Nucleotide sequence of DNA controlling expression of genes for maltosaccharide utilization in Streptococcus pneumoniae

An analysis of previous data indicated that four structural genes concerned with maltosaccharide utilization in Streptococcus pneumoniae are organized in two operons that are transcribed in opposite directions from a central control region. This region contains two strong promoters subject to repression by a regulatory gene product in the absence of maltose. The nucleotide sequence of the 554-bp control region DNA and adjacent portions of the malX and malM structural genes was determined. Unique reading frames and initiation codons allowed identification of the oppositely oriented structural genes. Putative ribosome binding sites and −10 and −35 RNA-polymerase-binding sites, as well as AT-rich regions farther upstream, were observed proximal to both the X and M genes. The similarity of these sequences to sites found in Escherichia coli and Bacillus subtilis indicated the conservation of control signals in bacteria, both Gram-negative and Gram-positive. A pair of 17-bp hyphenated repeat sequences in the control region may represent repressor binding sites. Two down promoter mutations, V11 and 69, were shown to be deletions in the control region. The V11 mutation, which affected only the MP operon, deleted the promoter adjacent to the M gene. Mutation 69, which reduced both X and M gene functions, deleted the entire segment between the promoters so that they now overlap at their −35 binding sites. As a consequence of this deletion, the AT-rich regions proximal to the promoters were lost. This suggests that the AT-rich regions are important for promoter strength.     

鱼类基因启动子的研究进展

启动子是基因的一个重要组成部分;控制基因的转录和表达。人们已经普遍认识到可以通过研究基因启动子来改变生物的特征;提高其优良性状。所以近年来;随着对启动子研究的不断深入;人们对鱼类基因启动子的分子结构、功能及其应用有了更多地了解。重点介绍鱼类启动子的特点;阐述启动子在鱼类代谢;生长发育和免疫中的应用以及双向启动子在转基因鱼研究中的应用。     

Computer System “Gene Discovery” to Search for Patterns in Eukaryotic Regulatory Nucleotide Sequences

A method is proposed to automatically search for patterns in the mutual location of context signals in regulatory DNA sequences. The procedure is based on the methods of Data Mining and Knowledge Discovery software, implemented in a computer system Gene Discovery. This system was used to study erythroid-specific promoters and promoters of the endocrine-system genes from TRRD. We detected some trends in occurrence and localization of specific oligonucleotide groups.     

Interactions in native binding sites cause a large change in protein dynamics

Cellular functions are regulated by molecules that interact with proteins and alter their activities. To enable such control, protein activity, and therefore protein conformational distributions, must be susceptible to alteration by molecular interactions at functional sites. Here we investigate whether interactions at functional sites cause a large change in the protein conformational distribution. We apply a computational method, called dynamics perturbation analysis (DPA), to identify sites at which interactions have a large allosteric potential D(x), which is the Kullback-Leibler divergence between protein conformational distributions with and without an interaction. In DPA, a protein is decorated with surface points that interact with neighboring protein atoms, and D(x) is calculated for each of the points in a coarse-grained model of protein vibrations. We use DPA to examine hundreds of protein structures from a standard small-molecule docking test set, and find that ligand-binding sites have elevated values of D(x): for 95% of proteins, the probability of randomly obtaining values as high as those in the binding site is 10(-3) or smaller. We then use DPA to develop a computational method to predict functional sites in proteins, and find that the method accurately predicts ligand-binding-site residues for proteins in the test set. The performance of this method compares favorably with that of a cleft analysis method. The results confirm that interactions at small-molecule binding sites cause a large change in the protein conformational distribution, and motivate using DPA for large-scale prediction of functional sites in proteins. They also suggest that natural selection favors proteins whose activities are capable of being regulated by molecular interactions.     

[3H]Muscimol Binding Site on Purified Benzodiazepine Receptor

The presence of a [3H]muscimol binding site on the purified benzodiazepine receptor was demonstrated. The purified protein was apparently homogeneous as shown by sodium dodecyl sulfate polyacrylamide gel electrophoresis (stained with silver), with a molecular weight of 60,000 +/- 3000. The benzodiazepine binding sites were characterized as being of the central type and the [3H]flunitrazepam binding was enhanced by GABA. This activation was antagonized by bicuculline. [3H]Muscimol specifically binds to the benzodiazepine receptor. The Scatchard plot indicates a Kd of 23 nM and the ratio [3H]flunitrazepam/[3H]muscimol is approximately unity.     

An internal AUU codon initiates a smaller peptide encoded by bacteriophage T4 baseplate gene 26

Summary Bacteriophage T4 baseplate gene 26 codes for two in-frame overlapping peptides with identical C-terminal regions. By site-directed mutagenesis we have now determined that an internal AUU, codon 114 of gene 26, is used as the initiation codon for the synthesis of a smaller peptide (gp26^*). Thus gene 26^* gives rise to a peptide of 95 amino acid residues with an M_r of 10873, while the complete gene 26 encodes a peptide of 208 amino acid residues of M_r 23 880. Expression of gene 26^* is shown to depend on the RNA secondary structure in the translational initiation region of this gene.     

Design, synthesis and DNA binding properties of orthogonally positioned diamino containing polyamide f-IPI

An orthogonally positioned diamino/dicationic polyamide f-IPI 2 was synthesized. It has enhanced binding affinity, and it showed comparable sequence specificity to its monoamino/monocationic counterpart f-IPI 1. Results from CD and DNase I footprinting studies confirmed the minor groove binding and selectivity of polyamides 1 and 2 for the cognate sequence 5′-ACGCGT-3′. SPR studies provided their binding constants: 2.4 × 10⁸ M⁻¹ for diamino 2, which is ∼4 times higher than 5.4 × 10⁷ M⁻¹ for its monoamino analogue 1.     

Refinement and Analysis of the Mature Zika Virus Cryo-EM Structure at 3.1 Å Resolution

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