Buried asparagines determine the dimerization specificities of leucine zipper mutants

Regulation of gene expression by many transcription factors is controlled by specific combinations of homo- and heterodimers through a short alpha-helical coiled-coil known as a leucine zipper. The dimer interface of a leucine zipper involves side chains of the residues at the a, d, e, and g positions of the (abcdefg)n heptad repeat. To understand the basis for the specificity of dimer formation, we characterized GCN4 leucine zipper mutants with all 16 possible permutations and combinations of isoleucines and asparagines at four a positions in the dimer interface, using a genetic test for the specificity of dimer formation by lambda repressor-leucine zipper fusions. Heterodimers were detected by loss of repressor activity in the presence of a fusion to a dominant-negative mutant form of the DNA-binding domain of repressor. Reconstruction experiments using leucine zippers from GCN4, Jun, Fos, and C/EBP showed that this assay distinguishes pairs that form heterodimers from those that do not. We found that the mutants have novel dimerization specificities determined by the positioning of buried asparagine residues at the a positions. The pattern of buried polar residues could also explain the dimerization specificities of some naturally occurring leucine zippers. The altered specificity mutants described here should be useful for the construction of artificial regulatory circuitry.

Detection of tetramerization domains in vivo by cooperative DNA binding to tandem lambda operator sites

Chimeric proteins comprising the N-terminal DNA binding domain of lambda repressor fused to a fragment of a foreign protein have been used to detect oligomerization of the latter. Fusions containing dimeric and tetrameric leucine zipper domains can be distinguished based on their in vivo repressor activities on a pair of cat-lacZ reporter strains. Repressor fusions are unable to efficiently repress transcription from a synthetic promoter that overlaps a weak operator site; repression by tetrameric, but not dimeric, fusion proteins is increased by the presence of a strong, upstream operator site. To construct reporters we developed a shuttle system that allows rapid construction of single-copy operon fusions in E. coli, with both cat and lacZ as reporters.

The role of platelet-derived growth factor in the development of mouse molars

Platelet-derived growth factor (PDGF) is a potent mitogen that functions in cytodifferentiation and wound healing. PDGF receptor-alpha (PDGFR-alpha) is required for the normal development of the dental ectomesenchyme (Stephenson et al., Proc. Natl. Acad. Sci. USA 88: 6-10, 1991). To investigate the regulatory potential of PDGF on tooth development, the expression of PDGF-AA was determined by reverse transcription-polymerase chain reaction (RT-PCR), the PDGF ligands and receptors were localized by immunohistochemistry. The growth-promoting effects of exogenous PDGF-AA on molar explants were determined by assaying for tritiated thymidine incorporation, the presence of type I collagen and amelogenin messenger RNA transcripts, and total DNA, RNA and protein accumulation. Based upon the temporal and spatial localization, PDGFs and their receptors are present in the enamel epithelia and pulpal mesenchyme of developing mouse molars. Exogenous PDGF-AA administration increased the total protein accumulation of mouse molar explants but produces no discernible effect on amelogenin and type I collagen expression.

Operator binding by lambda repressor heterodimers with one or two N-terminal arms

The first 6 amino acids (NH2-Ser1-Thr2-Lys3-Lys4-Lys5-Pro6) of bacteriophage lambda cI repressor form a flexible arm that wraps around the operator DNA. Homodimeric lambda repressor has two arms. To determine whether both arms are necessary or only one arm is sufficient for operator binding, we constructed heterodimeric repressors with two, one, or no arms by fusing the DNA binding domain of lambda repressor to leucine zippers from Fos and Jun. Although only one arm is visible in the cocrystal structure of the N-domain-operator complex, our results indicate that both arms are required for optimal operator binding and normal site discrimination.

Probing the roles of residues at the e and g positions of the GCN4 leucine zipper by combinatorial mutagenesis

Combinatorial mutagenesis with an alphabet limited to alanine, glutamic acid, lysine, and threonine was used to probe the role of interactions involving surface residues in stabilizing a short alpha-helical coiled coil. The residues at eight e and g positions in the leucine zipper of the Saccharomyces cerevisiae transcription factor GCN4 were randomized to these four residues in a lambda repressor-leucine zipper fusion protein, resulting in 65,536 possible residue combinations. Roughly three-fourths of these combinations allowed stable coiled-coil formation as assayed by DNA binding by the fusion protein. To understand the basis for the activity differences, functional and non-functional mutants were sequenced and statistical tests were applied to identify structure/function correlations. Helix-forming propensity and favorable intrasubunit and intersubunit charge-charge interactions were positively correlated with activity. These studies suggest that the identities of surface side chains at the e and g positions of coiled coils contribute modestly to stability; by comparison with previous work, however, the e and g positions are far less critical than residues at the a and d positions, which form the hydrophobic core of the dimer interface.

Disinfecting activities of non-peroxide soft contact lens cold disinfection solutions

The antimicrobial activities of three non-peroxide soft contact lens chemical disinfection systems--ReNu Multi-Purpose Solution (0.00005% polyaminopropyl biguanide), Opti-Soft Disinfecting Solution (0.001% polyquaternium-1), and Opti-Free Rinsing, Disinfecting & Storage Solution (0.001% polyquaternium-1)--were compared to Soft Mate Disinfecting Solution (0.005% chlorhexidine digluconate). Each product was separately inoculated with each of five microorganisms at approximately 10(6) microorganisms per mL. All of the solutions demonstrated excellent disinfecting activity against Pseudomonas aeruginosa and Staphylococcus epidermidis, with complete disinfection occurring within 4 hours. Only Soft Mate disinfected Serratia marcescens within 4 hours. ReNu reduced the microorganisms to 10-100 cells/mL and Opti-Soft and Opti-Free reduced the number to 10(2)-10(3) cells/mL. For the fungal species, Soft Mate showed excellent activity against Candida albicans (disinfection in 4 hours) and reduced Aspergillus fumigatus to 10(3) spores/mL in 4 hours. After 4 hours ReNu, Opti-Soft, and Opti-Free had reduced C. albicans only slightly, to 10(5) cells/mL and displayed virtually no disinfecting activity against A. fumigatus. For these newer chemical disinfection systems, diligent cleaning and rinsing of the soft contact lenses are the most important steps in the patient care regimen.

Sequence requirements for coiled-coils: analysis with lambda repressor-GCN4 leucine zipper fusions

A genetic system was developed in Escherichia coli to study leucine zippers with the amino-terminal domain of bacteriophage lambda repressor as a reporter for dimerization. This system was used to analyze the importance of the amino acid side chains at eight positions that form the hydrophobic interface of the leucine zipper dimer from the yeast transcriptional activator, GCN4. When single amino acid substitutions were analyzed, most functional variants contained hydrophobic residues at the dimer interface, while most nonfunctional sequence variants contained strongly polar or helix-breaking residues. In multiple randomization experiments, however, many combinations of hydrophobic residues were found to be nonfunctional, and leucines in the heptad repeat were shown to have a special function in leucine zipper dimerization.

Hobbies of retired people in the People's Republic of China: a preliminary study

This study describes and analyzes the hobbies of over 500 retired individuals (ages fifty to eighty-eight in the People's Republic of China. Data were obtained through questionnaires and compared with the responses of 100 younger people (twenty to thirty-nine years of age). Hobbies of the retired people were classified into five categories: reading, physical exercise, productive, visual-auditory, and recreational. This classification is at variance with the one proposed by some Western writers. The following conclusions were reached: 1) there are significant differences between the hobbies of retired people and those of younger people; 2) reading is the hobby most preferred by the retired person in China; and 3) gender, age, education, and previous occupation are the factors that most influence the retired person's choice of hobbies.

Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase

We have systematically assayed the in vivo promoter recognition properties of 13 mutations in rpoD, the gene that encodes the sigma 70 subunit of Escherichia coli RNA polymerase holoenzyme, using transcriptional fusions to 37 mutant and wild-type promoters. We found three classes of rpoD mutations: (1) mutations that suggest contacts between amino acid side-chains of sigma 70 and specific bases in the promoter; (2) mutations that appear to affect either sequence independent contacts to promoter DNA or isomerization of the polymerase; and (3) mutations that have little or no effect on promoter recognition. Our results lead us to suggest that a sequence near the C terminus of sigma 70, which is similar to the helix-turn-helix DNA binding motif of phage and bacterial DNA binding proteins, is responsible for recognition of the -35 region, and that a sequence internal to sigma 70, in a region which is highly conserved among sigma factors, recognizes the -10 region of the promoter. rpoD mutations that lie in the recognition helix of the proposed helix-turn-helix motif affect interactions with specific bases in the -35 region, while mutations in the upstream helix, which is thought to contact the phosphate backbone, have sequence-independent effect on promoter recognition.

Mutations in rpoD, the gene encoding the sigma 70 subunit of Escherichia coli RNA polymerase, that increase expression of the lac operon in the absence of CAP-cAMP

We have isolated a new class of mutations in rpoD, the gene encoding the sigma 70 subunit of Escherichia coli RNA polymerase, that alter the transcription initiation properties of RNA polymerase holoenzyme. The rpoD(Lac) mutations increase expression of the lac operon in the absence of CAP-cAMP, allowing a strain lacking adenyl cyclase to grow on lactose. Four of the six alleles isolated have three- to fivefold increases in the amount of lac mRNA and beta-galactosidase per cell. We show that these four mutations increase transcription initiation from the same promoter used by wild-type RNA polymerase. The mutations were mapped and sequenced. One mutation occurs in the codon for amino acid 389 of the sigma 70 polypeptide. The remaining five mutations are clustered, affecting residues 570, 571 and 575. These five mutations are within or near a proposed helix-turn-helix motif in the C terminus of sigma 70.

Mutations in rpoD that increase expression of genes in the mal regulon of Escherichia coli K-12

The sigma subunits of eubacterial RNA polymerases determine the site selectivity of initiation of transcription at promoters. Mutations in rpoD, the gene that encodes sigma 70, the major sigma factor in Escherichia coli, should be useful in determining the molecular details of the process of transcription initiation. However, such mutations are likely to be deleterious or lethal, since sigma70 is an essential gene product. We designed a system for the rapid isolation and fine structure mapping of mutations in rpoD, which allows selection of mutations that would otherwise be deleterious to the cell. We used this system to isolate a new class of mutations in rpoD, mutations that relieve the requirement for CAP-cAMP for initiation at promoters in the mal regulon. These mutations, which we designate rpoD(Mal) mutations, occur in two clusters in the rpoD gene within regions previously suggested by amino acid sequence comparisons to be important for sigma structure or function. We cannot distinguish whether the rpoD(Mal) mutations affect mal expression by altering interaction between RNA polymerase and mal promoters or between RNA polymerase and the accessory transcription factor MalT. However, the effects of the mutations on activator-independent transcription from the lac promoter (4 rpoD(Mal) mutations decrease CAP-independent expression of the lac promoter in vivo) suggest that the regions of sigma identified by our mutations may be directly involved in promoter recognition.

Mutations in the sigma subunit of E. coli RNA polymerase which affect positive control of transcription

The sigma subunits of bacterial RNA polymerases are required for the selective initiation of transcription. We have isolated and characterized mutations in rpoD, the gene which encodes the major form of sigma in E. coli, which affect the selectivity of transcription. These mutations increase the expression of araBAD up to 12-fold in the absence of CAP-cAMP. Expression of lac is unaffected, while expression of malT-activated operons is decreased. We determined the DNA sequence of 17 independently isolated mutations, and found that they consist of three different changes in a single CGC arginine codon at position 596 in the sigma polypeptide.

Structural features required for the binding of tRNATrp to avian myeloblastosis virus reverse transcriptase

The basis of the specific binding of tRNATrp by avian myeloblastosis virus reverse transcriptase was studied by chemical and enzymatic modification of the RNA. Binding does not depend on recognition of the tryptophan anticodon since molecules cleaved in the anticodon are stably bound by the enzyme. Modification of pseudouridine residues in the tRNA destroys binding to reverse transcriptase. These results are consistent with a model in which reverse transcriptase-tRNATrp interaction occurs not at the anticodon, but at regions in the tRNA which contain or are stabilized by pseudouridine residues.

Isolation and characterization of genomic mouse DNA clones containing sequences homologous to tRNAs and 5S rRNA

We have cloned and characterized three fragments of Balb/c mouse DNA which hybridize to mouse cell tRNAs. Fractionation of the tRNAs which hybridize to these clones reveals that two of the clones, lambda Mt-4A and lambda Mt-6A hybridize to only one or two tRNAs, while one clone, lambda Mt-4B, hybridizes to at least seven tRNAs. Two of the tRNAs were identified as tRNAProCCG and tRNAGlyGGA, and others have been identified as tRNAs which are selectively encapsidated into virions of murine leukemia virus and avian reticuloendotheliosis virus. The DNA sequences of putative genes for tRNAProCCG and tRNAGlyGGA, plus flanking regions, were determined. A clone of Balb/c mouse DNA which selectively hybridized to 5S rRNA was also isolated and partially characterized.

Marker rescue with plasmids bearing deletions in rpoD identifies a dispensable part of E. coli sigma factor

Recombinant DNA techniques allow rapid construction and characterization of tools for genetic dissection of essential genes. In this report, we describe construction of a set of deletions in rpoD, the gene which encodes the sigma subunit of E. coli RNA polymerase. We used this deletion set to identify a region of the sigma polypeptide which is dispensable for its function.