The response of E. coli to Hg(2+) exposure was investigated using proteomic and metalloproteomic approaches. E. coli was cultured in the LB medium containing HgCl2 and/or selenomethionine. The growth curve of E. coli was measured to estimate the toxicity of Hg(2+) or selenomethionine. After two-dimensional gel electrophoresis (2-DE), distribution of Hg in 2-DE gel was detected with synchrotron radiation X-ray fluorescence (SRXRF) at 4W1B, Beijing Synchrotron Radiation Facility. The proteins with differential expression and those containing Hg were identified with electrospray ionization tandem mass spectrometry (ESI-MS/MS) and peptide mass fingerprinting analysis. The results showed that Hg(2+) can inhibit the growth of E. coli, while supplement of selenomethionine can shorten the lag period induced by Hg(2+), indicating an antagonistic effect of selenomethionine against Hg(2+) toxicity. Mechanistically, Hg was observed to be able to bind pyruvate kinase, a glycolytic enzyme, and modulate the expression of five other proteins, including down-regulation of outer membrane protein W and up-regulation of transcription termination factor rho, cysteine synthase, transaldolase A and alkyl hydroperoxide reductase subunit C. Therefore, our results indicated that mercury may influence osmosis of plasma membrane, antioxidant defense, and glycometabolism of the microorganism. This study demonstrates the high sensitivity of SRXRF in identifying metal-associated proteins compared to conventional proteomic approaches.