scholarly journals New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

2011 ◽  
Vol 21 (11) ◽  
pp. 1929-1943 ◽  
Author(s):  
B. J. Parker ◽  
I. Moltke ◽  
A. Roth ◽  
S. Washietl ◽  
J. Wen ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Regulatory Rna ◽  
Rna Structures

scholarly journals Conformation-independent structural comparison of macromolecules with ProSMART

2014 ◽  
Vol 70 (a1) ◽  
pp. C494-C494 ◽  
Author(s):  
Robert Nicholls ◽  
Marcus Fischer ◽  
Garib Murshudov
Keyword(s):  
Comparative Analysis ◽  
Structural Alignment ◽  
Structural Data ◽  
Visual Assessment ◽  
Biological Macromolecules ◽  
Rna Structures ◽  
Structural Comparison ◽  
Biological Insight ◽  
High Sequence Homology ◽  
Insight Into

Structural comparison often aids insight into the function and mechanics of biological macromolecules. To make such analyses more accessible, we present the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART), which is designed to allow fast but detailed comparative analysis of macromolecular structures despite potential dissimilarities in global arrangement, such as domain motion and distortion. Whilst obtaining a residue alignment between structures is a prerequisite for comparative analysis, conventional alignment methods may fail in cases where conformational differences are dramatic. However, ProSMART achieves a conformation-independent structural alignment by focusing purely on local dissimilarities, rather than enforcing chain/domain rigidity. This allows the sensible comparison of protein (or DNA/RNA) structures in the presence of conformational change. ProSMART allows analysis of the structural conservation of local backbone and side chains in a wide variety of scenarios - the method is sensitive enough to allow identification of subtle dissimilarities between structures sharing high sequence homology, whilst being versatile enough to allow identification of local similarities between more distantly-related structures. In addition, ProSMART can be used for the identification of conserved rigid substructures, which may or may not represent functional domains. ProSMART is also used for the generation of external restraints for use in crystallographic refinement. Results from ProSMART can be visualised in either CCP4mg or PyMOL. All residue-based scores are illustrated using intuitive colour gradients, allowing easy visual assessment of local backbone and side chain conservation. Complementary structural comparison tools such as ProSMART can help break the complexity of the constantly growing pool of available structural data into a more readily accessible form, and consequently may aid biological insight into macromolecular structures.

scholarly journals Search for 5′-leader regulatory RNA structures based on gene annotation aided by the RiboGap database

Methods ◽  
2017 ◽  
Vol 117 ◽  
pp. 3-13 ◽  
Author(s):  
Mohammad Reza Naghdi ◽  
Katia Smail ◽  
Joy X. Wang ◽  
Fallou Wade ◽  
Ronald R. Breaker ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Regulatory Rna ◽  
Rna Structures

scholarly journals The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures

2016 ◽  
Vol 62 (1) ◽  
pp. 111-120 ◽  
Author(s):  
Nathan Pirakitikulr ◽  
Andrew Kohlway ◽  
Brett D. Lindenbach ◽  
Anna M. Pyle
Keyword(s):  
Regulatory Rna ◽  
Rna Structures ◽  
Coding Region

Identification of conserved regulatory RNA structures in prokaryotic metabolic pathway genes

Biosystems ◽  
2005 ◽  
Vol 80 (2) ◽  
pp. 145-154 ◽  
Author(s):  
Elena A. Lesnik ◽  
Gary B. Fogel ◽  
Dana Weekes ◽  
Timothy J. Henderson ◽  
Harold B. Levene ◽  
...  
Keyword(s):  
Metabolic Pathway ◽  
Regulatory Rna ◽  
Rna Structures

scholarly journals Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Hannah Steinert ◽  
Florian Sochor ◽  
Anna Wacker ◽  
Janina Buck ◽  
Christina Helmling ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Messenger Rna ◽  
Regulation Of Gene Expression ◽  
Untranslated Regions ◽  
Structural Description ◽  
Regulatory Rna ◽  
Structural Elements ◽  
Rna Structures ◽  
Cis Acting ◽  
Aptamer Domain

In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element. Here, we show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of the full-length transcripts is static: it exclusively populates the functional off-state but cannot switch to the on-state, regardless of the presence or absence of ligand. We show that only the combined matching of transcription rates and ligand binding enables transcription intermediates to undergo ligand-dependent conformational refolding.

Bacterial cis-regulatory RNA structures

2006 ◽  
Vol 40 (4) ◽  
pp. 541-550 ◽  
Author(s):  
M. S. Gelfand
Keyword(s):  
Regulatory Rna ◽  
Rna Structures

scholarly journals Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa:Kinship to coliphages and conservation of regulatory RNA structures

Virology ◽  
1995 ◽  
Vol 206 (1) ◽  
pp. 611-625 ◽  
Author(s):  
R.C.L. Olsthoorn ◽  
G. Garde ◽  
T. Dayhuff ◽  
J.F. Atkins ◽  
J. Van Duin
Keyword(s):  
Nucleotide Sequence ◽  
Regulatory Rna ◽  
Rna Structures ◽  
Rna Phage

scholarly journals Mutation in position of 32 (G>U) of S2M differentiate human SARS-CoV2 from Bat Coronavirus

2020 ◽  
Author(s):  
Majid Vahed ◽  
Mohammad Vahed ◽  
Aaron Sweeney ◽  
Farshad H Shirazi ◽  
Mehdi Mirsaeidi
Keyword(s):  
Genomic Sequence ◽  
Therapeutic Agents ◽  
Regulatory Rna ◽  
Host Defenses ◽  
Rna Structures ◽  
Host Proteins ◽  
Tertiary Structures ◽  
Stem Loop ◽  
The Impact ◽  
Bat Coronavirus

ABSTRACTThe new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a zoonotic pathogen that has rapidly mutated and become transmissible to humans. There is little existing data on the mutations in SARS-CoV-2 and the impact of these polymorphisms on its transmission and viral load. In this study, the SARS-CoV-2 genomic sequence was analyzed to identify variants within the 3’UTR region of its cis-regulatory RNA elements. A 43-nucleotide genetic element with a highly conserved stem-loop II-like motif (S2M), was discovered. The research revealed 32 G>U and 16 G>U/A mutations located within the S2M sequence in human SARS-CoV-2 models. These polymorphisms appear to make the S2M secondary and tertiary structures in human SARS-CoV-2 models less stable when compared to the S2M structures of bat/pangolin models. This grants the RNA structures more flexibility, which could be one of its escape mechanisms from host defenses or facilitate its entry into host proteins and enzymes. While this S2M sequence may not be omnipresent across all human SARS-CoV-2 models, when present, its sequence is always highly conserved. It may be used as a potential target for the development of vaccines and therapeutic agents.

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