Mapping the proteome landscape in Euglena gracilis: global, phospho, and ubiquitin proteomes under anaerobic response.

The photosynthetic flagellate Euglena gracilis (Euglena) exhibits a remarkable metabolic flexibility, enabling the dynamic coordination of energy production and resource partitioning during anaerobic adaptation. While the wax ester synthesis under hypoxia is well-documented, the regulatory interplay between protein abundance and post-translational modifications (PTMs) remains unexplored. A definitive understanding of this metabolic remodeling is hindered by the lack of high-depth proteomic resources and the fragmented genome annotations, which fail to capture Euglena's proteomic diversity and plasticity. Here, we provide a comprehensive Euglena proteome landscape through advanced LC-MS/MS analysis. By leveraging the recently refined proteome annotation, we identified 9,122 protein groups, 12,027 phospho-peptides, and 3,346 ubiquitinated peptides, establishing a comprehensive Euglena's proteome reference. Our results demonstrate that anaerobic adaptation is characterized by distinct phosphorylation and ubiquitination signatures that often occur independently of changes in global protein abundance, revealing a layer of PTM-mediated control over central metabolism during anaerobic adaptation in Euglena. This study provides a foundational resource that bridges the gap between genomic potential and functional metabolic in Euglena. By resolving the interplay between protein levels and PTM-driven regulation, our work offers a new resource for investigating environmental adaptation and provides a rigorous framework for future metabolic engineering in Euglena.