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Stojanovski BM, Di Cera E. Codon switching of conserved Ser residues in coagulation and fibrinolytic proteases. J Thromb Haemost 2024:S1538-7836(24)00307-6. [PMID: 38821294 DOI: 10.1016/j.jtha.2024.05.021] [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: 03/13/2024] [Revised: 04/30/2024] [Accepted: 05/21/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Unique among all amino acids, Ser is encoded by 2 sets of codons, TCN and AGY (N = any nucleotide, Y = pyrimidine), that cannot interconvert through single nucleotide substitutions. Both codons are documented at the essential residues S195 and S214 within the active site of serine proteases. However, it is not known how the codons interconverted during evolution because replacement of S195 or S214 by other amino acids typically results in loss of activity. OBJECTIVE To characterize the prevalence of codon switching among essential and non-essential Ser residues in coagulation and fibrinolytic proteases from different vertebrate lineages. METHODS TCN and AGY codon usage was analyzed in >550 sequences. RESULTS Evolutionary pressure to preserve the codon of S195 is absolute, with no evidence of interconversion. Pressure to preserve the codon of S214 is also strong, but an AGY↔TCN interconversion is observed in factor VII-inactive and protein C from ray-finned fish. In both cases, the interconversion occurred in genes that were rapidly evolving. In contrast, codon switching at nonessential Ser residues in the kringle domains of coagulation and fibrinolytic proteases is quite common and could be identified in half of the kringles analyzed. CONCLUSION Codon interconversion of essential Ser residues of coagulation and fibrinolytic proteases only occurred in genes that were rapidly evolving and that-at least in some cases-evolved following genome duplication. Interconversion is common at nonessential Ser residues as found in kringle domains.
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Affiliation(s)
- Bosko M Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri, USA.
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2
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Demir F, Kuppusamy M, Perrar A, Huesgen PF. Profiling Sequence Specificity of Proteolytic Activities Using Proteome-Derived Peptide Libraries. Methods Mol Biol 2022; 2447:159-174. [PMID: 35583780 DOI: 10.1007/978-1-0716-2079-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Substrate sequence specificity is a fundamental characteristic of proteolytic enzymes. Hundreds of proteases are encoded in plant genomes, but the vast majority of them have not been characterized and their distinct specificity remains largely unknown. Here we present our current protocol for profiling sequence specificity of plant proteases using Proteomic Identification of Cleavage Sites (PICS). This simple, cost-effective protocol is suited for detailed, time-resolved specificity profiling of purified or enriched proteases. The isolated active protease or fraction with enriched protease activity together with a suitable control are incubated with split aliquots of proteome-derived peptide libraries, followed by identification of specifically cleaved peptides using quantitative mass spectrometry. Detailed specificity profiles are obtained by alignment of many individual cleavage sites. The chapter covers preparation of complementary peptide libraries from heterologous sources, the cleavage assay itself, as well as mass spectrometry data analysis.
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Affiliation(s)
- Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Maithreyan Kuppusamy
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Andreas Perrar
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- Cologne Cluster of Excellence on Aging-related Disorders, CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany.
- Cologne Cluster of Excellence on Aging-related Disorders, CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
- Department for Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany.
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3
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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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4
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Chen S, Yim JJ, Bogyo M. Synthetic and biological approaches to map substrate specificities of proteases. Biol Chem 2020; 401:165-182. [PMID: 31639098 DOI: 10.1515/hsz-2019-0332] [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: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023]
Abstract
Proteases are regulators of diverse biological pathways including protein catabolism, antigen processing and inflammation, as well as various disease conditions, such as malignant metastasis, viral infection and parasite invasion. The identification of substrates of a given protease is essential to understand its function and this information can also aid in the design of specific inhibitors and active site probes. However, the diversity of putative protein and peptide substrates makes connecting a protease to its downstream substrates technically difficult and time-consuming. To address this challenge in protease research, a range of methods have been developed to identify natural protein substrates as well as map the overall substrate specificity patterns of proteases. In this review, we highlight recent examples of both synthetic and biological methods that are being used to define the substrate specificity of protease so that new protease-specific tools and therapeutic agents can be developed.
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Affiliation(s)
- Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua J Yim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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5
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Dall E, Zauner FB, Soh WT, Demir F, Dahms SO, Cabrele C, Huesgen PF, Brandstetter H. Structural and functional studies of Arabidopsis thaliana legumain beta reveal isoform specific mechanisms of activation and substrate recognition. J Biol Chem 2020; 295:13047-13064. [PMID: 32719006 PMCID: PMC7489914 DOI: 10.1074/jbc.ra120.014478] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/14/2020] [Indexed: 01/19/2023] Open
Abstract
The vacuolar cysteine protease legumain plays important functions in seed maturation and plant programmed cell death. Because of their dual protease and ligase activity, plant legumains have become of particular biotechnological interest, e.g. for the synthesis of cyclic peptides for drug design or for protein engineering. However, the molecular mechanisms behind their dual protease and ligase activities are still poorly understood, limiting their applications. Here, we present the crystal structure of Arabidopsis thaliana legumain isoform β (AtLEGβ) in its zymogen state. Combining structural and biochemical experiments, we show for the first time that plant legumains encode distinct, isoform-specific activation mechanisms. Whereas the autocatalytic activation of isoform γ (AtLEGγ) is controlled by the latency-conferring dimer state, the activation of the monomeric AtLEGβ is concentration independent. Additionally, in AtLEGβ the plant-characteristic two-chain intermediate state is stabilized by hydrophobic rather than ionic interactions, as in AtLEGγ, resulting in significantly different pH stability profiles. The crystal structure of AtLEGβ revealed unrestricted nonprime substrate binding pockets, consistent with the broad substrate specificity, as determined by degradomic assays. Further to its protease activity, we show that AtLEGβ exhibits a true peptide ligase activity. Whereas cleavage-dependent transpeptidase activity has been reported for other plant legumains, AtLEGβ is the first example of a plant legumain capable of linking free termini. The discovery of these isoform-specific differences will allow us to identify and rationally design efficient ligases with application in biotechnology and drug development.
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Affiliation(s)
- Elfriede Dall
- Department of Biosciences, University of Salzburg, Salzburg, Austria.
| | - Florian B Zauner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Wai Tuck Soh
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Sven O Dahms
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany; CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany; Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Salzburg, Austria.
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Soh WT, Demir F, Dall E, Perrar A, Dahms SO, Kuppusamy M, Brandstetter H, Huesgen PF. ExteNDing Proteome Coverage with Legumain as a Highly Specific Digestion Protease. Anal Chem 2020; 92:2961-2971. [PMID: 31951383 PMCID: PMC7075662 DOI: 10.1021/acs.analchem.9b03604] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Bottom-up
mass spectrometry-based proteomics utilizes proteolytic
enzymes with well characterized specificities to generate peptides
amenable for identification by high-throughput tandem mass spectrometry.
Trypsin, which cuts specifically after the basic residues lysine and
arginine, is the predominant enzyme used for proteome digestion, although
proteases with alternative specificities are required to detect sequences
that are not accessible after tryptic digest. Here, we show that the
human cysteine protease legumain exhibits a strict substrate specificity
for cleavage after asparagine and aspartic acid residues during in-solution
digestions of proteomes extracted from Escherichia
coli, mouse embryonic fibroblast cell cultures, and Arabidopsis thaliana leaves. Generating peptides
highly complementary in sequence, yet similar in their biophysical
properties, legumain (as compared to trypsin or GluC) enabled complementary
proteome and protein sequence coverage. Importantly, legumain further
enabled the identification and enrichment of protein N-termini not
accessible in GluC- or trypsin-digested samples. Legumain cannot cleave
after glycosylated Asn residues, which enabled the robust identification
and orthogonal validation of N-glycosylation sites based on alternating
sequential sample treatments with legumain and PNGaseF and vice versa.
Taken together, we demonstrate that legumain is a practical, efficient
protease for extending the proteome and sequence coverage achieved
with trypsin, with unique possibilities for the characterization of
post-translational modification sites.
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Affiliation(s)
- Wai Tuck Soh
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Elfriede Dall
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Andreas Perrar
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Sven O Dahms
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Maithreyan Kuppusamy
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Hans Brandstetter
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, Medical Faculty and University Hospital , University of Cologne , 50931 Cologne , Germany.,Institute for Biochemistry, Faculty of Mathematics and Natural Sciences , University of Cologne , 50674 Cologne , Germany
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7
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Dahms SO, Demir F, Huesgen PF, Thorn K, Brandstetter H. Sirtilins - the new old members of the vitamin K-dependent coagulation factor family. J Thromb Haemost 2019; 17:470-481. [PMID: 30644641 PMCID: PMC6850207 DOI: 10.1111/jth.14384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Indexed: 12/04/2022]
Abstract
Essentials Blood coagulation is driven by vitamin K (VK)-dependent proteases. We have identified and characterized 'sirtilin' as an additional VK-dependent protease. Sirtilins emerged early in the evolution of the coagulation system of vertebrates. Ubiquitous occurrence might indicate an important functional role of sirtilins. SUMMARY: Background Vitamin K (VK)-dependent proteases are major players in blood coagulation, including both the initiation and the regulation of the cascade. Five different members of this protease family have been described, comprising the following coagulation factors: factor VII, FIX, FX, protein C (PC), and prothrombin (FII). FVII, FIX, FX and PC share a typical domain architecture, with an N-terminal γ-carboxyglutamate (Gla) domain, two epidermal growth factor-like (EGF) domains, and a C-terminal trypsin-like serine protease (SP) domain. Objectives We have identified uncharacterized proteins in snake genomes showing the typical Gla-EGF1-EGF2-SP domain architecture but relatively low sequence conservation compared to known VK-dependent proteases. On the basis of sequence analysis, we hypothesized that these proteins are functional members of the VK-dependent protease family. Methods/results Using phylogenetic analyses, we confirmed the so-called 'sirtilins' as an additional VK-dependent protease class. These proteases were found in several vertebrates, including jawless fish, cartilaginous fish, bony fish, reptiles, birds, and marsupials, but not in other mammals. The recombinant zymogen form of Thamnophis sirtalis sirtilin was produced by in vitro renaturation, and was activated with human activated FXI. The activated form of sirtilin proteolytically cleaved peptide and protein substrates, including prothrombin. Mass spectrometry-based substrate profiling of sirtilin revealed a narrower sequence specificity than those of FIX and FX. Conclusions The ubiquitous occurrence of sirtilins in many vertebrate classes might indicate an important functional role. Understanding the detailed functions of sirtilins might contribute to a deeper understanding of the evolution and function of the vertebrate coagulation system.
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Affiliation(s)
- Sven O. Dahms
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Fatih Demir
- ZEA‐3 AnalyticsCentral Institute for Engineering, Electronics and AnalyticsForschungszentrum JülichJülichGermany
| | - Pitter F. Huesgen
- ZEA‐3 AnalyticsCentral Institute for Engineering, Electronics and AnalyticsForschungszentrum JülichJülichGermany
| | - Karina Thorn
- Haemophilia ResearchNovo Nordisk A/SMåløvDenmark
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