A variational perspective on accelerated methods in optimization
Andre Wibisono, Ashia C. Wilson, and Michael I. Jordan
Optimization problems arise naturally in statistical machine learning and other fields concerned with data analysis. The rapid growth in the scale and complexity of modern datasets has led to a focus on gradient-based methods and also on the class of accelerated methods, first proposed by Nesterov in 1983. Accelerated methods achieve faster convergence rates than gradient methods and indeed, under certain conditions, they achieve optimal rates. However, accelerated methods are not descent methods and remain a conceptual mystery. We propose a variational, continuous-time framework for understanding accelerated methods. We provide a systematic methodology for converting accelerated higher-order methods from continuous time to discrete time. Our work illuminates a class of dynamics that may be useful for designing better algorithms for optimization. (See pp. E7351–E7358.)
Rapid conversion of an oceanic spreading center to a subduction zone inferred from high-precision geochronology
Timothy E. Keenan, John Encarnación, Robert Buchwaldt, Dan Fernandez, James Mattinson, Christine Rasoazanamparany, and P. Benjamin Luetkemeyer
Subduction, the process by which tectonic plates sink into the mantle, is a fundamental tectonic process on Earth, yet the question of where and how new subduction zones form remains a matter of debate. In this study, we find that a divergent plate boundary, where two plates move apart, was forcefully and rapidly turned into a convergent boundary where one plate eventually began subducting. This finding is surprising because, although the plate material at a divergent boundary is weak, it is also buoyant and resists subduction. This study suggests that buoyant, but weak, plate material at a divergent boundary can be forced to converge until eventually older and denser plate material enters the nascent subduction zone, which then becomes self-sustaining. (See pp. E7359–E7366.)
Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium
Nathan G. Walworth, Michael D. Lee, Fei-Xue Fu, David A. Hutchins, and Eric A. Webb
The free-living cyanobacterium Trichodesmium is an important nitrogen-fixer in the global oceans, yet virtually nothing is known about its molecular evolution to increased CO2. Here we show that Trichodesmium can fix a plastic, short-term response upon long-term adaptation, potentially through genetic assimilation. We provide transcriptional evidence for molecular mechanisms that parallel the fixation of the plastic phenotype, thereby demonstrating an important evolutionary capability in Trichodesmium CO2 adaptation. Transcriptional shifts involve transposition and other regulatory mechanisms (sigma factors) that control a variety of metabolic pathways, suggesting alterations in upstream regulation to be important under genetic assimilation. Together, these data highlight potential biochemical evidence of genetic assimilation in a keystone marine N2-fixer, with broad implications for microbial evolution and biogeochemistry. (See pp. E7367–E7374.)
Disease resistance through impairment of α-SNAP–NSF interaction and vesicular trafficking by soybean Rhg1
Adam M. Bayless, John M. Smith, Junqi Song, Patrick H. McMinn, Alice Teillet, Benjamin K. August, and Andrew F. Bent
The Rhg1 resistance locus of soybean helps control one of the most damaging diseases in world agriculture. We found that Rhg1 (resistance to Heterodera glycines 1)-mediated resistance utilizes an unusual mechanism. Resistant soybeans carry a dysfunctional variant of the housekeeping protein α-SNAP [soluble NSF (N-ethylmaleimide–sensitive factor) attachment protein]. Rhg1 resistance-type α-SNAPs interact poorly with NSF and disrupt vesicle trafficking. High levels of resistance-type α-SNAPs interfere with wild-type α-SNAP activities, yet are functionally balanced in most tissues by sufficient wild-type α-SNAP levels. However, the biotrophic plant–pathogen interface is disabled by localized hyperaccumulation of resistance-type α-SNAPs. This study suggests a paradigm of resistance conferred by a dysfunctional version of a core cellular housekeeping protein. (See pp. E7375–E7382.)
Ultrahigh-throughput–directed enzyme evolution by absorbance-activated droplet sorting (AADS)
Fabrice Gielen, Raphaelle Hours, Stephane Emond, Martin Fischlechner, Ursula Schell, and Florian Hollfelder
Directed enzyme evolution is a powerful approach for discovering new catalysts with applications in green chemistry and elsewhere. However, “hits” in sequence space are rare: If too few members of a library are examined, the chances of success of a campaign are limited. Ultrahigh-throughput screening in emulsion droplets has dramatically increased the odds but requires a fluorescent reaction product that triggers selection of hits. We now introduce an absorbance-based microfluidic droplet sorter that broadens the scope of assays to those producing UV/Vis-active chromophores and demonstrate its usefulness by evolving a dehydrogenase based on the screening of half a million library members. Making ultrahigh-throughput screening possible for previously inaccessible reactions enables much wider use of microfluidic droplet sorters for laboratory evolution. (See pp. E7383–E7389.)
Emulating proton-induced conformational changes in the vesicular monoamine transporter VMAT2 by mutagenesis
Dana Yaffe, Ariela Vergara-Jaque, Lucy R. Forrest, and Shimon Schuldiner
Vesicular monoamine transporters (VMATs) are the targets of numerous psychoactive drugs, and play a critical role in the overall process of synaptic transmission by replenishing depleted monoamine stores in synaptic vesicles. VMATs transport monoamines in a process that involves exchange of two H+ per substrate. Here we show that two potent inhibitors of VMAT2, tetrabenazine and reserpine, bind to different conformations of the protein. The transition that generates a reserpine-binding site requires a proton gradient across the membrane. Here we emulate the effect of the proton gradient by tinkering with residues that form the cytoplasmic gate. These findings provide vital information about the conformational dynamics of a mammalian H+-coupled antiporter. Such conformational transitions constitute essential steps in all transport processes. (See pp. E7390–E7398.)
Distinct regions that control ion selectivity and calcium-dependent activation in the bestrophin ion channel
George Vaisey, Alexandria N. Miller, and Stephen B. Long
BEST1 is a Ca2+-activated chloride channel found in a variety of cell types that allows chloride to traverse the plasma membrane. Mutations in BEST1 can cause macular degeneration. The mechanisms for anion selectivity and Ca2+-dependent activation of BEST1 are unknown. Here, we show that a hydrophobic “neck” region of the channel’s pore does not play a major role in ion selectivity but acts as an effective gate, responding to Ca2+ binding at a cytosolic sensor. Mutation of a cytosolic “aperture” dramatically affects relative permeabilities among anions. These insights help rationalize how disease-causing mutations in BEST1 affect channel behavior and contribute to a broader understanding of ion channel gating and selectivity mechanisms. (See pp. E7399–E7408.)
Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences
Masahiko Imashimizu, Ariel Afek, Hiroki Takahashi, Lucyna Lubkowska, and David B. Lukatsky
How does RNA polymerase (RNAP) accurately and orderly control elongation of RNA in nanosystems dominated by random thermal fluctuations? Our statistical approach challenges this open question by identifying a linkage between thermal fluctuations, repetitive DNA sequences encoded in a genome, and RNAP pausing during elongation. Until now, it has been reasonably assumed that the structure of an elongation complex (EC) at any given location along DNA ultimately controls its enzymatic function. Contrary to this assumption, we show that nonlocal thermal fluctuations of the EC on repetitive DNA sequence elements statistically and robustly affect RNAP elongation by stabilizing pausing. This study also provides a proof of concept for the significance of thermal fluctuations in a wide variety of enzymatic systems. (See pp. E7409–E7417.)
Synthetic genome readers target clustered binding sites across diverse chromatin states
Graham S. Erwin, Matthew P. Grieshop, Devesh Bhimsaria, Truman J. Do, José A. Rodríguez-Martínez, Charu Mehta, Kanika Khanna, Scott A. Swanson, Ron Stewart, James A. Thomson, Parameswaran Ramanathan, and Aseem Z. Ansari
Targeting specific genomic loci with synthetic molecules remains a major goal in chemistry, biology, and precision medicine. Identifying how synthetic genome readers bind the chromatinized genome in cells would facilitate their development, but doing so remains a formidable challenge. We map the genome-wide binding patterns for two structurally distinct synthetic molecules. To achieve this goal, we couple our cross-linking of small molecules to isolate chromatin approach to next-generation sequencing. In addition to binding high-affinity sites, these molecules, surprisingly, bind clustered low-affinity sites. The data also show that these genome readers target sites in both open and closed chromatin. Our findings highlight the importance of genome-guided design for molecules that will serve as precision-targeted therapeutics. (See pp. E7418–E7427.)
Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast
Drew G. Michael, Ezekiel J. Maier, Holly Brown, Stacey R. Gish, Christopher Fiore, Randall H. Brown, and Michael R. Brent
The ability to engineer specific behaviors into cells would have a significant impact on biomedicine and biotechnology, including applications to regenerative medicine and biofuels production. One way to coax cells to behave in a desired way is to globally modify their gene expression state, making it more like the state of cells with the desired behavior. This paper introduces a broadly applicable algorithm for transcriptome engineering—designing transcription factor deletions or overexpressions to move cells to a gene expression state that is associated with a desired phenotype. This paper also presents an approach to benchmarking and validating such algorithms. The availability of systematic, objective benchmarks for a computational task often stimulates increased effort and rapid progress on that task. (See pp. E7428–E7437.)
Tertiary alphabet for the observable protein structural universe
Craig O. Mackenzie, Jianfu Zhou, and Gevorg Grigoryan
Proteins fold into intricate 3D structures, determined by their amino acid sequences. Different proteins can fold into drastically different structures, and the space of all possible structures appears hopelessly complex. However, this is precisely the space that needs to be described to understand how sequence encodes structure. In this paper, we decompose the set of known protein structures into standard reusable building blocks, which we call tertiary structural motifs (TERMs). Strikingly, we find that only ∼600 TERMs describe 50% of the known protein structural universe at sub-Angstrom resolution. Furthermore, we find the natural utilization of TERMs gives us a means of uncovering sequence–structure relationships. These insights can be harnessed for protein structure prediction, protein design, and other applications. (See pp. E7438–E7447.)
Highly selective inhibition of myosin motors provides the basis of potential therapeutic application
Serena Sirigu, James J. Hartman, Vicente José Planelles-Herrero, Virginie Ropars, Sheila Clancy, Xi Wang, Grace Chuang, Xiangping Qian, Pu-Ping Lu, Edward Barrett, Karin Rudolph, Christopher Royer, Bradley P. Morgan, Enrico A. Stura, Fady I. Malik, and Anne M. Houdusse
Defects in myosin function are linked to a number of widespread and debilitating diseases, including asthma, chronic obstructive pulmonary disease, and hypertrophic cardiomyopathy. We report here the discovery of an allosteric site that modulates myosin motor function with high specificity that opens the path toward new therapeutic solutions. Identification of specific antimyosin drugs that significantly alter a motor’s function is an imperative first step toward the development of targeted and effective treatments for such diseases. Highly specific drugs against different members of the superfamily would also provide exquisite tools to investigate in cells their functional role. Additionally, detailed, high-resolution studies of the interaction of drugs with their myosin targets provide insights into the molecular mechanism of motor function. (See pp. E7448–E7455.)
Design of a molecular support for cryo-EM structure determination
Thomas G. Martin, Tanmay A. M. Bharat, Andreas C. Joerger, Xiao-chen Bai, Florian Praetorius, Alan R. Fersht, Hendrik Dietz, and Sjors H. W. Scheres
As the scope of macromolecular structure determination by cryo-electron microscopy (cryo-EM) is expanding rapidly, it is becoming increasingly clear that many biological complexes are too fragile to withstand the harsh conditions involved in making cryo-EM samples. We describe an original approach to protect proteins from harmful forces during cryo-EM sample preparation by enclosing them inside a three-dimensional support structure that we designed using DNA origami techniques. By binding the transcription cofactor p53 to a specific DNA sequence, and by modifying the position of this sequence in our support structure, we also sought to control the relative orientation of individual p53:DNA complexes. (See pp. E7456–E7463.)
A Diaphanous-related formin links Ras signaling directly to actin assembly in macropinocytosis and phagocytosis
Alexander Junemann, Vedrana Filić, Moritz Winterhoff, Benjamin Nordholz, Christof Litschko, Helena Schwellenbach, Till Stephan, Igor Weber, and Jan Faix
Macropinocytosis and phagocytosis are two Ras-regulated, highly related processes of great physiological relevance collectively termed large-scale endocytosis. Both are actin-driven and entail engulfment of extracellular material by crown-like protrusions. Aside from the Arp2/3 complex, which serves as the main nucleator of branched actin filaments at the cup rim, the underlying mechanisms of actin assembly still remain elusive. Here, we analyzed the role of Diaphanous-related formin G (ForG) from Dictyostelium by biochemical, genetic, and imaging techniques. Our data demonstrate that this formin exhibits a rather weak nucleation activity and imply that ForG-mediated filament elongation synergizes with the Arp2/3 complex in actin assembly. Finally, we identify ForG as a Ras-regulated formin and show its significance for actin assembly in endocytic structures. (See pp. E7464–E7473.)
Protein aggregation as a cellular response to oxidative stress induced by heme and iron
Luiz R. C. Vasconcellos, Fabianno F. Dutra, Mariana S. Siqueira, Heitor A. Paula-Neto, Jennifer Dahan, Ellen Kiarely, Leticia A. M. Carneiro, Marcelo T. Bozza, and Leonardo H. Travassos
Hemolytic diseases include a variety of conditions with diverse etiologies in which red blood cells are destroyed and large amounts of hemeproteins are released. Heme has been described as a potent proinflammatory molecule that is able to induce multiple innate immune responses. The mechanisms by which eukaryotic cells respond to the toxic effects induced by heme to maintain homeostasis are not fully understood, however. Here we describe a previously uncharacterized cellular response induced by heme: the formation of p62/SQTM1 aggregates containing ubiquitinated proteins in structures known as aggresome-like induced structures (ALIS). This action is part of a response driven by the transcription factor NRF2 to the excessive generation of reactive oxygen species induced by heme. (See pp. E7474–E7482.)
Schizosaccharomyces pombe kinesin-5 switches direction using a steric blocking mechanism
Mishan Britto, Adeline Goulet, Syeda Rizvi, Ottilie von Loeffelholz, Carolyn A. Moores, and Robert A. Cross
Molecular motors organize cells by hauling molecular cargoes along polymer tracks (actin filaments or microtubules). Until recently, the stepping direction of each motor was thought to be fixed; however, it now emerges that yeast kinesin-5 motors can reverse their stepping direction. How does this work? We show that the stepping direction of Cut7, a yeast kinesin-5 motor, depends on the level of motor crowding on the microtubule, and that crowding of Cut7 by non-Cut7 proteins also can drive reversal. To explain this, we propose that stepping of Cut7 in one direction is blocked by collisions with neighbors, whereas stepping in the other direction, being less space-hungry, is not. Crowding-dependent directional reversal is a hitherto-unsuspected aspect of motor-driven self-organization in cells. (See pp. E7483–E7489.)
p62- and ubiquitin-dependent stress-induced autophagy of the mammalian 26S proteasome
Victoria Cohen-Kaplan, Ido Livneh, Noa Avni, Bertrand Fabre, Tamar Ziv, Yong Tae Kwon, and Aaron Ciechanover
Whereas the role of the ubiquitin system in protein degradation is well established, little is known regarding the regulation of its own components, including its catalytic arm, the 26S proteasome. Here we show that in stressed mammalian cells, the proteasome is targeted by autophagy, which requires site-specific ubiquitination of its ubiquitin receptors. The process is mediated by the p62/SQSTM1 adapter and requires its ubiquitin-associated domain. Independently, p62 serves also as a shuttling protein for ubiquitinated substrates, using its PB1 domain. This places p62 in a pivotal position where under certain conditions it binds to the proteasome as a protease, whereas in other conditions it recognizes the proteasome as a prey. The regulation of this intricate “decision making” process remains elusive. (See pp. E7490–E7499.)
Chemical and mechanical stimuli act on common signal transduction and cytoskeletal networks
Yulia Artemenko, Lucas Axiotakis Jr., Jane Borleis, Pablo A. Iglesias, and Peter N. Devreotes
Cells directionally migrate in response to a variety of external cues, including chemical, electrical, and mechanical stimuli; however, only response to chemoattractants has been characterized at the molecular level. Binding of chemoattractants to specific surface receptors triggers rapid, transient activation of many signal transduction and cytoskeletal events. We discovered that brief application of shear stress to cells likely elicits activation of all of the same events. Responses to chemoattractants and shear stress are susceptible to many of the same perturbations, although that to mechanical stimulation uniquely is blocked by disruption of the actin cytoskeleton. Our finding provides insight into the molecular mechanism of cellular response to mechanical stimuli and has important implications for integration of chemical and mechanical inputs. (See pp. E7500–E7509.)
Spatiotemporal dynamics of androgen signaling underlie sexual differentiation and congenital malformations of the urethra and vagina
Christine E. Larkins, Ana B. Enriquez, and Martin J. Cohn
Disorders of sex development (DSDs) and some non-DSD human syndromes result in female genitourinary malformations. The mechanisms of genitourinary development are beginning to be understood in males; however, little is known about female lower genitourinary organogenesis. Prenatal exposure to excessive endogenous or exogenous androgens can disrupt sexual differentiation of the female urethra and vagina, but the mechanisms responsible for these malformations are not well understood. This study sheds new light on development of vaginal anomalies in DSDs by (i) identifying the critical period of female development when vaginal position and feminization of the urethra is established and (ii) showing that this process is controlled by an androgen-responsive subpopulation of mesenchymal cells adjacent to the urogenital sinus. (See pp. E7510–E7517.)
An oscillating tragedy of the commons in replicator dynamics with game-environment feedback
Joshua S. Weitz, Ceyhun Eksin, Keith Paarporn, Sam P. Brown, and William C. Ratcliff
Classical game theory addresses how individuals make decisions given suitable incentives, for example, whether to use a commons rapaciously or with restraint. However, classical game theory does not typically address the consequences of individual actions that reshape the environment over the long term. Here, we propose a unified approach to analyze and understand the coupled evolution of strategies and the environment. We revisit the originating tragedy of the commons example and evaluate how overuse of a commons resource changes incentives for future action. In doing so, we identify an oscillatory tragedy of the commons in which the system cycles between deplete and replete environments and cooperation and defection behavior, highlighting new challenges for control and influence of feedback-evolving games. (See pp. E7518–E7525.)
Systematic autoantigen analysis identifies a distinct subtype of scleroderma with coincident cancer
George J. Xu, Ami A. Shah, Mamie Z. Li, Qikai Xu, Antony Rosen, Livia Casciola-Rosen, and Stephen J. Elledge
In this study, we created a barcoded whole-genome ORF mRNA display library and combined it with phage-immunoprecipitation sequencing to look for autoantibodies in sera from patients with scleroderma who also had coincident cancer without a known autoantibody biomarker. Using these two technologies, we found that 25% of these patients had autoantibodies to RNA Binding Region Containing 3 (RNPC3) and multiple other components of the minor spliceosome. There was evidence of intra- and intermolecular epitope spreading within RNPC3 and the complex. These combined technologies are highly effective for rapidly discovering autoantibodies in patient subgroups, which will be useful tools for patient stratification and discovery of pathogenic pathways. (See pp. E7526–E7534.)
Epigenetic inactivation of the p53-induced long noncoding RNA TP53 target 1 in human cancer
Angel Diaz-Lagares, Ana B. Crujeiras, Paula Lopez-Serra, Marta Soler, Fernando Setien, Ashish Goyal, Juan Sandoval, Yutaka Hashimoto, Anna Martinez-Cardús, Antonio Gomez, Holger Heyn, Catia Moutinho, Jesús Espada, August Vidal, Maria Paúles, Maica Galán, Núria Sala, Yoshimitsu Akiyama, María Martínez-Iniesta, Lourdes Farré, Alberto Villanueva, Matthias Gross, Sven Diederichs, Sonia Guil, and Manel Esteller
Long noncoding RNAs (lncRNAs) are starting to be recognized as critical molecules for cellular transformation, although only a few candidates have so far been characterized. Here we report that TP53TG1 is an lncRNA that is critical for the correct response of p53 to DNA damage. The cancer growth suppressor features of TP53TG1 are linked to its ability to block the tumorigenic activity of the RNA binding protein YBX1. The DNA methylation-associated silencing of TP53TG1 produces aggressive tumors that are resistant to cellular death when DNA-damaging agents and small targeted molecules are used. Our study provides an example of a tumor suppressor lncRNA undergoing an epigenetic lesion in cancer that is placed at the crossroads of DNA damage and oncogenic pathways. (See pp. E7535–E7544.)
Control of inflammation by stromal Hedgehog pathway activation restrains colitis
John J. Lee, Michael E. Rothenberg, E. Scott Seeley, Bryan Zimdahl, Sally Kawano, Wan-Jin Lu, Kunyoo Shin, Tomoyo Sakata-Kato, James K. Chen, Maximilian Diehn, Michael F. Clarke, and Philip A. Beachy
Inflammatory bowel disease (IBD) is a debilitating disorder with limited treatment options. Here, we report that manipulation of Hedgehog (Hh) pathway signaling affects disease severity in the well-established dextran sulfate mouse model of colitis. Genetic and pharmacologic manipulations that decrease Hh pathway signaling in the colon worsen colitis. Conversely, manipulations that increase Hh pathway signaling ameliorate colitis. We find that Hh pathway stimulation exerts its effects partially through increased expression of the antiinflammatory cytokine IL-10 in Hh pathway-responsive stromal cells and concomitant increases in CD4+Foxp3+ regulatory T cells in the colon. Our studies suggest that pharmacologic Hh pathway stimulation in colonic stromal cells may be a strategy to treat IBD. (See pp. E7545–E7553.)
Gut microbiota induce IGF-1 and promote bone formation and growth
Jing Yan, Jeremy W. Herzog, Kelly Tsang, Caitlin A. Brennan, Maureen A. Bower, Wendy S. Garrett, Balfour R. Sartor, Antonios O. Aliprantis, and Julia F. Charles
New interventions are needed to improve bone health and reduce the risk for osteoporosis and fracture. Dysbiosis is increasingly linked to metabolic abnormalities, although the effect of the microbiota on skeletal health is poorly understood. Previous studies suggest microbiota are detrimental to bone by increasing resorption. In this report, we show that the gut resident microbiota promote bone formation, as well as resorption, with long-term exposure to microbiota resulting in net skeletal growth. Microbiota induce the hormone insulin-like growth factor 1 (IGF-1), which promotes bone growth and remodeling. Short-chain fatty acids (SCFAs), produced when microbiota ferment fiber, also induce IGF-1, suggesting a mechanism by which microbiota affect bone health. Manipulating the microbiome or its metabolites may afford opportunities to optimize bone health and growth. (See pp. E7554–E7563.)
Role of sulfiredoxin as a peroxiredoxin-2 denitrosylase in human iPSC-derived dopaminergic neurons
Carmen R. Sunico, Abdullah Sultan, Tomohiro Nakamura, Nima Dolatabadi, James Parker, Bing Shan, Xuemei Han, John R. Yates III, Eliezer Masliah, Rajesh Ambasudhan, Nobuki Nakanishi, and Stuart A. Lipton
S-nitrosylation, addition of an NO group to a cysteine thiol, can regulate protein activity. Aberrant protein S-nitrosylation, however, can disrupt normal enzyme function, as is the case for S-nitrosylated peroxiredoxin (SNO-Prx), which would otherwise catabolize toxic peroxides that occur under neurodegenerative conditions such as Parkinson’s disease. Here, we describe a paradigm of N-phosphorylation–mediated denitrosylation by the enzyme sulfiredoxin that removes NO from Prx. The findings are at the center of redox control of the cell, explaining reactivation by sulfiredoxin of both Prx-SO2H and SNO-Prx and thus describe a master regulator of redox reactions that combats nitrosative and oxidative stress in cells. These results suggest that sulfiredoxin may be an important target for therapeutic intervention in neurodegenerative disorders. (See pp. E7564–E7571.)
IL-33/ST2 signaling excites sensory neurons and mediates itch response in a mouse model of poison ivy contact allergy
Boyi Liu, Yan Tai, Satyanarayana Achanta, Melanie M. Kaelberer, Ana I. Caceres, Xiaomei Shao, Jianqiao Fang, and Sven-Eric Jordt
In the United States, the most common cause of allergic contact dermatitis (ACD) is contact with poison ivy. Severe itch and skin inflammation are the major manifestations of poison ivy-induced ACD. In this study, we have established a critical role of IL-33/ST2 (interleukin 33/growth stimulation expressed gene 2) signaling in both itch and skin inflammation of poison ivy-induced ACD and revealed a previously unidentified interaction of IL-33/ST2 signaling with primary sensory neurons that may underlie the pruritic mechanisms of poison ivy-induced ACD. Blocking IL-33/ST2 signaling may represent a therapeutic approach to ameliorate itch and skin inflammation related to poison ivy dermatitis and, possibly, other chronic itch conditions in which IL-33/ST2 signaling may participate. (See pp. E7572–E7579.)
Motor neuron disease, TDP-43 pathology, and memory deficits in mice expressing ALS–FTD-linked UBQLN2 mutations
Nhat T. T. Le, Lydia Chang, Irina Kovlyagina, Polymnia Georgiou, Nathaniel Safren, Kerstin E. Braunstein, Mark D. Kvarta, Adam M. Van Dyke, Tara A. LeGates, Thomas Philips, Brett M. Morrison, Scott M. Thompson, Adam C. Puche, Todd D. Gould, Jeffrey D. Rothstein, Philip C. Wong, and Mervyn J. Monteiro
Animal models of human diseases provide important tools for mechanistic and preclinical investigations. Mutations in several genes cause ALS. One such gene is ubiquilin 2 (UBQLN2), mutations in which cause dominant inheritance of ALS with frontotemporal dementia (ALS–FTD). Several rodent models carrying UBQLN2 mutations have been described, but none develop motor neuron disease. We describe two transgenic (Tg) mouse models of ALS–FTD carrying different UBQLN2 mutations. Both models develop cognitive deficits, classic TAR-DNA binding protein 43 (TDP-43) pathology seen in ALS, and motor neuron disease. By contrast, Tg mouse lines expressing WT UBQLN2 had normal lifespans, no evidence of TDP-43 pathology, and mild signs of disease. These mouse lines provide valuable investigative tools for ALS–FTD research. (See pp. E7580–E7589.)
C-terminal domain of mammalian complexin-1 localizes to highly curved membranes
Jihong Gong, Ying Lai, Xiaohong Li, Mengxian Wang, Jeremy Leitz, Yachong Hu, Yunxiang Zhang, Ucheor B. Choi, Daniel Cipriano, Richard A. Pfuetzner, Thomas C. Südhof, Xiaofei Yang, Axel T. Brunger, and Jiajie Diao
The central nervous system utilizes Ca2+-triggered synaptic vesicle fusion mediated by SNAREs and other synaptic proteins for neurotransmitter release into the synaptic cleft. Complexin, a small cytosolic protein, plays a dual role in regulating spontaneous minirelease and in activating Ca2+-triggered fusion, but the molecular mechanisms are still unclear. Here we found that the C-terminal domain of mammalian complexin interacts with membranes in a curvature-dependent fashion similar to other curvature-sensing proteins, such as α-synuclein. Together with a previous study of worm complexin, this finding suggests that curvature-sensing of the C-terminal domain is evolutionarily conserved. Moreover, localization to the highly curved membrane of synaptic vesicles is important for regulating spontaneous release by complexin. (See pp. E7590–E7599.)
Reduced high-frequency motor neuron firing, EMG fractionation, and gait variability in awake walking ALS mice
Muhamed Hadzipasic, Weiming Ni, Maria Nagy, Natalie Steenrod, Matthew J. McGinley, Adi Kaushal, Eleanor Thomas, David A. McCormick, and Arthur L. Horwich
First recordings from awake walking symptomatic-stage amyotrophic lateral sclerosis (ALS) and control mice were made simultaneously from spinal cord motor pools and corresponding hindlimb flexor and extensor muscles. Spinal recordings revealed loss of high-frequency firing in ALS mice, and EMG showed an abnormal fractionated character with step-to-step variability and flexor/extensor coactivation, associated with step-to-step variability in kinematics and likely compensatory mechanisms that allow continued ability to walk in the face of motor neuron loss. (See pp. E7600–E7609.)
Illuminating a plant’s tissue-specific metabolic diversity using computational metabolomics and information theory
Dapeng Li, Sven Heiling, Ian T. Baldwin, and Emmanuel Gaquerel
Population geneticists have educated molecular biologists in how to harness the statistical power of variance arising from interindividual natural variation to elucidate gene function in plants. The metabolic differences among tissues within a plant provide another source of variance that can be harnessed in the quest to understand gene function. We combine the power of information theory statistics and computational metabolomics to parse metabolic diversity within an ecological model plant, Nicotiana attenuata, to reveal intriguing patterns of metabolic specialization in floral limb and anthers, the responsible mechanisms of which we parse further by detecting and silencing the expression of two UDP-glycosyltransferases involved in floral flavonoid metabolism. The workflow defines a framework for future evolutionary studies on plant tissue metabolic specialization. (See pp. E7610–E7618.)
The biosynthetic pathway of the nonsugar, high-intensity sweetener mogroside V from Siraitia grosvenorii
Maxim Itkin, Rachel Davidovich-Rikanati, Shahar Cohen, Vitaly Portnoy, Adi Doron-Faigenboim, Elad Oren, Shiri Freilich, Galil Tzuri, Nadine Baranes, Shmuel Shen, Marina Petreikov, Rotem Sertchook, Shifra Ben-Dor, Hugo Gottlieb, Alvaro Hernandez, David R. Nelson, Harry S. Paris, Yaakov Tadmor, Yosef Burger, Efraim Lewinsohn, Nurit Katzir, and Arthur Schaffer
We identified the biosynthetic pathway for the nonsugar sweetener mogroside V, a noncaloric with a sweetening strength 250-fold that of sucrose. This compound is produced by the fruit of the endemic Chinese cucurbit Siraitia grosvenoriii, also known as monk fruit and luo-han-guo. The metabolic pathway was identified using a combination of genomic and transcriptomic databases of the Siraitia plant, together with a large-scale functional expression of candidate genes. The novelty of the pathway could be attributed to a highly coordinated gene expression pattern responsible for the unique epoxidations, hydroxylations, and glucosylations leading to the sweet mogrosides. These discoveries will facilitate the development of alternative natural sweeteners. (See pp. E7619–E7628.)
Chloroplast division checkpoint in eukaryotic algae
Nobuko Sumiya, Takayuki Fujiwara, Atsuko Era, and Shin-ya Miyagishima
Chloroplasts arose from a cyanobacterial endosymbiont, which introduced photosynthesis into eukaryotes. It is widely believed that synchronization of division in the eukaryotic host cell and in the endosymbiont was critical for the host cell to maintain the endosymbiont/chloroplast permanently. However, it is unclear how the division of the endosymbiont (the chloroplast) and host cell became synchronized. Using the unicellular red alga Cyanidioschyzon merolae, we show that the host cell enters into the metaphase only when chloroplast division has commenced. A similar phenomenon also was observed in the glaucophyte alga Cyanophora paradoxa. It thus seems likely that the acquisition of the cell-cycle checkpoint of chloroplast division played an important role in the establishment of the chloroplast in ancient algae. (See pp. E7629–E7638.)