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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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Phylogenetic relationships of Hsp90 family members from eight plant species. Multiple alignment of Hsp90 proteins from A. thaliana (At), P. trichocarpa (Pt), O. sativa (Os), M. truncatula (Mt), S. bicolor, (Sb), B. distachyon (Bd), V. vinifera (Vv), and P. patens (Pp) was performed using Clustal X2.1, and a phylogenetic tree was constructed using full-length protein sequences by the maximum likelihood method using PhyML. Bootstrap support values are shown on selected branches.
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Figure 1: Phylogenetic relationships of Hsp90 family members from eight plant species. Multiple alignment of Hsp90 proteins from A. thaliana (At), P. trichocarpa (Pt), O. sativa (Os), M. truncatula (Mt), S. bicolor, (Sb), B. distachyon (Bd), V. vinifera (Vv), and P. patens (Pp) was performed using Clustal X2.1, and a phylogenetic tree was constructed using full-length protein sequences by the maximum likelihood method using PhyML. Bootstrap support values are shown on selected branches.

Mentions: To examine the phylogenetic relationships among the Hsp90 genes in P. trichocarpa and other plant species, we first generated a maximum likelihood phylogenetic tree by aligning full-length Hsp90 protein sequences from eight different plant species using PhyML. All of the sequences are classified into two major groups (group I and II), each of which is further divided into two subgroups (subgroup Ia, Ib, IIa and IIb) (Figure 1). The distribution of Hsp90 members in different species varies, and subgroups Ib and IIa are the largest two subgroups. There are two subgroup Ia members in P. trichocarpa, but none in moss and only one in the other species examined (Table 2). There are also more group Ib Hsp90 members in moss than these in the other species analyzed.


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)

Phylogenetic relationships of Hsp90 family members from eight plant species. Multiple alignment of Hsp90 proteins from A. thaliana (At), P. trichocarpa (Pt), O. sativa (Os), M. truncatula (Mt), S. bicolor, (Sb), B. distachyon (Bd), V. vinifera (Vv), and P. patens (Pp) was performed using Clustal X2.1, and a phylogenetic tree was constructed using full-length protein sequences by the maximum likelihood method using PhyML. Bootstrap support values are shown on selected branches.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750472&req=5

Figure 1: Phylogenetic relationships of Hsp90 family members from eight plant species. Multiple alignment of Hsp90 proteins from A. thaliana (At), P. trichocarpa (Pt), O. sativa (Os), M. truncatula (Mt), S. bicolor, (Sb), B. distachyon (Bd), V. vinifera (Vv), and P. patens (Pp) was performed using Clustal X2.1, and a phylogenetic tree was constructed using full-length protein sequences by the maximum likelihood method using PhyML. Bootstrap support values are shown on selected branches.
Mentions: To examine the phylogenetic relationships among the Hsp90 genes in P. trichocarpa and other plant species, we first generated a maximum likelihood phylogenetic tree by aligning full-length Hsp90 protein sequences from eight different plant species using PhyML. All of the sequences are classified into two major groups (group I and II), each of which is further divided into two subgroups (subgroup Ia, Ib, IIa and IIb) (Figure 1). The distribution of Hsp90 members in different species varies, and subgroups Ib and IIa are the largest two subgroups. There are two subgroup Ia members in P. trichocarpa, but none in moss and only one in the other species examined (Table 2). There are also more group Ib Hsp90 members in moss than these in the other species analyzed.

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