Dual Targeting of the Protein Methyltransferase PrmA Contributes to Both Chloroplastic and Mitochondrial Ribosomal Protein L11 Methylation in Arabidopsis

Abstract

Methylation of ribosomal proteins has long been described in prokaryotes and eukaryotes, but our knowledge about the enzymes responsible for these modifications in plants is scarce. The bacterial protein methyltransferase PrmA catalyzes the trimethylation of ribosomal protein L11 (RPL11) at three distinct sites. The role of these modifications is still unknown. Here, we show that PrmA from Arabidopsis thaliana (AtPrmA) is dually targeted to chloroplasts and mitochondria. Mass spectrometry and enzymatic assays indicated that the enzyme methylates RPL11 in plasto- and mitoribosomes in vivo. We determined that the Arabidopsis and Escherichia coli PrmA enzymes share similar product specificity, making trimethylated residues, but, despite an evolutionary relationship, display a difference in substrate site specificity. In contrast to the bacterial enzyme that trimethylates the ε-amino group of two lysine residues and the N-terminal α-amino group, AtPrmA methylates only one lysine in the MAFCK(D/E)(F/Y)NA motif of plastidial and mitochondrial RPL11. The plant enzyme possibly methylates the N-terminus of plastidial RPL11, whereas mitochondrial RPL11 is N-α-acetylated by an unknown acetyltransferase. Lastly, we found that an Arabidopsis prma-null mutant is viable in standard environmental conditions and no molecular defect could be associated with a lack of RPL11 methylation in leaf chloroplasts or mitochondria. However, the conservation of PrmA during the evolution of photosynthetic eukaryotes together with the location of methylated residues at the binding site of translation factors to ribosomes suggests that RPL11 methylation in plant organelles could be involved, in combination with other post-translational modifications, in optimizing ribosome function.

Determining the Mitochondrial Methyl Proteome in Saccharomyces cerevisiae using Heavy Methyl SILAC

“…Mnp1, Mrpl40, and Mrpl4 are all large subunit components 97 . Methylation of mitochondrial ribosomal protein L11 has been reported in Arabidopsis thaliana 98 ; we find no evidence for the methylation of the corresponding yeast protein in our study. A number of methylation sites of mitochondrial ribosomal proteins were also reported in Trypanosoma brucei 22 , but confirmatory isotope labeling was not used in that study.…”

Protein lysine methylation contributes to modulating the response of sensitive and tolerant Arabidopsis species to cadmium stress

“…In A. thaliana , 48 genes coding KMTs from the SDG have been identified (Serre et al, ). Only two KMTs belonging to the SBS superfamily have been characterized yet in plants, namely, the cytosolic enzyme CaMKMT that methylates calmodulin (CaM) (Banerjee et al, ) and the PrmA methyltransferase that modifies ribosomal protein L11 in plastids and mitochondria (Mazzoleni et al, ). Using BLAST searches, we identified 11 genes from A. thaliana that are orthologous to bacterial, yeast and human KMTs with a SBS structural fold (Figure S5) (Le S.Q.…”

“…In A. thaliana, 48 genes coding KMTs from the SDG have been identified (Serre et al, 2018). Only two KMTs belonging to the SBS superfamily have been characterized yet in plants, namely, the cytosolic enzyme CaMKMT that methylates calmodulin (CaM) (Banerjee et al, 2013) and the PrmA methyltransferase that modifies ribosomal protein L11 in plastids and mitochondria (Mazzoleni et al, 2015). Using BLAST searches, we identified 11 genes from A. thaliana that are orthologous to bacterial, yeast and human KMTs with a SBS structural fold ( Figure S5) In order to determine whether Cd could regulate the expression of KMT genes in A. thaliana, we analysed transcriptomic datasets from published works (Fischer et al, 2017;Herbette et al, 2006;Jobe et al, 2012;Khare et al, 2017;Li et al, 2010;Weber et al, 2006).…”

Protein lysine methylation is involved in modulating the response of sensitive and tolerant Arabidopsis species to cadmium stress

“…In A. thaliana, 48 genes coding KMTs from the SET domain-containing group (SDG) have been identified (Serre et al, 2018). Only two KMTs belonging to the seven-beta-strand (SBS) superfamily have been yet characterized in plants, namely the cytosolic enzyme CaMKMT that methylates calmodulin (CaM) (Banerjee et al, 2013) and the PrmA methyltransferase that modifies ribosomal protein L11 in plastids and mitochondria (Mazzoleni et al, 2015). Using BLAST searches, we identified 11 genes from A. thaliana that are orthologous to bacterial, yeast and human KMTs with a SBS structural fold ( Figure S4).…”