Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression

Abstract

Background: Arabidopsis thaliana transcript profiles indicate effects of abiotic and biotic stresses and tissue-specific and cell-specific gene expression. Organizing these datasets could reveal the structure and mechanisms of responses and crosstalk between pathways, and in which cells the plants perceive, signal, respond to, and integrate environmental inputs.

Results: We clustered Arabidopsis transcript profiles for various treatments, including abiotic, biotic, and chemical stresses. Ubiquitous stress responses in Arabidopsis, similar to those of fungi and animals, employ genes in pathways related to mitogen-activated protein kinases, Snf1-related kinases, vesicle transport, mitochondrial functions, and the transcription machinery. Induced responses to stresses are attributed to genes whose promoters are characterized by a small number of regulatory motifs, although secondary motifs were also apparent. Most genes that are downregulated by stresses exhibited distinct tissue-specific expression patterns and appear to be under developmental regulation. The abscisic acid-dependent transcriptome is delineated in the cluster structure, whereas functions that are dependent on reactive oxygen species are widely distributed, indicating that evolutionary pressures confer distinct responses to different stresses in time and space. Cell lineages in roots express stress-responsive genes at different levels. Intersections of stress-responsive and cell-specific profiles identified cell lineages affected by abiotic stress.

Conclusion: By analyzing the stress-dependent expression profile, we define a common stress transcriptome that apparently represents universal cell-level stress responses. Combining stress-dependent and tissue-specific and cell-specific expression profiles, and Arabidopsis 5'-regulatory DNA sequences, we confirm known stress-related 5' cis-elements on a genome-wide scale, identify secondary motifs, and place the stress response within the context of tissues and cell lineages in the Arabidopsis root.

Figure 1

Strategies to identify of Arabidopsis stress-regulated and tissue-regulated genes.

Figure 2

Clustering of genes in the Arabidopsis transcriptome. Out of 22,746 genes, 10,671 genes exhibited significant membership values in 180 clusters. The 17 most populated clusters include 7,039 genes (66% of total). Rows represent individual genes; columns (from left to right, as listed below) represent treatment conditions. A total of 180 clusters emerged. Outlined is cluster 12 (216 genes) including genes that responded to all stress treatment conditions (see Additional data files). (a) Time course experiments include cold (12 time points), osmotic (12), salt (12), drought (12), oxidative (12), and wounding (14) treatments. (b) Hormone treatments include ABA (3), ACC (3) and MeJA (3). (c) Biotic stress treatments include bacteria-derived elicitors (12), Pseudomonas syringae pt. tomato (Pst) DC300 (3), Pst avrRPM1 (3), Pst DC3000hrcC- (3), P. syringae pv. phaseolicola (3), Erysyphe oromoti (7), Phytophtera infestans (3), P. syringae ES4325 avrRPT2 (5), and P. syingae ES4325 (5). (d) Different light conditions (14). (e) Chemical treatments included t-zeatin, tri-iodobenzoic acid, AgNO₃, and cycloheximide.

Figure 3

Diagram of common stress response pathway genes. Representation of genes with known functions in clusters that respond to most stresses in cluster N12. Genes are identified by name or Gene Ontology assignment (see Additional data file 5).

Figure 4

Conserved or cluster-specific cis-elements. (a) Motifs identified in clusters N1, N8, N3, N9, N10, N12, and N13. These clusters were induced by light or ABA. A common motif ABRE united genes within these clusters. Additional motifs that distinguish genes in individual clusters are included (I-Box or DRE). See Table 2 for identified motifs. (b) 5'-regulatory motifs identified from clusters N0 and N19. The WRKY motif was identified in both clusters, whereas the HSF motif was present only in cluster N0.

Figure 5

Tissue-specific characteristics of abiotic stress-regulated transcripts. The expression of 12,360 transcripts in different tissues, cell lineages, and at three developmental stages in Arabidopsis root [19], separated into 19 clusters.

Figure 6

Stress down-regulated genes highly expressed in Stele during stage 3 development. AT5G04960, pectinesterase family protein; AT4G26010, peroxidase, putative, peroxidase ATP13a; AT3G59370, expressed protein; AT1G05250, peroxidase, putative, similar to peroxidase ATP11a; AT3G49960, peroxidase, putative, identical to peroxidase ATP21a; AT5G05500, pollen Ole e1 allergen and extensin family protein; AT4G00680, actin-depolymerizing factor, putative; AT2G47540, pollen Ole e1 allergen and extensin family protein; AT4G02270, pollen Ole e1 allergen and extensin family protein; AT1G01750, actin-depolymerizing factor, putative; AT1G48930, endo-1,4-beta-glucanase, putative cellulase; AT4G20210, terpene synthase/cyclase family protein; AT5G67400, peroxidase 73 (PER73) (P73) (PRXR11); AT5G19790, encodes a member of the ERF (ethylene response factor) subfamily B-6 of ERF/AP2 transcription factor family (RAP2.11); AT3G26610, polygalacturonase, putative pectinase; AT1G62980, expansin, putative (EXP18); AT1G12560, expansin, putative (EXP7); AT2G44110, seven transmembrane MLO family protein/MLO-like protein 15 (MLO15); AT1G30870, cationic peroxidase, putative; AT4G40090, arabinogalactan-protein (AGP3); AT4G09990, expressed protein; AT5G35190, proline-rich extensin-like family protein; No match, no match; AT1G12080, expressed protein; AT3G62680, proline-rich family protein.

Figure 7

Stress and ABA upregulated genes in mature roots are also expressed in shoots. AT2G04350, long-chain-fatty-acid-CoA ligase family protein; AT4G10955, lipase class 3 family protein; AT1G77450, no apical meristem (NAM) family protein, similar to GRAB1; AT4G33905, peroxisomal membrane protein 22 kDa; AT3G04240, O-linked N-acetyl glucosamine transferase; AT2G39800, delta 1-pyrroline-5-carboxylate synthetase A/P5CS A (P5CS1); AT4G34230, cinnamyl-alcohol dehydrogenase, putative; AT4G11220, reticulon family protein (RTNLB2); AT1G75170, SEC14 cytosolic factor family protein/phosphoglyceride transfer family; AT3G19290, ABA-responsive element-binding protein 2 (AREB2); AT5G37540, aspartyl protease family protein, weak similarity to CND41; AT1G58360, amino acid permease I (AAP1); AT1G78610, mechanosensitive ion channel domain-containing protein; AT4G34710, arginine decarboxylase 2 (SPE2); AT3G17790, acid phosphatase type 5 (ACP5); AT1G50630, expressed protein; AT1G13195, zinc finger (C3HC4-type RING finger) family protein; AT2G32800, protein kinase family protein, contains dual protein kinase domains; AT5G35460, expressed protein; AT2G32510, protein kinase family protein, contains protein kinase domain; AT1G07870, protein kinase family protein, contains protein kinase domain; AT1G43160, encodes a member of the ERF (ethylene response factor) subfamily B-4 of ERF/AP2 transcription factor family (RAP2.6); AT3G62700, glutathione-conjugate transporter, putative, similar to AtMRP4; AT2G31980, cysteine proteinase inhibitor-related; AT5G17860, cation exchanger, putative (CAX7), similar to NKX3_HUMAN sodium/potassium/calcium exchanger 3 precursor; AT1G08920, sugar transporter, putative, similar to ERD6 protein (Arabidopsis thaliana); AT4G15120, VQ, motif-containing protein; AT2G03240, EXS family protein/ERD1/XPR1/SYG1 family protein, similar to PHO1; AT5G01200, myb family transcription factor; AT1G48320, thioesterase family protein; AT5G01600, ferritin 1 (FER1).