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Nature Microbiology

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https://www.readbyqxmd.com/read/29133884/epha2-is-an-epithelial-cell-pattern-recognition-receptor-for-fungal-%C3%AE-glucans
#1
Marc Swidergall, Norma V Solis, Michail S Lionakis, Scott G Filler
Oral epithelial cells discriminate between pathogenic and non-pathogenic stimuli, and only induce an inflammatory response when they are exposed to high levels of a potentially harmful microorganism. The pattern recognition receptors (PRRs) in epithelial cells that mediate this differential response are poorly understood. Here, we demonstrate that the ephrin type-A receptor 2 (EphA2) is an oral epithelial cell PRR that binds to exposed β-glucans on the surface of the fungal pathogen Candida albicans. Binding of C...
November 13, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29133883/pseudomonas-aeruginosa-defends-against-phages-through-type-iv-pilus-glycosylation
#2
Hanjeong Harvey, Joseph Bondy-Denomy, Hélène Marquis, Kristina M Sztanko, Alan R Davidson, Lori L Burrows
Since phages present a major challenge to survival in most environments, bacteria express a battery of anti-phage defences including CRISPR-Cas, restriction-modification and abortive infection systems (1-4) . Such strategies are effective, but the phage genome-which encodes potentially inhibitory gene products-is still allowed to enter the cell. The safest way to preclude phage infection is to block initial phage adsorption to the cell. Here, we describe a cell-surface modification that blocks infection by certain phages...
November 13, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29133882/discovery-of-an-expansive-bacteriophage-family-that-includes-the-most-abundant-viruses-from-the-human-gut
#3
Natalya Yutin, Kira S Makarova, Ayal B Gussow, Mart Krupovic, Anca Segall, Robert A Edwards, Eugene V Koonin
Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery (1-3) . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome (4) . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study...
November 13, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29109479/viral-and-cellular-n-6-methyladenosine-and-n-6-2-o-dimethyladenosine-epitranscriptomes-in-the-kshv-life-cycle
#4
Brandon Tan, Hui Liu, Songyao Zhang, Suzane Ramos da Silva, Lin Zhang, Jia Meng, Xiaodong Cui, Hongfeng Yuan, Océane Sorel, Shao-Wu Zhang, Yufei Huang, Shou-Jiang Gao
N(6)-methyladenosine (m(6)A) and N(6),2'-O-dimethyladenosine (m(6)Am) modifications (m(6)A/m) of messenger RNA mediate diverse cellular functions. Oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV) has latent and lytic replication phases that are essential for the development of KSHV-associated cancers. To date, the role of m(6)A/m in KSHV replication and tumorigenesis is unclear. Here, we provide mechanistic insights by examining the viral and cellular m(6)A/m epitranscriptomes during KSHV latent and lytic infection...
November 6, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29109478/a-bacterial-pioneer-produces-cellulase-complexes-that-persist-through-community-succession
#5
Sebastian Kolinko, Yu-Wei Wu, Firehiwot Tachea, Evelyn Denzel, Jennifer Hiras, Raphael Gabriel, Nora Bäcker, Leanne Jade G Chan, Stephanie A Eichorst, Dario Frey, Qiushi Chen, Parastoo Azadi, Paul D Adams, Todd R Pray, Deepti Tanjore, Christopher J Petzold, John M Gladden, Blake A Simmons, Steven W Singer
Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs)...
November 6, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29109477/plasmodium-uis3-sequesters-host-lc3-to-avoid-elimination-by-autophagy-in-hepatocytes
#6
Eliana Real, Lénia Rodrigues, Ghislain G Cabal, Francisco J Enguita, Liliana Mancio-Silva, João Mello-Vieira, Wandy Beatty, Iset M Vera, Vanessa Zuzarte-Luís, Tiago N Figueira, Gunnar R Mair, Maria M Mota
The causative agent of malaria, Plasmodium, replicates inside a membrane-bound parasitophorous vacuole (PV), which shields this intracellular parasite from the cytosol of the host cell (1) . One common threat for intracellular pathogens is the homeostatic process of autophagy, through which cells capture unwanted intracellular material for lysosomal degradation (2) . During the liver stage of a malaria infection, Plasmodium parasites are targeted by the autophagy machinery of the host cell, and the PV membrane (PVM) becomes decorated with several autophagy markers, including LC3 (microtubule-associated protein 1 light chain 3) (3,4) ...
November 6, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29109476/the-major-targets-of-acute-norovirus-infection-are-immune-cells-in-the-gut-associated-lymphoid-tissue
#7
Katrina R Grau, Alexa N Roth, Shu Zhu, Abel Hernandez, Natacha Colliou, Bayli B DiVita, Drake T Philip, Cara Riffe, Benoit Giasson, Shannon M Wallet, Mansour Mohamadzadeh, Stephanie M Karst
Noroviruses are the leading cause of food-borne gastroenteritis outbreaks and childhood diarrhoea globally, estimated to be responsible for 200,000 deaths in children each year (1-4) . Thus, reducing norovirus-associated disease is a critical priority. Development of vaccines and therapeutics has been hindered by the limited understanding of basic norovirus pathogenesis and cell tropism. While macrophages, dendritic cells, B cells and stem-cell-derived enteroids can all support infection of certain noroviruses in vitro (5-7) , efforts to define in vivo norovirus cell tropism have generated conflicting results...
November 6, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29093550/author-correction-evolution-of-host-adaptation-in-the-salmonella-typhoid-toxin
#8
Xiang Gao, Lingquan Deng, Gabrielle Stack, Hai Yu, Xi Chen, Yuko Naito-Matsui, Ajit Varki, Jorge E Galán
The original version of this Letter has been modified in the abstract and main text to better reflect the distribution of Neu5Ac sialoglycans in humans. Additionally, co-author Lingquan Deng's present address has been further clarified.
November 1, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29085077/quantification-of-diverse-virus-populations-in-the-environment-using-the-polony-method
#9
Nava Baran, Svetlana Goldin, Ilia Maidanik, Debbie Lindell
Viruses are globally abundant and extremely diverse in their genetic make-up and in the hosts they infect. Although they influence the abundance, diversity and evolution of their hosts, current methods are inadequate for gaining a quantitative understanding of their impact on these processes. Here we report the adaptation of the solid-phase single-molecule PCR polony method for the quantification of taxonomically relevant groups of diverse viruses. Using T7-like cyanophages as our model, we found the polony method to be far superior to regular quantitative PCR methods and droplet digital PCR when degenerate primers were used to encompass the group's diversity...
October 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29085076/disarm-is-a-widespread-bacterial-defence-system-with-broad-anti-phage-activities
#10
Gal Ofir, Sarah Melamed, Hila Sberro, Zohar Mukamel, Shahar Silverman, Gilad Yaakov, Shany Doron, Rotem Sorek
The evolutionary pressure imposed by phage predation on bacteria and archaea has resulted in the development of effective anti-phage defence mechanisms, including restriction-modification and CRISPR-Cas systems. Here, we report on a new defence system, DISARM (defence island system associated with restriction-modification), which is widespread in bacteria and archaea. DISARM is composed of five genes, including a DNA methylase and four other genes annotated as a helicase domain, a phospholipase D (PLD) domain, a DUF1998 domain and a gene of unknown function...
October 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29085075/dynamic-biofilm-architecture-confers-individual-and-collective-mechanisms-of-viral-protection
#11
Lucia Vidakovic, Praveen K Singh, Raimo Hartmann, Carey D Nadell, Knut Drescher
In nature, bacteria primarily live in surface-attached, multicellular communities, termed biofilms (1-6) . In medical settings, biofilms cause devastating damage during chronic and acute infections; indeed, bacteria are often viewed as agents of human disease (7) . However, bacteria themselves suffer from diseases, most notably in the form of viral pathogens termed bacteriophages (8-12) , which are the most abundant replicating entities on Earth. Phage-biofilm encounters are undoubtedly common in the environment, but the mechanisms that determine the outcome of these encounters are unknown...
October 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29062088/a-crispr-cas9-based-gene-drive-platform-for-genetic-interaction-analysis-in-candida-albicans
#12
Rebecca S Shapiro, Alejandro Chavez, Caroline B M Porter, Meagan Hamblin, Christian S Kaas, James E DiCarlo, Guisheng Zeng, Xiaoli Xu, Alexey V Revtovich, Natalia V Kirienko, Yue Wang, George M Church, James J Collins
Candida albicans is the leading cause of fungal infections; yet, complex genetic interaction analysis remains cumbersome in this diploid pathogen. Here, we developed a CRISPR-Cas9-based 'gene drive array' platform to facilitate efficient genetic analysis in C. albicans. In our system, a modified DNA donor molecule acts as a selfish genetic element, replaces the targeted site and propagates to replace additional wild-type loci. Using mating-competent C. albicans haploids, each carrying a different gene drive disabling a gene of interest, we are able to create diploid strains that are homozygous double-deletion mutants...
October 23, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29062087/predicted-microbial-secretomes-and-their-target-substrates-in-marine-sediment
#13
William D Orsi, Thomas A Richards, Warren R Francis
Scientific drilling has identified a biosphere in marine sediments (1) , which contain many uncultivated microbial groups known only by their DNA sequences (2-4) . Recycling of organic matter in sediments is an important component of biogeochemical cycles because marine sediments are critical for long-term carbon storage (5) . Turnover of carbon is hypothesized to be driven by the secretion of enzymes by microbial organisms (5-7) , which act to break down macromolecules into constitutive monomers that can be transported into cells...
October 23, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29057995/author-correction-surface-properties-of-sar11-bacteria-facilitate-grazing-avoidance
#14
Ayelet Dadon-Pilosof, Keats R Conley, Yuval Jacobi, Markus Haber, Fabien Lombard, Kelly R Sutherland, Laura Steindler, Yaron Tikochinski, Michael Richter, Frank Oliver Glöckner, Marcelino T Suzuki, Nyree J West, Amatzia Genin, Gitai Yahel
In the version of this Letter originally published, the authors incorrectly stated that primers 28F-519R were reported in ref. 54 to underestimate the abundance of SAR11 in the ocean. This statement has now been amended in all versions of the Letter.
October 20, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29038467/self-sensing-in-bacillus-subtilis-quorum-sensing-systems
#15
Tasneem Bareia, Shaul Pollak, Avigdor Eldar
Bacterial cell-cell signalling, or quorum sensing, is characterized by the secretion and groupwide detection of small diffusible signal molecules called autoinducers. This mechanism allows cells to coordinate their behaviour in a density-dependent manner. A quorum-sensing cell may directly respond to the autoinducers it produces in a cell-autonomous and quorum-independent manner, but the strength of this self-sensing effect and its impact on bacterial physiology are unclear. Here, we explore the existence and impact of self-sensing in the Bacillus subtilis ComQXP and Rap-Phr quorum-sensing systems...
October 16, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29038444/structural-basis-for-maintenance-of-bacterial-outer-membrane-lipid-asymmetry
#16
Javier Abellón-Ruiz, Shreyas S Kaptan, Arnaud Baslé, Beatrice Claudi, Dirk Bumann, Ulrich Kleinekathöfer, Bert van den Berg
The Gram-negative bacterial outer membrane (OM) is a unique bilayer that forms an efficient permeation barrier to protect the cell from noxious compounds (1)(,)(2) . The defining characteristic of the OM is lipid asymmetry, with phospholipids comprising the inner leaflet and lipopolysaccharides comprising the outer leaflet (1-3) . This asymmetry is maintained by the Mla pathway, a six-component system that is widespread in Gram-negative bacteria and is thought to mediate retrograde transport of misplaced phospholipids from the outer leaflet of the OM to the cytoplasmic membrane (4) ...
October 16, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28993624/structure-of-the-calcium-dependent-type-2-secretion-pseudopilus
#17
Aracelys López-Castilla, Jenny-Lee Thomassin, Benjamin Bardiaux, Weili Zheng, Mangayarkarasi Nivaskumar, Xiong Yu, Michael Nilges, Edward H Egelman, Nadia Izadi-Pruneyre, Olivera Francetic
Many Gram-negative bacteria use type 2 secretion systems (T2SSs) to secrete proteins involved in virulence and adaptation. Transport of folded proteins via T2SS nanomachines requires the assembly of inner membrane-anchored fibres called pseudopili. Although efficient pseudopilus assembly is essential for protein secretion, structure-based functional analyses are required to unravel the mechanistic link between these processes. Here, we report an atomic model for a T2SS pseudopilus from Klebsiella oxytoca, obtained by fitting the NMR structure of its calcium-bound subunit PulG into the ~5-Å-resolution cryo-electron microscopy reconstruction of assembled fibres...
October 9, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28993620/d-alanylation-of-teichoic-acids-contributes-to-lactobacillus-plantarum-mediated-drosophila-growth-during-chronic-undernutrition
#18
Renata C Matos, Martin Schwarzer, Hugo Gervais, Pascal Courtin, Pauline Joncour, Benjamin Gillet, Dali Ma, Anne-Laure Bulteau, Maria Elena Martino, Sandrine Hughes, Marie-Pierre Chapot-Chartier, François Leulier
The microbial environment influences animal physiology. However, the underlying molecular mechanisms of such functional interactions are largely undefined. Previously, we showed that during chronic undernutrition, strains of Lactobacillus plantarum, a major commensal partner of Drosophila, promote host juvenile growth and maturation partly through enhanced expression of intestinal peptidases. By screening a transposon insertion library of Lactobacillus plantarum in gnotobiotic Drosophila larvae, we identify a bacterial cell-wall-modifying machinery encoded by the pbpX2-dlt operon that is critical to enhance host digestive capabilities and promote animal growth and maturation...
October 9, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28993611/natural-product-diversity-associated-with-the-nematode-symbionts-photorhabdus-and-xenorhabdus
#19
Nicholas J Tobias, Hendrik Wolff, Bardya Djahanschiri, Florian Grundmann, Max Kronenwerth, Yi-Ming Shi, Svenja Simonyi, Peter Grün, David Shapiro-Ilan, Sacha J Pidot, Timothy P Stinear, Ingo Ebersberger, Helge B Bode
Xenorhabdus and Photorhabdus species dedicate a large amount of resources to the production of specialized metabolites derived from non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS). Both bacteria undergo symbiosis with nematodes, which is followed by an insect pathogenic phase. So far, the molecular basis of this tripartite relationship and the exact roles that individual metabolites and metabolic pathways play have not been well understood. To close this gap, we have significantly expanded the database for comparative genomics studies in these bacteria...
October 9, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28993610/evolution-of-host-adaptation-in-the-salmonella-typhoid-toxin
#20
Xiang Gao, Lingquan Deng, Gabrielle Stack, Hai Yu, Xi Chen, Yuko Naito-Matsui, Ajit Varki, Jorge E Galán
The evolution of virulence traits is central for the emergence or re-emergence of microbial pathogens and for their adaptation to a specific host (1-5) . Typhoid toxin is an essential virulence factor of the human-adapted bacterial pathogen Salmonella Typhi (6,7) , the cause of typhoid fever in humans (8-12) . Typhoid toxin has a unique A2B5 architecture with two covalently linked enzymatic 'A' subunits, PltA and CdtB, associated with a homopentameric 'B' subunit made up of PltB, which has binding specificity for the N-acetylneuraminic acid (Neu5Ac) sialoglycans (6,13) prominently present in humans (14) ...
October 9, 2017: Nature Microbiology
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