Guard cell purification and RNA isolation suitable for high-throughput transcriptional analysis of cell-type responses to biotic stresses

Molecular Plant-Microbe Interactions

Volumn 26, Issue 8, 2013, Pages 844-849

  Obulareddy, Nisita ^a   Panchal, Shweta ^a   Melotto, Maeli ^a  

^a UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT RNA;

ARABIDOPSIS; ARTICLE; CULTURE TECHNIQUE; CYTOLOGY; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; METHODOLOGY; PHYSIOLOGICAL STRESS; PHYSIOLOGY; PROTOPLAST;

ARABIDOPSIS; CELL CULTURE TECHNIQUES; GENE EXPRESSION REGULATION, PLANT; PROTOPLASTS; RNA, PLANT; STRESS, PHYSIOLOGICAL; TRANSCRIPTION, GENETIC;

EID: 84880055331     PISSN: 08940282     EISSN: None     Source Type: Journal    
DOI: 10.1094/MPMI-03-13-0081-TA     Document Type: Article

References (25)

1. Bates, G. W., Rosenthal, D. M., Sun, J., Chattopadhyay, M., Peffer, E., Yang, J., Ort, D. R., and Jones, A. M. 2012. A comparative study of the Arabidopsis thaliana guard cell transcriptome and its modulation by sucrose. PLoS ONE 7(11): e49641. Published online.
2. Chitrakar, R., and Melotto, M. 2010. Assessing stomatal response to live bacterial cells using whole leaf imaging. J. Vis. Exp. 44: 2185.
3. Chung, H. S., Koo, A. J. K., Gao, X., Jayanty, S., Thines, B., Jones, A. D., and Howe, G. A. 2008. Regulation and function of Arabidopsis JASMONATE ZIM-Domain genes in response to wounding and herbivory. Plant Physiol. 146: 952-964.
4. Du, Z., Zhou, X., Ling, Y., Zhang, Z., and Su, Z. 2010. AgriGO: A GO analysis tool kit for the agricultural community. Nucleic Acids Res. 38: W64-W70.
5. Gudesblat, G. E., Torres, P. S., and Vojnov A. A. 2009. Xanthomonas campestris overcomes Arabidopsis stomatal innate immunity through a DSF cell-to-cell signal-regulated virulence factor. Plant Physiol. 149: 1017-1027.
6. Leonhardt, N., Kwak, J. M., Robert, N., Waner, D., Leonhardt, G., and Schroeder, J. I. 2004. Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant. Plant Cell 16: 596-615.
7. Livak, K. J., and Schmittgen, T. D. 2001. Analysis of relative gene expression data using real time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25: 402-408.
8. Melotto, M., Underwood, W., Koczan, J., Nomura, K., and He, S. Y. 2006. Plant stomata function in innate immunity against bacterial invasion. Cell 126: 969-980.
9. Narsai, R., Howell, K. A., Millar, A. H., O'Toole, N., Small, I., and Whelan, J. 2007. Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. Plant Cell 19: 3418-3436.
10. Pandey, S., Wang, X.-Q., Coursol, S. A., and Assmann, S. M. 2002. Preparation and applications of Arabidopsis thaliana guard cell protoplasts. New Phytol. 153: 517-526.
11. Pandey, S., Wang, R. S., Wilson, L., Li, S., Zhao, Z., Gookin, T. E., Assmann, S. M., and Albert, R. 2010. Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action. Mol. Syst. Biol. 6: 372.
12. Schellenberg, B., Ramel, C., and Dudler R. 2010. Pseudomonas syringae virulence factor syringolin A counteracts stomatal immunity by proteasome inhibition. Mol. Plant-Microbe Interact. 23: 1287-1293.
13. Schmittgen, T. D., and Livak, K. J. 2008. Analyzing real-time PCR data by the comparative CT method. Nat. Protoc. 3: 1101-1108.
14. Schroeder, J. I., Kwak, J. M., and Allen, G. J. 2001. Guard cell abscisic acid signaling and engineering drought hardiness in plants. Nature 410: 327-410.
15. Trapnell, C., Pachter, L., and Salzberg, S. L. 2009. TopHat: Discovering splice junctions with RNA-seq. Bioinformatics 25: 1105-1111.
16. Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., and Pachter, L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28: 511-515.
17. Wang, R.-S., Pandey, S., Li, S., Gookin, T. E., Zhao, Z., Albert, R., and Assmann, S. M. 2011. Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells. BMC Genomics 12: 216.
18. Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., Dicuccio, M., Edgar, R., Federhen, S., Feolo, M., Geer, L. Y., Helmberg, W., Kapustin, Y., Khovayko, O., Landsman, D., Lipman, D. J., Madden, T. L., Maglott, D. R., Miller, V., Ostell, J., Pruitt, K. D., Schuler, G. D., Shumway, M., Sequeira, E., Sherry, S. T., Sirotkin, K., Souvorov, A., Starchenko, G., Tatusov, R. L., Tatusova, T. A., Wagner, L., and Yaschenko, E. 2008. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 36: D13-21.
19. Zeng, W., Melotto, M., and He, S. Y. 2010. Plant stomata: A checkpoint of host immunity and pathogen virulence. Curr. Op. Biotechnol. 21: 599-603.
20. agriGO database: bioinfo.cau.edu.cn/agriGO
21. The Arabidopsis Information Resource TAIR10: arabidopsis.org
22. Cufflinks software: cufflinks.cbcb.umd.edu
23. Integrated DNA Technologies (IDT) SciTools: www.idtdna.com/Primerquest/ Home/Index
24. National Center for Biotechnology Information Sequence Read Archive: www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi
25. TopHat program: tophat.cbcb.umd.edu