From DNA to lytic proteins: transcription and translation of the bacteriophage T5 holin/endolysin operon.

The analysis of transcriptional activity of the bacteriophage T5 hol/endo operon conducted in the paper revealed a strong constitutive promoter recognized by E. coli RNA polymerase and a transcription initiation point of the operon. It was also shown that the only translational start codon for holin was a non-canonical TTG.

Dynamics of Open States and Promoter Functioning in the Y_red and Y_green Genetic Constructions Based on the pPF1 Plasmid.

Background: Although the role of dynamic factors in DNA function still remains unclear, research in this direction is a rapidly developing area of molecular biology. In this work, the genetic constructions Y_red and Y_green, based on the plasmid pPF1 and containing a fragment of () DNA with predicted promoter-like regions, are considered complex dynamic systems in which local sites of double helix unwinding, called open states, can arise and propagate. The purpose of the article is to show the existence of a connection between the dynamics of open states and the functioning of predicted promoters.

Proliferation, migration, and resistance to oxidative and thermal stresses of HT1080 cells with knocked out genes encoding Hsp90α and Hsp90β.

Heat shock protein 90 (Hsp90) fulfils essential housekeeping functions in the cell associated with the folding, stabilization, and turnover of various proteins. In mammals, there exist two Hsp90 isoforms, stress-inducible Hsp90α and constitutively expressed Hsp90β. In an attempt to identify cellular processes dependent on Hsp90α and Hsp90β, we generated a panel of clones of human fibrosarcoma HT1080 cells with the knocked out HSP90AA1 or HSP90AB1 genes encoding, respectively, Hsp90α and Hsp90β.

Divergently Transcribed ncRNAs in : Refinement of the Transcription Starts Assumes Functional Diversification.

Non-coding regulatory RNAs (ncRNAs) comprise specialized group of essential genetically encoded biological molecules involved in the wide variety of cellular metabolic processes. The progressive increase in the number of newly identified ncRNAs and the defining of their genome location indicate their predominant nesting in intergenic regions and expression under the control of their own regulatory elements. At the same time, the regulation of ncRNA's transcription cannot be considered in isolation from the processes occurring in the immediate genetic environment.

Excessive Promoters as Silencers of Genes Horizontally Acquired by .

Horizontally acquired genes are usually transcriptionally inactive, although most of them are associated with genomic loci enriched with promoter-like sequences forming "promoter islands." We hypothesized that lateral DNA transfer induces local mutagenesis, accumulating AT base pairs and creating promoter-like sequences, whose occupancy with RNA polymerase and a specific silencer H-NS suppresses the transcription of foreign genes. Error-prone mutagenesis was implemented for the "promoter island" of a foreign gene and the promoter region of an inherent gene .

Between computational predictions and high-throughput transcriptional profiling: in depth expression analysis of the OppB trans-membrane subunit of Escherichia coli OppABCDF oligopeptide transporter.

Bacterial oligopeptide transporters encoded by arrays of opp genes are implicated in a wide variety of physiological functions including nutrient acquisition, cell-to-cell communication, host-pathogen interaction. Combining the five opp genes in one oppABCDF operon of Escherichia coli assumes unified principle of their transcriptional regulation, which should provide a comparable amounts of translated products. This, however, contradicts the experimentally detected disproportion in the abundance of periplasmic OppA and the trans-membrane subunits OppB and OppC.

Visualizing the activity of Escherichia coli divergent promoters and probing their dependence on superhelical density using dual-colour fluorescent reporter vector.

Mosaic pattern of transcription in alternating directions is a common feature of prokaryotic and eukaryotic genomes which rationality and origin remain enigmatic. In Escherichia coli approximately 25% of genes comprise pairs of topologically linked divergently transcribed units. Given that transcriptional complex formation at each promoter in the pair induces topological changes and is itself sensitive to DNA structural perturbations, study of the functional anatomy in such areas requires special approaches.

[Antisense transcription within the hns locus of Escherichia coli].

Scanning the entire genome of E. coli by means of pattern-recognition software PlatProm spotted out more than a thousand of potential start points for antisense transcription. Taking into account possible role of antisense RNAs in the cell regulatory networks, our top-priority interest was focused on the promoter-like sites found within genes of transcription regulators.

Gains and unexpected lessons from genome-scale promoter mapping.

Potential promoters in the genome of Escherichia coli were searched by pattern recognition software PlatProm and classified on the basis of positions relative to gene borders. Beside the expected promoters located in front of the coding sequences we found a considerable amount of intragenic promoter-like signals with a putative ability to drive either antisense or alternative transcription and revealed unusual genomic regions with extremely high density of predicted transcription start points (promoter 'islands'), some of which are located in coding sequences. PlatProm scores converted into probability of RNA polymerase binding demonstrated certain correlation with the enzyme retention registered by ChIP-on-chip technique; however, in 'dense' regions the value of correlation coefficient is lower than throughout the entire genome.

Intragenic promotor-like sites in the genome of Escherichia coli discovery and functional implication.

Mapping of putative promoters within the entire genome of Escherichia coli (E. coli) by means of pattern-recognition software PlatProm revealed several thousand of sites having high probability to perform promoter function. Along with the expected promoters located upstream of coding sequences, PlatProm identified more than a thousand potential promoters for antisense transcription and several hundred very similar signals within coding sequences having the same direction with the genes.

The Rhizobium etli sigma70 (SigA) factor recognizes a lax consensus promoter.

A collection of Rhizobium etli promoters was isolated from a genomic DNA library constructed in the promoter-trap vector pBBMCS53, by their ability to drive the expression of a gusA reporter gene. Thirty-seven clones were selected, and their transcriptional start-sites were determined. The upstream sequence of these 37 start-sites, and the sequences of seven previously identified promoters were compared.

[Levels in the structural organization of Escherichia coli promoter DNA].

A number of additional structural elements were identified by statistic analysis of nucleotide sequences in promoters recognized by Escherichia coli RNA polymerase. Together with canonical hexanucleotides, these elements characterize different levels in the structural organization of promoter DNA. Sequence motifs exhibiting the highest statistical significance, which dominate in the contact regions with RNA polymerase alpha and sigma subunits, are considered as targets for specific interaction with RNA polymerase.

[Distribution and functional significance of A/T tracts in promotor sequences of Escherichia coli].

Distribution of the A/T tracts described in earlier publications in the region extending from nucleotide -250 to +150 relative to the transcription initiation site of gene transcribed regions adjacent to promoter was studied. Upstream of the -35 region a succession of A/T tracts was discovered distributed at a shorter distance one from another than in analogous elements of the transcribed region (1 and 1.5 helix turns, respectively).

Flexible elements in the structure of promoter DNA as probed by cationic surfactant binding.

A susceptibility of promoter DNA for adaptive conformational transitions has been studied using a cationic surfactant dodecyltrimethylammonium bromide (C(12)TAB) as a model DNA-binding ligand. DNAse 1 and KMnO(4) were utilized as structure-specific reagents. Both reagents revealed ligand-induced perturbations in the double helix of promoters T7A1 and T7D.

[Sequence-determined conformational changes in the coding region of the promoter DNA on transcription complex formation].

Chemical footprinting was used to study the spatial structure of bacteriophage T7 promoter D upon formation of the transcriptionally active complex with Escherichia coli RNA polymerase. Enzyme binding was shown to induce conformational changes in sites located at positions 43 and 57, several helix turns away from the transcription start. This was the first finding of a structural deformation induced by assembly of the transcription complex.

Structural organization and phase behavior of DNA-calcium-dipalmitoylphosphatidylcholine complex.

Freeze-fracture study of ultrastructure of DNA--calcium--dipalmitoylphosphatidylcholine (DPPC) complex was carried out at different temperatures. For high-speed cryofixation from controllable initial temperatures, a special thermostatic chamber was designed. The fracture surface of the complex was found to be considerably different from the initial DPPC liposomes: 1) the period of ripple phase was 25 nm in contrast to 15 nm for control samples; 2) the ripple phase was observed at temperatures ranging from 6 degreesC to lipid melting temperature; 3) at temperature above the lipid melting unordered worm-like folds were formed on the fracture surface.

Interaction of bacterial RNA-polymerase with two different promoters of phage T7 DNA. Conformational analysis.

Using a rifampicin-resistant RNA polymerase with altered specificity to different promoters, the D promoter of T7 phage DNA with increased affinity to the mutant enzyme was chosen. This promoter and the T7 A1 promoter with unchanged affinity as well as some nonpromoter DNA fragments were used to compare temperature-induced conformational transitions of RNA polymerase in the course of complex formation. Conformational alterations of RNA polymerase were monitored by the fluorescent label method.