Evolution of RNA-Protein Interactions: Non-Specific Binding Led to RNA Splicing Activity of Fungal Mitochondrial Tyrosyl-tRNA Synthetases

Studies of tRNA synthetases that adapted to assist the splicing of group I introns provide insight into how proteins can evolve new RNA-binding functions.

• Publication year

  2014

• Venue

  PLoS Biology

• Publication date

  2014-12-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1371/journal.pbio.1002028PMID 25536042PMCID 4275181
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The role of miRNAs in regulating gene expression networks.

  2013cited by this paper
• Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing

  2013cited by this paper
• Noncanonical functions of aminoacyl-tRNA synthetases

  2012cited by this paper
• Evolutionary origin of RNA editing.

  2012cited by this paper
• New developments in the ATSAS program package for small-angle scattering data analysis

  2012cited by this paper
• Crystal structure of Prp8 reveals active site cavity of the spliceosome

  2012cited by this paper
• Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase.

  2011cited by this paper
• NMR Structure of the C-terminal domain of a tyrosyl-tRNA synthetase that functions in group I intron splicing.

  2011cited by this paper
• I-TASSER: a unified platform for automated protein structure and function prediction

  2010cited by this paper
• Production of glycoprotein-deleted rabies viruses for monosynaptic tracing and high-level gene expression in neurons

  2010influential reference
• Small‐angle scattering for structural biology—Expanding the frontier while avoiding the pitfalls

  2010cited by this paper
• Irremediable Complexity?

  2010cited by this paper
• New functions of aminoacyl-tRNA synthetases beyond translation

  2010cited by this paper
• Bridging the gap between ribosomal and nonribosomal protein synthesis

  2010cited by this paper
• Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

  2008cited by this paper
• Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA

  2008cited by this paper
• Distinct domains of tRNA synthetase recognize the same base pair

  2008cited by this paper
• RNA‐binding proteins and post‐transcriptional gene regulation

  2008cited by this paper
• Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity

  2008influential reference
• Aminoacyl tRNA synthetases and their connections to disease

  2008cited by this paper
• Toward predicting self-splicing and protein-facilitated splicing of group I introns.

  2008cited by this paper
• Structural characterization of flexible proteins using small-angle X-ray scattering.

  2007cited by this paper
• The evolution of genetic networks by non-adaptive processes

  2007cited by this paper
• ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis

  2007influential reference
• RNA regulons: coordination of post-transcriptional events

  2007cited by this paper
• Introns and the origin of nucleus–cytosol compartmentalization

  2006cited by this paper
• Evolution of the tRNA(Tyr)/TyrRS aminoacylation systems.

  2005cited by this paper
• Protein production by auto-induction in high density shaking cultures.

  2005cited by this paper
• Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.

  2005cited by this paper
• Global rigid body modeling of macromolecular complexes against small-angle scattering data.

  2005influential reference
• A tyrosyl-tRNA synthetase adapted to function in group I intron splicing by acquiring a new RNA binding surface.

  2005influential reference
• The natural history of group I introns.

  2005cited by this paper
• Crystal structure of a phage Twort group I ribozyme–product complex

  2005cited by this paper
• Corrigendum to “Structural Snapshots of the KMSKS Loop Rearrangement for Amino Acid Activation by Bacterial Tyrosyl-tRNA Synthetase” [J. Mol. Biol. (2005) 346, 105–117]

  2005cited by this paper
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.

  2004cited by this paper
• The Neurospora crassa CYT-18 protein C-terminal RNA-binding domain helps stabilize interdomain tertiary interactions in group I introns.

  2004cited by this paper
• Small-angle scattering studies of biological macromolecules in solution

  2003cited by this paper
• The Solution Structure of YbcJ from Escherichia coli Reveals a Recently Discovered αL Motif Involved in RNA Binding

  2003cited by this paper
• Preliminary structure analysis of the DH/PH domains of leukemia-associated RhoGEF.

  2003cited by this paper
• Uniqueness of ab initio shape determination in small-angle scattering

  2003cited by this paper
• RNA-protein interactions.

  2002cited by this paper
• The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

  2002cited by this paper
• Mobile Introns: Pathways and Proteins

  2002cited by this paper
• Crystal structure of a human aminoacyl-tRNA synthetase cytokine

  2002cited by this paper
• tRNA-like recognition of group I introns by a tyrosyl-tRNA synthetase

  2002cited by this paper
• Class I tyrosyl‐tRNA synthetase has a class II mode of cognate tRNA recognition

  2002cited by this paper
• Determination of domain structure of proteins from X-ray solution scattering.

  2001cited by this paper
• Function of the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase in RNA splicing. Role of the idiosyncratic N-terminal extension and different modes of interaction with different group I introns.

  2001influential reference
• Crystal structure of Staphylococcus aureus tyrosyl‐tRNA synthetase in complex with a class of potent and specific inhibitors

  2001cited by this paper
• Automated matching of high- and low-resolution structural models

  2001cited by this paper
• A recurrent RNA‐binding domain is appended to eukaryotic aminoacyl‐tRNA synthetases

  2000cited by this paper
• Structure of Hsp15 reveals a novel RNA‐binding motif

  2000cited by this paper
• A novel anti-tumor cytokine contains an RNA binding motif present in aminoacyl-tRNA synthetases.

  2000cited by this paper
• A New Heat Shock Protein That Binds Nucleic Acids*

  1999cited by this paper
• Novel Predicted RNA-Binding Domains Associated with the Translation Machinery

  1999cited by this paper
• Two distinct cytokines released from a human aminoacyl-tRNA synthetase.

  1999cited by this paper
• Species Barrier to RNA Recognition Overcome with Nonspecific RNA Binding Domains*

  1999cited by this paper
• Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

  1999cited by this paper
• On the Possibility of Constructive Neutral Evolution

  1999cited by this paper
• Mutant bacteriophage T7 RNA polymerases with altered termination properties.

  1997cited by this paper
• Human Tyrosyl-tRNA Synthetase Shares Amino Acid Sequence Homology with a Putative Cytokine*

  1997cited by this paper
• Characterization of Neurospora mitochondrial group I introns reveals different CYT-18 dependent and independent splicing strategies and an alternative 3' splice site for an intron ORF.

  1997cited by this paper
• Rapid mutagenesis and purification of phage RNA polymerases.

  1997cited by this paper
• Rescuing an essential enzyme–RNA complex with a non‐essential appended domain

  1997cited by this paper
• A tyrosyl-tRNA synthetase protein induces tertiary folding of the group I intron catalytic core.

  1996cited by this paper
• Evolutionary origins of apoB mRNA editing: catalysis by a cytidine deaminase that has acquired a novel RNA-binding motif at its active site.

  1995cited by this paper
• Involvement of Neurospora mitochondrial tyrosyl-tRNA synthetase in RNA splicing. A new method for purifying the protein and characterization of physical and enzymatic properties pertinent to splicing.

  1995cited by this paper
• Species-specific microhelix aminoacylation by a eukaryotic pathogen tRNA synthetase dependent on a single base pair.

  1995cited by this paper
• Discrimination between transfer-RNAs by tyrosyl-tRNA synthetase.

  1993cited by this paper
• Introns as mobile genetic elements.

  1993cited by this paper
• On the evolution of RNA editing.

  1993cited by this paper
• The neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core.

  1992cited by this paper
• A tyrosyl-tRNA synthetase binds specifically to the group I intron catalytic core.

  1992cited by this paper
• The Neurospora mitochondrial tyrosyl-tRNA synthetase is sufficient for group I intron splicing in vitro and uses the carboxy-terminal tRNA-binding domain along with other regions.

  1991cited by this paper
• Function of Neurospora mitochondrial tyrosyl-tRNA synthetase in RNA splicing requires an idiosyncratic domain not found in other synthetases.

  1990cited by this paper
• Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing.

  1990influential reference
• Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs

  1990influential reference
• Crystal structure of a deletion mutant of a tyrosyl-tRNA synthetase complexed with tyrosine.

  1987cited by this paper
• A protein required for splicing group I introns in Neurospora mitochondria is mitochondrial tyrosyl-tRNA synthetase or a derivative thereof.

  1987cited by this paper
• Construction of heterodimer tyrosyl-tRNA synthetase shows tRNATyr interacts with both subunits.

  1986cited by this paper
• New reactions of the ribosomal RNA precursor of Tetrahymena and the mechanism of self-splicing.

  1986cited by this paper
• RNA splicing in Neurospora mitochondria. Defective splicing of mitochondrial mRNA precursors in the nuclear mutant cyt18-1.

  1985cited by this paper
• The primary structure of yeast mitochondrial tyrosine tRNA

  1983cited by this paper
• In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence.

  1981cited by this paper
• Interesting and unusual features in the sequence of Neurospora crassa mitochondrial tyrosine transfer RNA.

  1979cited by this paper
• Defective splicing of mitochondrial rRNA in cytochrome-deficient nuclear mutants of Neurospora crassa.

  1979cited by this paper
• Tyrosyl-tRNA synthetase from Escherichia coli. Stoichiometry of ligand binding and half-of-the-sites reactivity in aminoacylation.

  1975cited by this paper
• The nucleotide sequences of tyrosine transfer RNAs of Escherichia coli.

  1970cited by this paper
• Sequencing

  year unknowncited by this paper

• Comprehensive characterization of mRNAs associated with yeast cytosolic aminoacyl-tRNA synthetases

  2021cites this paper
• RNA mimicry in post‐transcriptional regulation by aminoacyl tRNA synthetases

  2020cites this paper
• Localization and RNA Binding of Mitochondrial Aminoacyl tRNA Synthetases

  2020cites this paper
• Shaping the regulation of the p53 mRNA tumour suppressor: the co-evolution of genetic signatures

  2019cites this paper
• The functional variant of NTN1 contributes to the risk of nonsyndromic cleft lip with or without cleft palate

  2019cites this paper
• The generality of Constructive Neutral Evolution

  2018cites this paper
• The generality of Constructive Neutral Evolution

  2018cites this paper
• Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.

  2017cites this paper
• SAXS studies of RNA: structures, dynamics, and interactions with partners

  2016cites this paper
• Structural Divergence of the Group I Intron Binding Surface in Fungal Mitochondrial Tyrosyl-tRNA Synthetases That Function in RNA Splicing*

  2016cites this paper
• Pre‐mRNA splicing is modulated by antifungal drugs in the filamentous fungus Neurospora crassa

  2016cites this paper
• Using Group II Introns for Attenuating the In Vitro and In Vivo Expression of a Homing Endonuclease

  2016cites this paper