Fig 1.
The ECM of pre-rRNA interacts with WDR75, UTP4, and UTP18 proteins in the Homo sapiens SSU processome.
The ECM (green) is a portion of the ETS (yellow) which is part of the SSU pre-rRNA. The ECM interacts with WDR75 (blue), UTP4 (pink), and UTP18 (orange). This 3D structure (PDB: 7MQ8) was determined through Cryo-electron microscopy and visualized in PyMOL (Schrödinger, 2020).
Fig 2.
WD Repeats found in the WDR75 reference sequence: Homo sapiens (NM_032168).
(A) Translation of the first 1845 out of 2493 bp are shown for the Homo sapiens sequence. WD repeats are shown with grey annotations spanning the repeat. The 13 WD repeats in WDR75 are annotated with grey arrows with each repeat containing approximately 40 amino acids. A summary diagram of the entire CDS and the relative location and size of the WD repeats for the humans shown in (B). Red boxes in (B) indicate known interacting sites based on the literature (Singh et al. 2021).
Fig 3.
Maximum likelihood phylogram of mammalian WDR75 based on DNA sequences.
This RAxML tree of mammals is rooted with reptiles, contains bootstrap values along the branches which are shown proportional to their inferred number of substitutions (subs/site). Green branches identify the reptile outgroups rooted with Alligator mississippiensis. Chiroptera (red), Rodentia (blue), and primates (purple) are identified as colored branches and with tip labels. The remaining mammals, mostly Carnivora and Artiodactyla, are shown in black. The three exceptionally long branches have been labeled (A) Myotis (bats), (B) the rodent suborder Myomorpha, and (C) the rodent Microtus oregoni (creeping vole). The asterisk identifies the transcript variants for Homo sapiens and Pan paniscus. The scale bar is in units of substitutions per site.
Table 1.
Clade support and stem branch lengths from the maximum likelihood phylogram of mammals’ WDR75 coding sequences.
Fig 4.
Homo sapiens WDR75 interactions within 4 Å of the ECM, UTP18 and UTP4.
The image of the PDB 7MQ8 is taken using PyMOL and displays cartoon WDR75 in blue, UTP4 in pink, UTP18 in orange, and the ECM in green. The remaining, non-interacting proteins present in the SSU processome multimer are hidden for simplicity. In panel A, WDR75 amino acids interacting with ECM and UTP4 are boxed in yellow and are located from amino acid sites 237 to 246. Beta sheets are shown as arrows. Panel B shows polar interactions (yellow dashed line) between WDR75 and UTP4 (pink) and ECM (green). Panel C show polar interactions between WDR75, UTP18, and ECM while panel D shows polar interactions between WDR75, and the ECM.
Fig 5.
Predicted secondary and 3D structures of human and bonobo WDR75 and their WDR75 transcript variants.
Predicted secondary structure of the reference human WDR75 sequence in panel A with predicted 3D structure in panel B (Q8IWA0). Predicted secondary structure of the human WDR75 transcript variant in panel C with predicted 3D structure in panel D (d1143). Predicted secondary structure of the bonobo WDR75 reference sequence in panel E with predicted 3D structure in panel F (A0A2R8ZEG9). Predicted secondary structure of the bonobo WDR75 transcript variant in panel G with predicted 3D structure in panel H (5e91a). Colors in the 3D structures represent model confidence (pLDDT out of 100) with dark blue as very high (pLDDT > 90), light blue as high (90 > pLDDT > 70), yellow as low (70> pLDDT> 50) and orange as very low (pLDDT< 50) confidence.
Table 2.
Evidence of selection on WDR75 of Homo sapiens and related mammals at known interacting sites with UTP4, UTP18, and the ECM.
Fig 6.
Homo sapiens and Pan paniscus transcript variants X2 start at base pair 193 in the reference WDR75 CDS.
Shown above is the ingroup multiple sequence alignment of the WDR75 coding sequence in Geneious using translation align. Homo sapiens and Pan paniscus transcript variant X2 CDSs are indicated with red stars. The black boxes show the first seven amino acids in the transcript variant sequence.
Fig 7.
Amino acid insertion in the Myotis WDR75 coding sequence at base pair 2419 of the reference sequence.
Shown above is the ingroup multiple sequence alignment of the WDR75 coding sequence in Geneious using translation align. The red box indicates the insertion of 3 amino acids in the Myotis sequences: Myotis myotis, Myotis daubentonii, Myotis davidii. The sequences in the alignment are sorted by the # of differences from the reference sequence, Homo sapiens, which is highlighted in yellow.