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A Populus TIR1 gene family survey reveals differential expression patterns and responses to 1-naphthaleneacetic acid and stress treatments.

Shu W, Liu Y, Guo Y, Zhou H, Zhang J, Zhao S, Lu M - Front Plant Sci (2015)

Bottom Line: Interestingly, PtrFBL1 and 7 were expressed mainly in vascular and cambial tissues, respectively, indicating their potential but different roles in wood formation.Finally, over-expression studies indicated a role of FBL1 in poplar stem growth and response to drought stress.Collectively, these observations lay the foundation for further investigations into the potential roles of PtrFBL genes in tree growth and development.

View Article: PubMed Central - PubMed

Affiliation: Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University Nanjing, China ; State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.

ABSTRACT
The plant hormone auxin is a central regulator of plant growth. TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) is a component of the E3 ubiquitin ligase complex SCF(TIR1/AFB) and acts as an auxin co-receptor for nuclear auxin signaling. The SCF(TIR1/AFB)-proteasome machinery plays a central regulatory role in development-related gene transcription. Populus trichocarpa, as a model tree, has a unique fast-growth trait to which auxin signaling may contribute. However, no systematic analyses of the genome organization, gene structure, and expression of TIR1-like genes have been undertaken in this woody model plant. In this study, we identified a total of eight TIR1 genes in the Populus genome that are phylogenetically clustered into four subgroups, PtrFBL1/PtrFBL2, PtrFBL3/PtrFBL4, PtrFBL5/PtrFBL6, and PtrFBL7/PtrFBL8, representing four paralogous pairs. In addition, the gene structure and motif composition were relatively conserved in each paralogous pair and all of the PtrFBL members were localized in the nucleus. Different sets of PtrFBLs were strongly expressed in the leaves, stems, roots, cambial zones, and immature xylem of Populus. Interestingly, PtrFBL1 and 7 were expressed mainly in vascular and cambial tissues, respectively, indicating their potential but different roles in wood formation. Furthermore, Populus FBLs responded differentially upon exposure to various stresses. Finally, over-expression studies indicated a role of FBL1 in poplar stem growth and response to drought stress. Collectively, these observations lay the foundation for further investigations into the potential roles of PtrFBL genes in tree growth and development.

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Phylogenetic relationship, gene structures, and motif composition of TIR1 genes in A. thaliana (At), and P. trichocarpa (Ptr). (A) A phylogenetic tree was constructed using MEGA 5 by the neighbor-joining (NJ) method with 1000 bootstrap replicates. The jasmonic acid receptor CONSTANS-LIKE 1 (AtCOL1) in Arabidopsis was used as an outgroup. (B) Exon/intron positions in the TIR1 receptors. Green boxes represent exons and black lines represent introns. (C) Schematic representation of conserved motifs (obtained using MEME) in TIR1 proteins. Different motifs are indicated by colored boxes.
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Figure 1: Phylogenetic relationship, gene structures, and motif composition of TIR1 genes in A. thaliana (At), and P. trichocarpa (Ptr). (A) A phylogenetic tree was constructed using MEGA 5 by the neighbor-joining (NJ) method with 1000 bootstrap replicates. The jasmonic acid receptor CONSTANS-LIKE 1 (AtCOL1) in Arabidopsis was used as an outgroup. (B) Exon/intron positions in the TIR1 receptors. Green boxes represent exons and black lines represent introns. (C) Schematic representation of conserved motifs (obtained using MEME) in TIR1 proteins. Different motifs are indicated by colored boxes.

Mentions: To investigate the evolutionary relationship among TIR1/AFB receptors from Arabidopsis and P. trichocarpa, a phylogenetic tree was constructed, and the TIR1 proteins were classified into four clades that include the pairs of PtrFBL1/PtrFBL2 (AtTIR1/AtAFB1), PtrFBL3/PtrFBL4 (AtAFB2/AtAFB3), PtrFBL7/PtrFBL8 (AtAFB4/AtAFB5), and PtrFBL5/PtrFBL6 (Figure 1A), suggesting that these pairs are paralogs. Each of the Populus paralogous pairs shared 78–90% in sequence identity, but only had 40–78% identity to Arabidopsis TIR1/AFBs. Surprisingly, PtrFBL5 and PtrFBL6 had no homologous counterparts in Arabidopsis. We decided it may be more accurate to ascertain the evolutionary relationships using conserved domain sequences (Marchler-Bauer et al., 2009). Therefore, we constructed the phylogenetic tree with TIR1/AFBs motif sequences from Arabidopsis and Populus using the maximum likelihood method with 1000 bootstrap replicates (Figure S1). The resulted phylogenetic tree was consistent with the one generated based on the full-length protein sequences.


A Populus TIR1 gene family survey reveals differential expression patterns and responses to 1-naphthaleneacetic acid and stress treatments.

Shu W, Liu Y, Guo Y, Zhou H, Zhang J, Zhao S, Lu M - Front Plant Sci (2015)

Phylogenetic relationship, gene structures, and motif composition of TIR1 genes in A. thaliana (At), and P. trichocarpa (Ptr). (A) A phylogenetic tree was constructed using MEGA 5 by the neighbor-joining (NJ) method with 1000 bootstrap replicates. The jasmonic acid receptor CONSTANS-LIKE 1 (AtCOL1) in Arabidopsis was used as an outgroup. (B) Exon/intron positions in the TIR1 receptors. Green boxes represent exons and black lines represent introns. (C) Schematic representation of conserved motifs (obtained using MEME) in TIR1 proteins. Different motifs are indicated by colored boxes.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4585115&req=5

Figure 1: Phylogenetic relationship, gene structures, and motif composition of TIR1 genes in A. thaliana (At), and P. trichocarpa (Ptr). (A) A phylogenetic tree was constructed using MEGA 5 by the neighbor-joining (NJ) method with 1000 bootstrap replicates. The jasmonic acid receptor CONSTANS-LIKE 1 (AtCOL1) in Arabidopsis was used as an outgroup. (B) Exon/intron positions in the TIR1 receptors. Green boxes represent exons and black lines represent introns. (C) Schematic representation of conserved motifs (obtained using MEME) in TIR1 proteins. Different motifs are indicated by colored boxes.
Mentions: To investigate the evolutionary relationship among TIR1/AFB receptors from Arabidopsis and P. trichocarpa, a phylogenetic tree was constructed, and the TIR1 proteins were classified into four clades that include the pairs of PtrFBL1/PtrFBL2 (AtTIR1/AtAFB1), PtrFBL3/PtrFBL4 (AtAFB2/AtAFB3), PtrFBL7/PtrFBL8 (AtAFB4/AtAFB5), and PtrFBL5/PtrFBL6 (Figure 1A), suggesting that these pairs are paralogs. Each of the Populus paralogous pairs shared 78–90% in sequence identity, but only had 40–78% identity to Arabidopsis TIR1/AFBs. Surprisingly, PtrFBL5 and PtrFBL6 had no homologous counterparts in Arabidopsis. We decided it may be more accurate to ascertain the evolutionary relationships using conserved domain sequences (Marchler-Bauer et al., 2009). Therefore, we constructed the phylogenetic tree with TIR1/AFBs motif sequences from Arabidopsis and Populus using the maximum likelihood method with 1000 bootstrap replicates (Figure S1). The resulted phylogenetic tree was consistent with the one generated based on the full-length protein sequences.

Bottom Line: Interestingly, PtrFBL1 and 7 were expressed mainly in vascular and cambial tissues, respectively, indicating their potential but different roles in wood formation.Finally, over-expression studies indicated a role of FBL1 in poplar stem growth and response to drought stress.Collectively, these observations lay the foundation for further investigations into the potential roles of PtrFBL genes in tree growth and development.

View Article: PubMed Central - PubMed

Affiliation: Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University Nanjing, China ; State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry Beijing, China.

ABSTRACT
The plant hormone auxin is a central regulator of plant growth. TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) is a component of the E3 ubiquitin ligase complex SCF(TIR1/AFB) and acts as an auxin co-receptor for nuclear auxin signaling. The SCF(TIR1/AFB)-proteasome machinery plays a central regulatory role in development-related gene transcription. Populus trichocarpa, as a model tree, has a unique fast-growth trait to which auxin signaling may contribute. However, no systematic analyses of the genome organization, gene structure, and expression of TIR1-like genes have been undertaken in this woody model plant. In this study, we identified a total of eight TIR1 genes in the Populus genome that are phylogenetically clustered into four subgroups, PtrFBL1/PtrFBL2, PtrFBL3/PtrFBL4, PtrFBL5/PtrFBL6, and PtrFBL7/PtrFBL8, representing four paralogous pairs. In addition, the gene structure and motif composition were relatively conserved in each paralogous pair and all of the PtrFBL members were localized in the nucleus. Different sets of PtrFBLs were strongly expressed in the leaves, stems, roots, cambial zones, and immature xylem of Populus. Interestingly, PtrFBL1 and 7 were expressed mainly in vascular and cambial tissues, respectively, indicating their potential but different roles in wood formation. Furthermore, Populus FBLs responded differentially upon exposure to various stresses. Finally, over-expression studies indicated a role of FBL1 in poplar stem growth and response to drought stress. Collectively, these observations lay the foundation for further investigations into the potential roles of PtrFBL genes in tree growth and development.

No MeSH data available.


Related in: MedlinePlus