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IBR3, a novel peroxisomal acyl-CoA dehydrogenase-like protein required for indole-3-butyric acid response

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Abstract

Indole-3-butyric acid (IBA) is an endogenous auxin that acts in Arabidopsis primarily via its conversion to the principal auxin indole-3-acetic acid (IAA). Genetic and biochemical evidence indicates that this conversion is similar to peroxisomal fatty acid β-oxidation, but the specific enzymes catalyzing IBA β-oxidation have not been identified. We identified an IBA-response mutant (ibr3) with decreased responses to the inhibitory effects of IBA on root elongation or the stimulatory effects of IBA on lateral root formation. However, ibr3 mutants respond normally to other forms of auxin, including IAA. The mutant seedlings germinate and develop normally, even in the absence of sucrose, suggesting that fatty acid β-oxidation is unaffected. Additionally, double mutants between ibr3 and acx3, which is defective in an acyl-CoA oxidase acting in fatty acid β-oxidation, have enhanced IBA resistance, consistent with a distinct role for IBR3. Positional cloning revealed that IBR3 encodes a putative acyl-CoA dehydrogenase with a consensus peroxisomal targeting signal. Based on the singular defect of this mutant in responding to IBA, we propose that IBR3 may act directly in the oxidation of IBA to IAA.

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Abbreviations

2,4-D:

2,4-Dichlorophenoxyacetic acid

2,4-DB:

2,4-Dichlorophenoxybutyric acid

ACAD:

Acyl-CoA dehydrogenase

ACX:

Acyl-CoA oxidase

APH:

Aminoglycoside phosphotransferase

IAA:

Indole-3-acetic acid

IBA:

Indole-3-butyric acid

IBR:

IBA-response

IVD:

Isovaleryl-CoA dehydrogenase

JA:

Jasmonic acid

NAA:

1-Naphthaleneacetic acid

PEX:

Peroxin

PTS1:

Peroxisomal targeting signal type 1

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Acknowledgments

We thank the ABRC at Ohio State University for seeds, the Salk Institute Genomic Analysis Laboratory for the sequence-indexed Arabidopsis T-DNA insertion mutants, the RIKEN BioResource Center for the full-length IBR3 cDNA clone R18687, and André Andalcio for preliminary mapping of ibr3–11. We are grateful to Naxhiely Martinez, Melanie Monroe-Augustus, Jeanne Rasbery, and Lucia Strader for critical comments on the manuscript. This work was supported by the University of Missouri-St Louis start-up funds, the University of Missouri Research Board, the National Science Foundation (IBN-0315596), and the Robert A. Welch Foundation (C-1309).

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  1. Department of Biology, University of Missouri-St Louis, One University Boulevard, R223 Research Building, St Louis, MO, 63121, USA

    Bethany K. Zolman & Michelle Nyberg

  2. Department of Biochemistry and Cell Biology, Rice University, Houston, TX, USA

    Bonnie Bartel

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  1. Bethany K. Zolman
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Correspondence to Bethany K. Zolman.

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ACAD domain alignment of IBR3 and IBR3 homologs. IBR3 was compared to similar proteins from Arabidopsis (At), rice (Os), chicken (Gg), humans (Hs), Tetrahymena (Tt), mouse (Mm), Caenorhabditis elegans (Ce), rat (Rn), pig (Ss), and the bacterium Megasphaera elsdenii (Me), using only the ACAD domain for the multidomain proteins and the ACAD domain without the predicted mitochondrial targeting sequences for the other proteins (IVD, SCAD, and MCAD). The alignment was generated in the MegAlign program (DNAStar) using the Clustal W method. Amino acid residues identical in at least seven sequences are shaded in black; chemically similar amino acids are shaded in grey. Hyphens indicate gaps introduced to maximize alignment. The locations of the mutations in ibr3-1 and ibr3-2 are indicated above the sequence by arrows, and the catalytic glutamate residues in Ss MCAD and Hs IVD (Kim and Miura 2004) are indicated below the sequence. This alignment was used to generate the phylogenetic tree shown in Figure 7 (DOC 20 kb)

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Zolman, B.K., Nyberg, M. & Bartel, B. IBR3, a novel peroxisomal acyl-CoA dehydrogenase-like protein required for indole-3-butyric acid response. Plant Mol Biol 64, 59–72 (2007). https://doi.org/10.1007/s11103-007-9134-2

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