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Genome-wide analysis of the Populus Hsp90 gene family reveals differential expression patterns, localization, and heat stress responses.

Zhang J, Li J, Liu B, Zhang L, Chen J, Lu M - BMC Genomics (2013)

Bottom Line: Furthermore, microarray and semi-quantitative real-time RT-PCR analyses show that a number of Populus Hsp90 genes are differentially expressed upon exposure to various stresses.Microarray and RT-PCR analyses show that most PtHsp90s were induced by various stresses, including heat stress.Collectively, these observations lay the foundation for future efforts to unravel the biological roles of PtHsp90 genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.

ABSTRACT

Background: Members of the heat shock protein 90 (Hsp90) class of proteins are evolutionarily conserved molecular chaperones. They are involved in protein folding, assembly, stabilization, activation, and degradation in many normal cellular processes and under stress conditions. Unlike many other well-characterized molecular chaperones, Hsp90s play key roles in signal transduction, cell-cycle control, genomic silencing, and protein trafficking. However, no systematic analysis of genome organization, gene structure, and expression compendium has been performed in the Populus model tree genus to date.

Results: We performed a comprehensive analysis of the Populus Hsp90 gene family and identified 10 Populus Hsp90 genes, which were phylogenetically clustered into two major groups. Gene structure and motif composition are relatively conserved in each group. In Populus trichocarpa, we identified three paralogous pairs, among which the PtHsp90-5a/PtHsp90-5b paralogous pair might be created by duplication of a genome segment. Subcellular localization analysis shows that PtHsp90 members are localized in different subcellular compartments. PtHsp90-3 is localized both in the nucleus and in the cytoplasm, PtHsp90-5a and PtHsp90-5b are in chloroplasts, and PtHsp90-7 is in the endoplasmic reticulum (ER). Furthermore, microarray and semi-quantitative real-time RT-PCR analyses show that a number of Populus Hsp90 genes are differentially expressed upon exposure to various stresses.

Conclusions: The gene structure and motif composition of PtHsp90s are highly conserved among group members, suggesting that members of the same group may also have conserved functions. Microarray and RT-PCR analyses show that most PtHsp90s were induced by various stresses, including heat stress. Collectively, these observations lay the foundation for future efforts to unravel the biological roles of PtHsp90 genes.

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Expression profiles of PtHsp90 genes. A. Heat map showing 10 PtHsp90 genes under heat stress. Expression is indicated as the fold-change in photosynthetic optimum (31.75°C, temperature producing the maximum net CO2 assimilation rate), 20% inhibition of optimum (38.4°C) and 30% inhibition of optimum (40.5°C) relative to baseline (22°C, the growth temperature), and was visualized using heat maps (see Methods). Microarray data were obtained from GEO (GSE26199). B. Heat map showing 10 PtHsp90 genes across various tissues and genotypes (GEO: GSE16786). The genotypes analyzed were P. fremontii × P. angustifolia clones 1979, 3200, and RM5; P. tremuloides clones 271 and L4; and P. deltoids clones Soligo and Carpaccio. The tissues analyzed were young leaves (YL), expanding leaves (EL), mature leaves (L), root tips (RT), and suspension cell cultures (C). Stress treatments were nitrogen limitation (low N), methyl jasmonate elicitation (MeJ), and wounding, with sampling either 1 week or 90 h after wounding. C. Heat map showing 10 PtHsp90 genes under conditions of short- and long-term water deficit (GEO: GSE17230). EAR, early response to water deficit (by 36 h), LMI, long-term (10-day) response to mild stress with a soil relative extractable water (REW) level of 20–35%, LMO, long-term (10-day) response to moderate stress with a soil REW level of 10–20%.
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Figure 5: Expression profiles of PtHsp90 genes. A. Heat map showing 10 PtHsp90 genes under heat stress. Expression is indicated as the fold-change in photosynthetic optimum (31.75°C, temperature producing the maximum net CO2 assimilation rate), 20% inhibition of optimum (38.4°C) and 30% inhibition of optimum (40.5°C) relative to baseline (22°C, the growth temperature), and was visualized using heat maps (see Methods). Microarray data were obtained from GEO (GSE26199). B. Heat map showing 10 PtHsp90 genes across various tissues and genotypes (GEO: GSE16786). The genotypes analyzed were P. fremontii × P. angustifolia clones 1979, 3200, and RM5; P. tremuloides clones 271 and L4; and P. deltoids clones Soligo and Carpaccio. The tissues analyzed were young leaves (YL), expanding leaves (EL), mature leaves (L), root tips (RT), and suspension cell cultures (C). Stress treatments were nitrogen limitation (low N), methyl jasmonate elicitation (MeJ), and wounding, with sampling either 1 week or 90 h after wounding. C. Heat map showing 10 PtHsp90 genes under conditions of short- and long-term water deficit (GEO: GSE17230). EAR, early response to water deficit (by 36 h), LMI, long-term (10-day) response to mild stress with a soil relative extractable water (REW) level of 20–35%, LMO, long-term (10-day) response to moderate stress with a soil REW level of 10–20%.

Mentions: In order to reveal the responses of Populus Hsp90 genes to abiotic stresses, we analyzed the expression profiles of PtHsp90s under abiotic stresses such as heat, low nitrogen levels, mechanical wounding, drought, and methyl jasmonate (MeJ) treatment. Affymetrix microarray data (series accession numbers GSE26199, GSE16786 and GSE17230 in the Gene Expression Omnibus [GEO]) [38] were used to analyze the global expression profiles of Populus Hsp90 genes. Previous study divided the physiological condition into four states according to Populus photosynthetic activity from 22°C to 42°C: baseline (22°C, the growth temperature), optimum (31.75°C, temperature producing the maximum net CO2 assimilation rate), 20% inhibition of optimum (38.4°C) and 30% inhibition of optimum (40.5°C) [39]. Most PtHsp90 genes are upregulated under heat stress. The expression of PtHsp90-1a and PtHsp90-1b is highly induced immediately when temperature increases to optimum. PtHsp90-5a and PtHsp90-6 are highly induced when the photosynthesis is inhibited by 30% under heat stress (Figure 5A). In PtHsp90 group I, PtHsp90-1a, PtHsp90-1b, and PtHsp90-3 in both the Soligo and Carpacio genotypes are upregulated under almost all drought stresses tested, including the early response (EAR) to drought at 36 h, and the long-term (10 days) responses to mild stress (LMI) and moderate stress (LMO) (Figure 5C). Nitrogen deficiency stress causes different responses among Hsp90 genes. For instance, PtHsp90-1a and PtHsp90-1b are upregulated in 4-week-old young leaves (YL) and 8-week-old expanded leaves (EL) of genotype 1979 and genotype 3200; PtHsp90-5a and PtHsp90-5b are upregulated in 8-week-old expanded leaves (EL) of the same two genotypes. However, PtHsp90-3, PtHsp90-4a, and PtHsp90-6 are downregulated in 8-week-old expanded leaves in genotype 1979 and/or genotype 3200 (Figure 5B). In response to mechanical wounding stress, six genes (PtHsp90-1a, PtHsp90-1b, PtHsp90-3, PtHsp90-5b, PtHsp90-6, and PtHsp90-7) are significantly downregulated in young leaves and/or expanding leaves 1 week after wounding. In response to MeJ feeding in cell culture, only PtHsp90-1a and PtHsp90-1b are slightly downregulated (Figure 5B).


Genome-wide analysis of the Populus Hsp90 gene family reveals differential expression patterns, localization, and heat stress responses.

Zhang J, Li J, Liu B, Zhang L, Chen J, Lu M - BMC Genomics (2013)

Expression profiles of PtHsp90 genes. A. Heat map showing 10 PtHsp90 genes under heat stress. Expression is indicated as the fold-change in photosynthetic optimum (31.75°C, temperature producing the maximum net CO2 assimilation rate), 20% inhibition of optimum (38.4°C) and 30% inhibition of optimum (40.5°C) relative to baseline (22°C, the growth temperature), and was visualized using heat maps (see Methods). Microarray data were obtained from GEO (GSE26199). B. Heat map showing 10 PtHsp90 genes across various tissues and genotypes (GEO: GSE16786). The genotypes analyzed were P. fremontii × P. angustifolia clones 1979, 3200, and RM5; P. tremuloides clones 271 and L4; and P. deltoids clones Soligo and Carpaccio. The tissues analyzed were young leaves (YL), expanding leaves (EL), mature leaves (L), root tips (RT), and suspension cell cultures (C). Stress treatments were nitrogen limitation (low N), methyl jasmonate elicitation (MeJ), and wounding, with sampling either 1 week or 90 h after wounding. C. Heat map showing 10 PtHsp90 genes under conditions of short- and long-term water deficit (GEO: GSE17230). EAR, early response to water deficit (by 36 h), LMI, long-term (10-day) response to mild stress with a soil relative extractable water (REW) level of 20–35%, LMO, long-term (10-day) response to moderate stress with a soil REW level of 10–20%.
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Figure 5: Expression profiles of PtHsp90 genes. A. Heat map showing 10 PtHsp90 genes under heat stress. Expression is indicated as the fold-change in photosynthetic optimum (31.75°C, temperature producing the maximum net CO2 assimilation rate), 20% inhibition of optimum (38.4°C) and 30% inhibition of optimum (40.5°C) relative to baseline (22°C, the growth temperature), and was visualized using heat maps (see Methods). Microarray data were obtained from GEO (GSE26199). B. Heat map showing 10 PtHsp90 genes across various tissues and genotypes (GEO: GSE16786). The genotypes analyzed were P. fremontii × P. angustifolia clones 1979, 3200, and RM5; P. tremuloides clones 271 and L4; and P. deltoids clones Soligo and Carpaccio. The tissues analyzed were young leaves (YL), expanding leaves (EL), mature leaves (L), root tips (RT), and suspension cell cultures (C). Stress treatments were nitrogen limitation (low N), methyl jasmonate elicitation (MeJ), and wounding, with sampling either 1 week or 90 h after wounding. C. Heat map showing 10 PtHsp90 genes under conditions of short- and long-term water deficit (GEO: GSE17230). EAR, early response to water deficit (by 36 h), LMI, long-term (10-day) response to mild stress with a soil relative extractable water (REW) level of 20–35%, LMO, long-term (10-day) response to moderate stress with a soil REW level of 10–20%.
Mentions: In order to reveal the responses of Populus Hsp90 genes to abiotic stresses, we analyzed the expression profiles of PtHsp90s under abiotic stresses such as heat, low nitrogen levels, mechanical wounding, drought, and methyl jasmonate (MeJ) treatment. Affymetrix microarray data (series accession numbers GSE26199, GSE16786 and GSE17230 in the Gene Expression Omnibus [GEO]) [38] were used to analyze the global expression profiles of Populus Hsp90 genes. Previous study divided the physiological condition into four states according to Populus photosynthetic activity from 22°C to 42°C: baseline (22°C, the growth temperature), optimum (31.75°C, temperature producing the maximum net CO2 assimilation rate), 20% inhibition of optimum (38.4°C) and 30% inhibition of optimum (40.5°C) [39]. Most PtHsp90 genes are upregulated under heat stress. The expression of PtHsp90-1a and PtHsp90-1b is highly induced immediately when temperature increases to optimum. PtHsp90-5a and PtHsp90-6 are highly induced when the photosynthesis is inhibited by 30% under heat stress (Figure 5A). In PtHsp90 group I, PtHsp90-1a, PtHsp90-1b, and PtHsp90-3 in both the Soligo and Carpacio genotypes are upregulated under almost all drought stresses tested, including the early response (EAR) to drought at 36 h, and the long-term (10 days) responses to mild stress (LMI) and moderate stress (LMO) (Figure 5C). Nitrogen deficiency stress causes different responses among Hsp90 genes. For instance, PtHsp90-1a and PtHsp90-1b are upregulated in 4-week-old young leaves (YL) and 8-week-old expanded leaves (EL) of genotype 1979 and genotype 3200; PtHsp90-5a and PtHsp90-5b are upregulated in 8-week-old expanded leaves (EL) of the same two genotypes. However, PtHsp90-3, PtHsp90-4a, and PtHsp90-6 are downregulated in 8-week-old expanded leaves in genotype 1979 and/or genotype 3200 (Figure 5B). In response to mechanical wounding stress, six genes (PtHsp90-1a, PtHsp90-1b, PtHsp90-3, PtHsp90-5b, PtHsp90-6, and PtHsp90-7) are significantly downregulated in young leaves and/or expanding leaves 1 week after wounding. In response to MeJ feeding in cell culture, only PtHsp90-1a and PtHsp90-1b are slightly downregulated (Figure 5B).

Bottom Line: Furthermore, microarray and semi-quantitative real-time RT-PCR analyses show that a number of Populus Hsp90 genes are differentially expressed upon exposure to various stresses.Microarray and RT-PCR analyses show that most PtHsp90s were induced by various stresses, including heat stress.Collectively, these observations lay the foundation for future efforts to unravel the biological roles of PtHsp90 genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.

ABSTRACT

Background: Members of the heat shock protein 90 (Hsp90) class of proteins are evolutionarily conserved molecular chaperones. They are involved in protein folding, assembly, stabilization, activation, and degradation in many normal cellular processes and under stress conditions. Unlike many other well-characterized molecular chaperones, Hsp90s play key roles in signal transduction, cell-cycle control, genomic silencing, and protein trafficking. However, no systematic analysis of genome organization, gene structure, and expression compendium has been performed in the Populus model tree genus to date.

Results: We performed a comprehensive analysis of the Populus Hsp90 gene family and identified 10 Populus Hsp90 genes, which were phylogenetically clustered into two major groups. Gene structure and motif composition are relatively conserved in each group. In Populus trichocarpa, we identified three paralogous pairs, among which the PtHsp90-5a/PtHsp90-5b paralogous pair might be created by duplication of a genome segment. Subcellular localization analysis shows that PtHsp90 members are localized in different subcellular compartments. PtHsp90-3 is localized both in the nucleus and in the cytoplasm, PtHsp90-5a and PtHsp90-5b are in chloroplasts, and PtHsp90-7 is in the endoplasmic reticulum (ER). Furthermore, microarray and semi-quantitative real-time RT-PCR analyses show that a number of Populus Hsp90 genes are differentially expressed upon exposure to various stresses.

Conclusions: The gene structure and motif composition of PtHsp90s are highly conserved among group members, suggesting that members of the same group may also have conserved functions. Microarray and RT-PCR analyses show that most PtHsp90s were induced by various stresses, including heat stress. Collectively, these observations lay the foundation for future efforts to unravel the biological roles of PtHsp90 genes.

Show MeSH
Related in: MedlinePlus