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Nature Microbiology

Christien P Laber, Jonathan E Hunter, Filipa Carvalho, James R Collins, Elias J Hunter, Brittany M Schieler, Emmanuel Boss, Kuldeep More, Miguel Frada, Kimberlee Thamatrakoln, Christopher M Brown, Liti Haramaty, Justin Ossolinski, Helen Fredricks, Jozef I Nissimov, Rebecca Vandzura, Uri Sheyn, Yoav Lehahn, Robert J Chant, Ana M Martins, Marco J L Coolen, Assaf Vardi, Giacomo R DiTullio, Benjamin A S Van Mooy, Kay D Bidle
Marine phytoplankton account for approximately half of global primary productivity1 , making their fate an important driver of the marine carbon cycle. Viruses are thought to recycle more than one-quarter of oceanic photosynthetically fixed organic carbon2 , which can stimulate nutrient regeneration, primary production and upper ocean respiration2 via lytic infection and the 'virus shunt'. Ultimately, this limits the trophic transfer of carbon and energy to both higher food webs and the deep ocean2 . Using imagery taken by the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard the Aqua satellite, along with a suite of diagnostic lipid- and gene-based molecular biomarkers, in situ optical sensors and sediment traps, we show that Coccolithovirus infections of mesoscale (~100 km) Emiliania huxleyi blooms in the North Atlantic are coupled with particle aggregation, high zooplankton grazing and greater downward vertical fluxes of both particulate organic and particulate inorganic carbon from the upper mixed layer...
March 12, 2018: Nature Microbiology
Daniel R Garza, Marcel C van Verk, Martijn A Huynen, Bas E Dutilh
The environmental metabolome and metabolic potential of microorganisms are dominant and essential factors shaping microbial community composition. Recent advances in genome annotation and systems biology now allow us to semiautomatically reconstruct genome-scale metabolic models (GSMMs) of microorganisms based on their genome sequence1 . Next, growth of these models in a defined metabolic environment can be predicted in silico, mechanistically linking the metabolic fluxes of individual microbial populations to the community dynamics...
March 12, 2018: Nature Microbiology
Jonathan J Knowlton, Isabel Fernández de Castro, Alison W Ashbrook, Daniel R Gestaut, Paula F Zamora, Joshua A Bauer, J Craig Forrest, Judith Frydman, Cristina Risco, Terence S Dermody
Viruses are molecular machines sustained through a life cycle that requires replication within host cells. Throughout the infectious cycle, viral and cellular components interact to advance the multistep process required to produce progeny virions. Despite progress made in understanding the virus-host protein interactome, much remains to be discovered about the cellular factors that function during infection, especially those operating at terminal steps in replication. In an RNA interference screen, we identified the eukaryotic chaperonin T-complex protein-1 (TCP-1) ring complex (TRiC; also called CCT for chaperonin containing TCP-1) as a cellular factor required for late events in the replication of mammalian reovirus...
March 12, 2018: Nature Microbiology
James A Thomas, Michele S Y Tan, Claudine Bisson, Aaron Borg, Trishant R Umrekar, Fiona Hackett, Victoria L Hale, Gema Vizcay-Barrena, Roland A Fleck, Ambrosius P Snijders, Helen R Saibil, Michael J Blackman
In the version of this Letter originally published, Michele S. Y. Tan was incorrectly listed as Michele Y. S. Tan due to a technical error. This has now been amended in all online versions of the Letter.
March 6, 2018: Nature Microbiology
Fei He, Yuvaraj Bhoobalan-Chitty, Lan B Van, Anders L Kjeldsen, Matteo Dedola, Kira S Makarova, Eugene V Koonin, Ditlev E Brodersen, Xu Peng
Viruses employ a range of strategies to counteract the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas), including mutational escape and physical blocking of enzymatic function using anti-CRISPR proteins (Acrs). Acrs have been found in many bacteriophages but so far not in archaeal viruses, despite the near ubiquity of CRISPR-Cas systems in archaea. Here, we report the functional and structural characterization of two archaeal Acrs from the lytic rudiviruses, SIRV2 and SIRV3...
March 5, 2018: Nature Microbiology
Andrew R J Curson, Beth T Williams, Benjamin J Pinchbeck, Leanne P Sims, Ana Bermejo Martínez, Peter Paolo L Rivera, Deepak Kumaresan, Elena Mercadé, Lewis G Spurgin, Ornella Carrión, Simon Moxon, Rose Ann Cattolico, Unnikrishnan Kuzhiumparambil, Paul Guagliardo, Peta L Clode, Jean-Baptiste Raina, Jonathan D Todd
Dimethylsulfoniopropionate (DMSP) is a globally important organosulfur molecule and the major precursor for dimethyl sulfide. These compounds are important info-chemicals, key nutrients for marine microorganisms, and are involved in global sulfur cycling, atmospheric chemistry and cloud formation1-3 . DMSP production was thought to be confined to eukaryotes, but heterotrophic bacteria can also produce DMSP through the pathway used by most phytoplankton4 , and the DsyB enzyme catalysing the key step of this pathway in bacteria was recently identified5 ...
February 26, 2018: Nature Microbiology
Kaitlyn D LaCourse, S Brook Peterson, Hemantha D Kulasekara, Matthew C Radey, Jungyun Kim, Joseph D Mougous
Bacteria in polymicrobial habitats contend with a persistent barrage of competitors, often under rapidly changing environmental conditions1 . The direct antagonism of competitor cells is thus an important bacterial survival strategy2 . Towards this end, many bacterial species employ an arsenal of antimicrobial effectors with multiple activities; however, the benefits conferred by the simultaneous deployment of diverse toxins are unknown. Here we show that the multiple effectors delivered to competitor bacteria by the type VI secretion system (T6SS) of Pseudomonas aeruginosa display conditional efficacy and act synergistically...
February 19, 2018: Nature Microbiology
James A Thomas, Michele Y S Tan, Claudine Bisson, Aaron Borg, Trishant R Umrekar, Fiona Hackett, Victoria L Hale, Gema Vizcay-Barrena, Roland A Fleck, Ambrosius P Snijders, Helen R Saibil, Michael J Blackman
Malaria parasites replicate within a parasitophorous vacuole in red blood cells (RBCs). Progeny merozoites egress upon rupture of first the parasitophorous vacuole membrane (PVM), then poration and rupture of the RBC membrane (RBCM). Egress is protease-dependent1 , but none of the effector molecules that mediate membrane rupture have been identified and it is unknown how sequential rupture of the two membranes is controlled. Minutes before egress, the parasite serine protease SUB1 is discharged into the parasitophorous vacuole2-6 where it cleaves multiple substrates2,5,7-9 including SERA6, a putative cysteine protease10-12 ...
February 19, 2018: Nature Microbiology
Paul I Costea, Falk Hildebrand, Manimozhiyan Arumugam, Fredrik Bäckhed, Martin J Blaser, Frederic D Bushman, Willem M de Vos, S Dusko Ehrlich, Claire M Fraser, Masahira Hattori, Curtis Huttenhower, Ian B Jeffery, Dan Knights, James D Lewis, Ruth E Ley, Howard Ochman, Paul W O'Toole, Christopher Quince, David A Relman, Fergus Shanahan, Shinichi Sunagawa, Jun Wang, George M Weinstock, Gary D Wu, Georg Zeller, Liping Zhao, Jeroen Raes, Rob Knight, Peer Bork
In the version of this Perspective originally published, the first and last name of co-author Manimozhiyan Arumugam were switched. This has now been corrected in all versions of the Perspective.
February 13, 2018: Nature Microbiology
Marc Swidergall, Norma V Solis, Michail S Lionakis, Scott G Filler
In the version of this Article originally published, technical problems led to errors in Figs. 2d and 5b. In the western blot panel in Fig. 2d, actin bands were misaligned at the bottom of the image and did not line up with the other bands in the panel; the corrected figure is shown below. In Fig. 5b, the upper right panel had an incorrect title of 'CXCL3/KC'; it should have instead been 'CXCL1/KC'. These errors have now been corrected in all versions of the Article.
February 13, 2018: Nature Microbiology
Bradley M Hover, Seong-Hwan Kim, Micah Katz, Zachary Charlop-Powers, Jeremy G Owen, Melinda A Ternei, Jeffrey Maniko, Andreia B Estrela, Henrik Molina, Steven Park, David S Perlin, Sean F Brady
Despite the wide availability of antibiotics, infectious diseases remain a leading cause of death worldwide1 . In the absence of new therapies, mortality rates due to untreatable infections are predicted to rise more than tenfold by 2050. Natural products (NPs) made by cultured bacteria have been a major source of clinically useful antibiotics. In spite of decades of productivity, the use of bacteria in the search for new antibiotics was largely abandoned due to high rediscovery rates2,3 . As only a fraction of bacterial diversity is regularly cultivated in the laboratory and just a fraction of the chemistries encoded by cultured bacteria are detected in fermentation experiments, most bacterial NPs remain hidden in the global microbiome...
February 12, 2018: Nature Microbiology
Laurent Dortet, Charlotte Lombardi, François Cretin, Andréa Dessen, Alain Filloux
Recent studies highlight that bacterial pathogens can reprogram target cells by influencing epigenetic factors. The type III secretion system (T3SS) is a bacterial nanomachine that resembles a syringe on the bacterial surface. The T3SS 'needle' delivers translocon proteins into eukaryotic cell membranes, subsequently allowing injection of bacterial effectors into the cytosol. Here we show that Pseudomonas aeruginosa induces early T3SS-dependent dephosphorylation and deacetylation of histone H3 in eukaryotic cells...
February 5, 2018: Nature Microbiology
Satomi Banno, Keiji Nishida, Takayuki Arazoe, Hitoshi Mitsunobu, Akihiko Kondo
In eukaryotes, the CRISPR-Cas9 system has now been widely used as a revolutionary genome engineering tool1, 2. However, in prokaryotes, the use of nuclease-mediated genome editing tools has been limited to negative selection for the already modified cells because of its lethality3, 4. Here, we report on deaminase-mediated targeted nucleotide editing (Target-AID) 5 adopted in Escherichia coli. Cytidine deaminase PmCDA1 fused to the nuclease-deficient CRISPR-Cas9 system achieved specific point mutagenesis at the target sites in E...
February 5, 2018: Nature Microbiology
Juliane Behler, Kundan Sharma, Viktoria Reimann, Annegret Wilde, Henning Urlaub, Wolfgang R Hess
Specialized RNA endonucleases for the maturation of clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNAs (crRNAs) are critical in CRISPR-CRISPR-associated protein (Cas) defence mechanisms. The Cas6 and Cas5d enzymes are the RNA endonucleases in many class 1 CRISPR-Cas systems. In some class 2 systems, maturation and effector functions are combined within a single enzyme or maturation proceeds through the combined actions of RNase III and trans-activating CRISPR RNAs (tracrRNAs). Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp...
February 5, 2018: Nature Microbiology
Jian Chen, Yi-Feng Yang, Yu Yang, Peng Zou, Jun Chen, Yongquan He, Sai-Lan Shui, Yan-Ru Cui, Ru Bai, Ya-Jun Liang, Yunwen Hu, Biao Jiang, Lu Lu, Xiaoyan Zhang, Jia Liu, Jianqing Xu
Zika virus (ZIKV) is associated with neonatal microcephaly and Guillain-Barré syndrome1,2. While progress has been made in understanding the causal link between ZIKV infection and microcephaly3-9, the life cycle and pathogenesis of ZIKV are less well understood. In particular, there are conflicting reports on the role of AXL, a TAM family kinase receptor that was initially described as the entry receptor for ZIKV10-22. Here, we show that while genetic ablation of AXL protected primary human astrocytes and astrocytoma cell lines from ZIKV infection, AXL knockout did not block the entry of ZIKV...
January 29, 2018: Nature Microbiology
Jeff Nivala, Seth L Shipman, George M Church
The adaptation phase of CRISPR-Cas immunity depends on the precise integration of short segments of foreign DNA (spacers) into a specific genomic location within the CRISPR locus by the Cas1-Cas2 integration complex. Although off-target spacer integration outside of canonical CRISPR arrays has been described in vitro, no evidence of non-specific integration activity has been found in vivo. Here, we show that non-canonical off-target integrations can occur within bacterial chromosomes at locations that resemble the native CRISPR locus by characterizing hundreds of off-target integration locations within Escherichia coli...
January 29, 2018: Nature Microbiology
Alexander J Probst, Bethany Ladd, Jessica K Jarett, David E Geller-McGrath, Christian M K Sieber, Joanne B Emerson, Karthik Anantharaman, Brian C Thomas, Rex R Malmstrom, Michaela Stieglmeier, Andreas Klingl, Tanja Woyke, M Cathryn Ryan, Jillian F Banfield
An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths...
January 29, 2018: Nature Microbiology
Xiaodi Qiu, Yingfeng Lei, Pan Yang, Qiang Gao, Nan Wang, Lei Cao, Shuai Yuan, Xiaofang Huang, Yongqiang Deng, Wenyu Ma, Tianbing Ding, Fanglin Zhang, Xingan Wu, Junjie Hu, Shan-Lu Liu, Chengfeng Qin, Xiangxi Wang, Zhikai Xu, Zihe Rao
Japanese encephalitis virus (JEV), closely related to dengue, Zika, yellow fever and West Nile viruses, remains neglected and not well characterized 1 . JEV is the leading causative agent of encephalitis, and is responsible for thousands of deaths each year in Asia. Humoral immunity is essential for protecting against flavivirus infections and passive immunization has been demonstrated to be effective in curing disease2,3. Here, we demonstrate that JEV-specific monoclonal antibodies, 2F2 and 2H4, block attachment of the virus to its receptor and also prevent fusion of the virus...
January 29, 2018: Nature Microbiology
Alexey Gurevich, Alla Mikheenko, Alexander Shlemov, Anton Korobeynikov, Hosein Mohimani, Pavel A Pevzner
Peptidic natural products (PNPs) include many antibiotics and other bioactive compounds. While the recent launch of the Global Natural Products Social (GNPS) molecular networking infrastructure is transforming PNP discovery into a high-throughput technology, PNP identification algorithms are needed to realize the potential of the GNPS project. GNPS relies on the assumption that each connected component of a molecular network (representing related metabolites) illuminates the 'dark matter of metabolomics' as long as it contains a known metabolite present in a database...
January 22, 2018: Nature Microbiology
Sebastian Zoll, Harriet Lane-Serff, Shahid Mehmood, Jonathan Schneider, Carol V Robinson, Mark Carrington, Matthew K Higgins
Only two trypanosome subspecies are able to cause human African trypanosomiasis. To establish an infection in human blood, they must overcome the innate immune system by resisting the toxic effects of trypanolytic factor 1 and trypanolytic factor 2 (refs. 1,2). These lipoprotein complexes contain an active, pore-forming component, apolipoprotein L1 (ApoL1), that causes trypanosome cell death 3 . One of the two human-infective subspecies, Trypanosoma brucei rhodesiense, differs from non-infective trypanosomes solely by the presence of the serum resistance-associated protein, which binds directly to ApoL1 and blocks its pore-forming capacity3-5...
January 22, 2018: Nature Microbiology
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