Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana

Abstract

Background: Pre-exposing plants to diverse abiotic stresses may alter their physiological and transcriptional responses to a subsequent stress, suggesting a form of "stress memory". Arabidopsis thaliana plants that have experienced multiple exposures to dehydration stress display transcriptional behavior suggesting "memory" from an earlier stress. Genes that respond to a first stress by up-regulating or down-regulating their transcription but in a subsequent stress provide a significantly different response define the 'memory genes' category. Genes responding similarly to each stress form the 'non-memory' category. It is unknown whether such memory responses exists in other Angiosperm lineages and whether memory is an evolutionarily conserved response to repeated dehydration stresses.

Results: Here, we determine the transcriptional responses of maize (Zea mays L.) plants that have experienced repeated exposures to dehydration stress in comparison with plants encountering the stress for the first time. Four distinct transcription memory response patterns similar to those displayed by A. thaliana were revealed. The most important contribution is the evidence that monocot and eudicot plants, two lineages that have diverged 140 to 200 M years ago, display similar abilities to 'remember' a dehydration stress and to modify their transcriptional responses, accordingly. The highly sensitive RNA-Seq analyses allowed to identify genes that function similarly in the two lineages, as well as genes that function in species-specific ways. Memory transcription patterns indicate that the transcriptional behavior of responding genes under repeated stresses is different from the behavior during an initial dehydration stress, suggesting that stress memory is a complex phenotype resulting from coordinated responses of multiple signaling pathways.

Conclusions: Structurally related genes displaying the same memory responses in the two species would suggest conservation of the genes' memory during the evolution of plants' dehydration stress response systems. On the other hand, divergent transcription memory responses by genes encoding similar functions would suggest occurrence of species-specific memory responses. The results provide novel insights into our current knowledge of how plants respond to multiple dehydration stresses, as compared to a single exposure, and may serve as a reference platform to study the functions of memory genes in adaptive responses to water deficit in monocot and eudicot plants.

Figure 1

Relative water content (RWC, %) in response to dehydration stress in leaves of trained or non-trained maize plants. RWC was measured in leaves harvested after air drying for the indicated times (in min, shown on the ‘x’-axis), for plants experiencing their first stress (dark blue line) or for trained plants exposed to three stress cycles (pink line). Points are the mean, and error bars are ± SE from three independent experiments, each performed with 8–10 leaves from three separate plants.

Figure 2

Distribution of dehydration stress responding genes in Z. mays and A. thaliana in S1 and S3. A) Transcript levels from dehydration stress responding genes that are up-regulated or down-regulated during S1 (color key at the bottom) plotted by the log2 of their S1 levels along the x-axis, and by log2 of their S1/watered ratio along the y-axis (left-hand panel); in the right-hand panel, transcript levels of dehydration stress memory genes are as above, except the y-axis is the log2 of the S3/watered ratio. The clustering of the four colors illustrates the distribution of the four distinct memory response types: revised response [+/-] and [-/+] memory genes clustering closer to their pre-stressed (W) levels, while the [+/+] and [-/-] increasing separation from these levels. B) Transcript levels from dehydration stress responding genes and from the memory genes in A. thaliana. Data are from Ding et al. 2013.

Figure 3

Transcription patterns of maize dehydration stress responding genes under initial pre-stressed watered (W) conditions, upon the first exposure (S1), during watered recovery (R2), and upon a subsequent stress (S3) measured by real time qRT-PCR. A) Higher transcript levels in S3 than in S1 produced by [+/+] memory genes: GRMZM2G179462 encodes a putative low-temperature ABA-induced protein integral to the plasma membrane; GRMZM2G053669 encodes a putative asparagine synthase; GRMZM2G011598 encodes a NAC domain protein involved in hypersensitive response; B) lower transcripts in S3 than in S1 produced by [-/-] memory genes: GRMZM2G306104 encodes a putative plastid gene; GRMZM2G151365 encodes unknown protein; GRMZM2G303993 encodes putative RNA-helicase; C) genes induced in S1 but revising response in S3 [+/-] memory genes: GRMZM2G390804 encodes a protein with unknown function; GRMZM2G012453 encodes a putative microtubule organizing protein; GRMZM2G013170 encodes a putative disease resistance protein from the RPP family; D) genes repressed in S1 but regaining activity in R1 and maintaining it in S3 [-/+] memory genes: GRMZM2G082830 encodes a putative membrane-associated kinase; GRMZM2G068519 encodes a putative Flavin-binding oxygenase; GRMZM2G110192 is an NCED4 homolog; E) and F) genes repetitiously providing similar transcript amounts during each exposure to the dehydration stress: [+/=] GRMZM2G159700 and GRMZM2G026892 encoding a protein of the cupin-superfamily and an unknown protein, respectively. The [-/=] nontrainable genes GRMZM2G055973 and GRMZM2G467576 encode putative Zn-finger proteins from the RING family.

Figure 4

Heat map illustrating the distribution of maize dehydration stress memory and non-memory classes according to different functional, biological process, and cellular component groups. Heat maps follow the percentage-wise distributions of genes (Table 2, and Additional file 6) over various groups according to GO categories from the four memory classes (A) or the non-memory class (B). Distribution of TFs encoded by memory genes (C) and non-memory genes (D)in Z. mays. Pitch-black indicates 0%, and red is a linear increase in brightness to a maximum of 60% recalculated to follow the total number of transcription factor genes in the memory or non-memory categories. The heatmap function in MATLAB® was used to generate Figure 4.

Figure 5

Distribution of the response patterns to repeated dehydration stress by homologous genes in the two species. A) Overall maize memory genes and their homologs in Arabidopsis are shown in the larger frames. The numbers of Arabidopsis homologous genes distributed according to the patterns of their responses to repeated dehydration stress are in the smaller frames below. Comparable numbers of the homologs respond to dehydration stress by providing memory or non-memory responses in Arabidopsis. The largest numbers of homologous genes not belonging in the dehydration response category are indicated. Members of gene families homologous to a maize memory gene account for the higher numbers of genes in Arabidopsis. B) Distribution of the maize homologs in Arabidopsis according to the memory response type. The numbers of maize genes of a particular memory category are in larger frames. The numbers of respective homologs according to their responses in Arabidopsis are in smaller frames: memory response genes are in shaded brackets (bottom rows); conserved-memory responses are shaded in green; non-memory genes and Arabidopsis homologs that do not respond in S1 (indicated by the =/* sign) are in brackets on top. Multiple members with a gene family responding differently to dehydration stress account for the higher numbers of summed up genes in both species.

Figure 6

Pair-wise comparison of Z. mays and A. thaliana memory and non-memory genes according to different functional, biological process, and cellular component groups. Heat maps follow the percentage-wise distributions of the genes (Table 2, Additional file 7) over various groups according to GO categories from the four memory classes (A) or the non-memory class (B) for Z. mays (ZM) and A. thaliana (AT). Distribution of TFs encoded by memory genes (C) and non-memory genes (D) in Z. mays and A. thaliana. Pitch-black indicates 0%, and red is a linear increase in brightness to a maximum of 60% recalculated to follow the total number of transcription factor genes in the memory or non-memory categories. The heatmap function in MATLAB® was used to generate Figure 6.