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Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM).
J Exp Bot. 2008; 59(7):1875-94.JE

Abstract

The common ice plant (Mesembryanthemum crystallinum L.) has emerged as a useful model for molecular genetic studies of Crassulacean acid metabolism (CAM) because CAM can be induced in this species by water deficit or salinity stress. Non-redundant sequence information from expressed sequence tag data was used to fabricate a custom oligonucleotide microarray to compare large-scale mRNA expression patterns in M. crystallinum plants conducting C(3) photosynthesis versus CAM. Samples were collected every 4 h over a 24 h time period at the start of the subjective second day from plants grown under constant light and temperature conditions in order to capture variation in mRNA expression due to salinity stress and circadian clock control. Of 8455 genes, a total of 2343 genes (approximately 28%) showed a significant change as judged by analysis of variance (ANOVA) in steady-state mRNA abundance at one or more time points over the 24 h period. Of these, 858 (10%) and 599 (7%) exhibited a greater than two-fold ratio (TFR) increase or decrease in mRNA abundance, respectively. Functional categorization of these TFR genes revealed that many genes encoding products that function in CAM-related C(4) acid carboxylation/decarboxylation, glycolysis/gluconeogenesis, polysaccharide, polyol, and starch biosynthesis/degradation, protein degradation, transcriptional activation, signalling, stress response, and transport facilitation, and novel, unclassified proteins exhibited stress-induced increases in mRNA abundance. In contrast, salt stress resulted in a significant decrease in transcript abundance for genes encoding photosynthetic functions, protein synthesis, and cellular biogenesis functions. Many genes with CAM-related functions exhibited phase shifts in their putative circadian expression patterns following CAM induction. This report establishes an extensive catalogue of gene expression patterns for future investigations aimed at understanding the complex, transcriptional hierarchies that govern CAM-specific expression patterns. A novel graph-theoretic approach called 'Max Clique Builder' is introduced that identifies and organizes sets of coordinately regulated genes, such as those encoding subunits of the vacuolar H(+)-ATPase complex, into tighter functionally related clusters with more similar expression patterns compared with standard hierarchical clustering methods.

Links

Publisher Full Text (DOI)

Authors+Show Affiliations

Cushman JC
Department of Biochemistry, MS200, University of Nevada, Reno, NV 89557-0014, USA. jcushman@unr.edu
Tillett RL
No affiliation info available
Wood JA
No affiliation info available
Branco JM
No affiliation info available
Schlauch KA
No affiliation info available

MeSH

Circadian RhythmGene Expression ProfilingGene Expression Regulation, PlantHot TemperatureMesembryanthemumPhotosynthesisPlant ProteinsRNA, MessengerRNA, PlantSodium Chloride

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

18319238

Citation

Cushman, John C., et al. "Large-scale mRNA Expression Profiling in the Common Ice Plant, Mesembryanthemum Crystallinum, Performing C3 Photosynthesis and Crassulacean Acid Metabolism (CAM)." Journal of Experimental Botany, vol. 59, no. 7, 2008, pp. 1875-94.
Cushman JC, Tillett RL, Wood JA, et al. Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM). J Exp Bot. 2008;59(7):1875-94.
Cushman, J. C., Tillett, R. L., Wood, J. A., Branco, J. M., & Schlauch, K. A. (2008). Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM). Journal of Experimental Botany, 59(7), 1875-94. https://doi.org/10.1093/jxb/ern008
Cushman JC, et al. Large-scale mRNA Expression Profiling in the Common Ice Plant, Mesembryanthemum Crystallinum, Performing C3 Photosynthesis and Crassulacean Acid Metabolism (CAM). J Exp Bot. 2008;59(7):1875-94. PubMed PMID: 18319238.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM). AU - Cushman,John C, AU - Tillett,Richard L, AU - Wood,Joshua A, AU - Branco,Joshua M, AU - Schlauch,Karen A, Y1 - 2008/03/03/ PY - 2008/3/6/pubmed PY - 2008/10/31/medline PY - 2008/3/6/entrez SP - 1875 EP - 94 JF - Journal of experimental botany JO - J Exp Bot VL - 59 IS - 7 N2 - The common ice plant (Mesembryanthemum crystallinum L.) has emerged as a useful model for molecular genetic studies of Crassulacean acid metabolism (CAM) because CAM can be induced in this species by water deficit or salinity stress. Non-redundant sequence information from expressed sequence tag data was used to fabricate a custom oligonucleotide microarray to compare large-scale mRNA expression patterns in M. crystallinum plants conducting C(3) photosynthesis versus CAM. Samples were collected every 4 h over a 24 h time period at the start of the subjective second day from plants grown under constant light and temperature conditions in order to capture variation in mRNA expression due to salinity stress and circadian clock control. Of 8455 genes, a total of 2343 genes (approximately 28%) showed a significant change as judged by analysis of variance (ANOVA) in steady-state mRNA abundance at one or more time points over the 24 h period. Of these, 858 (10%) and 599 (7%) exhibited a greater than two-fold ratio (TFR) increase or decrease in mRNA abundance, respectively. Functional categorization of these TFR genes revealed that many genes encoding products that function in CAM-related C(4) acid carboxylation/decarboxylation, glycolysis/gluconeogenesis, polysaccharide, polyol, and starch biosynthesis/degradation, protein degradation, transcriptional activation, signalling, stress response, and transport facilitation, and novel, unclassified proteins exhibited stress-induced increases in mRNA abundance. In contrast, salt stress resulted in a significant decrease in transcript abundance for genes encoding photosynthetic functions, protein synthesis, and cellular biogenesis functions. Many genes with CAM-related functions exhibited phase shifts in their putative circadian expression patterns following CAM induction. This report establishes an extensive catalogue of gene expression patterns for future investigations aimed at understanding the complex, transcriptional hierarchies that govern CAM-specific expression patterns. A novel graph-theoretic approach called 'Max Clique Builder' is introduced that identifies and organizes sets of coordinately regulated genes, such as those encoding subunits of the vacuolar H(+)-ATPase complex, into tighter functionally related clusters with more similar expression patterns compared with standard hierarchical clustering methods. SN - 1460-2431 UR - https://www.unboundmedicine.com/medline/citation/18319238/Large_scale_mRNA_expression_profiling_in_the_common_ice_plant_Mesembryanthemum_crystallinum_performing_C3_photosynthesis_and_Crassulacean_acid_metabolism__CAM__ DB - PRIME DP - Unbound Medicine ER -
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