Abstract
The heat shock protein 70 (HSP70) gene family plays a key role in protecting plant cells or tissues from thermal or oxidative stress. Although many studies have elucidated the molecular functions of individual family members, genome-wide analysis of this family is still limited, especially for crop species. Our objective was to integrate various meta-profiling data into the context of a phylogenetic tree, which would enable us to perform fine evaluation of functional dominancy or redundancy within this family. Our data indicated that a loss-of-function mutant of a rice cytosolic HSP70 gene (OsctHSP70-1) did not show a clear defective phenotype in response to high temperature because of the existence of another gene family member that was closely clustered with OsctHSP70-1 and had similar expression patterns. Moreover, the second gene showed much stronger anatomical expression. We indirectly analyzed the function of OsctHSP70-1 by studying GUS activity under the control of the endogenous promoter. We also designed a probable interaction network mediated by OsctHSP70-1 and used co-expression analysis among its components to refine the network, suggesting more probable model to explain the function of OsctHSP70-1.
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Abbreviations
- ER:
-
Endoplasmic reticulum
- GEO:
-
Gene expression omnibus
- IDs:
-
Identifiers
- MS:
-
Murashige and Skoog
- PCD:
-
Programmed cell death
- RT-PCR:
-
Reverse transcription polymerase chain reaction
- TPR:
-
Tetratricopeptide repeat
- WT:
-
Wild-type
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Acknowledgments
We are grateful to Dr. Pamela C. Ronald at the University of California, Davis, and Dr. Peijian Cao in the Zhengzhou Tobacco Research Institute for supporting the development of this phylogenomics tool, and to Mrs. Priscilla Licht for critical reading of the manuscript. This work is supported by the Next-Generation BioGreen 21 Program by South Korea (PJ008079 and PJ009514 to KHJ), and the young scientist supporting grant (20100615 to KHJ) from Kyung Hee University in 2010.
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Fig. S1
Phylogenomics analysis of rice Hsp70 family by integration of Agilent 44K anatomical meta-profiling data. Log2 normalized intensity of 209 Agilent 44K data from NCBI GEO data series GSE21494 was generated by the quantile normalization method (Bolstad et al. 2003). Cluster I, green; Cluster II, blue; Cluster III, light green; Cluster IV, dark green; Cluster V, light brown; Cluster VI, pink. Blue color on heat map indicates boundary of low-expression data; yellow indicates boundary of high-expression data. White boxes, samples collected in daytime (light); dark boxes, samples collected at night (darkness). Numbers below the blue-red bar in the heatmap indicate log2 transformed intensity for each sample (JPEG 6082 kb)
Fig. S2
Phylogenomics analysis of rice Hsp70 family, integrating anatomical expression patterns based on 983 Affymetrix arrays (JPEG 7470 kb)
Fig. S3
Evaluation of functional redundancy among OsctHsp70-1 and two closely linked OsctHsp70 genes by RT-PCR analysis. Expression patterns of OsctHsp70-1, Os01g62290, and Os11g47760 were analyzed in wild type (WT) and homozygous progenies of osctHsp70-1 mutant. OsUbi1 and OsUbi5 were used as internal controls for RT-PCR. The number of PCR cycles was 26 for Os01g62290, Os11g47760, OsUbi1, OsUbi5, and 32 for OsctHsp70-1 (JPEG 2077 kb)
Table S1
Protein sequences for combined phylogenetics analysis of rice and Arabidopsis Hsp70 protein family (TXT 45 kb)
Table S3
Primer sequences used for RT-PCR analyses (TXT 6 kb)
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Jung, KH., Gho, HJ., Nguyen, M.X. et al. Genome-wide expression analysis of HSP70 family genes in rice and identification of a cytosolic HSP70 gene highly induced under heat stress. Funct Integr Genomics 13, 391–402 (2013). https://doi.org/10.1007/s10142-013-0331-6
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DOI: https://doi.org/10.1007/s10142-013-0331-6