A Regex-Based Screening Model for 8-Ligand Metal-Binding RING and CHY Zinc Finger Domains in the Tea Proteome

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Eminoğlu A.

8TH INTERNATIONAL BLACK SEA MODERN SCIENTIFIC RESEARCH CONGRESS, Giresun, Türkiye, 21 - 22 Şubat 2026, ss.1, (Özet Bildiri)

  • Yayın Türü: Bildiri / Özet Bildiri
  • Basıldığı Şehir: Giresun
  • Basıldığı Ülke: Türkiye
  • Sayfa Sayıları: ss.1
  • Açık Arşiv Koleksiyonu: AVESİS Açık Erişim Koleksiyonu
  • Recep Tayyip Erdoğan Üniversitesi Adresli: Evet

Özet

ABSTRACT

Introduction and Purpose: In plants, CHY-type zinc finger motifs predominantly co-occur with C3H-type RING domains in CHYR proteins, forming Zn-dependent E3 ligases that integrate metal/iron sensing, protein ubiquitination, and abiotic stress signaling. In contrast, C3HC4-type RING fingers represent a structurally distinct class of RING zinc fingers that regulate growth, organ development, and broader signaling processes through targeted protein degradation. In this study, within the scope of metal-binding domains in the tea plant proteome, a regular expression (regex)-based screening model is developed based on an eight-metal-ligand (Cys/His) motif architecture characteristic of RING and CHY zinc finger families.

 

Materials and Methods: Two complementary approaches are employed for metal-binding motif detection. First, regex-based screening identifies C2H2-like zinc finger motifs, RING finger-like C3HC4 arrangements, and H/C-rich motif patterns. The proteome is analyzed on a per-protein basis in the R environment, and protein length together with histidine (H) and cysteine (C) contents are calculated. Regions of ≥60 amino acid satisfying at least one of the following criteria are selected as candidates: H ≥6, C ≥6, or (H+C) ≥8. At the protein level, sequences with a histidine fraction ≥0.12 or a cysteine fraction ≥0.08 are considered generally enriched. Conformity to the 8-ligand RING configuration is re-evaluated using two regex patterns representing C3H2C3 and C3HC4 arrangements. When multiple matches occur within a protein, the longest match with the highest C/H content is selected.

 

Results: 99 candidate proteins meeting these strict structural criteria are independently validated using CDD/CD-Search and InterPro analyses. Discussion and Conclusion: Unlike previous genome and annotation based studies reporting over 300 RING finger proteins in tea plants, this work applies the eight-ligand metal-binding motif architecture as a structural prerequisite, yielding a high-confidence and structurally refined candidate set.

 

Key Words: Metal-binding motifs; RING zinc finger; CHY-type zinc finger; E3 ubiquitin ligases; Camellia sinensis