Although transcription and pre-mRNA processing are colocalized in eukaryotic nuclei, molecules linking these processes have not previously been described. We have identified four novel rat proteins by their ability to interact with the repetitive C-terminal domain (CTD) of RNA polymerase II in a yeast two-hybrid assay. A yeast homolog of one of the rat proteins has also been shown to interact with the CTD. These CTD-binding proteins are all similar to the SR (serine/arginine-rich) family of proteins that have been shown to be involved in constitutive and regulated splicing. In addition to alternating Ser-Arg domains, these proteins each contain discrete N-terminal or C-terminal CTD-binding domains. We have identified SR-related proteins in a complex that can be immunoprecipitated from nuclear extracts with antibodies directed against RNA polymerase II. In addition, in vitro splicing is inhibited either by an antibody directed against the CTD or by wild-type but not mutant CTD peptides. Thus, these results suggest that the CTD and a set of CTDbinding proteins may act to physically and functionally link transcription and pre-mRNA processing.The C-terminal domain of the largest subunit of RNA polymerase II (CTD) consists of tandem repeats of the consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser (1, 2). Deletion studies demonstrated that the ClD is essential for cell growth (3-6), but the nature of this essential function is not known. The CID is only found on RNA polymerase II (pol II), suggesting that it plays a unique role in mRNA biogenesis (7 Despite identification of interaction partners, the role of the CTD in transcription remains unclear. The CTD is not required for either basalV(14, 15) or activated (16, 17) transcription of some genes in vitro. Furthermore, inhibition of CTD kinase does not block in vitro transcription from the adenovirus major late promoter or from a GAL4 VP16-activated promoter (18,19). Thus, these results indicate that the CTD is not essential for specific initiation at some promoters.CTD function may be required for postinitiation steps in the biogenesis of mRNA. O'Brien et al. (20) have demonstrated that several genes contain paused pol IIA complexes that can reenter the elongation mode coincident with CTD phosphorylation. In yeast, CTD-truncated pol II synthesizes an excess of GAL4-induced promoter proximal transcripts (D. L. Bentley, personal communication). Thus, these results argue that the CTD plays an important role subsequent to initiation. While the CTD has previously been proposed to function in premRNA processing (refs. 7 and 21 and H. Rienhoff and J. Boeke, personal communication), no experimental data have yet supported these models.We used the yeast two-hybrid system (22) to identify proteins that interact with the CTD. This unbiased approach did not yield proteins that are expected to be involved in transcription initiation, like TBP or the SRBs, but rather a set of proteins similar to RNA processing factors. In this paper we report the identification and characte...

Peptide binding reactions of class II MHC proteins exhibit unusual kinetics, with extremely slow apparent rate constants for the overall association (<100 M -1 s -1 ) and dissociation (<10 -5 s -1 ) processes. Various linear and branched pathways have been proposed to account for these data. Using fluorescence resonance energy transfer between tryptophan residues in the MHC peptide binding site and aminocoumarin-labeled peptides, we measured real-time kinetics of peptide binding to empty class II MHC proteins. Our experiments identified an obligate intermediate in the binding reaction. The observed kinetics were consistent with a binding mechanism that involves an initial bimolecular binding step followed by a slow unimolecular conformational change. The same mechanism is observed for different peptide antigens. In addition, we noted a reversible inactivation of the empty MHC protein that competes with productive binding. The implications of this kinetic mechanism for intracellular antigen presentation pathways are discussed.Proteins encoded by the major histocompatibility complex (MHC) 1 gene locus bind peptide antigens and display them at the cell surface for inspection by the immune system as part of the mechanism by which foreign material in the body is recognized and removed (1). Class II MHC proteins generally are found on specialized immune system cells such as B cells, macrophages, and dendritic cells, but they can be expressed by most cell types in response to inflammation or infection (2). Newly synthesized class II MHC R-and -glycoprotein subunits associate with a chaperonin-like invariant chain protein, which places an extended loop in the class II peptide binding site and directs transport to an endosomal compartment (3). Endosomal proteins cleave the invariant chain, and the bound fragment is exchanged for peptides generated from cell-surface and endocytosed proteins, in a poorly characterized process catalyzed by the peptide-exchange factor HLA-DM (4). MHC-peptide complexes then are transported to the cell surface for inspection by T-cell receptors on CD4 + T lymphocytes. Crystal structures have been determined for several human and murine class II MHC proteins in complex with defined peptides (5-13). In each case, the peptide was bound in a polyproline type II-like conformation, with several side chains projecting into specificity-determining pockets within the overall peptide binding groove, and with many additional contacts between the MHC proteins and the main chain of the bound peptide.Initially, in vitro kinetic measurements of peptide binding to purified class II MHC proteins were interpreted in terms of the simple bimolecular reaction shown in Scheme 1 (14): Physical and chemical characterization of purified class II MHC revealed that they carried complex mixtures of tightly bound endogenous peptides (15-19). The stoichiometry of binding for peptide added to these preparations was quite low. Many of the natural peptide ligands had extremely long half-lives, often on the order of ...

The plasminogen cascade of serine proteases directs both development and tumorigenesis in the mammary gland. Plasminogen can be activated to plasmin by urokinase-type plasminogen activator (uPA), tissue-type plasminogen activator (tPA), and plasma kallikrein (PKal). The dominant plasminogen activator for mammary involution is PKal, a serine protease that participates in the contact activation system of blood coagulation. We observed that the prekallikrein gene (Klkb1) is expressed highly in the mammary gland during stromal remodeling periods including puberty and postlactational involution. We used a variant of ecotin (ecotin-PKal), a macromolecular inhibitor of serine proteases engineered to be highly specific for active PKal, to demonstrate that inhibition of PKal with ecotinPKal delays alveolar apoptosis, adipocyte replenishment, and stromal remodeling in the involuting mammary gland, producing a phenotype resembling that resulting from plasminogen deficiency. Using biotinylated ecotin-PKal, we localized active PKal to connective tissue-type mast cells in the mammary gland. Taken together, these results implicate PKal as an effector of the plasminogen cascade during mammary development.The plasminogen cascade of serine proteases regulates both development and tumorigenesis in the mammary gland (1, 2). The ultimate effector in this cascade, plasminogen as its active form, plasmin, is mediated by an intricate cascade of plasminogen activators and protease inhibitors. Plasminogen-deficient mice exhibit significant defects in lactational competence and post-lactational mammary gland involution (2), the process by which the differentiated, lactating gland remodels after the cessation of lactation to a state approaching that of the non-pregnant animal. The effect of plasminogen loss is exacerbated after a round of pregnancy and lactation: plasminogen-null mammary glands have poorly developed secretory alveoli during lactation, and upon involution, never fully involute. Instead, the secretory alveoli fail to regress normally. Moreover, the stroma becomes fibrotic and is cleared incompletely of partially degraded epithelial basement membrane. Because plasminogen-deficient mice largely are unable to support a second round of pregnancy and lactation (2), this suggests that the involution defect is not overcome by activities of other proteases eventually. These studies establish plasminogen as a crucial protease in normal mammary gland biology.Plasminogen is synthesized in the liver and circulates as a zymogen through blood plasma to all vascularized tissues of the body. As this expression and circulation are constant,

Engineering of protein-protein interactions is used to enhance the affinity or specificity of proteins, such as antibodies or protease inhibitors, for their targets. However, fully diversifying all residues in a protein-protein interface is often unfeasible. Therefore, we limited our phage library for the serine protease inhibitor ecotin by restricting it to only tetranomial diversity and then targeted all 20 amino acid residues involved in protein recognition. This resulted in a high-affinity and highly specific plasma kallikrein inhibitor, ecotin-Pkal. To validate this approach we dissected the energetic contributions of each wild type (wt) or mutated surface loop to the binding of either plasma kallikrein (PKal) or membrane-type serine protease 1. The analysis demonstrated that a mutation in one loop has opposing effects depending on the sequence of surrounding loops. This finding stresses the cooperative nature of loop-loop interactions and justifies targeting multiple loops with a limited diversity. In contrast to ecotin wt, the specific loop combination of ecotin-Pkal discriminates the subtle structural differences between the active enzymes, PKal and Factor XIIa, and their respective zymogen forms. We used ecotin-Pkal to specifically inhibit contact activation of human plasma at the level mediated by plasma kallikrein.

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