Unknown,Transcriptomics,Genomics,Proteomics

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Time-course expression analysis of the low pH (pH 4.6) response in Arabidopsis whole roots

ABSTRACT: We preformed at time-course of the expression of whole Arabidopsis roots for 30 minutes, 1H, 3H, 6H 12H, 24H, and 48H after transfer to low pH (pH 4.6). Controls at the standard pH (pH 5.7) were included at each time-point. We combined these data with 13 other datasests and performed a meta-analysis to ask whether a universal stress response exists in Arabidopsis roots. Stress responses in plants are tightly coordinated with developmental processes, but the interaction between these pathways is poorly understood. Here we use genome-wide assays at high spatial and temporal resolution to understand the processes that lnk development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. Common stress responses appear to exists and, analagous to animal systems, many of them show cell-type specificity, suggesting a convergent evolutionary theme in multicellular organisms. Common stress responses may be mediated by cell identity regulators, as mutations in these genes resulted in altered responses to stress. Our results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide datasets to elucidate biological processes. 28 samples: 7 time points, with two replicates for each timepoint for both the control (pH 5.7) and treatment (pH 4.6)

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Anjali Iyer-Pascuzzi

PROVIDER: E-GEOD-30097 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Cell identity regulators link development and stress responses in the Arabidopsis root.

Iyer-Pascuzzi Anjali S AS Jackson Terry T Cui Hongchang H Petricka Jalean J JJ Busch Wolfgang W Tsukagoshi Hironaka H Benfey Philip N PN

Developmental cell 20111001 4

Stress responses in plants are tightly coordinated with developmental processes, but interaction of these pathways is poorly understood. We used genome-wide assays at high spatiotemporal resolution to understand the processes that link development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. However, common stress responses appear to exist with many showing cell type specificity. Common stress responses may be mediated by cell ident ...[more]

PMID: 22014526

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Project description:In Escherichia coli, pH-dependent gene expression varies with oxygen level. Anaerobic pH-dependent expression ratios were analyzed and compared to the published analysis of aerated cultures (Maurer et al, 2005). E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Gene expression profiles were obtained by cDNA hybridization to Affymetrix arrays. pH-dependent expression was seen for 1,394 genes, of which 1,002 show no pH dependence under aeration. Four intergenic regions containing regulatory sRNAs were up-regulated by acid anaerobically (ryeA, csrB, gadY, rybC) and one sRNA (ryhA) by acid with aeration. Acid and anaerobiosis co-regulated the gad regulon; drug transporters (mdtEF, mdtL); catabolism of sugar derivatives whose fermentation minimized acid production; and all hydrogenases (hya, hyb, hyc, hyf, hyp). The hydrogenases however were up-regulated at high pH under aeration (observed by real-time PCR). Acid with anaerobiosis down-regulated penicillin-binding proteins (dacACD, mreBC) and ribosome biosynthesis. Ribosome down-regulation may be caused by restriction of anaerobic metabolism at low pH. A core group of 236 genes showed similar pH response with or without aeration. Core genes up-regulated by acid included fimbriae (fimAC), periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa), the â??constitutiveâ?? Na+/H+ antiporter (nhaB), and over thirty unidentified proteins. Core genes at high pH included maltodextrin transport (lamB, malEFGKMPQT), ATP synthase, and DNA repair (recA and mutL). Overall, pH and anaerobiosis co-regulated metabolism and transport so as to maximize alternative catabolic options while minimizing acidification or alkalinization of the cytoplasm. Experiment Overall Design: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH during growth without aeration. The experiment was designed for direct comparison with the pH profile under aerobic conditions reported previously (GSE4511). Non-aerated overnight cultures were diluted 1:1000 and incubated in closed tubes containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.7, pH 7.0, and pH 8.5. Tubes were incubated at37Â°C with slow rotation (8 rpm) to an optical density at 600 nm of 0.2. For each of the three pH conditions, RNA was isolated from five independent cultures. Labeled cDNA was hybridized to Affymetrix antisense arrays according to standard procedures. To analyze the expression levels, Dchip software was used to generate model-based expression indices normalized to sample pH 7 replicate 1. ANOVA was used to identify genes with sitnificant expression differences among the three pH classes (p = 0.001). For genes showing significant differences, the Log2 expression ratios were determined for each pair of pH classes, and significance was determined by Tukey's test (p = 0.001).

Dataset Information

Time-course expression analysis of the low pH (pH 4.6) response in Arabidopsis whole roots

Publications

Cell identity regulators link development and stress responses in the Arabidopsis root.

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