Table 3

Relationship between the methylation status and nitrate regulation of TCA cycle genes.

AGI number

Gene Annotation

Responsiveness to nitrate

Methylation statusa


At3g47520

MDH (malate dehydrogenase); malate dehydrogenase

3

U

At1g04410

malate dehydrogenase, cytosolic, putative

0

A

At1g53240

malate dehydrogenase (NAD), mitochondrial

0

M

At2g22780

PMDH1 (PEROXISOMAL NAD-MALATE DEHYDROGENASE 1); malate dehydrogenase

0

M

At3g15020

malate dehydrogenase (NAD), mitochondrial, putative

0

U

At5g09660

PMDH2 (PEROXISOMAL NAD-MALATE DEHYDROGENASE 2), PMDH2 (PEROXISOMAL NAD-MALATE DEHYDROGENASE 2); malate dehydrogenase

0

M

At5g56720

malate dehydrogenase, cytosolic, putative

0

M

At5g58330

malate dehydrogenase (NADP), chloroplast, putative

0

M

At5g43330

malate dehydrogenase, cytosolic, putative

0

U

At5g03290

isocitrate dehydrogenase, putative/NAD+ isocitrate dehydrogenase, putative

2

U

At4g35260

IDH1 (ISOCITRATE DEHYDROGENASE 1); isocitrate dehydrogenase (NAD+)

2

U

At1g65930

isocitrate dehydrogenase, putative/NADP+ isocitrate dehydrogenase, putative

1

U

At3g09810

isocitrate dehydrogenase, putative/NAD+ isocitrate dehydrogenase, putative

0

M

At4g35650

isocitrate dehydrogenase, putative/NAD+ isocitrate dehydrogenase, putative

0

U

At5g14590

isocitrate dehydrogenase, putative/NADP+ isocitrate dehydrogenase, putative

0

M

At1g54340

ICDH (ICDH); isocitrate dehydrogenase (NADP+)

0

M


This table provides the AGI number, the gene annotation, regulation by nitrate as determined from four independent experiments (see main text) and the methylation status according to the two methylome datasets used in this work. This table includes all the different malate dehydrogenase and isocitrate dehydrogenase isozyme-coding genes present in the Arabidopsis genome, according to VirtualPlant http://www.virtualplant.org webcite. aMethylation code: U, unmethylated in both datasets; M, methylated in both datasets; A, ambiguous according to Zilberman et al. [25] but unmethylated according to Zhang et al. [24].

Aceituno et al. BMC Genomics 2008 9:438   doi:10.1186/1471-2164-9-438

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