Abstract
DEAD-box proteins are a large family of RNA helicases that play important roles in almost all cellular RNA processes in model plants. However, little is known about this family of proteins in crops such as soybean. Here, we identified 80 DEAD-box family genes in the Glycine max (soybean) genome. These DEAD-box genes were distributed on 19 chromosomes, and some genes were clustered together. The majority of DEAD-box family proteins were highly conserved in Arabidopsis and soybean, but Glyma.08G231300 and Glyma.14G115100 were specific to soybean. The promoters of these DEAD-box genes share cis-acting elements involved in plant responses to MeJA, salicylic acid (SA), low temperature and biotic as well as abiotic stresses; interestingly, half of the genes contain nodulation-related cis elements in their promoters. Microarray data analysis revealed that the DEAD-box genes were differentially expressed in the root and nodule. Notably, 31 genes were induced by rhizobia and/or were highly expressed in the nodule. Real-time quantitative PCR analysis validated the expression patterns of some DEAD-box genes, and among them, Glyma.08G231300 and Glyma.14G115100 were induced by rhizobia in root hair. Thus, we provide a comprehensive view of the DEAD-box family genes in soybean and highlight the crucial role of these genes in symbiotic nodulation.
Highlights
Helicases are essential enzymes found in all prokaryotes and eukaryotes and play important roles in essentially all nucleic acid metabolism processes
The results showed that only 39 DDX genes in soybean were the orthologs of 16 members in Arabidopsis (Figure S2)
The expression patterns of Glyma.08G231300 and Glyma.14G115100 mRNAs were similar in both mature nodules and infected root hair (Figure 6). They were expressed at low levels in root nodules, but both genes were induced by rhizobial infection at 24 h after inoculation (HAI)
Summary
Helicases are essential enzymes found in all prokaryotes and eukaryotes and play important roles in essentially all nucleic acid metabolism processes. These helicase proteins can be divided into different families based on different conserved motifs [1]. The majority of RNA helicases are DExD/H-box proteins, which share conserved motifs and domain structures [3] These RNA helicases have more than seven conserved motifs, which form two domains. The proteins form a cleft with an ATP binding site on one side and an RNA binding site on the other This core structure of RNA helicases ensures that
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