Shotgun glycomics of pig lung identifies natural endogenous receptors for influenza viruses
Lauren Byrd-Leotis, Renpeng Liu, Konrad C. Bradley, Yi Lasanajak, Sandra F. Cummings, Xuezheng Song, Jamie Heimburg-Molinaro, Summer E. Galloway, Marie R. Culhane, David F. Smith, David A. Steinhauer, and Richard D. Cummings
Studies using novel “shotgun glycan microarray” technology identify, for the first time to our knowledge, the endogenous receptors for influenza viruses from a natural host, the pig. Libraries of total N-glycans from pig lung were probed for binding properties using a panel of influenza viruses isolated from humans, birds, and swine. Natural glycan receptors were identified for all viruses examined, and although some displayed the rather broad α2,3 or α2,6 sialic acid linkage specificity conventionally associated with avian or human viruses, other strains were highly specific, revealing a complexity that has not been demonstrated previously (pp. E2241–E2250). Because pigs are often implicated as intermediate hosts for pandemic viruses, these results and the approaches described will transform our understanding of influenza host range, transmission, and pathogenicity.
The unique regulation of iron-sulfur cluster biogenesis in a Gram-positive bacterium
Joana A. Santos, Noelia Alonso-García, Sandra Macedo-Ribeiro, and Pedro José Barbosa Pereira
Iron-sulfur clusters are ubiquitous cofactors of proteins intervening in disparate biological processes. Iron-sulfur cluster biosynthesis pathways are tightly regulated in Gram-negative bacteria. One of the participating transcription factors, iron-sulfur cluster pathway (ISC) regulator (IscR), can itself bind an iron-sulfur cluster. Depending on its ligation status, IscR recognizes and binds to distinct promoters, therefore modulating cluster biosynthesis. This unique protein at the crossroad between the ISC and sulfur assimilation (SUF) iron-sulfur cluster biosynthetic pathways was thought to be restricted to Gram-negative bacteria. We demonstrated (pp. E2251–E2260) the existence of a functional IscR in the unique Gram-positive bacterium Thermincola potens. Structural and functional analysis of T. potens and Escherichia coli IscR unveiled a conserved mechanism of promoter discrimination, along with subtle structural differences that explain their distinct DNA sequence recognition specificity.
Mechanisms controlling the smooth muscle cell death in progeria via down-regulation of poly(ADP-ribose) polymerase 1
Haoyue Zhang, Zheng-Mei Xiong, and Kan Cao
Patients with Hutchinson–Gilford progeria syndrome (HGPS) almost always die of cardiovascular disease in their teens. Moreover, overlapping cardiovascular pathologies have been identified in HGPS and geriatric patients, including the loss of vascular smooth muscle cells in large vessels. However, how progerin leads to smooth muscle cell loss is still largely unknown. Here (pp. E2261–E2270), using induced pluripotent stem cells as a model, we examined the role of progerin in smooth muscle cell differentiation and maintenance. Our study identified poly(ADP-ribose) polymerase 1 as a central regulator of smooth muscle cell survival in progeria and elucidated a molecular pathway underlying heart disease in progeria. This study may provide key insights into future medical interventions for the cardiovascular dysfunction in progeria and normal aging.
Activation of the endoplasmic reticulum unfolded protein response by lipid disequilibrium without disturbed proteostasis in vivo
Nicole S. Hou, Aljona Gutschmidt, Daniel Y. Choi, Keouna Pather, Xun Shi, Jennifer L. Watts, Thorsten Hoppe, and Stefan Taubert
The unfolded protein response of the endoplasmic reticulum (UPRER) is induced by proteotoxic conditions. Lipid disequilibrium also activates the UPRER, but whether this activation is accompanied by disturbed proteostasis in vivo remains controversial. In this study (pp. E2271–E2280), we show that in the nematode Caenorhabditis elegans compromised fatty acid desaturation and reduced phosphatidylcholine production activate the UPRER without overt proteostatic imbalance, as assessed by molecular, pharmacological, and genetic analyses. This finding suggests that membrane composition is a direct input able to activate UPRER signaling even when proteostasis in the ER is largely intact. The activation of the UPRER by independent inputs may reflect the central role of the ER in both lipid and protein biosynthesis.
Golgi and plasma membrane pools of PI(4)P contribute to plasma membrane PI(4,5)P2 and maintenance of KCNQ2/3 ion channel current
Eamonn J. Dickson, Jill B. Jensen, and Bertil Hille
Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is a key informational phospholipid, localized to and defining the inner leaflet of the plasma membrane (PM). How PM PI(4,5)P2 is sourced and regulated is critically important to the understanding of cellular trafficking, cell motility, membrane identity, and ion channel activity. The immediate precursor of PI(4,5)P2 is PI(4)P. Direct evidence detailing the location and contribution of PI(4)P pool(s) maintaining steady-state PM PI(4,5)P2 is lacking. We find (pp. E2281–E2290) that PM PI(4,5)P2 levels are supported by at least two continuously supplying precursor pools of PI(4)P, one in the PM and the other in the Golgi. The contribution of the Golgi pool of PI(4)P highlights the possibility that PM PI(4,5)P2 production is coupled to important cell biological processes.
DA-Raf–dependent inhibition of the Ras-ERK signaling pathway in type 2 alveolar epithelial cells controls alveolar formation
Haruko Watanabe-Takano, Kazunori Takano, Akemi Sakamoto, Kenji Matsumoto, Takeshi Tokuhisa, Takeshi Endo, and Masahiko Hatano
Alveoli participating in gas exchange are essential for maintaining life in air-breathing vertebrates. In developing lungs, alveolar myofibroblasts (AMYFs) cause morphological changes of interalveolar walls and consequently generate alveoli. Although the Ras-ERK signaling pathway is known to regulate alveolar formation, the molecular and cellular mechanisms underlying its role remain largely obscure. Here (pp. E2291–E2300), we clarified a critical role of DA-Raf1 (DA-Raf)—a dominant-negative antagonist of the Ras-ERK signaling pathway—in alveolar formation. DA-Raf–deficient mice displayed alveolar dysgenesis resulting from defective AMYF differentiation. DA-Raf–dependent MEK1/2 inhibition in type 2 alveolar epithelial cells induces activation of matrix metalloproteinases, which is required for AMYF differentiation. Our findings reveal a pivotal role of DA-Raf–mediated regulation of the Ras-ERK signaling pathway in alveolar formation.
Inferring fitness landscapes by regression produces biased estimates of epistasis
Jakub Otwinowski and Joshua B. Plotkin
The dynamics of evolution depend on an organism’s fitness landscape: the mapping from genotypes to reproductive capacity. Knowledge of the fitness landscape can help resolve questions, such as how quickly a pathogen will acquire drug resistance or by what pattern of mutations. However, direct measurement of a fitness landscape is impossible because of the vast number of genotypes. Here, we critically examine regression techniques used to approximate fitness landscapes from data. We find (pp. E2301–E2309) that such regressions are subject to two inherent biases that distort the biological quantities of greatest interest, often making evolution seem less predictable than it actually is. We discuss methods that may mitigate these biases in some cases.
Precise estimates of mutation rate and spectrum in yeast
Yuan O. Zhu, Mark L. Siegal, David W. Hall, and Dmitri A. Petrov
Spontaneous mutations are rare and difficult to observe in large numbers experimentally. By sequencing the genomes of 145 diploid mutation accumulation (MA) lines of the budding yeast Saccharomyces cerevisiae, we identified nearly 1,000 mutations, a larger number than in any prior eukaryotic MA experiment as far as we are aware. For the first time, to our knowledge, in MA data, we were able to estimate rates of context-dependent single-nucleotide mutations. We were also able to observe mutational classes not seen in earlier yeast MA experiments and infer the rate of strongly deleterious mutations from patterns of missing mutations in each mutational class. Our findings (pp. E2310–E2318) both answer outstanding questions in the field, as well as highlight the need for more studies of spontaneous mutation.
Insulin regulates carboxypeptidase E by modulating translation initiation scaffolding protein eIF4G1 in pancreatic β cells
Chong Wee Liew, Anke Assmann, Andrew T. Templin, Jeffrey C. Raum, Kathryn L. Lipson, Sindhu Rajan, Guifen Qiang, Jiang Hu, Dan Kawamori, Iris Lindberg, Louis H. Philipson, Nahum Sonenberg, Allison B. Goldfine, Doris A. Stoffers, Raghavendra G. Mirmira, Fumihiko Urano, and Rohit N. Kulkarni
Elevated circulating proinsulin and a poor biological response to insulin are observed early in individuals with type 2 diabetes. Genome-wide association studies have recently identified genes associated with proinsulin processing, and clinical observations suggest that elevated proinsulin and its intermediates are markers of dysfunctional insulin-secreting β cells. Here (pp. E2319–E2328), we propose a previously unidentified mechanism in the regulation of an enzyme that is involved in proinsulin processing called carboxypeptidase E (CPE). Disruption of insulin signaling in β cells reduces expression of a scaffolding protein, eukaryotic translation initiation factor 4 gamma 1, that is required for the initiation of translation and occurs via regulation of two transcription factors, namely, pancreatic and duodenal homeobox 1 and sterol regulatory element-binding protein 1. Together, these effects lead to reduced levels of CPE protein and poor proinsulin processing in β cells.
Relating the metatranscriptome and metagenome of the human gut
Eric A. Franzosa, Xochitl C. Morgan, Nicola Segata, Levi Waldron, Joshua Reyes, Ashlee M. Earl, Georgia Giannoukos, Matthew R. Boylan, Dawn Ciulla, Dirk Gevers, Jacques Izard, Wendy S. Garrett, Andrew T. Chan, and Curtis Huttenhower
Recent years have seen incredible growth in both the scale and specificity of projects analyzing the microbial organisms living in and on the human body (the human microbiome). Such studies typically require subjects to report to clinics for sample collection, a complicated practice that is impractical for large studies. To address these issues, we developed a protocol that allows subjects to collect microbiome samples at home and ship them to laboratories for multiple different types of molecular analysis (pp. E2329–E2338). Measurements of microbial species, gene, and gene transcript composition within self-collected samples were consistent across sampling methods. In addition, our subsequent analysis of these samples revealed interesting similarities and differences between the measured functional potential and functional activity of the human microbiome.
Subthreshold resonance properties contribute to the efficient coding of auditory spatial cues
Michiel W. H. Remme, Roberta Donato, Jason Mikiel-Hunter, Jimena A. Ballestero, Simon Foster, John Rinzel, and David McAlpine
Locating the source of a sound is critical to the survival of many species and an important factor in human communication. Auditory spatial cues—differences in the timing and intensity of sounds arriving at the two ears—are processed by specialized neurons in the brainstem. The importance of these cues varies with sound frequency. Through in vitro recordings we show that the biophysical properties of brainstem neurons vary with their presumed sound frequency tuning. Using neural modeling we demonstrate that the cell properties are well suited to extract spatial cues from natural sounds, including in background noise. Our findings (pp. E2339–E2348) also provide an explanation for human listening performance limits under noisy conditions and have implications for further development of cochlear implants.
Two-photon imaging of remyelination of spinal cord axons by engrafted neural precursor cells in a viral model of multiple sclerosis
Milton L. Greenberg, Jason G. Weinger, Melanie P. Matheu, Kevin S. Carbajal, Ian Parker, Wendy B. Macklin, Thomas E. Lane, and Michael D. Cahalan
Stem cell transplantation has emerged as a promising cell-based therapy for the treatment of demyelinating diseases such as multiple sclerosis (MS). This study (pp. E2349–E2355) provides the first real-time imaging of transplanted stem cell-mediated remyelination in a mouse model of MS. Whereas current treatments solely delay disease progression, transplanted stem cells actively reverse clinical disease in animal models. Using two-photon microscopy and viral-induced demyelination, we describe a technique to visualize cellular migration and remyelination in the mouse spinal cord. Transplanted neural precursor cells physically wrap damaged axons with newly formed myelin, preserving axonal health.