Transfer RNA modifications and genes for modifying enzymes in Arabidopsis thaliana

Peng Chen; Jäger, Gunilla; Bo Zheng
January 2010
BMC Plant Biology;2010, Vol. 10, p201
Academic Journal
Background: In all domains of life, transfer RNA (tRNA) molecules contain modified nucleosides. Modifications to tRNAs affect their coding capacity and influence codon-anticodon interactions. Nucleoside modification deficiencies have a diverse range of effects, from decreased virulence in bacteria, neural system disease in human, and gene expression and stress response changes in plants. The purpose of this study was to identify genes involved in tRNA modification in the model plant Arabidopsis thaliana, to understand the function of nucleoside modifications in plant growth and development. Results: In this study, we established a method for analyzing modified nucleosides in tRNAs from the model plant species, Arabidopsis thaliana and hybrid aspen (Populus tremula x tremuloides). 21 modified nucleosides in tRNAs were identified in both species. To identify the genes responsible for the plant tRNA modifications, we performed global analysis of the Arabidopsis genome for candidate genes. Based on the conserved domains of homologs in Sacccharomyces cerevisiae and Escherichia coli, more than 90 genes were predicted to encode tRNA modifying enzymes in the Arabidopsis genome. Transcript accumulation patterns for the genes in Arabidopsis and the phylogenetic distribution of the genes among different plant species were investigated. Transcripts for the majority of the Arabidopsis candidate genes were found to be most abundant in rosette leaves and shoot apices. Whereas most of the tRNA modifying gene families identified in the Arabidopsis genome was found to be present in other plant species, there was a big variation in the number of genes present for each family. Through a loss of function mutagenesis study, we identified five tRNA modification genes (AtTRM10, AtTRM11, AtTRM82, AtKTI12 and AtELP1) responsible for four specific modified nucleosides (m¹G, m²G, m7G and ncm5U), respectively (two genes: AtKTI12 and AtELP1 identified for ncm5U modification). The AtTRM11 mutant exhibited an early-flowering phenotype, and the AtELP1 mutant had narrow leaves, reduced root growth, an aberrant silique shape and defects in the generation of secondary shoots. Conclusions: Using a reverse genetics approach, we successfully isolated and identified five tRNA modification genes in Arabidopsis thaliana. We conclude that the method established in this study will facilitate the identification of tRNA modification genes in a wide variety of plant species.


Related Articles

  • Plant dicistronic tRNA-snoRNA genes: a new mode of expression of the small nucleolar RNAs processed by RNase Z. Kruszka, Katarzyna; Barneche, Fredy; Guyot, Romain; Ailhas, Jérôme; Meneau, Isabelle; Schiffer, Steffen; Marchfelder, Anita; Echeverría, Manuel // EMBO Journal;2/1/2003, Vol. 22 Issue 3, p621 

    Small nucleolar RNAs (snoRNAs) guiding modifications of ribosomal RNAs and other RNAs display diverse modes of gene organization and expression depending on the eukaryotic system: in animals most are intron encoded, in yeast many are monocistronic genes and in plants most are polycistronic...

  • The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana. Camiolo, Salvatore; Farina, Lorenzo; Porceddu, Andrea // Genetics;Oct2012, Vol. 192 Issue 2, p641 

    The codon composition of coding sequences plays an important role in the regulation of gene expression. Herein, we report systematic differences in the usage of synonymous codons among Arabidopsis thaliana genes that are expressed specifically in distinct tissues. Although we observed that both...

  • EMBRYONIC FACTOR 31 encodes a tyrosyl-tRNA synthetase that is essential for seed development. Jiang, Li; Wang, Shu; Li, Huijie; Zhang, Guoxin; Li, Hengde // Molecular Biology Reports;Aug2012, Vol. 39 Issue 8, p8297 

    Aminoacyl-tRNA synthetases (AARSs) involve the process of catalyzing the ligation of specific amino acids to their cognate tRNAs. Here we identified an Arabidopsis mutant embryonic factor 31 ( fac31), its embryos arrested at development from one cell to globular stage. The FAC31 gene was...

  • Ubiquitin-Related Modifiers of Arabidopsis thaliana Influence Root Development. John, Florian; Philipp, Matthias; Leiber, Ruth-Maria; Errafi, Sanae; Ringli, Christoph // PLoS ONE;Jan2014, Vol. 9 Issue 1, p1 

    Ubiquitins are small peptides that allow for posttranslational modification of proteins. Ubiquitin-related modifier (URM) proteins belong to the class of ubiquitin-like proteins. A primary function of URM proteins has been shown to be the sulfur transfer reaction leading to thiolation of tRNAs,...

  • Loss of function of the Fusarium oxysporum SNF1 gene reduces virulence on cabbage and Arabidopsis. Ospina-Giraldo, Manuel D.; Mullins, Ewen; Kang, Seogchan // Current Genetics;Jul2003, Vol. 44 Issue 1, p49 

    Fusarium oxysporum pathogenicity is believed to require the activity of cell wall-degrading enzymes. Production of these enzymes in fungi is subject to carbon catabolite repression, a process that in yeast is mostly controlled by the SNF1 (sucrose non-fermenting 1) gene. To elucidate the role of...

  • Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family. Rautengarten, Carsten; Steinhauser, Dirk; Büssis, Dirk; Stintzi, Annick; Schaller, Andreas; Kopka, Joachim; Altmann, Thomas; Alexandrov, Nikolai N. // PLoS Computational Biology;Sep2005, Vol. 1 Issue 4, p297 

    The gene family of subtilisin-like serine proteases (subtilases) in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens...

  • Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. Kusano, Miyako; Fukushima, Atsushi; Arita, Masanori; Jonsson, Pär; Moritz, Thomas; Kobayashi, Makoto; Hayashi, Naomi; Tohge, Takayuki; Saito, Kazuki // BMC Systems Biology;2007, Vol. 1, p53 

    Background: Metabolites are not only the catalytic products of enzymatic reactions but also the active regulators or the ultimate phenotype of metabolic homeostasis in highly complex cellular processes. The modes of regulation at the metabolome level can be revealed by metabolic networks. We...

  • A Comprehensive Expression Analysis of all Members of a Gene Family Encoding Cell-Wall Enzymes Allowed us to Predict cis-Regulatory Regions Involved in Cell-Wall Construction in Specific Organs of Arabidopsis. Yokoyama, Ryusuke; Nishitani, Kazuhiko // Plant & Cell Physiology;Oct2001, Vol. 42 Issue 10, p1025 

    The Arabidopsis thaliana genome sequencing project has revealed that multigene families, such as those generated by genome duplications, are more abundant among plant genomes than among animal genomes. To gain insight into the evolutionary implications of the multigene families in higher plants,...

  • Functional diversity inside the Arabidopsis polyamine oxidase gene family. Fincato, Paola; Moschou, Panagiotis N.; Spedaletti, Valentina; Tavazza, Raffaela; Angelini, Riccardo; Federico, Rodolfo; Roubelakis-Angelakis, Kalliopi A.; Tavladoraki, Paraskevi // Journal of Experimental Botany;Jan2011, Vol. 62 Issue 3, p1155 

    Polyamine oxidases (PAOs) are FAD-dependent enzymes involved in polyamine catabolism. All so far characterized PAOs from monocotyledonous plants, such as the apoplastic maize PAO, oxidize spermine (Spm) and spermidine (Spd) to produce 1,3-diaminopropane, H2O2, and an aminoaldehyde, and are thus...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics