scholarly journals Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure–Function Map

2021 ◽  
Vol 89 (1-2) ◽  
pp. 103-116
Author(s):  
Julie Baker Phillips ◽  
David H. Ardell
Keyword(s):  
Structure Function ◽  
Metal Ion ◽  
Binding Pocket ◽  
Trna Synthetase ◽  
Heterologous Gene ◽  
Multigene Families ◽  
Ion Binding ◽  
Trna Genes ◽  
Structural Factors ◽  
Trna Structure

AbstractThe evolution of tRNA multigene families remains poorly understood, exhibiting unusual phenomena such as functional conversions of tRNA genes through anticodon shift substitutions. We improved FlyBase tRNA gene annotations from twelve Drosophila species, incorporating previously identified ortholog sets to compare substitution rates across tRNA bodies at single-site and base-pair resolution. All rapidly evolving sites fell within the same metal ion-binding pocket that lies at the interface of the two major stacked helical domains. We applied our tRNA Structure–Function Mapper (tSFM) method independently to each Drosophila species and one outgroup species Musca domestica and found that, although predicted tRNA structure–function maps are generally highly conserved in flies, one tRNA Class-Informative Feature (CIF) within the rapidly evolving ion-binding pocket—Cytosine 17 (C17), ancestrally informative for lysylation identity—independently gained asparaginylation identity and substituted in parallel across tRNAAsn paralogs at least once, possibly multiple times, during evolution of the genus. In D. melanogaster, most tRNALys and tRNAAsn genes are co-arrayed in one large heterologous gene cluster, suggesting that heterologous gene conversion as well as structural similarities of tRNA-binding interfaces in the closely related asparaginyl-tRNA synthetase (AsnRS) and lysyl-tRNA synthetase (LysRS) proteins may have played a role in these changes. A previously identified Asn-to-Lys anticodon shift substitution in D. ananassae may have arisen to compensate for the convergent and parallel gains of C17 in tRNAAsn paralogs in that lineage. Our results underscore the functional and evolutionary relevance of our tRNA structure–function map predictions and illuminate multiple genomic and structural factors contributing to rapid, parallel and compensatory evolution of tRNA multigene families.

scholarly journals Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure-Function Map

2020 ◽  
Author(s):  
Julie Baker Phillips ◽  
David H. Ardell
Keyword(s):  
Structure Function ◽  
Metal Ion ◽  
Gene Families ◽  
Gene Clusters ◽  
Binding Pocket ◽  
Trna Synthetase ◽  
Heterologous Gene ◽  
Ion Binding ◽  
Trna Genes ◽  
Trna Structure

AbstractThe evolution of tRNA multi-gene families remains poorly understood, exhibiting unusual phenomena such as functional conversions of tRNA genes through anticodon shift substitutions. We improved FlyBase tRNA gene annotations from twelve Drosophila species, incorporating previously identified orthologies to compare substitution rates across tRNA bodies at single-site resolution. All rapidly evolving sites fell within the same metal-ion-binding pocket at the interface of the two major stacked helical domains. We applied our tRNA Structure-Function Mapper (tSFM) method independently to each Drosophila species and one outgroup species Musca domestica. We found that, although predicted tRNA structure-function maps are generally highly conserved in flies, one tRNA Class-Informative Feature (CIF) within the rapidlyevolving ion-binding pocket — Cytosine 17 (C17), ancestrally informative for lysylation identity — independently gained asparaginylation identity and substituted in parallel across tRNAAsn paralogs at least once, possibly at least three times, in evolution of the genus. In D. melanogaster, most tRNALys and tRNAAsn genes are co-arrayed in nearby heterologous gene clusters, suggesting that heterologous gene conversion as well as structural similarities of the closely related asparaginyl-tRNA synthetase (AsnRS) and lysyl-tRNA synthetase (LysRS) proteins may have played a role in these changes. A previously identified Asn-to-Lys anticodon shift substitution in D. ananassae may have arisen to compensate for the convergent and parallel gains of C17 in tRNAAsn paralogs of the D. ananassae lineage. Our results underscore the functional and evolutionary relevance of our tRNA structure-function map predictions and illuminate multiple genomic and structural factors contributing to rapid, parallel and compensatory evolution of tRNA multi-gene families.

Photophysical Characterisation, Metal Ion Binding and Enantiomeric Recognition of Chiral Ligands Containing Phenazine Fluorophore

2004 ◽  
Vol 69 (4) ◽  
pp. 885-896 ◽  
Author(s):  
Luisa Stella Dolci ◽  
Péter Huszthy ◽  
Erika Samu ◽  
Marco Montalti ◽  
Luca Prodi ◽  
...  
Keyword(s):  
Metal Ion ◽  
Photophysical Properties ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Ammonium Ions ◽  
Enantiomerically Pure ◽  
Binding Process ◽  
High Affinity ◽  
Enantiomeric Recognition ◽  
Chiral Species

Enantiomerically pure dimethyl- and diisobutyl-substituted phenazino-18-crown-6 ligands bind metal and ammonium ions and also primary aralkylammonium perchlorates in acetonitrile with high affinity, causing pronounced changes in their luminescence properties. In addition, they show enantioselectivity towards chiral primary aralkylammonium perchlorates. The possibility to monitor the binding process by photoluminescence spectroscopy can gain ground for the design of very efficient enantioselective chemosensors for chiral species. The observed changes in the photophysical properties are also an important tool for understanding the interactions present in the adduct.

scholarly journals Snapshots of a Non-Canonical RdRP in Action

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1260
Author(s):  
Diego S. Ferrero ◽  
Michela Falqui ◽  
Nuria Verdaguer
Keyword(s):  
Metal Ion ◽  
Rna Viruses ◽  
Ion Binding ◽  
Genome Replication ◽  
Metal Ion Binding ◽  
Insect Virus ◽  
X Ray ◽  
Template Strand ◽  
Nucleotide Incorporation ◽  
Elongation Process

RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication and transcription. The closed “right hand” architecture of RdRPs encircles seven conserved structural motifs (A to G) that regulate the polymerization activity. The four palm motifs, arranged in the sequential order A to D, are common to all known template dependent polynucleotide polymerases, with motifs A and C containing the catalytic aspartic acid residues. Exceptions to this design have been reported in members of the Permutotetraviridae and Birnaviridae families of positive single stranded (+ss) and double-stranded (ds) RNA viruses, respectively. In these enzymes, motif C is located upstream of motif A, displaying a permuted C–A–B–D connectivity. Here we study the details of the replication elongation process in the non-canonical RdRP of the Thosea asigna virus (TaV), an insect virus from the Permutatetraviridae family. We report the X-ray structures of three replicative complexes of the TaV polymerase obtained with an RNA template-primer in the absence and in the presence of incoming rNTPs. The structures captured different replication events and allowed to define the critical interactions involved in: (i) the positioning of the acceptor base of the template strand, (ii) the positioning of the 3’-OH group of the primer nucleotide during RNA replication and (iii) the recognition and positioning of the incoming nucleotide. Structural comparisons unveiled a closure of the active site on the RNA template-primer binding, before rNTP entry. This conformational rearrangement that also includes the repositioning of the motif A aspartate for the catalytic reaction to take place is maintained on rNTP and metal ion binding and after nucleotide incorporation, before translocation.

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