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Nature Microbiology

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https://www.readbyqxmd.com/read/28628133/hbv-rna-pre-genome-encodes-specific-motifs-that-mediate-interactions-with-the-viral-core-protein-that-promote-nucleocapsid-assembly
#1
Nikesh Patel, Simon J White, Rebecca F Thompson, Richard Bingham, Eva U Weiß, Daniel P Maskell, Adam Zlotnick, Eric C Dykeman, Roman Tuma, Reidun Twarock, Neil A Ranson, Peter G Stockley
Formation of the hepatitis B virus nucleocapsid is an essential step in the viral lifecycle, but its assembly is not fully understood. We report the discovery of sequence-specific interactions between the viral pre-genome and the hepatitis B core protein that play roles in defining the nucleocapsid assembly pathway. Using RNA SELEX and bioinformatics, we identified multiple regions in the pre-genomic RNA with high affinity for core protein dimers. These RNAs form stem-loops with a conserved loop motif that trigger sequence-specific assembly of virus-like particles (VLPs) at much higher fidelity and yield than in the absence of RNA...
June 19, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28628099/toxoplasma-depends-on-lysosomal-consumption-of-autophagosomes-for-persistent-infection
#2
Manlio Di Cristina, Zhicheng Dou, Matteo Lunghi, Geetha Kannan, My-Hang Huynh, Olivia L McGovern, Tracey L Schultz, Aric J Schultz, Alyssa J Miller, Beth M Hayes, Wouter van der Linden, Carla Emiliani, Matthew Bogyo, Sébastien Besteiro, Isabelle Coppens, Vern B Carruthers
Globally, nearly 2 billion people are infected with the intracellular protozoan Toxoplasma gondii(1). This persistent infection can cause severe disease in immunocompromised people and is epidemiologically linked to major mental illnesses(2) and cognitive impairment(3). There are currently no options for curing this infection. The lack of effective therapeutics is due partly to a poor understanding of the essential pathways that maintain long-term infection. Although it is known that Toxoplasma replicates slowly within intracellular cysts demarcated with a cyst wall, precisely how it sustains itself and remodels organelles in this niche is unknown...
June 19, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28628098/short-chain-alkanes-fuel-mussel-and-sponge-cycloclasticus-symbionts-from-deep-sea-gas-and-oil-seeps
#3
Maxim Rubin-Blum, Chakkiath Paul Antony, Christian Borowski, Lizbeth Sayavedra, Thomas Pape, Heiko Sahling, Gerhard Bohrmann, Manuel Kleiner, Molly C Redmond, David L Valentine, Nicole Dubilier
Cycloclasticus bacteria are ubiquitous in oil-rich regions of the ocean and are known for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). In this study, we describe Cycloclasticus that have established a symbiosis with Bathymodiolus heckerae mussels and poecilosclerid sponges from asphalt-rich, deep-sea oil seeps at Campeche Knolls in the southern Gulf of Mexico. Genomic and transcriptomic analyses revealed that, in contrast to all previously known Cycloclasticus, the symbiotic Cycloclasticus appears to lack the genes needed for PAH degradation...
June 19, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28604710/erratum-conserved-patterns-hidden-within-group-a-streptococcus-m-protein-hypervariability-recognize-human-c4b-binding-protein
#4
Cosmo Z Buffalo, Adrian J Bahn-Suh, Sophia P Hirakis, Tapan Biswas, Rommie E Amaro, Victor Nizet, Partho Ghosh
This corrects the article DOI: 10.1038/nmicrobiol.2016.155.
June 12, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28604700/excess-of-non-conservative-amino-acid-changes-in-marine-bacterioplankton-lineages-with-reduced-genomes
#5
Haiwei Luo, Yongjie Huang, Ramunas Stepanauskas, Jijun Tang
Surface ocean waters are dominated by planktonic bacterial lineages with highly reduced genomes. The best examples are the cyanobacterial genus Prochlorococcus, the alphaproteobacterial clade SAR11 and the gammaproteobacterial clade SAR86, which together represent over 50% of the cells in surface oceans. Several studies have identified signatures of selection on these lineages in today's ocean and have postulated selection as the primary force throughout their evolutionary history. However, massive loss of genomic DNA in these lineages often occurred in the distant past, and the selective pressures underlying these ancient events have not been assessed...
June 12, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28604679/a-stabilized-microbial-ecosystem-of-self-limiting-bacteria-using-synthetic-quorum-regulated-lysis
#6
Spencer R Scott, M Omar Din, Philip Bittihn, Liyang Xiong, Lev S Tsimring, Jeff Hasty
Microbial ecologists are increasingly turning to small, synthesized ecosystems(1-5) as a reductionist tool to probe the complexity of native microbiomes(6,7). Concurrently, synthetic biologists have gone from single-cell gene circuits(8-11) to controlling whole populations using intercellular signalling(12-16). The intersection of these fields is giving rise to new approaches in waste recycling(17), industrial fermentation(18), bioremediation(19) and human health(16,20). These applications share a common challenge(7) well-known in classical ecology(21,22)-stability of an ecosystem cannot arise without mechanisms that prohibit the faster-growing species from eliminating the slower...
June 12, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28581505/a-decade-of-discovery-crispr-functions-and-applications
#7
REVIEW
Rodolphe Barrangou, Philippe Horvath
This year marks the tenth anniversary of the identification of the biological function of CRISPR-Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR-Cas systems has established a novel means of adaptive immunity in bacteria and archaea and deepened our understanding of the interplay between prokaryotes and their environment, and CRISPR-based molecular machines have been repurposed to enable a genome editing revolution. Here, we look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and discuss the related technological applications that have emerged, with a focus on microbiology...
June 5, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28581456/epigenetic-silencing-of-irf1-dysregulates-type-iii-interferon-responses-to-respiratory-virus-infection-in-epithelial-to-mesenchymal-transition
#8
Jun Yang, Bing Tian, Hong Sun, Roberto P Garofalo, Allan R Brasier
Chronic oxidative injury produced by airway disease triggers a transforming growth factor-β (TGF-β)-mediated epigenetic reprogramming known as the epithelial-mesenchymal transition (EMT). We observe that EMT silences protective mucosal interferon (IFN)-I and III production associated with enhanced rhinovirus (RV) and respiratory syncytial virus (RSV) replication. Mesenchymal transitioned cells are defective in inducible interferon regulatory factor 1 (IRF1) expression by occluding RelA and IRF3 access to the promoter...
June 5, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28581455/attenuation-of-rna-viruses-by-redirecting-their-evolution-in-sequence-space
#9
Gonzalo Moratorio, Rasmus Henningsson, Cyril Barbezange, Lucia Carrau, Antonio V Bordería, Hervé Blanc, Stephanie Beaucourt, Enzo Z Poirier, Thomas Vallet, Jeremy Boussier, Bryan C Mounce, Magnus Fontes, Marco Vignuzzi
RNA viruses pose serious threats to human health. Their success relies on their capacity to generate genetic variability and, consequently, on their adaptive potential. We describe a strategy to attenuate RNA viruses by altering their evolutionary potential. We rationally altered the genomes of Coxsackie B3 and influenza A viruses to redirect their evolutionary trajectories towards detrimental regions in sequence space. Specifically, viral genomes were engineered to harbour more serine and leucine codons with nonsense mutation targets: codons that could generate Stop mutations after a single nucleotide substitution...
June 5, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28555641/a-parts-list-for-fungal-cellulosomes-revealed-by-comparative-genomics
#10
Charles H Haitjema, Sean P Gilmore, John K Henske, Kevin V Solomon, Randall de Groot, Alan Kuo, Stephen J Mondo, Asaf A Salamov, Kurt LaButti, Zhiying Zhao, Jennifer Chiniquy, Kerrie Barry, Heather M Brewer, Samuel O Purvine, Aaron T Wright, Matthieu Hainaut, Brigitte Boxma, Theo van Alen, Johannes H P Hackstein, Bernard Henrissat, Scott E Baker, Igor V Grigoriev, Michelle A O'Malley
Cellulosomes are large, multiprotein complexes that tether plant biomass-degrading enzymes together for improved hydrolysis(1). These complexes were first described in anaerobic bacteria, where species-specific dockerin domains mediate the assembly of enzymes onto cohesin motifs interspersed within protein scaffolds(1). The versatile protein assembly mechanism conferred by the bacterial cohesin-dockerin interaction is now a standard design principle for synthetic biology(2,3). For decades, analogous structures have been reported in anaerobic fungi, which are known to assemble by sequence-divergent non-catalytic dockerin domains (NCDDs)(4)...
May 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28555626/discovery-of-extremely-halophilic-methyl-reducing-euryarchaea-provides-insights-into-the-evolutionary-origin-of-methanogenesis
#11
Dimitry Y Sorokin, Kira S Makarova, Ben Abbas, Manuel Ferrer, Peter N Golyshin, Erwin A Galinski, Sergio Ciordia, María Carmen Mena, Alexander Y Merkel, Yuri I Wolf, Mark C M van Loosdrecht, Eugene V Koonin
Methanogenic archaea are major players in the global carbon cycle and in the biotechnology of anaerobic digestion. The phylum Euryarchaeota includes diverse groups of methanogens that are interspersed with non-methanogenic lineages. So far, methanogens inhabiting hypersaline environments have been identified only within the order Methanosarcinales. We report the discovery of a deep phylogenetic lineage of extremophilic methanogens in hypersaline lakes and present analysis of two nearly complete genomes from this group...
May 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28555625/co-infecting-microorganisms-dramatically-alter-pathogen-gene-essentiality-during-polymicrobial-infection
#12
Carolyn B Ibberson, Apollo Stacy, Derek Fleming, Justine L Dees, Kendra Rumbaugh, Michael S Gilmore, Marvin Whiteley
Identifying genes required by pathogens during infection is critical for antimicrobial development. Here, we use a Monte Carlo simulation-based method to analyse high-throughput transposon sequencing data to determine the role of infection site and co-infecting microorganisms on the in vivo 'essential' genome of Staphylococcus aureus. We discovered that co-infection of murine surgical wounds with Pseudomonas aeruginosa results in conversion of ∼25% of the in vivo S. aureus mono-culture essential genes to non-essential...
May 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28555622/zooming-in-on-the-phycosphere-the-ecological-interface-for-phytoplankton-bacteria-relationships
#13
REVIEW
Justin R Seymour, Shady A Amin, Jean-Baptiste Raina, Roman Stocker
By controlling nutrient cycling and biomass production at the base of the food web, interactions between phytoplankton and bacteria represent a fundamental ecological relationship in aquatic environments. Although typically studied over large spatiotemporal scales, emerging evidence indicates that this relationship is often governed by microscale interactions played out within the region immediately surrounding individual phytoplankton cells. This microenvironment, known as the phycosphere, is the planktonic analogue of the rhizosphere in plants...
May 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28540935/a-microbiologist-s-guide-to-the-galaxy
#14
Emily White
No abstract text is available yet for this article.
May 25, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28540930/host-response-cross-fit-t-cells-battle-zika-virus
#15
Matthew Collins, Aravinda de Silva
No abstract text is available yet for this article.
May 25, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28540925/microorganisms-and-ocean-global-change
#16
REVIEW
David A Hutchins, Feixue Fu
The prokaryotic and eukaryotic microorganisms that drive the pelagic ocean's biogeochemical cycles are currently facing an unprecedented set of comprehensive anthropogenic changes. Nearly every important control on marine microbial physiology is currently in flux, including seawater pH, pCO2, temperature, redox chemistry, irradiance and nutrient availability. Here, we examine how microorganisms with key roles in the ocean carbon and nitrogen cycles may respond to these changes in the Earth's largest ecosystem...
May 25, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28540924/structural-biology-mycobacterial-esx-secrets-revealed
#17
Tracy Palmer
No abstract text is available yet for this article.
May 25, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28540923/archaeal-physiology-two-modes-of-a-dna-scissor
#18
Lennart Randau
No abstract text is available yet for this article.
May 25, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28540922/exploring-the-microbial-universe
#19
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
May 25, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28540921/the-path-towards-microbiome-based-metabolite-treatment
#20
Jotham Suez, Eran Elinav
The increasing evidence pointing towards the involvement of the gut microbiome in multiple diseases, as well as its plasticity, renders it a desirable potential therapeutic target. Nevertheless, classical therapies based on the consumption of live probiotic bacteria, or their enrichment by prebiotics, exhibit limited efficacy. Recently, a novel therapeutic approach has been suggested based on metabolites secreted, modulated or degraded by the microbiome. As many of the host-microorganism interactions pertaining to human health are mediated by metabolites, this approach may be able to provide therapeutic efficacy while overcoming caveats of current microbiome-targeting therapies, such as colonization resistance and inter-individual variation in microbial composition...
May 25, 2017: Nature Microbiology
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