4.8 Article

Rewiring of Aminoacyl-tRNA Synthetase Localization and Interactions in Plants With Extensive Mitochondrial tRNA Gene Loss

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

The tRNA identity landscape for aminoacylation and beyond

Richard Giege et al.

Summary: tRNAs play a crucial role in ribosome-dependent protein synthesis and their accuracy relies on specific identity elements within tRNA molecules. Although the understanding of these identity elements has expanded, the increasing number of reported functional differences has caused confusion. Furthermore, other processes involving tRNAs have been discovered, revealing multiple novel identities on the same tRNA molecule. This review highlights the mechanistic and evolutionary aspects of tRNA and tRNA-like identities, as well as new methods for identifying multiple identities on a single tRNA.

NUCLEIC ACIDS RESEARCH (2023)

Article Biochemistry & Molecular Biology

Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention

Konstantinos Giannakis et al.

Summary: This study utilized over 15,000 oDNA sequences and over 300 whole genome sequences across eukaryotes to identify the properties of genes and mechanisms that determine oDNA retention. The findings suggest that factors such as protein hydrophobicity and binding energy centrality within a protein complex play important roles in oDNA retention.

CELL SYSTEMS (2022)

Article Biochemistry & Molecular Biology

tRNA-Dependent Import of a Transit Sequence-Less Aminoacyl-tRNA Synthetase (LeuRS2) into the Mitochondria of Arabidopsis

Steffen Reinbothe et al.

Summary: A protein complex has been identified that facilitates the import of AaRS and tRNA into the mitochondria of Arabidopsis thaliana, shedding light on the process of transport of cytosolic AaRS and tRNA into mitochondria.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Genetics & Heredity

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora

Alissa M. Williams et al.

Summary: The angiosperm genus Silene is a model system for studying ecological and evolutionary traits in plants. This study provides genomic and transcriptomic resources for a hermaphroditic species of Silene, offering valuable insights for further research and development in plant ecology and evolution. The resources include high-quality full-length cDNA sequences and a draft assembly of the large genome size of the species, which is confirmed to be diploid.

G3-GENES GENOMES GENETICS (2021)

Article Biochemistry & Molecular Biology

Rapid Shifts in Mitochondrial tRNA Import in a Plant Line; e with Extensive Mitochondrial tRNA Gene Loss

Jessica M. Warren et al.

Summary: Research on mitochondrial genomes of Silene plants reveals the process of tRNA gene loss and replacement, as well as the import of nuclear-encoded tRNAs. Even in systems with recent mitochondrial tRNA gene loss, nuclear-encoded counterparts may likely replace mitochondrial tRNAs, providing insight into the evolutionary history of plant mitochondrial genomes.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Review Biochemistry & Molecular Biology

Aminoacyl-tRNA synthetases

Miguel Angel Rubio Gomez et al.

Article Biology

Detecting sequence signals in targeting peptides using deep learning

Jose Juan Almagro Armenteros et al.

LIFE SCIENCE ALLIANCE (2019)

Review Biochemistry & Molecular Biology

Plant mitochondrial protein import: the ins and outs

Abi S. Ghifari et al.

BIOCHEMICAL JOURNAL (2018)

Article Biochemistry & Molecular Biology

The Mutation Rate and the Age of the Sex Chromosomes in Silene latifolia

Marc Krasovec et al.

CURRENT BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses

Zhiqiang Wu et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Multidisciplinary Sciences

LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell

Jana Sperschneider et al.

SCIENTIFIC REPORTS (2017)

Article Biochemistry & Molecular Biology

Evolutionary gain of highly divergent tRNA specificities by two isoforms of human histidyl-tRNA synthetase

Yi-Hsueh Lee et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2017)

Article Evolutionary Biology

Cytonuclear Interactions in the Evolution of Animal Mitochondrial tRNA Metabolism

Walker Pett et al.

GENOME BIOLOGY AND EVOLUTION (2015)

Review Biochemistry & Molecular Biology

tRNA Biology in Mitochondria

Thalia Salinas-Giege et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2015)

Article Multidisciplinary Sciences

Massive gene loss in mistletoe (Viscum, Viscaceae) mitochondria

G. Petersen et al.

SCIENTIFIC REPORTS (2015)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Review Plant Sciences

Protein import into plant mitochondria: signals, machinery, processing, and regulation

Monika W. Murcha et al.

JOURNAL OF EXPERIMENTAL BOTANY (2014)

Review Biochemistry & Molecular Biology

Mitochondrial protein import: Common principles and physiological networks

Jan Dudek et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu et al.

BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

Crystal Structure of Human Mitochondrial PheRS Complexed with tRNAPhe in the Active Open State

Liron Klipcan et al.

JOURNAL OF MOLECULAR BIOLOGY (2012)

Article Biochemistry & Molecular Biology

ExPASy: SIB bioinformatics resource portal

Panu Artimo et al.

NUCLEIC ACIDS RESEARCH (2012)

Review Biochemistry & Molecular Biology

Mitochondrial tRNA Import and Its Consequences for Mitochondrial Translation

Andre Schneider

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 80 (2011)

Article Biochemistry & Molecular Biology

Evolutionary History of Arabidopsis thaliana Aminoacyl-tRNA Synthetase Dual-Targeted Proteins

Marcelo M. Brandao et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Article Plant Sciences

A global picture of tRNA genes in plant genomes

Morgane Michaud et al.

PLANT JOURNAL (2011)

Article Biochemistry & Molecular Biology

Parallel Loss of Nuclear-Encoded Mitochondrial Aminoacyl-tRNA Synthetases and mtDNA-Encoded tRNAs in Cnidaria

Karri M. Haen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Review Cell Biology

Mitochondrial protein import: from proteomics to functional mechanisms

Oliver Schmidt et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2010)

Review Cell Biology

Mitochondrial tRNA mutations and disease

John W. Yarham et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2010)

Review Genetics & Heredity

Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria

Anne-Marie Duchene et al.

CURRENT GENETICS (2009)

Article Biochemistry & Molecular Biology

Comparative Analysis of Structural Diversity and Sequence Evolution in Plant Mitochondrial Genes Transferred to the Nucleus

Shao-Lun Liu et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Article Biochemistry & Molecular Biology

Dual Targeting to Mitochondria and Chloroplasts: Characterization of Thr-tRNA Synthetase Targeting Peptide

Anna-Karin Berglund et al.

MOLECULAR PLANT (2009)

Article Biochemistry & Molecular Biology

Evidence for an adaptation mechanism of mitochondrial translation via tRNA import from the cytosol

Piotr Kamenski et al.

MOLECULAR CELL (2007)

Article Biochemistry & Molecular Biology

How can organellar protein N-terminal sequences be dual targeting signals?: In silico analysis and mutagenesis approach

Claire Pujol et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases

Bjorn Brindefalk et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms

Masaru Tsunoda et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

Loss of a primordial identity element for a mammalian mitochondrial aminoacylation system

Aurelie Fender et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2006)

Article Biochemistry & Molecular Biology

TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase

DH Ardell et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Multidisciplinary Sciences

Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in Arabidopsis thaliana

AM Duchêne et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

Sequence dependence of tRNAGly import into tobacco mitochondria

T Salinas et al.

BIOCHIMIE (2005)

Article Biochemistry & Molecular Biology

Human mitochondrial TyrRS disobeys the tyrosine identity rules

L Bonnefond et al.

Review Genetics & Heredity

Endosymbiotic gene transfer: Organelle genomes forge eukaryotic chromosomes

JN Timmis et al.

NATURE REVIEWS GENETICS (2004)

Article Biochemical Research Methods

Predotar:: A tool for rapidly screening proteomes for N-terminal targeting sequences

I Small et al.

PROTEOMICS (2004)

Article Biochemistry & Molecular Biology

In vitro import of a nuclearly encoded tRNA into mitochondria of Solanum tuberosum

L Delage et al.

MOLECULAR AND CELLULAR BIOLOGY (2003)

Article Multidisciplinary Sciences

Direct measurement of the transfer rate of chloroplast DNA into the nucleus

CY Huang et al.

NATURE (2003)

Review Plant Sciences

GATEWAY™ vectors for Agrobacterium-mediated plant transformation

M Karimi et al.

TRENDS IN PLANT SCIENCE (2002)

Review Biochemistry & Molecular Biology

The paradox of plastid transit peptides: conservation of function despite divergence in primary structure

BD Bruce

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2001)

Review Biochemistry & Molecular Biology

Dual targeting to mitochondria and chloroplasts

N Peeters et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2001)

Article Biochemistry & Molecular Biology

The chloroplast-derived trnW and trnM-e genes are not expressed in Arabidopsis mitochondria

AM Duchêne et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2001)

Review Plant Sciences

A guide to Agrobacterium binary Ti vectors

R Hellens et al.

TRENDS IN PLANT SCIENCE (2000)

Article Genetics & Heredity

The molecular evolution of signal peptides

EJB Williams et al.