Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates

The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the threedimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilised through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions (IDRs) of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provides a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.

CRISPR-ChIP reveals selective regulation of H3K79me2 by Menin in MLL leukemia

Chromatin regulation involves the selective recruitment of chromatin factors to facilitate DNA repair, replication and transcription. Here we demonstrate the utility of coupling unbiased functional genomics with chromatin immunoprecipitation (CRISPR-ChIP) to identify the factors associated with active chromatin modifications in mammalian cells. Specifically, an integrated reporter containing a cis-regulatory element of interest and a single guide RNA provide a chromatinized template for a direct readout for regulators of histone modifications associated with actively transcribed genes such as H3K4me3 and H3K79me2. With CRISPR-ChIP, we identify all the nonredundant COMPASS complex members required for H3K4me3 and demonstrate that RNA polymerase II is dispensable for the maintenance of H3K4me3. As H3K79me2 has a putative oncogenic function in leukemia cells driven by MLL translocations, using CRISPR-ChIP we reveal a functional partitioning of H3K79 methylation into two distinct regulatory units: an oncogenic DOT1L complex directed by the MLL fusion protein in a Menin-dependent manner and a separate endogenous DOT1L complex, where catalytic activity is directed by MLLT10. Overall, CRISPR-ChIP provides a powerful tool for the unbiased interrogation of the mechanisms underpinning chromatin regulation.

Development of a novel angiotensin converting enzyme 2 stimulator with broad implications in SARS-CoV2 and type 1 diabetes

Angiotensin-converting enzyme 2 (ACE2) is protective in cardiovascular disease, lung injury and diabetes yet paradoxically underlies our susceptibility to SARs-CoV2 infection and the fatal heart and lung disease it can induce. Furthermore, diabetic patients have chronic, systemic inflammation and altered ACE2 expression resulting in increased risk of severe COVID-19 and the associated mortality. A drug that could increase ACE2 activity and inhibit cellular uptake of severe acute respiratory syndrome coronavirus 2 (SARs-CoV2), thus decrease infection, would be of high relevance to cardiovascular disease, diabetes and SARs-CoV2 infection. While the need for such a drug lead was highlighted over a decade ago receiving over 600 citations,1 to date, no such drugs are available.2 Here, we report the development of a novel ACE2 stimulator, designated '2A'(international PCT filed), which is a 10 amino acid peptide derived from a snake venom, and demonstrate its in vitro and in vivo efficacy against SARs-CoV2 infection and associated lung inflammation. Peptide 2A also provides remarkable protection against glycaemic dysregulation, weight loss and disease severity in a mouse model of type 1 diabetes. No untoward effects of 2A were observed in these pre-clinical models suggesting its strong clinical translation potential.

The Melolontha melolontha entomopoxvirus fusolin protein is a chitin-active lytic polysaccharide monooxygenase that displays extreme stability

Spindles are intracellular crystals of the fusolin protein that enhance the oral virulence of insect poxviruses by disruption of the larval chitinous peritrophic matrix. The enigmatic fusolin protein is classified as a lytic polysaccharide monooxygenase (LPMO) by sequence and structure. Although circumstantial evidence points towards a role for fusolin in chitin degradation, no biochemical data exist to verify this claim. In the present study we demonstrate that fusolin released from over 40-year-old spindles, stored for 10 years at 4 °C, are chitin-degrading LPMOs. Not only were the fusolins active after long-term storage, but, in its crystalline form, fusolin also withstood high temperature and oxidative stress, highlighting an extreme stability that is beneficial to viral persistence and desirable for potential biotechnology applications.

SAGA and SAGA-like SLIK transcriptional coactivators are structurally and biochemically equivalent

The SAGA-like complex SLIK is a modified version of the Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex. SLIK is formed through C-terminal truncation of the Spt7 SAGA subunit, causing loss of Spt8, one of the subunits that interacts with the TATA-binding protein (TBP). SLIK and SAGA are both coactivators of RNA polymerase II transcription in yeast, and both SAGA and SLIK perform chromatin modifications. The two complexes have been speculated to uniquely contribute to transcriptional regulation, but their respective contributions are not clear. To investigate, we assayed the chromatin modifying functions of SAGA and SLIK, revealing identical kinetics on minimal substrates in vitro. We also examined the binding of SAGA and SLIK to TBP and concluded that interestingly, both protein complexes have similar affinity for TBP. Additionally, despite the loss of Spt8 and C-terminus of Spt7 in SLIK, TBP prebound to SLIK is not released in the presence of TATA-box DNA, just like TBP prebound to SAGA. Furthermore, we determined a low-resolution cryo-EM structure of SLIK, revealing a modular architecture identical to SAGA. Finally, we performed a comprehensive study of DNA-binding properties of both coactivators. Purified SAGA and SLIK both associate with ssDNA and dsDNA with high affinity (K_D = 10–17 nM), and the binding is sequence-independent. In conclusion, our study shows that the cleavage of Spt7 and the absence of the Spt8 subunit in SLIK neither drive any major conformational differences in its structure compared with SAGA, nor significantly affect HAT, DUB, or DNA-binding activities in vitro.

AgarFix: Simple and accessible stabilization of challenging single-particle cryo-EM specimens through crosslinking in a matrix of agar

Cryogenic electron microscopy (cryo-EM) allows structure determination of macromolecular assemblies that have resisted other structural biology approaches because of their size and heterogeneity. These challenging multi-protein targets are typically susceptible to dissociation and/or denaturation upon cryo-EM grid preparation, and often require crosslinking prior to freezing. Several approaches for gentle on-column or in-tube crosslinking have been developed. On-column crosslinking is not widely applicable because of the poor separation properties of gel filtration techniques. In-tube crosslinking frequently causes sample aggregation and/or precipitation. Gradient-based crosslinking through the GraFix method is more robust, but very time-consuming and necessitates specialised expensive equipment. Furthermore, removal of the glycerol typically involves significant sample loss and may cause destabilization detrimental to the sample quality. Here, we introduce an alternative procedure: AgarFix (Agarose Fixation). The sample is embedded in an agarose matrix that keeps the molecules separated, thus preventing formation of aggregates upon cross-inking. Gentle crosslinking is accomplished by diffusion of the cross-linker into the agarose drop. The sample is recovered by diffusion or electroelution and can readily be used for cryo-EM specimen preparation. AgarFix requires minimal equipment and basic lab experience, making it widely accessible to the cryo-EM community.

Supramolecular protein cages constructed from a crystalline protein matrix

Protein crystals are formed via ordered arrangements of proteins, which assemble to form supramolecular structures. Here, we show a method for the assembly of supramolecular protein cages within a crystalline environment. The cages are stabilized by covalent cross-linking allowing their release via dissolution of the crystal. The high stability of the desiccated protein crystals allows cages to be constructed.

Microcrystallography of Protein Crystals and In Cellulo Diffraction

The advent of high-quality microfocus beamlines at many synchrotron facilities has permitted the routine analysis of crystals smaller than 10 µm in their largest dimension, which used to represent a challenge. We present two alternative workflows for the structure determination of protein microcrystals by X-ray crystallography with a particular focus on crystals grown in vivo. The microcrystals are either extracted from cells by sonication and purified by differential centrifugation, or analyzed in cellulo after cell sorting by flow cytometry of crystal-containing cells. Optionally, purified crystals or crystal-containing cells are soaked in heavy atom solutions for experimental phasing. These samples are then prepared for diffraction experiments in a similar way by application onto a micromesh support and flash cooling in liquid nitrogen. We briefly describe and compare serial diffraction experiments of isolated microcrystals and crystal-containing cells using a microfocus synchrotron beamline to produce datasets suitable for phasing, model building and refinement. These workflows are exemplified with crystals of the Bombyx mori cypovirus 1 (BmCPV1) polyhedrin produced by infection of insect cells with a recombinant baculovirus. In this case study, in cellulo analysis is more efficient than analysis of purified crystals and yields a structure in ~8 days from expression to refinement.

Photoactivatable CO release from engineered protein crystals to modulate NF-κB activation

Photoactivatable CO releasing protein crystals were developed by immobilization of Mn carbonyl complexes in polyhedral crystals, which are spontaneously formed in insect cells. The photoactivatable CO release from the engineered protein crystals activates nuclear factor kappa B (NF-κB) upon stimulation by visible light irradiation with suppression of cytotoxicity of the Mn complex.

A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction

While structure determination from micrometre-sized crystals used to represent a challenge, serial X-ray crystallography on microfocus beamlines at synchrotron and free-electron laser facilities greatly facilitates this process today for microcrystals and nanocrystals. In addition to typical microcrystals of purified recombinant protein, these advances have enabled the analysis of microcrystals produced inside living cells. Here, a pipeline where crystals are grown in insect cells, sorted by flow cytometry and directly analysed by X-ray diffraction is presented and applied to in vivo-grown crystals of the recombinant CPV1 polyhedrin. When compared with the analysis of purified crystals, in cellulo diffraction produces data of better quality and a gain of ∼0.35 Å in resolution for comparable beamtime usage. Importantly, crystals within cells are readily derivatized with gold and iodine compounds through the cellular membrane. Using the multiple isomorphous replacement method, a near-complete model was autobuilt from 2.7 Å resolution data. Thus, in favourable cases, an in cellulo pipeline can replace the complete workflow of structure determination without compromising the quality of the resulting model. In addition to its efficiency, this approach maintains the protein in a cellular context throughout the analysis, which reduces the risk of disrupting transient or labile interactions in protein-protein or protein-ligand complexes.

Urodynamic changes in mice with experimental autoimmune encephalomyelitis correlate with neurological impairment

AIMS

Neurogenic bladder dysfunction is a major issue in Multiple Sclerosis (MS). High intravesical pressure should be treated early. Available therapies are insufficient and there is need for drug development and investigation of pathogenesis. Experimental Autoimmune Encephalomyelitis (EAE) in rodents is a well validated model to study MS. Previous research has shown that these animals develop urinary symptoms. However, from clinical studies, we know that symptoms do not necessarily reflect changes in bladder pressure. This paper aims to provide a complete overview of urodynamic changes in a model for detrusor overactivity in MS.

METHODS

Female C57Bl/6J mice, injected with MOG35-55 and control mice, injected with vehicle (Complete Freund's adjuvant), were monitored daily for neurologic symptoms. Within 1 month after symptom development, mice were used for cystometry or histology of the bladder.

RESULTS

Increasing disease score correlated with increased micturition frequency, basal pressure, and average pressure, and with a decrease in functional bladder capacity, voiding amplitude, and maximum pressure.

CONCLUSIONS

This paper provides a detailed description of bladder function in C57Bl/6J mice with Myelin Oligodendrocyte Glycoprotein peptide (MOG35-55 ) induced EAE. This EAE model induces detrusor overactivity in close relationship to neurological impairment. EAE in mice is a suitable model to study detrusor overactivity in MS. Neurourol. Urodynam. 35:450-456, 2016. © 2015 Wiley Periodicals, Inc.

In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology?

The serendipitous discovery of the spontaneous growth of protein crystals inside cells has opened the field of crystallography to chemically unmodified samples directly available from their natural environment. On the one hand, through in vivo crystallography, protocols for protein crystal preparation can be highly simplified, although the technique suffers from difficulties in sampling, particularly in the extraction of the crystals from the cells partly due to their small sizes. On the other hand, the extremely intense X-ray pulses emerging from X-ray free-electron laser (XFEL) sources, along with the appearance of serial femtosecond crystallography (SFX) is a milestone for radiation damage-free protein structural studies but requires micrometre-size crystals. The combination of SFX with in vivo crystallography has the potential to boost the applicability of these techniques, eventually bringing the field to the point where in vitro sample manipulations will no longer be required, and direct imaging of the crystals from within the cells will be achievable. To fully appreciate the diverse aspects of sample characterization, handling and analysis, SFX experiments at the Japanese SPring-8 angstrom compact free-electron laser were scheduled on various types of in vivo grown crystals. The first experiments have demonstrated the feasibility of the approach and suggest that future in vivo crystallography applications at XFELs will be another alternative to nano-crystallography.

Structure of viral spindles, in vivo crystals boosting insecticidal activity

Entomopoxviruses (EV) produce two types of microcrystals in infected cells: virus-containing spheroids representing their main infectious form; and spindles, bipyramidal crystals of the viral fusolin protein, that contribute to the oral virulence of these viruses. In co-feeding experiments, spindles also enhance the insecticidal activity of unrelated insect pathogens, which suggested their use as bioinsecticide additives. To understand how fusolin contributes to virulence and assembles in vivo, we determined the structures of EV spindles by X-ray microcrystallography using crystals isolated from EV-infected common cockchafers. This structure reveals that fusolin is composed of a fibronectin III domain followed by an extended C-terminal molecular arm (CT). The globular domain is structurally homologous to CBP21, a protein that is secreted by Gram-negative bacteria to degrade chitin as a source of energy. Like CBP21, fusolin has all the hallmarks of a lytic polysaccharide monooxygenase enzyme (LPMOs) with two conserved histidine residues forming a copper binding site and a prominent di-tryptophan motif positioned to bind the planar surface of crystalline chitin. The LPMO domain assembles in vivo into ultra-stable crystals crosslinked by CT. This molecular arm mediates the formation of domain-swapped dimers and their assembly into a crystalline lattice stabilized by a 3-D network of inter-dimer disulfide bonds. Overall, the molecular organization of spindles indicates a mode of action where controlled released of the LPMO domain of fusolin by proteolytic removal of the CT extension leads to disruption of the chitin-rich peritrophic matrix of larvae to facilitate the initial steps of viral invasion of the host.

Molecular determinants of the DprA-RecA interaction for nucleation on ssDNA

Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its loading on the incoming exogenous ssDNA. Although the 3D structures of both RecA and DprA have been solved, the mechanisms underlying their cross-talk remained elusive. By combining molecular docking simulations and experimental validation, we identified a region on RecA, buried at its self-assembly interface and involving three basic residues that contact an acidic triad of DprA previously shown to be crucial for the interaction. At the core of these patches, ^DprAM238 and ^RecAF230 are involved in the interaction. The other DprA binding regions of RecA could involve the N-terminal α-helix and a DNA-binding region. Our data favor a model of DprA acting as a cap of the RecA filament, involving a DprA−RecA interplay at two levels: their own oligomeric states and their respective interaction with DNA. Our model forms the basis for a mechanistic explanation of how DprA can act as a mediator for the loading of RecA on ssDNA.

Structural insights into the dimerization of the response regulator ComE from Streptococcus pneumoniae

Natural transformation contributes to the maintenance and to the evolution of the bacterial genomes. In Streptococcus pneumoniae, this function is reached by achieving the competence state, which is under the control of the ComD-ComE two-component system. We present the crystal and solution structures of ComE. We mimicked the active and non-active states by using the phosphorylated mimetic ComE(D58E) and the unphosphorylatable ComE(D58A) mutants. In the crystal, full-length ComE(D58A) dimerizes through its canonical REC receiver domain but with an atypical mode, which is also adopted by the isolated REC(D58A) and REC(D58E). The LytTR domain adopts a tandem arrangement consistent with the two direct repeats of its promoters. However ComE(D58A) is monomeric in solution, as seen by SAXS, by contrast to ComE(D58E) that dimerizes. For both, a relative mobility between the two domains is assumed. Based on these results we propose two possible ways for activation of ComE by phosphorylation.

Reflections on the Many Facets of Protein Microcrystallography

The use of X-ray crystallography for the structure determination of biological macromolecules has experienced a steady expansion over the last 20 years with the Protein Data Bank growing from <1000 deposited structures in 1992 to >100 000 in 2014. The large number of structures determined each year not only reflects the impact of X-ray crystallography on many disciplines in the biological and medical fields but also its accessibility to non-expert laboratories. Thus protein crystallography is now largely a mainstream research technique and is routinely integrated in high-throughput pipelines such as structural genomics projects and structure-based drug design. Yet, significant frontiers remain that continuously require methodological developments. In particular, membrane proteins, large assemblies, and proteins from scarce natural sources still represent challenging targets for which obtaining the large diffracting crystals required for classical crystallography is often difficult. These limitations have fostered the emergence of microcrystallography, novel approaches in structural biology that collectively aim at determining structures from the smallest crystals. Here, we review the state of the art of macromolecular microcrystallography and recent progress achieved in this field.

Transient receptor potential channels in bladder function

The transient receptor potential (TRP) superfamily of cationic ion channels includes proteins involved in the transduction of several physical and chemical stimuli to finely tune physiological functions. In the urinary bladder, they are highly expressed in, but not restricted to, primary afferent neurons. The urothelium and some interstitial cells also express several TRP channels. In this review, we describe the expression and the known roles of some members of TRP subfamilies, namely TRPV, TRPM and TRPA, in the urinary bladder. The therapeutic interest of modulating the activity of TRP channels to treat bladder dysfunctions is also discussed.

The structure of the NasR transcription antiterminator reveals a one-component system with a NIT nitrate receptor coupled to an ANTAR RNA-binding effector

The nitrate- and nitrite-sensing NIT domain is present in diverse signal-transduction proteins across a wide range of bacterial species. NIT domain function was established through analysis of the Klebsiella oxytoca NasR protein, which controls expression of the nasF operon encoding enzymes for nitrite and nitrate assimilation. In the presence of nitrate or nitrite, the NasR protein inhibits transcription termination at the factor-independent terminator site in the nasF operon transcribed leader region. We present here the crystal structure of the intact NasR protein in the apo state. The dimeric all-helical protein contains a large amino-terminal NIT domain that associates two four-helix bundles, and a carboxyl-terminal ANTAR (AmiR and NasR transcription antitermination regulator) domain. The analysis reveals unexpectedly that the NIT domain is structurally similar to the periplasmic input domain of the NarX two-component sensor that regulates nitrate and nitrite respiration. This similarity suggests that the NIT domain binds nitrate and nitrite between two invariant arginyl residues located on adjacent alpha helices, and results from site-specific mutagenesis showed that these residues are critical for NasR function. The resulting structural movements in the NIT domain would provoke an active configuration of the ANTAR domains necessary for specific leader mRNA binding.

Rhopalia are integrated parts of the central nervous system in box jellyfish

In cubomedusae, the central nervous system (CNS) is found both in the bell (the ring nerve) and in the four eye-bearing sensory structures (the rhopalia). The ring nerve and the rhopalia are connected via the rhopalial stalks and examination of the structure of the rhopalial stalks therefore becomes important when trying to comprehend visual processing. In the present study, the rhopalial stalk of the cubomedusae Tripedalia cystophora has been examined by light microscopy, transmission electron microscopy, and electrophysiology. A major part of the ring nerve is shown to continue into the stalk and to contact the rhopalial neuropil directly. Ultrastructural analysis of synapse distribution in the rhopalial stalk has failed to show any clustering, which indicates that integration of the visual input is probably spread throughout the CNS. Together, the results indicate that cubomedusae have one coherent CNS including the rhopalia. Additionally, a novel gastrodermal nerve has been found in the stalk; this nerve is not involved in visual processing but is likely to be mechanosensory and part of a proprioceptory system.