The Cdk8 kinase module regulates interaction of the mediator complex with RNA polymerase II.

The Cdk8 kinase module (CKM) is a dissociable part of the coactivator complex mediator, which regulates gene transcription by RNA polymerase II. The CKM has both negative and positive functions in gene transcription that remain poorly understood at the mechanistic level. In order to reconstitute the role of the CKM in transcription initiation, we prepared recombinant CKM from the yeast Saccharomyces cerevisiae. We showed that CKM bound to the core mediator (cMed) complex, sterically inhibiting cMed from binding to the polymerase II preinitiation complex (PIC) in vitro. We further showed that the Cdk8 kinase activity of the CKM weakened CKM-cMed interaction, thereby facilitating dissociation of the CKM and enabling mediator to bind the PIC in order to stimulate transcription initiation. Finally, we report that the kinase activity of Cdk8 is required for gene activation during the stressful condition of heat shock in vivo but not under steady-state growth conditions. Based on these results, we propose a model in which the CKM negatively regulates mediator function at upstream-activating sequences by preventing mediator binding to the PIC at the gene promoter. However, during gene activation in response to stress, the Cdk8 kinase activity of the CKM may release mediator and allow its binding to the PIC, thereby accounting for the positive function of CKM. This may impart improved adaptability to stress by allowing a rapid transcriptional response to environmental changes, and we speculate that a similar mechanism in metazoans may allow the precise timing of developmental transcription programs.

Mechanistic insight into the assembly of the HerA-NurA helicase-nuclease DNA end resection complex.

The HerA-NurA helicase-nuclease complex cooperates with Mre11 and Rad50 to coordinate the repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA. By combining hybrid mass spectrometry with cryo-EM, computational and biochemical data, we investigate the oligomeric formation of HerA and detail the mechanism of nucleotide binding to the HerA-NurA complex from thermophilic archaea. We reveal that ATP-free HerA and HerA-DNA complexes predominantly exist in solution as a heptamer and act as a DNA loading intermediate. The binding of either NurA or ATP stabilizes the hexameric HerA, indicating that HerA-NurA is activated by substrates and complex assembly. To examine the role of ATP in DNA translocation and processing, we investigated how nucleotides interact with the HerA-NurA. We show that while the hexameric HerA binds six nucleotides in an 'all-or-none' fashion, HerA-NurA harbors a highly coordinated pairwise binding mechanism and enables the translocation and processing of double-stranded DNA. Using molecular dynamics simulations, we reveal novel inter-residue interactions between the external ATP and the internal DNA binding sites. Overall, here we propose a stepwise assembly mechanism detailing the synergistic activation of HerA-NurA by ATP, which allows efficient processing of double-stranded DNA.

Rinsing Recommendations for Membrane Filters and Identification of Rinsables.

Filtration is universally used in biopharmaceutical processing. For example, in upstream processing for sterilizing-grade filtration of cell culture media or in various downstream operations, such as clarification, filtration of intermediates, and in critical final filling applications. It is well known that filtration devices can release a certain level of organic compounds within the first filtrate fractions, which can be measured as total organic carbon (TOC). The compounds are primarily released from the surface of its construction materials. This includes typical polymer constituents that migrate from the material, as well as compounds which are formed during sterilization by irradiation. The level of compounds present on a surface is reduced significantly during rinsing of filters. Therefore, these can be defined as "rinsables". A deeper understanding of filter rinsing characteristics and chemical composition of a rinse solution is relevant for process design and risk mitigation, especially in high-risk applications. This publication provides the analytical and mathematical tools to measure and evaluate rinsing curves obtained from different sterilizing-grade membrane filter capsules. Total organic carbon (TOC) content, high-resolution mass spectrometry, ion chromatography, and headspace GC-MS were used to determine the composition of rinsing fractions and to follow the course of the rinsing curve. The required, filter-specific parameters Bulk Volume per Surface area (BVS) and Rinsing Volume per Surface area (RVS) are introduced. They are used for calculating minimum bulk and rinsing volumes of filters that lead to TOC concentrations below the threshold of 500 µg/L for Water for Injection. Three relevant filtration cases in biopharmaceutical manufacturing are discussed together with best practices for evaluation and use of BVS and RVS parameters. Results of a verification test are presented and discussed.

Histone H3 Serine 28 Is Essential for Efficient Polycomb-Mediated Gene Repression in Drosophila.

Trimethylation at histone H3K27 is central to the polycomb repression system. Juxtaposed to H3K27 is a widely conserved phosphorylatable serine residue (H3S28) whose function is unclear. To assess the importance of H3S28, we generated a Drosophila H3 histone mutant with a serine-to-alanine mutation at position 28. H3S28A mutant cells lack H3S28ph on mitotic chromosomes but support normal mitosis. Strikingly, all methylation states of H3K27 drop in H3S28A cells, leading to Hox gene derepression and to homeotic transformations in adult tissues. These defects are not caused by active H3K27 demethylation nor by the loss of H3S28ph. Biochemical assays show that H3S28A nucleosomes are a suboptimal substrate for PRC2, suggesting that the unphosphorylated state of serine 28 is important for assisting in the function of polycomb complexes. Collectively, our data indicate that the conserved H3S28 residue in metazoans has a role in supporting PRC2 catalysis.