Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs

To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in...

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Published inNature communications Vol. 12; no. 1; pp. 6417 - 14
Main Authors Niu, Xiaolin, Sun, Ruirui, Chen, Zhifeng, Yao, Yirong, Zuo, Xiaobing, Chen, Chunlai, Fang, Xianyang
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 05.11.2021
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BASIC BIOLOGICAL SCIENCES
Biomedical materials
Dengue fever
Dynamics
Flavivirus - genetics
Folding
Humanities and Social Sciences
Laboratories
Life sciences
Magnesium
multidisciplinary
Mutation
Nucleic Acid Conformation
Regulatory mechanisms (biology)
Ribonucleic acid
RNA
RNA Folding - genetics
RNA Folding - physiology
Robustness
Science
Science (multidisciplinary)
Viruses
West Nile virus
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Abstract To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs’ folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg 2+ -dependent, furthermore, the Mg 2+ -dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg 2+ to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg 2+ , and tolerate mutations at key tertiary motifs at high Mg 2+ , which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs. Exoribonuclease-resistant RNAs (xrRNAs) are RNA elements that block the exoribonucleolytic degradation of RNA. Here the authors show how a long-range pseudoknot length modulates the Mg 2+ -dependence of flaviviral xrRNA’s folding, conformational dynamics and Xrn1 resistance.
AbstractList Exoribonuclease-resistant RNAs (xrRNAs) are RNA elements that block the exoribonucleolytic degradation of RNA. Here the authors show how a long-range pseudoknot length modulates the Mg2+-dependence of flaviviral xrRNA’s folding, conformational dynamics and Xrn1 resistance.
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs’ folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg2+-dependent, furthermore, the Mg2+-dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg2+ to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg2+, and tolerate mutations at key tertiary motifs at high Mg2+, which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.Exoribonuclease-resistant RNAs (xrRNAs) are RNA elements that block the exoribonucleolytic degradation of RNA. Here the authors show how a long-range pseudoknot length modulates the Mg2+-dependence of flaviviral xrRNA’s folding, conformational dynamics and Xrn1 resistance.
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs’ folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg 2+ -dependent, furthermore, the Mg 2+ -dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg 2+ to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg 2+ , and tolerate mutations at key tertiary motifs at high Mg 2+ , which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs' folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg -dependent, furthermore, the Mg -dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg , and tolerate mutations at key tertiary motifs at high Mg , which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assay. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved longrange pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs’ folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg2+- dependent, furthermore, the Mg2+-dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg2+ to stabilize its folding, exhibits reduced conformational dynamics and strong Xrn1 resistance even at low Mg2+, and tolerates mutations at key tertiary motifs at high Mg2+, which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs’ folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg 2+ -dependent, furthermore, the Mg 2+ -dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg 2+ to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg 2+ , and tolerate mutations at key tertiary motifs at high Mg 2+ , which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs. Exoribonuclease-resistant RNAs (xrRNAs) are RNA elements that block the exoribonucleolytic degradation of RNA. Here the authors show how a long-range pseudoknot length modulates the Mg 2+ -dependence of flaviviral xrRNA’s folding, conformational dynamics and Xrn1 resistance.
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs' folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg2+-dependent, furthermore, the Mg2+-dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg2+ to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg2+, and tolerate mutations at key tertiary motifs at high Mg2+, which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs' folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg2+-dependent, furthermore, the Mg2+-dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg2+ to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg2+, and tolerate mutations at key tertiary motifs at high Mg2+, which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.
ArticleNumber 6417
Author Chen, Chunlai
Fang, Xianyang
Niu, Xiaolin
Yao, Yirong
Sun, Ruirui
Chen, Zhifeng
Zuo, Xiaobing
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/34741027$$D View this record in MEDLINE/PubMed
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Snippet To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1...
Exoribonuclease-resistant RNAs (xrRNAs) are RNA elements that block the exoribonucleolytic degradation of RNA. Here the authors show how a long-range...
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BASIC BIOLOGICAL SCIENCES
Biomedical materials
Dengue fever
Dynamics
Flavivirus - genetics
Folding
Humanities and Social Sciences
Laboratories
Life sciences
Magnesium
multidisciplinary
Mutation
Nucleic Acid Conformation
Regulatory mechanisms (biology)
Ribonucleic acid
RNA
RNA Folding - genetics
RNA Folding - physiology
Robustness
Science
Science (multidisciplinary)
Viruses
West Nile virus
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Title Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs
URI https://link.springer.com/article/10.1038/s41467-021-26616-x
https://www.ncbi.nlm.nih.gov/pubmed/34741027
https://www.proquest.com/docview/2593744969
https://www.proquest.com/docview/2594298058
https://www.osti.gov/servlets/purl/1854162
https://pubmed.ncbi.nlm.nih.gov/PMC8571300
https://doaj.org/article/3b81654980444e4c84dfee67e84640e0
Volume 12
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