Analysis of Protein–Protein Interactions in Chlamydomonas reinhardtii CC125 by Co-Fractionation Mass Spectrometry

Abstract

Chlamydomonas reinhardtii, a unicellular eukaryotic green alga, is an important biological model. Previous studies on protein complexes in C. reinhardtii have primarily focused on photosynthesis and ciliary movement, while understanding the overall protein complex network is still limited. To address this issue, we used cofractionation mass spectrometry (CF-MS) to systematically analyze its protein–protein interaction (PPI) network. We identified 51,124 PPIs, of which 6774 are known interactions. Those PPIs were clustered into 490 protein complexes. Besides well-characterized complexes, we discovered 3467 new PPIs and some new components within conserved complexes, which are involved in processes such as photosynthesis, protein degradation, translation initiation, redox reactions, translocation, and signal transduction. These proteins might have functions according to their partners, such as Cre01.g025500.t1.1, HTV2, AGG4, and CPLD59 may participate in photosystem; Cre09.g402450.t1.2, Cre05.g230850.t1.1, FAP269, Cre01.g001100.t1.2, and Cre01.g030450.t1.1 may affect protein degradation. We also found protein complexes associated with substance transport, cellular signaling, and response mechanisms, reflecting the complex regulatory network of C. reinhardtii in adapting to environmental changes. Additionally, we found 46 flagellar-associated proteins, which have potential roles in translation regulation and calcium-signaling pathways. These results will provide valuable data sources and insights into understanding the molecular mechanisms underlying biological activities in C. reinhardtii.