Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.)

Wang, Yijun; Deng, Dexiang; Bian, Yunlong; Lv, Yanping; Xie, Qi

doi:10.1007/s11033-010-0058-6

Cited by 117 publications

(92 citation statements)

References 40 publications

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“…IAA proteins with LxLxLxL or LxLxLxLxL motifs are also found in the sequenced genomes of rice (Oryza sativa), sorghum (Sorghum bicolor), maize (Zea mays), and poplar (Populus trichocarpa; Jain et al, 2006;Kalluri et al, 2007;Wang et al, 2010aWang et al, , 2010b and in a wide variety of other plant species, indicating that these more extensive Leu-rich repression domains are conserved. Repression domains of different strengths (e.g.…”

Section: Discussionmentioning

confidence: 99%

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Identical Amino Acid Substitutions in the Repression Domain of Auxin/Indole-3-Acetic Acid Proteins Have Contrasting Effects on Auxin Signaling

Tiwari

Hagen

et al. 2011

Plant Physiology

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Auxin/indole-3-acetic acid (Aux/IAA) proteins function as repressors of auxin response gene expression when auxin concentrations in a cell are low. At elevated auxin concentrations, these repressors are destroyed via the ubiquitin-proteasome pathway, resulting in derepression/activation of auxin response genes. Most Aux/IAA repressors contain four conserved domains, with one of these being an active, portable repression domain (domain I) and a second being an auxin-dependent instability domain (domain II). Here, we have analyzed the effects of amino acid substitutions in the repression domain of selected Aux/IAA proteins. We show that stabilized versions of Aux/IAA proteins with amino acid substitutions in domain I display contrasting phenotypes when expressed in transformed Arabidopsis (Arabidopsis thaliana) plants. An alanine-forleucine substitution in the LxLxL (where L is leucine and x is another amino acid) repression domain of IAA3, IAA6, or IAA19 confers enhanced auxin response gene expression and "high-auxin" phenotypes when expressed from the 35S or IAA19 promoter (as tested with IAA19) in transformed Arabidopsis plants. In marked contrast, a single alanine-for-leucine substitution in domain I of IAA12 or IAA17 confers repression of auxin response genes and "low-auxin" phenotypes. These results point to intrinsic differences in the repression domain(s) of IAA proteins and suggest that some IAA proteins have stronger or more complex repression domains than others.

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Section: Discussionmentioning

confidence: 99%

“…In rice, OsIAA4, OsIAA22, OsIAA27, OsIAA28, and OsIAA29 lack domain I or domains I and II (Jain et al, 2006). Likewise, sorghum (Wang et al, 2010a) and maize (Wang et al, 2010b) along with a variety of other plants have examples of Aux/IAA proteins that lack domain I or both domains I and II.…”

Section: Discussionmentioning

confidence: 99%

Identical Amino Acid Substitutions in the Repression Domain of Auxin/Indole-3-Acetic Acid Proteins Have Contrasting Effects on Auxin Signaling

Tiwari

Hagen

et al. 2011

Plant Physiology

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“…According to the identified proteins of HD-ZIP family genes in Arabidopsis that were downloaded from TAIR database (Huala et al, 2001), the hidden Markov model (HMM) profile of the HD-ZIP family was extracted from the Pfam database as described by Wang et al (2010). With the aid of the HMM profile, searching against the peach proteins database in GDR was performed using identified proteins of the HD-ZIP family in Arabidopsis as query sequences.…”

Section: Isolation Of Predicted Hd-zip Genes In Peachmentioning

confidence: 99%

Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica)

Zhang¹,

J²,

Shen³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. In this study, 33 homeodomain-leucine zipper (HD-ZIP) genes were identified in peach using the HD-ZIP amino acid sequences of Arabidopsis thaliana as a probe. Based on the phylogenetic analysis and the individual gene or protein characteristics, the HD-ZIP gene family in peach can be classified into 4 subfamilies, HD-ZIP I, II, III, and IV, containing 14, 7, 4, and 8 members, respectively. The most closely related peach HD-ZIP members within the same subfamilies shared very similar gene structure in terms of either intron/exon numbers or lengths. Almost all members of the same subfamily shared common motif compositions, thereby implying that the HD-ZIP proteins within the same subfamily may have functional similarity. The 33 peach HD-ZIP genes were distributed across scaffolds 1 to 7. Although the primary structure varied among HD-ZIP family proteins, their tertiary structures were similar. The results from this study will 2655 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (2): 2654-2668 (2014) Analysis of the HD-ZIP family in peach be useful in selecting candidate genes from specific subfamilies for functional analysis.

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“…On the basis of the proteins identified in AP2/ERF superfamily genes of A. thaliana downloaded from the TAIR database (Huala et al, 2001), the hidden Markov model (HMM) profile of the AP2/ERF superfamily was extracted from the Pfam, as described by Wang et al (2010). With the aid of the HMM profile, a search against the peach proteins database in GDR was performed using the identified proteins of the AP2/ERF superfamily of A. thaliana as query sequences.…”

Section: Isolation Of Predicted Ap2/erf Genes In Peachmentioning

confidence: 99%

“…Parameters were set as described by Wang et al (2010): 0 or 1 occurrence of a single motif per sequence, motif width ranges of 10 to 300 amino acids, and 5 as the maximum number of motifs that must be found. All other parameters were set at default.…”

Section: Motif Display and Phylogenetic Analysis Of Predicted Ap2/erfmentioning

confidence: 99%

Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica)

Zhang

Shangguan²,

J³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. We identified 131 AP2/ERF (APETALA2/ethyleneresponsive factor) genes in material from peach using the gene sequences of AP2/ERF amino acids of Arabidopsis thaliana (Brassicaceae) as probes. Based on the number of AP2/ERF domains and individual gene characteristics, the AP2/ERF gene superfamily in peach can be classified broadly into three families, ERF (ethylene-responsive factor), RAV (related to ABI3/VP1), and AP2 (APETALA2), containing 104, 5, and 21 members, respectively, along with a solo gene (ppa005376m). The 104 genes in the ERF family were further divided into 11 groups based on the group classification made for Arabidopsis. The scaffold localizations of the AP2/ERF genes indicated that 129 AP2/ERF genes were all located on scaffolds 1 to 8, except for two genes, which were on scaffolds 17 and 10. Although the primary structure varied among AP2/ERF superfamily proteins, their tertiary structures were similar. Most ERF family genes have no introns, while members of the AP2 family have more introns than genes in the ERF and RAV families. All sequences of AP2 family genes were disrupted by introns into several segments of varying sizes. The expression of the AP2/ERF superfamily genes was highest in the mesocarp; it was far higher than in the other C.H. Zhang et al. ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research (2012) Ahead of Print seven tissues that we examined, implying that AP2/ERF superfamily genes play an important role in fruit growth and development in the peach. These results will be useful for selecting candidate genes from specific subgroups for functional analysis.

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Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.)

Cited by 117 publications

References 40 publications

Identical Amino Acid Substitutions in the Repression Domain of Auxin/Indole-3-Acetic Acid Proteins Have Contrasting Effects on Auxin Signaling

Identical Amino Acid Substitutions in the Repression Domain of Auxin/Indole-3-Acetic Acid Proteins Have Contrasting Effects on Auxin Signaling

Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica)

Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica)

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