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. 2017 Dec 21;17(1):261.
doi: 10.1186/s12870-017-1206-0.

Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

Youmei Wang  1   2 , Chaoqun Pang  1   2 , Xukai Li  3 , Zhen Hu  1   2 , Zhengyi Lv  1   2 , Bo Zheng  4   5 , Peng Chen  6   7
Affiliations

Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

Youmei Wang et al. BMC Plant Biol. .

Erratum in

Abstract

Background: Modification of nucleosides on transfer RNA (tRNA) is important either for correct mRNA decoding process or for tRNA structural stabilization. Nucleoside methylations catalyzed by MTase (methyltransferase) are the most common type among all tRNA nucleoside modifications. Although tRNA modified nucleosides and modification enzymes have been extensively studied in prokaryotic systems, similar research remains preliminary in higher plants, especially in crop species, such as rice (Oryza sativa). Rice is a monocot model plant as well as an important cereal crop, and stress tolerance and yield are of great importance for rice breeding.

Results: In this study, we investigated how the composition and abundance of tRNA modified nucleosides could change in response to drought, salt and cold stress, as well as in different tissues during the whole growth season in two model plants-O. sativa and Arabidopsis thaliana. Twenty two and 20 MTase candidate genes were identified in rice and Arabidopsis, respectively, by protein sequence homology and conserved domain analysis. Four methylated nucleosides, Am, Cm, m1A and m7G, were found to be very important in stress response both in rice and Arabidopsis. Additionally, three nucleosides,Gm, m5U and m5C, were involved in plant development. Hierarchical clustering analysis revealed consistency on Am, Cm, m1A and m7G MTase candidate genes, and the abundance of the corresponding nucleoside under stress conditions. The same is true for Gm, m5U and m5C modifications and corresponding methylation genes in different tissues during different developmental stages.

Conclusions: We identified candidate genes for various tRNA modified nucleosides in rice and Arabidopsis, especially on MTases for methylated nucleosides. Based on bioinformatics analysis, nucleoside abundance assessments and gene expression profiling, we propose four methylated nucleosides (Am, Cm, m1A and m7G) that are critical for stress response in rice and Arabidopsis, and three methylated nucleosides (Gm, m5U and m5C) that might be important during development.

Keywords: Development; Methyltransferase; Modified nucleoside; Stress; tRNA.

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Conflict of interest statement

Ethics approval and consent to participate

Nipponbare rice (Oryza sativa japonica) and Arabidopsis in Colombian-0 seeds were maintained in this lab. The cultivation and collection of plant material complied with institutional guidelines in accordance with legislation from Faculty of Plant Science and Technology, Huazhong Agricultural University.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Physical map of tRNA nucleoside methyltransferase candidate genes on rice (a) or Arabidopsis (b) genomes. a, Chromosome location of 22 rice MTases candidate genes. b, Chromosome location of 20 Arabidopsis MTases candidate genes. Chromosome size are indicated by relative lengths. Tandemly duplicated genes are indicated by boxes
Fig. 2
Fig. 2
Circular neighbor-joining (N-J) tree of rice and Arabidopsis MTase candidate genes. Supporting values from bootstrap analysis were shown for each branch. The three groups of Trm proteins clustered together were annotated with red lines for group I, blue lines for group II and green lines for group III, respectively
Fig. 3
Fig. 3
Conserved motif analysis of group I (a), group II (b) and group III (c) MTase candidate genes. X axis indicated position for each residue within the identified motifs, Y axis indicated bit score values. The size of the residue letter represented the degree of conservation within the group of proteins analyzed. The table below each graph illustrated the protein sequence for each member, with the name of the protein, starting position of the conserved motif and the whole motif sequence
Fig. 4
Fig. 4
Hierarchical clustering analysis between tRNA nucleoside modification and the Arabidopsis candidate genes expression under stress conditions. Heat map was generated using raw data of nucleosides abundance or MTase candidate genes expression level under stress conditions, respectively, horizontally normalized and logarithmically transformed. LN2 value was presented in color key, which corresponded with ratio of change on either nucleoside level of the gene expression level under various stress conditions. A hierarchy-clustering was shown on the left, showing similar patterns between nucleosides and MTase candidate genes. Solid boxes indicated nucleosides and corresponding genes clustered together
Fig. 5
Fig. 5
Hierarchical clustering analysis between tRNA nucleoside modification and the rice candidate genes expression under stress conditions. Heat map was generated using raw data of nucleosides abundance or MTase candidate genes expression level under stress conditions, respectively, horizontally normalized and logarithmically transformed. LN2 value was presented in color key, which corresponded with ratio of change on either nucleoside level of the gene expression level under various stress conditions. A hierarchy-clustering was shown on the left, showing similar patterns between nucleosides and MTase candidate genes. Solid boxes indicated nucleosides and corresponding genes clustered together
Fig. 6
Fig. 6
Hierarchical clustering analysis between tRNA nucleoside methylated modification and candidate genes expression level during development stage. Heatmap profiles about the abundance of methylated nucleosides and the expression level of the rice (a) or Arabidopsis (b) MTase candidate genes from developmental dataset. Heat map was generated from raw data of nucleoside levels and gene expression levels, normalized horizontally. LN2 values was shown above in color key. Solid boxes indicated nucleosides and the corresponding genes clustered into the same group. In panel B, green boxes indicated m5C nucleoside and the corresponding candidate genes in Arabidopsis. Solid boxes indicated nucleosides and corresponding genes clustered together
Fig. 7
Fig. 7
Selected methylated nucleosides that were potentially important for stress or development. (a and b) Quantification of Cm, m1A, Am, m7G nucleosides under stress conditions in Arabidopsis or rice. (c and d) Quantification of m5C, m5U and Gm nucleosides in different tissues during development
Fig. 8
Fig. 8
A model displaying the relationships within tRNA nucleoside methylation and stress/development. Green and red solid lines indicated nucleoside abundance and expression level of the corresponding MTase genes under stress or during development which could be clustered together, respectively. Green and red dashed lines showed nucleosides that changes under stress or during development, but shows no consistency with MTase gene expression
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