Linking yeast Gcn5p catalytic function and gene regulation using a quantitative, graded dominant mutant approach

Establishing causative links between protein functional domains and global gene regulation is critical for advancements in genetics, biotechnology, disease treatment, and systems biology. This task is challenging for multifunctional proteins when relying on traditional approaches such as gene deletions since they remove all domains simultaneously. Here, we describe a novel approach to extract quantitative, causative links by modulating the expression of a dominant mutant allele to create a function-specific competitive inhibition. Using the yeast histone acetyltransferase Gcn5p as a case study, we demonstrate the utility of this approach and (1) find evidence that Gcn5p is more involved in cell-wide gene repression, instead of the accepted gene activation associated with HATs, (2) identify previously unknown gene targets and interactions for Gcn5p-based acetylation, (3) quantify the strength of some Gcn5p-DNA associations, (4) demonstrate that this approach can be used to correctly identify canonical chromatin modifications, (5) establish the role of acetyltransferase activity on synthetic lethal interactions, and (6) identify new functional classes of genes regulated by Gcn5p acetyltransferase activity--all six of these major conclusions were unattainable by using standard gene knockout studies alone. We recommend that a graded dominant mutant approach be utilized in conjunction with a traditional knockout to study multifunctional proteins and generate higher-resolution data that more accurately probes protein domain function and influence.     

Recruitment of chromatin remodelling factors during gene activation via the glucocorticoid receptor N-terminal domain

We have shown that yeast mutants with defects in the Ada adaptor proteins are defective in hormone-dependent gene activation by ectopically expressed human glucocorticoid receptor (GR). Others have shown that the Ada2 protein is required for physical interactions between some activation domains and TBP (TATA-binding protein), whereas the Gcn5 (Ada4) protein has a histone acetyltransferase (HAT) activity. Although all HAT enzymes are able to acetylate histone substrates, some also acetylate non-histone proteins. Taken together, these observations suggest that the Ada proteins have the ability to effect different steps in the process of gene activation. It has recently been shown that the Ada proteins are present in two distinct protein complexes, the Ada complex and a larger SAGA complex. Our recent work has focused on determining (1) which of the Ada-containing complexes mediates gene activation by GR, (2) whether the HAT activity encoded by GCN5 is required for GR-dependent gene activation, (3) whether the Ada proteins contribute to GR-mediated activation at the level of chromatin remodelling and (4) how the role of these HAT complexes is integrated with other chromatin remodelling activities during GR-mediated gene activation. Our results suggest a model in which GR recruits the SAGA complex and that this contributes to chromatin remodelling via a mechanism involving the acetylation of histones. Furthermore, recruitment of the SWI/SNF remodelling complex also has a role in GR-mediated activation that is independent of the role of SAGA. These complexes are similar to analogous mammalian complexes and therefore these results are likely to be relevant to the human system.     

Structure and function of human prepro-orexin gene.

Orexin-A and -B are recently identified potent orexigenic peptides that are derived from the same precursor peptide and are highly specifically localized in neurons located in the lateral hypothalamic area, a region classically implicated in feeding behavior. We cloned the whole length of the human prepro-orexin gene and corresponding cDNA. The human prepro-orexin mRNA was predicted to encode a 131-residue precursor peptide (prepro-orexin). The human prepro-orexin gene consists of two exons and one intron distributed over 1432 base pairs. The 143-base pair first exon includes the 5'-untranslated region and a small part of the coding region that encodes the first seven residues of the secretory signal sequence. The second exon contains the remaining portion of the open reading frame and 3'-untranslated region. The 3.2 kilobase pairs of the 5'-upstream region from a cloned human prepro-orexin gene promoter is sufficient to direct the expression of the Escherichia coli beta-galactosidase (lacZ) gene in transgenic mice to neurons in the lateral hypothalamic area and adjacent regions. The lacZ-positive neurons were positively stained with anti-orexin antibody but not with anti-melanin-concentrating hormone antibody. These findings suggest that this genomic fragment contains all the necessary elements for appropriate expression of the gene and will be useful for the targeted expression of the exogenous gene in orexin-containing neurons. These mice might also be useful for examining the molecular mechanisms by which orexin gene expression is regulated.     

Structure and function of initiation complexes which accumulate during inhibition of protein synthesis by fluoride ion.

Incubation of the reticulocyte lysate cell-free system with KF results in the accumulation in polysomes of complexes containing deacylated tRNAMet and of complexes which can initiate globin chains in the presence of aurintricarboxylate. Degradation of these polysomes with T1RNase yields both 40 S and 80 S particles, and tRNAMet is found in both of these fractions. When the 80 S particles are reincubated with the soluble fraction of the lysate plus reagents for protein synthesis, short peptides which have the properties of the NH2-terminal regions of globin are synthesized de novo. These peptides are deficient in NH2-terminal methionine, but occur under conditions where nascent globin peptides of comparable length, containing NH2-terminal methionine, are completely protected from the methionine aminopeptidase.     

T cell activation by preformed, long-lived Ia-peptide complexes. Quantitative aspects

Planar membrane-bound complexes between a fluorescent peptide, FITC-OVA(323-339), and the class II MHC Ag, I-Ad, were analyzed by fluorescence microscopy and in biological assays to determine the optimum distance between peptide-Ia complexes required for maximum activation of IL-2 production by the Th cell hybridoma DO-11.10. Optimum responses were obtained when the average distance between peptide-Ia complexes was of the order of 200 A. This implies that T cell activation by Ag-MHC requires cross-linking of the TCR via closely packed Ag-MHC complexes. The same dose response curve to the preformed complexes was obtained whether one used a fixed concentration of Ia and varied the peptide concentration or a fixed concentration of peptide and varied the Ia concentration. In both cases there was a linear relationship between the number of peptide-Ia complexes and the response of the T cells. The association between Ia and peptide in vitro is an inefficient process, requiring prolonged incubation and a large excess of peptide over Ia. Once formed, however, the complex is extremely stable with no detectable dissociation at neutral pH after days at 4 degrees C. With several different preparations of Ia it was found that only about 10 to 20% of the purified Ia is capable of forming the long-lived complex with peptide.     

Structure and function of lipid droplet assembly complexes

Cells store lipids as a reservoir of metabolic energy and membrane component precursors in organelles called lipid droplets (LDs). LD formation occurs in the endoplasmic reticulum (ER) at LD assembly complexes (LDAC), consisting of an oligomeric core of seipin and accessory proteins. LDACs determine the sites of LD formation and are required for this process to occur normally. Seipin oligomers form a cage-like structure in the membrane that may serve to facilitate the phase transition of neutral lipids in the membrane to form an oil droplet within the LDAC. Modeling suggests that, as the LD grows, seipin anchors it to the ER bilayer and conformational shifts of seipin transmembrane segments open the LDAC dome toward the cytoplasm, enabling the emerging LD to egress from the ER.     

Structure and function of 2:1 DNA polymerase.DNA complexes

DNA polymerases are required for DNA replication and DNA repair in all of the living organisms. Different DNA polymerases are responsible different stages of DNA metabolism, and many of them are multifunctional enzymes. It was generally assumed that the different reactions are catalyzed by the same enzyme molecule. In addition to 1:1 DNA polymerase.DNA complex reported by crystallization studies, 2:1 and higher order DNA polymerase.DNA complexes have been identified in solution studies by various biochemical and biophysical approaches. Further, abundant evidences for the DNA polymerase-DNA interactions in several DNA polymerases suggested that the 2:1 complex represents the more active form. This review describes the current status of this emerging subject and explores their potential in vitro and in vivo functional significance, particularly for the 2:1 complexes of mammalian DNA polymerase beta (Pol beta), the Klenow fragment of E. coli DNA polymerase I (KF), and T4 DNA polymerase.     

chlD gene function in molybdate activation of nitrate reductase.

chlD mutants of Escherichia coli lack active nitrate reductase but form normal levels of this enzyme when the medium is supplemented with 10-3 M molybdate. When chlD mutants were grown in unsupplemented medium and then incubated with molybdate in the presence of chloramphenicol, they formed about 5% the normal level of nitrate reductase. Some chlD mutants or the wild type grown in medium supplemented with tungstate accumulated an inactive protein which was electrophoretically identical to active nitrate reductase. Addition of molybdate to those cells in the presence of chloramphenicol resulted in the formation of fully induced levels of nitrate reductase. Two chlD mutants, including a deletion mutant, failed to accumulate the inactive protein and to form active enzyme under the same conditions. Insertion of 99-Mo into the enzyme protein paralleled activation; 185-W could not be demonstrated to be associated with the accumulated inactive protein. The rates of activation of nitrate reductase at varying molybdate concentrations indicated that the chlD gene product facilitates the activation of nitrate reductase at concentrations of molybdate found in normal growth media. At high concentrations, molybdate circumvented this function in chlD mutants and appeared to activate nitrate reductase by a mass action process. We conclude that the chlD gene plays two distinguishable roles in the formation of nitrate reductase in E. coli. It is involved in the accumulation of fully induced levels of the nitrate reductase protein in the cell membrane and it facilitates the insertion of molybdenum to form the active enzyme.