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Background  Malic enzymes decarboxylate the tricarboxylic acid (TCA) cycle intermediate malate to the glycolytic end-product pyruvate and are well positioned to regulate metabolic flux in central carbon metabolism. Despite the wide distribution of these enzymes, their biological roles are unclear in part because the reaction catalyzed by these enzymes can be by-passed by other pathways. The N 2 -fixing alfalfa symbiont  Sinorhizobium meliloti  contains both a NAD(P)-malic enzyme (DME) and a separate NADP-malic enzyme (TME) and to help understand the role of these enzymes, we investigated growth, metabolomic, and transcriptional consequences resulting from loss of these enzymes in free-living cells.    Results  Loss of DME, TME, or both enzymes had no effect on growth with the glycolytic substrate, glucose. In contrast, the  dme  mutants, but not  tme , grew slowly on the gluconeogenic substrate succinate and this slow growth was further reduced upon the addition of glucose. The  dme  mutant strains incubated with succinate accumulated trehalose and hexose sugar phosphates, secreted malate, and relative to wild-type, these cells had moderately increased transcription of genes involved in gluconeogenesis and pathways that divert metabolites away from the TCA cycle. While  tme  mutant cells grew at the same rate as wild-type on succinate, they accumulated the compatible solute putrescine.    Conclusions  NAD(P)-malic enzyme (DME) of  S. meliloti  is required for efficient metabolism of succinate via the TCA cycle. In  dme  mutants utilizing succinate, malate accumulates and is excreted and these cells appear to increase metabolite flow via gluconeogenesis with a resulting increase in the levels of hexose-6-phosphates and trehalose. For cells utilizing succinate, TME activity alone appeared to be insufficient to produce the levels of pyruvate required for efficient TCA cycle metabolism. Putrescine was found to accumulate in  tme  cells growing with succinate, and whether this is related to altered levels of NADPH requires further investigation.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-016-0780-x) contains supplementary material, which is available to authorized users.

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