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Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Mining proteomes for zinc finger persulfidation.

Haoju Li1, Andrew T Stoltzfus1, Sarah L J Michel1

  • 1Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy Baltimore MD 21201 USA smichel@rx.umaryland.edu.

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Summary
This summary is machine-generated.

Hydrogen sulfide (H₂S) modifies zinc finger (ZF) proteins through persulfidation. This broad post-translational modification impacts all ZF classes across diverse eukaryotic species, influencing key cellular pathways.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Proteomics

Background:

  • Hydrogen sulfide (H₂S) is an endogenous gasotransmitter involved in cellular signaling via persulfidation.
  • Zinc finger (ZF) proteins, characterized by cysteine-rich domains, are known targets for H₂S-mediated modification.
  • Understanding the prevalence and scope of ZF persulfidation is crucial for deciphering H₂S signaling pathways.

Purpose of the Study:

  • To systematically evaluate the frequency and identify the types of zinc finger proteins undergoing persulfidation in cells.
  • To determine the breadth of ZF persulfidation across different eukaryotic species and ZF structural classes.

Main Methods:

  • A meta-analysis approach was employed, evaluating 22 datasets from 16 independent studies.
  • Persulfide-specific proteomics data were analyzed to identify modified cysteine residues within ZF proteins.
  • Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for pathway enrichment.

Main Results:

  • Persulfidated zinc finger proteins were identified in a wide array of eukaryotic organisms, including humans, mice, rats, plants, and phytoplankton.
  • All major classes of zinc finger proteins, defined by their cysteine and histidine ligand sets, were found to be susceptible to persulfidation.
  • Pathway analysis revealed enrichment in processes such as ubiquitin-dependent protein catabolism and viral carcinogenesis.

Conclusions:

  • Zinc finger protein persulfidation is a widespread and significant post-translational modification (PTM) affecting diverse species and all ZF protein types.
  • ZF persulfidation plays a role in fundamental cellular processes, including protein degradation and pathways implicated in viral carcinogenesis.
  • These findings highlight ZF persulfidation as a critical regulatory mechanism in cellular signaling and function.