Activation of Prp28 ATPase by phosphorylated Npl3 at a critical step of spliceosome remodeling

• Published in: Nature communications Vol. 12; no. 1; pp. 3082 - 9
• Main Authors: Yeh, Fu-Lung, Chang, Shang-Lin, Ahmed, Golam Rizvee, Liu, Hsin-I, Tung, Luh, Yeh, Chung-Shu, Lanier, Leah Stands, Maeder, Corina, Lin, Che-Min, Tsai, Shu-Chun, Hsiao, Wan-Yi, Chang, Wei-Hau, Chang, Tien-Hsien
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.05.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/1; 38/15; 38/22; 38/77; 631/337/1645/1792; 631/45/500; 82/16; 82/58; 82/80; 82/83; Adenosine triphosphatase; Adenosine Triphosphate - metabolism; Amino acids; Antibodies; DEAD-box RNA Helicases - genetics; DEAD-box RNA Helicases - metabolism; DNA helicase; Enzymes; Exons; Experiments; Gene expression; Humanities and Social Sciences; Humans; Hypotheses; Introns; Macromolecules; multidisciplinary; Multiprotein Complexes - genetics; Multiprotein Complexes - metabolism; Mutation; Nuclear Proteins - genetics; Nuclear Proteins - metabolism; Phosphorylation; Protein Binding; Proteins; Ribonuclease H - metabolism; Ribonucleoproteins (small nuclear); Ribonucleoproteins, Small Nuclear - metabolism; RNA Helicases - genetics; RNA Helicases - metabolism; RNA Precursors - genetics; RNA Precursors - metabolism; RNA Splicing; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Science; Science (multidisciplinary); Spliceosomes - genetics; Spliceosomes - metabolism; Splicing; Transfer RNA; Yeast
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-23459-4

Splicing, a key step in the eukaryotic gene-expression pathway, converts precursor messenger RNA (pre-mRNA) into mRNA by excising introns and ligating exons. This task is accomplished by the spliceosome, a macromolecular machine that must undergo sequential conformational changes to establish its active site. Each of these major changes requires a dedicated DExD/H-box ATPase, but how these enzymes are activated remain obscure. Here we show that Prp28, a yeast DEAD-box ATPase, transiently interacts with the conserved 5′ splice-site (5′SS) GU dinucleotide and makes splicing-dependent contacts with the U1 snRNP protein U1C, and U4/U6.U5 tri-snRNP proteins, Prp8, Brr2, and Snu114. We further show that Prp28’s ATPase activity is potentiated by the phosphorylated Npl3, but not the unphosphorylated Npl3, thus suggesting a strategy for regulating DExD/H-box ATPases. We propose that Npl3 is a functional counterpart of the metazoan-specific Prp28 N-terminal region, which can be phosphorylated and serves as an anchor to human spliceosome. Yeast helicase Prp28 promotes the first step of spliceosome remodeling. By placing a photoactivatable unnatural amino acid in Prp28, the authors capture Prp28 in action revealing its dynamic interactions and cofactor Npl3.