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Background  3′, 5′cAMP signaling in  Sinorhizobium meliloti  was recently shown to contribute to the autoregulation of legume infection.  In planta , three adenylate cyclases CyaD1, CyaD2 and CyaK, synthesizing 3′, 5′cAMP, together with the Crp-like transcriptional regulator Clr and  smc02178 , a gene of unknown function, are involved in controlling plant infection.    Results  Here we report on the characterization of a gene ( smc02179, spdA ) at the  cyaD1  locus that we predicted to encode a class III cytoplasmic phosphodiesterase.  First, we have shown that  spdA  had a similar pattern of expression as  smc02178 in planta  but did not require  clr  nor 3′, 5′cAMP for expression.  Second, biochemical characterization of the purified SpdA protein showed that, contrary to expectation, it had no detectable activity against 3′, 5′cAMP and, instead, high activity against the positional isomers 2′, 3′cAMP and 2′, 3′cGMP.  Third, we provide direct experimental evidence that the purified Clr protein was able to bind both 2′, 3′cAMP and 3′, 5′cAMP  in vitro  at high concentration. We further showed that Clr is a 3′, 5′cAMP-dependent DNA-binding protein and identified a DNA-binding motif to which Clr binds. In contrast, 2′, 3′cAMP was unable to promote Clr specific-binding to DNA and activate  smc02178  target gene expression  ex planta .  Fourth, we have shown a negative impact of exogenous 2′, 3′cAMP on 3′, 5′cAMP-mediated signaling  in vivo . A  spdA  null mutant was also partially affected in 3′, 5′cAMP signaling.    Conclusions  SpdA is a nodule-expressed 2′, 3′ specific phosphodiesterase whose biological function remains elusive. Circumstantial evidence suggests that SpdA may contribute insulating 3′, 5′cAMP-based signaling from 2′, 3′ cyclic nucleotides of metabolic origin.

Biochemical and functional characterization of SpdA, a 2′, 3′cyclic nucleotide phosphodiesterase from Sinorhizobium meliloti