Functional analysis of the methyltransferase SMYD in the single-cell model organism Tetrahymena thermophila

In order to resolve controversies concerning SMYD's substrates and functions, we studied SMYD1 (TTHERM_00578660), the only homologue in the unicellular eukaryote Tetrahymena thermophila. We epitope-tagged SMYD1, and analyzed its localization and interactome. We also characterized ΔSMYD1 cells, focusing on the replication and transcription phenotype. Our results show that: 1) SMYD1 is present in both cytoplasm and transcriptionally active macronucleus and shuttles between cytoplasm and macronucleus, which is consistent with its association with both histone and non-histone substrates; 2) SMYD1 is involved in DNA replication and regulates transcription of metabolism-related genes; 3) HSP90 is an potential substrate for SMYD1 and it may regulate target selection of HSP90, leading to pleiotropic effects in both the cytoplasm and the nucleus. To investigate the roles of SMYD1 in regulating gene transcription, we carried out RNA-seq analysis in wild-type (CU428) and the isogenic △SMYD1 cells. In total, 21461 well-annotated genes were included, among which 4841 (23%) were up-regulated (> 2-fold) and 1507 (7%) down-regulated (< 0.5-fold). KEGG pathway analysis revealed that the most affected pathways in △SMYD1 cells were metabolic pathway (ko01100) and biosynthesis of secondary metabolites (ko01110), supporting that SMYD1 plays important roles in regulating metabolic genes in Tetrahymena. The result of Gene Ontology (GO) term enrichment analysis was consistent with that of the KEGG pathway analysis, which revealed the single organism metabolic process as the most enriched pathway for the up-regulated genes in △SMYD1 cells. These results suggested that SMYD1 is involved in regulation of metabolism.