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. 2022 Jun 10:13:924490.
doi: 10.3389/fpls.2022.924490. eCollection 2022.

Integrated Transcriptomic and Proteomic Analyses Uncover the Regulatory Mechanisms of Myricaria laxiflora Under Flooding Stress

Linbao Li  1   2 , Guiyun Huang  1   2 , Weibo Xiang  2 , Haofei Zhu  1   2 , Haibo Zhang  1   2 , Jun Zhang  1   2 , Zehong Ding  3 , Jihong Liu  4 , Di Wu  1   2
Affiliations

Integrated Transcriptomic and Proteomic Analyses Uncover the Regulatory Mechanisms of Myricaria laxiflora Under Flooding Stress

Linbao Li et al. Front Plant Sci. .

Abstract

Flooding is one of the major environmental stresses that severely influence plant survival and development. However, the regulatory mechanisms underlying flooding stress remain largely unknown in Myricaria laxiflora, an endangered plant mainly distributed in the flood zone of the Yangtze River, China. In this work, transcriptome and proteome were performed in parallel in roots of M. laxiflora during nine time-points under the flooding and post-flooding recovery treatments. Overall, highly dynamic and stage-specific expression profiles of genes/proteins were observed during flooding and post-flooding recovery treatment. Genes related to auxin, cell wall, calcium signaling, and MAP kinase signaling were greatly down-regulated exclusively at the transcriptomic level during the early stages of flooding. Glycolysis and major CHO metabolism genes, which were regulated at the transcriptomic and/or proteomic levels with low expression correlations, mainly functioned during the late stages of flooding. Genes involved in reactive oxygen species (ROS) scavenging, mitochondrial metabolism, and development were also regulated exclusively at the transcriptomic level, but their expression levels were highly up-regulated upon post-flooding recovery. Moreover, the comprehensive expression profiles of genes/proteins related to redox, hormones, and transcriptional factors were also investigated. Finally, the regulatory networks of M. laxiflora in response to flooding and post-flooding recovery were discussed. The findings deepen our understanding of the molecular mechanisms of flooding stress and shed light on the genes and pathways for the preservation of M. laxiflora and other endangered plants in the flood zone.

Keywords: Myricaria laxiflora; flooding stress; post-flooding recovery; transcriptional and post-transcriptional regulation; transcriptome and proteome.

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Conflict of interest statement

LL, GH, HFZ, HBZ, JZ, and DW were employed by the China Three Gorges Corporation. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Transcriptome and proteome profiling of M. laxiflora at different time-points during flooding and post-flooding recovery treatment. (A,B) Up-regulated and down-regulated DEGs and DEPs, respectively, identified for a certain period of flooding compared with the control (R0). (C,D) Up-regulated and down-regulated DEGs and DEPs, respectively, identified between a time point and the preceding time point. R0, R6, R12, R18, R24, R30, R36, and R48 represent the samples collected at 0, 6, 12, 18, 24, 30, 36, and 48 h after the flooding treatment, respectively, while RR12 indicates the samples collected at 12 h after post-flooding recovery treatment.
FIGURE 2
FIGURE 2
Dynamic and stage-specific expression changes of genes and proteins upon flooding stress. (A) Profiles of DEGs identified exclusively at the transcriptomic level. A total of eight groups (gM1–gM8) were determined according to their expression patterns. (B) Profiles of DEGs/DEPs identified at both the transcriptomic and proteomic levels. Five groups (gpM1–gpM5) were found. (C) Profiles of DEPs identified exclusively at the proteomic level. Six groups (pM1–pM6) were found. (D) Functional category enrichment of DEGs/DEPs corresponding to those identified in (A–C). The samples/groups are prefixed as follows: g, transcriptomic level; p, proteomic level; gp, both transcriptomic and proteomic levels.
FIGURE 3
FIGURE 3
Summary of genes and pathways identified by integrated transcriptomic and proteomic analysis during flooding stress. The flooding treatment is divided into the early, late, and recovery stages.
FIGURE 4
FIGURE 4
Expression profiles of DEGs and DEPs related to sucrose-starch metabolism and glycolysis during flooding stress. (A) Summary of pathways of sucrose-starch metabolism and glycolysis. (B) Heatmap of DEGs and DEPs related to sucrose-starch metabolism. (C) Heatmap of DEGs and DEPs involved in glycolysis metabolism. The samples are prefixed as follows: g, transcriptomic level; p, proteomic level.
FIGURE 5
FIGURE 5
Expression profiles of DEGs and DEPs involved in redox metabolism during flooding stress. Each row represents a gene with its name at the right.
FIGURE 6
FIGURE 6
Expression profiles of DEGs and DEPs involved in hormone metabolism during flooding stress. (A) BR biosynthesis, (B) ABA biosynthesis, (C) ethylene biosynthesis, (D) GA biosynthesis, (E) JA biosynthesis. Each row represents a gene, and the cells (from left to right) indicate the normalized expression value of R0, R6, R12, R18, R24, R30, R36, R48, and RR12 at the transcriptomic and proteomic levels, respectively.
FIGURE 7
FIGURE 7
Expression profiles of transcriptional factors during flooding stress. Each row represents a TF with its name at the right. The cells (from left to right) indicate the normalized expression value of R0, R6, R12, R18, R24, R30, R36, R48, and RR12 at the transcriptomic and proteomic levels, respectively.
FIGURE 8
FIGURE 8
The transcriptional regulation model of M. laxiflora during flooding stress. (A) The transcriptional regulatory networks of M. laxiflora upon flooding (black lines) and post-flooding recovery (blue lines) treatment. The normal arrows and T-bars indicate positive and negative regulation relationships, respectively. Solid lines represent the relationships that are consistent with previously reported studies, while dash lines represent the relationships reported in other plants but not confirmed in our work. (B) The transcriptomic profiles of genes present in (A).
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