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Comparative analysis of plant lycopene cyclases
Ibrahim Koc1, Ertugrul Filiz2, Huseyin Tombuloglu3
1Gebze Technical University, Faculty of Science, Department of Molecular Biology and Genetics, Gebze, Kocaeli, 41400, Turkey; Crop Science, University of Illinois at Urbana-Champaign, United States.
Computational Biology and Chemistry
|June 21, 2015
Summary
Plant lycopene cyclases (LYC) are crucial for carotenoid production. This study reveals conserved motifs and structural similarities across plant LYC types, highlighting β-LCY genes
Area of Science:
- Plant biochemistry
- Molecular biology
- Genetics
Background:
- Carotenoids are vital plant pigments synthesized through carotenogenesis.
- Lycopene cyclase (LYC) enzymes catalyze a key branching step in carotenoid biosynthesis.
- Plants possess two main types of LYC: β-LCY and ϵ-LCY.
Purpose of the Study:
- To analyze plant lycopene cyclase (LYC) proteins.
- To investigate conserved features and evolutionary relationships among plant LYCs.
- To identify potential functional motifs and structural characteristics of LYCs.
Main Methods:
- Domain analysis to identify the lycopene cyclase domain (Pf05834).
- Motif analysis to detect conserved sequence patterns.
- Phylogenetic analysis to classify β-LCYs and ϵ-LCYs and differentiate monocots and dicots.
- Nucleotide diversity analysis of β-LCY and ϵ-LCY genes.
- 3D modeling for structural comparison.
- Co-expression analysis using the String server.
Main Results:
- All analyzed plant LYCs contain the conserved lycopene cyclase domain (Pf05834).
- Phylogenetic analysis clearly separated β-LCYs and ϵ-LCYs into distinct groups, with monocots and dicots also forming separate clades.
- β-LCY genes exhibited higher nucleotide diversity (π: 0.30) compared to ϵ-LCY genes (π: 0.25).
- 3D modeling revealed highly similar structures and conserved binding sites across analyzed monocot (Oryza sativa, Zea mays) and dicot (Vitis vinifera, Solanum lycopersicum) LYCs.
- A conserved V/IXGXGXXGXXXA motif, potentially involved in FAD binding via a Rossmann fold domain, was identified in both β-LCY and ϵ-LCY types.
Conclusions:
- Plant LYCs share conserved domains, motifs, and structures, indicating functional importance in carotenoid metabolism.
- The identified V/IXGXGXXGXXXA motif serves as a conserved signature for LYCs and can aid in annotating unknown proteins with lycopene cyclase domains.
- Comparative analysis of β-LCY and ϵ-LCY genes provides insights into their evolutionary divergence and diversity within plants.
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