iCysMod: an integrative database for protein cysteine modifications in eukaryotes

Wang, Panqin; Li, Shihua; Cheng, Ben; Han, Xue; Wei, Zhen; Shao, Tian; Liu, Zexian; Cheng, Han; Wang, Zhenlong

doi:10.1093/bib/bbaa400

Cited by 16 publications

(20 citation statements)

References 61 publications

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“…Cys residues in Hsp70 generally show modest reactivity in global profiling of the cysteinome [ 55 ]. Over the past twenty years development of methods for enrichment of Cys-modified proteins and mass spectrometry (MS) detection has allowed extensive identification of cysteine modifications in Hsp70 members ( Table S1 ), which have been summarized in databases for protein cysteine modifications [ 56 , 57 , 58 , 59 , 60 ]. Once cysteine modifications have been identified, the next goal is to identify the effects of cysteine modifications on the structure and function of Hsp70 and the physiological significance of these changes.…”

Section: Post-translational Modifications Of Hsp70 Under Oxidative St...mentioning

confidence: 99%

Hsp70 in Redox Homeostasis

Zhang

Gong

et al. 2022

Cells

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Cellular redox homeostasis is precisely balanced by generation and elimination of reactive oxygen species (ROS). ROS are not only capable of causing oxidation of proteins, lipids and DNA to damage cells but can also act as signaling molecules to modulate transcription factors and epigenetic pathways that determine cell survival and death. Hsp70 proteins are central hubs for proteostasis and are important factors to ameliorate damage from different kinds of stress including oxidative stress. Hsp70 members often participate in different cellular signaling pathways via their clients and cochaperones. ROS can directly cause oxidative cysteine modifications of Hsp70 members to alter their structure and chaperone activity, resulting in changes in the interactions between Hsp70 and their clients or cochaperones, which can then transfer redox signals to Hsp70-related signaling pathways. On the other hand, ROS also activate some redox-related signaling pathways to indirectly modulate Hsp70 activity and expression. Post-translational modifications including phosphorylation together with elevated Hsp70 expression can expand the capacity of Hsp70 to deal with ROS-damaged proteins and support antioxidant enzymes. Knowledge about the response and role of Hsp70 in redox homeostasis will facilitate our understanding of the cellular knock-on effects of inhibitors targeting Hsp70 and the mechanisms of redox-related diseases and aging.

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Section: Post-translational Modifications Of Hsp70 Under Oxidative St...mentioning

confidence: 99%

Hsp70 in Redox Homeostasis

Zhang

Gong

et al. 2022

Cells

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“…Previously, numerous informative databases have been constructed to store PTM-related data in plants. For example, some general resources, such as dbPTM ( 25 ) and SysPTM ( 26 ), contain various types of PTMs identified by experiments in eukaryotes, while several PTM-specific databases, including EPSD ( 27 ), PLMD ( 28 ) and iCysMod ( 29 ), host modified sites for phosphorylation, lysine modifications and cysteine modifications in eukaryotic proteins, respectively. However, these databases only cover a limited part of the experimentally identified PTM events in plants.…”

Section: Introductionmentioning

confidence: 99%

qPTMplants: an integrative database of quantitative post-translational modifications in plants

Han

Wang

Cao

et al. 2021

Nucleic Acids Research

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As a crucial molecular mechanism, post-translational modifications (PTMs) play critical roles in a wide range of biological processes in plants. Recent advances in mass spectrometry-based proteomic technologies have greatly accelerated the profiling and quantification of plant PTM events. Although several databases have been constructed to store plant PTM data, a resource including more plant species and more PTM types with quantitative dynamics still remains to be developed. In this paper, we present an integrative database of quantitative PTMs in plants named qPTMplants (http://qptmplants.omicsbio.info), which hosts 1 242 365 experimentally identified PTM events for 429 821 nonredundant sites on 123 551 proteins under 583 conditions for 23 PTM types in 43 plant species from 293 published studies, with 620 509 quantification events for 136 700 PTM sites on 55 361 proteins under 354 conditions. Moreover, the experimental details, such as conditions, samples, instruments and methods, were manually curated, while a variety of annotations, including the sequence and structural characteristics, were integrated into qPTMplants. Then, various search and browse functions were implemented to access the qPTMplants data in a user-friendly manner. Overall, we anticipate that the qPTMplants database will be a valuable resource for further research on PTMs in plants.

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“…Unlike external H2O2 addition, peroxisomal H2O2 production did not result in a po-IBD-SBP-YAP1C-mediated trapping of ACOX1 or MDH1. Nonetheless, such treatment did result in the trapping of various cytosolic, cytoskeletal, and plasma membrane-associated proteins (Table S4), many of which are known to be sulfenylated on at least one cysteine residue [Wang et al, 2021]. Importantly, given that (i) we have previously demonstrated that peroxisomederived H2O2 can efficiently permeate across the peroxisomal membrane [Lismont et al, 2019a], (ii) a small portion of po-IBD-SBP-YAP1C is mislocalized to the cytosol (Fig.…”

Section: The Cytosolic Mitochondrial and Peroxisomal Sulfenome Undergo Time-dependent Changes Upon Peroxisomal H2o2 Generationmentioning

confidence: 95%

Peroxisome-derived hydrogen peroxide can modulate the sulfenylation profiles of key redox signaling proteins

Lismont

Revenco

et al. 2021

Preprint

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Ever since the first characterization of peroxisomes, a central theme has been their involvement in cellular hydrogen peroxide (H2O2) metabolism. While the reputation of H2O2 drastically changed from an exclusively toxic molecule to a signaling messenger, the regulatory role of peroxisomes in these signaling events is still largely underappreciated. This is mainly because the number of known protein targets of peroxisome-derived H2O2 is rather limited and testing of specific targets is predominantly based on knowledge previously gathered in related fields of research. To gain a broader and more systematic insight into the role of peroxisomes in redox signaling, an unbiased approach is urgently needed. To accomplish this goal, we have combined a previously developed cell system in which peroxisomal H2O2 production can be modulated with a yeast AP-1-like-based sulfenome mining strategy to inventory protein thiol targets of peroxisome-derived H2O2 in different subcellular compartments. Using this unbiased approach, we were able to identify specific and common targets of peroxisome-derived and exogenous H2O2 in peroxisomes, the cytosol, and mitochondria. We also observed that the sulfenylation kinetics profiles of key targets belonging to different protein families can vary considerably. In addition, we obtained compelling but indirect evidence that peroxisome-derived H2O2 may oxidize at least some of its targets through a redox relay mechanism. In conclusion, given that sulfenic acids function as key intermediates in H2O2 signaling, the findings presented in this study provide initial but critical insight into how peroxisomes may be integrated in the cellular H2O2 signaling network.

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iCysMod: an integrative database for protein cysteine modifications in eukaryotes

Cited by 16 publications

References 61 publications

Hsp70 in Redox Homeostasis

Hsp70 in Redox Homeostasis

qPTMplants: an integrative database of quantitative post-translational modifications in plants

Peroxisome-derived hydrogen peroxide can modulate the sulfenylation profiles of key redox signaling proteins

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