Transcriptome Profiling of the Salt Stress Response in the Leaves and Roots of Halophytic Eutrema salsugineum

Abstract

Eutrema salsugineum can grow in natural harsh environments; however, the underlying mechanisms for salt tolerance of Eutrema need to be further understood. Herein, the transcriptome profiling of Eutrema leaves and roots exposed to 300 mM NaCl is investigated, and the result emphasized the role of genes involved in lignin biosynthesis, autophagy, peroxisome, and sugar metabolism upon salt stress. Furthermore, the expression of the lignin biosynthesis and autophagy-related genes, as well as 16 random selected genes, was validated by qRT-PCR. Notably, the transcript abundance of a large number of lignin biosynthesis genes such as CCoAOMT, C4H, CCR, CAD, POD, and C3′H in leaves was markedly elevated by salt shock. And the examined lignin content in leaves and roots demonstrated salt stress led to lignin accumulation, which indicated the enhanced lignin level could be an important mechanism for Eutrema responding to salt stress. Additionally, the differentially expressed genes (DEGs) assigned in the autophagy pathway including Vac8, Atg8, and Atg4, as well as DEGs enriched in the peroxisome pathway such as EsPEX7, EsCAT, and EsSOD2, were markedly induced in leaves and/or roots. In sugar metabolism pathways, the transcript levels of most DEGs associated with the synthesis of sucrose, trehalose, raffinose, and xylose were significantly enhanced. Furthermore, the expression of various stress-related transcription factor genes including WRKY, AP2/ERF-ERF, NAC, bZIP, MYB, C2H2, and HSF was strikingly improved. Collectively, the increased expression of biosynthesis genes of lignin and soluble sugars, as well as the genes in the autophagy and peroxisome pathways, suggested that Eutrema encountering salt shock possibly possess a higher capacity to adjust osmotically and facilitate water transport and scavenge reactive oxidative species and oxidative proteins to cope with the salt environment. Thus, this study provides a new insight for exploring the salt tolerance mechanism of halophytic Eutrema and discovering new gene targets for the genetic improvement of crops.

The Halophyte Dehydrin Sequence Landscape

“…Interestingly, it seems that for some DHNs, there is preference for some architectures by stress. We investigated, for instance, the changes in expression under salt stress of different architectures in the leaves, shoots, and roots of three species ( Puccinellia tenuiflora Eutrema salsugenium, and Hordeum marinum ), according to the previously reported studies [ 50 , 51 , 52 ]. As shown in Figure 5 , YnSKn dehydrins are significantly more induced by salt stress than SKn in Puccinellia tenuiflora in leaves and roots with log2-fold changes reaching up to 5.63 and 3.44, respectively ( Figure 5 A).…”

“…Expression data were collected from the previous reports [ 50 , 51 , 52 ]. Using gene IDs available in these studies, we have identified the protein sequences of dehydrins in the Phytozome v13 database and determined their architectures by using MEME.…”

“…( A ) Relative gene expression of several DHN architectures after 12 h and 48 h of salt stress (Nacl 300Mm) in Puccinellia tenuiflora leaves and roots [ 50 ]. ( B ) Relative gene expression of DHN architectures in Eutrema salsugenium leaves and root after 24 h of salt stress (NaCl 300 mM) [ 51 ]. ( C ) Relative gene expression of DHN architectures in Hordeum marinum shoots and roots after 5 days of salt stress (NaCl 300 mM) [ 52 ].…”

Adaptative Mechanisms of Halophytic Eutrema salsugineum Encountering Saline Environment

“…This indicates that the adjustment of metabolism and activation of the already existing enzymatic machinery could serve as a faster and more efficient strategy to cope with salt stress than the synthesis of new proteins (Pilarska et al, 2016 ; Figure 2 ). Furthermore, E. salsugineum exposed to 300 mM NaCl was used to investigate global transcriptional changes, and genes of several pathways mainly involved in lignin biosynthesis and accumulations of soluble sugars, as well as genes in autophagy and peroxisome pathways, were significantly enriched in the halophyte, suggesting these upregulated genes could contribute to salt tolerance of the halophytic Eutrema (Li et al, 2021 ).…”

“…Furthermore, 64 E. salsugineum LEA proteins were identified to be classified into eight families, based on transcriptome sequencing, as well as the domain structures, numbers, and composition of conserved repeat motifs in LEAs. The remarkably induced expression of EsLEA1, EsLEA4, EsLEA6 , and EsDehydrin genes was revealed in leaves and/or roots, which implies that the expression of LEA proteins could be one of the important strategies for E. salsugineum to deal with salt stress (Li et al, 2021 ).…”