GSE97140
Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA translation
Many cellular proteins are post-translationally modified by methylation of lysine residues. This has been most intensively studied in the case of histone proteins, where lysine methylations in the flexible tails are determinants of chromatin state and gene expression. Lysine methylations on non-histone proteins are also frequent, but in most cases the functional significance of the methylation event, as well as the identity of the responsible lysine (K) specific methyltransferase (KMT), remain unknown. While the majority of identified human KMTs belong to the SET (Su(var)3-9, Enhancer-of-zeste, Trithorax)-domain class of methyltransferases (MTases), several recently discovered KMTs belong to a different MTase class, the seven-beta-strand (7BS) MTases. Here, we have investigated an uncharacterized human 7BS MTase currently annotated as being part of the endothelin converting enzyme 2 (ECE2). However, transcriptomics data indicate that this MTase is not part of ECE2, and should be considered a separate protein. Combining in vitro enzymology and analyses of knockout cells, we demonstrate that this MTase efficiently methylates K36 in eukaryotic translation elongation factor 1 alpha (eEF1A) in vitro and in vivo. We suggest that this novel KMT is named eEF1A-KMT4 (gene name EEF1AKMT4), in agreement with the recently established nomenclature. Furthermore, by ribosome profiling we show that the absence of K36 methylation affects translation dynamics and changes translation speed of distinct codons. Finally, we demonstrate that eEF1A-KMT4 is part of a novel family of human KMTs, defined by a shared sequence motif in the active site, and we show the importance of this motif for catalytic activity. Overall design: Ribosome profiling and RNAseq data for wt and  EEF1AKMT4 knockout cells. This study includes the re-use of samples GSM2445294 and GSM2445295 from GSE93133. These two samples have been re-accessioned here so that the complete study is available from the SRP ID.