Interplay of structure, elasticity, and dynamics in actin-based nematic materials
Rui Zhang, Nitin Kumar, Jennifer L. Ross, Margaret L. Gardel, and Juan J. de Pablo
Thermotropic liquid crystals (LCs) are central to a wide range of commercial and emerging technologies. Lyotropic, aqueous-based LCs are common in nature, but applications have been scarce. The current understanding of their behavior is limited, and manipulating their mechanical and dynamic characteristics has been challenging. Here we show that the elasticity and temporal evolution of biopolymerbased nematic systems can be inferred from simple optical microscopy measurements, and that their mechanical properties can be manipulated by adjusting certain molecular characteristics, such as the product of length and concentration. It is also shown that the dynamic evolution of the resulting materials can be understood and predicted on the basis of a free energy functional originally developed for the study of thermotropic systems. (See pp. E124–E133.)
Interfacial curvature effects on the monolayer morphology and dynamics of a clinical lung surfactant
Amit Kumar Sachan and Joseph A. Zasadzinski
Confocal microscopy provides high-resolution images of highly curved interfaces with the surprising result that the morphology of phase-separated lung surfactant monolayers changes dramatically as the interfacial curvature approaches alveolar dimensions (radius, ∼100 µm). This is due to the anisotropic bending properties of the semicrystalline liquid-condensed (LC) domains that lead to a transition between discrete, discontinuous domains on a flat interface to an interconnected meshwork on alveolar-size bubbles. This may have important implications toward understanding the dilatational properties of the monolayer-covered interfaces which can dictate lung stability during breathing. (See pp. E134–E143.)
Quantitative historical analysis uncovers a single dimension of complexity that structures global variation in human social organization
Peter Turchin, Thomas E. Currie, Harvey Whitehouse, Pieter François, Kevin Feeney, Daniel Mullins, Daniel Hoyer, Christina Collins, Stephanie Grohmann, Patrick Savage, Gavin Mendel-Gleason, Edward Turner, Agathe Dupeyron, Enrico Cioni, Jenny Reddish, Jill Levine, Greine Jordan, Eva Brandl, Alice Williams, Rudolf Cesaretti, Marta Krueger, Alessandro Ceccarelli, Joe Figliulo-Rosswurm, Po-Ju Tuan, Peter Peregrine, Arkadiusz Marciniak, Johannes Preiser-Kapeller, Nikolay Kradin, Andrey Korotayev, Alessio Palmisano, David Baker, Julye Bidmead, Peter Bol, David Christian, Connie Cook, Alan Covey, Gary Feinman, Árni Daníel Júlíusson, Axel Kristinsson, John Miksic, Ruth Mostern, Cameron Petrie, Peter Rudiak-Gould, Barend ter Haar, Vesna Wallace, Victor Mair, Liye Xie, John Baines, Elizabeth Bridges, Joseph Manning, Bruce Lockhart, Amy Bogaard, and Charles Spencer
Do human societies from around the world exhibit similarities in the way that they are structured and show commonalities in the ways that they have evolved? To address these long-standing questions, we constructed a database of historical and archaeological information from 30 regions around the world over the last 10,000 years. Our analyses revealed that characteristics, such as social scale, economy, features of governance, and information systems, show strong evolutionary relationships with each other and that complexity of a society across different world regions can be meaningfully measured using a single principal component of variation. Our findings highlight the power of the sciences and humanities working together to rigorously test hypotheses about general rules that may have shaped human history. (See pp. E144–E151.)
Structural basis for the regulation of β-glucuronidase expression by human gut Enterobacteriaceae
Michael S. Little, Samuel J. Pellock, William G. Walton, Ashutosh Tripathy, and Matthew R. Redinbo
Commensal microbiota establish nutrient-utilization niches in the gastrointestinal tract. While the large intestine is dominated by the Bacteroidetes that degrade complex carbohydrates, the small intestine contains Proteobacteria and Firmicutes that compete with host tissues for small-molecule sources of carbon. Here, we show that the Enterobacteriaceae family of Proteobacteria, including Escherichia, Salmonella, Klebsiella, Shigella, and Yersinia pathobionts, maintains DNA operator- and glucuronidated ligand-specific glucuronide repressor (GusR) transcription factors that uniquely respond to glucuronidated ligands. (See pp. E152–E161.)
Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA
François Ferron, Lorenzo Subissi, Ana Theresa Silveira De Morais, Nhung Thi Tuyet Le, Marion Sevajol, Laure Gluais, Etienne Decroly, Clemens Vonrhein, Gérard Bricogne, Bruno Canard, and Isabelle Imbert
Emerging coronaviruses (CoVs; severe acute respiratory syndrome-CoV and Middle East respiratory syndrome-CoV) pose serious health threats globally, with no specific antiviral treatments available. These viruses are able to faithfully synthesize their large genomic RNA. We report, however, that their main RNA polymerase, nsp12, is not accurate. To achieve accuracy, CoVs have acquired nsp14, a bifunctional enzyme able to methylate the viral RNA cap [methyltransferase (MTase)] and excise erroneous mutagenic nucleotides inserted by nsp12. Strikingly, ribavirin can be excised from the viral genome, thus showing no antiviral activity. The crystal structure of nsp14 shows that it is unique, having been replaced by other MTase types during evolution. This unprecedented RNA correction machinery has allowed RNA genome size expansion, but also provided potential nucleoside drug resistance to these deadly pathogens. (See pp. E162–E171.)
Protonation state of glutamate 73 regulates the formation of a specific dimeric association of mVDAC1
Lucie A. Bergdoll, Michael T. Lerch, John W. Patrick, Kendrick Belardo, Christian Altenbach, Paola Bisignano, Arthur Laganowsky, Michael Grabe, Wayne L. Hubbell, and Jeff Abramson
Cellular acidification occurs in response to many cellular events, including ischemia and apoptosis. The voltage-dependent anion channel (VDAC) is the most abundant protein in the outer mitochondrial membrane and has been implicated in mitochondrial regulation, cell death, and assembling protein complexes with Bcl2 family of apoptotic regulating proteins. During apoptosis, VDAC has demonstrated rapid oligomerization followed by cytochrome c release into the cytoplasm. We report a new dimeric model of VDAC induced by minor acidification with a pKa of 7.4, which is regulated by the protonation state of transmembrane residue E73. This study links a specific dimer formation with cellular acidification, which may be a salient feature of the molecular mechanism(s) involved in mitochondrial regulation. (See pp. E172–E179.)
Genome-wide CRISPR screen for PARKIN regulators reveals transcriptional repression as a determinant of mitophagy
Christoph Potting, Christophe Crochemore, Francesca Moretti, Florian Nigsch, Isabel Schmidt, Carole Manneville, Walter Carbone, Judith Knehr, Rowena DeJesus, Alicia Lindeman, Rob Maher, Carsten Russ, Gregory McAllister, John S. Reece-Hoyes, Gregory R. Hoffman, Guglielmo Roma, Matthias Müller, Andreas W. Sailer, and Stephen B. Helliwell
In mitophagy, damaged mitochondria are targeted for disposal by the autophagy machinery. PARKIN promotes signaling of mitochondrial damage to the autophagy machinery for engagement, and PARKIN mutations cause Parkinson’s disease, possibly because damaged mitochondria accumulate in neurons. Because regulation of PARKIN abundance and the impact on signaling are poorly understood, we performed a genetic screen to identify PARKIN abundance regulators. Both positive and negative regulators were identified and will help us to further understand mitophagy and Parkinson’s disease. We show that some of the identified genes negatively regulate PARKIN gene expression, which impacts signaling of mitochondrial damage in mitophagy. This link between transcriptional repression and mitophagy is also apparent in neurons in culture, bearing implications for disease. (See pp. E180–E189.)
RSK2 drives cell motility by serine phosphorylation of LARG and activation of Rho GTPases
Geng-Xian Shi, Won Seok Yang, Ling Jin, Michelle L. Matter, and Joe W. Ramos
Cell motility is a dynamic process that requires the directed application of force and continuous coordinated changes in cell adhesion and cytoskeletal architecture often in response to extracellular stimuli. Here we have defined a mechanism by which RSK2 can promote cell migration and invasion in response to promotility stimuli. We show that in response to these signals RSK2 directly binds the RhoGEF LARG and phosphorylates it, thereby promoting LARG activation of RhoA GTPases. Moreover, we find that RSK2 is important for epidermal growth factor activation of Rho GTPases. These results advance our understanding of cell motility, RSK kinase function, and LARG/RhoA activation by revealing that these pathways are integrated and the precise mechanism by which that is accomplished. (See pp. E190–E199.)
Neuronal delivery of Hedgehog directs spatial patterning of taste organ regeneration
Wan-Jin Lu, Randall K. Mann, Allison Nguyen, Tingting Bi, Max Silverstein, Jean Y. Tang, Xiaoke Chen, and Philip A. Beachy
The maintenance of taste sensory organs (taste buds) in the tongue has been known for 140 years to depend on sensory innervation from distant neurons by an unknown mechanism. We find that maintenance and regeneration of taste receptor cells (TRCs) within taste buds requires neuronal delivery of the Sonic hedgehog (Shh) protein signal, thus explaining loss of taste sensation associated with Hedgehog pathway antagonism in patients and illustrating the principle that spatial patterning of TRC regeneration is specified by the projection pattern of Shh-expressing sensory neurons. We also find that pharmacologic Hedgehog pathway activation accelerates TRC recovery, suggesting a means to ameliorate the loss of taste sensation and appetite and the associated delay in recovery in cancer patients undergoing chemotherapy. (See pp. E200–E209.)
Listeria monocytogenes triggers noncanonical autophagy upon phagocytosis, but avoids subsequent growth-restricting xenophagy
Gabriel Mitchell, Mandy I. Cheng, Chen Chen, Brittney N. Nguyen, Aaron T. Whiteley, Sara Kianian, Jeffery S. Cox, Douglas R. Green, Kent L. McDonald, and Daniel A. Portnoy
Autophagy mediates the routing of cytoplasmic components to degradative membrane-bound compartments. During infection by intracellular pathogens, autophagy proteins orchestrate several antimicrobial responses by marking pathogen-containing vacuoles and protecting the host cytosol from invaders. However, intracellular pathogens such as Listeria monocytogenes circumvent the autophagy machinery to promote pathogenesis. By combining bacterial and host mutants, we have dissected the role of two distinct autophagy-related processes in controlling L. monocytogenes growth in macrophages. Our results showed that L. monocytogenes is oblivious to the initial marking of its vacuole by autophagy proteins, but that subsequent autophagic targeting restricts bacterial growth in the host cytosol. We suggest that processes coordinated by the autophagy machinery constitute a multilayered network of cell-autonomous defenses. (See pp. E210–E217.)
Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird
Alfredo O. Barrera-Guzmán, Alexandre Aleixo, Matthew D. Shawkey, and Jason T. Weir
Hybridization between species can produce reproductively isolated lineages by combining parental genotypes in novel ways. Here, we used thousands of genetic markers to demonstrate that the recently rediscovered golden-crowned manakin represents an avian hybrid species from the Amazon basin. This hybrid species has a unique golden-colored crown patch used for display, which differs from the brilliant white coloration of the parental species. We used microscopy to demonstrate that, despite its unique coloration, the crown has intermediate color-producing morphological features at the nanoscale. We propose that these intermediate features disrupted the high reflectivity of the parental species, resulting in a dull hybrid population. Selection then sequestered carotenoids to the crown to compensate for its low reflectivity. (See pp. E218–E225.)
Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas
Piotr Łukasik, Katherine Nazario, James T. Van Leuven, Matthew A. Campbell, Mariah Meyer, Anna Michalik, Pablo Pessacq, Chris Simon, Claudio Veloso, and John P. McCutcheon
Highly reduced genomes from bacteria that are long-term beneficial endosymbionts of insects often show remarkable structural stability. Endosymbionts in insects diverged by tens or hundreds of millions of years often have genomes almost completely conserved in gene order and content. Here, we show that an endosymbiont in some cicadas has repeatedly and independently fractured into complexes of distinct genomic and cellular lineages present in the same host. Individual endosymbiont lineages, having lost many of the essential ancestral genes, rely on each other for basic function and together seem to provide the same nutritional benefits as the ancestral single symbiont. These cicada endosymbionts show genomic parallels to mitochondria and provide another example of how normally stable genomes can lose structural stability. (See pp. E226–E235.)
Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex
Tao Ma, Kun Wang, Quanjun Hu, Zhenxiang Xi, Dongshi Wan, Qian Wang, Jianju Feng, Dechun Jiang, Hamid Ahani, Richard J. Abbott, Martin Lascoux, Eviatar Nevo, and Jianquan Liu
One of the outstanding questions in understanding how new species form is how reproductive isolation arises. In particular, the relative roles of gene flow and natural selection in creating two separate species remains open for debate. Here we show within the four continuously speciating lineages of a poplar that local genomic differentiation of populations is not associated with either rate of recent gene flow or time of species divergence. By contrast, we found that these genomic islands of divergence most likely came about by selective processes—sorting of ancient genetic polymorphisms and the incidental hitchhiking of linked variations. These findings substantially enhance our understanding of genomic changes in speciation. (See pp. E236–E243.)
Histone demethylase LSD1 regulates hematopoietic stem cells homeostasis and protects from death by endotoxic shock
Jianxun Wang, Kaoru Saijo, Dylan Skola, Chunyu Jin, Qi Ma, Daria Merkurjev, Christopher K. Glass, and Michael G. Rosenfeld
The histone demethylase LSD1, a critical regulator of mammalian hematopoiesis, serves as an important suppressor of endotoxic shock. Inflammation-induced deletion of LSD1 results in failure to generate all mature hematopoietic cells, and induces acute expansion of a pathological population of hyperproliferative and hyperinflammatory myeloid progenitors that cause “cytokine storm” and acute lethality. LSD1 proves to be a downstream target of Toll-like/cytokine receptors in HSCs during endotoxic shock, with its down-regulation caused by a cohort of inflammation-induced microRNAs. The resultant acute expansion of a population of pathological myeloid progenitors in bone marrow causes a septic shock phenotype. Inhibitors of these inflammation-induced microRNAs block the down-regulation of LSD1 and prevent LPS-induced mortality, suggesting a potential therapeutic approach for treatment of septic shock. (See pp. E244–E252.)
FoxP3 scanning mutagenesis reveals functional variegation and mild mutations with atypical autoimmune phenotypes
Ho-Keun Kwon, Hui-Min Chen, Diane Mathis, and Christophe Benoist
The transcription factor FoxP3 defines and controls regulatory T cells (Tregs), themselves essential components of immunoregulatory pathways. From a highly granular scanning mutagenesis, the results of our study point to very integrated functions of the protein’s domains, quite different from predictions of simple modular models. The phenotype of mutant mice carrying subtle mutations in Foxp3, which deviate from the acute lymphoproliferation and autoimmunity linked to Treg deficiency and become manifest only upon challenge, suggest that rare FOXP3 variants may contribute to a broader range of human diseases than previously recognized. (See pp. E253–E262.)
Designing a retrievable and scalable cell encapsulation device for potential treatment of type 1 diabetes
Duo An, Alan Chiu, James A. Flanders, Wei Song, Dahua Shou, Yen-Chun Lu, Lars G. Grunnet, Louise Winkel, Camilla Ingvorsen, Nicolaj Strøyer Christophersen, Johannes Josef Fels, Fredrik Wolfhagen Sand, Yewei Ji, Ling Qi, Yehudah Pardo, Dan Luo, Meredith Silberstein, Jintu Fan, and Minglin Ma
Cell encapsulation holds great potential as a better treatment for type 1 diabetes. An encapsulation system that is scalable to a clinically relevant capacity and can be retrieved or replaced whenever needed is highly desirable for clinical applications. Here we report a cell encapsulation device that is readily scalable and conveniently retrievable through a minimally invasive laparoscopic procedure. We demonstrated its mechanical robustness and facile mass transfer as well as its durable function in diabetic mice. We further showed, as a proof of concept, its scalability and retrievability in dogs. We believe this encapsulation device may contribute to a cellular therapy for type 1 diabetes and potentially other endocrine disorders and hormone-deficient diseases. (See pp. E263–E272.)
Stand-alone ClpG disaggregase confers superior heat tolerance to bacteria
Changhan Lee, Kamila B. Franke, Shady Mansour Kamal, Hyunhee Kim, Heinrich Lünsdorf, Jasmin Jäger, Manfred Nimtz, Janja Trček, Lothar Jänsch, Bernd Bukau, Axel Mogk, and Ute Römling
Severe heat stress causes massive protein loss by aggregation ultimately causing cell death. Cellular survival relies on protein disaggregation mediated by the Hsp70-ClpB (Hsp100) bichaperone system in most bacteria. Pseudomonas aeruginosa additionally codes for two stand-alone ClpG disaggregases, which had been acquired by horizontal gene transfer by the species and most abundant clone C strains, respectively. These ClpG disaggregases largely contribute to the resolution of protein aggregates to confer superior heat tolerance partially replacing the DnaK-ClpB system. (See pp. E273–E282.)
Colorectal cancer specific conditions promote Streptococcus gallolyticus gut colonization
Laetitia Aymeric, Françoise Donnadieu, Céline Mulet, Laurence du Merle, Giulia Nigro, Azadeh Saffarian, Marion Bérard, Claire Poyart, Sylvie Robine, Béatrice Regnault, Patrick Trieu-Cuot, Philippe J. Sansonetti, and Shaynoor Dramsi
Growing evidence indicates a correlation between colorectal cancer and intestinal dysbiosis or colonization by single bacterial species such as Streptococcus gallolyticus subsp. gallolyticus (SGG), yet a causality link remains to be established. To address this point experimentally, we colonized Apc+/− Notch-inducible mice with SGG. Apc+/− is a pioneer somatic mutation driving the occurrence of polyps. We did not observe significant changes in the occurrence or development of polyps in this model. However, we observed a strong SGG colonization in Apc+/− mice at the expense of resident enterococci. We related this ecological substitution to activation of a SGG-specific bacteriocin whose activity is induced in vivo by the detergent effect of an increased concentration of secondary bile acids in relation to oncogenic situation. (See pp. E283–E291.)
ATM and ATR play complementary roles in the behavior of excitatory and inhibitory vesicle populations
Aifang Cheng, Teng Zhao, Kai-Hei Tse, Hei-Man Chow, Yong Cui, Liwen Jiang, Shengwang Du, Michael M. T. Loy, and Karl Herrup
The symptoms of neurological diseases such as autism and schizophrenia are often attributed to a loss of excitatory/inhibitory balance of neural network function. By showing that ATR and ATM impact inhibitory and excitatory vesicle trafficking differently, our work expands the known repertoire of cytoplasmic functions for the two kinases and provides a new perspective on the origins of the symptoms of ataxia-telangiectasia (A-T) and Seckel syndrome (ATM and ATR deficiency, respectively). While these findings have their most immediate implications for the neurologic and cognitive symptoms of A-T and Seckel syndrome, they have potential relevance to a much broader range of neurologic conditions. (See pp. E292–E301.)
Cell-specific and region-specific transcriptomics in the multiple sclerosis model: Focus on astrocytes
Noriko Itoh, Yuichiro Itoh, Alessia Tassoni, Emily Ren, Max Kaito, Ai Ohno, Yan Ao, Vista Farkhondeh, Hadley Johnsonbaugh, Josh Burda, Michael V. Sofroniew, and Rhonda R. Voskuhl
Molecular mechanisms underlying distinct disabilities during neurological diseases may differ based on the neurological pathway involved. Multiple sclerosis (MS) is multifocal, characterized by distinct disabilities affecting walking, vision, cognition, and fatigue. Neuroprotective treatments tailored for each disability may be more effective than nonspecific treatments aiming to reduce a composite of disabilities in clinical trials. Here, we use the MS model to apply a cell-specific and region-specific gene expression approach to discover targets in distinct neuroanatomic regions. Altered cholesterol synthesis gene expression in astrocytes in spinal cord and optic nerve was identified as a potential target for walking and visual disabilities, respectively. This disability-specific discovery approach represents a strategy for finding neuroprotective treatments for multifocal neurodegenerative diseases. (See pp. E302–E309.)
Locus coeruleus input to hippocampal CA3 drives single-trial learning of a novel context
Akiko Wagatsuma, Teruhiro Okuyama, Chen Sun, Lillian M. Smith, Kuniya Abe, and Susumu Tonegawa
The ability to remember a new place is crucial for survival. The locus coeruleus (LC) in the brain stem is known to respond to novel sensory stimuli and can facilitate hippocampus-dependent memory, although the circuit and the role that LC plays in novelty-associated memory is unknown. We performed circuit-specific optogenetic inhibition and found that the hippocampal CA3 subregion is the crucial target of LC projections during the encoding of a novel context. Furthermore, we show with activity-dependent labeling and in vivo calcium imaging that LC inputs are necessary to provide stable neuronal representations of the context. This study provides evidence that LC neuromodulation, especially to the CA3 subregion, plays a crucial role in memory formation of a new context. (See pp. E310–E316.)
Heat activation is intrinsic to the pore domain of TRPV1
Feng Zhang, Andres Jara-Oseguera, Tsg-Hui Chang, Chanhyung Bae, Sonya M. Hanson, and Kenton J. Swartz
The TRPV1 channel is an important detector of noxious heat, yet the location of the heat sensor and the mechanism of heat activation remain poorly understood. Here we used structure-based engineering between the heat-activated TRPV1 channel and the Shaker Kv channel to demonstrate that transplantation of the pore domain of TRPV1 into Shaker gives rise to functional channels that can be activated by a TRPV1-selective tarantula toxin and by noxious heat, demonstrating that the pore of TRPV1 contains the structural elements sufficient for activation by temperature. (See pp. E317–E324.)
ALKBH5-dependent m6A demethylation controls splicing and stability of long 3′-UTR mRNAs in male germ cells
Chong Tang, Rachel Klukovich, Hongying Peng, Zhuqing Wang, Tian Yu, Ying Zhang, Huili Zheng, Arne Klungland, and Wei Yan
N6-methyladnosine (m6A) represents one of the most common RNA modifications. Biochemical analyses have identified ALKBH5 as an eraser of m6A. The present study represents the first molecular characterization of the Alkbh5 knockout mouse model. Our data associate m6A erasure with mRNA length control. Specifically, proper m6A demethylation is required for correct splicing and selective degradation of longer 3′-UTR transcripts, which are abundant in mitotic and meiotic male germ cells, but these longer 3′-UTR transcripts become rapidly degraded in the haploid male germ cells. Aberrant m6A levels in spermatogenic cells are incompatible with normal spermatogenesis and male fertility. (See pp. E325–E333.)
ZmCCT9 enhances maize adaptation to higher latitudes
Cheng Huang, Huayue Sun, Dingyi Xu, Qiuyue Chen, Yameng Liang, Xufeng Wang, Guanghui Xu, Jinge Tian, Chenglong Wang, Dan Li, Lishuan Wu, Xiaohong Yang, Weiwei Jin, John F. Doebley, and Feng Tian
Flowering time is a critical determinant of crop adaptation to local environments. As a result of natural and artificial selection, maize has evolved a reduced photoperiod sensitivity to adapt to regions over 90° of latitude in the Americas. Here we show that a distant Harbinger-like transposon acts as a cis-regulatory element to repress ZmCCT9 expression to promote flowering under the long days of higher latitudes. The transposon at ZmCCT9 and another functional transposon at a second flowering-time gene, ZmCCT10, arose sequentially following domestication and were targeted by selection as maize spread from the tropics to higher latitudes. Our results demonstrate that new functional variation created by transposon insertions helped maize to spread over a broad range of latitudes rapidly. (See pp. E334–E341.)