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

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.

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Tagging and Capturing of Lentiviral Vectors Using Short RNAs

International Journal of Molecular Sciences ◽

10.3390/ijms221910263 ◽

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.

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Crystal structure of a new RNA-binding domain from the antiterminator protein SacY of Bacillus subtilis

The EMBO Journal ◽

10.1093/emboj/16.16.5030 ◽

1997 ◽

Vol 16 (16) ◽

pp. 5030-5036 ◽

Cited By ~ 42

Author(s):

H. van Tilbeurgh

Keyword(s):

Crystal Structure ◽

Bacillus Subtilis ◽

Rna Binding ◽

Binding Domain ◽

Rna Binding Domain

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Specific interaction of the RNA-binding domain of the Bacillus subtilis transcriptional antiterminator GlcT with its RNA target, RAT 1 1Edited by M. Gottesman

Journal of Molecular Biology ◽

10.1006/jmbi.1999.3176 ◽

1999 ◽

Vol 293 (4) ◽

pp. 795-805 ◽

Cited By ~ 26

Author(s):

Ines Langbein ◽

Steffi Bachem ◽

Jörg Stülke

Keyword(s):

Bacillus Subtilis ◽

Rna Binding ◽

Specific Interaction ◽

Binding Domain ◽

Rna Binding Domain

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

Nucleic Acids Research ◽

10.1093/nar/gkaa652 ◽

2020 ◽

Vol 48 (16) ◽

pp. 9262-9272 ◽

Cited By ~ 1

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.

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