Protein tyrosine nitration in plants: Present knowledge, computational prediction and future perspectives

Area of Science:

• Biochemistry
• Plant Science
• Molecular Biology

Background:

• Nitric oxide (NO) and reactive nitrogen species regulate physiological processes via posttranslational modifications.
• Protein tyrosine nitration (PTN) is a specific modification of tyrosine residues, altering protein structure and function.
• Significant research has focused on identifying nitrated proteins, target sites, and functional impacts in plants.

Purpose of the Study:

• To review and evaluate existing knowledge on the biochemical mechanisms, structural/functional consequences, and selectivity of PTN in plants.
• To discuss the decomposition and conversion of nitrated proteins.
• To highlight unresolved questions, including the reversibility of PTN, proteasomal involvement, and effects on tyrosine phosphorylation.

Main Methods:

• Literature review and evaluation of accumulated knowledge on PTN in plants.
• In silico analysis of the Arabidopsis proteome using computational prediction tools (GPS-YNO2, iNitro-Tyr) to identify potential nitrated proteins.
• Selection of candidate proteins for future research based on prediction and experimental data.

Main Results:

• Accumulated knowledge on PTN mechanisms, consequences, and selectivity in plants has been evaluated.
• In silico analysis identified potential plant tyrosine nitroproteome candidates.
• Key unanswered questions regarding PTN reversibility, proteasomal degradation, and interplay with tyrosine phosphorylation were emphasized.

Conclusions:

• PTN is a significant regulatory mechanism in plants, with diverse implications for protein function.
• Computational tools aid in identifying potential nitration sites and proteins, guiding future research.
• Further investigation into the evolutionary aspects and unresolved questions of PTN is crucial for a comprehensive understanding.