title: Interaction between ribosome assembly factors Krr1 and Faf1 is essential for formation of small ribosomal subunit in yeast.
abstract: Ribosome formation in Saccharomyces cerevisiae requires a large number of transiently associated assembly factors that coordinate processing and folding of pre-rRNA and binding of ribosomal proteins. Krr1 and Faf1 are two interacting proteins present in early 90 S precursor particles of the small ribosomal subunit. Here, we determined a co-crystal structure of the core domain of Krr1 bound to a 19-residue fragment of Faf1 at 2.8 Å resolution. The structure reveals that Krr1 consists of two packed K homology (KH) domains, KH1 and KH2, and resembles archaeal Dim2-like proteins. We show that KH1 is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1. KH2 contains a canonical RNA-binding surface and additionally associates with an α-helix of Faf1. Specific disruption of the Krr1-Faf1 interaction impaired early 18 S rRNA processing at sites A0, A1, and A2 and caused cell lethality, but it did not prevent incorporation of the two proteins into pre-ribosomes. The Krr1-Faf1 interaction likely maintains a critical conformation of 90 S pre-ribosomes required for pre-rRNA processing. Our results illustrate the versatility of KH domains in protein interaction and provide insight into the role of Krr1-Faf1 interaction in ribosome biogenesis.
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875,; National Institute of Biological Sciences at Beijing, Beijing 102206, and.
authors.forename: Sanduo
authors.initials: S
authors.lastname: Zheng
authors.affiliation: National Institute of Biological Sciences at Beijing, Beijing 102206, and; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Lan
authors.affiliation: National Institute of Biological Sciences at Beijing, Beijing 102206, and.
authors.forename: Ximing
authors.initials: X
authors.lastname: Liu
authors.affiliation: National Institute of Biological Sciences at Beijing, Beijing 102206, and; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730,; Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: yekeqiong@nibs.ac.cn.
authors.forename: Keqiong
authors.initials: K
authors.lastname: Ye
mesh_terms: D020816:Amino Acid Motifs; D018360:Crystallography, X-Ray; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D012323:RNA Processing, Post-Transcriptional / Q000502:physiology; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012337:RNA, Ribosomal, 18S / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D054682:Ribosome Subunits, Small, Eukaryotic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: C490779:FAF1 protein, S cerevisiae; C099980:KRR1 protein, S cerevisiae; D012331:RNA, Fungal; D012337:RNA, Ribosomal, 18S; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins
keywords: Crystal Structure; Protein-Protein Interaction; RNA-binding Protein; Ribosome Assembly; rRNA Processing