The TATA binding protein (TBP) is required for the expression of nearly all genes and is highly regulated both positively and negatively. Here, we use DNA microarrays to explore the genome-wide interplay of several TBP-interacting inhibitors in the yeast Saccharomyces cerevisiae. Our findings suggest the following: The NC2 inhibitor turns down, but not off, highly active genes. Autoinhibition of TBP through dimerization contributes to transcriptional repression, even at repressive subtelomeric regions. The TAND domain of TAF1 plays a primary inhibitory role at very few genes, but its function becomes widespread when other TBP interactions are compromised. These findings reveal that transcriptional output is limited in part by a collaboration of different combinations of TBP inhibitory mechanisms.

The recruitment of the TATA box-binding protein (TBP) to promoters in vivo is often rate limiting in gene expression. We present evidence that TBP negatively autoregulates its accessibility to promoter DNA in yeast through dimerization. The crystal structure of TBP dimers was used to design point mutations in the dimer interface. These mutants are impaired for dimerization in vitro, and in vivo they generate large increases in activator-independent gene expression. Overexpression of wild-type TBP suppresses these mutants, possibly by heterodimerizing with them. In addition to loss of autorepression, dimerization-defective TBPs are rapidly degraded in vivo. Direct detection of TBP dimers in vivo was achieved through chemical cross-linking. Taken together, the data suggest that TBP dimerization prevents unregulated gene expression and its own degradation.

Host cell proteins (HCPs) are process-related impurities that may copurify with biopharmaceutical drug products. Within this class of impurities there are some that are more problematic. These problematic HCPs can be considered high-risk and can include those that are immunogenic, biologically active, or enzymatically active with the potential to degrade either product molecules or excipients used in formulation. Some have been shown to be difficult to remove by purification. Why should the biopharmaceutical industry worry about these high-risk HCPs? What approach could be taken to understand the origin of its copurification and address these *Marisa Jones and Nisha Palackal should be considered joint first authors About Biophorum Development Group (BPDG): Since its inception in 2004, BioPhorum has become a trusted environment in which senior leaders of the biopharmaceutical industry come together to share and discuss openly the emerging trends and challenges facing their industry.BioPhorum currently comprises more than 3800 active participants in seven "phorums" covering cell and gene therapy, drug substance, development, fill-finish, a technology roadmap, information technology, and supply partners. The Host Cell Protein (HCP) Workstream is part of the Development Group (BPDG). This article is a composite view of opinions shared by the whole of the BPDG-HCP Workstream and should not be attributed to the individual positions of the participating companies.

A kinetic analysis of dimer dissociation, TATA DNA binding, and thermal inactivation of the yeast Saccharomyces cerevisiae and human TATA binding proteins (TBP) was conducted. We find that yeast TBP dimers, like human TBP dimers, are slow to dissociate in vitro (t(1/2) approximately 20 min). Mild mutations in the crystallographic dimer interface accelerate the rate of dimer dissociation, whereas severe mutations prevent dimerization. In the presence of excess TATA DNA, which measures the entire active TBP population, dimer dissociation represents the rate-limiting step in DNA binding. These findings provide a biochemical extension to genetic studies demonstrating that TBP dimerization prevents unregulated gene expression in yeast [Jackson-Fisher, A. J., Chitikila, C., Mitra, M., and Pugh, B. F. (1999) Mol. Cell 3, 717-727]. In the presence of vast excesses of TBP over TATA DNA, which measures only a very small fraction of the total TBP, the monomer population in a monomer/dimer equilibrium binds DNA rapidly, which is consistent with a simultaneous binding and bending of the DNA. Under conditions where other studies failed to detect dimers, yeast TBP's DNA binding activity was extremely labile in the absence of TATA DNA, even at temperatures as low as 0 degrees C. Kinetic analyses of TBP instability in the absence of DNA at 30 degrees C revealed that even under fairly stabilizing solution conditions, TBP's DNA binding activity rapidly dissipated with t(1/2) values ranging from 6 to 26 min. TBP's stability appeared to vary with the square root of the TBP concentration, suggesting that TBP dimerization helps prevent TBP inactivation.

No abstract

Erythropoietin (EPO) is the cytokine essential for erythropoiesis; however, the expression of EPO and EPO receptor (EPOR) is not limited to cells of erythroid lineage. Erythropoietin and EPOR expression has been localized to numerous non-hematopoietic cells and tissues including endothelial, neuronal and ovarian. Moreover, several tumor types have been shown to express both EPO and EPOR and display increased expression upon hypoxia. To shed light on the potential biological role of EPOR and tumor cells we characterized the response of human colon carcinoma HT-29 cells to EPO. Functionality of the erythropoietin receptor was assessed by radio-labeled ligand binding, cellular proliferation/signaling, and gene expression using DNA microarrays. Receptor binding experiments using [125I]-EPO did not reveal measurable EPO binding activity present on the surface of HT-29 cells under both normoxic and hypoxic conditions. Moreover, EPO failed to induce cellular proliferation or an increase in the phosphorylation state of STAT5, EPOR or ERK1/2 under normoxic or hypoxic conditions at supra-pharmacological levels (25 IU/ml). Gene expression analysis revealed no significant change in gene expression in response to EPO (5 IU/ml) under normoxic conditions. On the other hand, over 347 genes exhibited greater than a 1.5 fold change in gene expression when cells were cultured under hypoxic conditions (1 % O2). When EPO was administered to cells in the hypoxic state, 36 additional genes were observed (9 and 27 up-regulated or down-regulated, respectively). That HT-29 cells exhibit minor transcriptional changes in response to EPO raises the possibility that EPO may signal in HT-29 cells. However, the mechanism for this response is not through the previously described EPO/EPOR signal transduction pathway. This conclusion is supported by the apparent lack of EPO receptor expression on the cell surface. These results suggest that tumor microenvironment, e.g., hypoxia, exerts a greater effect than that seen by exposure to erythropoietin.