New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology

N-degron and C-degron pathways of protein degradation

(2019) Alexander Varshavsky   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modulating Protein Stability to Switch Toxic Protein Function On and Off in Living Cells

(2019) Frederik Faden et al.   PLANT PHYSIOLOGY

Conditional Protein Function via N-Degron Pathway–Mediated Proteostasis in Stress Physiology

(2019) Nico Dissmeyer   Annual Review of Plant Biology

Regulation of autophagic proteolysis by the N-recognin SQSTM1/p62 of the N-end rule pathway

(2018) Hyunjoo Cha-Molstad et al.   Autophagy

Plant mitochondrial protein import: the ins and outs

(2018) Abi S. Ghifari et al.   BIOCHEMICAL JOURNAL

N-terminal acetylation: an essential protein modification emerges as an important regulator of stress responses

(2018) Eric Linster et al.   JOURNAL OF EXPERIMENTAL BOTANY

Increases in activity of proteasome and papain-like cysteine protease in Arabidopsis autophagy mutants: back-up compensatory effect or cell-death promoting effect?

(2018) Marien Havé et al.   JOURNAL OF EXPERIMENTAL BOTANY

Simple, scalable, and ultrasensitive tip-based identification of protease substrates

(2018) Gerta Shema et al.   MOLECULAR & CELLULAR PROTEOMICS

Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern

(2018) Benoit Castrec et al.   Nature Chemical Biology

New Perspectives on Chloroplast Protein Import

(2018) Masato Nakai   PLANT AND CELL PHYSIOLOGY

Alternative Splicing and Cross-Talk with Light Signaling

(2018) You-Liang Cheng et al.   PLANT AND CELL PHYSIOLOGY

N-terminal arginylation generates a bimodal degron that modulates autophagic proteolysis

(2018) Young Dong Yoo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alternative Splicing Control of Abiotic Stress Responses

(2018) Tom Laloum et al.   TRENDS IN PLANT SCIENCE

Distinct branches of the N-end rule pathway modulate the plant immune response

(2018) Jorge Vicente et al.   NEW PHYTOLOGIST

Alternative Splicing as a Regulator of Early Plant Development

(2018) Dóra Szakonyi et al.   Frontiers in Plant Science

Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics

(2018) Borjana Arsova et al.   Frontiers in Plant Science

Formyl-methionine as an N-degron of a eukaryotic N-end rule pathway

(2018) Jeong-Mok Kim et al.   SCIENCE

Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation inArabidopsis

(2017) Hui Dong et al.   GENES & DEVELOPMENT

N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana

(2017) Patrick Willems et al.   MOLECULAR & CELLULAR PROTEOMICS

Engineering peptide ligase specificity by proteomic identification of ligation sites

(2017) Amy M Weeks et al.   Nature Chemical Biology

Quantitative proteomics in plant protease substrate identification

(2017) Fatih Demir et al.   NEW PHYTOLOGIST

Real-time detection of N-end rule-mediated ubiquitination via fluorescently labeled substrate probes

(2017) Augustin C. Mot et al.   NEW PHYTOLOGIST

Life and death of proteins after protease cleavage: protein degradation by the N-end rule pathway

(2017) Nico Dissmeyer et al.   NEW PHYTOLOGIST

N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway

(2017) Hongtao Zhang et al.   NEW PHYTOLOGIST

An Approach to Incorporate Multi-Enzyme Digestion into C-TAILS for C-Terminomics Studies

(2017) Yang Zhang et al.   PROTEOMICS

Plant cysteine oxidases are dioxygenases that directly enable arginyl transferase-catalysed arginylation of N-end rule targets

(2017) Mark D. White et al.   Nature Communications

p62/SQSTM1/Sequestosome-1 is an N-recognin of the N-end rule pathway which modulates autophagosome biogenesis

(2017) Hyunjoo Cha-Molstad et al.   Nature Communications

Comprehensive analysis of human protein N-termini enables assessment of various protein forms

(2017) Jeonghun Yeom et al.   Scientific Reports

Depletion of internal peptides by site-selective blocking, phosphate labeling, and TiO2 adsorption for in-depth analysis of C-terminome

(2016) Lingfan Chen et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Hydrophobic Tagging-Assisted N-Termini Enrichment for In-Depth N-Terminome Analysis

(2016) Lingfan Chen et al.   ANALYTICAL CHEMISTRY

Modulation of SQSTM1/p62 activity by N-terminal arginylation of the endoplasmic reticulum chaperone HSPA5/GRP78/BiP

(2016) Hyunjoo Cha-Molstad et al.   Autophagy

The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins

(2016) Yanxialei Jiang et al.   Autophagy

Analyzing N-terminal Arginylation through the Use of Peptide Arrays and Degradation Assays

(2016) Brandon Wadas et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of Targets and Interaction Partners of Arginyl-tRNA Protein Transferase in the MossPhyscomitrella patens

(2016) Sebastian N. W. Hoernstein et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Phenotypes on demand via switchable target protein degradation in multicellular organisms

(2016) Frederik Faden et al.   Nature Communications

Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms

(2016) Om Singh Rathore et al.   Scientific Reports

A novel method to isolate protein N-terminal peptides from proteome samples using sulfydryl tagging and gold-nanoparticle-based depletion

(2015) Lanting Li et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Systematic Optimization of C-Terminal Amine-Based Isotope Labeling of Substrates Approach for Deep Screening of C-Terminome

(2015) Yang Zhang et al.   ANALYTICAL CHEMISTRY

Positive Enrichment of C-Terminal Peptides Using Oxazolone Chemistry and Biotinylation

(2015) Minbo Liu et al.   ANALYTICAL CHEMISTRY

Proteomic approaches to identify substrates of the three Deg/HtrA proteases of the cyanobacteriumSynechocystissp. PCC 6803

(2015) Lam X. Tam et al.   BIOCHEMICAL JOURNAL

Amino-terminal arginylation as a degradation signal for selective autophagy

(2015) Hyunjoo Cha-Molstad et al.   BMB Reports

Identification of cleavage sites and substrate proteins for two mitochondrial intermediate peptidases in Arabidopsis thaliana

(2015) Chris Carrie et al.   JOURNAL OF EXPERIMENTAL BOTANY

Amino-terminal arginylation targets endoplasmic reticulum chaperone BiP for autophagy through p62 binding

(2015) Hyunjoo Cha-Molstad et al.   NATURE CELL BIOLOGY

Spatio-temporal patterning of arginyl-tRNA protein transferase (ATE) contributes to gametophytic development in a moss

(2015) Christian Schuessele et al.   NEW PHYTOLOGIST

Two N-Terminal Acetyltransferases Antagonistically Regulate the Stability of a Nod-Like Receptor in Arabidopsis

(2015) Fang Xu et al.   PLANT CELL

Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage

(2015) Ansgar Gruber et al.   PLANT JOURNAL

Characterization of Chloroplast Protein Import without Tic56, a Component of the 1-Megadalton Translocon at the Inner Envelope Membrane of Chloroplasts

(2015) Daniel Köhler et al.   PLANT PHYSIOLOGY

Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots

(2015) Hongtao Zhang et al.   PROTEOMICS

Enrichment of protein N-termini by charge reversal of internal peptides

(2015) Zon W. Lai et al.   PROTEOMICS

An improved workflow for quantitative N-terminal charge-based fractional diagonal chromatography (ChaFRADIC) to study proteolytic events inArabidopsis thaliana

(2015) A. Saskia Venne et al.   PROTEOMICS

Molecular identification and functional characterization of the first Nα-acetyltransferase in plastids by global acetylome profiling

(2015) Trinh V. Dinh et al.   PROTEOMICS

Emerging Functions for N-Terminal Protein Acetylation in Plants

(2015) Daniel J. Gibbs   TRENDS IN PLANT SCIENCE

The paracaspase MALT1 cleaves HOIL1 reducing linear ubiquitination by LUBAC to dampen lymphocyte NF-κB signalling

(2015) Theo Klein et al.   Nature Communications

Downregulation of N-terminal acetylation triggers ABA-mediated drought responses in Arabidopsis

(2015) Eric Linster et al.   Nature Communications

Identification of protein N-termini in Cyanophora paradoxa cyanelles: transit peptide composition and sequence determinants for precursor maturation

(2015) Daniel Köhler et al.   Frontiers in Plant Science

Arginyltransferase ATE1 Catalyzes Midchain Arginylation of Proteins at Side Chain Carboxylates In Vivo

(2014) Junling Wang et al.   CHEMISTRY & BIOLOGY

N-terminomics and proteogenomics, getting off to a good start

(2014) Erica M. Hartmann et al.   PROTEOMICS

Ensembles of protein termini and specific proteolytic signatures as candidate biomarkers of disease

(2014) Pitter F. Huesgen et al.   Proteomics Clinical Applications

Approach for Identification and Quantification of C-Terminal Peptides: Incorporation of Isotopic Arginine Labeling Based on Oxazolone Chemistry

(2013) Minbo Liu et al.   ANALYTICAL CHEMISTRY

The N-end rule proteolytic system in autophagy

(2013) Sung Tae Kim et al.   Autophagy

Novel Highly Sensitive, Specific, and Straightforward Strategy for Comprehensive N-Terminal Proteomics Reveals Unknown Substrates of the Mitochondrial Peptidase Icp55

(2013) A. Saskia Venne et al.   JOURNAL OF PROTEOME RESEARCH

Absolute proteomic quantification of the activity state of proteases and proteolytic cleavages using proteolytic signature peptides and isobaric tags

(2013) Richard P. Fahlman et al.   Journal of Proteomics

Control of Protein Quality and Stoichiometries by N-Terminal Acetylation and the N-End Rule Pathway

(2013) Anna Shemorry et al.   MOLECULAR CELL

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

The Arabidopsis METACASPASE9 Degradome

(2013) L. Tsiatsiani et al.   PLANT CELL

Proteomic Amino-Termini Profiling Reveals Targeting Information for Protein Import into Complex Plastids

(2013) Pitter F. Huesgen et al.   PLoS One

Small molecule inhibitors of arginyltransferase regulate arginylation-dependent protein degradation, cell motility, and angiogenesis

(2012) Sougata Saha et al.   BIOCHEMICAL PHARMACOLOGY

Protein sorting in complex plastids

(2012) Lilach Sheiner et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Unbiased Selective Isolation of Protein N-terminal Peptides from Complex Proteome Samples Using Phospho Tagging (PTAG) and TiO2-based Depletion

(2012) Geert P. M. Mommen et al.   MOLECULAR & CELLULAR PROTEOMICS

Comparative Large Scale Characterization of PlantversusMammal Proteins Reveals Similar and IdiosyncraticN-α-Acetylation Features

(2012) Willy V. Bienvenut et al.   MOLECULAR & CELLULAR PROTEOMICS

The N-end rule pathway counteracts cell death by destroying proapoptotic protein fragments

(2012) K. I. Piatkov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chemoenzymatic Labeling of Protein C-Termini for Positive Selection of C-Terminal Peptides

(2011) Guoqiang Xu et al.   ACS Chemical Biology

Posttranslational arginylation as a global biological regulator

(2011) Sougata Saha et al.   DEVELOPMENTAL BIOLOGY

Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates

(2011) Oded Kleifeld et al.   Nature Protocols

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

(2011) An Staes et al.   Nature Protocols

N- and C-terminal degradomics: new approaches to reveal biological roles for plant proteases from substrate identification

(2011) Pitter F. Huesgen et al.   PHYSIOLOGIA PLANTARUM

Proteins of Diverse Function and Subcellular Location Are Lysine Acetylated in Arabidopsis

(2011) I. Finkemeier et al.   PLANT PHYSIOLOGY

The N-end rule pathway and regulation by proteolysis

(2011) Alexander Varshavsky   PROTEIN SCIENCE

Multiplex N-terminome Analysis of MMP-2 and MMP-9 Substrate Degradomes by iTRAQ-TAILS Quantitative Proteomics

(2010) Anna Prudova et al.   MOLECULAR & CELLULAR PROTEOMICS

Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products

(2010) Oded Kleifeld et al.   NATURE BIOTECHNOLOGY

Complementary positional proteomics for screening substrates of endo- and exoproteases

(2010) Petra Van Damme et al.   NATURE METHODS

Proteome-wide analysis of protein carboxy termini: C terminomics

(2010) Oliver Schilling et al.   NATURE METHODS

Generation of acetyllysine antibodies and affinity enrichment of acetylated peptides

(2010) Kun-Liang Guan et al.   Nature Protocols

N-Terminal Acetylation of Cellular Proteins Creates Specific Degradation Signals

(2010) C.-S. Hwang et al.   SCIENCE

Global Analysis of the Mitochondrial N-Proteome Identifies a Processing Peptidase Critical for Protein Stability

(2009) F.-Nora Vögtle et al.   CELL

Identification of N-terminally arginylated proteins and peptides by mass spectrometry

(2009) Tao Xu et al.   Nature Protocols

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

(2009) Paul J Boersema et al.   Nature Protocols

The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis

(2009) T. J. Holman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The N-end rule pathway controls multiple functions during Arabidopsis shoot and leaf development

(2009) E. Graciet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini

(2009) G. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions

(2009) C. Choudhary et al.   SCIENCE

Plant Proteases: From Phenotypes to Molecular Mechanisms

(2008) Renier A. L. van der Hoorn   Annual Review of Plant Biology

Tags for labeling protein N-termini with subtiligase for proteomics

(2008) Hikari A.I. Yoshihara et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini

(2008) Sami Mahrus et al.   CELL

Sorting Signals, N-Terminal Modifications and Abundance of the Chloroplast Proteome

(2008) Boris Zybailov et al.   PLoS One

Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)

(2008) An Staes et al.   PROTEOMICS