Plant Stress Physiology | Plant Stress Physiology ...-Fe-Fe-Fe-Fe-Fe-Fe-Fe-Fe +Fe +Fe +Fe+...
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-Fe -Fe -Fe -Fe -Fe -Fe -Fe -Fe +Fe +Fe +Fe +Fe +Fe +Fe +Fe 24 h 24 h 24 h 24 h 24 h 24 h 72 h Y 72 h Y 72 h Y 72 h Y 72 h Y 72 h Y 72 h Y 72 h W 72 h W 72 h W 72 h W 72 h W 72 h W -15 -10 -5 0 5 10 15 t1 -15 -10 -5 0 5 10 15 t2 -Fe -Fe -Fe -Fe -Fe -Fe -Fe -Fe +Fe +Fe +Fe +Fe +Fe +Fe +Fe 24 h 24 h 24 h 24 h 24 h 24 h 72 h Y 72 h Y 72 h Y 72 h Y 72 h Y 72 h Y 72 h Y 72 h W 72 h W 72 h W 72 h W 72 h W 72 h W Proteomic and metabolic profiles of Beta vulgaris root tips: changes induced in response to iron deficiency and resupply R. Rellán-Álvarez a , S. Andaluz a , A.F. López-Millán a , A. Álvarez-Fernández a , O. Fiehn b and J. Abadía a a Plant Nutrition Dept., Aula Dei Experimental Station, Council for Scientific Research (CSIC), Apdo. 13034, 50080 Zaragoza, Spain. Visit at: www.eead.csic.es/stressphysiology. b Genome Center, University of California, Davis, CA, USA. Visit at: www.fiehnlab.ucdavis.edu Background Iron-deficient Strategy I plants develop a series of biochemical and morphological changes in roots that lead to an increased capacity for Fe uptake. These responses at the uptake level are accompanied by several metabolic changes that support this adaptation mechanism to Fe-deficiency [1]. These metabolic changes include an induction of carbon metabolism pathways with a increase in the activities of PEPC and several enzymes of the glycolytic pathway and the TCA cycle. These changes can be partially reverted after Fe resupply [2, 3]. Other changes include accumulation of organic acids and flavins and excretion of phenolic compounds and flavins. In this work, a comprehensive analysis of the metabolic and proteomic changes observed in sugar beet root tips with Fe- deficiency and Fe-resupply has been carried out. Experimental ROOT TIPS were taken from Fe-sufficient (grown with 45 M Fe(III)-EDTA), Fe- deficient (grown with 0 M Fe), and Fe-resupplied Beta vulgaris plants (24 and 72 hours after Fe resupply with 45 M Fe(III)-EDTA). METABOLOMIC PROFILES: extracts were obtained as described elsewhere [5]. A mixture of internal retention index markers composed by different fatty acid markers were added to the dried extracts. Samples were derivatized in two steps with methoxiamine hydrochloride and MSTFA 1%, randomized and analyzed by GC-MS following the recommendations described by the Metabolomics Standards Initiative [3]. Mass chromatograms were deconvoluted using the Leco ChromaTOF software and peaks were exported to the BinBase database [5] and identified using the Fiehn Library (http://fiehnlab.ucdavis.edu/Metabolite-Library-2007). PROTEOMIC PROFILES: extracts were obtained according to Meyer et al. [4] and run in 2D gels. The first dimension was run with a pl linear gradient from 5 to 8 and focused at 20 ºC for a total of 14000 V.h. For the second dimension IPG strips were loaded into 12% SDS-PAGE and run at 20 mA for 1.5 h. Gels were stained with Comassie blue and analyzed with the Bio-Rad PD Quest 8.0 software. Protein spots were excised using a Proteineer DP protein station and analyzed using a Bruker Ultraflex MALDI TOF-TOF and LIFT TOF-TOF. Peptide masses were used as input to search the NCBInr database using Mascot Software. EXPRESSION OF 6,7-DIMETHYL-8-NBITYLLUMAZINE (DMRL) SYNTHASE transcripts in root tips was analyzed by semi-quantitative RT-PCR. Metabolomic profiles FIGURE 1. Score scatter plot of component 1 vs. component 2 after Partial Least Square analysis of identified metabolites. Fe sufficient (+Fe), Fe-deficient (- Fe), 24 Fe-resupplied (24h) and 72 h Fe-resupplied root tip yellow zone (72 h Y) and new white zone (72 h W). The red circle contains a +/- 3.00 STD Dev. Seventy six metabolites were identified in root tips. A principal component analysis of the identified metabolites shows a good separation between Fe- sufficient and Fe-deficient root tips. 24 h Fe-resupplied root tip metabolites fall between those of Fe-deficient and Fe-sufficient root tips. 72 h Fe-resupplied root tip metabolites show a larger degree of variation due to sampling difficulties. An increase in organic acid metabolism (TCA cycle) with Fe-deficiency was observed in agreement with previous results [1]. An activation of the raffinose series of oligosaccharides (RSOs), including raffinose, galactinol and myo- inositol was also observed in Fe-deficient and 24-h resupplied plants. This activation has never been described before in plants under Fe deficiency, although is a common response in plants under other stresses. References [1] Schmidt (1999) New Phytol. 141: 1-26. [2] López-Millán et al. (2000) Plant Physol. 124: 885-897. [3] López-Millán et al. (2001) Australian J Plant Physiol. 28: 171-180. [4] Meyer et al. (1988) Electrophoresis 9: 704-712. [5] Fiehn et al. (2008) Plant J. 53: 691-704. [6] Fiehn et al. (2005) Proc. Lect. Notes Bioinformatics 3615: 224-239. Conclusions Fe-deficiency increased the amount of many TCA cycle intermediates in Beta vulgaris root tips. An increase in the amount of the raffinose series of oligosaccharides, including raffinose, galactinol and myo-inositol was observed in Fe-deficient and 24 hours Fe-resupplied plant roots. Fe-deficiency induced significant intensity changes in a large number of proteins, many of them associated to carbohydrate catabolism. A protein identified as DMRL synthase was very abundant in root tips from Fe-deficient sugar beet and was not detectable in Fe-sufficient roots. This protein was found to be regulated transcriptionally by Fe status. Expression of DMRL synthase FIGURE 3. Semi-quantitative RT-PCR analysis of the BvDMRLs transcript in root tip extracts. Fe sufficient (+Fe), Fe-deficient (-Fe), 24 Fe-resupplied (24h) and 72 h Fe- resupplied root tip yellow zone (72 h yellow) and new white zone (72 h white). The largest change found in the proteome map of root tip extracts from plants grown in Fe-deficiency corresponds to appearance of a spot highlighted in Fig 2D and identified as DMRL synthase. The expression of DMRL synthase was also up-regulated in Fe-deficient conditions. Proteomic profiles FIGURE 2. 2-D IEF-SDS PAGE proteome maps of root tips from Fe-sufficient (A & C) and Fe-deficient (B & D) plants. Scans of real typical gels are shown in A and B. Virtual composite images (C & D) created containing all spots present in the real gels. Spots whose intensities decrease or disappear completely with Fe deficiency are labeled with blue and green marks, respectively (C), and those increasing with Fe deficiency or only present in Fe-deficient gels are labeled with orange and red marks, respectively (D). Fe-deficiency results in relative intensity changes in a large number of these proteins. Most of the proteins found to be up-regulated by Fe deficiency were identified as carbohydrate catabolism enzymes, including 5 out of 10 enzymes of the glycolytic pathway. Fe-deficiency also increased the activities of several enzymes of the citric acid cycle. Up-regulation of carbohydrate catabolism in roots of plants grown in Fe deficient conditions is probably a result of an increased demand of energy and reducing power in roots needed to sustain the increased activity of H + -ATPase and Fe-reductase. DMRL Acknowledgments This study was supported by the Spanish Ministry of Science and Innovation (projects AGL2006-1416 and AGL2007-61948, co-financed with FEDER), the European Commission (EU 6th Framework Integrated Project ISAFRUIT), and the Aragón Government (group A03).
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Proteomic and metabolic profiles of Beta vulgaris root tips: changes induced in response to iron deficiency and resupply
R. Rellán-Álvareza, S. Andaluza, A.F. López-Millána, A. Álvarez-Fernándeza, O. Fiehnb and J. Abadíaa
aPlant Nutrition Dept., Aula Dei Experimental Station, Council for Scientific Research (CSIC), Apdo. 13034, 50080 Zaragoza, Spain. Visitat: www.eead.csic.es/stressphysiology. bGenome Center, University of California, Davis, CA, USA. Visit at: www.fiehnlab.ucdavis.edu
BackgroundIron-deficient Strategy I plants develop a series of biochemical and morphologicalchanges in roots that lead to an increased capacity for Fe uptake. Theseresponses at the uptake level are accompanied by several metabolic changes thatsupport this adaptation mechanism to Fe-deficiency [1]. These metabolic changesinclude an induction of carbon metabolism pathways with a increase in theactivities of PEPC and several enzymes of the glycolytic pathway and the TCAcycle. These changes can be partially reverted after Fe resupply [2, 3]. Otherchanges include accumulation of organic acids and flavins and excretion ofphenolic compounds and flavins. In this work, a comprehensive analysis of themetabolic and proteomic changes observed in sugar beet root tips with Fe-deficiency and Fe-resupply has been carried out.
Experimental ROOT TIPS were taken from Fe-sufficient (grown with 45 M Fe(III)-EDTA), Fe-
deficient (grown with 0 M Fe), and Fe-resupplied Beta vulgaris plants (24 and 72hours after Fe resupply with 45 M Fe(III)-EDTA).
METABOLOMIC PROFILES: extracts were obtained as described elsewhere [5]. Amixture of internal retention index markers composed by different fatty acid markerswere added to the dried extracts. Samples were derivatized in two steps withmethoxiamine hydrochloride and MSTFA 1%, randomized and analyzed by GC-MSfollowing the recommendations described by the Metabolomics Standards Initiative[3]. Mass chromatograms were deconvoluted using the Leco ChromaTOF software andpeaks were exported to the BinBase database [5] and identified using the FiehnLibrary (http://fiehnlab.ucdavis.edu/Metabolite-Library-2007).
PROTEOMIC PROFILES: extracts were obtained according to Meyer et al. [4] andrun in 2D gels. The first dimension was run with a pl linear gradient from 5 to 8 andfocused at 20 ºC for a total of 14000 V.h. For the second dimension IPG strips wereloaded into 12% SDS-PAGE and run at 20 mA for 1.5 h. Gels were stained withComassie blue and analyzed with the Bio-Rad PD Quest 8.0 software. Protein spotswere excised using a Proteineer DP protein station and analyzed using a BrukerUltraflex MALDI TOF-TOF and LIFT TOF-TOF. Peptide masses were used as input tosearch the NCBInr database using Mascot Software.
EXPRESSION OF 6,7-DIMETHYL-8-NBITYLLUMAZINE (DMRL) SYNTHASE transcriptsin root tips was analyzed by semi-quantitative RT-PCR.
Metabolomic profilesFIGURE 1. Score scatter plot of component 1 vs. component 2 after PartialLeast Square analysis of identified metabolites. Fe sufficient (+Fe), Fe-deficient (-Fe), 24 Fe-resupplied (24h) and 72 h Fe-resupplied root tip yellow zone (72 h Y) and newwhite zone (72 h W). The red circle contains a +/- 3.00 STD Dev.
Seventy six metabolites were identified in root tips. A principal componentanalysis of the identified metabolites shows a good separation between Fe-sufficient and Fe-deficient root tips. 24 h Fe-resupplied root tip metabolites fallbetween those of Fe-deficient and Fe-sufficient root tips. 72 h Fe-resuppliedroot tip metabolites show a larger degree of variation due to samplingdifficulties.
An increase in organic acid metabolism (TCA cycle) with Fe-deficiency wasobserved in agreement with previous results [1]. An activation of the raffinoseseries of oligosaccharides (RSOs), including raffinose, galactinol and myo-inositol was also observed in Fe-deficient and 24-h resupplied plants. Thisactivation has never been described before in plants under Fe deficiency,although is a common response in plants under other stresses.
References[1] Schmidt (1999) New Phytol. 141: 1-26. [2] López-Millán et al. (2000) Plant Physol. 124:885-897. [3] López-Millán et al. (2001) Australian J Plant Physiol. 28: 171-180. [4] Meyer et al.(1988) Electrophoresis 9: 704-712. [5] Fiehn et al. (2008) Plant J. 53: 691-704. [6] Fiehn et al.(2005) Proc. Lect. Notes Bioinformatics 3615: 224-239.
Conclusions Fe-deficiency increased the amount of many TCA cycle intermediates in Beta
vulgaris root tips. An increase in the amount of the raffinose series ofoligosaccharides, including raffinose, galactinol and myo-inositol was observed inFe-deficient and 24 hours Fe-resupplied plant roots.
Fe-deficiency induced significant intensity changes in a large number ofproteins, many of them associated to carbohydrate catabolism. A proteinidentified as DMRL synthase was very abundant in root tips from Fe-deficientsugar beet and was not detectable in Fe-sufficient roots. This protein was foundto be regulated transcriptionally by Fe status.
Expression of DMRL synthaseFIGURE 3. Semi-quantitative RT-PCR analysis of the BvDMRLs transcript in roottip extracts. Fe sufficient (+Fe), Fe-deficient (-Fe), 24 Fe-resupplied (24h) and 72 h Fe-resupplied root tip yellow zone (72 h yellow) and new white zone (72 h white).
The largest change found in the proteome map of root tip extracts fromplants grown in Fe-deficiency corresponds to appearance of a spot highlighted inFig 2D and identified as DMRL synthase. The expression of DMRL synthase wasalso up-regulated in Fe-deficient conditions.
Proteomic profilesFIGURE 2. 2-D IEF-SDS PAGE proteome maps of root tips from Fe-sufficient (A& C) and Fe-deficient (B & D) plants. Scans of real typical gels are shown in A and B.Virtual composite images (C & D) created containing all spots present in the real gels.Spots whose intensities decrease or disappear completely with Fe deficiency are labeledwith blue and green marks, respectively (C), and those increasing with Fe deficiency oronly present in Fe-deficient gels are labeled with orange and red marks, respectively (D).
Fe-deficiency results in relative intensity changes in a large number of theseproteins. Most of the proteins found to be up-regulated by Fe deficiency wereidentified as carbohydrate catabolism enzymes, including 5 out of 10 enzymesof the glycolytic pathway. Fe-deficiency also increased the activities of severalenzymes of the citric acid cycle. Up-regulation of carbohydrate catabolism inroots of plants grown in Fe deficient conditions is probably a result of anincreased demand of energy and reducing power in roots needed to sustain theincreased activity of H+-ATPase and Fe-reductase.
DMRL
AcknowledgmentsThis study was supported by the Spanish Ministry of Science and Innovation (projects AGL2006-1416 and AGL2007-61948, co-financed with
FEDER), the European Commission (EU 6th Framework Integrated Project ISAFRUIT), and the Aragón Government (group A03).
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