| Literature DB >> 20565974 |
Rubén Rellán-Alvarez1, Sofía Andaluz, Jorge Rodríguez-Celma, Gert Wohlgemuth, Graziano Zocchi, Ana Alvarez-Fernández, Oliver Fiehn, Ana Flor López-Millán, Javier Abadía.
Abstract
BACKGROUND: Plants grown under iron deficiency show different morphological, biochemical and physiological changes. These changes include, among others, the elicitation of different strategies to improve the acquisition of Fe from the rhizosphere, the adjustment of Fe homeostasis processes and a reorganization of carbohydrate metabolism. The application of modern techniques that allow the simultaneous and untargeted analysis of multiple proteins and metabolites can provide insight into multiple processes taking place in plants under Fe deficiency. The objective of this study was to characterize the changes induced in the root tip proteome and metabolome of sugar beet plants in response to Fe deficiency and resupply.Entities:
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Year: 2010 PMID: 20565974 PMCID: PMC3017792 DOI: 10.1186/1471-2229-10-120
Source DB: PubMed Journal: BMC Plant Biol ISSN: 1471-2229 Impact factor: 4.215
Figure 12-D IEF-SDS PAGE proteome maps of root tips from Fe-sufficient and Fe-deficient . Proteins were separated in the first dimension in linear (pH 5-8) IPG gel strips and in the second dimension in 12% acrylamide vertical gels. Scans of real typical gels of root tips from Fe-sufficient and Fe-deficient plants are shown in A and B, respectively. Virtual composite images, showing all polypeptides present in root tips from Fe-deficient and Fe-sufficient plants are shown in panels C and D. Statistical significance was assessed with a t-test (p < 0.10), and a 2-fold change in spot intensity between treatments was used as a threshold. Only spots that fit both criteria are marked in panel C; spots whose intensities decrease or disappear completely with Fe deficiency were labelled with green and blue marks, respectively, and those increasing with Fe deficiency or only present in Fe-deficient gels were labelled with yellow and red marks, respectively. In panel D, polypeptides that had significant homologies with proteins in the databases (using MALDI-MS and MASCOT) are marked by squares and labelled with lower-case letters. Homologies are described in detail in Table 1.
Proteins identified by MALDI-MS in 2-D IEF-SDS PAGE gels
| Spot | Th. MW | Th. pI | Exp. MW | Exp. pI | Score(1,2) | Accession # | Homology | Species |
|---|---|---|---|---|---|---|---|---|
| Increased proteins in Fe-deficiency | ||||||||
| 39 | 7.6 | 42 | 5.9 | 761 | T48396 | fructose 1,6-bisphosphate aldolase | ||
| 27 | 5.5 | 35 | 5.4 | 1431 | gi|556171 | triose-phosphate isomerase | ||
| 31 | 4.9 | 45 | 5.4 | 1031 | gi|28172909 | cytosolic 3-phosphoglycerate kinase | ||
| 49 | 5.6 | 59 | 5.5 | 1881 | gi|1087071 | enolase | ||
| 49 | 5.6 | 58 | 5.4 | 1231 | T12341 | enolase | ||
| 36 | 5.9 | 40 | 6.2 | 1401 | CAB61618 | malate dehydrogenase | ||
| 36 | 5.9 | 40 | 5.8 | 771 | CAB61618 | malate dehydrogenase | ||
| 22 | 7.6 | 40 | 6.0 | 1241 | gi|48375044 | malate dehydrogenase | ||
| 55 | 6.0 | 60 | 6.0 | 1851 | O78692 | F1 ATPase α subunit | ||
| 49 | 5.1 | 58 | 5.3 | 1701 | gi|4388533 | F1 ATPase β subunit | ||
| 36 | 5.2 | 49 | 5.5 | 2991 | gi|1052973 | fructokinase | ||
| 41 | 6.5 | 44 | 6.3 | 1021 | gi|38636526 | formate dehydrogenase | ||
| 26 | 5.5 | 35 | 5.4 | 1131 | gi|21689609 | At1g79210/YUP8H12R_1 | ||
| 17 | 5.9 | 17 | 5.5 | 1162 | gi|16301 | glycine rich protein | ||
| New spots in Fe-deficiency | ||||||||
| 37 | 7.1 | 36 | 6.6 | 1011 | gi|19566 | glyceraldehyde 3-phosphate DH | ||
| 23 | 8.7 | 16 | 6.6 | 652 | Q9XH32 | DMRL synthase | ||
| Decreased spots in Fe-deficiency | ||||||||
| 16 | 6.3 | 15 | 6.4 | 1661 | gi|3309053 | nucleoside diphosphate kinase I | ||
| 23 | 6.4 | 30 | 6.8 | 2171 | gi|11496133 | oxalate oxidase-like germin 171 | ||
| 22 | 6.1 | 32 | 5.7 | 1881 | gi|34365651 | At4g27270 | ||
| Missing spots in Fe-deficiency | ||||||||
| 23 | 6.4 | 34 | 5.7 | 2171 | gi|11496133 | oxalate oxidase-like germin 171 | ||
| 9 | 6.0 | 49 | 5.7 | 492 | gi|2956703 | peroxidase | ||
| 29 | 5.1 | 38 | 5.3 | 692 | gi|5101868 | caffeoyl CoA O-methyltransferase | ||
Scores (equal to -10*Log P, P being the probability that the observed match is a random event) are based on: (1) MS1 Peptide mass fingerprint data, with protein scores >76 being statistically significant (p < 0.05), and (2)MS2 ion sequencing data, with individual ion scores > 40 indicating identity or extensive homology (p < 0.05). In both cases, protein scores are derived from ion scores as a non-probabilistic basis for ranking protein hits. Proteins are separated in different groups depending on whether they increased, decreased, appeared (new) or disappeared (missing) when compared to control plants.
Figure 2DMRL and flavin analysis. Semi-quantitative RT-PCR analysis of the BvDMRL and actin gene transcripts (A), zoom scans of typical gels containing the BvDMRL protein (B) and riboflavin sulphates (C) and riboflavin (D) concentrations in sugar beet root tips from Fe sufficient (+Fe), Fe-deficient (-Fe), 24 h Fe-resupplied, 72 h Fe-resupplied YZ and 72 h Fe-resupplied WZ. Letters in (C) and (D) indicate significant differences (n = 6, p < 0.05, Duncan test).
Figure 3Score scatter plot of identified metabolites. Partial Least Square (PLS) analysis, showing the score scatter plot of PLS vector 1 (t1) vs. PLS vector 2 (t2) of identified metabolites in sugar beet root tips from Fe sufficient (+Fe, green circles), Fe-deficient (-Fe, red circles), 24 h Fe-resupplied (24h, blue squares), 72 h Fe-resupplied YZ (72h YZ, grey squares) and 72 h Fe-resupplied WZ (72h WZ, orange squares).
Identified metabolite response ratios of the different treatments vs. Fe-sufficient controls (+Fe)
| # | metabolites | -Fe | 24h | 72hYZ | 72hWZ | |
|---|---|---|---|---|---|---|
| Aminoacid and Nitrogen Metabolism | ||||||
| 1 | nicotianamine | |||||
| 2 | 2-aminoadipic acid | 11.2 | 0300, 1100, 0310 | |||
| 3 | 2-hydroxyglutaric acid | 1.3 | 0650 | |||
| 4 | citrulline | 1.4 | 1.7 | 0330, 1100 | ||
| 5 | lysine | 2.5 | 0300, 1100, 0310, 0780, 0960, 0310 | |||
| 6 | serine | 0970, 1100, 0260, 0600, 0460, 0271, 0272, 0920, 0680 | ||||
| 7 | hydroxylamine | 1.1 | 0910 | |||
| 8 | urea | 1.0 | 1.0 | 6.2 | 0330, 1100, 0230, 0240 | |
| 9 | arginine + ornithine | 2.2 | 1.1 | 1.6 | 0.0 | 0330, 1100, 0970 |
| 10 | aspartic acid | 1.0 | 1.3 | 1.4 | 1.1 | 0970, 1100, 0260, 0760, 0710, 0300, 0910, 0252, 0460, 0410, 0330, 0770 |
| 11 | glutamic acid | 1.1 | 1.0 | 1.2 | -1.0 | 0970, 1100, 0480, 0860, 0650, 0251, 0340, 0330 |
| 12 | glycine | -1.3 | -1.3 | 1.3 | -1.5 | 0970, 1100, 0260, 0480, 0730, 0310, 0230, 0120, 0460, 0860, 0680 |
| 13 | phenylalanine | 1.2 | -1.1 | 1.2 | -1.1 | 0970, 1100, 0400, 0966, 0960, 0360, 0940 |
| 14 | tyrosine | 2.1 | -1.2 | 1.3 | -1.3 | 0970, 1100, 0950, 0730, 0960, 0350, 0940, 0966 |
| 15 | putrescine | -1.1 | -1.8 | -1.3 | -1.3 | 1100, 0960, 0480 |
| 16 | ornithine | 1.6 | -1.2 | 1.2 | -1.0 | 1100, 0330, 0480 |
| 17 | tryptophan | 1.0 | -1.2 | 1100, 0970, 0380, 0901, 0400, 0966 | ||
| 18 | oxoproline | -1.3 | -1.1 | -1.2 | 0330 | |
| 19 | valine | 1.2 | 1.0 | 1.4 | 0970, 0901, 0400, 0966, 0380, 1100 | |
| 20 | asparagine | -1.0 | -1.8 | -1.2 | 1100, 0970, 0910, 0252, 0460 | |
| 21 | alanine | -1.4 | 1.7 | 1.5 | 1100, 0970, 0252, 0710, 0450, 0430, 0272, 0720 | |
| 22 | glutamine | -1.6 | 1100, 0970, 0910, 0251, 0240, 0230 | |||
| Carbohydrate metabolism | ||||||
| 23 | galactinol | 7.6 | 0052 | |||
| 24 | raffinose | 9.9 | 0052 | |||
| 25 | sucrose | 2.2 | 0052, 1100, 0500 | |||
| 26 | lactobionic acid | |||||
| 27 | N-acetyl-D-mannosamine | 1100, 0530 | ||||
| 28 | arabinose | 1.4 | 1.4 | |||
| 29 | xylonic acid | 1.4 | ||||
| 30 | inulobiose | 2.1 | ||||
| 31 | cellobiose | 5.1 | 0500 | |||
| 32 | mannitol | -1.3 | 1.6 | 1.4 | 0052, 1100, 0053, 4070, 0562 | |
| 33 | xylitol | 1.1 | 1.3 | 1.4 | 1100, 0040 | |
| 34 | fructose | -1.8 | -1.7 | 1.9 | -1.3 | 0052, 1100, 0051, 0500 |
| 35 | suberyl glycine | 1.1 | -2.0 | -1.1 | ||
| Co-enzymes and alkaloid biosynthesis | ||||||
| 36 | ribitol | 5.6 | 2.0 | 1100, 0040, 0740 | ||
| 37 | pantothenic acid | 1.7 | 1.4 | 1100, 0410, 0770 | ||
| 38 | nicotinic acid | -1.3 | 1.3 | 1.8 | 1100, 0760, 0960 | |
| Glycolysis | ||||||
| 39 | glucose-1-phosphate | 1.4 | 2.5 | 1.7 | 0052, 1100, 0010, 0500, 0040, 0520 | |
| 40 | glucose | 1.1 | -3.9 | 1.8 | -2.4 | 0052, 1100, 0010, 0500, 0030, 0901 |
| 41 | fructose-6-phosphate | -1.1 | -1.3 | 1.2 | 1.2 | 0710, 1100, 0040, 0680, 0530 |
| 42 | glucose-6-phosphate 2 | -1.3 | -1.6 | 1.2 | -1.1 | 0500, 1100, 0562 |
| 43 | 3-phosphoglycerate | -1.3 | 1.2 | 0561, 0260, 0010, 0710, 0630, 1100 | ||
| Glyoxylate and dicarboxylate metabolism | ||||||
| 44 | glyceric acid | 1.3 | 1.7 | 0561, 0260, 0030, 0630, 1100 | ||
| 45 | glycolic acid | 2.9 | 2.0 | 3.1 | 0630, 1100, 0361 | |
| 46 | oxalic acid | 1.5 | 0630, 1100 | |||
| Lipid metabolism | ||||||
| 47 | behenic acid | 1040 | ||||
| 48 | y hexaric acid | 1.7 | ||||
| 49 | stearic acid | -1.2 | 4.1 | 0061, 1040 | ||
| 50 | glycerol | -1.2 | ||||
| 51 | cerotic acid | -1.1 | ||||
| 52 | myristic acid | 1.0 | 0061 | |||
| 53 | palmitic acid | -1.2 | 0061, 1040, 1100, 0062, 0071 | |||
| 54 | phosphoethanolamine | 1.7 | 1.5 | 1.7 | 0600, 0260, 1100, 0564 | |
| 55 | lauric acid | -1.1 | 2.1 | 2.3 | 0061 | |
| 56 | capric acid | -1.1 | 1.4 | 0061 | ||
| 57 | pentadecanoic acid | 1.0 | 1.2 | 2.9 | 3.0 | |
| 58 | pelargonic acid | -1.2 | 1.1 | 2.5 | 1.8 | |
| 59 | linoleic acid | -1.4 | 1.2 | 2.3 | 2.4 | 1040, 1100 |
| 60 | glycerol-alpha-phosphate | -1.0 | 1.0 | 1.5 | 1.5 | |
| Oxidative stress | ||||||
| 61 | threonic acid | 1.6 | 1.2 | 1.7 | ||
| 62 | dehydroascorbate | 1.4 | 1.4 | |||
| 63 | 2-hydroxypentanoic acid | -1.2 | 1.5 | 0982 | ||
| 64 | 1,2,4-benzenetriol | 1.5 | 3.0 | 1100, 0361, 0362, 0627 | ||
| 65 | y pentonic acid | 1.6 | -1.4 | -1.1 | -1.8 | |
| Pentose phosphate pathway | ||||||
| 66 | ribose | 1.5 | 1.9 | 1100, 0030 | ||
| 67 | gluconic acid | 1.6 | 2.5 | 1.6 | 1100, 0030, 0710, 0230 | |
| Signaling | ||||||
| 68 | myoinositol | 2.4 | ||||
| 69 | GABA | 1.8 | 4.5 | 1.5 | 1100, 0251, 0410, 0650 | |
| 70 | inositol-monophosphate | -1.2 | 4070, 0562 | |||
| TCA Cycle | ||||||
| 71 | aconitic acid | 1.8 | 1100, 0020, 0720, 0630 | |||
| 72 | citric acid | 1.5 | 1100, 0020, 0720, 0630, 0251, 0252 | |||
| 73 | malate | 1.8 | 1100, 0020, 0720, 0630, 0251, 0252, 0710, 0620 | |||
| 74 | succinic acid | 1.4 | 1.5 | 2.2 | 1100, 0020, 0720, 0630, 0251, 0252, 0350, 0650, 0632, 0361, 0190, 0640 | |
| Others | ||||||
| 75 | acetohydroxamic acid | 1.1 | -1.6 | |||
| 76 | phosphoric acid | -1.3 | -1.5 | 3.8 | 1100, 0190, 0195, 0550 | |
| 77 | adenosine-5-monophosphate | -1.2 | 1.3 | 1.1 | 1100, 0230, 0908 | |
When the response ratio (level in a given treatment divided by the level in the +Fe treatment) was lower than 1 the inverse was taken and the sign changed. Values indicated in bold represent a t-test significance of p < 0.05. The last column shows A. thaliana KEGG pathway numbers where the metabolite is predicted to be involved; all KEGG pathway numbers are hyper-linked to the corresponding KEGG website. To reach one specific pathway in KEGG type in your web browser: "http://www.genome.jp/kegg-bin/show_pathway?ath0XXXX" being XXXX the pathway number.
Figure 4Changes in metabolic pathways as affected by Fe status. Pathways related to metabolites and proteins were integrated according to the KEGG database. Statistical t-student tests were performed to both protein and metabolite data to show statistically relevant changes between samples. Red squares indicate metabolites showing significant, marked (more than 4-fold) up-accumulation compared to the controls, and yellow ones mean significant, moderate (less than 4-fold) up-accumulation. Blue squares mean significant, marked (more than 4-fold) down-accumulation, and green ones mean significant moderate (less than 4-fold) down-accumulation. The same colour code was used with proteins, represented by circles. Red circles are proteins detected only in Fe-deficient gels, and yellow ones mean significantly up-accumulated proteins using a 2-fold threshold. Decreased (at least 50%) and missing proteins in the Fe-deficient treatment were represented in green and blue respectively. Each number or letter corresponds to those shown in the corresponding protein and metabolite tables (Tables 1 and 2 respectively). Panels correspond to root tip extracts from plants Fe-deficient (A), 24h after Fe resupply (B), and 72h after Fe resupply (YZ in panel C and WZ in panel D).