Topological localization in out-of-equilibrium dissipative systems
Kinjal Dasbiswas, Kranthi K. Mandadapu, and Suriyanarayanan Vaikuntanathan
Topological insulators and their analogs in mechanical materials support conducting states only on their surface. We show that such topologically protected edge modes can also occur as the steady states of classical systems driven out of equilibrium. As proof of principle of the generic applicability of such notions, we show the existence of topologically localized states in a collection of interacting particles described by a hydrodynamic theory and discuss a general procedure to establish them in stochastic networks. In both cases, dissipative processes that break time-reversal symmetry are key to topological protection. Our results provide design principles for robust edge modes in synthetic systems as well as for the localization of flow of matter and information in biology. (See pp. E9031–E9040.)
Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways
Fangda Xu, Asanga Bandara, Hisashi Akiyama, Behnaz Eshaghi, David Stelter, Tom Keyes, John E. Straub, Suryaram Gummuluru, and Björn M. Reinhard
Membrane-wrapped noble metal nanoparticles provide a synthetic platform to investigate lipid-mediated, glycoprotein-independent virus–cell interactions. Different from membrane-wrapped virus-like particles (VLPs), these artificial virus nanoparticles (AVNs) are not derived from cellular systems and can contain organic or inorganic cores optimized for imaging or delivery purposes. A particular advantage is the rational control over the AVN membrane composition, which can be complex or undefined in VLP. This work shows that monosialodihexosylganglioside-presenting AVNs accumulate in virus-containing compartments (VCCs) that represent assembly sites for HIV-1. VCCs provide evasion for HIV-1 from the immune system as well as antiviral therapeutics. The ability to target VCCs with AVNs provides opportunities for eradicating a putative reservoir of HIV-1 persistence. (See pp. E9041–E9050.)
Macrocycle ring deformation as the secondary design principle for light-harvesting complexes
Luca De Vico, André Anda, Vladimir Al. Osipov, Anders Ø. Madsen, and Thorsten Hansen
Bacteriochlorophyll–protein complexes, such as LH2 and LH3 from Rhodoblastus acidophilus, represent the core of bacterial photosynthesis. While similar in many aspects, these two prototypical complexes show different absorption wavelengths, being the latter blue-shifted ca. 30 nm in its major peak respect to the former. These systems have been intensively studied so as to understand the underlying structural mechanisms controlling the difference in absorption and, ultimately, the photosynthetic process. Through highest level computational tools, we here demonstrate that, somewhat contrary to common belief, the major device steering the absorption of bacteriochlorophylls is the direction of their macrocycle ring curvature axis. This finding could lead to the design of novel, easily, and highly tunable chromophores, for future light-harvesting artificial systems. (See pp. E9051–E9057.)
Pendular alignment and strong chemical binding are induced in helium dimer molecules by intense laser fields
Qi Wei, Sabre Kais, Tomokazu Yasuike, and Dudley Herschbach
Intense electric fields, provided by pulsed lasers, can profoundly alter the electronic structure of atoms and molecules. For the helium dimer, we carry out a theoretical study of laser interactions in two realms: (I) fields not strong enough to dislodge electrons, but interact with the anisotropic polarizability to induce spatial alignment of the molecular axis; and (II) superintense, high-frequency lasers that impel electrons to undergo quiver oscillations that interact with the intrinsic Coulomb forces and induce an extremely strong chemical bond. By including in II an excited electronic state, we bring out features amenable to experimental observation that has been lacking. (See pp. E9058–E9066.)
The culture of social comparison
Matthew Baldwin and Thomas Mussweiler
Humans have the unique ability to coordinate behavior, economic exchange, political action, and social relationships across immense distances and times. To keep this level of coordination running smoothly, we often look to others as comparison standards for how to behave, think, and feel. A detailed understanding of the relation between social comparison and broad patterns of social life is lacking, however. The current research is a step in this direction—we show that social comparison is linked to cultural practices that promote strong norms and punishment for deviance (tightness) and those that promote relational self-construal (collectivism). These findings advance our understanding of the origins of social comparison and highlight the essential role of comparison for the development of social life. (See pp. E9067–E9074.)
Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase
Tricia A. Windgassen, Maxime Leroux, Kenneth A. Satyshur, Steven J. Sandler, and James L. Keck
DNA replication complexes are often prematurely ejected from sites of DNA replication. Left unrepaired, this situation results in incomplete genome replication and cell death. All cells have therefore evolved “replication restart” mechanisms to reload the replicative machinery. This process is orchestrated by the PriA DNA helicase in bacteria. We describe the structural mechanism by which PriA recognizes and processes branched DNA replication forks. PriA binds to each arm of the replication fork and interaction with the parental DNA is shown to be particularly important for targeting PriA’s lagging strand-specific functions in vitro and in vivo. Our work provides mechanistic insights into how genome maintenance proteins recognize DNA replication forks and how they couple those interactions to strand-specific functions. (See pp. E9075–E9084.)
Function and crystal structure of the dimeric P-loop ATPase CFD1 coordinating an exposed [4Fe-4S] cluster for transfer to apoproteins
Oliver Stehling, Jae-Hun Jeoung, Sven A. Freibert, Viktoria D. Paul, Sebastian Bänfer, Brigitte Niggemeyer, Ralf Rösser, Holger Dobbek, and Roland Lill
Eukaryotic iron-sulfur (Fe-S) proteins play essential roles in energy conversion, antiviral defense, protein translation, genome integrity, and iron homeostasis. Assembly of the metallo-cofactors is assisted by complex machineries involving more than 30 known components. The initial phase of Fe-S protein maturation in the human cytosol is poorly studied thus far, with the P-loop nucleoside triphosphatase NBP35 being the only known assembly factor. Here, we identified and characterized human CFD1 as an indispensable complex partner of NBP35 in cytosolic Fe-S protein assembly (CIA). The crystal structure of fungal holo-Cfd1 showed a surface-exposed [4Fe-4S] cluster. Its shared, surface-exposed coordination by two Cfd1 monomers has important mechanistic implications for the ATP-dependent de novo cluster assembly and subsequent transfer to apoproteins via downstream CIA components. (See pp. E9085–E9094.)
Structural basis for activation of voltage sensor domains in an ion channel TPC1
Alexander F. Kintzer, Evan M. Green, Pawel K. Dominik, Michael Bridges, Jean-Paul Armache, Dawid Deneka, Sangwoo S. Kim, Wayne Hubbell, Anthony A. Kossiakoff, Yifan Cheng, and Robert M. Stroud
This paper addresses how the structures of voltage-sensing domains within voltage-gated ion channels respond to physiological changes in electric potential across membranes. We report three new structures of TPC1 by cryo-EM and X-ray crystallography, two with voltage-sensing domains in intermediate activated conformations and a third structure representing the deactivated state under low cytoplasmic Ca2+. The intermediate states of the voltage sensor undergo significant rotation in the membrane plane and a twisting motion, with respect to our previously determined resting state, that alters access of gating charges from the inside to the outside of the membrane, with little vertical movement across the membrane. Together these structures suggest a general mechanism for the activation of voltage-gated ion channels. (See pp. E9095–E9104.)
Autonomous conformational regulation of β3 integrin and the conformation-dependent property of HPA-1a alloantibodies
Aye Myat Myat Thinn, Zhengli Wang, Dongwen Zhou, Yan Zhao, Brian R. Curtis, and Jieqing Zhu
Integrin inside-out activation is initiated by the α/β separation at the cytoplasmic and transmembrane domains. Such separation leads to complicated local and global conformational rearrangements of β subunit, while the conformational change of α subunit is relatively simple. It is unclear whether the global structural changes of β subunit depend on the α subunit. Using a single-chain β3 construct to mimic an extreme condition of fully separated α/β heterodimer, we show that the β3 subunit autonomously drives the membrane-dependent bent-to-extended conformational rearrangement in the absence of the α subunit. In addition, we show that the clinically important anti–HPA-1a (β3-L33) alloantibodies perform the conformation-dependent property when interfering with the β3 integrin, which may correlate with the pathogenesis of β3-mediated alloimmune thrombocytopenia. (See pp. E9105–E9114.)
LRRK2 and its substrate Rab GTPases are sequentially targeted onto stressed lysosomes and maintain their homeostasis
Tomoya Eguchi, Tomoki Kuwahara, Maria Sakurai, Tadayuki Komori, Tetta Fujimoto, Genta Ito, Shin-ichiro Yoshimura, Akihiro Harada, Mitsunori Fukuda, Masato Koike, and Takeshi Iwatsubo
LRRK2, a protein kinase related to Parkinson’s disease, is implicated in the maintenance of lysosomes, and a subset of Rab GTPases has been identified as bona fide substrates of LRRK2. Here, we reveal a key stress-responsive pathway composed of Rab7L1, LRRK2, and phosphorylated Rab8/10 involved in lysosomal homeostasis. Lysosomal overload stress induces translocation of Rab7L1 and LRRK2 to lysosomes, where LRRK2 is activated, and stabilizes Rab8 and Rab10 through phosphorylation. The activation of this machinery protects against lysosomal enlargement and upregulates lysosomal secretion through Rab effectors, EHBP1 and EHBP1L1. These findings elucidate a novel regulatory mechanism of Rab GTPases by phosphorylation by LRRK2 in stressed lysosomes, which may also be involved in the pathomechanism of LRRK2-related disorders. (See pp. E9115–E9124.)
Mutually inhibitory Ras-PI(3,4)P2 feedback loops mediate cell migration
Xiaoguang Li, Marc Edwards, Kristen F. Swaney, Nilmani Singh, Sayak Bhattacharya, Jane Borleis, Yu Long, Pablo A. Iglesias, Jie Chen, and Peter N. Devreotes
Cell migration is central in physiological and pathological conditions such as immune response and cancer metastasis. The excitable network hypothesis can account for recent observations of propagating waves of signal transduction and cytoskeleton events as well as behaviors of migrating cells. However, the molecular feedback loops involved in these networks that bring about excitability are poorly understood. Here, we provide evidence for a positive-feedback loop based on a mutual inhibitory interaction between Ras and phosphatidylinositol (3,4)-bisphosphate [PI(3,4)P2]. Our results uncover an important role of PI(3,4)P2 in the regulation of Ras activity, which may extend well beyond cell migration. (See pp. E9125–E9134.)
Bighead is a Wnt antagonist secreted by the Xenopus Spemann organizer that promotes Lrp6 endocytosis
Yi Ding, Gabriele Colozza, Eric A. Sosa, Yuki Moriyama, Samantha Rundle, Lukasz Salwinski, and Edward M. De Robertis
The early frog embryo provides a classical model system for the isolation of secreted molecules that regulate long-range cell–cell communication. Extensive screens of a region with embryonic induction activity, called Spemann organizer, have revealed a large number of secreted growth factor antagonists. Here, we used high-throughput sequencing of differentiating ectodermal explants to isolate yet another potent Wnt inhibitor expressed in Spemann organizer tissue. Bighead is a secreted protein that inhibits Wnt by causing the endocytosis and degradation in lysosomes of the Wnt coreceptor Lrp6. Its overexpression induces embryos with larger heads, and its knockdown reduces head development through the regulation of Wnt signaling. Many Wnt inhibitors exist, and we find that endocytosis regulation is crucial for function. (See pp. E9135–E9144.)
Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation
Anjar Wibowo, Claude Becker, Julius Durr, Jonathan Price, Stijn Spaepen, Sally Hilton, Hadi Putra, Ranjith Papareddy, Quentin Saintain, Sarah Harvey, Gary D. Bending, Paul Schulze-Lefert, Detlef Weigel, and Jose Gutierrez-Marcos
While clonally propagated individuals should share identical genomes, there is often substantial phenotypic variation among them. Both genetic and epigenetic modifications induced during regeneration have been associated with this phenomenon. Here we investigated the fate of the epigenome after asexual propagation by generating clonal individuals from differentiated somatic cells through the manipulation of a zygotic transcription factor. We found that phenotypic novelty in clonal progeny was linked to epigenetic imprints that reflect the organ used for regeneration. Some of these organ-specific imprints can be maintained during the cloning process and subsequent rounds of meiosis. Our findings are fundamental for understanding the significance of epigenetic variability arising from asexual reproduction and have significant implications for future biotechnological applications. (See pp. E9145–E9152.)
mRNA vaccination with charge-altering releasable transporters elicits human T cell responses and cures established tumors in mice
Ole A. W. Haabeth, Timothy R. Blake, Colin J. McKinlay, Robert M. Waymouth, Paul A. Wender, and Ronald Levy
The RNA delivery field is mostly focused on lipid nanoparticles (LNPs). Although promising, LNPs have several limitations with respect to pharmacokinetics, biodistribution, and toxicity. The mechanism of RNA charge-altering releasable transporters (CART) delivery and release is unique. It proceeds dynamically with a controllable change in physical properties. Differing from all mRNA delivery systems, a key attribute of CARTs is a charge-altering degradation mechanism, which transforms the initial polycationic CART into neutral byproducts, thereby enabling endosomal escape, release, and subsequent translation of the polyanionic mRNA cargo. With this study, we introduce a potentially general approach to therapeutic vaccination enabled by a dynamic drug-delivery system (mRNA-CART) and demonstrate its utility in suppressing tumor formation and in eliminating established tumors. (See pp. E9153–E9161.)
Interferon stimulation creates chromatin marks and establishes transcriptional memory
Rui Kamada, Wenjing Yang, Yubo Zhang, Mira C. Patel, Yanqin Yang, Ryota Ouda, Anup Dey, Yoshiyuki Wakabayashi, Kazuyasu Sakaguchi, Takashi Fujita, Tomohiko Tamura, Jun Zhu, and Keiko Ozato
Epigenetic memory for experience-based gene expression has not been well studied in higher organisms. Here we demonstrate that cells previously exposed to interferons exhibit a memory response and mount faster and higher transcription upon restimulation in fibroblasts and macrophages. Genome-wide analysis showed that memory was ascribed to accelerated recruitment of transcription factors to the genes. This process rested upon a distinct chromatin state involving the histone H3.3 and H3K36 modification. Our findings provide a mechanistic framework for the previously proposed idea of “trained innate immunity” representing memory, independent of adaptive immunity. Together, this study highlights learning as a fundamental faculty of mammalian somatic cells. (See pp. E9162–E9171.)
Deconvolution of pro- and antiviral genomic responses in Zika virus-infected and bystander macrophages
Aaron F. Carlin, Edward A. Vizcarra, Emilie Branche, Karla M. Viramontes, Lester Suarez-Amaran, Klaus Ley, Sven Heinz, Christopher Benner, Sujan Shresta, and Christopher K. Glass
Interpretation of genome-wide investigations of host–pathogen interactions are often obscured by analyses of mixed populations of infected and uninfected cells. Thus, we developed a system whereby we simultaneously characterize and compare genome-wide transcriptional and epigenetic changes in pure populations of virally infected and neighboring uninfected cells to identify viral-regulated host responses. Using patient-derived unmodified Zika viruses (ZIKV) infecting primary human macrophages, we reveal that ZIKV suppresses host transcription by multiple mechanisms. ZIKV infection causes both targeted suppression of type I interferon responses and general suppression by reducing RNA polymerase II protein levels and DNA occupancy. Simultaneous evaluation of transcriptomic and epigenetic features of infected and uninfected cells provides a powerful method for identifying coincident evolution of dominant proviral or antiviral mechanisms. (See pp. E9172–E9181.)
Engineered DNA plasmid reduces immunity to dystrophin while improving muscle force in a model of gene therapy of Duchenne dystrophy
Peggy P. Ho, Lauren J. Lahey, Foteini Mourkioti, Peggy E. Kraft, Antonio Filareto, Moritz Brandt, Klas E. G. Magnusson, Eric E. Finn, Jeffrey S. Chamberlain, William H. Robinson, Helen M. Blau, and Lawrence Steinman
Duchenne muscular dystrophy is a genetic disorder in which mutations in the dystrophin gene causes severe muscle wasting. A proposed treatment method involves systemic gene replacement therapy to introduce a functional dystrophin gene to the skeletal and cardiac muscles of the patient via rAAV6. A potentially serious problem may arise from immune recognition of dystrophin and the accompanying adeno-associated viral (AAV) vector. This unwanted immunity could interfere with successful long-term dystrophin expression by muscle cells. To suppress the unwanted immune response, a DNA vaccine was engineered to dampen immunity to both dystrophin and AAV6 capsid. Development of this engineered plasmid aims to improve gene replacement therapy and to overcome problems inherent with unwanted immunity to the encoded protein and to the delivery vector. (See pp. E9182–E9191.)
Elevated A20 promotes TNF-induced and RIPK1-dependent intestinal epithelial cell death
Ricard Garcia-Carbonell, Jerry Wong, Ju Youn Kim, Lisa Abernathy Close, Brigid S. Boland, Thomas L. Wong, Philip A. Harris, Samuel B. Ho, Soumita Das, Peter B. Ernst, Roman Sasik, William J. Sandborn, John Bertin, Pete J. Gough, John T. Chang, Michelle Kelliher, David Boone, Monica Guma, and Michael Karin
Excessive apoptosis is detected in the intestinal epithelium of patients with inflammatory bowel disease (IBD), where it is frequently TNF-dependent. We show that A20, a protein implicated in negative regulation of NF-κB, is expressed in intestinal epithelial cells (IECs) from patients with IBD in areas that exhibit apoptosis. Transgenic mice that overexpress A20 in IECs are highly susceptible to TNF-induced cell death. In these mice, A20 potentiates TNF-induced mucosal erosion and RIPK1-dependent IEC apoptosis through Ripoptosome/RIPK1 activation. A20-enhanced IEC damage and intestinal inflammation can be prevented by RIPK1 inhibitors, suggesting a new approach to IBD treatment. (See pp. E9192–E9200.)
Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor
Christopher A. Nelson, Craig B. Wilen, Ya-Nan Dai, Robert C. Orchard, Arthur S. Kim, Roderick A. Stegeman, Leon L. Hsieh, Thomas J. Smith, Herbert W. Virgin, and Daved H. Fremont
The mechanisms of norovirus capsid interactions with host receptors and the mechanisms by which soluble cofactors augment norovirus infection are not understood. We recently identified CD300lf as a cell surface receptor for murine norovirus (MNoV) and observed that a small molecule cofactor was critical for efficient binding of virus to CD300lf. Herein we identify the bile acid GCDCA as a cofactor enhancing MNoV infection and provide a biophysical characterization of the capsid–receptor and capsid–cofactor interactions, thereby providing a structure-based understanding of how noroviruses initiate cellular infection. This work has important implications for the design of norovirus therapeutics. (See pp. E9201–E9210.)
Homologous recombination is an intrinsic defense against antiviral RNA interference
Lauren C. Aguado, Tristan X. Jordan, Emily Hsieh, Daniel Blanco-Melo, John Heard, Maryline Panis, Marco Vignuzzi, and Benjamin R. tenOever
In an effort to determine whether host defenses can significantly influence the prevalence of different virus groups, we applied identical selective pressures onto four families of diverse viruses. Using an RNAi-like defense, we found that the capacity of positive-stranded RNA viruses to switch genomic templates during replication conferred an adaptability that exceeded that of negative-stranded RNA viruses that were less able to perform this biology. Together, this work suggests that in the absence of an antiviral antagonist, fundamental aspects of virus biology can provide an inherent advantage to evade host defenses. (See pp. E9211–E9219.)
Cortical circuit activity underlying sleep slow oscillations and spindles
Niels Niethard, Hong-Viet V. Ngo, Ingrid Ehrlich, and Jan Born
Slow oscillations and spindles are hallmarks of the EEG during slow-wave sleep. They are thought to support memory consolidation, particularly in instances where the faster spindle nests into the “upstate” of a slow oscillation. Using two-photon and wide-field imaging, we recorded calcium transients from distinct populations of cortical excitatory and inhibitory neurons during sleep in mice. Compared with spindles or slow oscillations occurring in isolation, events where spindles nested in a slow oscillation upstate were indeed accompanied by a unique pattern of calcium activity where high pyramidal cell activity appears to concur with high perisomatic inhibition through parvalbumin-positive interneurons and with low dendritic inhibition through somatostatin-positive interneurons. These conditions might foster dendritic plasticity. (See pp. E9220–E9229.)
Tissue plasminogen activator promotes white matter integrity and functional recovery in a murine model of traumatic brain injury
Yuguo Xia, Hongjian Pu, Rehana K. Leak, Yejie Shi, Hongfeng Mu, Xiaoming Hu, Zhengyu Lu, Lesley M. Foley, T. Kevin Hitchens, C. Edward Dixon, Michael V. L. Bennett, and Jun Chen
Tissue plasminogen activator (tPA) is employed in stroke patients to lyse blood clots, but its therapeutic potential in brain trauma victims is far from settled, partly due to fears of internal bleeding. The long-term effects of tPA upon the white matter of the brain and neurological outcomes after head trauma are also uncertain. To address these gaps, we performed electrophysiological, anatomical, and behavioral studies in genetically modified or wild-type mice subjected to traumatic brain injury and infused tPA through the nose. We found that natural or synthetic forms of tPA protect or repair white matter tracts without magnifying internal bleeding. Thus, tPA treatment after brain injury promotes communication across neuronal networks through nerve fiber tracts and improves long-term adaptive behavior. (See pp. E9230–E9238.)
AP2 transcription factor CBX1 with a specific function in symbiotic exchange of nutrients in mycorrhizal Lotus japonicus
Li Xue, Lompong Klinnawee, Yue Zhou, Georgios Saridis, Vinod Vijayakumar, Mathias Brands, Peter Dörmann, Tamara Gigolashvili, Franziska Turck, and Marcel Bucher
Arbuscular mycorrhizal (AM) fungi promote phosphorus uptake into host plants in exchange for organic carbon. Physiological tracer experiments showed that up to 100% of acquired phosphate can be delivered to plants via the mycorrhizal phosphate uptake pathway (MPU). Previous studies revealed that the CTTC cis-regulatory element (CRE) is required for promoter activation of mycorrhiza-specific phosphate transporter and H+-ATPase genes. However, the precise transcriptional mechanism directly controlling MPU is unknown. Here, we show that CBX1 binds CTTC and AW-box CREs and coregulates mycorrhizal phosphate transporter and H+-ATPase genes. Interestingly, genes involved in lipid biosynthesis are also regulated by CBX1 through binding to AW box, including RAM2. Our work suggests a common regulatory mechanism underlying complex trait control of symbiotic exchange of nutrients. (See pp. E9239–E9246.)
Universal method for robust detection of circadian state from gene expression
Rosemary Braun, William L. Kath, Marta Iwanaszko, Elzbieta Kula-Eversole, Sabra M. Abbott, Kathryn J. Reid, Phyllis C. Zee, and Ravi Allada
Determining the state of an individual's internal physiological clock has important implications for precision medicine, from diagnosing neurological disorders to optimizing drug delivery. To be useful, such a test must be accurate, minimally burdensome to the patient, and robust to differences in patient protocols, sample collection, and assay technologies. TimeSignature is a machine-learning approach to predict physiological time based on gene expression in human blood. A powerful feature is TimeSignature's generalizability, enabling it to be applied to samples from disparate studies and yield highly accurate results despite systematic differences between the studies. This quality is unique among expression-based predictors and addresses a major challenge in the development of reliable and clinically useful biomarker tests. (See pp. E9247–E9256.)