The structural and functional workings of KEOPS

Abstract

KEOPS (Kinase, Endopeptidase and Other Proteins of Small size) is a five-subunit protein complex that is highly conserved in eukaryotes and archaea and is essential for the fitness of cells and for animal development. In humans, mutations in KEOPS genes underlie Galloway–Mowat syndrome, which manifests in severe microcephaly and renal dysfunction that lead to childhood death. The Kae1 subunit of KEOPS catalyzes the universal and essential tRNA modification N6-threonylcarbamoyl adenosine (t6A), while the auxiliary subunits Cgi121, the kinase/ATPase Bud32, Pcc1 and Gon7 play a supporting role. Kae1 orthologs are also present in bacteria and mitochondria but function in distinct complexes with proteins that are not related in structure or function to the auxiliary subunits of KEOPS. Over the past 15 years since its discovery, extensive study in the KEOPS field has provided many answers towards understanding the roles that KEOPS plays in cells and in human disease and how KEOPS carries out these functions. In this review, we provide an overview into recent advances in the study of KEOPS and illuminate exciting future directions.

A prebiotically plausible scenario of an RNA–peptide world

“…The question of how this RNA world then advanced to the next stage, in which proteins became the catalysts of life and RNA reduced its function predominantly to information storage, is one of the most mysterious chicken-and-egg conundrums in evolution 3 – 5 . Here we show that non-canonical RNA bases, which are found today in transfer and ribosomal RNAs 6 , 7 , and which are considered to be relics of the RNA world 8 – 12 , are able to establish peptide synthesis directly on RNA. The discovered chemistry creates complex peptide-decorated RNA chimeric molecules, which suggests the early existence of an RNA–peptide world 13 from which ribosomal peptide synthesis 14 may have emerged 15 , 16 .…”

Commonality and diversity in tRNA substrate recognition in t6A biogenesis by eukaryotic KEOPSs

“…Indeed, mutation of a potential tRNA-binding residue (Arg 63 in the Pcc1 subunit of the archaeal KEOPS) abolishes the t 6 A modification activity of archaeal KEOPS ( 18 ). Gon7 subunit interacts with Pcc1 in an opposite side and is spatially far from tRNA anticodon loop ( 5 ); it is unlikely to be C32 binding partner. Nonetheless, the interaction between the tRNA anticodon loop and KEOPS need to be further explored in detail.…”

“…This evidence highlights the conserved feature of the critical role of the D-arm in both eukaryotic and archaeal KEOPS complexes. The G10–C25 and C11–G24 motifs probably interact with OSGEP and/or TP53RK according to the archaeal KEOPS–tRNA interaction model ( 5 , 18 ).…”

“…Among all positions of a given tRNA molecule, those in the anticodon loop, in particular positions 34 and 37, are the most extensively modified due to their critical roles in codon-anticodon base pairing strength and accuracy ( 3 , 4 ). N 6 -Threonylcarbamoyladenosine (t 6 A) is a modified nucleotide found exclusively at position 37 adjacent to the anticodon in ANN-decoding tRNAs across all three domains of life ( 5 , 6 ). Enzymes for t 6 A biogenesis have been studied in bacteria, archaea, and eukaryotes and in organelles.…”

“…In addition to the catalytic subunit Kae1 (OSGEP), Bud32 (TP53RK) is an ATPase that catalyzes the hydrolysis of ATP to ADP and Pi ( 19 ); however, the exact role of this subunit in t 6 A biogenesis remains unclear. Furthermore, the function of both Gon7 (GON7) and Pcc1 (LAGE3) remains unknown ( 5 ). TsaC has been reported to interact with the TsaD-TsaB-TsaE complex ( 10 ); however, Sua5/YRDC seems to be independent of the KEOPS complex in the cytoplasm or of OSGEPL1 in mitochondria ( 15 , 19 ).…”