: 34361849 PMCID: PMC8348681 DOI: 10.3390/molecules26154699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 01/02/2023] Open
Abstract
Proteases play a central role in various biochemical pathways catalyzing and regulating key biological events. Proteases catalyze an irreversible post-translational modification called proteolysis by hydrolyzing peptide bonds in proteins. Given the destructive potential of proteolysis, protease activity is tightly regulated. Dysregulation of protease activity has been reported in numerous disease conditions, including cancers, neurodegenerative diseases, inflammatory conditions, cardiovascular diseases, and viral infections. The proteolytic profile of a cell, tissue, or organ is governed by protease activation, activity, and substrate specificity. Thus, identifying protease substrates and proteolytic events under physiological conditions can provide crucial information about how the change in protease regulation can alter the cellular proteolytic landscape. In recent years, mass spectrometry-based techniques called N-terminomics have become instrumental in identifying protease substrates from complex biological mixtures. N-terminomics employs the labeling and enrichment of native and neo-N-termini peptides, generated upon proteolysis followed by mass spectrometry analysis allowing protease substrate profiling directly from biological samples. In this review, we provide a brief overview of N-terminomics techniques, focusing on their strengths, weaknesses, limitations, and providing specific examples where they were successfully employed to identify protease substrates in vivo and under physiological conditions. In addition, we explore the current trends in the protease field and the potential for future developments.
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An Updated review on production of food derived bioactive peptides; focus on the psychrotrophic bacterial proteases. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Kaminska M, Bruyat P, Malgorn C, Doladilhe M, Cassar-Lajeunesse E, Fruchart Gaillard C, De Souza M, Beau F, Thai R, Correia I, Galat A, Georgiadis D, Lequin O, Dive V, Bregant S, Devel L. Ligand-Directed Modification of Active Matrix Metalloproteases: Activity-based Probes with no Photolabile Group. Angew Chem Int Ed Engl 2021; 60:18272-18279. [PMID: 34096148 DOI: 10.1002/anie.202106117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Indexed: 12/12/2022]
Abstract
Activity-based probes enable discrimination between the active enzyme and its inactive or inactivated counterparts. Since metalloproteases catalysis is non-covalent, activity-based probes targeting them have been systematically developed by decorating reversible inhibitors with photo-crosslinkers. By exploiting two types of ligand-guided chemistry, we identified novel activity-based probes capable of covalently modifying the active site of matrix metalloproteases (MMPs) without any external trigger. The ability of these probes to label recombinant MMPs was validated in vitro and the identity of the main labelling sites within their S3 ' region unambiguously assigned. We also demonstrated that our affinity probes can react with rhMMP12 at nanogram scale (that is, at 0.07 % (w/w)) in complex proteomes. Finally, this ligand-directed chemistry was successfully applied to label active MMP-12 secreted by eukaryote cells. We believe that this approach could be transferred more widely to many other metalloproteases, thus contributing to tackle their unresolved proteomic profiling in vivo.
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Affiliation(s)
- Monika Kaminska
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Pierrick Bruyat
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Carole Malgorn
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Marion Doladilhe
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Evelyne Cassar-Lajeunesse
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Carole Fruchart Gaillard
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Mélissa De Souza
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Fabrice Beau
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Robert Thai
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Isabelle Correia
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, Ecole Normale Supérieure, PSL University, 75005, Paris, France
| | - Andrzej Galat
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Dimitris Georgiadis
- Department of Chemistry, Laboratory of Organic Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Olivier Lequin
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, Ecole Normale Supérieure, PSL University, 75005, Paris, France
| | - Vincent Dive
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Sarah Bregant
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Laurent Devel
- Université Paris-Saclay, CEA, INRAE, Medicaments et Technologies pour la Sante (MTS), SIMoS, 91191, Gif-sur-Yvette, France
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Lai X, Tang J, ElSayed MEH. Recent advances in proteolytic stability for peptide, protein, and antibody drug discovery. Expert Opin Drug Discov 2021; 16:1467-1482. [PMID: 34187273 DOI: 10.1080/17460441.2021.1942837] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: To discover and develop a peptide, protein, or antibody into a drug requires overcoming multiple challenges to obtain desired properties. Proteolytic stability is one of the challenges and deserves a focused investigation.Areas covered: This review concentrates on improving proteolytic stability by engineering the amino acids around the cleavage sites of a liable peptide, protein, or antibody. Peptidases are discussed on three levels including all peptidases in databases, mixtures based on organ and tissue types, and individual peptidases. The technique to identify cleavage sites is spotlighted on mass spectrometry-based approaches such as MALDI-TOF and LC-MS. For sequence engineering, the replacements that have been commonly applied with a higher chance of success are highlighted at the beginning, while the rarely used and more complicated replacements are discussed later. Although a one-size-fits-all approach does not exist to apply to different projects, this review provides a 3-step strategy for effectively and efficiently conducting the proteolytic stability experiments to achieve the eventual goal of improving the stability by engineering the molecule itself.Expert opinion: Improving the proteolytic stability is a spiraling up process sequenced by testing and engineering. There are many ways to engineer amino acids, but the choice must consider the cost and properties affected by the changes of the amino acids.
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Affiliation(s)
- Xianyin Lai
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Jason Tang
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Mohamed E H ElSayed
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
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64
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Tying up loose ends: the N-degron and C-degron pathways of protein degradation. Biochem Soc Trans 2021; 48:1557-1567. [PMID: 32627813 PMCID: PMC7458402 DOI: 10.1042/bst20191094] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022]
Abstract
Selective protein degradation by the ubiquitin-proteasome system (UPS) is thought to be governed primarily by the recognition of specific motifs — degrons — present in substrate proteins. The ends of proteins — the N- and C-termini – have unique properties, and an important subset of protein–protein interactions involve the recognition of free termini. The first degrons to be discovered were located at the extreme N-terminus of proteins, a finding which initiated the study of the N-degron (formerly N-end rule) pathways, but only in the last few years has it emerged that a diverse set of C-degron pathways target analogous degron motifs located at the extreme C-terminus of proteins. In this minireview we summarise the N-degron and C-degron pathways currently known to operate in human cells, focussing primarily on those that have been discovered in recent years. In each case we describe the cellular machinery responsible for terminal degron recognition, and then consider some of the functional roles of terminal degron pathways. Altogether, a broad spectrum of E3 ubiquitin ligases mediate the recognition of a diverse array of terminal degron motifs; these degradative pathways have the potential to influence a wide variety of cellular functions.
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65
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Juurikka K, Dufour A, Pehkonen K, Mainoli B, Campioni Rodrigues P, Solis N, Klein T, Nyberg P, Overall CM, Salo T, Åström P. MMP8 increases tongue carcinoma cell-cell adhesion and diminishes migration via cleavage of anti-adhesive FXYD5. Oncogenesis 2021; 10:44. [PMID: 34059618 PMCID: PMC8167110 DOI: 10.1038/s41389-021-00334-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/03/2021] [Accepted: 05/14/2021] [Indexed: 12/28/2022] Open
Abstract
Matrix metalloproteinases (MMPs) modify bioactive factors via selective processing or degradation resulting in tumour-promoting or tumour-suppressive effects, such as those by MMP8 in various cancers. We mapped the substrates of MMP8 to elucidate its previously shown tumour-protective role in oral tongue squamous cell carcinoma (OTSCC). MMP8 overexpressing (+) HSC-3 cells, previously demonstrated to have reduced migration and invasion, showed enhanced cell-cell adhesion. By analysing the secretomes of MMP8 + and control cells with terminal amine isotopic labelling of substrates (TAILS) coupled with liquid chromatography and tandem mass spectrometry (LC-MS/MS), we identified 36 potential substrates of MMP8, including FXYD domain-containing ion transport regulator 5 (FXYD5). An anti-adhesive glycoprotein FXYD5 has been previously shown to predict poor survival in OTSCC. Cleavage of FXYD5 by MMP8 was confirmed using recombinant proteins. Furthermore, we detected a loss of FXYD5 levels on cell membrane of MMP8 + cells, which was rescued by inhibition of the proteolytic activity of MMP8. Silencing (si) FXYD5 increased the cell-cell adhesion of control but not that of MMP8 + cells. siFXYD5 diminished the viability and motility of HSC-3 cells independent of MMP8 and similar effects were seen in another tongue cancer cell line, SCC-25. FXYD5 is a novel substrate of MMP8 and reducing FXYD5 levels either with siRNA or cleavage by MMP8 increases cell adhesion leading to reduced motility. FXYD5 being a known prognostic factor in OTSCC, our findings strengthen its potential as a therapeutic target.
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Affiliation(s)
- K Juurikka
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - A Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada.,Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - K Pehkonen
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - B Mainoli
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - P Campioni Rodrigues
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - N Solis
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - T Klein
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - P Nyberg
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Biobank Borealis of Northern Finland, Oulu University Hospital, Oulu, Finland
| | - C M Overall
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - T Salo
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Oral and Maxillofacial Diseases, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital, Helsinki, Finland.,Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland
| | - P Åström
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland. .,Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada. .,Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland.
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66
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Fahrner M, Kook L, Fröhlich K, Biniossek ML, Schilling O. A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines. Proteomes 2021; 9:proteomes9020026. [PMID: 34070654 PMCID: PMC8162549 DOI: 10.3390/proteomes9020026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 01/07/2023] Open
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become the most commonly used technique in explorative proteomic research. A variety of open-source tools for peptide-spectrum matching have become available. Most analyses of explorative MS data are performed using conventional settings, such as fully specific enzymatic constraints. Here we evaluated the impact of the fragment mass tolerance in combination with the enzymatic constraints on the performance of three search engines. Three open-source search engines (Myrimatch, X! Tandem, and MSGF+) were evaluated concerning the suitability in semi- and unspecific searches as well as the importance of accurate fragment mass spectra in non-specific peptide searches. We then performed a semispecific reanalysis of the published NCI-60 deep proteome data applying the most suited parameters. Semi- and unspecific LC-MS/MS data analyses particularly benefit from accurate fragment mass spectra while this effect is less pronounced for conventional, fully specific peptide-spectrum matching. Search speed differed notably between the three search engines for semi- and non-specific peptide-spectrum matching. Semispecific reanalysis of NCI-60 proteome data revealed hundreds of previously undescribed N-terminal peptides, including cases of proteolytic processing or likely alternative translation start sites, some of which were ubiquitously present in all cell lines of the reanalyzed panel. Highly accurate MS2 fragment data in combination with modern open-source search algorithms enable the confident identification of semispecific peptides from large proteomic datasets. The identification of previously undescribed N-terminal peptides in published studies highlights the potential of future reanalysis and data mining in proteomic datasets.
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Affiliation(s)
- Matthias Fahrner
- Institute for Surgical Pathology, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (M.F.); (K.F.)
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Lucas Kook
- Epidemiology, Biostatistics & Prevention Institute, University of Zurich, 8001 Zurich, Switzerland;
- Institute for Data Analysis and Process Design, Zurich University of Applied Sciences, 8401 Winterthur, Switzerland
| | - Klemens Fröhlich
- Institute for Surgical Pathology, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (M.F.); (K.F.)
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Martin L. Biniossek
- Institute for Molecular Medicine and Cell Research, University of Freiburg, 79104 Freiburg, Germany;
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (M.F.); (K.F.)
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
- Correspondence: ; Tel.: +49-761-270-80610
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67
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Villalba-Rodríguez AM, Martínez-González S, Sosa-Hernández JE, Parra-Saldívar R, Bilal M, Iqbal HMN. Nanoclay/Polymer-Based Hydrogels and Enzyme-Loaded Nanostructures for Wound Healing Applications. Gels 2021; 7:gels7020059. [PMID: 34068868 PMCID: PMC8162325 DOI: 10.3390/gels7020059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Multi-polymeric nanocomposite hydrogels with multi-functional characteristics have been engineered with high interest around the globe. The ease in fine tunability with maintained compliance makes an array of nanocomposite biomaterials outstanding candidates for the biomedical sector of the modern world. In this context, the present work intends to tackle the necessity of alternatives for the treatment of diabetic foot ulcers through the formulation of nanoclay and/or polymer-based nanocomposite hydrogels. Laponite RD, a synthetic 2-D nanoclay that becomes inert when in a physiological environment, while mixed with water, becomes a clear gel with interesting shear-thinning properties. Adding Laponite RD to chitosan or gelatin allows for the modification of the mechanical properties of such materials. The setup explored in this research allows for a promising polymeric matrix that can potentially be loaded with active compounds for antibacterial support in foot ulcers, as well as enzymes for wound debridement.
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Affiliation(s)
- Angel M. Villalba-Rodríguez
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; (A.M.V.-R.); (S.M.-G.); (J.E.S.-H.); (R.P.-S.)
| | - Sara Martínez-González
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; (A.M.V.-R.); (S.M.-G.); (J.E.S.-H.); (R.P.-S.)
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; (A.M.V.-R.); (S.M.-G.); (J.E.S.-H.); (R.P.-S.)
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; (A.M.V.-R.); (S.M.-G.); (J.E.S.-H.); (R.P.-S.)
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
- Correspondence: (M.B.); (H.M.N.I.)
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; (A.M.V.-R.); (S.M.-G.); (J.E.S.-H.); (R.P.-S.)
- Correspondence: (M.B.); (H.M.N.I.)
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Abstract
The Borrelia spp. are tick-borne pathogenic spirochetes that include the agents of Lyme disease and relapsing fever. As part of their life cycle, the spirochetes traffic between the tick vector and the vertebrate host, which requires significant physiological changes and remodeling of their outer membranes and proteome. This crucial proteome resculpting is carried out by a diverse set of proteases, adaptor proteins, and related chaperones. Despite its small genome, Borrelia burgdorferi has dedicated a large percentage of its genome to proteolysis, including a full complement of ATP-dependent proteases. Energy-driven proteolysis appears to be an important physiological feature of this dual-life-cycle bacterium. The proteolytic arsenal of Borrelia is strategically deployed for disposal of proteins no longer required as they move from one stage to another or are transferred from one host to another. Likewise, the Borrelia spp. are systemic organisms that need to break down and move through host tissues and barriers, and so their unique proteolytic resources, both endogenous and borrowed, make movement more feasible. Both the Lyme disease and relapsing fever Borrelia spp. bind plasminogen as well as numerous components of the mammalian plasminogen-activating system. This recruitment capacity endows the spirochetes with a borrowed proteolytic competency that can lead to increased invasiveness.
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69
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Cytosolic DNA sensing by cGAS: regulation, function, and human diseases. Signal Transduct Target Ther 2021; 6:170. [PMID: 33927185 PMCID: PMC8085147 DOI: 10.1038/s41392-021-00554-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/17/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Sensing invasive cytosolic DNA is an integral component of innate immunity. cGAS was identified in 2013 as the major cytosolic DNA sensor that binds dsDNA to catalyze the synthesis of a special asymmetric cyclic-dinucleotide, 2′3′-cGAMP, as the secondary messenger to bind and activate STING for subsequent production of type I interferons and other immune-modulatory genes. Hyperactivation of cGAS signaling contributes to autoimmune diseases but serves as an adjuvant for anticancer immune therapy. On the other hand, inactivation of cGAS signaling causes deficiency to sense and clear the viral and bacterial infection and creates a tumor-prone immune microenvironment to facilitate tumor evasion of immune surveillance. Thus, cGAS activation is tightly controlled. In this review, we summarize up-to-date multilayers of regulatory mechanisms governing cGAS activation, including cGAS pre- and post-translational regulations, cGAS-binding proteins, and additional cGAS regulators such as ions and small molecules. We will also reveal the pathophysiological function of cGAS and its product cGAMP in human diseases. We hope to provide an up-to-date review for recent research advances of cGAS biology and cGAS-targeted therapies for human diseases.
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70
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Chen P, Wang H, Wu H, Zou P, Wang C, Liu X, Pan Y, Liu Y, Liang G. Intracellular Synthesis of Hybrid Gallium-68 Nanoparticle Enhances MicroPET Tumor Imaging. Anal Chem 2021; 93:6329-6334. [PMID: 33848118 DOI: 10.1021/acs.analchem.1c00747] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Positron-emission tomography (PET) imaging enables cancer diagnosis at an early stage and to determine its pathological degree. However, tumor uptake efficiency of traditional PET radiotracers is usually low. Herein, we rationally designed a precursor CBT-NODA, the cold analogue CBT-NODA-Ga, and its corresponding radiotracer CBT-NODA-68Ga. Using these three compounds, we verified that coinjection of CBT-NODA-68Ga with CBT-NODA or CBT-NODA-Ga could lead to the synthesis of hybrid gallium-68 nanoparticles in furin-overexpressing cancer cells and enhance microPET tumor imaging in mice. In vivo experiments showed that coinjection of CBT-NODA-68Ga with CBT-NODA-Ga had the most prolonged retention of the radiotracer in blood, the highest radioactivity in tumor regions, and the most enhanced microPET tumor imaging in mice. We anticipate that, by combining the coinjection strategy with our CBT-Cys click condensation reaction, more radiotracers are developed for microPET imaging of more tumors in clinical settings in the future.
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Affiliation(s)
- Peiyao Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.,Hefei National Laboratory of Physical Sciences at Microscale, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hongyong Wang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Hao Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Pei Zou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Chenchen Wang
- Hefei National Laboratory of Physical Sciences at Microscale, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaoyang Liu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yue Pan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yaling Liu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Gaolin Liang
- Hefei National Laboratory of Physical Sciences at Microscale, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.,State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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71
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Azambuja FD, Moons J, Parac-Vogt TN. The Dawn of Metal-Oxo Clusters as Artificial Proteases: From Discovery to the Present and Beyond. Acc Chem Res 2021; 54:1673-1684. [PMID: 33600141 DOI: 10.1021/acs.accounts.0c00666] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The selective cleavage of peptide bonds in proteins is of paramount importance in many areas of the biological and medical sciences, playing a key role in protein structure/function/folding analysis, protein engineering, and targeted proteolytic drug design. Current applications that depend on selective protein hydrolysis largely rely on costly proteases such as trypsin, which are sensitive to the pH, ionic strength, and temperature conditions. Moreover, >95% of peptides deposited in databases are generated from trypsin digests, restricting the information within the analyzed proteomes. On the other hand, harsh and toxic chemical reagents such as BrCN are very active but cause permanent modifications of certain amino acid residues. Consequently, transition-metal complexes have emerged as smooth and selective artificial proteases owing to their ability to provide larger fragments and complementary structural information. In the past decade, our group has discovered the unique protease activity of diverse metal-oxo clusters (MOC) and pioneered a distinctive approach to the development of selective artificial proteases. In contrast to classical coordination complexes which often depend on amino acid side chains to control the regioselectivity, the selectivity profile of MOCs is determined by a complex combination of structural factors, such as the protein surface charge, metal coordination to specific side chains, and hydrogen bonding between the protein surface and the MOC scaffold.In this Account, we present a critical overview of our detailed kinetic, spectroscopic, and crystallographic studies in MOC-assisted peptide bond hydrolysis, from its origins to the current rational and detailed mechanistic understanding. To this end, reactivity trends related to the structure and properties of MOCs based on the hydrolysis of small model peptides and key structural aspects governing the selectivity of protein hydrolysis are presented. Finally, our endeavors in seeking the next generation of heterogeneous MOC-based proteases are briefly discussed by embedding MOCs in metal-organic frameworks or using them as discrete nanoclusters in the development of artificial protease-like materials (i.e., nanozymes). The deep and comprehensive understanding sought experimentally and theoretically over the years in aqueous systems with intrinsic polar and charged substrates provides a unique view of the reactivity between inorganic moieties and biomolecules, thereby broadly impacting several different fields (e.g., catalysis in biochemistry, inorganic chemistry, and organic chemistry).
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Affiliation(s)
| | - Jens Moons
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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72
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Demir F, Kizhakkedathu JN, Rinschen MM, Huesgen PF. MANTI: Automated Annotation of Protein N-Termini for Rapid Interpretation of N-Terminome Data Sets. Anal Chem 2021; 93:5596-5605. [PMID: 33729755 PMCID: PMC8027985 DOI: 10.1021/acs.analchem.1c00310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/04/2021] [Indexed: 12/23/2022]
Abstract
Site-specific proteolytic processing is an important, irreversible post-translational protein modification with implications in many diseases. Enrichment of protein N-terminal peptides followed by mass spectrometry-based identification and quantification enables proteome-wide characterization of proteolytic processes and protease substrates but is challenged by the lack of specific annotation tools. A common problem is, for example, ambiguous matches of identified peptides to multiple protein entries in the databases used for identification. We developed MaxQuant Advanced N-termini Interpreter (MANTI), a standalone Perl software with an optional graphical user interface that validates and annotates N-terminal peptides identified by database searches with the popular MaxQuant software package by integrating information from multiple data sources. MANTI utilizes diverse annotation information in a multistep decision process to assign a conservative preferred protein entry for each N-terminal peptide, enabling automated classification according to the likely origin and determines significant changes in N-terminal peptide abundance. Auxiliary R scripts included in the software package summarize and visualize key aspects of the data. To showcase the utility of MANTI, we generated two large-scale TAILS N-terminome data sets from two different animal models of chemically and genetically induced kidney disease, puromycin adenonucleoside-treated rats (PAN), and heterozygous Wilms Tumor protein 1 mice (WT1). MANTI enabled rapid validation and autonomous annotation of >10 000 identified terminal peptides, revealing novel proteolytic proteoforms in 905 and 644 proteins, respectively. Quantitative analysis indicated that proteolytic activities with similar sequence specificity are involved in the pathogenesis of kidney injury and proteinuria in both models, whereas coagulation processes and complement activation were specifically induced after chemical injury.
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Affiliation(s)
- Fatih Demir
- Department
of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark
- Central
Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum
Jülich GmbH, 52425 Jülich, Germany
| | - Jayachandran N. Kizhakkedathu
- Centre
for Blood Research, Department of Pathology & Laboratory Medicine,
School of Biomedical Engineering, Department of Chemistry, University of British Columbia, 251-2222 Health Sciences Mall, Vancouver V6T 1Z3, British Columbia, Canada
| | - Markus M. Rinschen
- Department
of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark
- III.
Department of Medicine, University Medical
Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Pitter F. Huesgen
- Central
Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum
Jülich GmbH, 52425 Jülich, Germany
- Cologne
Excellence Cluster Cellular Stress Response in Aging-Associated Diseases
(CECAD), Medical Faculty and University Hospital, Institute of Biochemistry,
Department of Chemistry, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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73
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Tau Is Truncated in Five Regions of the Normal Adult Human Brain. Int J Mol Sci 2021; 22:ijms22073521. [PMID: 33805376 PMCID: PMC8036332 DOI: 10.3390/ijms22073521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/01/2023] Open
Abstract
The truncation of Tau is thought to be important in promoting aggregation, with this feature characterising the pathology of dementias such as Alzheimer disease. Antibodies to the C-terminal and N-terminal regions of Tau were employed to examine Tau cleavage in five human brain regions: the entorhinal cortex, prefrontal cortex, motor cortex, hippocampus, and cerebellum. These were obtained from normal subjects ranging in age from 18 to 104 years. Tau fragments of approximately 40 kDa and 45 kDa with an intact N-terminus retained were found in soluble and insoluble brain fractions. In addition, smaller C-terminal Tau fragments ranging in mass from 17 kDa to 25 kDa were also detected. These findings are consistent with significant Tau cleavage taking place in brain regions from 18 years onwards. It appears that site-specific cleavage of Tau is widespread in the normal human brain, and that large Tau fragments that contain the N-terminus, as well as shorter C-terminal Tau fragments, are present in brain cells across the age range.
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74
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Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nat Commun 2021; 12:1693. [PMID: 33727531 PMCID: PMC7966775 DOI: 10.1038/s41467-021-21754-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Proteases are among the largest protein families and critical regulators of biochemical processes like apoptosis and blood coagulation. Knowledge of proteases has been expanded by the development of proteomic approaches, however, technology for multiplexed screening of proteases within native environments is currently lacking behind. Here we introduce a simple method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter, their analysis in a mass spectrometer and a custom data analysis pipeline. The method is significantly faster, cheaper, technically less demanding, easy to multiplex and produces accurate protease fingerprints. Using the blood cascade proteases as a case study, we obtain protease substrate profiles that can be used to map specificity, cleavage entropy and allosteric effects and to design protease probes. The data further show that protease substrate predictions enable the selection of potential physiological substrates for targeted validation in biochemical assays. Characterizing proteases in their native environment is still challenging. Here, the authors develop a proteomics workflow for analyzing protease-specific peptides from cell lysates in 96-well format, providing mechanistic insights into blood proteases and enabling the prediction of protease substrates.
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75
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Uzozie AC, Ergin EK, Rolf N, Tsui J, Lorentzian A, Weng SSH, Nierves L, Smith TG, Lim CJ, Maxwell CA, Reid GSD, Lange PF. PDX models reflect the proteome landscape of pediatric acute lymphoblastic leukemia but divert in select pathways. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:96. [PMID: 33722259 PMCID: PMC7958471 DOI: 10.1186/s13046-021-01835-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/10/2021] [Indexed: 12/22/2022]
Abstract
Background Murine xenografts of pediatric leukemia accurately recapitulate genomic aberrations. How this translates to the functional capacity of cells remains unclear. Here, we studied global protein abundance, phosphorylation, and protein maturation by proteolytic processing in 11 pediatric B- and T- cell ALL patients and 19 corresponding xenografts. Methods Xenograft models were generated for each pediatric patient leukemia. Mass spectrometry-based methods were used to investigate global protein abundance, protein phosphorylation, and limited proteolysis in paired patient and xenografted pediatric acute B- and T- cell lymphocytic leukemia, as well as in pediatric leukemia cell lines. Targeted next-generation sequencing was utilized to examine genetic abnormalities in patients and in corresponding xenografts. Bioinformatic and statistical analysis were performed to identify functional mechanisms associated with proteins and protein post-translational modifications. Results Overall, we found xenograft proteomes to be most equivalent with their patient of origin. Protein level differences that stratified disease subtypes at diagnostic and relapse stages were largely recapitulated in xenografts. As expected, PDXs lacked multiple human leukocyte antigens and complement proteins. We found increased expression of cell cycle proteins indicating a high proliferative capacity of xenografted cells. Structural genomic changes and mutations were reflected at the protein level in patients. In contrast, the post-translational modification landscape was shaped by leukemia type and host and only to a limited degree by the patient of origin. Of 201 known pediatric oncogenic drivers and drug-targetable proteins, the KMT2 protein family showed consistently high variability between patient and corresponding xenografts. Comprehensive N terminomics revealed deregulated proteolytic processing in leukemic cells, in particular from caspase-driven cleavages found in patient cells. Conclusion Genomic and host factors shape protein and post-translational modification landscapes differently. This study highlights select areas of diverging biology while confirming murine patient-derived xenografts as a generally accurate model system. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01835-8.
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Affiliation(s)
- Anuli C Uzozie
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Enes K Ergin
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Nina Rolf
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Janice Tsui
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Amanda Lorentzian
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Samuel S H Weng
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Lorenz Nierves
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Theodore G Smith
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - C James Lim
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Christopher A Maxwell
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Gregor S D Reid
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Philipp F Lange
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada. .,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada. .,Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada.
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76
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Prejanò M, Vidossich P, Russo N, De Vivo M, Marino T. Insights into the Catalytic Mechanism of Domains CD1 and CD2 in Histone Deacetylase 6 from Quantum Calculations. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Pietro Vidossich
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036 Arcavacata di Rende, Cosenza, Italy
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77
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Quantitative profiling of protease specificity. PLoS Comput Biol 2021; 17:e1008101. [PMID: 33617527 PMCID: PMC7932537 DOI: 10.1371/journal.pcbi.1008101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/04/2021] [Accepted: 01/28/2021] [Indexed: 12/30/2022] Open
Abstract
Proteases are an important class of enzymes, whose activity is central to many physiologic and pathologic processes. Detailed knowledge of protease specificity is key to understanding their function. Although many methods have been developed to profile specificities of proteases, few have the diversity and quantitative grasp necessary to fully define specificity of a protease, both in terms of substrate numbers and their catalytic efficiencies. We have developed a concept of “selectome”; the set of substrate amino acid sequences that uniquely represent the specificity of a protease. We applied it to two closely related members of the Matrixin family–MMP-2 and MMP-9 by using substrate phage display coupled with Next Generation Sequencing and information theory-based data analysis. We have also derived a quantitative measure of substrate specificity, which accounts for both the number of substrates and their relative catalytic efficiencies. Using these advances greatly facilitates elucidation of substrate selectivity between closely related members of a protease family. The study also provides insight into the degree to which the catalytic cleft defines substrate recognition, thus providing basis for overcoming two of the major challenges in the field of proteolysis: 1) development of highly selective activity probes for studying proteases with overlapping specificities, and 2) distinguishing targeted proteolysis from bystander proteolytic events. Proteases and proteolysis are intimately involved in virtually all biological processes from embryonic development to programmed cell death and cellular protein recycling. As the only irreversible posttranslational modification, proteolysis represents a committed step in regulation of biological networks and pathways. Imbalance of proteolytic activity has catastrophic implications and is the basis of many genetic disorders as well as a multitude of pathological states of varying etiologies. To understand protease function, one must gain insight into the repertoires of substrates targeted by these enzymes. As many proteases recognize a wide variety of sequences in proteins, it is a challenge to establish if a particular cleavage represents a targeted or a bystander proteolytic event. In addition, since many proteases have overlapping specificities, especially among closely related members of the same gene families, it is a challenge to develop highly selective tools for studying or inhibition of these enzymes. In this work, we used two closely related proteases (MMP-2 and 9) as a model system for development of an information theory-based approach to quantification of substrate specificity and demonstrated its potential for distinguishing between the target and bystander proteolytic events as well as for uncovering selectivity between closely related proteases.
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78
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Identification and characterization of a wolfberry carboxypeptidase inhibitor from Lycium barbarum. Food Chem 2021; 351:129338. [PMID: 33647700 DOI: 10.1016/j.foodchem.2021.129338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 01/22/2021] [Accepted: 02/06/2021] [Indexed: 01/13/2023]
Abstract
Hyperstable cysteine-rich peptides (CRPs) represent an underexplored superfamily of bioactives in functional foods. An example is wolfberry of the Lycium barbarum family. Previously, we discovered a CRP, designated α-lybatide, from L. barbarum bark. Herein, we report the discovery of β-lybatide, a novel carboxypeptidase inhibitor belonging to a different CRP family from the wolfberry plant. Proteomic and transcriptomic analyses showed that β-lybatide contains 36 amino acids with six cysteine residues. NMR spectroscopy revealed that β-lybatide displays a knottin-like structure that renders it highly resistant to thermal, chemical and enzymatic degradation, conditions important for keeping its structural integrity in gastrointestinal tract. Biochemical assays showed that β-lybatide is a potent carboxypeptidase inhibitor which could contribute to the wolfberry biological activities. Bioinformatics analysis revealed an additional 49 β-lybatide-like plant carboxypeptidase inhibitors. Together, our results show that β-lybatide is the first and the smallest plant-derived hyperstable carboxypeptidase inhibitor discovered from a functional food.
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79
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Liu F, Chen R, Song W, Li L, Lei C, Nie Z. Modular Combination of Proteolysis-Responsive Transcription and Spherical Nucleic Acids for Smartphone-Based Colorimetric Detection of Protease Biomarkers. Anal Chem 2021; 93:3517-3525. [DOI: 10.1021/acs.analchem.0c04894] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Fang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Ru Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Wenlu Song
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Liangwen Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
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80
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Choo J, Heo G, Pothoulakis C, Im E. Posttranslational modifications as therapeutic targets for intestinal disorders. Pharmacol Res 2021; 165:105412. [PMID: 33412276 DOI: 10.1016/j.phrs.2020.105412] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 02/08/2023]
Abstract
A variety of biological processes are regulated by posttranslational modifications. Posttranslational modifications including phosphorylation, ubiquitination, glycosylation, and proteolytic cleavage, control diverse physiological functions in the gastrointestinal tract. Therefore, a better understanding of their implications in intestinal diseases, including inflammatory bowel disease, irritable bowel syndrome, celiac disease, and colorectal cancer would provide a basis for the identification of novel biomarkers as well as attractive therapeutic targets. Posttranslational modifications can be common denominators, as well as distinct biomarkers, characterizing pathological differences of various intestinal diseases. This review provides experimental evidence that identifies changes in posttranslational modifications from patient samples, primary cells, or cell lines in intestinal disorders, and a summary of carefully selected information on the use of pharmacological modulators of protein modifications as therapeutic options.
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Affiliation(s)
- Jieun Choo
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Gwangbeom Heo
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Charalabos Pothoulakis
- Section of Inflammatory Bowel Disease & Inflammatory Bowel Disease Center, Division of Digestive Diseases, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Eunok Im
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea.
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81
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A highly efficient protein degradation system in Bacillus sp. CN2: a functional-degradomics study. Appl Microbiol Biotechnol 2021; 105:707-723. [PMID: 33386896 DOI: 10.1007/s00253-020-11083-z] [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: 09/02/2020] [Revised: 12/07/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
A novel protease-producing Bacillus sp. CN2 isolated from chicken manure composts exhibited a relatively high proteolytic specific activity. The strain CN2 degradome consisted of at least 149 proteases and homolog candidates, which were distributed into 4 aspartic, 30 cysteine, 55 metallo, 56 serine, and 4 threonine proteases. Extracellular proteolytic activity was almost completely inhibited by PMSF (phenylmethylsulfonyl fluoride) rather than o-P, E-64, or pepstatin A, suggesting that strain CN2 primarily secreted serine protease. More importantly, analysis of the extracellular proteome of strain CN2 revealed the presence of a highly efficient protein degradation system. Three serine proteases of the S8 family with different active site architectures firstly fragmented protein substrates which were then degraded to smaller peptides by a M4 metalloendopeptidase that prefers to degrade hydrophobic peptides and by a S13 carboxypeptidase. Those enzymes acted synergistically to degrade intact substrate proteins outside the cell. Furthermore, highly expressed sequence-specific intracellular aminopeptidases from multiple families (M20, M29, and M42) accurately degraded peptides into oligopeptides or amino acids, thus realizing the rapid acquisition and utilization of nitrogen sources. In this paper, a systematic study of the functional-degradome provided a new perspective for understanding the complexity of the protease hydrolysis system of Bacillus, and laid a solid foundation for further studying the precise degradation of proteins with the cooperative action of different family proteases. KEY POINTS: • Bacillus sp. CN2 has relatively high proteolytic specific activity. • Bacillus sp. CN2 harbors a highly efficient protein degradation system. • The site-specific endopeptidases were secreted extracellular, while the sequence-specific aminopeptidases played a role in the cell.
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82
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Irshad S, Siddiqui B, ur.Rehman A, Farooq RK, Ahmed N. Recent trends and development in targeted delivery of therapeutics through enzyme responsive intelligent nanoplatform. INT J POLYM MATER PO 2020. [DOI: 10.1080/00914037.2020.1848829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sundus Irshad
- Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Bazla Siddiqui
- Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Asim. ur.Rehman
- Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rai Khalid Farooq
- Department of Neuroscience Research, Institute of Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Naveed Ahmed
- Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
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83
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Kedia S, Ramakrishna P, Netrakanti PR, Singh N, Sisodia SS, Jose M, Kumar S, Mahadevan A, Ramanan N, Nadkarni S, Nair D. Alteration in synaptic nanoscale organization dictates amyloidogenic processing in Alzheimer's disease. iScience 2020; 24:101924. [PMID: 33409475 PMCID: PMC7773964 DOI: 10.1016/j.isci.2020.101924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/22/2020] [Accepted: 12/07/2020] [Indexed: 01/08/2023] Open
Abstract
Despite intuitive insights into differential proteolysis of amyloid precursor protein (APP), the stochasticity behind local product formation through amyloidogenic pathway at individual synapses remain unclear. Here, we show that the major components of amyloidogenic machinery namely, APP and secretases are discretely organized into nanodomains of high local concentration compared to their immediate environment in functional zones of the synapse. Additionally, with the aid of multiple models of Alzheimer's disease (AD), we confirm that this discrete nanoscale chemical map of amyloidogenic machinery is altered at excitatory synapses. Furthermore, we provide realistic models of amyloidogenic processing in unitary vesicles originating from the endocytic zone of excitatory synapses. Thus, we show how an alteration in the stochasticity of synaptic nanoscale organization contributes to the dynamic range of C-terminal fragments β (CTFβ) production, defining the heterogeneity of amyloidogenic processing at individual synapses, leading to long-term synaptic deficits as seen in AD. Components of amyloidogenic machinery are organized into nanodomains Assembly of nanodomains differs between functional zones of the synapse Stochasticity of nanoscale organization dictates dynamic range of APP proteolysis Variability in composition of amyloidogenic machinery is associated with AD
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Affiliation(s)
- Shekhar Kedia
- Centre for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | | | | | - Nivedita Singh
- Centre for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Sangram S Sisodia
- Center for Molecular Neurobiology, Department of Neurobiology, The University of Chicago, IL 60637, USA
| | - Mini Jose
- Centre for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Sathish Kumar
- Department of Neurology, University of Bonn, Bonn 53127, Germany
| | - Anita Mahadevan
- Department of Neuropathology, NIMHANS, Bangalore 560029, India
| | | | - Suhita Nadkarni
- Indian Institute of Science Education and Research, Pune 411008, India
| | - Deepak Nair
- Centre for Neuroscience, Indian Institute of Science, Bangalore 560012, India
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Affiliation(s)
- Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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85
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The challenge of detecting modifications on proteins. Essays Biochem 2020; 64:135-153. [PMID: 31957791 DOI: 10.1042/ebc20190055] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.
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86
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Chang CH, Chang HY, Rappsilber J, Ishihama Y. Isolation of Acetylated and Unmodified Protein N-Terminal Peptides by Strong Cation Exchange Chromatographic Separation of TrypN-Digested Peptides. Mol Cell Proteomics 2020; 20:100003. [PMID: 33517145 PMCID: PMC7857546 DOI: 10.1074/mcp.tir120.002148] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/22/2020] [Accepted: 11/02/2020] [Indexed: 12/25/2022] Open
Abstract
We developed a simple and rapid method to enrich protein N-terminal peptides, in which the protease TrypN is first employed to generate protein N-terminal peptides without Lys or Arg and internal peptides with two positive charges at their N termini, and then, the N-terminal peptides with or without N-acetylation are separated from the internal peptides by strong cation exchange chromatography according to a retention model based on the charge/orientation of peptides. This approach was applied to 20 μg of human HEK293T cell lysate proteins to profile the N-terminal proteome. On average, 1550 acetylated and 200 unmodified protein N-terminal peptides were successfully identified in a single LC/MS/MS run with less than 3% contamination with internal peptides, even when we accepted only canonical protein N termini registered in the Swiss-Prot database. Because this method involves only two steps, protein digestion and chromatographic separation, without the need for tedious chemical reactions, it should be useful for comprehensive profiling of protein N termini, including proteoforms with neo-N termini.
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Affiliation(s)
- Chih-Hsiang Chang
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Hsin-Yi Chang
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan; Graduate Institute of Metabolism and Obesity Sciences, Taipei Medical University, Taipei, Taiwan
| | - Juri Rappsilber
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany; Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan; Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan.
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87
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New strategies to identify protease substrates. Curr Opin Chem Biol 2020; 60:89-96. [PMID: 33220627 DOI: 10.1016/j.cbpa.2020.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/31/2022]
Abstract
Proteome dynamics is governed by transcription, translation, and post-translational modifications. Limited proteolysis is an irreversible post-translational modification that generates multiple but unique proteoforms from almost every native protein. Elucidating these proteoforms and understanding their dynamics at a system-wide level is of utmost importance because uncontrolled proteolytic cleavages correlate with many pathologies. Mass spectrometry-based degradomics has revolutionized protease research and invented workflows for global identification of protease substrates with resolution down to precise cleavage sites. In this review, we provide an overview of current strategies in protease substrate degradomics and introduce the concept of workflow, mass spectrometry-based and in silico enrichment of protein termini with the perspective of full deconvolution of digital proteome maps for precision medicine, and degradomics biomarker diagnostics.
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88
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Kampatsikas I, Pretzler M, Rompel A. Die Erzeugung von Tyrosinaseaktivität in einer Catecholoxidase erlaubt die Identifizierung der für die C‐H‐Aktivierung in Typ‐III‐Kupferenzymen verantwortlichen Aminosäurereste. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ioannis Kampatsikas
- Universität Wien Fakultät für Chemie Institut für Biophysikalische Chemie Althanstraße 14 1090 Wien Österreich
| | - Matthias Pretzler
- Universität Wien Fakultät für Chemie Institut für Biophysikalische Chemie Althanstraße 14 1090 Wien Österreich
| | - Annette Rompel
- Universität Wien Fakultät für Chemie Institut für Biophysikalische Chemie Althanstraße 14 1090 Wien Österreich
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89
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Kampatsikas I, Pretzler M, Rompel A. Identification of Amino Acid Residues Responsible for C-H Activation in Type-III Copper Enzymes by Generating Tyrosinase Activity in a Catechol Oxidase. Angew Chem Int Ed Engl 2020; 59:20940-20945. [PMID: 32701181 PMCID: PMC7693034 DOI: 10.1002/anie.202008859] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 12/12/2022]
Abstract
Tyrosinases (TYRs) catalyze the hydroxylation of phenols and the oxidation of the resulting o-diphenols to o-quinones, while catechol oxidases (COs) exhibit only the latter activity. Aurone synthase (AUS) is not able to react with classical tyrosinase substrates, such as tyramine and l-tyrosine, while it can hydroxylate its natural substrate isoliquiritigenin. The structural difference of TYRs, COs, and AUS at the heart of their divergent catalytic activities is still a puzzle. Therefore, a library of 39 mutants of AUS from Coreopsis grandiflora (CgAUS) was generated and the activity studies showed that the reactivity of the three conserved histidines (HisA2 , HisB1 , and HisB2 ) is tuned by their adjacent residues (HisB1 +1, HisB2 +1, and waterkeeper residue) either to react as stronger bases or / and to stabilize a position permissive for substrate proton shuffling. This provides the understanding for C-H activation based on the type-III copper center to be used in future biotechnological processes.
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Affiliation(s)
- Ioannis Kampatsikas
- Universität WienFakultät für ChemieInstitut für Biophysikalische ChemieAlthanstraße 141090WienAustria
| | - Matthias Pretzler
- Universität WienFakultät für ChemieInstitut für Biophysikalische ChemieAlthanstraße 141090WienAustria
| | - Annette Rompel
- Universität WienFakultät für ChemieInstitut für Biophysikalische ChemieAlthanstraße 141090WienAustria
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90
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Overall CM. The HUPO High-Stringency Inventory of Humanity's Shared Human Proteome Revealed. J Proteome Res 2020; 19:4211-4214. [PMID: 33074000 DOI: 10.1021/acs.jproteome.0c00794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences and Biochemistry & Molecular Biology, Faculty of Dentistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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91
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Lopez C, Adelfio A, Wall AM, Molloy B, Holton TA, Khaldi N. Human milk and infant formulae: Peptide differences and the opportunity to address the functional gap. Curr Res Food Sci 2020; 3:217-226. [PMID: 33426531 PMCID: PMC7782925 DOI: 10.1016/j.crfs.2020.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bovine-derived formula milk (FM) is a common substitute to human milk (HM), but lacks key functional benefits associated with HM. Accordingly, there have been significant efforts to humanise FM. Recent research has demonstrated that HM-derived peptides convey an array of beneficial bioactivities. Given that peptides serve as important signalling molecules offering high specificity and potency, they represent a prime opportunity to humanise FM. To further understand how HM-derived peptides contribute to infant health, we used peptidomics and bioinformatics to compare the peptide profile of HM to commercially available FM. We found clear and substantial differences between HM and FM in terms of peptide physicochemical properties, protein coverage and abundance. We additionally identified 618 peptides specific to HM that represent an important untapped source to be explored for novel bioactivities. While further study is required, our findings highlight the potential of a peptide-based approach to address the functional gap in FM.
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Affiliation(s)
- Cyril Lopez
- Nuritas Ltd, Joshua Dawson House, Dublin 2, D02 RY95, Ireland
| | | | - Audrey M. Wall
- Nuritas Ltd, Joshua Dawson House, Dublin 2, D02 RY95, Ireland
| | - Brendan Molloy
- Nuritas Ltd, Joshua Dawson House, Dublin 2, D02 RY95, Ireland
| | | | - Nora Khaldi
- Nuritas Ltd, Joshua Dawson House, Dublin 2, D02 RY95, Ireland
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92
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Zhu Y, Almuntashiri S, Han Y, Wang X, R. Somanath P, Zhang D. The Roles of CCN1/CYR61 in Pulmonary Diseases. Int J Mol Sci 2020; 21:ijms21217810. [PMID: 33105556 PMCID: PMC7659478 DOI: 10.3390/ijms21217810] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
CCN1 (cysteine-rich 61, connective tissue growth factor, and nephroblastoma-1), previously named CYR61 (cysteine-rich angiogenic inducer 61) belongs to the CCN family of matricellular proteins. CCN1 plays critical roles in the regulation of proliferation, differentiation, apoptosis, angiogenesis, and fibrosis. Recent studies have extensively characterized the important physiological and pathological roles of CCN1 in various tissues and organs. In this review, we summarize both basic and clinical aspects of CCN1 in pulmonary diseases, including acute lung injury (ALI), chronic obstructive pulmonary disease (COPD), lung fibrosis, pulmonary arterial hypertension (PAH), lung infection, and lung cancer. We also emphasize the important challenges for future investigations to better understand the CCN1 and its role in physiology and pathology, as well as the questions that need to be addressed for the therapeutic development of CCN1 antagonists in various lung diseases.
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Affiliation(s)
- Yin Zhu
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA 30912, USA; (Y.Z.); (S.A.); (Y.H.); (P.R.S.)
| | - Sultan Almuntashiri
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA 30912, USA; (Y.Z.); (S.A.); (Y.H.); (P.R.S.)
| | - Yohan Han
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA 30912, USA; (Y.Z.); (S.A.); (Y.H.); (P.R.S.)
| | - Xiaoyun Wang
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA;
| | - Payaningal R. Somanath
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA 30912, USA; (Y.Z.); (S.A.); (Y.H.); (P.R.S.)
- Department of Medicine, Augusta University, Augusta, GA 30912, USA
| | - Duo Zhang
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA 30912, USA; (Y.Z.); (S.A.); (Y.H.); (P.R.S.)
- Correspondence: ; Tel.: +1-706-721-6491; Fax: +1-706-721-3994
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93
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Khrenova MG, Nemukhin AV, Tsirelson VG. Discrimination of enzyme–substrate complexes by reactivity using the electron density analysis: peptide bond hydrolysis by the matrix metalloproteinase-2. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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94
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Li N, Zhan X. MASS SPECTROMETRY-BASED MITOCHONDRIAL PROTEOMICS IN HUMAN OVARIAN CANCERS. MASS SPECTROMETRY REVIEWS 2020; 39:471-498. [PMID: 32020673 DOI: 10.1002/mas.21618] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The prominent characteristics of mitochondria are highly dynamic and regulatory, which have crucial roles in cell metabolism, biosynthetic, senescence, apoptosis, and signaling pathways. Mitochondrial dysfunction might lead to multiple serious diseases, including cancer. Therefore, identification of mitochondrial proteins in cancer could provide a global view of tumorigenesis and progression. Mass spectrometry-based quantitative mitochondrial proteomics fulfils this task by enabling systems-wide, accurate, and quantitative analysis of mitochondrial protein abundance, and mitochondrial protein posttranslational modifications (PTMs). Multiple quantitative proteomics techniques, including isotope-coded affinity tag, stable isotope labeling with amino acids in cell culture, isobaric tags for relative and absolute quantification, tandem mass tags, and label-free quantification, in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides, increase flexibility for researchers to study mitochondrial proteomes. This article reviews isolation and purification of mitochondria, quantitative mitochondrial proteomics, quantitative mitochondrial phosphoproteomics, mitochondrial protein-involved signaling pathway networks, mitochondrial phosphoprotein-involved signaling pathway networks, integration of mitochondrial proteomic and phosphoproteomic data with whole tissue proteomic and transcriptomic data and clinical information in ovarian cancers (OC) to in-depth understand its molecular mechanisms, and discover effective mitochondrial biomarkers and therapeutic targets for predictive, preventive, and personalized treatment of OC. This proof-of-principle model about OC mitochondrial proteomics is easily implementable to other cancer types. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Na Li
- University Creative Research Initiatives Center, Shandong First Medical University, Shandong, 250062, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, Shandong, 250062, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- Department of Oncology, Xiangya Hospital, Central South University, 88 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 88 Xiangya Road, Changsha, Hunan, 410008, P. R. China
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95
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Hofsetz E, Demir F, Szczepanowska K, Kukat A, Kizhakkedathu JN, Trifunovic A, Huesgen PF. The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis. Mol Cell Proteomics 2020; 19:1330-1345. [PMID: 32467259 PMCID: PMC8014998 DOI: 10.1074/mcp.ra120.002082] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/24/2020] [Indexed: 12/29/2022] Open
Abstract
The mammalian mitochondrial proteome consists of more than 1100 annotated proteins and their proteostasis is regulated by only a few ATP-dependent protease complexes. Technical advances in protein mass spectrometry allowed for detailed description of the mitoproteome from different species and tissues and their changes under specific conditions. However, protease-substrate relations within mitochondria are still poorly understood. Here, we combined Terminal Amine Isotope Labeling of Substrates (TAILS) N termini profiling of heart mitochondria proteomes isolated from wild type and Clpp-/- mice with a classical substrate-trapping screen using FLAG-tagged proteolytically active and inactive CLPP variants to identify new ClpXP substrates in mammalian mitochondria. Using TAILS, we identified N termini of more than 200 mitochondrial proteins. Expected N termini confirmed sequence determinants for mitochondrial targeting signal (MTS) cleavage and subsequent N-terminal processing after import, but the majority were protease-generated neo-N termini mapping to positions within the proteins. Quantitative comparison revealed widespread changes in protein processing patterns, including both strong increases or decreases in the abundance of specific neo-N termini, as well as an overall increase in the abundance of protease-generated neo-N termini in CLPP-deficient mitochondria that indicated altered mitochondrial proteostasis. Based on the combination of altered processing patterns, protein accumulation and stabilization in CLPP-deficient mice and interaction with CLPP, we identified OAT, HSPA9 and POLDIP2 and as novel bona fide ClpXP substrates. Finally, we propose that ClpXP participates in the cooperative degradation of UQCRC1. Together, our data provide the first landscape of the heart mitochondria N terminome and give further insights into regulatory and assisted proteolysis mediated by ClpXP.
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Affiliation(s)
- Eduard Hofsetz
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Karolina Szczepanowska
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Alexandra Kukat
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, School of Biomedical Engineering, Department of Pathology & Laboratory Medicine, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aleksandra Trifunovic
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
| | - Pitter F Huesgen
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany; Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany; Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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96
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Gorelik A, van Aalten DMF. Tools for functional dissection of site-specific O-GlcNAcylation. RSC Chem Biol 2020; 1:98-109. [PMID: 34458751 PMCID: PMC8386111 DOI: 10.1039/d0cb00052c] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022] Open
Abstract
Protein O-GlcNAcylation is an abundant post-translational modification of intracellular proteins with the monosaccharide N-acetylglucosamine covalently tethered to serines and threonines. Modification of proteins with O-GlcNAc is required for metazoan embryo development and maintains cellular homeostasis through effects on transcription, signalling and stress response. While disruption of O-GlcNAc homeostasis can have detrimental impact on cell physiology and cause various diseases, little is known about the functions of individual O-GlcNAc sites. Most of the sites are modified sub-stoichiometrically which is a major challenge to the dissection of O-GlcNAc function. Here, we discuss the application, advantages and limitations of the currently available tools and technologies utilised to dissect the function of O-GlcNAc on individual proteins and sites in vitro and in vivo. Additionally, we provide a perspective on future developments required to decipher the protein- and site-specific roles of this essential sugar modification.
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Affiliation(s)
- Andrii Gorelik
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee Dundee UK
| | - Daan M F van Aalten
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee Dundee UK
- Institute for Molecular Precision Medicine, Xiangya Hospital, Central South University Changsha China
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97
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On the cutting edge: protease-based methods for sensing and controlling cell biology. Nat Methods 2020; 17:885-896. [PMID: 32661424 DOI: 10.1038/s41592-020-0891-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Sequence-specific proteases have proven to be versatile building blocks for tools that report or control cellular function. Reporting methods link protease activity to biochemical signals, whereas control methods rely on engineering proteases to respond to exogenous inputs such as light or chemicals. In turn, proteases have inherent control abilities, as their native functions are to release, activate or destroy proteins by cleavage, with the irreversibility of proteolysis allowing sustained downstream effects. As a result, protease-based synthetic circuits have been created for diverse uses such as reporting cellular signaling, tuning protein expression, controlling viral replication and detecting cancer states. Here, we comprehensively review the development and application of protease-based methods for reporting and controlling cellular function in eukaryotes.
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98
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Discovery of potent thrombin inhibitors from a protease-focused DNA-encoded chemical library. Proc Natl Acad Sci U S A 2020; 117:16782-16789. [PMID: 32641511 PMCID: PMC7382296 DOI: 10.1073/pnas.2005447117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To rapidly identify small-molecule lead compounds to target healthcare-associated proteases, we constructed a unique 9.8-million-membered protease-focused DNA-encoded chemical library. Affinity selection of this library with a healthcare-relevant protease (i.e., thrombin, a key protein necessary for blood coagulation) revealed potent inhibitors in the first screening attempt. Our results emphasize the utility of a structurally focused DNA-encoded chemical library approach to rapidly uncover hits for healthcare targets (e.g., proteases) where no drug exists (e.g., male contraception) and for emerging diseases (e.g., coronavirus disease 2019). DNA-encoded chemical libraries are collections of compounds individually coupled to unique DNA tags serving as amplifiable identification barcodes. By bridging split-and-pool combinatorial synthesis with the ligation of unique encoding DNA oligomers, million- to billion-member libraries can be synthesized for use in hundreds of healthcare target screens. Although structural diversity and desirable molecular property ranges generally guide DNA-encoded chemical library design, recent reports have highlighted the utility of focused DNA-encoded chemical libraries that are structurally biased for a class of protein targets. Herein, a protease-focused DNA-encoded chemical library was designed that utilizes chemotypes known to engage conserved catalytic protease residues. The three-cycle library features functional moieties such as guanidine, which interacts strongly with aspartate of the protease catalytic triad, as well as mild electrophiles such as sulfonamide, urea, and carbamate. We developed a DNA-compatible method for guanidinylation of amines and reduction of nitriles. Employing these optimized reactions, we constructed a 9.8-million-membered DNA-encoded chemical library. Affinity selection of the library with thrombin, a common protease, revealed a number of enriched features which ultimately led to the discovery of a 1 nM inhibitor of thrombin. Thus, structurally focused DNA-encoded chemical libraries have tremendous potential to find clinically useful high-affinity hits for the rapid discovery of drugs for targets (e.g., proteases) with essential functions in infectious diseases (e.g., severe acute respiratory syndrome coronavirus 2) and relevant healthcare conditions (e.g., male contraception).
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99
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Savickas S, Kastl P, auf dem Keller U. Combinatorial degradomics: Precision tools to unveil proteolytic processes in biological systems. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140392. [DOI: 10.1016/j.bbapap.2020.140392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/28/2022]
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100
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Opdenakker G, Abu El-Asrar A, Van Damme J. Remnant Epitopes Generating Autoimmunity: From Model to Useful Paradigm. Trends Immunol 2020; 41:367-378. [PMID: 32299652 DOI: 10.1016/j.it.2020.03.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 12/19/2022]
Abstract
Autoimmune diseases are defined as pathologies of adaptive immunity by the presence of autoantibodies or MHC-restricted autoantigen-reactive T cells. Because autoreactivity is a normal process based on mechanisms producing repertoires of antibodies and T cell receptors, crucial questions about disease mechanisms and key steps for interference have been outstanding. We defined 25 years ago the 'remnant epitopes generate autoimmunity' (REGA)-model in which extracellular proteases from innate immune cells generate autoantigens. Here, we refine the REGA-model, tested in diseases ranging from organ-specific autoimmune diseases to systemic lupus erythematosus. It now constitutes a paradigm in which remnant epitopes generate, maintain, and regulate autoimmunity; are dependent on genetic and epigenetic influences; are produced in a disease phase-specific manner; and have therapeutic implications when targeted.
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Affiliation(s)
- Ghislain Opdenakker
- Laboratory of Immunobiology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, University of Leuven, Leuven, Belgium.
| | - Ahmed Abu El-Asrar
- Laboratory of Immunobiology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, University of Leuven, Leuven, Belgium; Laboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, University of Leuven, Leuven, Belgium
| | - Jo Van Damme
- Laboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, University of Leuven, Leuven, Belgium
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