Identification of unexplored substrates of the serine protease, thrombin, using N-terminomics strategy

Siglecs family used by pathogens for immune escape may engaged in immune tolerance in pregnancy

The Siglecs family is a group of type I sialic acid-binding immunoglobulin-like receptors that regulate cellular signaling by recognizing sialic acid epitopes. Siglecs are predominantly expressed on the surface of leukocytes, where they play a crucial role in regulating immune activity. Pathogens can exploit inhibitory Siglecs by utilizing their sialic acid components to promote invasion or suppress immune functions, facilitating immune evasion. The establishing of an immune-balanced maternal-fetal interface microenvironment is essential for a successful pregnancy. Dysfunctional immune cells may lead to adverse pregnancy outcomes. Siglecs are important for inducing a phenotypic switch in leukocytes at the maternal-fetal interface toward a less toxic and more tolerant phenotype. Recent discoveries regarding Siglecs in the reproductive system have drawn further attention to their potential roles in reproduction. In this review, we primarily discuss the latest advances in understanding the impact of Siglecs as immune regulators on infections and pregnancy.

Non-canonical roles of Siglecs: Beyond sialic acid-binding and immune cell modulation

Siglecs (Sialic acid-binding immunoglobulin-type lectins) are I-type lectins that bind with sialic acid ligands (Sia). Most are expressed on the surface of leukocytes and are involved in immune regulation and possess immune tyrosine-based inhibitory motif (ITIM) in the intracellular domain, thus leading to inhibition of the immune response. This signaling is instrumental in maintaining quiescence under physiological conditions and acts as a brake for inflammatory cascades. By contrast, activating Siglecs carry positively charged residues in the transmembrane domain and interact with immune tyrosine-based activating motif (ITAM)-containing proteins, a DNAX-activating protein of 10-12 kDa (DAP10/12), to activate immune cells. There are various characteristics of Siglecs that do not fit within the classification of Siglec receptors as being either inhibitory or activating in nature. This review focuses on elucidating the non-canonical functions and interactions of Siglec receptors, which include Sia-independent interactions such as protein-protein interactions and interactions with lipids or other sugars. This review also summarizes Siglec expression and function on non-immune cells, and non-classical signaling of the receptor. Thus, this review will be beneficial to researchers interested in the field of Siglecs and sialic acid biology.

Identification of substrates of MBL Associated Serine Protease-1 (MASP-1) from human plasma using N-terminomics strategy

MBL Associated Serine Protease-1 (MASP-1) is an abundant enzyme of the lectin complement pathway. MASP-1 cleaves numerous substrates like MASP-2, MASP-3, C2, C3i, fibrinogen, FXIII and prothrombin. It has thrombin-like specificity and can cleave thrombin substrates. Owing to its high concentration and relaxed substrate specificity, MASP-1 has substrates outside the complement system and can influence other proteolytic cascades and physiological processes. The unidentified substrates may assist us to ascertain the role(s) of MASP-1. In this study, we used a high-throughput N-terminomics method to identify substrates of MASP-1 from human plasma. We have identified 35 putative substrates of MASP-1. Among the identified proteins, alpha 2-antiplasmin, alpha-1-acid glycoprotein, antithrombin III, and siglec-6 were demonstrated to be cleaved by MASP-1. We have discussed the physiological relevance of cleavage of these substrates by MASP-1. The expression of Siglec-6 and MASP-1 has been reported in the B cells. Alpha-1-acid glycoprotein cleavage by MASP-1 may occur in the acute phase as it is known to be an inhibitor of platelet aggregation, whereas MASP-1 triggers platelet aggregation. The cleavage alpha2 antiplasmin by MASP-1 implies that MASP-1 may be promoting plasmin-mediated fibrinolysis. Our study supports that MASP-1 may be implicated in thrombosis as well as thrombolysis.

A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms

Especially in eukaryotes, the N-terminal acetylation status of a protein reveals translation initiation sites and substrate specificities and activities of N-terminal acetyltransferases (NATs). Here, we discuss a bottom-up proteomics protocol for the enrichment of N-terminal peptides via strong cation exchange chromatography. This protocol is based on depleting internal tryptic peptides from proteome digests through their retention on strong cation exchangers, leaving N-terminally acetylated/blocked peptides enriched among the nonretained peptides. As such, one can identify novel N-terminal proteoforms and quantify the degree of N-terminal protein acetylation.

Proteomics in Thrombosis and Haemostasis

No Abstract.

Advances and Utility of the Human Plasma Proteome

The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophysiology. Here we provide views and perspectives about technological developments and possible clinical applications that use mass-spectrometry(MS)- or affinity-based methods. We discuss examples where plasma proteomics contributed valuable insights into SARS-CoV-2 infections, aging, and hemostasis and the opportunities offered by combining proteomics with genetic data. As a contribution to the Human Proteome Organization (HUPO) Human Plasma Proteome Project (HPPP), we present the Human Plasma PeptideAtlas build 2021-07 that comprises 4395 canonical and 1482 additional nonredundant human proteins detected in 240 MS-based experiments. In addition, we report the new Human Extracellular Vesicle PeptideAtlas 2021-06, which comprises five studies and 2757 canonical proteins detected in extracellular vesicles circulating in blood, of which 74% (2047) are in common with the plasma PeptideAtlas. Our overview summarizes the recent advances, impactful applications, and ongoing challenges for translating plasma proteomics into utility for precision medicine.

Insight into the human pathodegradome of the V8 protease from Staphylococcus aureus

Staphylococcus aureus possesses ten extracellular proteases with mostly unknown targets in the human proteome. To assist with bacterial protease target discovery, we have applied and compared two N-terminomics methods to investigate cleavage of human serum proteins by S. aureus V8 protease, discovering 85 host-protein targets. Among these are virulence-relevant complement, iron sequestration, clotting cascade, and host protease inhibitor proteins. Protein cleavage sites have been identified, providing insight into the disruption of host protein function by V8. Complement proteins are cleaved within peptidase and sushi domains, and host protease inhibitors are cleaved outside their protease-trapping motifs. Our data highlight the potential for further application of N-terminomics in discovery of bacterial protease substrates in other host niches and provide omics-scale insight into the role of the V8 protease in S. aureus pathogenesis.

S. aureus-secreted proteases are central to disease causation, but the discovery of their host substrates has been limited. Frey et al. use N-terminomic approaches to uncover human serum targets of the V8 protease that are from virulence-relevant processes such as the host inflammatory network and nutrient sequestration.

Protein amino-termini and how to identify them

INTRODUCTION

The N-terminus of a protein can encode several protein features, including its half-live and its localization. As the proteomics field remains dominated by bottom-up approaches and as N-terminal peptides only account for a fraction of all analyzable peptides, there is a need for their enrichment prior to analysis. COFRADIC, TAILS, and the subtiligase method were among the first N-terminomics methods developed, and several variants and novel methods were introduced that often reduce processing time and/or the amount of material required.

AREAS COVERED

We present an overview of how the field of N-terminomics developed, including a discussion of the founding methods, several updates made to these and introduce newer methods such as TMPP-labeling, biotin-based methods besides some necessary improvements in data analysis.

EXPERT OPINION

N-terminomic methods remain being used and improved methods are published however, more efficient use of contemporary mass spectrometers, promising data-independent approaches, and mass spectrometry-free single peptide or protein sequences may threat the N-terminomics field.