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A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.).

Qiao L, Zhang X, Han X, Zhang L, Li X, Zhan H, Ma J, Luo P, Zhang W, Cui L, Li X, Chang Z - Front Plant Sci (2015)

Bottom Line: The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family.However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern.Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, College of Life Science, Shanxi University Taiyuan, China ; Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences Taiyuan, China.

ABSTRACT
The Auxin/indole-3-acetic acid (Aux/IAA) gene family plays key roles in the primary auxin-response process and controls a number of important traits in plants. However, the characteristics of the Aux/IAA gene family in hexaploid bread wheat (Triticum aestivum L.) have long been unknown. In this study, a comprehensive identification of the Aux/IAA gene family was performed using the latest draft genome sequence of the bread wheat "Chinese Spring." Thirty-four Aux/IAA genes were identified, 30 of which have duplicated genes on the A, B or D sub-genome, with a total of 84 Aux/IAA sequences. These predicted Aux/IAA genes were non-randomly distributed in all the wheat chromosomes except for chromosome 2D. The information of wheat Aux/IAA proteins is also described. Based on an analysis of phylogeny, expression and adaptive evolution, we prove that the Aux/IAA family in wheat has been replicated twice in the two allopolyploidization events of bread wheat, when the tandem duplication also occurred. The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family. However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern. Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

No MeSH data available.


Motifs of wheat Aux/IAA proteins. The sequence logos are based on multiple alignment analysis of 84 wheat Aux/IAA proteins performed with Clustal W. The bit score indicates the information content for each position in the sequence. Positions of conserved domains are boxed.
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Figure 4: Motifs of wheat Aux/IAA proteins. The sequence logos are based on multiple alignment analysis of 84 wheat Aux/IAA proteins performed with Clustal W. The bit score indicates the information content for each position in the sequence. Positions of conserved domains are boxed.

Mentions: The results of multiple alignment and motif distribution analyses of TaIAA proteins showed that 48 out of 84 (57.1%) wheat Aux/IAA proteins contain the same domains, known as domains I, II, III and IV (Supplementary Figure 1). Motifs 1, 2, 3, and 4 are located in these four domains, respectively (Figures 1B, 4). Eighteen (21.4%) wheat Aux/IAA proteins missed one domain (I, II, or IV), while 17 (20.2%) proteins missed domains I & II; just one (1.2%) protein, TaIAA16-B, lacked three domains (I & II & III). Generally, TaIAA proteins within the same phylogenetic group have similar domains and motifs. Domain I (Motif 1) contains the LxLxLx motif, a typical leucine-rich region that was shown in most TaIAA proteins, which has been shown to act as a strong transcriptional repressor (Tiwari et al., 2004). Domain II contains VGWPP, the core sequence of the target site for wheat Aux/IAA protein degradation. Dominant mutation in this region causes Aux/IAA proteins to fail to resolve via the ubiquitin pathway (Kepinski and Leyser, 2005). Domains III and IV are comparatively more conserved. A βαα structure existing in domain III (Motif 3) appeared among all the TaIAA proteins except TaIAA16-B (Figure 1B). It was found that this fold plays an important role in the dimerization of Aux/IAA proteins. Most of the wheat Aux/IAA proteins include two hypothetical nuclear localization signals (NLS). The first bipartite NLS is comprised of two elements: one between domains I and II, and the other in domain II (Supplementary Figure 1). The second element, the SV40-type NLS, is located in domain IV (Supplementary Figure 1). The possible function of these NLSs may be to transfer TaIAA proteins into the nucleus. Interestingly, the conserved residue in the bipartite NLS is KP in TaIAA proteins, while it is KR in rice Aux/IAA proteins (Jain et al., 2006). Therefore, further study into the bipartite NLS in wheat is required. In addition, the existence of phosphorylation sites in several TaIAA proteins partly indicates that these proteins can be extrapolated as short-lived proteins (Supplementary Figure 1).


A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.).

Qiao L, Zhang X, Han X, Zhang L, Li X, Zhan H, Ma J, Luo P, Zhang W, Cui L, Li X, Chang Z - Front Plant Sci (2015)

Motifs of wheat Aux/IAA proteins. The sequence logos are based on multiple alignment analysis of 84 wheat Aux/IAA proteins performed with Clustal W. The bit score indicates the information content for each position in the sequence. Positions of conserved domains are boxed.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4588698&req=5

Figure 4: Motifs of wheat Aux/IAA proteins. The sequence logos are based on multiple alignment analysis of 84 wheat Aux/IAA proteins performed with Clustal W. The bit score indicates the information content for each position in the sequence. Positions of conserved domains are boxed.
Mentions: The results of multiple alignment and motif distribution analyses of TaIAA proteins showed that 48 out of 84 (57.1%) wheat Aux/IAA proteins contain the same domains, known as domains I, II, III and IV (Supplementary Figure 1). Motifs 1, 2, 3, and 4 are located in these four domains, respectively (Figures 1B, 4). Eighteen (21.4%) wheat Aux/IAA proteins missed one domain (I, II, or IV), while 17 (20.2%) proteins missed domains I & II; just one (1.2%) protein, TaIAA16-B, lacked three domains (I & II & III). Generally, TaIAA proteins within the same phylogenetic group have similar domains and motifs. Domain I (Motif 1) contains the LxLxLx motif, a typical leucine-rich region that was shown in most TaIAA proteins, which has been shown to act as a strong transcriptional repressor (Tiwari et al., 2004). Domain II contains VGWPP, the core sequence of the target site for wheat Aux/IAA protein degradation. Dominant mutation in this region causes Aux/IAA proteins to fail to resolve via the ubiquitin pathway (Kepinski and Leyser, 2005). Domains III and IV are comparatively more conserved. A βαα structure existing in domain III (Motif 3) appeared among all the TaIAA proteins except TaIAA16-B (Figure 1B). It was found that this fold plays an important role in the dimerization of Aux/IAA proteins. Most of the wheat Aux/IAA proteins include two hypothetical nuclear localization signals (NLS). The first bipartite NLS is comprised of two elements: one between domains I and II, and the other in domain II (Supplementary Figure 1). The second element, the SV40-type NLS, is located in domain IV (Supplementary Figure 1). The possible function of these NLSs may be to transfer TaIAA proteins into the nucleus. Interestingly, the conserved residue in the bipartite NLS is KP in TaIAA proteins, while it is KR in rice Aux/IAA proteins (Jain et al., 2006). Therefore, further study into the bipartite NLS in wheat is required. In addition, the existence of phosphorylation sites in several TaIAA proteins partly indicates that these proteins can be extrapolated as short-lived proteins (Supplementary Figure 1).

Bottom Line: The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family.However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern.Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, College of Life Science, Shanxi University Taiyuan, China ; Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences Taiyuan, China.

ABSTRACT
The Auxin/indole-3-acetic acid (Aux/IAA) gene family plays key roles in the primary auxin-response process and controls a number of important traits in plants. However, the characteristics of the Aux/IAA gene family in hexaploid bread wheat (Triticum aestivum L.) have long been unknown. In this study, a comprehensive identification of the Aux/IAA gene family was performed using the latest draft genome sequence of the bread wheat "Chinese Spring." Thirty-four Aux/IAA genes were identified, 30 of which have duplicated genes on the A, B or D sub-genome, with a total of 84 Aux/IAA sequences. These predicted Aux/IAA genes were non-randomly distributed in all the wheat chromosomes except for chromosome 2D. The information of wheat Aux/IAA proteins is also described. Based on an analysis of phylogeny, expression and adaptive evolution, we prove that the Aux/IAA family in wheat has been replicated twice in the two allopolyploidization events of bread wheat, when the tandem duplication also occurred. The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family. However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern. Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

No MeSH data available.