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Identification of RNA helicases in Medicago truncatula and their expression patterns under abiotic stress

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Abstract

RNA helicase catalyzes the denaturation of DNA or the unwinding of double-stranded RNA. It is vital to RNA splicing, transport, editing, degradation and the initiation of protein translation. However, the function of RNA helicase in Medicago truncatula has rarely been reported. In this study, 170 putative RNA helicase genes were identified in the M. truncatula genome, and classified into three subfamilies based on the presence of either a DEAD-box (52 genes), DEAH-box (38 genes), or DExD/H-box (80 genes) in their coding regions. Additionally, conserved helicase_C domains and other functional domains (e.g., the HA2, DUF, and ZnF domains) were also present in these genes. Chromosomal mapping and synteny analyses showed that there were tandem and segment duplications of RNA helicase genes. Furthermore, transcriptome and real-time PCR analysis showed that the expression of 35 RNA helicase genes was affected by abiotic stress. To be specific, 17, 12 and 19 genes were regulated by salt, drought and cold stress, respectively. It is worth noting that MtDEAD8, MtDEAH3, MtDExD/H18 and MtDExD/H23 responded to all three types of stress. These results provide valuable information for understanding the RNA helicase genes in M. truncatula and their abiotic stress-related functions.

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Fig. 1

taken from the Pfam or SMART database. Domain abbreviations: H, HELICc domain; HA2, Helicase associated domain; DUF, DUF domain; DSHCT, DSHCT domain; RING, RING finger domain; AAA, AAA domain; Sec, Sec63 domain; ZnF, Zinc finger domain; SANT, SANT domain; PAZ, PAZ domain; R, RIBOc domain; DS, DSRM domain; RQC,domain of DAPkinase; WW, WW domain

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Acknowledgements

This study was financed by the National Natural Science Foundation of China (32060069), and Natural Science Foundation of Jiangxi Province (20202BABL205023).

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Author notes

  1. Jie Cheng and Songsong Zhou have contributed equally to this work.

Authors and Affiliations

  1. College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045, People’s Republic of China

    Jie Cheng, Songsong Zhou, Kun Yang, Hongyang Yu, Rongrong Chen, Liming Zeng, Yihua Wang & Jianbo Song

  2. Camphor Engineering Technology Research Center for State Forestry Administration, Jiangxi Academy of Forestry, Nanchang, 330032, People’s Republic of China

    Songsong Zhou

  3. College of Science, Jiangxi Agricultural University, Nanchang, 330045, People’s Republic of China

    Yihua Wang

  4. College of Life Science, Henan Agricultural University, Zhengzhou, 450002, People’s Republic of China

    Hua Li

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  1. Jie Cheng
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Contributions

JC, SZ and KY carried out data collection and bioinformatics analysis. JC, SZ and RC performed the biological experiment. HY, LZ and HL prepared the plant sample. YW and JS designed the experiments and wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Yihua Wang or Jianbo Song.

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Supplementary Information

Below is the link to the electronic supplementary material.

12298_2021_1087_MOESM1_ESM.docx

Supplemental Fig. 1. Evolutionary relationship analysis of RNA Helicases in Medicago truncatula, Arabidopsis thaliana, and Oryza sativa. (DOCX 542 KB)

Supplemental Table 1. Primer sequences used for this study (XLS 25 KB)

12298_2021_1087_MOESM3_ESM.docx

Supplemental Table 2. Basic data of the DEAD-box, DEAH-box and DExD/H-box RNA helicase genes in the M. truncatula genome. (DOCX 62 KB)

Supplemental Table 3. Helicase family genes in Medicago truncatula, Arabidopsis thaliana and Oryza sativa. (XLS 541 KB)

Supplemental Table 4. Read abundance of all Helicase family genes in the drought, salt and cold stresses. (XLS 186 KB)

Supplemental Table 5. 15 type Cis-acting elements of each RNA helicase genes and its numbers. (XLS 68 KB)

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Cheng, J., Zhou, S., Yang, K. et al. Identification of RNA helicases in Medicago truncatula and their expression patterns under abiotic stress. Physiol Mol Biol Plants 27, 2283–2296 (2021). https://doi.org/10.1007/s12298-021-01087-y

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