The auxin response factor gene family in allopolyploid Brassica napus.

Jing Wen,Pengcheng Guo,Pengfeng Li,Yunwen Wu,Mangmang Wang,Jiana Li,Mingming Liu,Hai Du,Feng Ran,Yunzhuo Ke

doi:10.1371/journal.pone.0214885

Abstract

Auxin response factor (ARF) is a member of the plant-specific B3 DNA binding superfamily. Here, we report the results of a comprehensive analysis of ARF genes in allotetraploid Brassica napus (2n = 38, AACC). Sixty-seven ARF genes were identified in B. napus (BnARFs) and divided into four subfamilies (I–IV). Sixty-one BnARFs were distributed on all chromosomes except C02; the remaining were on Ann and Cnn. The full length of the BnARF proteins was highly conserved especially within each subfamily with all members sharing the N-terminal DNA binding domain (DBD) and the middle region (MR), and most contained the C-terminal dimerization domain (PBI). Twenty-one members had a glutamine-rich MR that may be an activator and the remaining were repressors. Accordingly, the intron patterns are highly conserved in each subfamily or clade, especially in DBD and PBI domains. Several members in subfamily III are potential targets for miR167. Many putative cis-elements involved in phytohormones, light signaling responses, and biotic and abiotic stress were identified in BnARF promoters, implying their possible roles. Most ARF proteins are likely to interact with auxin/indole-3-acetic acid (Aux/IAA) -related proteins, and members from different subfamilies generally shared many common interaction proteins. Whole genome-wide duplication (WGD) by hybridization between Brassica rapa and Brassica oleracea and segmental duplication led to gene expansion. Gene loss following WGD is biased with the An-subgenome retaining more ancestral genes than the Cn-subgenome. BnARFs have wide expression profiles across vegetative and reproductive organs during different developmental stages. No obvious expression bias was observed between An- and Cn-subgenomes. Most synteny-pair genes had similar expression patterns, indicating their functional redundancy. BnARFs were sensitive to exogenous IAA and 6-BA treatments especially subfamily III. The present study provides insights into the distribution, phylogeny, and evolution of ARF gene family.

Highlights

Auxin response factors (ARF) are a group of transcription factors generally consisting of an Nterminal DNA-binding domain (DBD), a middle region (MR), and a C-terminal dimerization domain (PBI) [1,2]
A total of 67 BnARFs were identified in the B. napus genome, consisting of 62 typical ARF genes with a complete open reading frame (ORF) and five putative genes with short fragment deletions in the BDs (BnaC03g57150D, BnaAnng13910D, BnaC09g52440D, BnaC09g23080D, and BnaA06g14090D)
As ARF genes are well-known for their roles in the auxin-response process, which is important for root development, we explored the expression patterns of BnARFs in B. napus roots under five exogenous hormone treatments (IAA, ACC, abscisic acid (ABA), GA3, and 6-BA) (Fig 7)

Summary

Introduction

Auxin response factors (ARF) are a group of transcription factors generally consisting of an Nterminal DNA-binding domain (DBD), a middle region (MR), and a C-terminal dimerization domain (PBI) [1,2]. The DBD of ARFs fulfills a critical role for a transcription factor: recognition of a DNA motif, called the auxin-responsive element (AuxRE). The PBI consists of domain III and domain IV. The N-terminal III region consists of an antiparallel β-sheet (β1–β2) and α1. The C-terminal IV region contains a second antiparallel β-sheet (β3–β5) and two α-helices (α2 and α3). The PBI domain is the most optional one and is similar to motifs III and IV of the Aux/IAA protein family [4], which is not present in certain ARF proteins such as AtARF3 and AtARF17 [5,6]. Transient expression assays and domain swaps have demonstrated that each of the three domains can act in isolation [2]

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Discussion

Conclusion