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Dash L, Swaminathan S, Šimura J, Gonzales CLP, Montes C, Solanki N, Mejia L, Ljung K, Zabotina OA, Kelley DR. Changes in cell wall composition due to a pectin biosynthesis enzyme GAUT10 impact root growth. PLANT PHYSIOLOGY 2023; 193:2480-2497. [PMID: 37606259 PMCID: PMC10663140 DOI: 10.1093/plphys/kiad465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/23/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) root development is regulated by multiple dynamic growth cues that require central metabolism pathways such as β-oxidation and auxin. Loss of the pectin biosynthesizing enzyme GALACTURONOSYLTRANSFERASE 10 (GAUT10) leads to a short-root phenotype under sucrose-limited conditions. The present study focused on determining the specific contributions of GAUT10 to pectin composition in primary roots and the underlying defects associated with gaut10 roots. Using live-cell microscopy, we determined reduced root growth in gaut10 is due to a reduction in both root apical meristem size and epidermal cell elongation. In addition, GAUT10 was required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Specifically, loss of GAUT10 led to a reduction in galacturonic acid and xylose in root cell walls and altered the presence of rhamnogalacturonan-I (RG-I) and homogalacturonan (HG) polymers in the root. Transcriptomic analysis of gaut10 roots compared to wild type uncovered hundreds of genes differentially expressed in the mutant, including genes related to auxin metabolism and peroxisome function. Consistent with these results, both auxin signaling and metabolism were modified in gaut10 roots. The sucrose-dependent short-root phenotype in gaut10 was linked to β-oxidation based on hypersensitivity to indole-3-butyric acid (IBA) and an epistatic interaction with TRANSPORTER OF IBA1 (TOB1). Altogether, these data support a growing body of evidence suggesting that pectin composition may influence auxin pathways and peroxisome activity.
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Affiliation(s)
- Linkan Dash
- Department of Genetics, Development and Cell Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Sivakumar Swaminathan
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Jan Šimura
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå 901 83, Sweden
| | - Caitlin Leigh P Gonzales
- Department of Genetics, Development and Cell Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Iowa City, IA 50011, USA
| | - Neel Solanki
- Department of Genetics, Development and Cell Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Ludvin Mejia
- Department of Genetics, Development and Cell Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå 901 83, Sweden
| | - Olga A Zabotina
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Iowa City, IA 50011, USA
| | - Dior R Kelley
- Department of Genetics, Development and Cell Biology, Iowa State University, Iowa City, IA 50011, USA
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Robin AHK, Saha G, Laila R, Park JI, Kim HT, Nou IS. Expression and Role of Biosynthetic, Transporter, Receptor, and Responsive Genes for Auxin Signaling during Clubroot Disease Development. Int J Mol Sci 2020; 21:ijms21155554. [PMID: 32756478 PMCID: PMC7432499 DOI: 10.3390/ijms21155554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 01/07/2023] Open
Abstract
Auxins play a pivotal role in clubroot development caused by the obligate biotroph Plasmodiophora brassicae. In this study, we investigated the pattern of expression of 23 genes related to auxin biosynthesis, reception, and transport in Chinese cabbage (Brassica rapa) after inoculation with P. brassicae. The predicted proteins identified, based on the 23 selected auxin-related genes, were from protein kinase, receptor kinase, auxin responsive, auxin efflux carrier, transcriptional regulator, and the auxin-repressed protein family. These proteins differed in amino acids residue, molecular weights, isoelectric points, chromosomal location, and subcellular localization. Leaf and root tissues showed dynamic and organ-specific variation in expression of auxin-related genes. The BrGH3.3 gene, involved in auxin signaling, exhibited 84.4-fold increase in expression in root tissues compared to leaf tissues as an average of all samples. This gene accounted for 4.8-, 2.6-, and 5.1-fold higher expression at 3, 14, and 28 days post inoculation (dpi) in the inoculated root tissues compared to mock-treated roots. BrNIT1, an auxin signaling gene, and BrPIN1, an auxin transporter, were remarkably induced during both cortex infection at 14 dpi and gall formation at 28 dpi. BrDCK1, an auxin receptor, was upregulated during cortex infection at 14 dpi. The BrLAX1 gene, associated with root hair development, was induced at 1 dpi in infected roots, indicating its importance in primary infection. More interestingly, a significantly higher expression of BrARP1, an auxin-repressed gene, at both the primary and secondary phases of infection indicated a dynamic response of the host plant towards its resistance against P. brassicae. The results of this study improve our current understanding of the role of auxin-related genes in clubroot disease development.
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Affiliation(s)
- Arif Hasan Khan Robin
- Department of Horticulture, Sunchon National University, Suncheon 57922, Korea; (A.H.K.R.); (G.S.); (R.L.); (J.-I.P.); (H.-T.K.)
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 02202, Bangladesh
| | - Gopal Saha
- Department of Horticulture, Sunchon National University, Suncheon 57922, Korea; (A.H.K.R.); (G.S.); (R.L.); (J.-I.P.); (H.-T.K.)
- Department of Agronomy, Patuakhali Science and Technology University, Patuakhali 8602, Bangladesh
| | - Rawnak Laila
- Department of Horticulture, Sunchon National University, Suncheon 57922, Korea; (A.H.K.R.); (G.S.); (R.L.); (J.-I.P.); (H.-T.K.)
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon 57922, Korea; (A.H.K.R.); (G.S.); (R.L.); (J.-I.P.); (H.-T.K.)
| | - Hoy-Taek Kim
- Department of Horticulture, Sunchon National University, Suncheon 57922, Korea; (A.H.K.R.); (G.S.); (R.L.); (J.-I.P.); (H.-T.K.)
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon 57922, Korea; (A.H.K.R.); (G.S.); (R.L.); (J.-I.P.); (H.-T.K.)
- Correspondence: ; Tel.: +82-617-503-249
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Katz E, Bagchi R, Jeschke V, Rasmussen ARM, Hopper A, Burow M, Estelle M, Kliebenstein DJ. Diverse Allyl Glucosinolate Catabolites Independently Influence Root Growth and Development. PLANT PHYSIOLOGY 2020; 183:1376-1390. [PMID: 32321840 PMCID: PMC7333702 DOI: 10.1104/pp.20.00170] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/30/2020] [Indexed: 05/15/2023]
Abstract
Glucosinolates (GSLs) are sulfur-containing defense metabolites produced in the Brassicales, including the model plant Arabidopsis (Arabidopsis thaliana). Previous work suggests that specific GSLs may function as signals to provide direct feedback regulation within the plant to calibrate defense and growth. These GSLs include allyl-GSL, a defense metabolite that is one of the most widespread GSLs in Brassicaceae and has also been associated with growth inhibition. Here we show that at least three separate potential catabolic products of allyl-GSL or closely related compounds affect growth and development by altering different mechanisms influencing plant development. Two of the catabolites, raphanusamic acid and 3-butenoic acid, differentially affect processes downstream of the auxin signaling cascade. Another catabolite, acrylic acid, affects meristem development by influencing the progression of the cell cycle. These independent signaling events propagated by the different catabolites enable the plant to execute a specific response that is optimal to any given environment.
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Affiliation(s)
- Ella Katz
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Rammyani Bagchi
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093
| | - Verena Jeschke
- DynaMo Center of Excellence, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
| | | | - Aleshia Hopper
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Meike Burow
- DynaMo Center of Excellence, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
| | - Mark Estelle
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, California 95616
- DynaMo Center of Excellence, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
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Plant nitrilase: a new job for an old enzyme. Biochem J 2019; 476:1105-1107. [PMID: 30971459 DOI: 10.1042/bcj20190060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 11/17/2022]
Abstract
Nitrilases are versatile enzymes that hydrolyze nitriles to carboxylic acids and ammonia, but many members of this family lack defined biological functions. In plants, nitrilases have been associated with detoxification of cyanide-containing compounds and auxin biosynthesis; however, recent work suggests that the chemical versatility of these proteins contributes to metabolite repair. In this issue of the Biochemical Journal, Niehaus et al. demonstrate that the Nit1 nitrilase from Arabidopsis thaliana functions as a metabolite repair enzyme that removes deaminated glutathione from the cytoplasm and plastids.
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Günther J, Irmisch S, Lackus ND, Reichelt M, Gershenzon J, Köllner TG. The nitrilase PtNIT1 catabolizes herbivore-induced nitriles in Populus trichocarpa. BMC PLANT BIOLOGY 2018; 18:251. [PMID: 30348089 PMCID: PMC6196558 DOI: 10.1186/s12870-018-1478-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 10/10/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Nitrilases are nitrile-converting enzymes commonly found within the plant kingdom that play diverse roles in nitrile detoxification, nitrogen recycling, and phytohormone biosynthesis. Although nitrilases are present in all higher plants, little is known about their function in trees. Upon herbivory, poplars produce considerable amounts of toxic nitriles such as benzyl cyanide, 2-methylbutyronitrile, and 3-methylbutyronitrile. In addition, as byproduct of the ethylene biosynthetic pathway upregulated in many plant species after herbivory, toxic β-cyanoalanine may accumulate in damaged poplar leaves. In this work, we studied the nitrilase gene family in Populus trichocarpa and investigated the potential role of the nitrilase PtNIT1 in the catabolism of herbivore-induced nitriles. RESULTS A BLAST analysis revealed three putative nitrilase genes (PtNIT1, PtNIT2, PtNIT3) in the genome of P. trichocarpa. While PtNIT1 was expressed in poplar leaves and showed increased transcript accumulation after leaf herbivory, PtNIT2 and PtNIT3 appeared not to be expressed in undamaged or herbivore-damaged leaves. Recombinant PtNIT1 produced in Escherichia coli accepted biogenic nitriles such as β-cyanoalanine, benzyl cyanide, and indole-3-acetonitrile as substrates in vitro and converted them into the corresponding acids. In addition to this nitrilase activity, PtNIT1 showed nitrile hydratase activity towards β-cyanoalanine, resulting in the formation of the amino acid asparagine. The kinetic parameters of PtNIT1 suggest that the enzyme utilizes β-cyanoalanine and benzyl cyanide as substrates in vivo. Indeed, β-cyanoalanine and benzyl cyanide were found to accumulate in herbivore-damaged poplar leaves. The upregulation of ethylene biosynthesis genes after leaf herbivory indicates that herbivore-induced β-cyanoalanine accumulation is likely caused by ethylene formation. CONCLUSIONS Our data suggest a role for PtNIT1 in the catabolism of herbivore-induced β-cyanoalanine and benzyl cyanide in poplar leaves.
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Affiliation(s)
- Jan Günther
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
| | - Sandra Irmisch
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
- Present Address: Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Nathalie D. Lackus
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
| | - Michael Reichelt
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
| | - Tobias G. Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
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Urbancsok J, Bones AM, Kissen R. Benzyl Cyanide Leads to Auxin-Like Effects Through the Action of Nitrilases in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:1240. [PMID: 30197652 PMCID: PMC6117430 DOI: 10.3389/fpls.2018.01240] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/06/2018] [Indexed: 05/19/2023]
Abstract
Plants within the Brassicales order generate glucosinolate hydrolysis products that can exert different biological effects on several organisms. Here, we evaluated the physiological effects of one of these compounds, benzyl cyanide (phenylacetonitrile), when exogenously applied on Arabidopsis thaliana. Treatment with benzyl cyanide led to a dose-dependent reduction of primary root length and total biomass. Further morphological changes like elongated hypocotyls, epinastic cotyledons, and increased formation of adventitious roots resembled a severe auxin-overproducer phenotype. The elevated auxin response was confirmed by histochemical staining and gene expression analysis of auxin-responsive genes. Nitriles are converted by specific enzymes, nitrilases (NIT1-3), to their corresponding carboxylic acids. The nitrilase mutants nit1 and nit2 tolerated benzyl cyanide treatments better than the wild type, with nit2 being less resistant than nit1. A NIT2RNAi line suppressing several nitrilases was resistant to all tested benzyl cyanide concentrations. When exposed to phenylacetic acid (PAA) - the corresponding carboxylic acid of benzyl cyanide - wild type and mutant seedlings were, however, equally susceptible and showed a more severe auxin phenotype than upon cyanide treatment. Here, we demonstrate that the auxin-like effects triggered by benzyl cyanide on Arabidopsis are due to its nitrilase-mediated conversion to the natural auxin PAA.
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Affiliation(s)
| | | | - Ralph Kissen
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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Zidenga T, Siritunga D, Sayre RT. Cyanogen Metabolism in Cassava Roots: Impact on Protein Synthesis and Root Development. FRONTIERS IN PLANT SCIENCE 2017; 8:220. [PMID: 28286506 PMCID: PMC5323461 DOI: 10.3389/fpls.2017.00220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/06/2017] [Indexed: 05/14/2023]
Abstract
Cassava (Manihot esculenta Crantz), a staple crop for millions of sub-Saharan Africans, contains high levels of cyanogenic glycosides which protect it against herbivory. However, cyanogens have also been proposed to play a role in nitrogen transport from leaves to roots. Consistent with this hypothesis, analyses of the distribution and activities of enzymes involved in cyanide metabolism provides evidence for cyanide assimilation, derived from linamarin, into amino acids in cassava roots. Both β-cyanoalanine synthase (CAS) and nitrilase (NIT), two enzymes involved in cyanide assimilation to produce asparagine, were observed to have higher activities in roots compared to leaves, consistent with their proposed role in reduced nitrogen assimilation. In addition, rhodanese activity was not detected in cassava roots, indicating that this competing means for cyanide metabolism was not a factor in cyanide detoxification. In contrast, leaves had sufficient rhodanese activity to compete with cyanide assimilation into amino acids. Using transgenic low cyanogen plants, it was shown that reducing root cyanogen levels is associated with elevated root nitrate reductase activity, presumably to compensate for the loss of reduced nitrogen from cyanogens. Finally, we overexpressed Arabidopsis CAS and NIT4 genes in cassava roots to study the feasibility of enhancing root cyanide assimilation into protein. Optimal overexpression of CAS and NIT4 resulted in up to a 50% increase in root total amino acids and a 9% increase in root protein accumulation. However, plant growth and morphology was altered in plants overexpressing these enzymes, demonstrating a complex interaction between cyanide metabolism and hormonal regulation of plant growth.
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Affiliation(s)
- Tawanda Zidenga
- Bioscience Division, Los Alamos National Laboratory, Los AlamosNM, USA
| | - Dimuth Siritunga
- Department of Biology, University of Puerto Rico, MayaguezPR, USA
| | - Richard T. Sayre
- Bioscience Division, Los Alamos National Laboratory, Los AlamosNM, USA
- New Mexico Consortium, Los AlamosNM, USA
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Rehman HM, Shah ZH, Nawaz MA, Ahmad MQ, Yang SH, Kho KH, Chung G. RETRACTED ARTICLE: Beta-cyanoalanine synthase pathway as a homeostatic mechanism for cyanide detoxification as well as growth and development in higher plants. PLANTA 2017; 245:235. [PMID: 27744484 DOI: 10.1007/s00425-016-2606-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/09/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdul-Aziz University, Jeddah, 21577, Saudi Arabia
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 6000, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Kang Hee Kho
- Department of Aquatic Biology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea.
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Lehmann T, Janowitz T, Sánchez-Parra B, Alonso MMP, Trompetter I, Piotrowski M, Pollmann S. Arabidopsis NITRILASE 1 Contributes to the Regulation of Root Growth and Development through Modulation of Auxin Biosynthesis in Seedlings. FRONTIERS IN PLANT SCIENCE 2017. [PMID: 28174581 DOI: 10.3389/fpls.2017.00036.ecollection] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nitrilases consist of a group of enzymes that catalyze the hydrolysis of organic cyanides. They are found ubiquitously distributed in the plant kingdom. Plant nitrilases are mainly involved in the detoxification of ß-cyanoalanine, a side-product of ethylene biosynthesis. In the model plant Arabidopsis thaliana a second group of Brassicaceae-specific nitrilases (NIT1-3) has been found. This so-called NIT1-subfamily has been associated with the conversion of indole-3-acetonitrile (IAN) into the major plant growth hormone, indole-3-acetic acid (IAA). However, apart of reported functions in defense responses to pathogens and in responses to sulfur depletion, conclusive insight into the general physiological function of the NIT-subfamily nitrilases remains elusive. In this report, we test both the contribution of the indole-3-acetaldoxime (IAOx) pathway to general auxin biosynthesis and the influence of altered nitrilase expression on plant development. Apart of a comprehensive transcriptomics approach to explore the role of the IAOx route in auxin formation, we took a genetic approach to disclose the function of NITRILASE 1 (NIT1) of A. thaliana. We show that NIT1 over-expression (NIT1ox) results in seedlings with shorter primary roots, and an increased number of lateral roots. In addition, NIT1ox plants exhibit drastic changes of both free IAA and IAN levels, which are suggested to be the reason for the observed phenotype. On the other hand, NIT2RNAi knockdown lines, capable of suppressing the expression of all members of the NIT1-subfamily, were generated and characterized to substantiate the above-mentioned findings. Our results demonstrate for the first time that Arabidopsis NIT1 has profound effects on root morphogenesis in early seedling development.
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Affiliation(s)
- Thomas Lehmann
- Lehrstuhl für Pflanzenphysiologie Ruhr-Universität Bochum, Bochum, Germany
| | - Tim Janowitz
- Lehrstuhl für Pflanzenphysiologie Ruhr-Universität Bochum, Bochum, Germany
| | - Beatriz Sánchez-Parra
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Pozuelo de Alarcón, Spain
| | - Marta-Marina Pérez Alonso
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Pozuelo de Alarcón, Spain
| | - Inga Trompetter
- Lehrstuhl für Pflanzenphysiologie Ruhr-Universität Bochum, Bochum, Germany
| | - Markus Piotrowski
- Lehrstuhl für Pflanzenphysiologie Ruhr-Universität Bochum, Bochum, Germany
| | - Stephan Pollmann
- Lehrstuhl für PflanzenphysiologieRuhr-Universität Bochum, Bochum, Germany; Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Pozuelo de Alarcón, Spain
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Lehmann T, Janowitz T, Sánchez-Parra B, Alonso MMP, Trompetter I, Piotrowski M, Pollmann S. Arabidopsis NITRILASE 1 Contributes to the Regulation of Root Growth and Development through Modulation of Auxin Biosynthesis in Seedlings. FRONTIERS IN PLANT SCIENCE 2017; 8:36. [PMID: 28174581 PMCID: PMC5258727 DOI: 10.3389/fpls.2017.00036] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/09/2017] [Indexed: 05/20/2023]
Abstract
Nitrilases consist of a group of enzymes that catalyze the hydrolysis of organic cyanides. They are found ubiquitously distributed in the plant kingdom. Plant nitrilases are mainly involved in the detoxification of ß-cyanoalanine, a side-product of ethylene biosynthesis. In the model plant Arabidopsis thaliana a second group of Brassicaceae-specific nitrilases (NIT1-3) has been found. This so-called NIT1-subfamily has been associated with the conversion of indole-3-acetonitrile (IAN) into the major plant growth hormone, indole-3-acetic acid (IAA). However, apart of reported functions in defense responses to pathogens and in responses to sulfur depletion, conclusive insight into the general physiological function of the NIT-subfamily nitrilases remains elusive. In this report, we test both the contribution of the indole-3-acetaldoxime (IAOx) pathway to general auxin biosynthesis and the influence of altered nitrilase expression on plant development. Apart of a comprehensive transcriptomics approach to explore the role of the IAOx route in auxin formation, we took a genetic approach to disclose the function of NITRILASE 1 (NIT1) of A. thaliana. We show that NIT1 over-expression (NIT1ox) results in seedlings with shorter primary roots, and an increased number of lateral roots. In addition, NIT1ox plants exhibit drastic changes of both free IAA and IAN levels, which are suggested to be the reason for the observed phenotype. On the other hand, NIT2RNAi knockdown lines, capable of suppressing the expression of all members of the NIT1-subfamily, were generated and characterized to substantiate the above-mentioned findings. Our results demonstrate for the first time that Arabidopsis NIT1 has profound effects on root morphogenesis in early seedling development.
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Affiliation(s)
- Thomas Lehmann
- Lehrstuhl für PflanzenphysiologieRuhr-Universität Bochum, Bochum, Germany
| | - Tim Janowitz
- Lehrstuhl für PflanzenphysiologieRuhr-Universität Bochum, Bochum, Germany
| | - Beatriz Sánchez-Parra
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Pozuelo de Alarcón, Spain
| | - Marta-Marina Pérez Alonso
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Pozuelo de Alarcón, Spain
| | - Inga Trompetter
- Lehrstuhl für PflanzenphysiologieRuhr-Universität Bochum, Bochum, Germany
| | - Markus Piotrowski
- Lehrstuhl für PflanzenphysiologieRuhr-Universität Bochum, Bochum, Germany
| | - Stephan Pollmann
- Lehrstuhl für PflanzenphysiologieRuhr-Universität Bochum, Bochum, Germany
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Pozuelo de Alarcón, Spain
- *Correspondence: Stephan Pollmann
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Li A, Zhou M, Wei D, Chen H, You C, Lin J. Transcriptome Profiling Reveals the Negative Regulation of Multiple Plant Hormone Signaling Pathways Elicited by Overexpression of C-Repeat Binding Factors. FRONTIERS IN PLANT SCIENCE 2017; 8:1647. [PMID: 28983312 PMCID: PMC5613223 DOI: 10.3389/fpls.2017.01647] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 09/07/2017] [Indexed: 05/18/2023]
Abstract
C-repeat binding factors (CBF) are a subfamily of AP2 transcription factors that play critical roles in the regulation of plant cold tolerance and growth in low temperature. In the present work, we sought to perform a detailed investigation into global transcriptional regulation of plant hormone signaling associated genes in transgenic plants engineered with CBF genes. RNA samples from Arabidopsis thaliana plants overexpressing two CBF genes, CBF2 and CBF3, were subjected to Illumina HiSeq 2000 RNA sequencing (RNA-Seq). Our results showed that more than half of the hormone associated genes that were differentially expressed in CBF2 or CBF3 transgenic plants were related to auxin signal transduction and metabolism. Most of these alterations in gene expression could lead to repression of auxin signaling. Accordingly, the IAA content was significantly decreased in young tissues of plants overexpressing CBF2 and CBF3 compared with wild type. In addition, genes associated with the biosynthesis of Jasmonate (JA) and Salicylic acid (SA), as well as the signal sensing of Brassinolide (BR) and SA, were down-regulated, while genes associated with Gibberellin (GA) deactivation were up-regulated. In general, overexpression of CBF2 and CBF3 negatively affects multiple plant hormone signaling pathways in Arabidopsis. The transcriptome analysis using CBF2 and CBF3 transgenic plants provides novel and integrated insights into the interaction between CBFs and plant hormones, particularly the modulation of auxin signaling, which may contribute to the improvement of crop yields under abiotic stress via molecular engineering using CBF genes.
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Choi DS, Lim CW, Hwang BK. Proteomics and functional analyses of Arabidopsis nitrilases involved in the defense response to microbial pathogens. PLANTA 2016; 244:449-465. [PMID: 27095107 DOI: 10.1007/s00425-016-2525-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/07/2016] [Indexed: 06/05/2023]
Abstract
Proteomics and functional analyses of the Arabidopsis - Pseudomonas syringae pv. tomato interactions reveal that Arabidopsis nitrilases are required for plant defense and R gene-mediated resistant responses to microbial pathogens. A high-throughput in planta proteome screen has identified Arabidopsis nitrilase 2 (AtNIT2), which was de novo-induced by Pseudomonas syringae pv. tomato (Pst) infection. The AtNIT2, AtNIT3, and AtNIT4 genes, but not AtNIT1, were distinctly induced in Arabidopsis leaves by Pst infection. Notably, avirulent Pst DC3000 (avrRpt2) infection led to significant induction of AtNIT2 and AtNIT4 in leaves. Pst DC3000 and Pst DC3000 (avrRpt2) significantly grew well in leaves of nitrilase transgenic (nit2i-2) and mutant (nit1-1 and nit3-1) lines compared to the wild-type leaves. In contrast, NIT2 overexpression in nit2 mutants led to significantly high growth of the two Pst strains in leaves. The nitrilase transgenic and mutant lines exhibited enhanced susceptibility to Hyaloperonospora arabidopsidis infection. The nit2 mutation enhanced Pst DC3000 (avrRpt2) growth in salicylic acid (SA)-deficient NahG transgenic and sid2 and npr1 mutant lines. Infection with Pst DC3000 or Pst DC3000 (avrRpt2) induced lower levels of indole-3-acetic acid (IAA) in nit2i and nit2i NahG plants than in wild-type plants, but did not alter the IAA level in NahG transgenic plants. This suggests that Arabidopsis nitrilase 2 is involved in IAA signaling of defense and R gene-mediated resistance responses to Pst infection. Quantification of SA in these transgenic and mutant plants demonstrates that Arabidopsis nitrilase 2 is not required for SA-mediated defense response to the virulent Pst DC3000 but regulates SA-mediated resistance to the avirulent Pst DC3000 (avrRpt2). These results collectively suggest that Arabidopsis nitrilase genes are involved in plant defense and R gene-mediated resistant responses to microbial pathogens.
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Affiliation(s)
- Du Seok Choi
- Laboratory of Molecular Plant Pathology, College of Life Sciences and Biotechnology, Korea University, Anam-dong, Sungbuk-ku, Seoul, 02841, Republic of Korea
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, CA, 92521, USA
| | - Chae Woo Lim
- Laboratory of Molecular Plant Pathology, College of Life Sciences and Biotechnology, Korea University, Anam-dong, Sungbuk-ku, Seoul, 02841, Republic of Korea
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Byung Kook Hwang
- Laboratory of Molecular Plant Pathology, College of Life Sciences and Biotechnology, Korea University, Anam-dong, Sungbuk-ku, Seoul, 02841, Republic of Korea.
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Tohge T, Scossa F, Fernie AR. Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation. PLANT PHYSIOLOGY 2015; 169:1499-511. [PMID: 26371234 PMCID: PMC4634077 DOI: 10.1104/pp.15.01006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/10/2015] [Indexed: 05/05/2023]
Abstract
Huge insight into molecular mechanisms and biological network coordination have been achieved following the application of various profiling technologies. Our knowledge of how the different molecular entities of the cell interact with one another suggests that, nevertheless, integration of data from different techniques could drive a more comprehensive understanding of the data emanating from different techniques. Here, we provide an overview of how such data integration is being used to aid the understanding of metabolic pathway structure and regulation. We choose to focus on the pairwise integration of large-scale metabolite data with that of the transcriptomic, proteomics, whole-genome sequence, growth- and yield-associated phenotypes, and archival functional genomic data sets. In doing so, we attempt to provide an update on approaches that integrate data obtained at different levels to reach a better understanding of either single gene function or metabolic pathway structure and regulation within the context of a broader biological process.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
| | - Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
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Ramteke PW, Maurice NG, Joseph B, Wadher BJ. Nitrile-converting enzymes: an eco-friendly tool for industrial biocatalysis. Biotechnol Appl Biochem 2014; 60:459-81. [PMID: 23826937 DOI: 10.1002/bab.1139] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/21/2013] [Indexed: 11/10/2022]
Abstract
Nitriles are organic compounds bearing a − C ≡ N group; they are frequently known to occur naturally in both fauna and flora and are also synthesized chemically. They have wide applicability in the fields of medicine, industry, and environmental monitoring. However, the majority of nitrile compounds are considered to be lethal, mutagenic, and carcinogenic in nature and are known to cause potential health problems such as nausea, bronchial irritation, respiratory distress, convulsions, coma, and skeletal deformities in humans. Nitrile-converting enzymes, which are extracted from microorganisms, are commonly termed nitrilases and have drawn the attention of researchers all over the world to combat the toxicity of nitrile compounds. The present review focuses on the utility of nitrile-converting enzymes, sources, classification, structure, properties, and applications, as well as the future perspective on nitrilases.
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Affiliation(s)
- Pramod W Ramteke
- Department of Biological Sciences, Sam Higginbotom Institute of Agriculture, Technology and Sciences, Allahabad, India
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Yao P, Li J, Yuan J, Han C, Liu X, Feng J, Wu Q, Zhu D. Enzymatic Synthesis of a Key Intermediate for Rosuvastatin by Nitrilase-Catalyzed Hydrolysis of Ethyl (R)-4-Cyano-3-hydroxybutyate at High Substrate Concentration. ChemCatChem 2014. [DOI: 10.1002/cctc.201402877] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Influences of halogen atoms on indole-3-acetonitrile (IAN): Crystal structure and Hirshfeld surfaces analysis. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.07.069] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. BIOINFORMATICS (OXFORD, ENGLAND) 2014; 151:3-12. [PMID: 24695404 DOI: 10.1111/ppl.12098] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/30/2013] [Accepted: 08/15/2013] [Indexed: 05/09/2023]
Abstract
MOTIVATION Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. RESULTS The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. AVAILABILITY AND IMPLEMENTATION Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic CONTACT usadel@bio1.rwth-aachen.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anthony M Bolger
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, GermanyDepartment Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany
| | - Marc Lohse
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany
| | - Bjoern Usadel
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, GermanyDepartment Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany
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Phylogenetic analysis of putative genes involved in the tryptophan-dependent pathway of auxin biosynthesis in rice. Appl Biochem Biotechnol 2014; 172:2480-95. [PMID: 24398922 DOI: 10.1007/s12010-013-0710-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/25/2013] [Indexed: 12/31/2022]
Abstract
Plant proteome databases were mined for a flavin monooxygenase (YUCCA), tryptophan decarboxylase (TDC), nitrilase (NIT), and aldehyde oxidase (AO) enzymes that could be involved in the tryptophan-dependent pathway of auxin biosynthesis. Phylogenetic trees for enzyme sequences obtained were constructed. The YUCCA and TDC trees showed that these enzymes were conserved across the plant kingdom and therefore could be involved in auxin synthesis. YUCCAs branched into two clades. Most experimentally studied YUCCAs were found in the first clade. The second clade which has representatives from only seed plants contained Arabidopsis sequences linked to embryonic development. Therefore, sequences in this clade were suggested to be evolved with seed development. Examination of TDC activity and expression had previously linked this enzyme to secondary products synthesis. However, the phylogenetic finding of a conserved TDC clade across land plants suggested its essential role in plant growth. Phylogenetic analysis of AOs showed that plants inherited one AO. Recent gene duplication was suggested as AO sequences from each species were similar to each other rather than to AO from other species. Taken together and based on the experimental support of the involvement of AO in abscisic synthesis, AO was excluded as an intermediate in IAA production. Phylogenetic tree for NIT showed that the first clade contained sequences from species across the plant kingdom whereas the second branch contained sequences from only Brassicaceae. Even though NIT4 orthologues were conserved in the second clade, their major role seems to be detoxification of hydrogen cyanide rather than producing IAA.
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Mano Y, Nemoto K. The pathway of auxin biosynthesis in plants. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2853-72. [PMID: 22447967 DOI: 10.1093/jxb/ers091] [Citation(s) in RCA: 295] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The plant hormone auxin, which is predominantly represented by indole-3-acetic acid (IAA), is involved in the regulation of plant growth and development. Although IAA was the first plant hormone identified, the biosynthetic pathway at the genetic level has remained unclear. Two major pathways for IAA biosynthesis have been proposed: the tryptophan (Trp)-independent and Trp-dependent pathways. In Trp-dependent IAA biosynthesis, four pathways have been postulated in plants: (i) the indole-3-acetamide (IAM) pathway; (ii) the indole-3-pyruvic acid (IPA) pathway; (iii) the tryptamine (TAM) pathway; and (iv) the indole-3-acetaldoxime (IAOX) pathway. Although different plant species may have unique strategies and modifications to optimize their metabolic pathways, plants would be expected to share evolutionarily conserved core mechanisms for auxin biosynthesis because IAA is a fundamental substance in the plant life cycle. In this review, the genes now known to be involved in auxin biosynthesis are summarized and the major IAA biosynthetic pathway distributed widely in the plant kingdom is discussed on the basis of biochemical and molecular biological findings and bioinformatics studies. Based on evolutionarily conserved core mechanisms, it is thought that the pathway via IAM or IPA is the major route(s) to IAA in plants.
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Affiliation(s)
- Yoshihiro Mano
- Graduate School of Bioscience, Tokai University, 317 Nishino, Numazu, Shizuoka 410-0321, Japan.
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Zhao Y. Auxin biosynthesis: a simple two-step pathway converts tryptophan to indole-3-acetic acid in plants. MOLECULAR PLANT 2012; 5:334-8. [PMID: 22155950 PMCID: PMC3309920 DOI: 10.1093/mp/ssr104] [Citation(s) in RCA: 289] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 11/21/2011] [Indexed: 05/18/2023]
Abstract
Indole-3-acetic acid (IAA), the main naturally occurring auxin, is essential for almost every aspect of plant growth and development. However, only recently have studies finally established the first complete auxin biosynthesis pathway that converts tryptophan (Trp) to IAA in plants. Trp is first converted to indole-3-pyruvate (IPA) by the TAA family of amino transferases and subsequently IAA is produced from IPA by the YUC family of flavin monooxygenases. The two-step conversion of Trp to IAA is the main auxin biosynthesis pathway that plays an essential role in many developmental processes.
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Affiliation(s)
- Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, USA.
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Chen Y, Pang Q, Dai S, Wang Y, Chen S, Yan X. Proteomic identification of differentially expressed proteins in Arabidopsis in response to methyl jasmonate. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:995-1008. [PMID: 21377756 DOI: 10.1016/j.jplph.2011.01.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 01/06/2011] [Accepted: 01/10/2011] [Indexed: 05/25/2023]
Abstract
Jasmonates (JAs) are the well characterized fatty acid-derived cyclopentanone signals involved in the plant response to biotic and abiotic stresses. JAs have been shown to regulate many aspects of plant metabolism, including glucosinolate biosynthesis. Glucosinolates are natural plant products that function in defense against herbivores and pathogens. In this study, we applied a proteomic approach to gain insight into the physiological processes, including glucosinolate metabolism, in response to methyl jasmonate (MeJA). We identified 194 differentially expressed protein spots that contained proteins that participated in a wide range of physiological processes. Functional classification analysis showed that photosynthesis and carbohydrate anabolism were repressed after MeJA treatment, while carbohydrate catabolism was up-regulated. Additionally, proteins related to the JA biosynthesis pathway, stress and defense, and secondary metabolism were up-regulated. Among the differentially expressed proteins, many were involved in oxidative tolerance. The results indicate that MeJA elicited a defense response at the proteome level through a mechanism of redirecting growth-related metabolism to defense-related metabolism.
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Affiliation(s)
- Yazhou Chen
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China
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Kaplan O, Bezouška K, Plíhal O, Ettrich R, Kulik N, Vaněk O, Kavan D, Benada O, Malandra A, Sveda O, Veselá AB, Rinágelová A, Slámová K, Cantarella M, Felsberg J, Dušková J, Dohnálek J, Kotik M, Křen V, Martínková L. Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10. BMC Biotechnol 2011; 11:2. [PMID: 21210990 PMCID: PMC3023689 DOI: 10.1186/1472-6750-11-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 01/06/2011] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Nitrilases attract increasing attention due to their utility in the mild hydrolysis of nitriles. According to activity and gene screening, filamentous fungi are a rich source of nitrilases distinct in evolution from their widely examined bacterial counterparts. However, fungal nitrilases have been less explored than the bacterial ones. Nitrilases are typically heterogeneous in their quaternary structures, forming short spirals and extended filaments, these features making their structural studies difficult. RESULTS A nitrilase gene was amplified by PCR from the cDNA library of Aspergillus niger K10. The PCR product was ligated into expression vectors pET-30(+) and pRSET B to construct plasmids pOK101 and pOK102, respectively. The recombinant nitrilase (Nit-ANigRec) expressed in Escherichia coli BL21-Gold(DE3)(pOK101/pTf16) was purified with an about 2-fold increase in specific activity and 35% yield. The apparent subunit size was 42.7 kDa, which is approx. 4 kDa higher than that of the enzyme isolated from the native organism (Nit-ANigWT), indicating post-translational cleavage in the enzyme's native environment. Mass spectrometry analysis showed that a C-terminal peptide (Val327 - Asn₃₅₆) was present in Nit-ANigRec but missing in Nit-ANigWT and Asp₂₉₈-Val₃₁₃ peptide was shortened to Asp₂₉₈-Arg₃₁₀ in Nit-ANigWT. The latter enzyme was thus truncated by 46 amino acids. Enzymes Nit-ANigRec and Nit-ANigWT differed in substrate specificity, acid/amide ratio, reaction optima and stability. Refolded recombinant enzyme stored for one month at 4°C was fractionated by gel filtration, and fractions were examined by electron microscopy. The late fractions were further analyzed by analytical centrifugation and dynamic light scattering, and shown to consist of a rather homogeneous protein species composed of 12-16 subunits. This hypothesis was consistent with electron microscopy and our modelling of the multimeric nitrilase, which supports an arrangement of dimers into helical segments as a plausible structural solution. CONCLUSIONS The nitrilase from Aspergillus niger K10 is highly homologous (≥86%) with proteins deduced from gene sequencing in Aspergillus and Penicillium genera. As the first of these proteins, it was shown to exhibit nitrilase activity towards organic nitriles. The comparison of the Nit-ANigRec and Nit-ANigWT suggested that the catalytic properties of nitrilases may be changed due to missing posttranslational cleavage of the former enzyme. Nit-ANigRec exhibits a lower tendency to form filaments and, moreover, the sample homogeneity can be further improved by in vitro protein refolding. The homogeneous protein species consisting of short spirals is expected to be more suitable for structural studies.
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Affiliation(s)
- Ondřej Kaplan
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Robles P, Fleury D, Candela H, Cnops G, Alonso-Peral MM, Anami S, Falcone A, Caldana C, Willmitzer L, Ponce MR, Van Lijsebettens M, Micol JL. The RON1/FRY1/SAL1 gene is required for leaf morphogenesis and venation patterning in Arabidopsis. PLANT PHYSIOLOGY 2010; 152:1357-72. [PMID: 20044451 PMCID: PMC2832283 DOI: 10.1104/pp.109.149369] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 12/26/2009] [Indexed: 05/19/2023]
Abstract
To identify genes involved in vascular patterning in Arabidopsis (Arabidopsis thaliana), we screened for abnormal venation patterns in a large collection of leaf shape mutants isolated in our laboratory. The rotunda1-1 (ron1-1) mutant, initially isolated because of its rounded leaves, exhibited an open venation pattern, which resulted from an increased number of free-ending veins. We positionally cloned the RON1 gene and found it to be identical to FRY1/SAL1, which encodes an enzyme with inositol polyphosphate 1-phosphatase and 3' (2'),5'-bisphosphate nucleotidase activities and has not, to our knowledge, previously been related to venation patterning. The ron1-1 mutant and mutants affected in auxin homeostasis share perturbations in venation patterning, lateral root formation, root hair length, shoot branching, and apical dominance. These similarities prompted us to monitor the auxin response using a DR5-GUS auxin-responsive reporter transgene, the expression levels of which were increased in roots and reduced in leaves in the ron1-1 background. To gain insight into the function of RON1/FRY1/SAL1 during vascular development, we generated double mutants for genes involved in vein patterning and found that ron1 synergistically interacts with auxin resistant1 and hemivenata-1 but not with cotyledon vascular pattern1 (cvp1) and cvp2. These results suggest a role for inositol metabolism in the regulation of auxin responses. Microarray analysis of gene expression revealed that several hundred genes are misexpressed in ron1-1, which may explain the pleiotropic phenotype of this mutant. Metabolomic profiling of the ron1-1 mutant revealed changes in the levels of 38 metabolites, including myoinositol and indole-3-acetonitrile, a precursor of auxin.
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Janowitz T, Trompetter I, Piotrowski M. Evolution of nitrilases in glucosinolate-containing plants. PHYTOCHEMISTRY 2009; 70:1680-6. [PMID: 19698961 DOI: 10.1016/j.phytochem.2009.07.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 07/21/2009] [Accepted: 07/22/2009] [Indexed: 05/08/2023]
Abstract
Nitrilases, enzymes that catalyze the hydrolysis of organic cyanides, are ubiquitous in the plant kingdom. The typical plant nitrilase is a nitrilase 4 homolog which is involved in the cyanide detoxification pathway. In this pathway, nitrilase 4 converts beta-cyanoalanine, the intermediate product of cyanide detoxification, into asparagine, aspartic acid and ammonia. In the Brassicaceae, a new family of nitrilases has evolved, the nitrilase 1 homologs. These enzymes are not able to use beta-cyanoalanine as a substrate. Instead, they display rather broad substrate specificities and are able to hydrolyze nitriles that result from the decomposition of glucosinolates, the typical secondary metabolites of the Brassicaceae. Here we summarize and discuss data indicating that nitrilase 1 homologs have evolved to function in glucosinolate catabolism.
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Affiliation(s)
- Tim Janowitz
- Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany
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Desclos M, Etienne P, Coquet L, Jouenne T, Bonnefoy J, Segura R, Reze S, Ourry A, Avice JC. A combined 15N tracing/proteomics study in Brassica napus reveals the chronology of proteomics events associated with N remobilisation during leaf senescence induced by nitrate limitation or starvation. Proteomics 2009; 9:3580-608. [PMID: 19609964 DOI: 10.1002/pmic.200800984] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Our goal was to identify the leaf proteomic changes which appeared during N remobilisation that were associated or not associated with senescence of oilseed rape in response to contrasting nitrate availability. Remobilisation of N and leaf senescence status were followed using (15)N tracing, patterns of chlorophyll level, total protein content and a molecular indicator based on expression of senescence-associated gene 12/Cab genes. Three phases associated with N remobilisation were distinguished. Proteomics revealed that 55 proteins involved in metabolism, energy, detoxification, stress response, proteolysis and protein folding, were significantly induced during N remobilisation. Four proteases were specifically identified. FtsH, a chloroplastic protease, was induced transiently during the early stages of N remobilisation. Considering the dynamics of N remobilisation, chlorophyll and protein content, the pattern of FtsH expression indicated that this protease could be involved in the degradation of chloroplastic proteins. Aspartic protease increased at the beginning of senescence and was maintained at a high level, implicating this protease in proteolysis during the course of leaf senescence. Two proteases, proteasome beta subunit A1 and senescence-associated gene 12, were induced and continued to increase during the later phase of senescence, suggesting that these proteases are more specifically involved in the proteolysis processes occurring at the final stages of leaf senescence.
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Affiliation(s)
- Marie Desclos
- INRA, UMR INRA/UCBN 950 Ecophysiologie Végétale, Agronomie et nutritions N C S, IFR 146 ICORE, Institut de Biologie Fondamentale et Appliquée, Université de CAEN Basse-Normandie, Caen, France
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Kim JS, Tiwari MK, Moon HJ, Jeya M, Ramu T, Oh DK, Kim IW, Lee JK. Identification and characterization of a novel nitrilase from Pseudomonas fluorescens Pf-5. Appl Microbiol Biotechnol 2009; 83:273-83. [DOI: 10.1007/s00253-009-1862-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 12/07/2008] [Accepted: 01/06/2009] [Indexed: 11/29/2022]
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Thuku R, Brady D, Benedik M, Sewell B. Microbial nitrilases: versatile, spiral forming, industrial enzymes. J Appl Microbiol 2009; 106:703-27. [DOI: 10.1111/j.1365-2672.2008.03941.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Piotrowski M. Primary or secondary? Versatile nitrilases in plant metabolism. PHYTOCHEMISTRY 2008; 69:2655-67. [PMID: 18842274 DOI: 10.1016/j.phytochem.2008.08.020] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 08/26/2008] [Indexed: 05/08/2023]
Abstract
The potential of plant nitrilases to convert indole-3-acetonitrile into the plant growth hormone indole-3-acetic acid has earned them the interim title of "key enzyme in auxin biosynthesis". Although not widely recognized, this view has changed considerably in the last few years. Recent work on plant nitrilases has shown them to be involved in the process of cyanide detoxification, in the catabolism of cyanogenic glycosides and presumably in the catabolism of glucosinolates. All plants possess at least one nitrilase that is homologous to the nitrilase 4 isoform of Arabidopsis thaliana. The general function of these nitrilases lies in the process of cyanide detoxification, in which they convert the intermediate detoxification product beta-cyanoalanine into asparagine, aspartic acid and ammonia. Cyanide is a metabolic by-product in biosynthesis of the plant hormone ethylene, but it may also be released from cyanogenic glycosides, which are present in a large number of plants. In Sorghum bicolor, an additional nitrilase isoform has been identified, which can directly use a catabolic intermediate of the cyanogenic glycoside dhurrin, thus enabling the plant to metabolize its cyanogenic glycoside without releasing cyanide. In the Brassicaceae, a family of nitrilases has evolved, the members of which are able to hydrolyze catabolic products of glucosinolates, the predominant secondary metabolites of these plants. Thus, the general theme of nitrilase function in plants is detoxification and nitrogen recycling, since the valuable nitrogen of the nitrile group is recovered in the useful metabolites asparagine or ammonia. Taken together, a picture emerges in which plant nitrilases have versatile functions in plant metabolism, whereas their importance for auxin biosynthesis seems to be minor.
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Affiliation(s)
- Markus Piotrowski
- Department of Plant Physiology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany.
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Transcriptional regulation of the nitrile hydratase gene cluster in Pseudomonas chlororaphis B23. J Bacteriol 2008; 190:4210-7. [PMID: 18408036 DOI: 10.1128/jb.00061-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An enormous amount of nitrile hydratase (NHase) is inducibly produced by Pseudomonas chlororaphis B23 after addition of methacrylamide as the sole nitrogen source to a medium. The expression pattern of the P. chlororaphis B23 NHase gene cluster in response to addition of methacrylamide to the medium was investigated. Recently, we reported that the NHase gene cluster comprises seven genes (oxdA, amiA, nhpA, nhpB, nhpC, nhpS, and acsA). Sequence analysis of the 1.5-kb region upstream of the oxdA gene revealed the presence of a 936-bp open reading frame (designated nhpR), which should encode a protein with a molecular mass of 35,098. The deduced amino acid sequence of the nhpR product showed similarity to the sequences of transcriptional regulators belonging to the XylS/AraC family. Although the transcription of the eight genes (nhpR, oxdA, amiA, nhpABC, nhpS, and acsA) in the NHase gene cluster was induced significantly in the P. chlororaphis B23 wild-type strain after addition of methacrylamide to the medium, transcription of these genes in the nhpR disruptant was not induced, demonstrating that nhpR codes for a positive transcriptional regulator in the NHase gene cluster. A reverse transcription-PCR experiment revealed that five genes (oxdA, amiA, nhpA, nhpB, and nhpC) are cotranscribed, as are two other genes (nhpS and acsA). The transcription start sites for nhpR, oxdA, nhpA, and nhpS were mapped by primer extension analysis, and putative -12 and -24 sigma(54)-type promoter binding sites were identified. NhpR was found to be the first transcriptional regulator of NHase belonging to the XylS/AraC family.
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Batista R, Saibo N, Lourenço T, Oliveira MM. Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proc Natl Acad Sci U S A 2008; 105:3640-5. [PMID: 18303117 PMCID: PMC2265136 DOI: 10.1073/pnas.0707881105] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Indexed: 12/27/2022] Open
Abstract
Controversy regarding genetically modified (GM) plants and their potential impact on human health contrasts with the tacit acceptance of other plants that were also modified, but not considered as GM products (e.g., varieties raised through conventional breeding such as mutagenesis). What is beyond the phenotype of these improved plants? Should mutagenized plants be treated differently from transgenics? We have evaluated the extent of transcriptome modification occurring during rice improvement through transgenesis versus mutation breeding. We used oligonucleotide microarrays to analyze gene expression in four different pools of four types of rice plants and respective controls: (i) a gamma-irradiated stable mutant, (ii) the M1 generation of a 100-Gy gamma-irradiated plant, (iii) a stable transgenic plant obtained for production of an anticancer antibody, and (iv) the T1 generation of a transgenic plant produced aiming for abiotic stress improvement, and all of the unmodified original genotypes as controls. We found that the improvement of a plant variety through the acquisition of a new desired trait, using either mutagenesis or transgenesis, may cause stress and thus lead to an altered expression of untargeted genes. In all of the cases studied, the observed alteration was more extensive in mutagenized than in transgenic plants. We propose that the safety assessment of improved plant varieties should be carried out on a case-by-case basis and not simply restricted to foods obtained through genetic engineering.
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Affiliation(s)
- Rita Batista
- Instituto Nacional de Saúde Dr. Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal.
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Spaepen S, Vanderleyden J, Remans R. Indole-3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol Rev 2007; 31:425-48. [PMID: 17509086 DOI: 10.1111/j.1574-6976.2007.00072.x] [Citation(s) in RCA: 762] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Diverse bacterial species possess the ability to produce the auxin phytohormone indole-3-acetic acid (IAA). Different biosynthesis pathways have been identified and redundancy for IAA biosynthesis is widespread among plant-associated bacteria. Interactions between IAA-producing bacteria and plants lead to diverse outcomes on the plant side, varying from pathogenesis to phyto-stimulation. Reviewing the role of bacterial IAA in different microorganism-plant interactions highlights the fact that bacteria use this phytohormone to interact with plants as part of their colonization strategy, including phyto-stimulation and circumvention of basal plant defense mechanisms. Moreover, several recent reports indicate that IAA can also be a signaling molecule in bacteria and therefore can have a direct effect on bacterial physiology. This review discusses past and recent data, and emerging views on IAA, a well-known phytohormone, as a microbial metabolic and signaling molecule.
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Affiliation(s)
- Stijn Spaepen
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Heverlee, Belgium
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Brenner WG, Romanov GA, Köllmer I, Bürkle L, Schmülling T. Immediate-early and delayed cytokinin response genes of Arabidopsis thaliana identified by genome-wide expression profiling reveal novel cytokinin-sensitive processes and suggest cytokinin action through transcriptional cascades. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 44:314-33. [PMID: 16212609 DOI: 10.1111/j.1365-313x.2005.02530.x] [Citation(s) in RCA: 241] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cytokinins are hormones that regulate many developmental and physiological processes in plants. Recent work has revealed that the cytokinin signal is transduced by two-component systems to the nucleus where target genes are activated. Most of the rapid transcriptional responses are unknown. We measured immediate-early and delayed cytokinin responses through genome-wide expression profiling with the Affymetrix ATH1 full genome array (Affymetrix Inc., Santa Clara, CA, USA). Fifteen minutes after cytokinin treatment of 5-day-old Arabidopsis seedlings, 71 genes were upregulated and 11 genes were downregulated. Immediate-early cytokinin response genes include a high portion of transcriptional regulators, among them six transcription factors that had previously not been linked to cytokinin. Five plastid transcripts were rapidly regulated as well, indicating a rapid transfer of the signal to plastids or direct perception of the cytokinin signal by plastids. After 2 h of cytokinin treatment genes coding for transcriptional regulators, signaling proteins, developmental and hormonal regulators, primary and secondary metabolism, energy generation and stress reactions were over-represented. A significant number of the responding genes are known to regulate light (PHYA, PSK1, CIP8, PAT1, APRR), auxin (Aux/IAA), ethylene (ETR2, EIN3, ERFs/EREBPs), gibberellin (GAI, RGA1, GA20 oxidase), nitrate (NTR2, NIA) and sugar (STP1, SUS1) dependent processes, indicating intense crosstalk with environmental cues, other hormones and metabolites. Analysis of cytokinin-deficient 35S:AtCKX1 transgenic seedlings has revealed additional, long-lasting cytokinin-sensitive changes of transcript abundance. Comparative overlay-analysis with the software tool mapman identified previously unknown cytokinin-sensitive metabolic genes, for example in the metabolism of trehalose-6-phosphate. Taken together, we present a genome-wide view of changes in cytokinin-responsive transcript abundance of genes that might be functionally relevant for the many biological processes that are governed by cytokinins.
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Affiliation(s)
- Wolfram G Brenner
- Max Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
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Abstract
BACKGROUND The phytohormone auxin is critical for plant growth and orchestrates many developmental processes. SCOPE This review considers the complex array of mechanisms plants use to control auxin levels, the movement of auxin through the plant, the emerging view of auxin-signalling mechanisms, and several interactions between auxin and other phytohormones. Though many natural and synthetic compounds exhibit auxin-like activity in bioassays, indole-3-acetic acid (IAA) is recognized as the key auxin in most plants. IAA is synthesized both from tryptophan (Trp) using Trp-dependent pathways and from an indolic Trp precursor via Trp-independent pathways; none of these pathways is fully elucidated. Plants can also obtain IAA by beta-oxidation of indole-3-butyric acid (IBA), a second endogenous auxin, or by hydrolysing IAA conjugates, in which IAA is linked to amino acids, sugars or peptides. To permanently inactivate IAA, plants can employ conjugation and direct oxidation. Consistent with its definition as a hormone, IAA can be transported the length of the plant from the shoot to the root; this transport is necessary for normal development, and more localized transport is needed for tropic responses. Auxin signalling is mediated, at least in large part, by an SCFTIR1 E3 ubiquitin ligase complex that accelerates Aux/IAA repressor degradation in response to IAA, thereby altering gene expression. Two classes of auxin-induced genes encode negatively acting products (the Aux/IAA transcriptional repressors and GH3 family of IAA conjugating enzymes), suggesting that timely termination of the auxin signal is crucial. Auxin interaction with other hormone signals adds further challenges to understanding auxin response. CONCLUSIONS Nearly six decades after the structural elucidation of IAA, many aspects of auxin metabolism, transport and signalling are well established; however, more than a few fundamental questions and innumerable details remain unresolved.
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Hashimoto Y, Hosaka H, Oinuma KI, Goda M, Higashibata H, Kobayashi M. Nitrile pathway involving acyl-CoA synthetase: overall metabolic gene organization and purification and characterization of the enzyme. J Biol Chem 2005; 280:8660-7. [PMID: 15632196 DOI: 10.1074/jbc.m405686200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two open reading frames (nhpS and acsA) were identified immediately downstream of the previously described Pseudomonas chlororaphis B23 nitrile hydratase (NHase) gene cluster (encoding aldoxime dehydratase, amidase, the two NHase subunits, and an uncharacterized protein). The amino acid sequence deduced from acsA shows similarity to that of acyl-CoA synthetase (AcsA). The acsA gene product expressed in Escherichia coli showed acyl-CoA synthetase activity toward butyric acid and CoA as substrates, with butyryl-CoA being synthesized. From the E. coli transformant, AcsA was purified to homogeneity and characterized. The quality of the recombinant protein was verified by the NH2-terminal amino acid sequence and the results of matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The apparent Km values for butyric acid, CoA, and ATP were 0.32 +/- 0.04, 0.37 +/- 0.02, and 0.22 +/- 0.02 mm, respectively. AcsA was shown to be a short-chain acyl-CoA synthetase, according to the catalytic efficiencies (kcat/Km) for various acids. The substrate specificity of AcsA was similar to those of aldoxime dehydratase, NHase, and amidase, the genes of which coexist in the same orientation in the gene cluster. P. chlororaphis B23 grew when cultured in a medium containing butyraldoxime as the sole carbon and nitrogen source. The activities of aldoxime dehydratase, NHase, and amidase were detected together with that of acyl-CoA synthetase under the culture conditions used. Moreover, on culture in a medium containing butyric acid as the sole carbon source, acyl-CoA synthetase activity was also detected. Together with the adjacent locations of the aldoxime dehydratase, NHase, amidase, and acyl-CoA synthetase genes, these findings suggest that the four enzymes are sequentially correlated with one another in vivo to utilize butyraldoxime as a carbon and nitrogen source. This is the first report of an overall "nitrile pathway" (aldoxime-->nitrile-->amide-->acid-->acyl-CoA) comprising these enzymes.
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Affiliation(s)
- Yoshiteru Hashimoto
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Konishi K, Ishida K, Oinuma KI, Ohta T, Hashimoto Y, Higashibata H, Kitagawa T, Kobayashi M. Identification of Crucial Histidines Involved in Carbon-Nitrogen Triple Bond Synthesis by Aldoxime Dehydratase. J Biol Chem 2004; 279:47619-25. [PMID: 15339918 DOI: 10.1074/jbc.m407223200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aldoxime dehydratase (OxdA), which is a novel heme protein, catalyzes the dehydration of an aldoxime to a nitrile even in the presence of water in the reaction mixture. The combination of site-directed mutagenesis of OxdA (mutation of all conserved histidines in the aldoxime dehydratase superfamily), estimation of the heme contents and specific activities of the mutants, and CD and resonance Raman spectroscopic analyses led to the identification of the proximal and distal histidines in this unique enzyme. The heme contents and CD spectra in the far-UV region of all mutants except for the H299A one were almost identical to those of the wild-type OxdA, whereas the H299A mutant lost the ability of binding heme, demonstrating that His(299) is the proximal histidine. On the other hand, substitution of alanine for His(320) did not affect the overall structure of OxdA but caused loss of its ability of carbon-nitrogen triple bond synthesis and a lower shift of the Fe-C stretching band in the resonance Raman spectrum for the CO-bound form. Furthermore, the pH dependence of the wild-type OxdA closely followed the His protonation curves observed for other proteins. These findings suggest that His(320) is located in the distal heme pocket of OxdA and would donate a proton to the substrate in the aldoxime dehydration mechanism.
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Affiliation(s)
- Kazunobu Konishi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Sewell BT, Berman MN, Meyers PR, Jandhyala D, Benedik MJ. The cyanide degrading nitrilase from Pseudomonas stutzeri AK61 is a two-fold symmetric, 14-subunit spiral. Structure 2004; 11:1413-22. [PMID: 14604531 DOI: 10.1016/j.str.2003.10.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The quaternary structure of the cyanide dihydratase from Pseudomonas stutzeri AK61 was determined by negative stain electron microscopy and three-dimensional reconstruction using the single particle technique. The structure is a spiral comprising 14 subunits with 2-fold symmetry. Interactions across the groove cause a decrease in the radius of the spiral at the ends and the resulting steric hindrance prevents the addition of further subunits. Similarity to two members of the nitrilase superfamily, the Nit domain of NitFhit and N-carbamyl-D-amino acid amidohydrolase, enabled the construction of a partial atomic model that could be unambiguously fitted to the stain envelope. The model suggests that interactions involving two significant insertions in the sequence relative to these structures leads to the left-handed spiral assembly.
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Affiliation(s)
- B T Sewell
- Electron Microscope Unit, University of Cape Town, Private Bag, 7701 Rondebosch, South Africa.
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Oinuma KI, Ohta T, Konishi K, Hashimoto Y, Higashibata H, Kitagawa T, Kobayashi M. Heme environment in aldoxime dehydratase involved in carbon-nitrogen triple bond synthesis. FEBS Lett 2004; 568:44-8. [PMID: 15196918 DOI: 10.1016/j.febslet.2004.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2004] [Revised: 03/27/2004] [Accepted: 05/05/2004] [Indexed: 11/30/2022]
Abstract
Resonance Raman spectra have been measured to characterize the heme environment in aldoxime dehydratase (OxdA), a novel hemoprotein, which catalyzes the dehydration of aldoxime into nitrile. The spectra showed that the ferric heme in the enzyme is six-coordinate low spin, whereas the ferrous heme is five-coordinate high spin. We assign a prominent vibration that occurs at 226 cm(-1) in the ferrous enzyme to the Fe-proximal histidine stretching vibration. In the CO-bound form of OxdA, the correlation between the Fe-CO stretching (512 cm(-1)) and C-O stretching (1950 cm(-1)) frequencies also supports our assignment of proximal histidine coordination.
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Affiliation(s)
- Ken-Ichi Oinuma
- Institute of Applied Biochemistry, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Abstract
The enzymes nitrilase, cyanide dihydratase and cyanide hydratase are a group of closely related proteins. The proteins show significant similarities at the amino acid and protein structure level but the enzymes show many differences in catalytic capability. Nitrilases, while catalysing the hydration of nitrile to the corresponding acid, vary widely in substrate specificity. Cyanide dihydratase and cyanide hydratase use HCN as the only efficient substrate but produce acid and amide products, respectively. The similarities of all these enzymes at the amino acid level but the functional differences between them provide a rich source of material for the study of structure/function relationships in this biotechnologically important group of enzymes. This review provides an overview of current understanding of the genetics and biochemistry of this interesting group of enzymes.
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Affiliation(s)
- C O'Reilly
- Department of Chemical and Life Sciences, Waterford Institute of Technology, Cork Road, Waterford, Ireland.
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Park WJ, Kriechbaumer V, Möller A, Piotrowski M, Meeley RB, Gierl A, Glawischnig E. The Nitrilase ZmNIT2 converts indole-3-acetonitrile to indole-3-acetic acid. PLANT PHYSIOLOGY 2003; 133:794-802. [PMID: 12972653 PMCID: PMC219053 DOI: 10.1104/pp.103.026609] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2003] [Revised: 07/01/2003] [Accepted: 07/08/2003] [Indexed: 05/18/2023]
Abstract
We isolated two nitrilase genes, ZmNIT1 and ZmNIT2, from maize (Zea mays) that share 75% sequence identity on the amino acid level. Despite the relatively high homology to Arabidopsis NIT4, ZmNIT2 shows no activity toward beta-cyano-alanine, the substrate of Arabidopsis NIT4, but instead hydrolyzes indole-3-acetonitrile (IAN) to indole-3-acetic acid (IAA). ZmNIT2 converts IAN to IAA at least seven to 20 times more efficiently than AtNIT1/2/3. Quantitative real-time polymerase chain reaction revealed the gene expression of both nitrilases in maize kernels where high concentrations of IAA are synthesized tryptophan dependently. Nitrilase protein and endogenous nitrilase activity are present in maize kernels together with the substrate IAN. These results suggest a role for ZmNIT2 in auxin biosynthesis.
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Affiliation(s)
- Woong June Park
- Lehrstuhl für Genetik, Technische Universität München, D-85350 Freising, Germany
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40
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Oinuma KI, Hashimoto Y, Konishi K, Goda M, Noguchi T, Higashibata H, Kobayashi M. Novel aldoxime dehydratase involved in carbon-nitrogen triple bond synthesis of Pseudomonas chlororaphis B23. Sequencing, gene expression, purification, and characterization. J Biol Chem 2003; 278:29600-8. [PMID: 12773527 DOI: 10.1074/jbc.m211832200] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Analysis of the nitrile hydratase gene cluster involved in nitrile metabolism of Pseudomonas chlororaphis B23 revealed that it contains one open reading frame encoding aldoxime dehydratase upstream of the amidase gene. The amino acid sequence deduced from this open reading frame shows similarity (32% identity) with that of Bacillus phenylacetaldoxime dehydratase (Kato, Y., Nakamura, K., Sakiyama, H., Mayhew, S. G., and Asano, Y. (2000) Biochemistry 39, 800-809). The gene product expressed in Escherichia coli catalyzed the dehydration of aldoxime into nitrile. The Pseudomonas aldoxime dehydratase (OxdA) was purified from the E. coli transformant and characterized. OxdA shows an absorption spectrum with a Soret peak that is characteristic of heme, demonstrating that it is a hemoprotein. For its activity, this enzyme required a reducing reagent, Na2S2O4, but did not require FMN, which is crucial for the Bacillus enzyme. The enzymatic reaction was found to be catalyzed when the heme iron of the enzyme was in the ferrous state. Calcium as well as iron was included in the enzyme. OxdA reduced by Na2S2O4 had a molecular mass of 76.2 kDa and consisted of two identical subunits. The kinetic parameters of OxdA indicated that aliphatic aldoximes are more effective substrates than aromatic aldoximes. A variety of spectral shifts in the absorption spectra of OxdA were observed upon the addition of each of various compounds (i.e. redox reagents and heme ligands). Moreover, the addition of the substrate to OxdA gave a peak that would be derived from the intermediate in the nitrile synthetic reaction. P. chlororaphis B23 grew and showed the OxdA activity when cultured in a medium containing aldoxime as the sole carbon and nitrogen source. Together with these findings, Western blotting analysis of the extracts using anti-OxdA antiserum revealed that OxdA is responsible for the metabolism of aldoxime in vivo in this strain.
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Affiliation(s)
- Ken-Ichi Oinuma
- Institute of Applied Biochemistry, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Ludwig-Müller J, Cohen JD. Identification and quantification of three active auxins in different tissues of Tropaeolum majus. PHYSIOLOGIA PLANTARUM 2002; 115:320-329. [PMID: 12060252 DOI: 10.1034/j.1399-3054.2002.1150220.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Indole-3-acetic acid (IAA), indole-3-butyric acid (IBA) and phenylacetic acid (PAA) were identified as endogenous compounds with auxin activity in nasturtium (Tropaeolum majus L.) by full scan gas chromatography-mass spectrometry. The endogenous concentrations of the three auxins were measured by GC-selected ion monitoring-MS and isotope dilution analysis using stable labelled isotopes. PAA was present at concentrations about 10- to 100-fold lower than IAA, whereas IBA was found to be in the same concentration range as IAA. Free IAA was highest in roots followed by young leaves. IBA was also highest in the roots, and relatively high concentrations were found in young leaves and flowers. The distribution of PAA was quite different from that found for IBA. No PAA could be detected in young leaves and flowers, and in all other tissues studied the concentrations were well below those of the other two auxin compounds. The presence of a nitrilase gene family and nitrilase activity in extracts from T. majus suggests that PAA might be synthesized by the nitrilase pathway using benzylglucosinolate as precursor.
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Affiliation(s)
- Jutta Ludwig-Müller
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 22, D-01062, Dresden, Germany Department of Horticultural Science, University of Minnesota, 305 Alderman Hall, Saint Paul, MN 55108, USA
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Kutz A, Müller A, Hennig P, Kaiser WM, Piotrowski M, Weiler EW. A role for nitrilase 3 in the regulation of root morphology in sulphur-starving Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 30:95-106. [PMID: 11967096 DOI: 10.1046/j.1365-313x.2002.01271.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Arabidopsis thaliana expresses four nitrilases, three of which (NIT1, NIT2 and NIT3) are able to convert indole-3-acetonitrile to indole-3-acetic acid (IAA), the plant growth hormone, while the isozyme NIT4 is a beta-cyano-l-alanine hydratase/nitrilase. NIT3 promoter activity is marginal in leaves or roots of vegetative plants and undetectable in bolting and flowering plants, but its level increases strongly when plants experience sulphur deprivation. No other nitrilase genes respond to sulphur supply/deficiency. Neither N- nor P-deprivation cause detectable changes in NIT3 promoter activity. In transgenic plants expressing uidA under the control of the NIT3 promoter (NIT3p::uidA), sulphate deprivation leads to the appearance of beta-glucuronidase activity in shoots and particularly in roots, most strongly in the conductive tissues and lateral root primordia. Deletion analysis allowed localization of the sulphur-responsive element to a 317 bp segment of the NIT3 promoter encompassing nt -2151 to -1834 upstream of the transcriptional start point. Both nitrilase polypeptide and nitrilase activity were also induced by sulphur starvation. NIT3 promoter activity was strongly induced by O-acetylserine, suggesting that, as is the case with enzymes of sulphate assimilation, sulphate deficiency may be communicated to NIT3 via an increase in the level of the cysteine precursor, O-acetylserine. During sulphur deprivation, a preferential depletion of the pool of the indole-3-acetonitrile precursor glucobrassicin compared with that of total glucosinolates was noticed. In the absence of an external sulphate supply, plants developed longer roots with a higher number of lateral roots. The increased growth of the root system occurred at the expense of shoot growth which was retarded under conditions of sulphur starvation. Taken together, these results suggest that a regulatory loop appears to exist by which sulphate deficiency, through an increase in glucobrassicin turnover and nitrilase 3 accumulation, initiates the production of extra auxin leading to increased root growth and branching, thus allowing the root system to penetrate new areas of soil effectively to gain access to fresh supplies of sulphur.
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Affiliation(s)
- Alexandra Kutz
- Lehrstuhl für Pflanzenphysiologie, Ruhr-Universität, Universitätsstr. 150, D-44780 Bochum, Germany
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Nitz I, Berkefeld H, Puzio PS, Grundler FM. Pyk10, a seedling and root specific gene and promoter from Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2001; 161:337-346. [PMID: 11448764 DOI: 10.1016/s0168-9452(01)00412-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Pyk10 is a root and hypocotyl specific myrosinase from Arabidopsis thaliana. Northern analysis revealed the root specific expression of pyk10. In order to study the pyk10 promoter and the genomic structure of the gene, a genomic clone was isolated and sequenced. The clone contained the complete pyk10 gene and a promoter region of 3569 bp. The gene spans 2963 bp and consists of 12 exons and 11 introns, a structure that reflects the common gene organization of myrosinases. Within the promoter sequence, different development specific, organ specific, elicitor and plant hormone responsive regulatory elements could be identified, which also occur in other promoters. To determine the pattern of expression, four different 5'-promoter deletion fragments were linked to a ss-glucuronidase (gus) reporter gene and transformed into A. thaliana. The results demonstrated that the pyk10 promoter mediates a developmental gene activity with a strong emphasis in the root. Cis-acting sequences regulating root specific expression were identified to reside in the two promoter fragments B and C.
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Affiliation(s)
- I Nitz
- Institut für Phytopathologie, Universität Kiel, D-24098, Kiel, Germany
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Piotrowski M, Schönfelder S, Weiler EW. The Arabidopsis thaliana isogene NIT4 and its orthologs in tobacco encode beta-cyano-L-alanine hydratase/nitrilase. J Biol Chem 2001; 276:2616-21. [PMID: 11060302 DOI: 10.1074/jbc.m007890200] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitrilases (nitrile aminohydrolases, EC ) are enzymes that catalyze the hydrolysis of nitriles to the corresponding carbon acids. Among the four known nitrilases of Arabidopsis thaliana, the isoform NIT4 is the most divergent one, and homologs of NIT4 are also known from species not belonging to the Brassicaceae like Nicotiana tabacum and Oryza sativa. We expressed A. thaliana NIT4 as hexahistidine tag fusion protein in Escherichia coli. The purified enzyme showed a strong substrate specificity for beta-cyano-l-alanine (Ala(CN)), an intermediate product of cyanide detoxification in higher plants. Interestingly, not only aspartic acid but also asparagine were identified as products of NIT4-catalyzed Ala(CN) hydrolysis. Asn itself was no substrate for NIT4, indicating that it is not an intermediate but one of two reaction products. NIT4 therefore has both nitrilase and nitrile hydratase activity. Several lines of evidence indicate that the catalytic center for both reactions is the same. The NIT4 homologs of N. tabacum were found to catalyze the same reactions and protein extracts of A. thaliana, N. tabacum and Lupinus angustifolius also converted Ala(CN) to Asp and Asn in vitro. NIT4 may play a role in cyanide detoxification during ethylene biosynthesis because extracts from senescent leaves of A. thaliana showed higher Ala(CN) hydratase/nitrilase activities than extracts from nonsenescent tissue.
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Affiliation(s)
- M Piotrowski
- Department of Plant Physiology, Ruhr-Universität, Universitätsstrasse 150, D-44801 Bochum, Germany.
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Bak S, Tax FE, Feldmann KA, Galbraith DW, Feyereisen R. CYP83B1, a cytochrome P450 at the metabolic branch point in auxin and indole glucosinolate biosynthesis in Arabidopsis. THE PLANT CELL 2001; 13:101-11. [PMID: 11158532 PMCID: PMC102201 DOI: 10.1105/tpc.13.1.101] [Citation(s) in RCA: 245] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2000] [Accepted: 10/23/2000] [Indexed: 05/17/2023]
Abstract
Auxins are growth regulators involved in virtually all aspects of plant development. However, little is known about how plants synthesize these essential compounds. We propose that the level of indole-3-acetic acid is regulated by the flux of indole-3-acetaldoxime through a cytochrome P450, CYP83B1, to the glucosinolate pathway. A T-DNA insertion in the CYP83B1 gene leads to plants with a phenotype that suggests severe auxin overproduction, whereas CYP83B1 overexpression leads to loss of apical dominance typical of auxin deficit. CYP83B1 N-hydroxylates indole-3-acetaldoxime to the corresponding aci-nitro compound, 1-aci-nitro-2-indolyl-ethane, with a K(m) of 3 microM and a turnover number of 53 min(-1). The aci-nitro compound formed reacts non-enzymatically with thiol compounds to produce an N-alkyl-thiohydroximate adduct, the committed precursor of glucosinolates. Thus, indole-3-acetaldoxime is the metabolic branch point between the primary auxin indole-3-acetic acid and indole glucosinolate biosynthesis in Arabidopsis.
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Affiliation(s)
- S Bak
- Departments of Plant Sciences, Molecular and Cellular Biology, and Entomology, University of Arizona, Tucson, Arizona 85721, USA
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Müller A, Weiler EW. IAA-synthase, an enzyme complex from Arabidopsis thaliana catalyzing the formation of indole-3-acetic acid from (S)-tryptophan. Biol Chem 2000; 381:679-86. [PMID: 11030425 DOI: 10.1515/bc.2000.088] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
An enzyme complex was isolated from Arabidopsis thaliana that catalyzes the entire pathway of biosynthesis of the major plant growth hormone, indole-3-acetic acid (IAA), from (S)-tryptophan. The 160-180 kDa, soluble complex catalyzes a strictly O2-dependent reaction which requires no further added factors and is stereospecific for the substrate (S)-tryptophan (app. Km = 120 microM). H2(18)O labeling proved that both oxygen atoms of IAA were delivered via H2O. This, as well as immunological evidence for the presence of a nitrilase-like protein in the complex, suggests the reaction to proceed via the intermediate indole-3-acetonitrile. IAA-synthase forms a tight metabolite channel committed to IAA production and occurs in shoots, roots and cell cultures of A. thaliana.
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Affiliation(s)
- A Müller
- Lehrstuhl für Pflanzenphysiologie, Ruhr-Universität Bochum, Germany
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Glawischnig E, Tomas A, Eisenreich W, Spiteller P, Bacher A, Gierl A. Auxin biosynthesis in maize kernels. PLANT PHYSIOLOGY 2000; 123:1109-19. [PMID: 10889260 PMCID: PMC59074 DOI: 10.1104/pp.123.3.1109] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/1999] [Accepted: 03/28/2000] [Indexed: 05/20/2023]
Abstract
Auxin biosynthesis was analyzed in a maize (Zea mays) kernel culture system in which the seeds develop under physiological conditions similar to the in vivo situation. This system was modified for precursor feeding experiments. Tryptophan (Trp) is efficiently incorporated into indole-3-acetic acid (IAA) with retention of the 3, 3' bond. Conversion of Trp to IAA is not competed by indole. Labeling with the general precursors [U-(13)C(6)]glucose and [1, 2-(13)C(2)]acetate followed by retrobiosynthetic analysis strongly suggest that Trp-dependent IAA synthesis is the predominant route for auxin biosynthesis in the maize kernel. The synthesis of IAA from indole glycerol phosphate and IAA formation via condensation of indole with an acetyl-coenzyme A or phosphoenolpyruvate derived metabolite can be excluded.
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Affiliation(s)
- E Glawischnig
- Lehrstuhl für Genetik, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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Grsic-Rausch S, Kobelt P, Siemens JM, Bischoff M, Ludwig-Müller J. Expression and localization of nitrilase during symptom development of the clubroot disease in Arabidopsis. PLANT PHYSIOLOGY 2000; 122:369-378. [PMID: 10677430 DOI: 10.1021/jf00123a006] [Citation(s) in RCA: 209] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The expression of nitrilase in Arabidopsis during the development of the clubroot disease caused by the obligate biotroph Plasmodiophora brassicae was investigated. A time course study showed that only during the exponential growth phase of the clubs was nitrilase prominently enhanced in infected roots compared with controls. NIT1 and NIT2 are the nitrilase isoforms predominantly expressed in clubroot tissue, as shown by investigating promoter-beta-glucuronidase fusions of each. Two peaks of beta-glucuronidase activity were visible: an earlier peak (21 d post inoculation) consisting only of the expression of NIT1, and a second peak at about 32 d post inoculation, which predominantly consisted of NIT2 expression. Using a polyclonal antibody against nitrilase, it was shown that the protein was mainly found in infected cells containing sporulating plasmodia, whereas in cells of healthy roots and in uninfected cells of inoculated roots only a few immunosignals were detected. To determine which effect a missing nitrilase isoform might have on symptom development, the P. brassicae infection in a nitrilase mutant (nit1-3) of Arabidopsis was investigated. As a comparison, transgenic plants overexpressing NIT2 under the control of the cauliflower mosaic virus 35S promoter were studied. Root galls were smaller in nit1-3 plants compared with the wild type. The phenotype of smaller clubs in the mutant was correlated with a lower free indole-3-acetic acid content in the clubs compared with the wild type. Overexpression of nitrilase did not result in larger clubs compared with the wild type. The putative role of nitrilase and auxins during symptom development is discussed.
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Affiliation(s)
- S Grsic-Rausch
- Botanisches Institut, Johann Wolfgang Goethe-Universität, Siesmayerstrasse 70, 60054 Frankfurt, Germany
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Swango KL, Hymes J, Brown P, Wolf B. Amino acid homologies between human biotinidase and bacterial aliphatic amidases: putative identification of the active site of biotinidase. Mol Genet Metab 2000; 69:111-5. [PMID: 10720437 DOI: 10.1006/mgme.2000.2959] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A search of protein databases revealed amino acid homologies among human biotinidase, bacterial aliphatic amidases, and bacterial and plant nitrilases. Amino acids YRK(210-212) of biotinidase are conserved among the enzyme families. This homology and naturally occurring mutations that cause biotinidase deficiency suggest that this region is essential for enzyme activity and is conserved from bacteria. Cys(245) is likely the cysteine in the active site of biotinidase.
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Affiliation(s)
- K L Swango
- Department of Human Genetics, Medical College of Virginia of Virginia Commonwealth University, Richmond, Virginia, 23298, USA
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50
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Grsic-Rausch S, Kobelt P, Siemens JM, Bischoff M, Ludwig-Müller J. Expression and localization of nitrilase during symptom development of the clubroot disease in Arabidopsis. PLANT PHYSIOLOGY 2000; 122:369-78. [PMID: 10677430 PMCID: PMC58874 DOI: 10.1104/pp.122.2.369] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/1999] [Accepted: 10/20/1999] [Indexed: 05/18/2023]
Abstract
The expression of nitrilase in Arabidopsis during the development of the clubroot disease caused by the obligate biotroph Plasmodiophora brassicae was investigated. A time course study showed that only during the exponential growth phase of the clubs was nitrilase prominently enhanced in infected roots compared with controls. NIT1 and NIT2 are the nitrilase isoforms predominantly expressed in clubroot tissue, as shown by investigating promoter-beta-glucuronidase fusions of each. Two peaks of beta-glucuronidase activity were visible: an earlier peak (21 d post inoculation) consisting only of the expression of NIT1, and a second peak at about 32 d post inoculation, which predominantly consisted of NIT2 expression. Using a polyclonal antibody against nitrilase, it was shown that the protein was mainly found in infected cells containing sporulating plasmodia, whereas in cells of healthy roots and in uninfected cells of inoculated roots only a few immunosignals were detected. To determine which effect a missing nitrilase isoform might have on symptom development, the P. brassicae infection in a nitrilase mutant (nit1-3) of Arabidopsis was investigated. As a comparison, transgenic plants overexpressing NIT2 under the control of the cauliflower mosaic virus 35S promoter were studied. Root galls were smaller in nit1-3 plants compared with the wild type. The phenotype of smaller clubs in the mutant was correlated with a lower free indole-3-acetic acid content in the clubs compared with the wild type. Overexpression of nitrilase did not result in larger clubs compared with the wild type. The putative role of nitrilase and auxins during symptom development is discussed.
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Affiliation(s)
- S Grsic-Rausch
- Botanisches Institut, Johann Wolfgang Goethe-Universität, Siesmayerstrasse 70, 60054 Frankfurt, Germany
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