Discovery of AAA+ Protease Substrates through Trapping Approaches

Liao, Jui‐Yun Rei; Wijk, Klaas J. van

doi:10.1016/j.tibs.2018.12.006

Cited by 30 publications

(19 citation statements)

References 77 publications

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“…It is imperative to examine peptidomes in an in vivo context, as in vitro peptidase cleavage assays may reveal activity against an array of putative substrates that are otherwise irrelevant. Plant peptidomics is a nascent research area, mainly focusing on plant development, thus requiring method development and optimization for robust quantitative analysis (Gemperline et al, 2016; Majsec et al, 2017; Rei Liao and van Wijk, 2019). Peptidome extractions are often accompanied by unwanted metabolites and other non‐peptidic features (Maes et al, 2019).…”

Section: Resultsmentioning

confidence: 99%

“…Peptides significantly more abundant in the top1top2 mutant in vivo represent putative direct substrates or pleotropic effects displaying increased accumulation due to the loss of TOP activity (Rei Liao and van Wijk, 2019). Therefore in vitro validation is required to differentiate between these outcomes.…”

Section: Resultsmentioning

confidence: 99%

“…For example, the plant elicitor peptide 1 has increased release from metacaspase‐mediated proteolysis of PROPEP upon plant wounding and activates defensin gene transcription (Hander et al, 2019; Huffaker et al, 2006; Qia et al, 2010; Shen et al, 2019). However, uncovering the role of peptidases in plant stress response is limited by the ability to identify substrates, characterize features of substrate recognition, as well as understand how cleavage products elicit downstream signaling effects due to the perceived stress (Majsec et al, 2017; Rei Liao and van Wijk, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Profiling thimet oligopeptidase‐mediated proteolysis in Arabidopsis thaliana

et al. 2021

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Protein homeostasis (proteostasis) is crucial for proper cellular function, including the production of peptides with biological functions through controlled proteolysis. Proteostasis has roles in maintenance of cellular functions and plant interactions with the environment under physiological conditions. Plant stress continues to reduce agricultural yields causing substantial economic losses; thus, it is critical to understand how plants perceive stress signals to elicit responses for survival. As previously shown in Arabidopsis thaliana, thimet oligopeptidases (TOPs) TOP1 (also referred to as organellar oligopeptidase) and TOP2 (also referred to as cytosolic oligopeptidase) are essential components in plant response to pathogens, but further characterization of TOPs and their peptide substrates is required to understand their contributions to stress perception and defense signaling. Herein, label-free peptidomics via liquid chromatography-tandem mass spectrometry was used to differentially quantify 1111 peptides, originating from 369 proteins, between the Arabidopsis Col-0 wild type and top1top2 knock-out mutant. This revealed 350 peptides as significantly more abundant in the mutant, representing accumulation of these potential TOP substrates. Ten direct substrates were validated using in vitro enzyme assays with recombinant TOPs and synthetic candidate peptides. These TOP substrates are derived from proteins involved in photosynthesis, glycolysis, protein folding, biogenesis, and antioxidant defense, implicating TOP involvement in processes aside from defense signaling. Sequence motif analysis revealed TOP cleavage preference for non-polar residues in the positions surrounding the cleavage site. Identification of these substrates provides a framework for TOP signaling networks, through which the interplay between proteolytic pathways and defense signaling can be further characterized.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Profiling thimet oligopeptidase‐mediated proteolysis in Arabidopsis thaliana

et al. 2021

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“…Following short-term stress, mRNA and proteins levels of ClpC did not change [122], whereas after intensive-light treatments for 2.5 h, the transcript levels increased [128]. In vivo trapping studies for the discovery of the substrates for Clp proteases also revealed that most ClpC components are involved in the stress responses [129].…”

Section: Roles Of Clp Protease Complexes In Land Plants During Stressmentioning

confidence: 98%

Protective Roles of Cytosolic and Plastidal Proteasomes on Abiotic Stress and Pathogen Invasion

Ali

Baek

2020

Plants

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Protein malfunction is typically caused by abiotic stressors. To ensure cell survival during conditions of stress, it is important for plant cells to maintain proteins in their respective functional conformation. Self-compartmentalizing proteases, such as ATP-dependent Clp proteases and proteasomes are designed to act in the crowded cellular environment, and they are responsible for degradation of misfolded or damaged proteins within the cell. During different types of stress conditions, the levels of misfolded or orphaned proteins that are degraded by the 26S proteasome in the cytosol and nucleus and by the Clp proteases in the mitochondria and chloroplasts increase. This allows cells to uphold feedback regulations to cellular-level signals and adjust to altered environmental conditions. In this review, we summarize recent findings on plant proteolytic complexes with respect to their protective functions against abiotic and biotic stressors.

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“…Often because of severe and pleiotropic mutant phenotypes in combination with a lack of clear cleavage site (Box 1) motifs – instead of cleaving a substrate once, resulting in a defined cleavage site motif, the enzyme can cleave at many sites in the substrate with lesser site specificity and so it is hard to assign a substrate through prediction of cleavage sites or matching to a known protease specificity profile. To obtain evidence for bona fide substrates, multiple follow-up experiments are required with substrate trapping being a particularly promising way forward (Rei Liao and van Wijk, 2019). In a substantial advance for serine and cysteine proteases, a proof-of-concept was recently established for substrate trapping by replacement of the active site cysteine or serine with the non-native amino acid 2,3-diaminopropionic acid (DAP) (Huguenin-Dezot et al , 2019).…”

Section: Protease Substratesmentioning

confidence: 99%