DNA microarrays were used to probe the transcriptional response of Escherichia coli to N, N, N, N-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN). Fifty-five transcripts were significantly up-regulated, including all of the genes that are regulated by Zur and many that are regulated by Fur. In the same TPEN-treated cells, 46 transcripts were significantly down-regulated.The transcriptional response of Escherichia coli to elevated levels of metal ions such as Zn(II), Cd(II), Co(II), Ni(II), and Fe(II) has been probed in an effort to understand the mechanisms by which the homeostatic levels of these metal ions are maintained (10,15,51,95,96). In contrast, very few studies have probed the global response of E. coli to low levels of metal ions, presumably due to the difficulty of sufficiently depleting the growth medium of metal ions. In this study, cDNA microarrays were used to probe the transcriptional response of E. coli to stress by N, N, NЈ, NЈ-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN). TPEN (58, 81), a cell-permeative, divalent metal chelator, is often called "Zn(II) specific" (17,33,38,48,59,64,71,79,80,83,88). Our data show significant changes in the transcription of several genes in cells stressed with TPEN.To identify genes that are differentially expressed in response to TPEN, E. coli BL21(DE3) cells were grown in minimal medium (76) until the cultures reached mid-log phase. TPEN was introduced, and the cells were cultured for 5 h; this time was chosen so that the results would correspond to previous transcriptional response studies with excess Zn(II) (51). The cultures containing 5 M TPEN were analyzed with DNA microarrays (E. coli K12 V2 array slides from MWG-BIOTECH), and the results were compared to those from E. coli cells grown in minimal medium containing no TPEN. A minimum of six slides was used for each experiment (three slides with one combination of Cy3 and Cy5 dyes and three slides with swapped dyes). Fifty-five transcripts were significantly up-regulated (twofold) ( Table 1). Four genes (ykgM, znuA, znuC, and yodA) that are regulated by Zur, the Zn(II) uptake regulator (30), exhibited significant increases in expression. The remaining Zur-regulated transcript, znuB, was also up-regulated; however, this transcript did not meet our filtering criteria: (i) P values of Յ0.5, (ii) Ն2-fold changes in expression, and (iii) consistent data in all six slides. The expression of zntA, which is regulated by ZntR and encodes the high-affinity Zn(II) exporter in E. coli (7,14,78), was unchanged in E. coli cultures stressed with TPEN (see the complete set of DNA array data).Twenty-nine of the up-regulated genes from TPEN-supplemented cultures are transcriptionally regulated by Fur, the iron uptake regulator (Table 1), and several are involved in Fe transport. The genes (entB, entA, entD, entE, and fes) which encode proteins involved with enterobactin synthesis and uptake (26, 29, 54) and the fec genes (fecR and fecI), which encode proteins involved in Fe import (23), were significantly up-regulated. S...