Tho2 is critical for the recruitment of Rrp6 to chromatin in response to perturbed mRNP biogenesis.

The eukaryotic THO complex coordinates the assembly of so-called messenger RNA-ribonucleoprotein particles (mRNPs), a process that involves cotranscriptional coating of nascent mRNAs with proteins. Once formed, mRNPs undergo a quality control step that marks them either for active transport to the cytoplasm, or Rrp6/RNA exosome-mediated degradation in the nucleus. However, the mechanism behind the quality control of nascent mRNPs is still unclear.

Regulation of the conserved 3'-5' exoribonuclease EXOSC10/Rrp6 during cell division, development and cancer.

The conserved 3'-5' exoribonuclease EXOSC10/Rrp6 processes and degrades RNA, regulates gene expression and participates in DNA double-strand break repair and control of telomere maintenance via degradation of the telomerase RNA component. EXOSC10/Rrp6 is part of the multimeric nuclear RNA exosome and interacts with numerous proteins. Previous clinical, genetic, biochemical and genomic studies revealed the protein's essential functions in cell division and differentiation, its RNA substrates and its relevance to autoimmune disorders and oncology.

Yeast RNA exosome activity is necessary for maintaining cell wall stability through proper protein glycosylation.

Nuclear RNA exosome is the main 3'→5' RNA degradation and processing complex in eukaryotic cells and its dysregulation therefore impacts gene expression and viability. In this work we show that RNA exosome activity is necessary for maintaining cell wall stability in yeast . While the essential RNA exosome catalytic subunit Dis3 provides exoribonuclease catalytic activity, the second catalytic subunit Rrp6 has a noncatalytic role in this process.

Protocol for efficient fluorescence 3' end-labeling of native noncoding RNA domains.

Noncoding RNAs (ncRNAs) comprise a class of versatile transcripts that are highly involved in the regulation of a wide range of biological processes. Functional long ncRNAs (> 200 nts in length) often adopt secondary structures that arise co-transcriptionally. To maintain the secondary structure elements as well as preparation homogeneity of such transcripts, native-like conditions should be maintained throughout the synthesis, purification and chemical tagging processes.

Deciphering the Dynamic Landscape of Transcription-Associated mRNP Quality Control Components Over the Whole Yeast Genome.

In eukaryotic cells, aberrant mRNPs with processing and packaging defects are targeted co-transcriptionally by a surveillance system that triggers their nuclear retention and ultimately the degradation of their mRNA component by the 3'-5' activity of the exosome-associated exonuclease Rrp6. This mRNP quality control process is stimulated by the NNS complex (Nrd1-Nab3-Sen1), which otherwise mediates termination, processing, and decay of ncRNAs. The process involves also the exosome co-activator TRAMP complex (Trf4-Air2-Mtr4).

Modulation of Maillard reaction and protein aggregation in bovine meat following exposure to microwave heating and possible impact on digestive processes: An FTIR spectroscopy study.

The aim of this study was to highlight the existence of a correlation between Maillard reaction and protein aggregation in bovine meat as a function of power level and exposure time used by microwave heating. The obtained results are compared with those of convective heating. For this, Fourier Transform-Infrared Spectroscopy was used to analyze the effects of microwave heating on different samples of bovine meat cooked in microwave ovens at three power levels of 700, 900 and 1100 W, and in conventional electric oven at the temperature of 170°C.

Chromosome aberration in typical biological systems under exposure to low- and high-intensity magnetic fields.

The aim of this study was to investigate the response of chromosomes in typical human and plant cells under applied low-frequency magnetic fields at low and high intensities. Neuronal-like cells and roots of and were used to investigate chromosome's response to a static and 50 Hz magnetic fields at intensities ranging from 1 mT to 0.8 T, generated by two Helmholtz coils driven by direct current or alternate current voltage.

mRNA with Mammalian Codon Bias Accumulates in Yeast Mutants with Constitutive Stress Granules.

Stress granules and P bodies are cytoplasmic structures assembled in response to various stress factors and represent sites of temporary storage or decay of mRNAs. Depending on the source of stress, the formation of these structures may be driven by distinct mechanisms, but several stresses have been shown to stabilize mRNAs via inhibition of deadenylation. A recent study identified yeast gene deletion mutants with constitutive stress granules and elevated P bodies; however, the mechanisms which trigger its formation remain poorly understood.

Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome.

Eukaryotic cells have evolved a nuclear quality control (QC) system to monitor the co-transcriptional mRNA processing and packaging reactions that lead to the formation of export-competent ribonucleoprotein particles (mRNPs). Aberrant mRNPs that fail to pass the QC steps are retained in the nucleus and eliminated by the exonuclease activity of Rrp6. It is still unclear how the surveillance system is precisely coordinated both physically and functionally with the transcription machinery to detect the faulty events that may arise at each step of transcript elongation and mRNP formation.

Infrared spectroscopic demonstration of magnetic orientation in SH-SY5Y neuronal-like cells induced by static or 50 Hz magnetic fields.

To study the response of neuronal-like cells to an applied static or low-frequency magnetic field. Fourier Transform Infrared (FTIR) Spectroscopy was used to investigate the overall behavior of SH-SY5Y neuronal-like cells exposed to a static or 50 Hz magnetic fields at intensities up to 1 mT generated by two Helmholtz coils driven by direct current or alternate current voltage. The Helmholtz coils were placed into an incubator in a 5% CO/95% air humidified at 37 °C.

Thermal restraint of a bacterial exopolysaccharide of shallow vent origin.

To dynamically characterize the thermal properties of the fructose-rich exopolysaccharide (EPS1-T14), produced by the marine thermophilic Bacillus licheniformis T14, the Attenuated Total Reflectance Fourier Transform Infra-Red spectroscopy was coupled to variable temperature ranging from ambient to 80°C. The spectra were analyzed by the following innovative mathematical tools: i) non-ideal spectral deviation, ii) OH-stretching band frequency center shift, iii) spectral distance, and iv) wavelet cross-correlation analysis. The thermal restraint analysis revealed that the whole EPS1-T14 system possessed high stability until 80°C, and suggested that fucose was mainly involved in the EPS1-T14 thermal stability, whereas glucose was responsible for its molecular flexibility.

Recombinant yeast and human cells as screening tools to search for antibacterial agents targeting the transcription termination factor Rho.

The alarming issue of antibiotic resistance expansion requires a continuous search for new and efficient antibacterial agents. Here we describe the design of new tools to screen for target-specific inhibitors of the bacterial Rho factor directly inside eukaryotic cells. Rho factor is a global regulator of gene expression which is essential to most bacteria, especially Gram-negative.

In situ footprinting of E. coli transcription elongation complex with chloroacetaldehyde.

The structure and dynamics of Escherichia coli transcription elongation complex are now well documented. However, most of the studies have been conducted in vitro and frequently under artificial conditions that facilitate the biochemical characterization of the complex. Thus, little is known about relevance of these results for the regulatory aspects of transcription elongation inside the cell.

Cdk5 induces constitutive activation of 5-HT6 receptors to promote neurite growth.

The serotonin6 receptor (5-HT6R) is a promising target for treating cognitive deficits of schizophrenia often linked to alterations of neuronal development. This receptor controls neurodevelopmental processes, but the signaling mechanisms involved remain poorly understood. Using a proteomic strategy, we show that 5-HT6Rs constitutively interact with cyclin-dependent kinase 5 (Cdk5).

Cotranscriptional recruitment of RNA exosome cofactors Rrp47p and Mpp6p and two distinct Trf-Air-Mtr4 polyadenylation (TRAMP) complexes assists the exonuclease Rrp6p in the targeting and degradation of an aberrant messenger ribonucleoprotein particle (mRNP) in yeast.

The cotranscriptional mRNA processing and packaging reactions that lead to the formation of export-competent messenger ribonucleoprotein particles (mRNPs) are under the surveillance of quality control steps. Aberrant mRNPs resulting from faulty events are retained in the nucleus with ensuing elimination of their mRNA component. The molecular mechanisms by which the surveillance system recognizes defective mRNPs and stimulates their destruction by the RNA degradation machinery are still not completely elucidated.

Ligand binding in a spherical region randomly crowded by receptors.

This paper reports on some results concerning the binding of diffusing ligands in a spherical 3D region randomly filled by free receptors. It is shown that commonly accepted mean-field theory which is successfully used for bulk diffusion-controlled reactions cannot describe the behavior of ligand concentration in the diffusion layer close to the region boundary. To eliminate this drawback of the theory, we introduce a new complementary diffusion equation in the boundary layer with an appropriate matching condition.

Nuclear mRNA quality control in yeast is mediated by Nrd1 co-transcriptional recruitment, as revealed by the targeting of Rho-induced aberrant transcripts.

The production of mature export-competent transcripts is under the surveillance of quality control steps where aberrant mRNP molecules resulting from inappropriate or inefficient processing and packaging reactions are subject to exosome-mediated degradation. Previously, we have shown that the heterologous expression of bacterial Rho factor in yeast interferes in normal mRNP biogenesis leading to the production of full-length yet aberrant transcripts that are degraded by the nuclear exosome with ensuing growth defect. Here, we took advantage of this new tool to investigate the molecular mechanisms by which an integrated system recognizes aberrancies at each step of mRNP biogenesis and targets the defective molecules for destruction.

Expression of bacterial Rho factor in yeast identifies new factors involved in the functional interplay between transcription and mRNP biogenesis.

In eukaryotic cells, the nascent pre-mRNA molecule is coated sequentially with a large set of processing and binding proteins that mediate its transformation into an export-competent ribonucleoprotein particle (mRNP) that is ready for translation in the cytoplasm. We have implemented an original assay that monitors the dynamic interplay between transcription and mRNP biogenesis and that allows the screening for new factors linking mRNA synthesis to translation in Saccharomyces cerevisiae. The assay is based on the perturbation of gene expression induced by the bacterial Rho factor, an RNA-dependent helicase/translocase that acts as a competitor at one or several steps of mRNP biogenesis in yeast.

Insight into the intrinsic flexibility of the SL1 stem-loop from genomic RNA of HIV-1 as probed by molecular dynamics simulation.

The SL1 stem-loop is the dimerization initiation site for linking the two copies of the RNA forming the HIV-1 genome. The 26 nucleotides stem contains a defect consisting on a highly conserved G-rich 1-3 asymmetrical internal loop, which is a major site for nucleocapsid protein binding. Several NMR attempts were undertaken to determine the internal loop structure in the SL1 monomer.

Molecular dynamics simulation for probing the flexibility of the 35 nucleotide SL1 sequence kissing complex from HIV-1Lai genomic RNA.

The SL1 stem-loop located in the encapsidation domain is responsible for initiating the dimerisation of HIV-1 genomic RNA by means of a loop-loop interaction known as Kissing Complex (KC). The SL1 secondary structure has been predicted as a 35 nucleotides [K. G.

Mannose-6-phosphate/insulin-like growth factor II receptor expression and tumor development.

The mannose-6-phosphate/insulin-like growth factor II receptor (M6P/IGF-IIR) is a multi-functional transmembrane glycoprotein whose major function is to bind and transport M6P-bearing glycoproteins from the trans-Golgi network or the cell surface to lysosomes. The cell surface M6P/IGF-IIR also bind and internalizes the insulin-like growth factor II. The receptor gene is considered a "candidate" tumor suppressor gene.

Conformational pathway for the kissing complex-->extended dimer transition of the SL1 stem-loop from genomic HIV-1 RNA as monitored by targeted molecular dynamics techniques.

HIV-1 retroviral genomic RNA dimerization is initiated by loop-loop interactions between the SL1 stem-loops of two identical RNA molecules. The SL1-SL1 unstable resulting kissing complex (KC) then refolds irreversibly into a more stable complex called extended dimer (ED). Although the structures of both types of complex have been determined, very little is known about the conformational pathway corresponding to the transition, owing to the difficulty of observing experimentally intermediate conformations.

Transcriptional pausing in vivo: a nascent RNA hairpin restricts lateral movements of RNA polymerase in both forward and reverse directions.

Transcriptional pausing by RNA polymerase has been the subject of extensive investigations in vitro, yet little is known about its occurrence and significance in vivo. The transient nature of the pausing events makes them difficult to observe inside the cell, whereas their studies in vitro by classical biochemical methods are usually conducted under non-physiological conditions that increase the pause duration. Here, we have used an Escherichia coli system in which several RNA polymerase molecules transcribing in tandem traverse a pausing sequence while approaching a protein roadblock.

Topological insulators inhibit diffusion of transcription-induced positive supercoils in the chromosome of Escherichia coli.

The double helical nature of DNA implies that progression of transcription machinery that cannot rotate easily around the DNA axis creates waves of positive supercoils ahead of it and negative supercoils behind it. Using topological reporters that detect local variations in DNA supercoiling, we have characterized the diffusion of transcription-induced (TI) positive supercoils in plasmids or in the chromosome of wild type Escherichia coli cells. Transcription-induced positive supercoils were able to diffuse and affect local supercoiling several kilobases away from the site of origin.

Improvement of exogenous DNA nuclear importation by nuclear localization signal-bearing vectors: a promising way for non-viral gene therapy?

Several vectors have been developed in order to target genes to specific cells. Virus-based vectors lead to a high transfection efficiency in vitro, but display important disadvantages such as pathological risks, which they expose to patients. Plasmid-associated chemical vectors lack these disadvantages, but allow only a very low efficiency of transgene expression.