Eukaryotic translation initiation factors (eIFs) are essential protein complexes involved in the translation of mRNA into proteins. These initiation factors are generally used as targets in the control of plant RNA virus infections. In the present study, we identified a total 190 eIFs, clustered phylogenetically into 40 distinct subfamilies in the allopolyploid Brassica juncea. Extensive evolutionary duplications of the eIFs in B. juncea suggest their increased genetic diversity and wide adaptability. The induction of expressions in some of the eIFs after inoculation against Turnip mosaic virus (TuMV) provided candidate targets to be used in the control of viral infections. In addition, the expression profiles of eIFs under different temperatures suggested that the TuMV epidemic was temperature dependent. The eIFs expressions suggested that the systemic viral infections were more acute in plants grown between 20 °C and 28 °C. In addition, our results revealed that new subgroups of eIFs, eIF2β, eIF2α, eIF2Bβ, EF1A, and PABP could be represented as targets for antiviral strategies in B. juncea. In summary, our findings would be helpful in studying the complex mechanisms of eIF-mediated, temperature-dependent RNA virus control in B. juncea.
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This work was supported by grants from the National Natural Science Foundation of Zhejiang Province (Grant No. Z20C150008) and the National Natural Science Foundation of China (Grant No. 31872095). We thank LetPub (https://www.letpub.com) for its linguistic assistance during the preparation of this manuscript.
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Visualization of the eIF linkage groups. Chromosomal distributions of eIF-related genes in the B. juncea genome. The lines represent putative orthologs of eIF genes in Arabidopsis and B. juncea. At1 to At5, Bj1 to Bj10, and Bj11 to Bj18 represent the Arabidopsis, B. juncea subgenome A, and B. juncea subgenome B chromosome numbers, respectively. Fig. S2 Phylogenetic relationships, gene structures, and protein structures of the B. junceae subgenome B eIF genes. (A) The phylogenetic tree was constructed with MEGA 5.0 using the NJ method with 1,000 bootstrap replicates based on a multiple alignment of 91 eIF aa sequences from BjuBeIF. The 38 major subfamilies are indicated by name and are marked with backgrounds colored differently. (B) Exon/intron structures of eIF genes from BjuBeIF. Exons and introns are represented by blue boxes and black lines, respectively. The sizes of the exons and introns are estimated using the scale at the bottom. (C) Schematic of the conserved motifs in the eIF proteins from BjuB, elucidated by MEME. Every motif is represented by one colored box with a number. The black lines represent the non-conserved sequences. Fig. S3 Sequence logos for the conserved motifs of eIFBjuB domain proteins. Fig. S4 Sequence comparisons of eIF2Bβ, eIF4E, and eIFiso4E duplicated genes between A and B subgenome promoter regions in B. juncea. Pairs of horizontal bars represent subgenome A (upper) and subgenome B (lower) promoter region sequences. Highly similar regions are illustrated by black lines and inverted regions by red lines. Similar sequences are connected by black lines. Similar sequences but in reverse orientation are connected with red lines. Unfilled boxes represent sequences absent in one or another contig. Red broken lines connect similar regions in the inverted match and solid dark lines connect similar regions. Fig. S5 Graphical representation of phosphorylation site predictions in BjuAeIFs. Fig. S6 Graphical representation of phosphorylation site predictions in BjuBeIFs. Fig. S7 Graphical representation of signal peptide predictions in BjuAeIFs. Fig. S8 Graphical representation of signal peptide predictions in BjuBeIFs. (DOCX 9504 kb)
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Shopan, J., Liu, C., Hu, Z. et al. Identification of eukaryotic translation initiation factors and the temperature-dependent nature of Turnip mosaic virus epidemics in allopolyploid Brassica juncea. 3 Biotech 10, 75 (2020). https://doi.org/10.1007/s13205-020-2058-0
- Eukaryotic translation initiation factors
- Phylogenetic evolution
- Virus epidemic