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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

Phylogenetic relationships, gene structures and motif compositions ofHsfandsHspfamily members inA. thaliana(At) andP. trichocarpa(Pt). Multiple alignment of Hsf (A) and sHsp (B) proteins from A. thaliana (At) and P. trichocarpa (Pt) was performed using MEGA 5.0 by the Neighbor-Joining (NJ) method with 1000 bootstrap replicates (left panel). Exon/intron structures of the Hsf and sHsp genes are shown in the middle panel. Green boxes represent exons and black lines represent introns. The numbers indicate the splicing phases of the Hsf and sHsp genes: 0, phase 0; 1, phase 1; and 2, phase 2. A schematic representation of conserved motifs (obtained using MEME) in Hsf and sHsp proteins is displayed in the right panel. Different motifs are represented by different colored boxes. Details of the individual motifs are in the Additional file 4: Table S4 and Additional file 5: Table S5.
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Fig1: Phylogenetic relationships, gene structures and motif compositions ofHsfandsHspfamily members inA. thaliana(At) andP. trichocarpa(Pt). Multiple alignment of Hsf (A) and sHsp (B) proteins from A. thaliana (At) and P. trichocarpa (Pt) was performed using MEGA 5.0 by the Neighbor-Joining (NJ) method with 1000 bootstrap replicates (left panel). Exon/intron structures of the Hsf and sHsp genes are shown in the middle panel. Green boxes represent exons and black lines represent introns. The numbers indicate the splicing phases of the Hsf and sHsp genes: 0, phase 0; 1, phase 1; and 2, phase 2. A schematic representation of conserved motifs (obtained using MEME) in Hsf and sHsp proteins is displayed in the right panel. Different motifs are represented by different colored boxes. Details of the individual motifs are in the Additional file 4: Table S4 and Additional file 5: Table S5.

Mentions: To evaluate the evolutionary relationship of the Hsf and Hsp proteins, a phylogenetic analysis of each family was performed based on the full-length amino acid sequences from both P. trichocarpa and Arabidopsis (Figures 1 and 2, left panel). Each family could be classified into different subfamilies. The PtHsf family contains three subfamilies: type A (17 genes), type B (10 genes), and type C (1 gene). However the subfamilies in each of the PtHsp families could be assigned based on the proteins’ predicted subcellular localization. The sHsp family was classified into cytosolic, endoplasmic reticulum (ER), peroxisome (PX), chloroplast (CP), and mitochondrial (MT) subfamilies in P. trichocarpa. There are six groups of cytosolic sHsp genes, C-I, C-II, C-III, C-IV, C-V, and C-VI, and two groups of mitochondrial sHsp genes, MT and MT II, in P. trichocarpa. Notably, the C-I sHsp group in the genome of P. trichocarpa is large, containing 19 genes compared with 6 in Arabidopsis (Figure 1). The Hsp60 family was divided into four subfamilies in P. trichocarpa: cytosol-localized Cpn60 (18 genes), mitochondrion-localized Hsp60 (3 genes), and chloroplast-localized Cpn60-a (4 genes) and Cpn60-b (3 genes). The Hsp70 family contains genes encoding 10 cytosolic Hsp70s, 4 binding proteins (BIPs, Hsp70 homologs in the ER), 2 plastid Hsp70s (cpHsc70s), 2 mitochondrial Hsp70s (mtHsc70s), and 2 truncated Hsp70s (Hsp70ts). The Hsp100 family can be divided into three classes in P. trichocarpa, cytoplasmic (Cyt, 2 genes), chloroplastic (CP, 2 genes), and mitochondrial (MT, 1 gene) (Figure 2).Figure 1


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)

Phylogenetic relationships, gene structures and motif compositions ofHsfandsHspfamily members inA. thaliana(At) andP. trichocarpa(Pt). Multiple alignment of Hsf (A) and sHsp (B) proteins from A. thaliana (At) and P. trichocarpa (Pt) was performed using MEGA 5.0 by the Neighbor-Joining (NJ) method with 1000 bootstrap replicates (left panel). Exon/intron structures of the Hsf and sHsp genes are shown in the middle panel. Green boxes represent exons and black lines represent introns. The numbers indicate the splicing phases of the Hsf and sHsp genes: 0, phase 0; 1, phase 1; and 2, phase 2. A schematic representation of conserved motifs (obtained using MEME) in Hsf and sHsp proteins is displayed in the right panel. Different motifs are represented by different colored boxes. Details of the individual motifs are in the Additional file 4: Table S4 and Additional file 5: Table S5.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Phylogenetic relationships, gene structures and motif compositions ofHsfandsHspfamily members inA. thaliana(At) andP. trichocarpa(Pt). Multiple alignment of Hsf (A) and sHsp (B) proteins from A. thaliana (At) and P. trichocarpa (Pt) was performed using MEGA 5.0 by the Neighbor-Joining (NJ) method with 1000 bootstrap replicates (left panel). Exon/intron structures of the Hsf and sHsp genes are shown in the middle panel. Green boxes represent exons and black lines represent introns. The numbers indicate the splicing phases of the Hsf and sHsp genes: 0, phase 0; 1, phase 1; and 2, phase 2. A schematic representation of conserved motifs (obtained using MEME) in Hsf and sHsp proteins is displayed in the right panel. Different motifs are represented by different colored boxes. Details of the individual motifs are in the Additional file 4: Table S4 and Additional file 5: Table S5.
Mentions: To evaluate the evolutionary relationship of the Hsf and Hsp proteins, a phylogenetic analysis of each family was performed based on the full-length amino acid sequences from both P. trichocarpa and Arabidopsis (Figures 1 and 2, left panel). Each family could be classified into different subfamilies. The PtHsf family contains three subfamilies: type A (17 genes), type B (10 genes), and type C (1 gene). However the subfamilies in each of the PtHsp families could be assigned based on the proteins’ predicted subcellular localization. The sHsp family was classified into cytosolic, endoplasmic reticulum (ER), peroxisome (PX), chloroplast (CP), and mitochondrial (MT) subfamilies in P. trichocarpa. There are six groups of cytosolic sHsp genes, C-I, C-II, C-III, C-IV, C-V, and C-VI, and two groups of mitochondrial sHsp genes, MT and MT II, in P. trichocarpa. Notably, the C-I sHsp group in the genome of P. trichocarpa is large, containing 19 genes compared with 6 in Arabidopsis (Figure 1). The Hsp60 family was divided into four subfamilies in P. trichocarpa: cytosol-localized Cpn60 (18 genes), mitochondrion-localized Hsp60 (3 genes), and chloroplast-localized Cpn60-a (4 genes) and Cpn60-b (3 genes). The Hsp70 family contains genes encoding 10 cytosolic Hsp70s, 4 binding proteins (BIPs, Hsp70 homologs in the ER), 2 plastid Hsp70s (cpHsc70s), 2 mitochondrial Hsp70s (mtHsc70s), and 2 truncated Hsp70s (Hsp70ts). The Hsp100 family can be divided into three classes in P. trichocarpa, cytoplasmic (Cyt, 2 genes), chloroplastic (CP, 2 genes), and mitochondrial (MT, 1 gene) (Figure 2).Figure 1

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