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 The PUMILIO−RNA Interaction:  A Single RNA-Binding Domain Monomer Recognizes a Bipartite Target Sequence†

Biochemistry ◽  
1999 ◽  
Vol 38 (2) ◽  
pp. 596-604 ◽  
Author(s):  
Phillip D. Zamore ◽  
David P. Bartel ◽  
Ruth Lehmann ◽  
James R. Williamson
Keyword(s):  
Rna Binding ◽  
Binding Domain ◽  
Target Sequence ◽  
Rna Binding Domain ◽  
Rna Interaction

scholarly journals Tagging and Capturing of Lentiviral Vectors Using Short RNAs

2021 ◽  
Vol 22 (19) ◽  
pp. 10263
Author(s):  
Martin Panigaj ◽  
Michael P. Marino ◽  
Jakob Reiser
Keyword(s):  
Nucleic Acid ◽  
Rna Binding ◽  
Binding Domain ◽  
Rna Aptamer ◽  
Rna Sequences ◽  
Rna Binding Domain ◽  
Transgene Delivery ◽  
Vector Particles ◽  
Nucleic Acid Sequences

Lentiviral (LV) vectors have emerged as powerful tools for transgene delivery ex vivo but in vivo gene therapy applications involving LV vectors have faced a number of challenges, including the low efficiency of transgene delivery, a lack of tissue specificity, immunogenicity to both the product encoded by the transgene and the vector, and the inactivation of the vector by the human complement cascade. To mitigate these issues, several engineering approaches, involving the covalent modification of vector particles or the incorporation of specific protein domains into the vector’s envelope, have been tested. Short synthetic oligonucleotides, including aptamers bound to the surface of LV vectors, may provide a novel means with which to retarget LV vectors to specific cells and to shield these vectors from neutralization by sera. The purpose of this study was to develop strategies to tether nucleic acid sequences, including short RNA sequences, to LV vector particles in a specific and tight fashion. To bind short RNA sequences to LV vector particles, a bacteriophage lambda N protein-derived RNA binding domain (λN), fused to the measles virus hemagglutinin protein, was used. The λN protein bound RNA sequences bearing a boxB RNA hairpin. To test this approach, we used an RNA aptamer specific to the human epidermal growth factor receptor (EGFR), which was bound to LV vector particles via an RNA scaffold containing a boxB RNA motif. The results obtained confirmed that the EGFR-specific RNA aptamer bound to cells expressing EGFR and that the boxB containing the RNA scaffold was bound specifically to the λN RNA binding domain attached to the vector. These results show that LV vectors can be equipped with nucleic acid sequences to develop improved LV vectors for in vivo applications.

scholarly journals Structure of the RBD-PRDI fragment of the antiterminator protein GlcT

2012 ◽  
Vol 68 (7) ◽  
pp. 751-756 ◽  
Author(s):  
Sebastian Himmel ◽  
Christian Grosse ◽  
Sebastian Wolff ◽  
Claudia Schwiegk ◽  
Stefan Becker
Keyword(s):  
Bacillus Subtilis ◽  
Glucose Metabolism ◽  
Rna Binding ◽  
Hydrophobic Interactions ◽  
Binding Domain ◽  
Regulatory Domain ◽  
Asymmetric Unit ◽  
Rna Sequences ◽  
Rna Binding Domain

GlcT is a transcriptional antiterminator protein that is involved in regulation of glucose metabolism inBacillus subtilis. Antiterminator proteins bind specific RNA sequences, thus preventing the formation of overlapping terminator stem-loops. The structure of a fragment (residues 3–170) comprising the RNA-binding domain (RBD) and the first regulatory domain (PRDI) of GlcT was solved at 2.0 Å resolution with one molecule in the asymmetric unit. The two domains are connected by a helical linker. Their interface is mostly constituted by hydrophobic interactions.

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 RNA Binding Domain of Telomerase Reverse Transcriptase

2001 ◽  
Vol 21 (4) ◽  
pp. 990-1000 ◽  
Author(s):  
Cary K. Lai ◽  
James R. Mitchell ◽  
Kathleen Collins
Keyword(s):  
Catalytic Activity ◽  
Reverse Transcriptase ◽  
Rna Binding ◽  
Binding Domain ◽  
Amino Terminus ◽  
Telomerase Reverse Transcriptase ◽  
Telomerase Rna ◽  
Sequence Motifs ◽  
Rna Binding Domain ◽  
Rna Interaction

ABSTRACT Telomerase is a ribonucleoprotein reverse transcriptase that extends the ends of chromosomes. The two telomerase subunits essential for catalysis in vitro are the telomerase reverse transcriptase (TERT) and the telomerase RNA. Using truncations and site-specific mutations, we identified sequence elements of TERT and telomerase RNA required for catalytic activity and protein-RNA interaction for Tetrahymena thermophila telomerase. We found that the TERT amino and carboxyl termini, although evolutionarily poorly conserved, are nonetheless important for catalytic activity. In contrast, high-affinity telomerase RNA binding requires only a small region in the amino terminus of TERT. Surprisingly, the TERT region necessary and sufficient for telomerase RNA binding is completely separable from the reverse transcriptase motifs. The minimalTetrahymena TERT RNA binding domain contains two sequence motifs with ciliate-specific conservation and one TERT motif with conservation across all species. With human TERT, we demonstrate that a similar region within the TERT amino terminus is essential for human telomerase RNA binding as well. Finally, we defined theTetrahymena telomerase RNA sequences that are essential for TERT interaction. We found that a four-nucleotide region 5′ of the template is critical for TERT binding and that the 5′ end of telomerase RNA is sufficient for TERT binding. Our results reveal at least one evolutionarily conserved molecular mechanism by which the telomerase reverse transcriptase is functionally specialized for obligate use of an internal RNA template.

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.

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