Genome identification and analysis of genes encoding the key enzymes involved in organic acid biosynthesis pathway in apple, grape, and sweet orange

• Identified the important genes by whole genome proteins and ESTs.
• MDH, FUM, and CS could be the key genes in malic acid and citric acid biosynthesis.
• SDH, SAT, NAD-ICDH, and ACO may play key roles in the malic acid–citric acid cycle.
• GME, GGalPP, and GalDH may play key roles in the Smirnoff–Wheeler pathway for l-ascorbic acid biosynthesis.
• l-lanDH does not function in converting l-ascorbic acid to l-tartaric acid.

Fruit taste depends on the amounts and types of soluble sugars and organic acids in the fruit. However, a large-scale investigation to identify and compare the genes involved in organic acid biosynthesis across multiple plants has not yet been undertaken. To address this void, we have identified some key enzymes involved in organic acid biosynthetic pathways by comparing the gene copy numbers and related-ESTs (expressed sequence tags) in different fruits. The results show that malic acid is mainly synthesized in mitochondria. Therefore, the malic acid that participates in citric acid biosynthesis, which occurs in glyoxysomes, is transported from the cytoplasm to glyoxysomes to participate in that pathway. The different expression levels of malate dehydrogenase (MDH), fumarase (FUM), citrate synthase (CS), succinate dehydrogenase (SDH), succinate thiokinase (SAT), NAD-isocitrate dehydrogenase (NAD-ICDH), aconitase (ACO), GDP-d-mannose-3, 5-epimerase (GME), GDP-l-galactose pyrophosphatase (GGalPP) and l-galactose dehydrogenase (GalDH) between apples, grapes, and sweet oranges caused differences in the fruits’ predominant organic acids. MDH, FUM, and CS enzymes were found to be the key enzymes in the malic acid and citric acid biosynthetic pathways, while SDH, SAT, NAD-ICDH, and ACO enzymes may play key roles in the malic acid–citric acid cycle, whereby citric acid is decomposed and malic acid is created. GME, GGalPP, and GalDH enzymes may play key roles in the Smirnoff–Wheeler pathway for l-ascorbic acid biosynthesis. Because we determined that l-lanDH does not function in converting l-ascorbic acid to l-tartaric acid, the key enzyme involved in that pathway is still unknown. Overall, this study provides a new and quick way to compare the key enzymes involved in specific biosynthetic pathways for many species using publicly available sequence information.