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Expression of the H+-ATPase AHA10 proton pump is associated with citric acid accumulation in lemon juice sac cells

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Abstract

The sour taste of lemons (Citrus limon (L.) Burm.) is determined by the amount of citric acid in vacuoles of juice sac cells. Faris is a “sweet” lemon variety since it accumulates low levels of citric acid. The University of California Riverside Citrus Variety Collection includes a Faris tree that produces sweet (Faris non-acid; FNA) and sour fruit (Faris acid; FA) on different branches; it is apparently a graft chimera with layer L1 derived from Millsweet limetta and layer L2 from a standard lemon. The transcription profiles of Faris sweet lemon were compared with Faris acid lemon and Frost Lisbon (L), which is a standard sour lemon genetically indistinguishable from Faris in prior work with SSR markers. Analysis of microarray data revealed that the transcriptomes of the two sour lemon genotypes were nearly identical. In contrast, the transcriptome of Faris sweet lemon was very different from those of both sour lemons. Among about 1,000 FNA-specific, presumably pH-related genes, the homolog of Arabidopsis H+-ATPase proton pump AHA10 was not expressed in FNA, but highly expressed in FA and L. Since Arabidopsis AHA10 is involved in biosynthesis and acidification of vacuoles, the lack of expression of the AHA10 citrus homolog represents a very conspicuous molecular feature of the FNA sweet phenotype. In addition, high expression of several 2-oxoglutarate degradation-related genes in FNA suggests activation of the GABA shunt and degradation of valine and tyrosine as components of the mechanism that reduces the level of citric acid in sweet lemon.

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Acknowledgments

The authors would like to thank Ottilia Bier for bringing to our attention the presence of sour fruit on the Faris lemon trees, Ray Fenton for isolating the RNA, Jan Svensson for cooperation on identification of reference transcripts, and Barbara Walter for labeling the RNA and processing the gene chips. Avi Sadka provided helpful advice and comments on the results.

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Authors and Affiliations

  1. Department of Biotechnology and Environmental Science, University of Salento, Lecce, Prov.le Lecce-Monteroni, 73100, Italy

    Alessio Aprile & Luigi De Bellis

  2. Department of Botany and Plant Sciences and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521-0124, USA

    Alessio Aprile, Claire Federici, Timothy J. Close & Mikeal L. Roose

  3. CRA-Genomic Research Centre, Fiorenzuola d’Arda (PC), Via S.Protaso 302, Fiorenzuola, 29017, Italy

    Alessio Aprile & Luigi Cattivelli

Authors
  1. Alessio Aprile
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  2. Claire Federici
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  3. Timothy J. Close
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  4. Luigi De Bellis
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  5. Luigi Cattivelli
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  6. Mikeal L. Roose
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Corresponding author

Correspondence to Alessio Aprile.

Additional information

Financial Source: California Citrus Research Board, University of California Industry-University Cooperative Research Program, Affymetrix Inc. Italian Ministry of Agriculture special project “CITRUSTART”

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Figure S1

All QT clusters. Three genotypes are plotted on the x-axis, young samples on the left and mature samples on the right. The relative expression level (data normalized to the median for each probe set) is plotted on the y-axis. The lines represent the average expression of all probe sets of a cluster. The cluster “unclassified” contain the 1,202 probe sets that did not satisfy either of the two selected thresholds. FNA Faris non-acid, FA Faris acid, L Frost Lisbon (JPEG 140 kb)

High resolution image (TIFF 943 kb)

Figure S2

Branched-chain amino acids catabolism pathway. Differentially expressed genes are in solid line boxes. Not differentially expressed genes are in dotted line boxes. BCAT branched-chain amino acid transaminase, BDKD branched-chain keto-acid dehydrogenase, BDH 3-hydroxyisobutyrate dehydrogenase (JPEG 121 kb)

High resolution image (TIFF 1088 kb)

Table S1

Summary of all differentially expressed genes. In column A are listed the probe set IDs. “Comparisons” columns show the results of t test analysis. An empty cell means a non-significant result. For each probe set the relative gene ontology (GO) and Arabidopsis best match are shown (“Annotation” columns). Columns R to W report expression levels and columns X to AA the fold changes in sweet vs sour lemons (XLS 2208 kb)

Table S2

Functional classification of the cluster 1 genes using FunCat (Ruepp et al. 2004). Each category is sorted by increasing p value. Categories with p value lower than 0.05 (red) were considered over-represented in cluster 1 relative to observed Arabidopsis genome frequencies (XLS 91 kb)

Table S3

Functional classification of the cluster 2 genes using FunCat (Ruepp et al. 2004). Each category is sorted by increasing p value. Categories with p value lower than 0.05 (red) were considered over-represented in cluster 2 relative to observed Arabidopsis genome frequencies (XLS 90 kb)

Table S4

List of the probe sets that were not expressed in FNA samples and were expressed in FA and L samples. We report the probe set ID, the relative QT cluster, gene ontologies, Arabidopsis best match and expression level (XLS 38 kb)

Table S5

List of all the probe sets represented on Affymetrix Citrus GeneChip® related to glycolysis, acetyl-CoA synthesis, TCA cycle, citrate catabolism, glutamate synthesis, GABA shunt, tyrosine catabolism, branched-chain amino acid catabolism, and proton pumps. The last columns show the relative expression levels and fold changes in sweet vs sour lemons (XLS 125 kb)

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Aprile, A., Federici, C., Close, T.J. et al. Expression of the H+-ATPase AHA10 proton pump is associated with citric acid accumulation in lemon juice sac cells. Funct Integr Genomics 11, 551–563 (2011). https://doi.org/10.1007/s10142-011-0226-3

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