Publications

• Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases.

  Pulicherla N., Pogorzala L.A., Xu Z., O'Farrell H.C., Musayev F.N., Scarsdale J.N., Sia E.A., Culver G.M., Rife J.P.

  The enzymes of the KsgA/Dim1 family are universally distributed throughout all phylogeny; however, structural and functional differences are known to exist. The well-characterized function of these enzymes is to dimethylate two adjacent adenosines of the small ribosomal subunit in the normal cours ... >> More

  The enzymes of the KsgA/Dim1 family are universally distributed throughout all phylogeny; however, structural and functional differences are known to exist. The well-characterized function of these enzymes is to dimethylate two adjacent adenosines of the small ribosomal subunit in the normal course of ribosome maturation, and the structures of KsgA from Escherichia coli and Dim1 from Homo sapiens and Plasmodium falciparum have been determined. To this point, no examples of archaeal structures have been reported. Here, we report the structure of Dim1 from the thermophilic archaeon Methanocaldococcus jannaschii. While it shares obvious similarities with the bacterial and eukaryotic orthologs, notable structural differences exist among the three members, particularly in the C-terminal domain. Previous work showed that eukaryotic and archaeal Dim1 were able to robustly complement for KsgA in E. coli. Here, we repeated similar experiments to test for complementarity of archaeal Dim1 and bacterial KsgA in Saccharomyces cerevisiae. However, neither the bacterial nor the archaeal ortholog could complement for the eukaryotic Dim1. This might be related to the secondary, non-methyltransferase function that Dim1 is known to play in eukaryotic ribosomal maturation. To further delineate regions of the eukaryotic Dim1 critical to its function, we created and tested KsgA/Dim1 chimeras. Of the chimeras, only one constructed with the N-terminal domain from eukaryotic Dim1 and the C-terminal domain from archaeal Dim1 was able to complement, suggesting that eukaryotic-specific Dim1 function resides in the N-terminal domain also, where few structural differences are observed between members of the KsgA/Dim1 family. Future work is required to identify those determinants directly responsible for Dim1 function in ribosome biogenesis. Finally, we have conclusively established that none of the methyl groups are critically important to growth in yeast under standard conditions at a variety of temperatures. << Less

  J. Mol. Biol. 391:884-893(2009) [PubMed] [EuropePMC]

• The DIM1 gene responsible for the conserved m6(2)Am6(2)A dimethylation in the 3'-terminal loop of 18 S rRNA is essential in yeast.

  Lafontaine D., Delcour J., Glasser A.L., Desgres J., Vandenhaute J.

  Biogenesis of cytoplasmic ribosomes universally involves methylation of ribosomal RNA. Little genetic evidence is available about the functional role(s) of this conserved posttranscriptional modification. The only known methylase gene involved in rRNA maturation is ksgA in Escherichia coli, which ... >> More

  Biogenesis of cytoplasmic ribosomes universally involves methylation of ribosomal RNA. Little genetic evidence is available about the functional role(s) of this conserved posttranscriptional modification. The only known methylase gene involved in rRNA maturation is ksgA in Escherichia coli, which directs dimethylation of two adjacent adenosines (m6(2)A1518m6(2)A1519) in the loop of a conserved hairpin near the 3'-end of 16 S rRNA. This tandem methylation is the only rRNA modification common to pro and eukaryotes. Disruption of ksgA confers resistance to the aminoglycoside antibiotic kasugamycin without significantly impairing viability. Here we report the cloning of the DIM1 gene encoding the homolog 18 S rRNA dimethylase in Saccharomyces cerevisiae. The yeast enzyme is evolutionary related to the ksgA protein. It carries a distinctive lysine-rich-N-terminal extension with a potential protein kinase C phosphorylation site. Like ksgA, DIM1 belongs to the erm family of prokaryotic 23 S rRNA dimethylases responsible for erythromycin resistance. Surprisingly, disruption of DIM1 turns out to be lethal in yeast. << Less

  J. Mol. Biol. 241:492-497(1994) [PubMed] [EuropePMC]