Abstract
BackgroundDuring the photosynthesis, two isoforms of the fructose-1,6-bisphosphatase (FBPase), the chloroplastidial (cFBP1) and the cytosolic (cyFBP), catalyse the first irreversible step during the conversion of triose phosphates (TP) to starch or sucrose, respectively. Deficiency in cyFBP and cFBP1 isoforms provokes an imbalance of the starch/sucrose ratio, causing a dramatic effect on plant development when the plastidial enzyme is lacking.ResultsWe study the correlation between the transcriptome and proteome profile in rosettes and roots when cFBP1 or cyFBP genes are disrupted in Arabidopsis thaliana knock-out mutants. By using a 70-mer oligonucleotide microarray representing the genome of Arabidopsis we were able to identify 1067 and 1243 genes whose expressions are altered in the rosettes and roots of the cfbp1 mutant respectively; whilst in rosettes and roots of cyfbp mutant 1068 and 1079 genes are being up- or down-regulated respectively. Quantitative real-time PCR validated 100% of a set of 14 selected genes differentially expressed according to our microarray analysis. Two-dimensional (2-D) gel electrophoresis-based proteomic analysis revealed quantitative differences in 36 and 26 proteins regulated in rosettes and roots of cfbp1, respectively, whereas the 18 and 48 others were regulated in rosettes and roots of cyfbp mutant, respectively. The genes differentially expressed and the proteins more or less abundant revealed changes in protein metabolism, RNA regulation, cell signalling and organization, carbon metabolism, redox regulation, and transport together with biotic and abiotic stress. Notably, a significant set (25%) of the proteins identified were also found to be regulated at a transcriptional level.ConclusionThis transcriptomic and proteomic analysis is the first comprehensive and comparative study of the gene/protein re-adjustment that occurs in photosynthetic and non-photosynthetic organs of Arabidopsis mutants lacking FBPase isoforms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0945-7) contains supplementary material, which is available to authorized users.
Highlights
During the photosynthesis, two isoforms of the fructose-1,6-bisphosphatase (FBPase), the chloroplastidial and the cytosolic, catalyse the first irreversible step during the conversion of triose phosphates (TP) to starch or sucrose, respectively
We found that: (i) cfbp1 and cyfbp mutants affect the expression of a broad range of genes, representing the reprogramming of near to 10% of the Arabidopsis genome; (ii) chloroplastic fructose-1 (cFBP1) or cytosolic fructose1 (cyFBP) gene disruption induces different expression profiles in rosettes and roots; (iii) differentially expressed genes/proteins are related to carbon metabolism, protein metabolism, cell signalling, gene regulation, transport, and stress responses; and (iv) the transcriptome and the proteome data were correlated
Expressed genes in Arabidopsis knock-out mutants lacking cFBP1 and cyFBP genes To analyse the genome-wide effects of cFBP1 or cyFBP gene disruption in rosettes and roots tissues, we performed a microarray analysis comparing cfbp1 and cyfbp knock-out mutants with the wild-type plants using a 70mer oligonucleotide microarray representing the genome of Arabidopsis
Summary
Two isoforms of the fructose-1,6-bisphosphatase (FBPase), the chloroplastidial (cFBP1) and the cytosolic (cyFBP), catalyse the first irreversible step during the conversion of triose phosphates (TP) to starch or sucrose, respectively. To maintain an optimum photosynthetic rate, this carbon partitioning needs to be highly regulated [1] This regulation is strongly dependent on the circadian rhythm of the plant and carbon metabolite levels and is carried out through the export of triose phosphate intermediates produced in the chloroplast during the reductive pentose phosphate pathway or the Calvin-Benson cycle [2]. A chloroplastic isoform (cFBP1), found in photosynthetic eukaryotes [5], is regulated by the reduction of disulphide bonds via thioredoxin (TRX) as well as by changes in the pH and Mg2+ concentration that results from illumination [3]. The function of cFBP2 in sucrose synthesis and the control of carbohydrate distribution still has to be elucidated
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