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JOURNAL OF BACTERIOLOGY, Sept. 2006, p. 6709–6713 0021-9193/06/$08.00⫹0 doi:10.1128/JB.00680-06 Copyright © 2006, American Society for Microbiology. All Rights Reserved.
DNA microarrays were used to probe the transcriptional response of Escherichia coli to N, N, Nⴕ, Nⴕ-tetrakis(2pyridylmethyl)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. mented 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. Several other genes (fhuA, exbB, exbD, fhuD, fhuC, and fhuF) associated with ferrichrome transport in E. coli were also up-regulated (19, 56, 62). Forty-six transcripts were significantly down-regulated in E. coli cells stressed with TPEN (Table 2). Two operons in E. coli, flgBCDEFGHIJKL and flgAMN, possess genes that encode proteins involved in flagellar biosynthesis (8). Some of these motility-related genes, namely, flgB, fliM, and motB, were previously reported as being up-regulated in E. coli cells stressed with excess Zn(II) (51). In addition, the expression of flagellar biosynthetic proteins in E. coli is affected by the concentration of copper, possibly exerting its effect via the OmpR or H-NS transcriptional regulators (42). All of the genes in the cus and cue systems, which confer copper tolerance to E. coli (68), were also down-regulated, although cusA and copA were filtered out of the data shown in Table 2. Previous studies have demonstrated that the expression levels of the cus and cue genes are dependent on aerobic/anaerobic conditions as well as on the levels of copper in the periplasm/cytoplasm (68). The expression levels of cytoplasmic ferritin (3) were also significantly down-regulated in TPEN-treated cells. To validate the microarray data, two representative genes were selected for real-time PCR and assayed for the level of mRNA by a two-step, real-time PCR technique. The genes yodA and pdxH, which were up-regulated (21-fold) and exhibited no change (1.1-fold), respectively, were analyzed with realtime PCR. Real-time PCR results were as follows: yodA upregulated, 17 ⫾ 1; pdxH up-regulated, 1.1 ⫾ 0.1. In order to probe whether the changes observed in cells grown in the presence of TPEN were due to the chelator, RT-PCR was used to probe for the expression levels of yodA in E. coli cells grown in minimal medium containing 5 ␮M TPEN and 30 ␮M Zn(II). There was no change in transcript levels of yodA when E. coli was cultured in this medium. Despite the fact that TPEN is often referred to as a Zn(II)specific chelator (17, 33, 38, 48, 59, 64, 71, 79, 80, 83, 88), the analyses of our microarray data suggest that the levels of other metal ions may have been affected by the presence of TPEN.
PTS, phosphotransferase system. ID, identifier.
with the accession number GSE5356 (www.ncbi.nlm.nih.gov /geo). We thank Paul Christopher Wood and Maria Lia Molas from the Center for Bioinformatics and Functional Genomics (CBFG) for helping with the microarray scanner and real-time PCR experiments. We are also grateful to Herbert Auer, Director of the Affymetrix Core, Columbus Children’s Research Institute, for training and assistance in the analysis of cDNA microarray data. We acknowledge Miami University (Committee on Faculty Research and OARS) and the National Institutes of Health (GM079411) for funding this work.
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