Planta

, Volume 233, Issue 3, pp 433–438

Plant response to stress meets dedifferentiation

Authors

    • French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert ResearchBen-Gurion University of the Negev
  • Vered Chalifa-Caspi
    • The National Institute for BiotechnologyBen-Gurion University of the Negev
  • Tal Nagar
    • The National Institute for BiotechnologyBen-Gurion University of the Negev
  • Inbar Plaschkes
    • The National Institute for BiotechnologyBen-Gurion University of the Negev
  • Simon Barak
    • French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert ResearchBen-Gurion University of the Negev
  • Vanessa Ransbotyn
    • French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert ResearchBen-Gurion University of the Negev
Review

DOI: 10.1007/s00425-011-1366-3

Cite this article as:
Grafi, G., Chalifa-Caspi, V., Nagar, T. et al. Planta (2011) 233: 433. doi:10.1007/s00425-011-1366-3

Abstract

Plant response to various stress conditions often results in expression of common genes, known as stress-responsive/inducible genes. Accumulating data point to a common, yet elusive process underlying the response of plant cells to stress. Evidence derived from transcriptome profiling of shoot apical meristem stem cells, dedifferentiating protoplast cells as well as from senescing cells lends support to a model in which a common response of cells to certain biotic and abiotic stresses converges on cellular dedifferentiation whereby cells first acquire a stem cell-like state before assuming a new fate.

Keywords

Chromatin structureDedifferentiationSenescenceStem cellsStress responseTranscription factors

Abbreviations

iPSCs

Induced pluripotent stem cells

SAM

Shoot apical meristem

SAGs

Senescence-associated genes

TF

Transcription factor

NHEJ

Non-homologous end-joining

Dedifferentiation

Cellular dedifferentiation signifies the withdrawal of cells from a given differentiated state into a transient, stem cell-like state (Hay 1959; Grafi 2004)—a process preceding trans/redifferentiation, reentry into the cell cycle, and even the commitment to cell death. In recent years, this process has drawn much attention due to its potential as a fundamental approach for obtaining autologous stem cell lineages to be used in regenerative medicine. Accordingly, somatic animal cells can be reprogrammed, though at a very low rate of success, to acquire pluripotency by retroviral transduction of Oct4, Sox2, Klf4 and c-Myc—a process known to induce formation of pluripotent stem cells (iPSCs; Takahashi and Yamanaka 2006). In plants, cellular dedifferentiation is exemplified by the transition of differentiated leaf cells to protoplasts (plant cells devoid of cell walls; Jamet et al. 1990; Zhao et al. 2001), which assume a unique transient state with features resembling animal stem cells. Protoplasts are characterized by widespread chromatin decondensation (Zhao et al. 2001; Tessadori et al. 2007)—a distinguishing feature of animal stem cells (Meshorer and Misteli 2006)—and foremost by their capability to differentiate into different cell types following application of various stimuli (Takebe et al. 1971; Valente et al. 1998; Zhao et al. 2001; Pasternak et al. 2002). Commonly, auxin and cytokinin induce protoplasts to reenter the cell cycle, proliferate and form calli, which under appropriate conditions can form shoots and roots, eventually giving rise to an entire fertile plant (Takebe et al. 1971). The sole application of auxin induces endoreduplication and formation of elongated cells (Valente et al. 1998), whereas in the absence of growth factors dedifferentiating protoplast cells die, exhibiting hallmark events of programmed cell death (Zhao et al. 2001). Thus, dedifferentiation appears to precede any switch in cell fate including transdifferentiation (i.e. the conversion of one cell type to another), reentry into the cell cycle as well as cell death (Grafi 2004).

Stem cells and dedifferentiating cells

Animal stem cells have been intensively studied in recent years in an attempt to uncover the genes determining the stem cell state. However, contrary to the assumption that stem cells selectively express specific stem cell genes, often referred to as a “stem cell signature” or ‘stemness genes’, these cells appear to display a promiscuous gene expression profile (Zipori 2004; Meshorer and Misteli 2006; Efroni et al. 2008). Accumulating data emphasize two attributes of animal stem cells: they assume a transcriptionally competent chromatin state and display widespread expression of most markers of differentiated cells but at a very low level (Zipori 2004; Meshorer and Misteli 2006). Indeed, animal stem cells, like dedifferentiating plant cells, acquire an open, decondensed chromatin architecture (Zhao et al. 2001; Meshorer and Misteli 2006; Tessadori et al. 2007), which is essential, though not sufficient, for initiation of gene transcription. The existence of flexible chromatin architecture has been proposed for Arabidopsis shoot apical meristem (SAM) stem cells whose transcriptome shows overrepresentation of genes involved in chromatin modification pathways (Yadav et al. 2009).

In both plants and animals, the quiescent nature characteristic of stem cells is reflected in dedifferentiating protoplast cells by structural changes in the nucleolus, which can undergo shrinkage or disruption that is often accompanied by condensation of rRNA gene clusters (Williams et al. 2003; Damri et al. 2009). Consequently, dedifferentiating cells exhibit significantly reduced ribosome biogenesis, which could lead to reduction in protein synthesis and acquisition of a quiescent state. Notably, ultrastructural studies revealed a lower density of ribosomes in the central region of SAM as compared to the peripheral zone (Gifford and Steward 1967). This observation is consistent with the low and high frequency of cell division in the SAM central and peripheral zones, respectively (Steeves and Sussex 1989).

Senescence meets dedifferentiation

Plant senescence, often induced following exposure to biotic and abiotic stresses, is an integral stage of plant development that leads to the death of cells, tissues, or organs and even to death of the entire plant. It is an actively programmed process accompanied by changes in metabolic activities involving the degradation of macromolecules and remobilization of their constituents to other parts of the plants (e.g. seeds, young leaves, stem; Buchanan-Wollaston et al. 2003; Lim et al. 2007). During senescence, many hundreds of genes, collectively known as senescence-associated genes (SAGs), become up-regulated including genes encoding transcription factors (TFs), kinases, as well as genes encoding proteases and RNases (Gepstein et al. 2003; Andersson et al. 2004; Guo et al. 2004; Lin and Wu 2004; Buchanan-Wollaston et al. 2005). Senescence is not necessarily a terminal process leading to cell death but rather a transient phase that still retains developmental capabilities. Accordingly, under certain circumstances such as removal of young leaves or application of cytokinins, yellowish, senescing leaves can turn green and resume their photosynthetic capacity (Venkatarayappa et al. 1984; Gan and Amasino 1995; Buchanan-Wollaston et al. 2003). Thus, senescence appears to represent a unique transient state, which is not necessarily defined by the expression of specific ‘senescent signature genes’ but rather by promiscuous expression of genes whose function is not fully understood. Damri et al. (2009) have recently proposed that this transient state of senescence can well be defined as a dedifferentiated, stem cell-like state. Indeed, senescing cells and dedifferentiating protoplast cells share common features. Both cell types display a large increase in the expression of genes encoding specific TF families including ANAC, WRKY and b-ZIP, which are often up-regulated under various biotic and abiotic stress conditions (Chen et al. 2002; Cheong et al. 2002; Balazadeh et al. 2008). In a similar manner, SAM stem cells also displayed a large increase in expression of TFs (Table 1). Furthermore, senescing cells displayed features characteristic of stem cells and dedifferentiating protoplast cells including widespread chromatin decondensation, shrinkage/disruption of the nucleolus and condensation of rRNA genes (Williams et al. 2003; Avivi et al. 2004; Damri et al. 2009). Consistent with the changes observed in chromatin structure, the microarray data revealed similar expression profiles of chromatin modifying genes in dedifferentiating protoplasts and senescing cells, which favor the acquisition of a decondensed chromatin configuration (Damri et al. 2009). Likewise, the transcriptome profile of the Arabidopsis SAM showed overrepresentation of genes involved in epigenetic pathways in stem cells, which might confer flexibility over chromatin structure (Yadav et al. 2009). Thus, paradoxically, cells undergoing senescence share common features with cells capable of undergoing rejuvenation. These seemingly contradicting states raise the idea that somatic cells destined for death first enter a dedifferentiated, stem cell-like state before their commitment to death is established (Fig. 1). This idea can be extended to include any endogenous signal (e.g. phytohormones) or environmental cue (e.g. pathogen attack, drought) that eventually leads to premature senescence and death, or to a switch in cell fate—i.e. reentry into the cell cycle or transdifferentiation.
Table 1

Summary of the expression of several major Arabidopsis transcription factor families in dedifferentiating protoplasts and their expression in leaves, senescing cells and in the shoot apical meristem (SAM) stem cells

Gene ID

Gene name

Leavesa

Protoplastsa

Senescenceb

SAM CLV3c

SAM FILc

SAM WUSc

ANAC family

 AT1G01010

ANAC1

+

+

 AT1G01720

ANAC2

+

+

+

+

+

 AT1G02220

ANAC3

+

 AT1G32870

ANAC13

+

+

 AT1G52890

ANAC19

+

+

+

+

 AT1G69490

ANAC29

+

+

+

 AT1G77450

ANAC32

+

+

+

+

+

 AT2G43000

ANAC42

+

 AT3G04070

ANAC47

+

+

 AT3G10500

ANAC53

+

+

+

+

+

 AT3G15500

ANAC55

+

+

 AT3G49530

ANAC62

+

+

+

+

+

 AT4G27410

ANAC72

+

+

+

+

+

 AT5G04410

ANAC78

+

+

+

+

+

+

 AT5G09330

ANAC82

+

+

+

+

+

 AT5G22290

ANAC89

+

+

+

+

+

 AT5G24590

ANAC91

+

+

+

+

+

 AT5G39610

ANAC92

+

+

 AT5G63790

ANAC102

+

+

+

+

+

+

WRKY family

 AT1G13960

AtWRKY4

+

+

+

+

+

 AT1G62300

AtWRKY6

+

+

 AT1G80840

AtWRKY40

+

+

+

+

+

 AT2G23320

AtWRKY15

+

+

+

+

+

 AT2G30250

AtWRKY25

+

+

 AT2G38470

AtWRKY33

+

+

+

+

+

 AT3G56400

AtWRKY70

+

+

+

+

+

 AT4G01250

AtWRKY22

+

+

+

+

+

 AT4G18170

AtWRKY28

+

+

 AT4G22070

AtWRKY31

+

 AT4G31550

AtWRKY11

+

+

+

+

+

 AT5G13080

AtWRKY75

+

+

 AT5G49520

AtWRKY48

+

+

+

+

+

b-ZIP family

 AT1G42990

AtbZIP60

+

+

+

+

+

 AT1G43700

AtbZIP51/VIP1

+

+

+

+

+

+

 AT1G77920

AtbZIP50

+

+

 AT2G18160

AtbZIP2

+

+

+

+

+

+

 AT3G10800

AtbZIP28

+

+

+

+

+

 AT3G19290

AtbZIP38

+

+

+

+

+

 AT3G54620

AtbZIP25

+

+

+

+

+

 AT4G34000

AtbZIP37

+

+

+

+

+

+

 AT4G35040

AtbZIP19

+

+

+

+

+

 AT5G28770

AtbZIP63

+

 AT5G49450

AtbZIP1

+

+

+

+

+

 AT5G65210

AtbZIP47

+

+

(+) and (−) indicate genes displaying expression signal (log2) above or below 8, respectively

aBased on transcriptome profile of Ler protoplasts and leaves (Damri et al. 2009)

bBased on transcriptome profile of senescing leaves, i.e. 5 days after exposure to dark (Lin and Wu 2004)

cBased on transcriptome profile of SAM stem cells (Yadav et al. 2009)

https://static-content.springer.com/image/art%3A10.1007%2Fs00425-011-1366-3/MediaObjects/425_2011_1366_Fig1_HTML.gif
Fig. 1

Plant response to stress encounters dedifferentiation. Differentiated leaf cells can undergo dedifferentiation (senescence) and acquire a stem cell-like state following exposure to stress. Cell response to stress involves global chromatin decondensation accompanied by extensive reprogramming of gene expression (Damri et al. 2009). Stress-induced dedifferentiation may lead to ‘irreversible genomic modifications’ (McClintock 1984) driven by DNA transposition and DNA recombination and consequently to genetic hazard and cell death. Depending on the type of stimulus, dedifferentiated cells can be induced to redifferentiate, transdifferentiate or reenter the cell cycle. *Notably, many of the dedifferentiation-derived cells may possess a genotype, which is not identical to the genotype of the original differentiated cell(s)

Plant-stress responses meet dedifferentiation

Several lines of evidence support the hypothesis that plant response to stress may converge on cellular dedifferentiation. First, it has long been known that protein synthesis is reduced significantly in a variety of plant species following exposure to various stress conditions (Barnett and Naylor 1966; Ben-Zioni et al. 1967; Dhindsa and Cleland 1975). This reduction in protein synthesis could facilitate the acquisition of a quiescent state, a characteristic of stem cells. Second, chromatin remodeling—a fundamental theme of cellular dedifferentiation—is induced following exposure of plants to various stress conditions. Various lines of Zea mays subjected to UV-B irradiation showed increased acetylation on the N-terminal tails of histones H3 and H4 (Casati et al. 2008)—a modification associated with chromatin relaxation and gene transcription (Eberharter and Becker 2002; Chen and Tian 2007). In a similar manner, increase in H3K4 trimethylation and H3K9 acetylation, modifications associated with open chromatin configuration, was observed in Arabidopsis thaliana under drought stress conditions (Kim et al. 2008). In maize seedlings, cold stress induced widespread demethylation of genomic DNA (Steward et al. 2002), which is likely to lead to chromatin decondensation, while in Arabidopsis prolonged exposure to heat stress resulted in decondensation of higher order heterochromatin (Pecinka et al. 2010).

Finally, to further assess the possible link between stem cell state, dedifferentiation and plant response to stress, the list of TF genes whose expression was altered in dedifferentiating cells (Damri et al. 2009; see also Supplementary Table 1) was compared with the data obtained from “high quality” ATH1 microarrays examining the response of Arabidopsis to various biotic and abiotic stresses (Fig. 2). The microarray data were viewed from the “stimulus” perspective, such that for each gene in each microarray experiment, log2 fold-change expression ratios of treatment versus control were calculated, and hierarchical clustering analysis was used to produce a dendrogram and associated heat map depicted as colored squares on a red-black-green scale (from up- to down-regulation, respectively). This analysis revealed that a variety of stress conditions including oxidative stress, UV-B irradiation, salt, drought and pathogen infection exhibit similar up- and down-regulated expression of regulatory genes as is observed in dedifferentiating cells.
https://static-content.springer.com/image/art%3A10.1007%2Fs00425-011-1366-3/MediaObjects/425_2011_1366_Fig2_HTML.gif
Fig. 2

Hierarchical clustering analysis reveals similarity in expression of transcription factor-encoding genes between dedifferentiation, senescence and various abiotic and biotic stresses. Transcription factor genes differentially expressed (fold-change ≥ 2, P value < 0.05) in dedifferentiating cells (see Supplementary Table 1 derived from gene expression omnibus GSE15515) were compared to the expression profile of these same transcription factors in a range of biotic and abiotic stresses (publicly available data from TAIR: ME00340; ME00341, ME00342; ArrayExpress: E-MEXP-1443, E-MEXP-1725, E-MEXP-98, E-ATMX-19, E-GEOD-6154 and Gene Expression Omnibus: GSE5521, GSE5535, GSE10522, GSE6583, GSE3533, GSE5621, GSE5622, GSE5623, GSE5624, GSE5626, GSE5628, GSE5686, GSE5525, GSE6516, GSE17464, GSE4638, GSE20009, GSE8927, GSE8925, GSE8913, GSE8912, GSE8926, GSE6831). Senescence data were kindly provided by S.H. Wu (Lin and Wu 2004). Cluster analysis was performed using Spearman rank correlation by centroid linkage (Do and Choi 2008) employing the Cluster 3.0 Software (de Hoon et al. 2004). a The clustering analysis with associated heat map (log2 expression value) where a red color represents up-regulated genes and green represents down-regulated genes. From the heat map, the region with the most highly correlated expression pattern to that of dedifferentiation is highlighted (r = 0.52, yellow box). b Enlargement of the dendrogram presented in a where treatments with a similar expression pattern are highlighted in yellow (r = 0.52). A more highly correlated cluster is also highlighted (r = 0.60, blue line). hpi hours post-inoculation, hpt hours post-treatment, dpi days post-inoculation

It may be argued that because protoplasting imposes an acute stress on leaf cells, it is not surprising that ‘dedifferentiating’ protoplast cells display high similarity with stressed cells. Yet, the very purpose of this article is to highlight the idea that stressed cells are in fact dedifferentiating cells assuming a stem cell-like state. If this hypothesis is true, then one might predict that naturally occurring stem cells (e.g. SAM stem cells) should display features of stressed cells. Support for this view came from a recent study addressing the transcriptome profile of Arabidopsis SAM cells (Yadav et al. 2009). This analysis revealed enrichment in genes encoding protein factors involved in mismatch repair and non-homologous end-joining (NHEJ) DNA repair pathways, leading the authors to conclude that “SAM stem cells exhibit typical characteristics of cells experiencing stress”.

The emerging picture supports the idea that stress-related responses might promote genomic reprogramming leading to substantial alterations in gene transcription, which are necessary for somatic cells to acquire an embryonic state (Verdeil et al. 2007; Zavattieri et al. 2010). Accordingly, it is suggested that a general response of cells to certain biotic and abiotic stresses, particularly those that induce premature senescence or a switch in cell fate, features dedifferentiation and acquisition of a stem cell-like state prior to a switch in cell fate (e.g. reentry into the cell cycle or cell death).

Acknowledgments

We thank Esti Yeger-Lotem for bioinformatics discussions and Yigal Avivi for critical reading of the manuscript. This work was supported by The Israel Science Foundation (ISF) grant No. 476/09 to G.G. and V.C.-C.

Supplementary material

425_2011_1366_MOESM1_ESM.xls (114 kb)
Supplementary Table 1 (XLS 114 kb)

Copyright information

© Springer-Verlag 2011