In Vivo and in Vitro Analyses of the AmyR Binding Site of the Aspergillus nidulans agdA Promoter; Requirement of the CGG Direct Repeat for Induction and High Affinity Binding of AmyR

The α-glucosidase gene (agdA) of Aspergillus nidulans has a single CGGN₈CGG type AmyR binding site in its promoter region. The binding site is functional in vivo as a cis-element responsible for induction by starch, and mutational studies indicated that both the CGG triplets are required for high-level induction. A part of AmyR (residues 1-411; AmyR_1-411), which was produced as a MalE fusion protein in E. coli, bound to the CGGN₈CGG site of the agdA promoter. DNA binding profiles to the mutant binding sites that lacked both or either one of the CGG triplets suggested that AmyR_1-411 can bind to a single CGG triplet site with low affinity and that two AmyR molecules cooperatively bind to the CGG direct repeat.     

A high affinity binding site for the HIV-1 nucleocapsid protein.

The nucleocapsid protein (NC) of HIV-1 is a small zinc finger protein that contributes to multiple steps of the viral life cycle, including the proper encapsidation of HIV RNA. This is accomplished through an interaction between NC and a region at the 5'-end of the RNA, defined as the Psi element. However, the specificity of NC for Psi or for RNA in general is not well understood. To study this problem, we used SELEX to identify high affinity RNA ligands that bind to NC. A 'winner' molecule (SelPsi), as well as a subregion of Psi RNA, were further characterized to understand the interaction between NC and SelPsi and its relationship to the interaction between NC and Psi. The comparison makes predictions about the sequence and structure of a high affinity binding site within the HIV-1 Psi element.     

In vitro induction systems for analyses of amphibian organogenesis and body patterning

The discovery that some well-known growth factors have inducing activity in embryogenesis has accelerated our understanding of embryonic induction. Relevant receptors, signal transduction pathways and patterns of gene expression have been characterized over the past decade. Amphibian embryos have provided an excellent model for analysis of embryonic induction because they are easily surgically manipulated and cultured in vitro, and with the addition of treatment with various inducing factors we have been able to control organogenesis and body patterning during early development in vitro. Activin A, a TGF-beta family protein, has a potent mesoderm-inducing activity on the isolated ectoderm called the animal cap. Activin induces animal caps to differentiate into various mesodermal and endodermal tissues, including beating hearts, in a dose-dependent fashion. Activin, in combination with retinoic acid, also induces the formation of the pronephros, a primitive embryonic kidney. The in vitro induced kidney was confirmed to function in vivo in a transplantation experiment. Furthermore, the activin-induced animal caps organize heads or trunk-and-tails in exactly the same manner as the organizer. The potential use of in vitro induction systems to further our understanding of vertebrate organogenesis and body patterning will be discussed.     

Cloning of a murine IL-11 receptor alpha-chain; requirement for gp130 for high affinity binding and signal transduction.

An adult mouse liver cDNA library was screened with oligonucleotides corresponding to the conserved WSXWS motif of the haemopoietin receptor family. Using this method, cDNA clones encoding a novel receptor were isolated. The new receptor, named NR1, was most similar in sequence and predicted structure to the alpha-chain of the IL-6 receptor and mRNA was expressed in the 3T3-L1 pre-adipocytic cell line and in a range of primary tissues. Expression of NR1 in the factor-dependent haemopoietic cell line Ba/F3 resulted in the generation of low affinity receptors for IL-11 (Kd approximately 10 nM). The capacity to bind IL-11 with high affinity (Kd = 300-800 pM) appeared to require coexpression of both NR1 and gp130, the common subunit of the IL-6, leukaemia inhibitory factor (LIF), oncostatin M (OSM) and ciliary neurotrophic factor (CNTF) receptors. The expression of both NR1 and gp130 was also necessary for Ba/F3 cells to proliferate and M1 cells to undergo macrophage differentiation in response to IL-11.     

In vivo and in vitro studies of nitrate reductase regulation in Asperillus nidulans.

Summary Induced wildtype cells ofA. nidulans rapidly lost NADPH — linked nitrate reductase activity when subjected to carbon and or nitrogen starvation. A constitutive mutant at the regulatory gene for nitrate reductase,nirA ^c1, rapidly lost nitrate reductase activity upon carbon starvation. This loss of activity is thought to be due to a decrease in the NADPH concentration in the cells. Cell free extracts from wild-type cells grown in the presence of nitrate, rapidly lost their nitrate reductase activity when incubated at 25° C. NADPH prevented this loss of activity. Wildtype cells grown in the presence of nitrate and urea have a higher initial NADPH: NADP⁺ ratio and cell free extracts from such cells lost their nitrate reductase activity slower than extracts of cells grown with nitrate alone.The Pentose Phosphate Pathway mutant,pppB-1, had a lower NADPH concentration compared with the wildtype grown under the same conditions and cell free extracts lost their nitrate reductase activity more rapidly than the wildtype. Cell free extracts ofnirA ^c-1 and a non-inducible mutant for nitrate reductase,nirA ^--14, upon incubation lost little of their nitrate reductase activity.     

A novel binding assay identifies high affinity ligands to the rosiglitazone binding site of mitoNEET

A novel outer mitochondrial membrane protein containing [2Fe-2S] clusters, mitoNEET was first identified through its binding to the anti-diabetic drug pioglitazone. Pioglitazone belongs to a family of drugs that are peroxisome proliferator-activated receptor (PPAR) gamma agonists, collectively known as glitazones. With the lack of pharmacological tools available to fully elucidate mitoNEET's function, we developed a binding assay to probe the glitazone binding site with the aim of developing selective and high affinity compounds. We used multiple thiazolidine-2,4-dione (TZD), 2-thioxothiazolidin-4-one (TTD), and 2-iminothiazolidin-4-one (ITD) compounds to establish several trends to enhance ligand development for the purpose of elucidating mitoNEET function.     

The cartilage-specific fibronectin isoform has a high affinity binding site for the small proteoglycan decorin

Binding of fibronectin to the small proteoglycan decorin plays an important role in cell differentiation and cell migration. The cartilage-specific (V+C)(-) fibronectin isoform, in which nucleotides that normally encode the protein segments V, III(15), and I(10) are spliced out, is one of the major splice variants present in cartilage matrices. Full-length and truncated cDNA constructs were used to express recombinant versions of fibronectin. Results demonstrated that the (V+C)(-) isoform has a higher affinity for decorin. Dissociation constants for decorin and fibronectin interaction were calculated to be 93 nm for the V(+)C(+) isoform and 24 nm and 223 nm for (V+C)(-) fibronectin. Because heparin competed with decorin competitively, binding of decorin to fibronectin likely occurs at a heparin-binding region. We propose that alternative splicing of the V and C regions changes the global conformation of fibronectin in such a way that it opens an additional decorin-binding site. This conformational change is responsible for the higher affinity of the (V+C)(-) fibronectin isoform for decorin.     

The high affinity binding site on polyoma virus DNA for the viral large-T protein.

In order to map the high affinity binding site for the viral large-T protein on polyoma virus DNA, we have developed an assay which does not require purified protein. It is based on the specific elution of the large-T ATPase activity from calf thymus DNA cellulose by recombinant DNA molecules including known sequences of the viral DNA. Using this assay, a high affinity binding site has been mapped on the early region side of the ori region. Binding requires the integrity of a sequence /AGAGGC/TTCC/AGAGGC/ (nucleotides 49 to 64 in the DNA sequence of the A2 strain). Similar repeats of a PuGPuGGC sequence within less than 20 bases are not found within the viral coding regions, but are strikingly common in the control regions of papovaviruses and other eukaryotic DNAs.