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Engineering the type III secretion system in non-replicating bacterial minicells for antigen delivery
Bacterial type III secretion systems (T3SS) improve the delivery of vaccine antigens and antigen-specific immune responses but require the use of live vaccines. Carleton et al. report the assembly of a functional T3SS in replication-incompetent bacterial minicells that can deliver vaccine antigens in vitro and in vivo.
- Heather A. Carleton
- , María Lara-Tejero
- & Jorge E. Galán
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Actin-based confinement of calcium responses during Shigella invasion
Shigella triggers an increase in intracellular calcium during invasion of host cells. Here the authors show that increased actin polymerization at the invasion site slows the diffusion of signalling mediators, thus sustaining localized calcium influx at invasion sites.
- Guy Tran Van Nhieu
- , Bing Kai Liu
- & Laurent Combettes
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| Open AccessSir2a regulates rDNA transcription and multiplication rate in the human malaria parasite Plasmodium falciparum
The factors that modulate growth rate of the human malaria parasite Plasmodium falciparum remain poorly understood. Here Scherf and collaborators demonstrate that the Plasmodiumsirtuin PfSir2a regulates the transcription of ribosomal DNA, thereby modulating parasite proliferation rate and virulence.
- Liliana Mancio-Silva
- , Jose Juan Lopez-Rubio
- & Artur Scherf
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A synthetic nanomaterial for virus recognition produced by surface imprinting
The recognition of viruses by synthetic materials is historically difficult. Here, a templating procedure using silica nanoparticles coated with organosilanes is used to form virus-imprinted particles, possessing both shape and chemical imprints, capable of virus recognition at picomolar concentrations.
- Alessandro Cumbo
- , Bernard Lorber
- & Patrick Shahgaldian
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| Open AccessCell wall elongation mode in Gram-negative bacteria is determined by peptidoglycan architecture
Bacterial cell wall peptidoglycan is essential for viability and shape determination. Using high-resolution microscopy, Foster and colleagues elucidate the peptidoglycan architecture and insertion pattern in Escherichia coliand other Gram-negative bacteria, and propose a new model for cell wall elongation.
- Robert D. Turner
- , Alexander F. Hurd
- & Simon J. Foster
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Influenza neuraminidase operates via a nucleophilic mechanism and can be targeted by covalent inhibitors
New influenza neuramidase inhibitors may increase preparedness against influenza outbreaks. Vavricka et al.confirm the catalytic mechanism of neuramidase and show that it can be inhibited irreversibly with covalent inhibitors.
- Christopher J. Vavricka
- , Yue Liu
- & George F. Gao
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Mechanism of tetracycline resistance by ribosomal protection protein Tet(O)
The bacterial tetracycline resistance protein Tet(O) binds to the ribosome, preventing tetracycline from inhibiting translation. Using cryo-electron microscopic reconstruction, the authors present an atomic model of Tet(O) bound to the 70S ribosome, and reveal how Tet(O) promotes antibiotic resistance.
- Wen Li
- , Gemma C. Atkinson
- & Joachim Frank
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Bacteroides fragilis polysaccharide A is necessary and sufficient for acute activation of intestinal sensory neurons
Commensal bacteria in gut lumen are known to interact with the enteric nervous system. Mao and colleagues test the effects of Lactobacillus rhamnosus and Bacteroides fragilis ex vivo, in the myenteric plexus, and find that the polysaccharide A is necessary for intestinal sensory neuron sensitization.
- Yu-Kang Mao
- , Dennis L. Kasper
- & Wolfgang A. Kunze
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Cytotoxicity of botulinum neurotoxins reveals a direct role of syntaxin 1 and SNAP-25 in neuron survival
Botulinum toxins can cause substantial neurodegeneration. Peng et al. study cultured rat hippocampal neurons and find that botulinum toxin-induced cytotoxicity occurs only when there is effective cleavage of the SNARE proteins, syntaxin 1 or SNAP-25, by type C and type E botulinum toxins.
- Lisheng Peng
- , Huisheng Liu
- & Min Dong
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Self-organization of the vesicular stomatitis virus nucleocapsid into a bullet shape
The bullet shape of Rhabdoviruses is thought to depend on their matrix protein, which stabilizes the nucleocapsid coil. Desfosses and colleagues show that the nucleoprotein of the vesicular stomatitis virus can fold the genome into a bullet-shaped skeleton in the absence of other viral components.
- Ambroise Desfosses
- , Euripedes A. Ribeiro Jr
- & Irina Gutsche
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Strong bias in the bacterial CRISPR elements that confer immunity to phage
Bacterial CRISPR–Cas systems provide adaptive immunity against phage by transcribing interfering RNA from phage DNA inserted into the bacterial genome. Using deep-sequencing, the authors detect a bias in the phage genome locations sampled, suggestive of selection.
- David Paez-Espino
- , Wesley Morovic
- & Jillian F. Banfield
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Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity
In microbial biogeography, little is known about processes involved in soil bacterial diversity turnover. By conducting a wide-scale investigation, this study shows that dispersal limitation and environmental selection of bacteria are not mutually exclusive, highlighting the importance of landscape diversity.
- L. Ranjard
- , S. Dequiedt
- & P. Lemanceau
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The microbiome extends to subepidermal compartments of normal skin
Microbes living in human skin are known to influence the immune system; however, the deeper layers in which immune cells reside were thought to be largely impervious to bacteria. Nakatsuji et al.show that the skin microbiome extends into the dermis, enabling contact with cells below the basement membrane.
- Teruaki Nakatsuji
- , Hsin-I. Chiang
- & Richard L. Gallo
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| Open AccessMethylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen
Rumen methanogenic archaea are major sources of methane emissions and potential targets for methane mitigation strategies. Poulsen et al.now show that dietary rapeseed oil (RSO) supplementation can reduce the abundance of methanogenic Thermoplasmata archaea inhabiting the bovine rumen.
- Morten Poulsen
- , Clarissa Schwab
- & Tim Urich
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| Open AccessInterferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals
A variant in the IFITM3gene increases the risk of severe influenza, but homozygosity is rare in Caucasians. The authors show that the variant gene is homozygous in 25% of healthy Chinese people, and 69% of those with severe pandemic influenza, suggesting that this gene influences the epidemiology of influenza in South-East Asia.
- Yong-Hong Zhang
- , Yan Zhao
- & Tao Dong
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| Open AccessThe evolution and pathogenic mechanisms of the rice sheath blight pathogen
The rice sheath blight pathogen, Rhizoctonia solani, is an important fungal pathogen that can devastate rice and maize crops. Zheng and colleagues sequence and assemble the R. solani AG1 IA genome—the first to be sequenced from the Rhizoctoniagenus—using Illumina sequencing technology.
- Aiping Zheng
- , Runmao Lin
- & Ping Li
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| Open AccessSpatial association with PTEX complexes defines regions for effector export into Plasmodium falciparum-infected erythrocytes
During red blood cell infection, malaria parasites export hundreds of proteins that remodel the host cell surface. Cowman and colleagues identify a putative protein translocator complex spatially associated with exported proteins, revealing the cellular domains involved in protein export.
- David T. Riglar
- , Kelly L. Rogers
- & Alan F. Cowman
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Modular optimization of multi-gene pathways for fatty acids production in E. coli
Microbial fatty acid-derived fuels represent promising alternatives to the traditionally used fossil fuels. Koffas and colleagues report that E. colicentral metabolism can be modified to produce large quantities of fatty acids through a modular pathway engineering strategy.
- Peng Xu
- , Qin Gu
- & Mattheos A.G. Koffas
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Environmental conditions and community evenness determine the outcome of biological invasion
Biological invasion varies under different environmental stressors. Here, using a fully controlled system of bacterial communities, De Roy et al. find that community evenness affects the level of invasion, and that the community’s response depends on specific environmental conditions as well as the community evenness.
- Karen De Roy
- , Massimo Marzorati
- & Nico Boon
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| Open AccessTransgenerational gene silencing causes gain of virulence in a plant pathogen
Plant pathogens encode effector proteins that trigger immunity in plants carrying appropriate resistance genes. Here Qutob et al. show non-Mendelian interactions between naturally occurring Phytophthora sojaealleles that result in transgenerational gene silencing and gain of virulence in soybean plants.
- Dinah Qutob
- , B. Patrick Chapman
- & Mark Gijzen
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Different types of synchrony in chaotic and cyclic communities
Natural populations are complex systems where interactions can lead to chaotic dynamics. This study tests how cyclic and chaotic microbial predator–prey communities synchronize, showing different phase-locking responses for cyclic and chaotic systems.
- Lutz Becks
- & Hartmut Arndt
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A structural basis for streptomycin-induced misreading of the genetic code
The antibiotic streptomycin increases errors in protein translation, but it is unclear how streptomycin exerts its effect on the ribosome. Demirci et al. present X-ray crystal structures that reveal conformational changes induced by streptomycin, which may inspire future efforts in antibiotics design.
- Hasan Demirci
- , Frank Murphy IV
- & Gerwald Jogl
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Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans
Systemic infection with the fungal pathogenC. albicans is characterized by high mortality, and the precise antifungal defence mechanisms in humans are poorly defined. Using a systems approach, Smeekens et al. describe a previously unknown role for type I interferons in human anti-Candidadefence.
- Sanne P. Smeekens
- , Aylwin Ng
- & Ramnik J. Xavier
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In vivo imaging of virological synapses
In vitro, retroviruses spread between cells via structures resembling synapses. Sewaldet al. now demonstrate that virological synapses can also be observed in living mice by intravital microscopy, validating this concept in vivo.
- Xaver Sewald
- , David G. Gonzalez
- & Walther Mothes
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Predator richness increases the effect of prey diversity on prey yield
The functioning of bacterial communities is affected by selection, but the role of predation by single or multiple predators is unclear. In a study of 465 bacterial microcosms, Saleem et al.find that multiple predation causes positive bacterial diversity effects due to increased evenness among bacterial species.
- Muhammad Saleem
- , Ingo Fetzer
- & Antonis Chatzinotas
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| Open AccessProteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes
Selected reaction monitoring mass spectrometry (SRM-MS) can quantify dynamic changes in protein expression with high sensitivity. Karlsson et al. define optimal detection parameters for 10,412 distinct group A Streptococcus pyogenespeptides, which facilitates proteome-wide SRM-MS studies in this bacterium.
- Christofer Karlsson
- , Lars Malmström
- & Johan Malmström
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| Open AccessVirus-like glycodendrinanoparticles displaying quasi-equivalent nested polyvalency upon glycoprotein platforms potently block viral infection
Host–pathogen relationships can be mediated by polyvalent glycan ligand–protein interactions. Here well-defined highly valent glycodendrimeric constructs are synthesized that can mimic pathogens, and can inhibit a model of infection by the Ebola virus.
- Renato Ribeiro-Viana
- , Macarena Sánchez-Navarro
- & Benjamin G. Davis
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Plasmodium falciparum heat shock protein 110 stabilizes the asparagine repeat-rich parasite proteome during malarial fevers
The proteome of the malarial parasite Plasmodium falciparum has an overabundance of aggregation-prone asparagine repeat-containing proteins. Muralidharan et al. show that PlasmodiumHsp110 protein potently prevents aggregation of asparagine-rich proteins, thereby allowing the parasite to survive febrile episodes.
- Vasant Muralidharan
- , Anna Oksman
- & Daniel E. Goldberg
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Cooperation between different RNA virus genomes produces a new phenotype
RNA viruses are known to rapidly evolve new features through errors in replication and reshuffling of genomic segments. These authors report another strategy used by the measles virus to improve infectivity; the cooperation between wild-type and mutant fusion proteins in the same viral particle.
- Yuta Shirogane
- , Shumpei Watanabe
- & Yusuke Yanagi
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Competition–colonization dynamics in experimental bacterial metacommunities
Species coexistence can be explained by the competition–colonization trade-off theory. Here, Livingston et al. illustrate this theory in a metacommunity experiment using two bacterial strains, finding a negative correlation between diversity and productivity when scaled to full metacommunities.
- George Livingston
- , Miguel Matias
- & Nicolas Mouquet
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| Open AccessSymptomatic atherosclerosis is associated with an altered gut metagenome
The gut microbiota has emerged as an environmental factor that can influence the development of obesity and diabetes. Here, Karlsson et al. report compositional and functional alterations of the gut metagenome in patients with symptomatic atherosclerosis.
- Fredrik H. Karlsson
- , Frida Fåk
- & Jens Nielsen
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| Open AccessFactors determining the occurrence of submicroscopic malaria infections and their relevance for control
Malaria can persist at levels that escape detection by standard microscopy, but can be detected by PCR. Okell et al.now show that rates of submicroscopic infection can be predicted using more widely available microscopy data, and are most epidemiologically significant in areas with low malaria transmission.
- Lucy C. Okell
- , Teun Bousema
- & Chris J. Drakeley
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Warming and nitrogen deposition lessen microbial residue contribution to soil carbon pool
Microbes appear to play an important role in carbon sequestration. Here, the composition of microbial residues in a California grassland with elevated carbon dioxide, warming and nitrogen deposition reveals that warming and nitrogen deposition can both alter the fraction of carbon derived from microbes in soils.
- Chao Liang
- & Teri C. Balser
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Chimpanzees and humans harbour compositionally similar gut enterotypes
Humans tend to adopt one of a limited number of different bacterial community structures in the gut, known as enterotypes. Moeller et al.now show that these microbial fingerprints are conserved in chimpanzees, and that individuals can switch between enterotypes over periods of several years.
- Andrew H. Moeller
- , Patrick H. Degnan
- & Howard Ochman
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Virtual metagenome reconstruction from 16S rRNA gene sequences
Large-scale sequencing techniques have helped to understand the genetic diversity of little-known microbial communities. These authors demonstrate a cheaper alternative to direct sequencing—the construction of virtual metagenomes using gel electrophoresis and related genome sequences.
- Shujiro Okuda
- , Yuki Tsuchiya
- & Hisao Morisaki
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Tyrosine sulfation in a Gram-negative bacterium
The sulfation of protein tyrosine residues is a common post-translational modification in eukaryotes. Here, Han et al.show that the protein RaxST, produced by a plant bacterium, has tyrosine sulfotransferase activity, demonstrating for the first time tyrosine sulfation in prokaryotes.
- Sang-Wook Han
- , Sang-Won Lee
- & Pamela C. Ronald
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Annotation of microsporidian genomes using transcriptional signals
Microsporidia are widespread human parasites, but limited genome annotation has hampered efforts to understand their biology. Peyretailladeet al. use sequence motifs upstream of start codons to annotate or re-annotate microsporidian genomes and find new genes potentially involved in interactions with the host.
- Eric Peyretaillade
- , Nicolas Parisot
- & Pierre Peyret
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Phylogenetic constraints on ecosystem functioning
It has been proposed that phylogenetic diversity can be used as a proxy to estimate functional diversity and to predict ecosystem functioning. Here, the rapid evolutionary response of marine bacteria is used to study the positive effects of evolutionary history and species diversity on ecosystem productivity.
- Dominique Gravel
- , Thomas Bell
- & Nicolas Mouquet
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| Open AccessA multi-omic map of the lipid-producing yeast Rhodosporidium toruloides
The ability of oleaginous fungi to produce lipids for biofuels remains untapped, in part due to a lack of genetic information required to engineer industrial strains. Zhuet al. present the genome of R. toruloides, and identify transcriptomic and proteomic changes associated with lipid production.
- Zhiwei Zhu
- , Sufang Zhang
- & Zongbao K. Zhao
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| Open AccessStructure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing
Sodium-gated ion channels open and close in response to the flow of ions. Here, McCusker et al.report the open structure of a sodium-gated ion channel pore from a bacterial homologue, and show, by comparison with the closed structure, that the movement of a C-terminal helix is sufficient to open the channel.
- Emily C. McCusker
- , Claire Bagnéris
- & B.A. Wallace
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Evidence for methane production by saprotrophic fungi
Methane is an important anthropogenic greenhouse gas and is thought to be produced by industrial processes and prokaryotic methanogenic Archaea. In this study, the saprotrophic fungi,Basidiomycetes, is shown to produce methane in the absence of methanogenic Archaea.
- Katharina Lenhart
- , Michael Bunge
- & Frank Keppler
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Organellar mechanosensitive channels in fission yeast regulate the hypo-osmotic shock response
Mechanosensitive channels are required to sense cell swelling in response to osmotic shock. Nakayamaet al.report that Msy1 and Msy2 are the fission yeast homologues of the bacterial mechanosensitive channel MscS, and are required for regulating intracellular calcium in response to cell swelling.
- Yoshitaka Nakayama
- , Kenjiro Yoshimura
- & Hidetoshi Iida
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Controlled delivery of bioactive molecules into live cells using the bacterial mechanosensitive channel MscL
The bacterial channel protein MscL opens in response to mechanical forces and could be exploited for vesicular-based drug delivery. Doerneret al. show that functional MscL can be expressed in mammalian cells and facilitate the controlled cellular uptake of relatively large, membrane-impermeable bioactive molecules.
- Julia F. Doerner
- , Sebastien Febvay
- & David E. Clapham
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| Open AccessMolecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system
The clustered regularly interspaced short palindromic repeats (CRISPR) system protects prokaryotes from foreign DNA. Here, bacteriophage DNA containing mutations that can circumvent this response are shown to be incorporated into the CRISPR locus, allowing bacteria to remember previous infections in an adaptive manner.
- Kirill A. Datsenko
- , Ksenia Pougach
- & Ekaterina Semenova
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| Open AccessGenome sequence of the model medicinal mushroom Ganoderma lucidum
Ganoderma lucidumis a macrofungus in traditional Chinese medicine known to produce different bioactive compounds. In this study, the genome ofG. lucidumis sequenced, making this organism a potential model system for future studies of secondary metabolic pathways and their regulation in medicinal fungi.
- Shilin Chen
- , Jiang Xu
- & Chao Sun
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Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription
How DNA cytosine methylation affects gene expression inEscherichia coli is poorly understood. Here, the first genome-wide study of cytosine methylation in E. coliat single-base resolution reveals that cytosine methylation controls the expression of genes during the stationary growth phase.
- Christina Kahramanoglou
- , Ana I. Prieto
- & Aswin S.N. Seshasayee
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| Open AccessContrasting arbuscular mycorrhizal responses of vascular and non-vascular plants to a simulated Palaeozoic CO2 decline
Vascular plants with root systems evolved in the mid-Palaeozoic with symbiotic fungi. Fieldet al. show that in contrast to non-vascular plants lacking roots, the efficiency of plant–fungal symbiosis increased for vascular plants with root systems as carbon dioxide levels declined in the mid-Palaeozoic.
- Katie J. Field
- , Duncan D. Cameron
- & David J. Beerling
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Adaptive mutations in NEP compensate for defective H5N1 RNA replication in cultured human cells
Adaptive mutations in the avian influenza virus permit replication in mammals but how these mutations enable this effect is unclear. In this study, mutations found in the nuclear export protein of human isolates of H5N1 are shown to enhance the replication of viral RNA in human cells in culture.
- Benjamin Mänz
- , Linda Brunotte
- & Martin Schwemmle
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| Open AccessThe C-terminal helical bundle of the tetrameric prokaryotic sodium channel accelerates the inactivation rate
Many channels have cytosolic domains which regulate channel function. Irieet al. show that the cytosolic C-terminal region of NavSulP, a prokaryotic voltage-gated sodium channel, forms a four-helix bundle which stabilises the tetrameric channel and accelerates channel inactivation.
- Katsumasa Irie
- , Takushi Shimomura
- & Yoshinori Fujiyoshi
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