Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function

Abstract

Mitochondria are essential molecular machinery for the maintenance of cellular energy supply by the oxidative phosphorylation system (OXPHOS). Mitochondrial transcription factor B1 (TFB1M) is a dimethyltransferase that maintains mitochondrial homeostasis by catalyzing dimethylation of two adjacent adenines located in helix45 (h45) of 12S rRNA. This m62A modification is indispensable for the assembly and maturation of human mitochondrial ribosomes. However, both the mechanism of TFB1M catalysis and the precise function of TFB1M in mitochondrial homeostasis are unknown. Here we report the crystal structures of a ternary complex of human (hs) TFB1M–h45–S-adenosyl-methionine and a binary complex hsTFB1M–h45. The structures revealed a distinct mode of hsTFB1M interaction with its rRNA substrate and with the initial enzymatic state involved in m62A modification. The suppression of hsTFB1M protein level or the overexpression of inactive hsTFB1M mutants resulted in decreased ATP production and reduced expression of components of the mitochondrial OXPHOS without affecting transcription of the corresponding genes and their localization to the mitochondria. Therefore, hsTFB1M regulated the translation of mitochondrial genes rather than their transcription via m62A modification in h45.

Shared requirements for key residues in the antibiotic resistance enzymes ErmC and ErmE suggest a common mode of RNA recognition

“…Recent structural data has emerged for two members of the RRAD family, a low-resolution cryo-EM structure of RsmA (KsgA) bound to the 30S ribosome and a crystal structure of TFB1M bound to helix 45 of mitochondrial 12S rRNA (Figs. 1E and 7A) (20,24). Both structures possess a similar mode of interaction with their rRNA substrate in which the helical axis of helix 45 is perpendicular to the long axis of the methyltransferase which can be best seen in Figure 7A.…”

Methylation of Ribosomal RNA: A Mitochondrial Perspective

“…Initially, mitochondrial TFB1M was considered to function as a transcription factor alongside TFB2M. However, it was instead shown to be a dimethyltransferase responsible for m 6 2 A modification of the 12S rRNA (Cotney and Shadel, 2006;Liu et al, 2019). This modification occurs within two adjacent adenines, A936 and A937 (human mtDNA position: m.1583A and m.1584A, respectively), located in the tetraloop "GGAA" of helix 45 at the 3′-end of the mt-12S rRNA, which is extremely conserved in both sequence and structure (McCulloch et al, 2002).…”

“…Recently, the crystal structure of TFB1M in complex with helix 45 and SAM has revealed its unique properties compared to its paralogue TFB2M (Liu et al, 2019). Notably, TFB1M has a clear acid-active pocket, which accommodates SAM, while the same region in TFB2M is highly positively charged, thus facilitating interaction with DNA molecules.…”

Epitranscriptomics of Mammalian Mitochondrial Ribosomal RNA

“…In mammalian mitoribosomes nucleotides m 2 6 A936 and m 2 6 A937 ( Figure 2 ) are modified by TFB1M [ 63 ] in a sequential order starting with A937 [ 64 ]. TFB1M and its paralogue, TFB2M, may also act as a transcription factor to activate transcription by POLRMT in vitro [ 65 ].…”

“…Inactivation of Tfb1m gene caused a decreased amount of the small ribosomal subunits, diminished efficiency of mitochondrial translation [ 64 ], and decrease in the abundance of ETC complexes subunits, encoded in the mitochondrial genome [ 70 ]. Tfb1m inactivation in murine pancreatic β-cells also causes mitochondrial disfunction: such cells have decreased ETC complex activity, while the amount of mitochondria is elevated.…”