Human AATF/Che-1 forms a nucleolar protein complex with NGDN and NOL10 required for 40S ribosomal subunit synthesis

Abstract

Mammalian AATF/Che-1 is essential for embryonic development, however, the underlying molecular mechanism is unclear. By immunoprecipitation of human AATF we discovered that AATF forms a salt-stable protein complex together with neuroguidin (NGDN) and NOL10, and demonstrate that the AATF-NGDN-NOL10 (ANN) complex functions in ribosome biogenesis. All three ANN complex members localize to nucleoli and display a mutual dependence with respect to protein stability. Mapping of protein-protein interaction domains revealed the importance of both the evolutionary conserved WD40 repeats in NOL10 and the UTP3/SAS10 domain in NGDN for complex formation. Functional analysis showed that the ANN complex supports nucleolar steps of 40S ribosomal subunit biosynthesis. All complex members were required for 18S rRNA maturation and their individual depletion affected the same nucleolar cleavage steps in the 5′ETS and ITS1 regions of the ribosomal RNA precursor. Collectively, we identified the ANN complex as a novel functional module supporting the nucleolar maturation of 40S ribosomal subunits. Our data help to explain the described role of AATF in cell proliferation during mouse development as well as its requirement for malignant tumor growth.

A protein-RNA interaction atlas of the ribosome biogenesis factor AATF

“…AATF had previously been associated with ribosome biogenesis due to its nucleolar localization and the impact of loss of the protein on the generation of the 40S subunit and rRNA maturation 15,16 . In our study, depletion of AATF led to a reduction in mature rRNA levels and previously published work had shown an accumulation of rRNA precursors upon loss of AATF 15,21 . Furthermore, AATF has been shown to be part of a protein complex (ANN complex) required for efficient generation of the SSU 21 .…”

“…Interestingly, Bfr2 -the budding yeast orthologue of AATF -was identified in a screen that analyzed constituents of yeast 90S particles assembled using truncated pre-18S RNAs and was shown to be specifically bound to the 5'ETS 40 . Furthermore, Bammert et al 21 had…”

“…As mentioned above, none of the ANN complex constituents -including AATF -possess a canonical RNA binding domain. While Bammert et al 21 argued that RNA binding of the ANN complex may be mediated by the WD40 domain of NOL10 which had previously been shown to mediate RNA-binding of other proteins 44 , the intrinsically disordered, basic Cterminus of AATF, 20% of which is made up of lysine (K) and arginine (R) residues, appears likely to promote RNA binding. This is also in line with recent studies that could emphasize the importance of intrinsically disordered regions (IDR) for RNA-protein interactions 24,27,45 and the results of recent proteome-wide screens for RNA-binding domains 26,45 .…”

“…However, the mode of action of AATF in ribosome maturation has remained unclear. A first insight came recently from a study by Bammert et al 21 that could show AATF as part of a nucleolar protein complex (termed ANN complex).…”

Proteome and phosphoproteome changes associated with prognosis in acute myeloid leukemia

“…RRP1B (P < .0002, FC 1.09) and AATF (P < .0002, FC 0.91) were the most significant proteins in this cluster. AATF (also known as CHE1) is participating in several cellular pathways, such as 40S ribosomal subunit synthesis in complex with NGDN (P = .0014, FC 0.95) and NOL10 (P = .0007, FC 0.85)49 , and high AATF expression has been linked to variants of leukemia50,51 . Other proteins in this cluster were CEBPZ, a transcription factor in the CEBP family, several WD repeat-containing proteins (e.g.…”