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Determination of protein-protein interactions is an important component in assigning function and discerning the biological relevance of proteins within a broader cellular context. In vitro protein-protein interaction methodologies, including affinity chromatography, coimmunoprecipitation, and newer approaches such as protein chip arrays, hold much promise in the detection of protein interactions, particularly in well-characterized organisms with sequenced genomes. However, each of these approaches attracts certain background proteins that can thwart detection and identification of true interactors. In addition, recombinant proteins expressed in Escherichia coli are also extensively used to assess protein-protein interactions, and background proteins in these isolates can thus contaminate interaction studies. Rigorous validation of a true interaction thus requires not only that an interaction be found by alternate techniques, but more importantly that researchers be aware of and control for matrix/support dependence. Here, we evaluate these methods for proteins interacting with DmsD (an E. coli redox enzyme maturation protein chaperone), in vitro, using E. coli subcellular fractions as prey sources. We compare and contrast the various in vitro interaction methods to identify some of the background proteins and protein profiles that are inherent to each of the methods in an E. coli system.

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The Escherichia coli chromosomal determinant for tellurite resistance consists of two genes (tehA and tehB) which, when expressed on a multicopy plasmid, confer resistance to K 2 TeO 3 at 128 g/ml, compared to the MIC of 2 g/ml for the wild type. TehB is a cytoplasmic protein which possesses three conserved motifs (I, II, and III) found in S-adenosyl-L-methionine (SAM)-dependent non-nucleic acid methyltransferases. Replacement of the conserved aspartate residue in motif I by asparagine or alanine, or of the conserved phenylalanine in motif II by tyrosine or alanine, decreased resistance to background levels. Our results are consistent with motifs I and II in TehB being involved in SAM binding. Additionally, conformational changes in TehB are observed upon binding of both tellurite and SAM. The hydrodynamic radius of TehB measured by dynamic light scattering showed a ϳ20% decrease upon binding of both tellurite and SAM. These data suggest that TehB utilizes a methyltransferase activity in the detoxification of tellurite.Tellurite (TeO 3 2Ϫ ) resistance, which is found in many microorganisms (37), is carried on plasmids of IncHI, IncHII, and IncP incompatibility groups (3, 36, 39) and/or on chromosomes (9, 10, 29, 33). Tellurite resistance (Te r ) determinants are very diverse, and at least five different determinants have been identified (37). Te r determinants are unrelated, and probably different resistance mechanisms are involved. Except for that encoded by the Pseudomonas syringae tpm gene, Te r mechanisms are not clearly understood. tpm encodes a methyltransferase that catalyzes S-adenosyl-L-methionine (SAM) methylation of 6-mercaptopurine, a substrate for human thiopurine methyltransferase. It was assumed that tellurite is also a substrate for this enzyme (11).The Te r determinant tehAB, an operon located at 32.3 min on the Escherichia coli K-12 chromosome (38), encodes proteins of 330 (TehA) and 197 (TehB) amino acids. TehA is a membrane protein with 10 transmembrane segments, whereas TehB is a soluble protein. The closest homologues of these two genes are found in Haemophilus influenzae (15).A sequence search performed with the BLAST program (National Center for Biotechnology Information), followed by alignment analysis with the Genetics Computer Group software package (University of Wisconsin) (12), demonstrated that TehB displays some amino acid sequence similarity to many SAM-dependent non-nucleic acid methyltransferases. These proteins have three shared motifs, and the TehB proteins show homologies within all regions with comparable sequence interval distances (Fig.

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