scholarly journals RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

2017 ◽  
Author(s):  
Nila Roy Choudhury ◽  
Gregory Heikel ◽  
Maryia Trubitsyna ◽  
Peter Kubik ◽  
Jakub Stanislaw Nowak ◽  
...  
Keyword(s):  
Cell Biology ◽  
Rna Binding ◽  
Ubiquitin Ligases ◽  
Binding Activity ◽  
Binding Domain ◽  
E3 Ubiquitin Ligases ◽  
Spry Domain ◽  
Binding Partners ◽  
Rna Targets ◽  
Rna Binding Domain

ABSTRACTTRIM25 is a novel RNA-binding protein and a member of the Tripartite Motif (TRIM) family of E3 ubiquitin ligases, which plays a pivotal role in the innate immune response. Almost nothing is known about its RNA-related roles in cell biology. Furthermore, its RNA-binding domain has not been characterized. Here, we reveal that RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain, which we postulate to be a novel RNA-binding domain. Using CLIP-seq and SILAC-based co-immunoprecipitation assays, we uncover TRIM25’s endogenous RNA targets and protein binding partners. Finally, we show that the RNA-binding activity of TRIM25 is important for its ubiquitin ligase function. These results reveal new insights into the molecular roles and characteristics of RNA-binding E3 ubiquitin ligases and demonstrate that RNA could be an essential factor for their biological functions.

scholarly journals LOTUS domain is a novel class of G-rich and G-quadruplex RNA binding domain

2020 ◽  
Vol 48 (16) ◽  
pp. 9262-9272 ◽  
Author(s):  
Deqiang Ding ◽  
Chao Wei ◽  
Kunzhe Dong ◽  
Jiali Liu ◽  
Alexander Stanton ◽  
...  
Keyword(s):  
Rna Binding ◽  
Specific Interaction ◽  
Binding Activity ◽  
Binding Domain ◽  
Binding Property ◽  
Domain Family ◽  
Rna Sequences ◽  
G Quadruplex ◽  
Rna Binding Domain ◽  
Rna Interaction

Abstract LOTUS domains are helix-turn-helix protein folds identified in essential germline proteins and are conserved in prokaryotes and eukaryotes. Despite originally predicted as an RNA binding domain, its molecular binding activity towards RNA and protein is controversial. In particular, the most conserved binding property for the LOTUS domain family remains unknown. Here, we uncovered an unexpected specific interaction of LOTUS domains with G-rich RNA sequences. Intriguingly, LOTUS domains exhibit high affinity to RNA G-quadruplex tertiary structures implicated in diverse cellular processes including piRNA biogenesis. This novel LOTUS domain-RNA interaction is conserved in bacteria, plants and animals, comprising the most ancient binding feature of the LOTUS domain family. By contrast, LOTUS domains do not preferentially interact with DNA G-quadruplexes. We further show that a subset of LOTUS domains display both RNA and protein binding activities. These findings identify the LOTUS domain as a specialized RNA binding domain across phyla and underscore the molecular mechanism underlying the function of LOTUS domain-containing proteins in RNA metabolism and regulation.

scholarly journals Mutations in the RNA Binding Domain of Stem-Loop Binding Protein Define Separable Requirements for RNA Binding and for Histone Pre-mRNA Processing

2001 ◽  
Vol 21 (6) ◽  
pp. 2008-2017 ◽  
Author(s):  
Zbigniew Dominski ◽  
Judith A. Erkmann ◽  
John A. Greenland ◽  
William F. Marzluff
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Binding Activity ◽  
Mrna Processing ◽  
Binding Domain ◽  
Stem Loop ◽  
Amino Acid Region ◽  
Stem Loop Structure ◽  
U7 Snrnp ◽  
Rna Binding Domain

ABSTRACT Expression of replication-dependent histone genes at the posttranscriptional level is controlled by stem-loop binding protein (SLBP). One function of SLBP is to bind the stem-loop structure in the 3′ untranslated region of histone pre-mRNAs and facilitate 3′ end processing. Interaction of SLBP with the stem-loop is mediated by the centrally located RNA binding domain (RBD). Here we identify several highly conserved amino acids in the RBD mutation of which results in complete or substantial loss of SLBP binding activity. We also identify residues in the RBD which do not contribute to binding to the stem-loop RNA but instead are required for efficient recruitment of U7 snRNP to histone pre-mRNA. Recruitment of the U7 snRNP to the pre-mRNA also depends on the 20-amino-acid region located immediately downstream of the RBD. A critical region of the RBD contains the sequence YDRY. The tyrosines are required for RNA binding, and the DR dipeptide is essential for processing but not for RNA binding. It is likely that the RBD of SLBP interacts directly with both the stem-loop RNA and other processing factor(s), most likely the U7 snRNP, to facilitate histone pre-mRNA processing.

scholarly journals Requirement for C-terminal Extension to the RNA Binding Domain for Efficient RNA Binding by Ribosomal Protein L2

2002 ◽  
Vol 66 (3) ◽  
pp. 682-684 ◽  
Author(s):  
Takeshi HAYASHI ◽  
Maino TAHARA ◽  
Kenta IWASAKI ◽  
Yoshiaki KOUZUMA ◽  
Makoto KIMURA
Keyword(s):  
Ribosomal Protein ◽  
Rna Binding ◽  
Binding Domain ◽  
Ribosomal Protein L2 ◽  
Rna Binding Domain

K160 in the RNA‐binding domain of the orf virus virulence factor OV20.0 is critical for its functions in counteracting host antiviral defense

FEBS Letters ◽  
2021 ◽  
Author(s):  
Guan‐Ru Liao ◽  
Yeu‐Yang Tseng ◽  
Ching‐Yu Tseng ◽  
Ying‐Ping Huang ◽  
Ching‐Hsiu Tsai ◽  
...  
Keyword(s):  
Virulence Factor ◽  
Rna Binding ◽  
Binding Domain ◽  
Orf Virus ◽  
Antiviral Defense ◽  
Rna Binding Domain

scholarly journals Characterization of an RNA-binding domain in the bacteriophage phi 29 connector.

1993 ◽  
Vol 268 (27) ◽  
pp. 20198-20204
Author(s):  
L.E. Donate ◽  
J.M. Valpuesta ◽  
C Mier ◽  
F Rojo ◽  
J.L. Carrascosa
Keyword(s):  
Rna Binding ◽  
Binding Domain ◽  
Rna Binding Domain
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