Proteome characterization of single gene deletion mutants lacking zinc finger µ-proteins in Haloferax volcanii

Microproteins (≤70 amino acids) have important and often essential roles in all kingdoms of life, influencing cell motility, regulation of membrane transport and as transcription factors. In the halophilic archaeon and model system Haloferax volcanii a significant number of µ-proteins were predicted to be zinc finger proteins. Here we used mass spectrometry-based proteomics to systematically investigate the impact of single gene deletions of 19 zinc finger µ-proteins on the proteome of H. volcanii grown in synthetic medium with glucose as sole carbon and energy source. We employed a state-of-the-art dia-PASEF acquisition strategy, detecting over 3400 proteins across the 19 deletion strains and the wild type. The comprehensive proteome coverage enabled a systematic analysis of proteome remodeling. We found that in 11 out of the 19 mutants the proteome remodeling involved proteins annotated to play a role in cell motility, matching swarming and growth rate phenotypes we observed for these strains. Taken together, our data provide the most comprehensive proteome coverage of H. volcanii to date, and the effect of 19 different zinc-finger µ-proteins deletion strains on the proteome of this organism. The combined data (available via ProteomeXchange with identifier PXD066008) provide a valuable resource for future research in the field.