Structural basis for sequestration and autoinhibition of cGAS by chromatin.

Cyclic GMP-AMP synthase (cGAS) is an innate immune sensor for cytosolic microbial DNA1. After binding DNA, cGAS synthesizes the messenger 2'3'-cyclic GMP-AMP (cGAMP)2-4, which triggers cell-autonomous defence and the production of type I interferons and pro-inflammatory cytokines via the activation of STING5. In addition to responding to cytosolic microbial DNA, cGAS also recognizes mislocalized cytosolic self-DNA and has been implicated in autoimmunity and sterile inflammation6,7. Specificity towards pathogen- or damage-associated DNA was thought to be caused by cytosolic confinement. However, recent findings place cGAS robustly in the nucleus8-10, where tight tethering of chromatin is important to prevent autoreactivity to self-DNA8. Here we show how cGAS is sequestered and inhibited by chromatin. We provide a cryo-electron microscopy structure of the cGAS catalytic domain bound to a nucleosome, which shows that cGAS does not interact with the nucleosomal DNA, but instead interacts with histone 2A-histone 2B, and is tightly anchored to the 'acidic patch'. The interaction buries the cGAS DNA-binding site B, and blocks the formation of active cGAS dimers. The acidic patch robustly outcompetes agonistic DNA for binding to cGAS, which suggests that nucleosome sequestration can efficiently inhibit cGAS, even when accessible DNA is nearby, such as in actively transcribed genomic regions. Our results show how nuclear cGAS is sequestered by chromatin and provides a mechanism for preventing autoreactivity to nuclear self-DNA.

BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture.

The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with proteins such as potassium channels, the second messenger also specifically binds to transcription factors, thereby altering the processes in the cell on the transcriptional level. We here describe the structural and biochemical characterization of BusR from the human pathogen Streptococcus agalactiae. BusR is a member of a yet structurally uncharacterized subfamily of the GntR family of transcription factors that downregulates transcription of the genes for the BusA (OpuA) glycine-betaine transporter upon c-di-AMP binding. We report crystal structures of full-length BusR, its apo and c-di-AMP bound effector domain, as well as cryo-EM structures of BusR bound to its operator DNA. Our structural data, supported by biochemical and biophysical data, reveal that BusR utilizes a unique domain assembly with a tetrameric coiled-coil in between the binding platforms, serving as a molecular ruler to specifically recognize a 22 bp separated bipartite binding motif. Binding of c-di-AMP to BusR induces a shift in equilibrium from an inactivated towards an activated state that allows BusR to bind the target DNA, leading to transcriptional repression.

c-di-AMP hydrolysis by the phosphodiesterase AtaC promotes differentiation of multicellular bacteria.

Antibiotic-producing Streptomyces use the diadenylate cyclase DisA to synthesize the nucleotide second messenger c-di-AMP, but the mechanism for terminating c-di-AMP signaling and the proteins that bind the molecule to effect signal transduction are unknown. Here, we identify the AtaC protein as a c-di-AMP-specific phosphodiesterase that is also conserved in pathogens such as Streptococcus pneumoniae and Mycobacterium tuberculosis AtaC is monomeric in solution and binds Mn2+ to specifically hydrolyze c-di-AMP to AMP via the intermediate 5'-pApA. As an effector of c-di-AMP signaling, we characterize the RCK_C domain protein CpeA. c-di-AMP promotes interaction between CpeA and the predicted cation/proton antiporter, CpeB, linking c-di-AMP signaling to ion homeostasis in Actinobacteria. Hydrolysis of c-di-AMP is critical for normal growth and differentiation in Streptomyces, connecting ionic stress to development. Thus, we present the discovery of two components of c-di-AMP signaling in bacteria and show that precise control of this second messenger is essential for ion balance and coordinated development in Streptomyces.

Chemical Synthesis of the Fluorescent, Cyclic Dinucleotides cth GAMP.

The cGAS-STING pathway is known for its role in sensing cytosolic DNA introduced by a viral infection, bacterial invasion or tumorigenesis. Free DNA is recognized by the cyclic GMP-AMP synthase (cGAS) catalyzing the production of 2',3'-cyclic guanosine monophosphate-adenosine monophosphate (2',3'-cGAMP) in mammals. This cyclic dinucleotide acts as a second messenger, activating the stimulator of interferon genes (STING) that finally triggers the transcription of interferon genes and inflammatory cytokines. Due to the therapeutic potential of this pathway, both the production and the detection of cGAMP via fluorescent moieties for assay development is of great importance. Here, we introduce the paralleled synthetic access to the intrinsically fluorescent, cyclic dinucleotides 2'3'-cth GAMP and 3'3'-cth GAMP based on phosphoramidite and phosphate chemistry, adaptable for large scale synthesis. We examine their binding properties to murine and human STING and confirm biological activity including interferon induction by 2'3'-cth GAMP in THP-1 monocytes. Two-photon imaging revealed successful cellular uptake of 2'3'-cth GAMP in THP-1 cells.

Regioselective Fluorination of Acenes: Tailoring of Molecular Electronic Levels and Solid-State Properties.

Optoelectronic properties of molecular solids are important for organic electronic devices and are largely determined by the adopted molecular packing motifs. In this study, we analyzed such structure-property relationships for the partially regioselective fluorinated tetracenes 1,2,12-trifluorotetracene, 1,2,10,12-tetrafluorotetracene and 1,2,9,10,11-pentafluorotetracene that were further compared with tetracene and perfluoro-tetracene. Quantum chemical DFT calculations in combination with optical absorption spectroscopy data show that the frontier orbital energies are lowered with the degree of fluorination, while their optical gap is barely affected. However, the crystal structure changes from a herringbone packing motif of tetracene towards a planar stacking motif of the fluorinated tetracene derivatives, which is accompanied by the formation of excimers and leads to strongly red-shifted photoluminescence with larger lifetimes.

Template and Temperature-Controlled Polymorph Formation in Squaraine Thin Films.

Controlling the polymorph formation in organic semiconductor thin films by the choice of processing parameters is a key factor for targeted device performance. Small molecular semiconductors such as the prototypical anilino squaraine compound with branched butyl chains as terminal functionalization (SQIB) allow both solution and vapor phase deposition methods. SQIB has been considered for various photovoltaic applications mainly as amorphous isotropic thin films due to its broad absorption within the visible to deep-red spectral range. The two known crystalline polymorphs adopting a monoclinic and orthorhombic crystal phase show characteristic Frenkel excitonic spectral signatures of overall H-type and J-type aggregates, respectively, with additional pronounced Davydov splitting. This gives a recognizable polarized optical response of crystalline thin films suitable for identification of the polymorphs. Both phases emerge with a strongly preferred out-of-plane and rather random in-plane orientation in spin-casted thin films depending on subsequent thermal annealing. By contrast, upon vapor deposition on dielectric and conductive substrates, such as silicon dioxide, potassium chloride, graphene, and gold, the polymorph expression depends basically on the choice of growth substrate. The same pronounced out-of-plane orientation is adopted in all crystalline cases, but with a surface templated in-plane alignment in case of crystalline substrates. Strikingly, the amorphous isotropic thin films obtained by vapor deposition cannot be crystallized by thermal postannealing, which is a key feature for the spin-casted thin films, here monitored by polarized in situ microscopy. Combining X-ray diffraction, atomic force microscopy, ellipsometry, and polarized spectro-microscopy, we identify the processing-dependent evolution of the crystal phases, correlating morphology and molecular orientations within the textured SQIB films.

Novel Poxin Stable cGAMP-Derivatives Are Remarkable STING Agonists.

2',3'-cGAMP is a cyclic A- and G-containing dinucleotide second messenger, which is formed upon cellular recognition of foreign cytosolic DNA as part of the innate immune response. The molecule binds to the adaptor protein STING, which induces an immune response characterized by the production of type I interferons and cytokines. The development of STING-binding molecules with both agonistic as well as antagonistic properties is currently of tremendous interest to induce or enhance antitumor or antiviral immunity on the one hand, or to treat autoimmune diseases on the other hand. To escape the host innate immune recognition, some viruses encode poxin endonucleases that cleave 2',3'-cGAMP. Here we report that dideoxy-2',3'-cGAMP (1) and analogs thereof, which lack the secondary ribose-OH groups, form a group of poxin-stable STING agonists. Despite their reduced affinity to STING, particularly the compound constructed from two A nucleosides, dideoxy-2',3'-cAAMP (2), features an unusually high antitumor response in mice.

Selective saturation of step-edges as a tool to control the growth of molecular fibres.

The concept of bottom-up self-organisation has become a promising alternative for structuring molecular materials, which are hardly accessible by conventional top-down approaches such as lithography due to their limited chemical robustness. While these materials often tend to form three-dimensional, crystalline islands or fibres upon film growth, the size and orientation of such fibres are mainly governed by appropriate preparation conditions as well as microscopic interactions at the interface with the supporting surface. Substrate surface defects such as vacancies or step-edges, which cannot be completely ruled out on real surfaces on the mesoscopic scale, can act as preferred nucleation sites for molecules that leads to parasitic film growth competing with their intrinsic alignment prevailing on an ideal surface. In the present study, we demonstrate for the case of para-quaterphenyl (p-4P) that the presence of azimuthally disordered, fibres on Ag(111) surfaces can be understood as a superposition of step-mediated nucleation and the intrinsic epitaxial fibre growth on ideal surfaces. We validate the concept by purposely exposing the silver substrates briefly to oxygen or even ambient air to passivate the more reactive step-sites, which hampers subsequently grown molecular films to nucleate at these step-edges. This yields a truly epitaxial alignment as well as an enlargement of the fibres present on the whole sample.

Low-lying excited states in crystalline perylene.

Organic materials are promising candidates for advanced optoelectronics and are used in light-emitting diodes and photovoltaics. However, the underlying mechanisms allowing the formation of excited states responsible for device functionality, such as exciton generation and charge separation, are insufficiently understood. This is partly due to the wide range of existing crystalline polymorphs depending on sample preparation conditions. Here, we determine the linear optical response of thin-film single-crystal perylene samples of distinct polymorphs in transmission and reflection geometries. The sample quality allows for unprecedented high-resolution spectroscopy, which offers an ideal opportunity for judicious comparison between theory and experiment. Excellent agreement with first-principles calculations for the absorption based on the GW plus Bethe-Salpeter equation (GW-BSE) approach of many-body perturbation theory (MBPT) is obtained, from which a clear picture of the low-lying excitations in perylene emerges, including evidence of an exciton-polariton stopband, as well as an assessment of the commonly used Tamm-Dancoff approximation to the GW-BSE approach. Our findings on this well-controlled system can guide understanding and development of advanced molecular solids and functionalization for applications.

Chemical Surface Reactivity and Morphological Changes of Bismuth Triiodide (BiI3) under Different Environmental Conditions.

Layered metal halides like BiI3 are of current interest in connection with both 2D materials and photovoltaics. Here, we present a facile new method for the preparation of millimeter-sized BiI3 single crystals. We use these crystals to study the surface reactivity of their (001) cleavage planes toward various environmental conditions by measuring morphological changes using atomic force microscopy and analyzing the formed species by means of X-ray photoelectron spectroscopy and X-ray diffraction methods. We find that freshly cleaved samples show atomically flat surface regions extending over several micrometers and reveal steps corresponding to single BiI3 layers. However, we also find that the surface deteriorates in air on a time scale of hours. By studying samples cleaved and stored under different conditions, we identify water as the agent initiating the changes in surface morphology, while under inert gas and dry oxygen, the surface stays intact. On the basis of the analysis of deteriorated long-term-stored samples we identify BiOI as the main product of hydrolysis. We also observe a second long-term decomposition route for samples stored under dynamic vacuum, where formation of BiI whiskers occurs. Overall, our findings emphasize the challenges associated with the surface reactivity of BiI3 but also demonstrate that well-ordered BiI3 surfaces can be obtained, which indicates that preparation of extended, atomically smooth BiI3 monolayers by exfoliation from bulk crystals should be possible.

Unilaterally Fluorinated Acenes: Synthesis and Solid-State Properties.

The rapid development of organic electronics is closely related to the availability of molecular materials with specific electronic properties. Here, we introduce a novel synthetic route enabling a unilateral functionalization of acenes along their long side, which is demonstrated by the synthesis of 1,2,10,11,12,14-hexafluoropentacene (1) and the related 1,2,9,10,11-pentafluorotetracene (2). Quantum chemical DFT calculations in combination with optical and X-ray absorption spectroscopy data indicate that the single-molecule properties of 1 are a connecting link between the organic semiconductor model systems pentacene (PEN) and perfluoropentacene (PFP). In contrast, the crystal structure analysis reveals a different packing motif than for the parent molecules. This can be related to distinct F⋅⋅⋅H interactions identified in the corresponding Hirshfeld surface analysis and also affects solid-state properties such as the exciton binding energy and the sublimation enthalpy.

A Click-Chemistry Linked 2'3'-cGAMP Analogue.

2'3'-cGAMP is an uncanonical cyclic dinucleotide where one A and one G base are connected via a 3'-5' and a unique 2'-5' linkage. The molecule is produced by the cyclase cGAS in response to cytosolic DNA binding. cGAMP activates STING and hence one of the most powerful pathways of innate immunity. cGAMP analogues with uncharged linkages that feature better cellular penetrability are currently highly desired. Here, the synthesis of a cGAMP analogue with one amide and one triazole linkage is reported. The molecule is best prepared via a first CuI -catalyzed click reaction, which establishes the triazole, while the cyclization is achieved by macrolactamization.

Orientational and Crystalline Order of Copper-Phthalocyanine Films on Gold: the Role of Substrate Roughness and Cleanliness.

Although metal phthalocyanines are widely used in optoelectronic devices, e.g., as hole-transport and electron-blocking layers, or as UV-stable dyes, their multilayer growth on metal substrates has surprisingly not been studied very systematically. Even for CuPc, one of the most widely studied representatives of phthalocyanines, contradictory structures are reported for films grown on gold, a common electrode material, suggesting that the influence of actual substrate surface properties on film growth has not been sufficiently considered. In this study, we analyze the growth of CuPc films on gold substrates for thicknesses ranging from the initial seed layer to thick multilayers (50 nm) by combining near-edge X-ray absorption spectroscopy with atomic force microscopy and X-ray diffraction. To study the influence of surface roughness, we compare the formation of CuPc films on well-ordered Au(111) and sputter-deposited polycrystalline gold substrates and also investigate the influence of surface contamination by exposing these gold surfaces to air before film growth. While on clean gold substrates, CuPc molecules exclusively adopt a recumbent orientation and form (112̅)-oriented films, they also grow in an upright orientation on contaminated gold surfaces. On Au(111), this leads to the coexistence of (112̅)- and (100)-oriented regions, whereas only (100)-oriented films are formed on contaminated polycrystalline gold. Remarkably, the (112̅)-oriented films consist of extended but isolated crystalline islands, resulting in large overall roughness, whereas the (100)-oriented films consist of rather small domains but have significantly lower film roughness.

cGAS produces a 2'-5'-linked cyclic dinucleotide second messenger that activates STING.

Detection of cytoplasmic DNA represents one of the most fundamental mechanisms of the innate immune system to sense the presence of microbial pathogens. Moreover, erroneous detection of endogenous DNA by the same sensing mechanisms has an important pathophysiological role in certain sterile inflammatory conditions. The endoplasmic-reticulum-resident protein STING is critically required for the initiation of type I interferon signalling upon detection of cytosolic DNA of both exogenous and endogenous origin. Next to its pivotal role in DNA sensing, STING also serves as a direct receptor for the detection of cyclic dinucleotides, which function as second messenger molecules in bacteria. DNA recognition, however, is triggered in an indirect fashion that depends on a recently characterized cytoplasmic nucleotidyl transferase, termed cGAMP synthase (cGAS), which upon interaction with DNA synthesizes a dinucleotide molecule that in turn binds to and activates STING. We here show in vivo and in vitro that the cGAS-catalysed reaction product is distinct from previously characterized cyclic dinucleotides. Using a combinatorial approach based on mass spectrometry, enzymatic digestion, NMR analysis and chemical synthesis we demonstrate that cGAS produces a cyclic GMP-AMP dinucleotide, which comprises a 2'-5' and a 3'-5' phosphodiester linkage >Gp(2'-5')Ap(3'-5')>. We found that the presence of this 2'-5' linkage was required to exert potent activation of human STING. Moreover, we show that cGAS first catalyses the synthesis of a linear 2'-5'-linked dinucleotide, which is then subject to cGAS-dependent cyclization in a second step through a 3'-5' phosphodiester linkage. This 13-membered ring structure defines a novel class of second messenger molecules, extending the family of 2'-5'-linked antiviral biomolecules.

Structural mechanism of cytosolic DNA sensing by cGAS.

Cytosolic DNA arising from intracellular bacterial or viral infections is a powerful pathogen-associated molecular pattern (PAMP) that leads to innate immune host defence by the production of type I interferon and inflammatory cytokines. Recognition of cytosolic DNA by the recently discovered cyclic-GMP-AMP (cGAMP) synthase (cGAS) induces the production of cGAMP to activate the stimulator of interferon genes (STING). Here we report the crystal structure of cGAS alone and in complex with DNA, ATP and GTP along with functional studies. Our results explain the broad DNA sensing specificity of cGAS, show how cGAS catalyses dinucleotide formation and indicate activation by a DNA-induced structural switch. cGAS possesses a remarkable structural similarity to the antiviral cytosolic double-stranded RNA sensor 2'-5'oligoadenylate synthase (OAS1), but contains a unique zinc thumb that recognizes B-form double-stranded DNA. Our results mechanistically unify dsRNA and dsDNA innate immune sensing by OAS1 and cGAS nucleotidyl transferases.

Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth.

Cell growth is regulated during RNA polymerase (Pol) I transcription initiation by the conserved factor Rrn3/TIF-IA in yeast/humans. Here we provide a structure-function analysis of Rrn3 based on a combination of structural biology with in vivo and in vitro functional assays. The Rrn3 crystal structure reveals a unique HEAT repeat fold and a surface serine patch. Phosphorylation of this patch represses human Pol I transcription, and a phospho-mimetic patch mutation prevents Rrn3 binding to Pol I in vitro and reduces cell growth and Pol I gene occupancy in vivo. Cross-linking indicates that Rrn3 binds Pol I between its subcomplexes, AC40/19 and A14/43, which faces the serine patch. The corresponding region of Pol II binds the Mediator head that cooperates with transcription factor (TF) IIB. Consistent with this, the Rrn3-binding factor Rrn7 is predicted to be a TFIIB homolog. This reveals the molecular basis of Rrn3-regulated Pol I initiation and cell growth, and indicates a general architecture of eukaryotic transcription initiation complexes.

Atomic Structure and Biochemical Characterization of an RNA Endonuclease in the N Terminus of Andes Virus L Protein.

Andes virus (ANDV) is a human-pathogenic hantavirus. Hantaviruses presumably initiate their mRNA synthesis by using cap structures derived from host cell mRNAs, a mechanism called cap-snatching. A signature for a cap-snatching endonuclease is present in the N terminus of hantavirus L proteins. In this study, we aimed to solve the atomic structure of the ANDV endonuclease and characterize its biochemical features. However, the wild-type protein was refractory to expression in Escherichia coli, presumably due to toxic enzyme activity. To circumvent this problem, we introduced attenuating mutations in the domain that were previously shown to enhance L protein expression in mammalian cells. Using this approach, 13 mutant proteins encompassing ANDV L protein residues 1-200 were successfully expressed and purified. Protein stability and nuclease activity of the mutants was analyzed and the crystal structure of one mutant was solved to a resolution of 2.4 Å. Shape in solution was determined by small angle X-ray scattering. The ANDV endonuclease showed structural similarities to related enzymes of orthobunya-, arena-, and orthomyxoviruses, but also differences such as elongated shape and positively charged patches surrounding the active site. The enzyme was dependent on manganese, which is bound to the active site, most efficiently cleaved single-stranded RNA substrates, did not cleave DNA, and could be inhibited by known endonuclease inhibitors. The atomic structure in conjunction with stability and activity data for the 13 mutant enzymes facilitated inference of structure-function relationships in the protein. In conclusion, we solved the structure of a hantavirus cap-snatching endonuclease, elucidated its catalytic properties, and present a highly active mutant form, which allows for inhibitor screening.

cGAS Senses Human Cytomegalovirus and Induces Type I Interferon Responses in Human Monocyte-Derived Cells.

Human cytomegalovirus (HCMV) infections of healthy individuals are mostly unnoticed and result in viral latency. However, HCMV can also cause devastating disease, e.g., upon reactivation in immunocompromised patients. Yet, little is known about human immune cell sensing of DNA-encoded HCMV. Recent studies indicated that during viral infection the cyclic GMP/AMP synthase (cGAS) senses cytosolic DNA and catalyzes formation of the cyclic di-nucleotide cGAMP, which triggers stimulator of interferon genes (STING) and thus induces antiviral type I interferon (IFN-I) responses. We found that plasmacytoid dendritic cells (pDC) as well as monocyte-derived DC and macrophages constitutively expressed cGAS and STING. HCMV infection further induced cGAS, whereas STING expression was only moderately affected. Although pDC expressed particularly high levels of cGAS, and the cGAS/STING axis was functional down-stream of STING, as indicated by IFN-I induction upon synthetic cGAMP treatment, pDC were not susceptible to HCMV infection and mounted IFN-I responses in a TLR9-dependent manner. Conversely, HCMV infected monocyte-derived cells synthesized abundant cGAMP levels that preceded IFN-I production and that correlated with the extent of infection. CRISPR/Cas9- or siRNA-mediated cGAS ablation in monocytic THP-1 cells and primary monocyte-derived cells, respectively, impeded induction of IFN-I responses following HCMV infection. Thus, cGAS is a key sensor of HCMV for IFN-I induction in primary human monocyte-derived DC and macrophages.

Polarized absorbance and Davydov splitting in bulk and thin-film pentacene polymorphs.

Pentacene is one of the most studied organic materials and in particular its optical properties have been the subject of intense research during the last two decades. In spite of such a widespread interest and of the extensive knowledge achieved so far, a number of issues are still debated. One of the most relevant questions concerns the role of polymorphism and how it affects the lowest-energy exciton, which appears in the visible region and is subject to a sizable Davydov splitting. We address this problem in a combined theoretical and experimental work, where the optical absorption properties of three pentacene polymorphs are investigated within the whole energy range of visible light. Optical spectra computed from first principles in the framework of many-body perturbation theory are directly compared with the polarization-resolved absorbance, measured for three different pentacene phases (the two bulk polymorphs and the thin-film phase). In this way, we unambiguously identify the two Davydov components of the first exciton and the optical fingerprints of each considered phase. With very good agreement between theory and experiment, we show that all polymorphs exhibit common features at the absorption onset, while phase-dependent characteristics appear only above 2 eV. We discuss the character of the lowest-lying singlet and triplet excitons, including dark ones, highlighting the contributions from the electronic bands and the role of the electron-hole interaction and of the local-field effects.

Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes.

The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sensor. These 'Twitch' sensors are based on the C-terminal domain of Opsanus troponin C. Their FRET responses were optimized by a large-scale functional screen in bacterial colonies, refined by a secondary screen in rat hippocampal neuron cultures. We tested the in vivo performance of the most sensitive variants in the brain and lymph nodes of mice. The sensitivity of the Twitch sensors matched that of synthetic calcium dyes and allowed visualization of tonic action potential firing in neurons and high resolution functional tracking of T lymphocytes. Given their ratiometric readout, their brightness, large dynamic range and linear response properties, Twitch sensors represent versatile tools for neuroscience and immunology.