Genome-wide and molecular characterization of the DNA replication helicase 2 (DNA2) gene family in rice under drought and salt stress

Bilal Saleem; Umer Farooq; Obaid Ur Rehman; Muhammad Aqeel; Muhammad Shahbaz Farooq; Muhammad Kashif Naeem; Safeena Inam; Wajya Ajmal; Amna Abdul Rahim; Ming Chen; Rabia Kalsoom; Muhammad Uzair; Sajid Fiaz; Kotb Attia; Hayat Ali Alafari; Muhammad Ramzan Khan; Guoping Yu

doi:10.3389/fgene.2022.1039548

Genome-wide and molecular characterization of the DNA replication helicase 2 (DNA2) gene family in rice under drought and salt stress

Front Genet. 2022 Nov 22:13:1039548. doi: 10.3389/fgene.2022.1039548. eCollection 2022.

Authors

Bilal Saleem¹, Umer Farooq¹, Obaid Ur Rehman^{1

2}, Muhammad Aqeel¹, Muhammad Shahbaz Farooq¹, Muhammad Kashif Naeem¹, Safeena Inam¹, Wajya Ajmal¹, Amna Abdul Rahim¹, Ming Chen², Rabia Kalsoom³, Muhammad Uzair^{1

4}, Sajid Fiaz⁵, Kotb Attia⁶, Hayat Ali Alafari⁷, Muhammad Ramzan Khan¹, Guoping Yu^{8

9

10}

Affiliations

¹ National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan.
² Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China.
³ School of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
⁴ National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
⁵ Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan.
⁶ Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.
⁷ Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia.
⁸ National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China.
⁹ China National Rice Research Institute, Hangzhou, China.
¹⁰ Hainan Yazhou Bay Seed Lab, Sanya, China.

Abstract

Rice plants experience various biotic (such as insect and pest attack) and abiotic (such as drought, salt, heat, and cold etc.) stresses during the growing season, resulting in DNA damage and the subsequent losses in rice production. DNA Replication Helicase/Nuclease2 (DNA2) is known to be involved in DNA replication and repair. In animals and yeast DNA2 are well characterized because it has the abilities of both helicase and nuclease, it plays a crucial role in DNA replication in the nucleus and mitochondrial genomes. However; they are not fully examined in plants due to less focused on plants damage repair. To fill this research gap, the current study focused on the genome-wide identification and characterization of OsDNA2 genes, along with analyses of their transcriptional expression, duplication, and phylogeny in rice. Overall, 17 OsDNA2 members were reported to be found on eight different chromosomes (2, 3, 4, 6, 7, 9, 10, and 11). Among these chromosomes (Chr), Chr4 contained a maximum of six OsDNA2 genes. Based on phylogenetic analysis, the OsDNA2 gene members were clustered into three different groups. Furthermore, the conserved domains, gene structures, and cis-regulatory elements were systematically investigated. Gene duplication analysis revealed that OsDNA2_2 had an evolutionary relationship with OsDNA2_14, OsDNA2_5 with OsDNA2_6, and OsDNA2_1 with OsDNA2_8. Moreover, results showed that the conserved domain (AAA_11 superfamily) were present in the OsDNA2 genes, which belongs to the DEAD-like helicase superfamily. In addition, to understand the post-transcriptional modification of OsDNA2 genes, miRNAs were predicted, where 653 miRNAs were reported to target 17 OsDNA2 genes. The results indicated that at the maximum, OsDNA2_1 and OsDNA2_4 were targeted by 74 miRNAs each, and OsDNA2_9 was less targeted (20 miRNAs). The three-dimensional (3D) structures of 17 OsDNA2 proteins were also predicted. Expression of OsDNA2 members was also carried out under drought and salt stresses, and conclusively their induction indicated the possible involvement of OsDNA2 in DNA repair under stress when compared with the control. Further studies are recommended to confirm where this study will offer valuable basic data on the functioning of DNA2 genes in rice and other crop plants.

Keywords: DNA damage-repair; DNA2; abiotic stress; gene expression; rice.