1H, 13C, 15N backbone NMR resonance assignments for the rRNA methyltransferase Dim1 from the hyperthermophilic archaeon Pyrococcus horikoshii

The protein dimethyladenosine transferase 1 (Dim1) is a highly conserved protein occurring in organisms ranging from bacteria such as E. coli where it is named KsgA to humans. Since Dim1 is involved in the biogenesis of the small ribosomal subunit it is an essential protein. During ribosome biogenesis Dim1 acts as an rRNA modification enzyme and dimethylates two adjacent adenosine residues of the small ribosomal subunit rRNA. In eukaryotes it is also required to ensure the proper endonucleolytic processing of the small ribosomal subunit rRNA precursor. Recently, a third function was proposed for eukaryotic Dim1. Karbstein and coworkers suggested that Dim1 interacts with the essential ribosome assembly factor Fap7 and that Fap7 is responsible for the dissociation of Dim1 from the nascent small ribosomal subunit. Here, we report the backbone ¹H, ¹³C and ¹⁵N NMR resonance assignments for the 30.9 kDa Dim1 homologue from the hyperthermophilic archaeon Pyrococcus horikoshii (PhDim1) as a prerequisite for a detailed structural investigation of the PhDim1/PhFap7 interaction.

The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation

Late in their maturation, nascent small (40S) ribosomal subunits bind 60S subunits to produce 80S-like ribosomes. Because of the analogy of this translation-like cycle to actual translation, and because 80S-like ribosomes do not produce any protein, it has been suggested that this represents a quality control mechanism for subunit functionality. Here we use genetic and biochemical experiments to show that the essential ATPase Fap7 promotes formation of the rotated state, a key intermediate in translocation, thereby releasing the essential assembly factor Dim1 from pre-40S subunits. Bypassing this quality control step produces defects in reading frame maintenance. These results show how progress in the maturation cascade is linked to a test for a key functionality of 40S ribosomes: their ability to translocate the mRNA⋅tRNA pair. Furthermore, our data demonstrate for the first time that the translation-like cycle is a quality control mechanism that ensures the fidelity of the cellular ribosome pool.

Defective entry into mitosis 1 (Dim1) negatively regulates osteoclastogenesis by inhibiting the expression of nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 (NFATc1)

Bone remodeling is a continuous process of osteoblastic bone formation and osteoclastic bone resorption to maintain normal bone mass. NFATc1 is the master regulator of osteoclastogensis and transcriptionally activated by c-Fos and NF-κB in response to receptor activator of NF-κB ligand (RANKL) treatment. Defective entry into mitosis 1 (Dim1) is a nuclear protein that is implicated in pre-mRNA splicing and cell cycle progression, but the possible role of Dim1 in regulating other cellular processes remains unknown. Here, we demonstrate that Dim1 attenuates RANKL-induced osteoclastogenesis by targeting NFATc1 signaling pathway. Expression levels of Dim1 and NFATc1 are significantly increased during the formation of multinucleated osteoclasts. RNAi-mediated knockdown of Dim1 markedly enhances the expression of NFATc1 and its target genes, leading to the increase of RANKL-induced osteoclastogenesis in bone marrow-derived macrophages. Conversely, ectopic expression of Dim1 decreases RANKL-induced osteoclast differentiation by silencing NFATc1 and its target genes, further linking Dim1 to the dynamic regulation of osteoclastogenesis. Consistent with this notion, ChIP and interaction studies show that Dim1 directly associates with c-Fos and prevents c-Fos from binding to the NFATc1 promoter, resulting in targeted inactivation of the NFATc1 gene. Therefore, our studies reveal an unrecognized role for Dim1 as a master modulator of osteoclast differentiation, as well as the molecular mechanism underlying its repressive action toward osteoclastogensis.