Single molecule studies on the dynamics of the transcription initiation complex of yeast mitochondria

Department of Biomedical EngineeringThe transcription initiation complex in the yeast mitochondria of Saccharomyces cerevisiae comprises the RNA polymerase, Rpo41, the initiation factor, Mtf1, and the DNA including 6 base pair promoter sequence. The Mtf1 is known to recognize and help to open the promoter region during the initiation stage, but its exact role and mechanism still remains unclear. We designed a multi-color single molecule FRET assay to directly measure the dynamics of the complex during transcription initiation. The labels on the DNA report on its opening-closing dynamics, while the label on Mtf1 report on the recruitment, dynamics, and dissociation of the initiation factor. From these measurements, we can correlate the promoter opening dynamics, factor binding/dissociation, and the transition to the elongation phase. Mtf1 is also associated with controlling the production of abortive RNA transcripts. We observed the scrunching motion during transcription by stepping along the DNA template with various combinations of nucleotide substrates. The FRET distribution shifted toward the high FRET region as we stepped further. From these observations, we propose a mechanistic model of the transcription initiation in the yeast mitochondria.ope

Translation initiation factor eIF3 promotes programmed stop codon readthrough.

Programmed stop codon readthrough is a post-transcription regulatory mechanism specifically increasing proteome diversity by creating a pool of C-terminally extended proteins. During this process, the stop codon is decoded as a sense codon by a near-cognate tRNA, which programs the ribosome to continue elongation. The efficiency of competition for the stop codon between release factors (eRFs) and near-cognate tRNAs is largely dependent on its nucleotide context; however, the molecular mechanism underlying this process is unknown. Here, we show that it is the translation initiation (not termination) factor, namely eIF3, which critically promotes programmed readthrough on all three stop codons. In order to do so, eIF3 must associate with pre-termination complexes where it interferes with the eRF1 decoding of the third/wobble position of the stop codon set in the unfavorable termination context, thus allowing incorporation of near-cognate tRNAs with a mismatch at the same position. We clearly demonstrate that efficient readthrough is enabled by near-cognate tRNAs with a mismatch only at the third/wobble position. Importantly, the eIF3 role in programmed readthrough is conserved between yeast and humans

A three-dimensional multiscale model of intergranular hydrogen-assisted cracking

We present a three-dimensional model of intergranular hydrogen-embrittlement (HE) that accounts for: (i) the degradation of grain-boundary strength that arises from hydrogen coverage; (ii) grain-boundary diffusion of hydrogen; and (iii) a continuum model of plastic deformation that explicitly resolves the three-dimensional polycrystalline structure of the material. The polycrystalline structure of the specimen along the crack propagation path is resolved explicitly by the computational mesh. The texture of the polycrystal is assumed to be random and the grains are elastically anisotropic and deform plastically by crystallographic slip. We use the impurity-dependent cohesive model in order to account for the embrittling of grain boundaries due to hydrogen coverage. We have carried out three-dimensional finite-element calculations of crack-growth initiation and propagation in AISI 4340 steel double-cantilever specimens in contact with an aggressive environment and compared the predicted initiation times and crack-growth curves with the experimental data. The calculated crack-growth curves exhibit a number of qualitative features that are in keeping with observation, including: an incubation time followed by a well-defined crack-growth initiation transition for sufficiently large loading; the existence of a threshold intensity factor K_(Iscc) below which there is no crack propagation; a subsequent steeply rising part of the curve known as stage I; a plateau, or stage II, characterized by a load-insensitive crack-growth rate; and a limiting stress-intensity factor K_(Ic), or toughness, at which pure mechanical failure occurs. The calculated dependence of the crack-growth initiation time on applied stress-intensity factor exhibits power-law behavior and the corresponding characteristic exponents are in the ball-park of experimental observation. The stage-II calculated crack-growth rates are in good overall agreement with experimental measurements

Solving the Structure of eIF2 Bound to eIF2B Using Cryogenic Electron Microscopy

Translation begins when initiation factor-2 (eIF2) delivers methionyl initiator tRNA (Met-tRNAi) to the ribosome. The exchange of GDP bound to eIF2 for GTP is a prerequisite to binding Met-tRNAi and is mediated by a second initiation factor, eIF2B. Regulation of mRNA translation is achieved through phosphorylation of eIF2 α at Ser51 which converts eIF2 from a substrate into a competitive inhibitor of eIF2B. Using the latest cryo-electron microscopy (cryoEM) technologies in both collection and data processing we were able to obtain three high resolution structures to interrogate the structural basis of the integrated stress response

Factors associated with antiretroviral treatment initiation amongst HIV-positive individuals linked to care within a universal test and treat programme: early findings of the ANRS 12249 TasP trial in rural South Africa

Prompt uptake of antiretroviral treatment (ART) is essential to ensure the success of universal test and treat (UTT) strategies to prevent HIV transmission in high-prevalence settings. We describe ART initiation rates and associated factors within an ongoing UTT cluster-randomized trial in rural South Africa. HIV-positive individuals were offered immediate ART in the intervention arm vs. national guidelines recommended initiation (CD4≤350 cells/mm3) in the control arm. We used data collected up to July 2015 among the ART-eligible individuals linked to TasP clinics before January 2015. ART initiation rates at one (M1), three (M3) and six months (M6) from baseline visit were described by cluster and CD4 count strata (cells/mm3) and other eligibility criteria: ≤100; 100–200; 200–350; CD4>350 with WHO stage 3/4 or pregnancy; CD4>350 without WHO stage 3/4 or pregnancy. A Cox model accounting for covariate effect changes over time was used to assess factors associated with ART initiation. The 514 participants had a median [interquartile range] follow-up duration of 1.08 [0.69; 2.07] months until ART initiation or last visit. ART initiation rates at M1 varied substantially (36.9% in the group CD4>350 without WHO stage 3/4 or pregnancy, and 55.2–71.8% in the three groups with CD4≤350) but less at M6 (from 85.3% in the first group to 96.1–98.3% in the three other groups). Factors associated with lower ART initiation at M1 were a higher CD4 count and attending clinics with both high patient load and higher cluster HIV prevalence. After M1, having a regular partner was the only factor associated with higher likelihood of ART initiation. These findings suggest good ART uptake within a UTT setting, even among individuals with high CD4 count. However, inadequate staffing and healthcare professional practices could result in prioritizing ART initiation in patients with the lowest CD4 counts

Inhibition of translation by poliovirus: Inactivation of a specific initiation factor

Translation of vesicular stomatitis virus (VSV) mRNA, like host mRNA translation, is inhibited in cells infected with poliovirus. To study the mechanism of poliovirus-induced inhibition of protein synthesis, we prepared extracts from poliovirus-infected and uninfected HeLa cells. Poliovirus mRNA was translated in lysates from both infected and uninfected cells, while VSV mRNA was translated only in the lysate from uninfected cells. Addition of purified translation initiation factors to the extract from infected cells showed that one factor, eIF-4B, could restore VSV mRNA translation in the infected lysate, but did not increase poliovirus mRNA translation. Further experiments involving translation of VSV mRNA in mixed extracts from poliovirus-infected and uninfected cells showed (i) that there was not an excess of an inhibitor of VSV mRNA translation in the infected lysate, but (ii) that an activity that caused a slow inactivation of eIF-4B was present in the infected lysate. Inactivation of eIF-4B appears to be the mechanism by which poliovirus infection causes a selective inhibition of translation

Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation.

The initiation of protein synthesis plays an essential regulatory role in human biology. At the center of the initiation pathway, the 13-subunit eukaryotic translation initiation factor 3 (eIF3) controls access of other initiation factors and mRNA to the ribosome by unknown mechanisms. Using electron microscopy (EM), bioinformatics and biochemical experiments, we identify two highly conserved RNA-binding motifs in eIF3 that direct translation initiation from the hepatitis C virus internal ribosome entry site (HCV IRES) RNA. Mutations in the RNA-binding motif of subunit eIF3a weaken eIF3 binding to the HCV IRES and the 40S ribosomal subunit, thereby suppressing eIF2-dependent recognition of the start codon. Mutations in the eIF3c RNA-binding motif also reduce 40S ribosomal subunit binding to eIF3, and inhibit eIF5B-dependent steps downstream of start codon recognition. These results provide the first connection between the structure of the central translation initiation factor eIF3 and recognition of the HCV genomic RNA start codon, molecular interactions that likely extend to the human transcriptome

Crafting better team climate: the benefits of using creative methods during team initiation

This study employs a mixed methods approach to investigate the effect of creative methods, the combinative use of model building and storytelling, during team initiation on team climate, a critical people-related factor in the management of collective innovation work. Qualitative analysis provides empirical evidence that creative methods benefit team initiation by raising participative confidence, engagement with the social environment as well as the team activities, friendly competition among team members, and by reducing fear of failure and habitual thinking. We also find support that the use of creative methods initiates and supports the development of positive team climate over the span of a team’s life. A quantitative comparison with two control groups using the 14-item team climate inventory (TCI) 13 weeks after the team initiation indicates that the test group has significantly higher values in all dimensions of the TCI than the two control groups. Overall, this examination informs the work of innovation managers and scholars with vital insights about the effectiveness of using creative methods during team initiation