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PMID: 17277896 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Plant molecular biology ·Vol. 64 ·No. 1-2 ·2007-05-00 ·Pages 59-72

Zolman BK, Nyberg M, Bartel B

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 beta-oxidation, but the specific enzymes catalyzing IBA beta-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 beta-oxidation is unaffected. Additionally, double mutants between ibr3 and acx3, which is defective in an acyl-CoA oxidase acting in fatty acid beta-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.

MeSH Terms
Acyl-CoA Dehydrogenase/chemistry,genetics,physiology Acyl-CoA Oxidase/genetics Amino Acid Sequence Arabidopsis/enzymology,genetics,metabolism Arabidopsis Proteins/chemistry,genetics,physiology Butyrates/metabolism Cloning, Molecular Indoleacetic Acids/metabolism Molecular Sequence Data Mutation Peroxisomes/physiology Phylogeny Sequence Alignment
Chemicals
Arabidopsis Proteins Butyrates Indoleacetic Acids indoleacetic acid ACX3 protein, Arabidopsis Acyl-CoA Oxidase Acyl-CoA Dehydrogenase IBR3 protein, Arabidopsis
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Zolman Bethany K
Department of Biology, University of Missouri-St Louis, One University Boulevard, R223 Research Building, St Louis, MO 63121, USA. [email protected]
Nyberg Michelle
Bartel Bonnie
References (72)
72 references, click to expand
  1. High efficiency Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana leaf and cotyledon explants.
    Plant Cell Rep. 1988 Dec;7(7):583-6 PMID: 24240423
  2. The mitochondrial isovaleryl-coenzyme a dehydrogenase of arabidopsis oxidizes intermediates of leucine and valine catabolism.
    Plant Physiol. 2001 Jun;126(2):601-12 PMID: 11402190
  3. Genetic analysis of variation for auxin-induced adventitious root formation among eighteen ecotypes of Arabidopsis thaliana L. Heynh.
    J Hered. 1998 Nov-Dec;89(6):481-7 PMID: 9864859
  4. Genome-wide insertional mutagenesis of Arabidopsis thaliana.
    Science. 2003 Aug 1;301(5633):653-7 PMID: 12893945
  5. 2,4-Dichlorophenoxybutyric acid-resistant mutants of Arabidopsis have defects in glyoxysomal fatty acid beta-oxidation.
    Plant Cell. 1998 Feb;10(2):183-95 PMID: 9490742
  6. Postgerminative growth and lipid catabolism in oilseeds lacking the glyoxylate cycle.
    Proc Natl Acad Sci U S A. 2000 May 9;97(10):5669-74 PMID: 10805817
  7. The Arabidopsis thaliana multifunctional protein gene (MFP2) of peroxisomal beta-oxidation is essential for seedling establishment.
    Plant J. 2006 Mar;45(6):930-41 PMID: 16507084
  8. The Arabidopsis pxa1 mutant is defective in an ATP-binding cassette transporter-like protein required for peroxisomal fatty acid beta-oxidation.
    Plant Physiol. 2001 Nov;127(3):1266-78 PMID: 11706205
  9. Peroxisomal Acyl-CoA synthetase activity is essential for seedling development in Arabidopsis thaliana.
    Plant Cell. 2004 Feb;16(2):394-405 PMID: 14742880
  10. Arabidopsis mutants in short- and medium-chain acyl-CoA oxidase activities accumulate acyl-CoAs and reveal that fatty acid beta-oxidation is essential for embryo development.
    J Biol Chem. 2003 Jun 13;278(24):21370-7 PMID: 12682048
  11. No induction of beta-oxidation in leaves of Arabidopsis that over-produce lauric acid.
    Planta. 1999 Jan;207(3):385-92 PMID: 9951734
  12. Changes in targeting efficiencies of proteins to plant microbodies caused by amino acid substitutions in the carboxy-terminal tripeptide.
    Plant Cell Physiol. 1997 Jun;38(6):759-68 PMID: 9249991
  13. High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper.
    Plant J. 1998 Sep;15(5):707-20 PMID: 9778851
  14. A library of Arabidopsis 35S-cDNA lines for identifying novel mutants.
    Plant Mol Biol. 2001 Aug;46(6):695-703 PMID: 11575724
  15. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana.
    Plant J. 1998 Dec;16(6):735-43 PMID: 10069079
  16. Activation tagging in Arabidopsis.
    Plant Physiol. 2000 Apr;122(4):1003-13 PMID: 10759496
  17. Functional analysis of methylthioribose kinase genes in plants.
    Plant Physiol. 2004 Dec;136(4):4061-71 PMID: 15557090
  18. Analysis of indole-3-butyric acid-induced adventitious root formation on Arabidopsis stem segments.
    J Exp Bot. 2005 Aug;56(418):2095-105 PMID: 15955788
  19. AtPex14p maintains peroxisomal functions by determining protein targeting to three kinds of plant peroxisomes.
    EMBO J. 2000 Nov 1;19(21):5701-10 PMID: 11060021
  20. Functional differentiation of peroxisomes revealed by expression profiles of peroxisomal genes in Arabidopsis thaliana.
    Plant Cell Physiol. 2003 Dec;44(12):1275-89 PMID: 14701923
  21. AraPerox. A database of putative Arabidopsis proteins from plant peroxisomes.
    Plant Physiol. 2004 Sep;136(1):2587-608 PMID: 15333753
  22. Molecular characterization of a glyoxysomal long chain acyl-CoA oxidase that is synthesized as a precursor of higher molecular mass in pumpkin.
    J Biol Chem. 1998 Apr 3;273(14):8301-7 PMID: 9525937
  23. Mutations in Arabidopsis acyl-CoA oxidase genes reveal distinct and overlapping roles in beta-oxidation.
    Plant J. 2005 Mar;41(6):859-74 PMID: 15743450
  24. Auxin: regulation, action, and interaction.
    Ann Bot. 2005 Apr;95(5):707-35 PMID: 15749753
  25. Jasmonic acid levels are reduced in COMATOSE ATP-binding cassette transporter mutants. Implications for transport of jasmonate precursors into peroxisomes.
    Plant Physiol. 2005 Mar;137(3):835-40 PMID: 15761209
  26. Controlling electron transfer in Acyl-CoA oxidases and dehydrogenases: a structural view.
    J Biol Chem. 2006 Oct 13;281(41):31012-20 PMID: 16887802
  27. Cloning and characterization of a human cDNA ACAD10 mapped to chromosome 12q24.1.
    Mol Biol Rep. 2004 Sep;31(3):191-5 PMID: 15560374
  28. Acyl-CoA dehydrogenases. A mechanistic overview.
    Eur J Biochem. 2004 Feb;271(3):494-508 PMID: 14728676
  29. Sucrose rescues seedling establishment but not germination of Arabidopsis mutants disrupted in peroxisomal fatty acid catabolism.
    Plant J. 2005 Sep;43(6):861-72 PMID: 16146525
  30. Arabidopsis contains a large superfamily of acyl-activating enzymes. Phylogenetic and biochemical analysis reveals a new class of acyl-coenzyme a synthetases.
    Plant Physiol. 2003 Jun;132(2):1065-76 PMID: 12805634
  31. Biosynthesis, conjugation, catabolism and homeostasis of indole-3-acetic acid in Arabidopsis thaliana.
    Plant Mol Biol. 2002 Sep;50(2):309-32 PMID: 12175022
  32. Aminoglycoside antibiotic phosphotransferases are also serine protein kinases.
    Chem Biol. 1999 Jan;6(1):11-8 PMID: 9889150
  33. Long-chain acyl-CoA oxidases of Arabidopsis.
    Plant J. 1999 Oct;20(1):1-13 PMID: 10571860
  34. Facile transformation of Arabidopsis.
    Plant Cell Rep. 1991 Aug;10(5):235-9 PMID: 24221586
  35. Chewing the fat: beta-oxidation in signalling and development.
    Trends Plant Sci. 2006 Mar;11(3):124-32 PMID: 16490379
  36. Ped3p is a peroxisomal ATP-binding cassette transporter that might supply substrates for fatty acid beta-oxidation.
    Plant Cell Physiol. 2002 Jan;43(1):1-11 PMID: 11828016
  37. Control of germination and lipid mobilization by COMATOSE, the Arabidopsis homologue of human ALDP.
    EMBO J. 2002 Jun 17;21(12):2912-22 PMID: 12065405
  38. Structure of an enzyme required for aminoglycoside antibiotic resistance reveals homology to eukaryotic protein kinases.
    Cell. 1997 Jun 13;89(6):887-95 PMID: 9200607
  39. A pathway for lateral root formation in Arabidopsis thaliana.
    Genes Dev. 1995 Sep 1;9(17):2131-42 PMID: 7657165
  40. A family of auxin-conjugate hydrolases that contributes to free indole-3-acetic acid levels during Arabidopsis germination.
    Plant Physiol. 2004 Jun;135(2):978-88 PMID: 15155875
  41. Arabidopsis contains nine long-chain acyl-coenzyme a synthetase genes that participate in fatty acid and glycerolipid metabolism.
    Plant Physiol. 2002 Aug;129(4):1710-22 PMID: 12177484
  42. Identification and functional characterization of Arabidopsis PEROXIN4 and the interacting protein PEROXIN22.
    Plant Cell. 2005 Dec;17(12):3422-35 PMID: 16272432
  43. beta-hydroxyisobutyryl coenzyme A deacylase deficiency: a defect in valine metabolism associated with physical malformations.
    Pediatrics. 1982 Oct;70(4):532-8 PMID: 7122152
  44. A novel acyl-CoA oxidase that can oxidize short-chain acyl-CoA in plant peroxisomes.
    J Biol Chem. 1999 Apr 30;274(18):12715-21 PMID: 10212254
  45. Requirement for 3-ketoacyl-CoA thiolase-2 in peroxisome development, fatty acid beta-oxidation and breakdown of triacylglycerol in lipid bodies of Arabidopsis seedlings.
    Plant J. 2001 Oct;28(1):1-12 PMID: 11696182
  46. The metabolism of 3-indolylalkanecarboxylic acids, and their amides, nitriles and methyl esters in plant tissues.
    Proc R Soc Lond B Biol Sci. 1960 May 17;152:231-54 PMID: 13849765
  47. Identification and analysis of the plant peroxisomal targeting signal 1 receptor NtPEX5.
    Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):13336-41 PMID: 9789089
  48. age Mutants of Arabidopsis exhibit altered auxin-regulated gene expression.
    Plant Cell. 1998 Oct;10(10):1649-62 PMID: 9761792
  49. Functional annotation of a full-length Arabidopsis cDNA collection.
    Science. 2002 Apr 5;296(5565):141-5 PMID: 11910074
  50. Preventing photochemistry in culture media by long-pass light filters alters growth of cultured tissues.
    Plant Physiol. 1990 Aug;93(4):1365-9 PMID: 16667626
  51. Role of beta-oxidation in jasmonate biosynthesis and systemic wound signaling in tomato.
    Plant Cell. 2005 Mar;17(3):971-86 PMID: 15722469
  52. Lateral root initiation or the birth of a new meristem.
    Plant Mol Biol. 2006 Apr;60(6):871-87 PMID: 16724258
  53. ACX3, a novel medium-chain acyl-coenzyme A oxidase from Arabidopsis.
    Plant Physiol. 2000 Jun;123(2):733-42 PMID: 10859203
  54. Acyl-CoA dehydrogenases and acyl-CoA oxidases. Structural basis for mechanistic similarities and differences.
    Eur J Biochem. 2004 Feb;271(3):483-93 PMID: 14728675
  55. A knowledge base for predicting protein localization sites in eukaryotic cells.
    Genomics. 1992 Dec;14(4):897-911 PMID: 1478671
  56. chy1, an Arabidopsis mutant with impaired beta-oxidation, is defective in a peroxisomal beta-hydroxyisobutyryl-CoA hydrolase.
    J Biol Chem. 2001 Aug 17;276(33):31037-46 PMID: 11404361
  57. A defect in beta-oxidation causes abnormal inflorescence development in Arabidopsis.
    Plant Cell. 1999 Oct;11(10):1911-24 PMID: 10521521
  58. Aminoglycoside phosphotransferases: proteins, structure, and mechanism.
    Front Biosci. 1999 Jan 01;4:D9-21 PMID: 9872733
  59. Genetic analysis of indole-3-butyric acid responses in Arabidopsis thaliana reveals four mutant classes.
    Genetics. 2000 Nov;156(3):1323-37 PMID: 11063705
  60. CD-Search: protein domain annotations on the fly.
    Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31 PMID: 15215404
  61. Fatty acid-derived signals in plants.
    Trends Plant Sci. 2002 May;7(5):217-24 PMID: 11992827
  62. Pathways of straight and branched chain fatty acid catabolism in higher plants.
    Prog Lipid Res. 2002 Mar;41(2):156-81 PMID: 11755682
  63. Aminoglycoside-modifying enzymes: mechanisms of catalytic processes and inhibition.
    Drug Resist Updat. 2001 Apr;4(2):106-17 PMID: 11512519
  64. The growth regulating activity of certain omega-substituted alkyl carboxylic acids in relation to their beta-oxidation within the plant.
    Proc R Soc Lond B Biol Sci. 1954 Sep 27;142(909):525-36 PMID: 13215509
  65. Specification of the peroxisome targeting signals type 1 and type 2 of plant peroxisomes by bioinformatics analyses.
    Plant Physiol. 2004 Jun;135(2):783-800 PMID: 15208424
  66. The multifunctional protein AtMFP2 is co-ordinately expressed with other genes of fatty acid beta-oxidation during seed germination in Arabidopsis thaliana (L.) Heynh.
    Biochem Soc Trans. 2000 Feb;28(2):95-9 PMID: 10816107
  67. An Arabidopsis indole-3-butyric acid-response mutant defective in PEROXIN6, an apparent ATPase implicated in peroxisomal function.
    Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1786-91 PMID: 14745029
  68. In plants a putative isovaleryl-CoA-dehydrogenase is located in mitochondria.
    Plant Mol Biol. 1999 Apr;39(6):1275-82 PMID: 10380813
  69. Promoter trapping of a novel medium-chain acyl-CoA oxidase, which is induced transcriptionally during Arabidopsis seed germination.
    J Biol Chem. 2000 Nov 3;275(44):34375-81 PMID: 10918060
  70. SMART 5: domains in the context of genomes and networks.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D257-60 PMID: 16381859
  71. Two long-chain acyl-CoA synthetases from Arabidopsis thaliana involved in peroxisomal fatty acid beta-oxidation.
    Plant J. 2002 Oct;32(1):93-103 PMID: 12366803
  72. An Arabidopsis mutant disrupted in valine catabolism is also compromised in peroxisomal fatty acid beta-oxidation.
    FEBS Lett. 2004 Jul 30;571(1-3):147-53 PMID: 15280033
Article Info
Journal
Plant molecular biology
Abbr.
Plant Mol Biol
ISSN
0167-4412
DOI
10.1007/s11103-007-9134-2
Email
[email protected]
Published
2007-05-00
Epub
2007-00-03
Pages
59-72
Language
English
Region
Netherlands
NLM ID
9106343
Subset
IM
External Links
PubMed source DOI: 10.1007/s11103-007-9134-2 View journal details
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