Specificity in auxin responses is not explained by the promoter preferences of activator ARFs

AbstractAuxin is essential for almost every developmental process within plants. How a single small molecule can lead to a plethora of downstream responses has puzzled researchers for decades. It has been hypothesized that one source for such diversity is distinct promoter-binding and activation preferences for different members of the AUXIN RESPONSE FACTOR (ARF) family of transcription factors. We systematically tested this hypothesis by engineering varied promoter sequences in a heterologous yeast system and quantifying transcriptional activation by ARFs from two species, Arabidopsis thaliana and Zea mays. By harnessing the user-defined and scalable nature of our synthetic system, we elucidated promoter design rules for optimal ARF function, discovered novel ARF-responsive promoters, and characterized the impact of ARF dimerization on their activation potential. We found no evidence for specificity in ARF-promoter interactions, suggesting that the diverse auxin responses observed in plants may be driven by factors outside the core auxin response machinery.

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Genome-wide analysis of the auxin response factor (ARF) gene family in maize (Zea mays)

Plant Growth Regulation ◽

10.1007/s10725-010-9519-0 ◽

2010 ◽

Vol 63 (3) ◽

pp. 225-234 ◽

Cited By ~ 46

Author(s):

Yan Liu ◽

HaiYang Jiang ◽

Wenjuan Chen ◽

Yexiong Qian ◽

Qing Ma ◽

...

Keyword(s):

Zea Mays ◽

Gene Family ◽

Auxin Response Factor ◽

Response Factor ◽

Auxin Response ◽

Genome Wide Analysis ◽

Genome Wide

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Distinct modes of manipulation of rice auxin response factor OsARF17 by different plant RNA viruses for infection

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1918254117 ◽

2020 ◽

Vol 117 (16) ◽

pp. 9112-9121 ◽

Cited By ~ 6

Author(s):

Hehong Zhang ◽

Lulu Li ◽

Yuqing He ◽

Qingqing Qin ◽

Changhai Chen ◽

...

Keyword(s):

Transcription Factors ◽

Transcriptional Activation ◽

Rna Viruses ◽

Rna Virus ◽

Viral Proteins ◽

Plant Viruses ◽

Auxin Response Factor ◽

Auxin Signaling ◽

Response Factor ◽

Auxin Response

Plant auxin response factor (ARF) transcription factors are an important class of key transcriptional modulators in auxin signaling. Despite the well-studied roles of ARF transcription factors in plant growth and development, it is largely unknown whether, and how, ARF transcription factors may be involved in plant resistance to pathogens. We show here that two fijiviruses (double-stranded RNA viruses) utilize their proteins to disturb the dimerization of OsARF17 and repress its transcriptional activation ability, while a tenuivirus (negative-sense single-stranded RNA virus) directly interferes with the DNA binding activity of OsARF17. These interactions impair OsARF17-mediated antiviral defense. OsARF17 also confers resistance to a cytorhabdovirus and was directly targeted by one of the viral proteins. Thus, OsARF17 is the common target of several very different viruses. This suggests that OsARF17 plays a crucial role in plant defense against different types of plant viruses, and that these viruses use independently evolved viral proteins to target this key component of auxin signaling and facilitate infection.

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Proper regeneration from in vitro cultured Arabidopsis thaliana requires the microRNA-directed action of an auxin response factor

The Plant Journal ◽

10.1111/j.1365-313x.2012.04944.x ◽

2012 ◽

Vol 71 (1) ◽

pp. 14-22 ◽

Cited By ~ 54

Author(s):

Meng Qiao ◽

Zhongjuan Zhao ◽

Yuguang Song ◽

Zhenhua Liu ◽

Lingxue Cao ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Auxin Response Factor ◽

Response Factor ◽

Auxin Response ◽

Directed Action

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Functional analysis of molecular interactions in synthetic auxin response circuits

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1604379113 ◽

2016 ◽

Vol 113 (40) ◽

pp. 11354-11359 ◽

Cited By ~ 25

Author(s):

Edith Pierre-Jerome ◽

Britney L. Moss ◽

Amy Lanctot ◽

Amber Hageman ◽

Jennifer L. Nemhauser

Keyword(s):

Transcriptional Activation ◽

Function Analysis ◽

Response Factor ◽

Quantitative Structure ◽

Auxin Response ◽

Transcriptional Responses ◽

Synthetic Auxin ◽

Promoter Architecture ◽

Repressor Proteins ◽

Indole 3 Acetic Acid

Auxin-regulated transcription pivots on the interaction between the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) repressor proteins and the AUXIN RESPONSE FACTOR (ARF) transcription factors. Recent structural analyses of ARFs and Aux/IAAs have raised questions about the functional complexes driving auxin transcriptional responses. To parse the nature and significance of ARF–DNA and ARF–Aux/IAA interactions, we analyzed structure-guided variants of synthetic auxin response circuits in the budding yeast Saccharomyces cerevisiae. Our analysis revealed that promoter architecture could specify ARF activity and that ARF19 required dimerization at two distinct domains for full transcriptional activation. In addition, monomeric Aux/IAAs were able to repress ARF activity in both yeast and plants. This systematic, quantitative structure-function analysis identified a minimal complex—comprising a single Aux/IAA repressing a pair of dimerized ARFs—sufficient for auxin-induced transcription.

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AINTEGUMENTA negatively regulates age-dependent leaf senescence downstream of AUXIN RESPONSE FACTOR 2 in Arabidopsis thaliana

Plant Biotechnology ◽

10.5511/plantbiotechnology.16.0222a ◽

2016 ◽

Vol 33 (2) ◽

pp. 71-76 ◽

Cited By ~ 8

Author(s):

Guanping Feng ◽

Qiang Xu ◽

Zhenyang Wang ◽

Qiangjiu Zhuoma

Keyword(s):

Arabidopsis Thaliana ◽

Leaf Senescence ◽

Auxin Response Factor ◽

Response Factor ◽

Auxin Response ◽

Age Dependent

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Blue light alters miR167 expression and microRNA-targeted auxin response factor genes in Arabidopsis thaliana plants

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2016.03.018 ◽

2016 ◽

Vol 104 ◽

pp. 146-154 ◽

Cited By ~ 12

Author(s):

Pavel P. Pashkovskiy ◽

Alexander V. Kartashov ◽

Ilya E. Zlobin ◽

Sergei I. Pogosyan ◽

Vladimir V. Kuznetsov

Keyword(s):

Arabidopsis Thaliana ◽

Blue Light ◽

Auxin Response Factor ◽

Response Factor ◽

Auxin Response

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Four AUXIN RESPONSE FACTOR genes downregulated by microRNA167 are associated with growth and development in Oryza sativa

Functional Plant Biology ◽

10.1071/fp12106 ◽

2012 ◽

Vol 39 (9) ◽

pp. 736 ◽

Cited By ~ 24

Author(s):

Hai Liu ◽

Shenghua Jia ◽

Defeng Shen ◽

Jin Liu ◽

Jie Li ◽

...

Keyword(s):

Transgenic Rice ◽

Growth And Development ◽

Target Genes ◽

High Efficiency ◽

Developmental Process ◽

Auxin Response Factor ◽

Response Factor ◽

Mrna Levels ◽

Auxin Response

MicroRNA167 (miR167), as a conserved miRNA, has been implicated in auxin signalling by regulating the expression of certain auxin response factor (ARF) genes to determine the plant developmental process. Among the 10 MIR167 genes of rice, the precursor structures derived from MIR167a, MIR167b and MIR167c produce miR167 with high efficiency. To explore the biological function of miR167 in rice, four of its predicted target genes, OsARF6, OsARF12, OsARF17 and OsARF25, were identified in vivo. Although the expression levels of miR167 and its target OsARFs did not show an obvious negative correlation, the enhanced miR167 level in transgenic rice overexpressing miR167 resulted in a substantial decrease in mRNA levels of the four OsARF genes. Moreover, the transgenic rice plants were small in stature with remarkably reduced tiller number. These results suggest that miR167 is important for the appropriate expression of at least four OsARFs, which mediate the auxin response, to contribute to the normal growth and development of rice.

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