Proteomic identification of protease cleavage sites: cell-biological and biomedical applications

Abstract

Proteolysis shapes proteomes by protein degradation or restricted proteolysis, which generates stable cleavage products. Proteolytic (in-)activation of enzymes and cytokines is an essential aspect of the functional proteome status. Proteome-wide identification and quantification of proteolytic processing is accessible by complementary techniques for the focused analysis of protein termini. These innovative strategies are now widely applied and have transformed protease research. Pioneering studies portrayed apoptotic and caspase-dependent cleavage events. Protease-centric investigations focused predominantly on matrix metalloproteinases (MMPs), granzymes and aspartyl and cysteine cathepsins. The first in vivo degradomic studies were performed with mice lacking either cysteine cathepsins or matrix metalloproteinases. Process-centric degradomic analyses investigated infectious processes and mitochondrial import. Peptidomic analyses yielded disease biomarkers representing cleavage fragments from bodily fluids. The diversity of degradomic endeavors illustrates the importance of portraying proteolytic processing in health and disease. The present review provides an overview of the current status of degradomic studies.

Keywords::

• caspases
• cathepsins
• degradomics
• granzymes
• limited proteolysis
• matrix metalloproteinases
• pharmacological protease inhibition
• peptidomics
• protease specificity

Financial & competing interests disclosure

O Schilling is supported by an Emmy-Noether grant of the Deutsche Forschungsgemeinschaft (DFG) (SCHI 871/2), a starting grant of the European Research Council (Programme “Ideas” - Call identifier: ERC-2011-StG 282111-ProteaSys), and the Excellence Initiative of the German Federal and State Governments (EXC 294, BIOSS). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Key issues

• • Proteolysis is a ubiquitous post-translational modification, involved in almost every (patho-)physiological process.

• • Pharmacological protease inhibition is increasingly applied.

• • Proteases inhibitor development is hampered by incomplete understanding of protease substrates.

• • Several proteomic methods have been developed to identify protease cleavage sites in biological samples.

• • Degradomic analysis is now a straightforward endeavor, applicable to cellular and in vivo (tissue) samples.

• • Biochemical protease specificity is useful as a first-line validation for cellular protease substrates.

• • Proteases function in highly interdependent networks with gain or loss of protease function leading to secondary downstream effects.

• • Peptidomics has yielded valuable biomarker profiles, largely representing proteolytic cleavage fragments.

Notes