Loss of malic enzymes leads to metabolic imbalance and altered levels of trehalose and putrescine in the bacterium Sinorhizobium meliloti

Table 1 Overview of the differential expression patterns based on gene function categories^a

Gene category	No. of genes significantly regulated^b (increased/decreased)
Gene category	Glucose vs succinate (wt)^c	dme vs wt (succinate)^d	tme vs wt (succinate)^e	dme vs wt (glucose)^f	tme vs wt (glucose)^g
Amino acid metabolism	3/0	17/0	4/0	3/2	2/0
Cofactor and vitamin metabolism	3/0	12/0	1/0	0/0	0/0
Fatty acid, ester, and phospholipid	1/1	4/0	2/0	0/0	1/0
Carbohydrate metabolism	13/3	13/0	2/0	0/0	0/0
Purine, pyrimidine, and nucleotide	0/1	1/0	3/0	1/0	1/1
Regulatory function	7/0	3/0	2/3	3/1	1/1
DNA replication and repair	1/1	4/0	1/1	0/0	0/1
Transport system	16/5	54/0	9/0	3/5	3/5
Energy metabolism	2/2	17/0	8/0	0/3	2/3
Other categories	4/3	7/3	3/2	2/2	5/0
Hypothetical protein	14/31	47/16	21/8	11/4	12/8
Total (6269)	64/47	179/19	56/14	23/17	27/19

^aThe complete list of differentially regulated genes can be found in Additional file 1: Tables S3–S6
^bGenes significantly regulated have a fold change of ≥ 3 and a P-value (Student’s t test) of ≤ 0.05
^cComparing S. meliloti wild type grown in glucose and succinate
^dComparing dme mutant & wild type grown in succinate (includes smb20178 and smb2080 Additional file 1: Table S2)
^eComparing tme mutant and wild type grown in succinate
^fComparing dme mutant and wild type grown in glucose
^gComparing tme mutant and wild type grown in glucose

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