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Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses.

Zhang J, Liu B, Li J, Zhang L, Wang Y, Zheng H, Lu M, Chen J - BMC Genomics (2015)

Bottom Line: In Populus trichocarpa, we identified 42 paralogous pairs, 66.7% resulting from a whole genome duplication.A coexpression network between Populus Hsf and Hsp genes was generated based on their expression.Coordinated relationships were validated by transient overexpression and subsequent qPCR analyses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China. zhang007jin@163.com.

ABSTRACT

Background: Heat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in stress responses have been well characterized in Arabidopsis, their roles in perennial woody species undergoing various environmental stresses remain unclear.

Results: Here, a comprehensive identification and analysis of Hsf and Hsp families in poplars is presented. In Populus trichocarpa, we identified 42 paralogous pairs, 66.7% resulting from a whole genome duplication. The gene structure and motif composition are relatively conserved in each subfamily. Microarray and quantitative real-time RT-PCR analyses showed that most of the Populus Hsf and Hsp genes are differentially expressed upon exposure to various stresses. A coexpression network between Populus Hsf and Hsp genes was generated based on their expression. Coordinated relationships were validated by transient overexpression and subsequent qPCR analyses.

Conclusions: The comprehensive analysis indicates that different sets of PtHsps are downstream of particular PtHsfs and provides a basis for functional studies aimed at revealing the roles of these families in poplar development and stress responses.

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Related in: MedlinePlus

Expression profiles ofPopulus HsfsandHspsacross different tissues. Heatmap showing expression of Hsf and Hsp genes across various tissues and different stem development/growth stages. The Affymetrix microarray data (GSE13990) and the NimbleGen microarray data (GSE13043) were obtained from NCBI Gene Expression Omnibus (GEO) database. CL, continuous light-grown seedling; DL, etiolated dark-grown seedling transferred to light for 3 h; DS, dark-grown seedlings; YL, young leaf; ML, mature leaf; R, root; DX, differentiating xylem; FC, female catkins; MC, male catkins; IN2-IN5, and IN9, stem internode 2 to internode 5, and internode 9. Background corrected expression intensities were log transformed and visualized as heatmaps (see Methods). Color scale represents log2 expression values, green represents low level and red indicates high level of transcript abundance. Blank represents a gene has no corresponding probe sets in the microarray data.
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Fig4: Expression profiles ofPopulus HsfsandHspsacross different tissues. Heatmap showing expression of Hsf and Hsp genes across various tissues and different stem development/growth stages. The Affymetrix microarray data (GSE13990) and the NimbleGen microarray data (GSE13043) were obtained from NCBI Gene Expression Omnibus (GEO) database. CL, continuous light-grown seedling; DL, etiolated dark-grown seedling transferred to light for 3 h; DS, dark-grown seedlings; YL, young leaf; ML, mature leaf; R, root; DX, differentiating xylem; FC, female catkins; MC, male catkins; IN2-IN5, and IN9, stem internode 2 to internode 5, and internode 9. Background corrected expression intensities were log transformed and visualized as heatmaps (see Methods). Color scale represents log2 expression values, green represents low level and red indicates high level of transcript abundance. Blank represents a gene has no corresponding probe sets in the microarray data.

Mentions: We then investigated the global expression profiles of Hsf and Hsp genes by examining previously published microarray data in poplars. At first, Affymetrix (GSE13990) [44] and a Nimblegen (GSE13043) [45] microarray data from Gene Expression Omnibus [46] were used to analyze the expression patterns of Hsf and Hsp genes in different tissues. Most Populus Hsf and Hsp genes were detected in the two different platforms. The majority of Hsf and Hsp genes showed a tissue-specific expression pattern (Figure 4). Four sHsps (Pt16.2I-sHsp, Pt18.3I-sHsp, Pt18.5I-sHsp, and Pt21.8ER-sHsp) and two Hsp60s (PtCpn60-5.1 and PtCpn60-7.2) had high transcript levels in the differentiating xylem. Two Hsfs (PtHsf-A3 and PtHsf-B3a), one sHsp (Pt16.5I-sHsp) and one Hsp70 (PtHsp70-BIP3) were preferentially expressed in male and female catkins, but almost all of the Hsp60s had low transcript levels in catkins (Figure 4). During stem development, 9 Hsfs, 13 sHsps, and 2 Hsp100s had high levels in the basal stem undergoing the secondary growth (internode 9). In comparison, most Hsp60 and Hsp70 genes showed high expression levels in the upper stem (internode 2 and 3) (Figure 4).Figure 4


Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses.

Zhang J, Liu B, Li J, Zhang L, Wang Y, Zheng H, Lu M, Chen J - BMC Genomics (2015)

Expression profiles ofPopulus HsfsandHspsacross different tissues. Heatmap showing expression of Hsf and Hsp genes across various tissues and different stem development/growth stages. The Affymetrix microarray data (GSE13990) and the NimbleGen microarray data (GSE13043) were obtained from NCBI Gene Expression Omnibus (GEO) database. CL, continuous light-grown seedling; DL, etiolated dark-grown seedling transferred to light for 3 h; DS, dark-grown seedlings; YL, young leaf; ML, mature leaf; R, root; DX, differentiating xylem; FC, female catkins; MC, male catkins; IN2-IN5, and IN9, stem internode 2 to internode 5, and internode 9. Background corrected expression intensities were log transformed and visualized as heatmaps (see Methods). Color scale represents log2 expression values, green represents low level and red indicates high level of transcript abundance. Blank represents a gene has no corresponding probe sets in the microarray data.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4373061&req=5

Fig4: Expression profiles ofPopulus HsfsandHspsacross different tissues. Heatmap showing expression of Hsf and Hsp genes across various tissues and different stem development/growth stages. The Affymetrix microarray data (GSE13990) and the NimbleGen microarray data (GSE13043) were obtained from NCBI Gene Expression Omnibus (GEO) database. CL, continuous light-grown seedling; DL, etiolated dark-grown seedling transferred to light for 3 h; DS, dark-grown seedlings; YL, young leaf; ML, mature leaf; R, root; DX, differentiating xylem; FC, female catkins; MC, male catkins; IN2-IN5, and IN9, stem internode 2 to internode 5, and internode 9. Background corrected expression intensities were log transformed and visualized as heatmaps (see Methods). Color scale represents log2 expression values, green represents low level and red indicates high level of transcript abundance. Blank represents a gene has no corresponding probe sets in the microarray data.
Mentions: We then investigated the global expression profiles of Hsf and Hsp genes by examining previously published microarray data in poplars. At first, Affymetrix (GSE13990) [44] and a Nimblegen (GSE13043) [45] microarray data from Gene Expression Omnibus [46] were used to analyze the expression patterns of Hsf and Hsp genes in different tissues. Most Populus Hsf and Hsp genes were detected in the two different platforms. The majority of Hsf and Hsp genes showed a tissue-specific expression pattern (Figure 4). Four sHsps (Pt16.2I-sHsp, Pt18.3I-sHsp, Pt18.5I-sHsp, and Pt21.8ER-sHsp) and two Hsp60s (PtCpn60-5.1 and PtCpn60-7.2) had high transcript levels in the differentiating xylem. Two Hsfs (PtHsf-A3 and PtHsf-B3a), one sHsp (Pt16.5I-sHsp) and one Hsp70 (PtHsp70-BIP3) were preferentially expressed in male and female catkins, but almost all of the Hsp60s had low transcript levels in catkins (Figure 4). During stem development, 9 Hsfs, 13 sHsps, and 2 Hsp100s had high levels in the basal stem undergoing the secondary growth (internode 9). In comparison, most Hsp60 and Hsp70 genes showed high expression levels in the upper stem (internode 2 and 3) (Figure 4).Figure 4

Bottom Line: In Populus trichocarpa, we identified 42 paralogous pairs, 66.7% resulting from a whole genome duplication.A coexpression network between Populus Hsf and Hsp genes was generated based on their expression.Coordinated relationships were validated by transient overexpression and subsequent qPCR analyses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China. zhang007jin@163.com.

ABSTRACT

Background: Heat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in stress responses have been well characterized in Arabidopsis, their roles in perennial woody species undergoing various environmental stresses remain unclear.

Results: Here, a comprehensive identification and analysis of Hsf and Hsp families in poplars is presented. In Populus trichocarpa, we identified 42 paralogous pairs, 66.7% resulting from a whole genome duplication. The gene structure and motif composition are relatively conserved in each subfamily. Microarray and quantitative real-time RT-PCR analyses showed that most of the Populus Hsf and Hsp genes are differentially expressed upon exposure to various stresses. A coexpression network between Populus Hsf and Hsp genes was generated based on their expression. Coordinated relationships were validated by transient overexpression and subsequent qPCR analyses.

Conclusions: The comprehensive analysis indicates that different sets of PtHsps are downstream of particular PtHsfs and provides a basis for functional studies aimed at revealing the roles of these families in poplar development and stress responses.

Show MeSH
Related in: MedlinePlus