Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination

AbstractRNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. As anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutations in vivo.

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The Structural Basis of 5′ Triphosphate Double-Stranded RNA Recognition by RIG-I C-Terminal Domain

Structure ◽

10.1016/j.str.2010.05.007 ◽

2010 ◽

Vol 18 (8) ◽

pp. 1032-1043 ◽

Cited By ~ 148

Author(s):

Cheng Lu ◽

Hengyu Xu ◽

C.T. Ranjith-Kumar ◽

Monica T. Brooks ◽

Tim Y. Hou ◽

...

Keyword(s):

Structural Basis ◽

Rna Recognition ◽

Double Stranded Rna ◽

Terminal Domain

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Structural basis for initiation of transcription from an RNA polymerase–promoter complex

Nature ◽

10.1038/19999 ◽

1999 ◽

Vol 399 (6731) ◽

pp. 80-83 ◽

Cited By ~ 207

Author(s):

Graham M. T. Cheetham ◽

David Jeruzalmi ◽

Thomas A Steitz

Keyword(s):

Rna Polymerase ◽

Structural Basis ◽

Promoter Complex ◽

Initiation Of Transcription ◽

Rna Polymerase Promoter

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Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein

PLoS Pathogens ◽

10.1371/journal.ppat.1009100 ◽

2020 ◽

Vol 16 (12) ◽

pp. e1009100 ◽

Cited By ~ 1

Author(s):

Dhurvas Chandrasekaran Dinesh ◽

Dominika Chalupska ◽

Jan Silhan ◽

Eliska Koutna ◽

Radim Nencka ◽

...

Keyword(s):

Rna Binding ◽

Mutational Analysis ◽

Rna Virus ◽

Structural Basis ◽

Rna Recognition ◽

Nonstructural Proteins ◽

Viral Membrane ◽

Intrinsically Disordered ◽

Binding Cleft ◽

Rna Complex

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19). SARS-CoV-2 is a single-stranded positive-sense RNA virus. Like other coronaviruses, SARS-CoV-2 has an unusually large genome that encodes four structural proteins and sixteen nonstructural proteins. The structural nucleocapsid phosphoprotein N is essential for linking the viral genome to the viral membrane. Both N-terminal RNA binding (N-NTD) and C-terminal dimerization domains are involved in capturing the RNA genome and, the intrinsically disordered region between these domains anchors the ribonucleoprotein complex to the viral membrane. Here, we characterized the structure of the N-NTD and its interaction with RNA using NMR spectroscopy. We observed a positively charged canyon on the surface of the N-NTD that might serve as a putative RNA binding site similarly to other coronaviruses. The subsequent NMR titrations using single-stranded and double-stranded RNA revealed a much more extensive U-shaped RNA-binding cleft lined with regularly distributed arginines and lysines. The NMR data supported by mutational analysis allowed us to construct hybrid atomic models of the N-NTD/RNA complex that provided detailed insight into RNA recognition.

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Faculty Opinions recommendation of Structural basis for transcription antitermination at bacterial intrinsic terminator.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.736187458.793563740 ◽

2019 ◽

Author(s):

Katsuhiko Murakami

Keyword(s):

Structural Basis ◽

Transcription Antitermination

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Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch

Nature Communications ◽

10.1038/s41467-021-27400-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Chris H. Hill ◽

Lukas Pekarek ◽

Sawsan Napthine ◽

Anuja Kibe ◽

Andrew E. Firth ◽

...

Keyword(s):

Optical Tweezers ◽

Protein A ◽

Ribosomal Subunit ◽

Viral Gene Expression ◽

Structural Basis ◽

Viral Gene ◽

Rna Recognition ◽

Translational Initiation ◽

Multiple Copies ◽

Rna Pseudoknot

AbstractProgrammed –1 ribosomal frameshifting (PRF) in cardioviruses is activated by the 2A protein, a multi-functional virulence factor that also inhibits cap-dependent translational initiation. Here we present the X-ray crystal structure of 2A and show that it selectively binds to a pseudoknot-like conformation of the PRF stimulatory RNA element in the viral genome. Using optical tweezers, we demonstrate that 2A stabilises this RNA element, likely explaining the increase in PRF efficiency in the presence of 2A. Next, we demonstrate a strong interaction between 2A and the small ribosomal subunit and present a cryo-EM structure of 2A bound to initiated 70S ribosomes. Multiple copies of 2A bind to the 16S rRNA where they may compete for binding with initiation and elongation factors. Together, these results define the structural basis for RNA recognition by 2A, show how 2A-mediated stabilisation of an RNA pseudoknot promotes PRF, and reveal how 2A accumulation may shut down translation during virus infection.

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Structural basis for mRNA recognition by human RBM38

Biochemical Journal ◽

10.1042/bcj20190652 ◽

2020 ◽

Vol 477 (1) ◽

pp. 161-172 ◽

Cited By ~ 3

Author(s):

Kaiyue Qian ◽

Mengyu Li ◽

Junchao Wang ◽

Min Zhang ◽

Mingzhu Wang

Keyword(s):

Rna Binding ◽

Structural Information ◽

Protein Translation ◽

Effector Proteins ◽

Structural Basis ◽

Binding Property ◽

Rna Recognition ◽

Recognition Mechanism ◽

Rrm Domain ◽

Regulate Protein

RNA-binding protein RBM38 was reported to bind the mRNA of several p53-related genes through its RRM domain and to up-regulate or down-regulate protein translation by increasing mRNA stability or recruitment of other effector proteins. The recognition mechanism, however, for RNA-binding of RBM38 remains unclear. Here, we report the crystal structure of the RRM domain of human RBM38 in complex with a single-stranded RNA. Our structural and biological results revealed that RBM38 recognizes G(U/C/A)GUG sequence single-stranded RNA in a sequence-specific and structure-specific manner. Two phenylalanine stacked with bases of RNA were crucial for RNA binding, and a series of hydrogen bonds between the base atoms of RNA and main-chain or side-chain atoms of RBM38 determine the sequence-specific recognition. Our results revealed the RNA-recognition mechanism of human RBM38 and provided structural information for understanding the RNA-binding property of RBM38.

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