Microbiology articles within Nature

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  • Letter |

    Many cellular and virus messenger RNAs are methylated at the 2′-O positions of the 5′ guanosine cap. The role of 2′-O methylation in virus infection has been unclear. These authors show that this form of methylation enables several unrelated viruses to evade the antiviral effects of genes stimulated by type I interferon.

    • Stephane Daffis
    • , Kristy J. Szretter
    •  & Michael S. Diamond

  • Letter |

    Contact-dependent growth inhibition (CDI) through a two-component system was first described in Escherichia coli as a mechanism to inhibit growth of bacterial cells that do not possess this system. Now the widespread occurrence of CDI in bacteria and the molecular basis for some of these interactions have been elucidated. The data suggest that CDI is a common mechanism by which microbes compete with each other in the environment.

    • Stephanie K. Aoki
    • , Elie J. Diner
    •  & David A. Low

  • Article |

    The first crystal structure for an arenavirus nucleoprotein is solved, revealing some new functions. The C-terminal domain has 3′ to 5′ exonuclease activity, and it is confirmed that Lassa virus nucleoprotein is capable of cleaving short RNAs and suppressing virus-induced interferon induction. The N-terminal domain contains a unique cap-binding feature, which has implications for understanding the distinctive cap-snatching mechanism of arenaviruses.

    • Xiaoxuan Qi
    • , Shuiyun Lan
    •  & Changjiang Dong

  • Letter |

    In his study of Brownian motion, Einstein realized that the same random molecular movements characterizing a substance at rest should affect, for example, the drag it opposes to a particle pushed through it. This was later generalized as the fluctuation–response theorem (FRT), but whether and how it may apply to biological systems, which operate far from equilibrium, has remained an open question. Based on the unmatched fine-scale measurements possible in the study of bacterial chemotaxis, it is now revealed that the FRT does apply in this case, and ways to dissect which features in the biochemical network couple its internal states with its responses to external stimuli are suggested.

    • Heungwon Park
    • , William Pontius
    •  & Philippe Cluzel

  • Article |

    tRNAs are synthesized in a premature form that requires trimming of the 5′ and 3′ ends and modification of specific nucleotides. RNase P, a complex containing a long catalytic RNA and a protein cofactor, catalyses the cleavage that generates the mature 5′ end. Here, the structure of RNase P bound to mature tRNAPhe is solved. Recognition of the leader sequence and its mechanism of cleavage is determined by soaking an oligonucleotide corresponding to the premature 5′ end into the crystal.

    • Nicholas J. Reiter
    • , Amy Osterman
    •  & Alfonso Mondragón

  • Letter |

    Insertion of retrovirus genome into host genome to replicate is mediated by a tetramer of the virus-encoded integrase protein. The structure of a related integrase from prototype foamy virus bound to the cleaved viral DNA ends, a complex called the intasome, was previously revealed. These authors solve the structure of the intasome interacting with the target host DNA both before and after it is cleaved, revealing new details of the integration process that may help in designing improved inhibitors of HIV.

    • Goedele N. Maertens
    • , Stephen Hare
    •  & Peter Cherepanov

  • Letter |

    It is thought that rises in atmospheric oxygen concentrations occurred about 2.3 and 0.8 billion years ago, with the latter implicated in the subsequent evolutionary expansion of complex biota. Sulphur isotope fractionation data from an ancient sedimentary succession in Scotland now suggest that the terrestrial environment was already sufficiently oxygenated to support a biota adapted to an oxygen-rich atmosphere about 1.2 billion years ago.

    • John Parnell
    • , Adrian J. Boyce
    •  & Sam Spinks

  • News & Views |

    Many bacteria and archaea protect themselves from viruses and other invasive genomes through a genetic interference pathway. The small RNAs that guide this defence specify the direct cleavage of foreign DNA. See Article p.67

    • Erik J. Sontheimer
    •  & Luciano A. Marraffini

  • News Feature |

    Behind the walls of the J. Craig Venter Institute, Ham Smith and Clyde Hutchison quietly worked to bring a synthetic cell to life.

    • Roberta Kwok

  • Article |

    CRISPR/Cas is a microbial immune system that is known to protect bacteria from virus infection. These authors show that the Streptococcus thermophilus CRISPR/Cas system can prevent both plasmid carriage and phage infection through cleavage of invading double-stranded DNA.

    • Josiane E. Garneau
    • , Marie-Ève Dupuis
    •  & Sylvain Moineau

  • Article
    | Open Access

    Using newly derived genome sequences of 137 marine microbial isolates as well as previously obtained genome and metagenome data, this study presents a functional analysis of picoplankton residing in the ocean's surface layer.

    • Shibu Yooseph
    • , Kenneth H. Nealson
    •  & J. Craig Venter

  • News & Views |

    The crystal structure of a protein channel provides clues about the mechanisms that control the closure of pores found in the epidermis of plant leaves. Excitingly, the protein channel folds in a way never seen before. See Article p.1074

    • Sébastien Thomine
    •  & Hélène Barbier-Brygoo

  • Letter |

    Bacterial chromosomes often carry integrated genetic elements (such as plasmids and prophages) that contribute to the evolutionary fitness of the host bacterium. In Vibrio cholerae, a prophage encodes cholera toxin. Here, the events that led to the acquisition of phage DNA have been reconstructed, revealing the cooperative interactions between multiple filamentous phages that contributed to the emergence of virulent V. cholerae strains.

    • Faizule Hassan
    • , M. Kamruzzaman
    •  & Shah M. Faruque

  • Letter |

    Entry of herpes simplex virus-1 into cells requires cellular receptors for both envelope glycoprotein B and envelope glycoprotein D. These authors show that the interaction of non-muscle myosin heavy chain IIA with envelope glycoprotein B is important for entry of herpes simplex virus-1.

    • Jun Arii
    • , Hideo Goto
    •  & Yasushi Kawaguchi

  • Letter |

    During infection, Bacillus anthracis secretes two potent toxins called lethal factor and oedema factor. Using Drosophila melanogaster as a model system, these authors show that these toxins interact with the Rab11/Sec15 exocyst, which is involved in endocytic recycling. This interaction may explain vascular leakage during infection.

    • Annabel Guichard
    • , Shauna M. McGillivray
    •  & Ethan Bier

  • News & Views |

    The bacterium Clostridium difficile can cause life-threatening human disease. The question is which of the organism's two toxins is the more crucial to its pathogenicity. The answer is one or the other, or both. See Letter p.711

    • Jimmy D. Ballard

  • Letter |

    During immune responses, antibodies are selected for their ability to bind to foreign antigens with high affinity, in part by their ability to undergo homotypic bivalent binding. However, this type of binding is not always possible. Here, the monoclonal antibodies produced in two infected subjects in response to human immunodeficiency virus (HIV) glycoprotein have been analysed. The results provide evidence for polyreactivity, which may be required when the density of glycoprotein spikes is so low that bivalent binding is unlikely.

    • Hugo Mouquet
    • , Johannes F. Scheid
    •  & Michel C. Nussenzweig

  • News & Views |

    Spikes on the surface of HIV to which antibodies can bind are sparse. One of nature's solutions is to sometimes produce antibodies that bind tightly to a spike with one arm and grab another structure with the other arm. See Letter p.591

    • Andreas Plückthun

  • Article |

    Salmonella enterica serotype Typhimurium causes acute gut inflammation, which promotes the growth of the pathogen through unknown mechanisms. It is now shown that the reactive oxygen species generated during inflammation react with host-derived sulphur compounds to produce tetrathionate, which the pathogen uses as a terminal electron acceptor to support its growth. The ability to use tetrathionate provides the pathogen with a competitive advantage over bacteria that lack this property.

    • Sebastian E. Winter
    • , Parameth Thiennimitr
    •  & Andreas J. Bäumler

  • Article |

    The evolutionary origin of the human malaria parasite Plasmodium falciparum has been much debated. Genetic analysis of a large number of faecal samples from wild-living African apes now shows that Plasmodium parasites from Western gorillas are most closely related to the human parasite. The data suggest that human P. falciparum evolved from a gorilla parasite after a single host transfer event.

    • Weimin Liu
    • , Yingying Li
    •  & Beatrice H. Hahn

  • Editorial |

    Plan to cull badgers in England shows the new government does not respect scientific advice.

  • News & Views |

    Plasmodium falciparum is the agent of the deadliest form of human malaria. A survey of Plasmodium diversity in African apes reveals that western gorillas are the reservoir species for this parasite. See Article p. 420

    • Edward C. Holmes

  • News & Views |

    How does a Salmonella pathogen outcompete beneficial intestinal microorganisms? It triggers an immune response that generates a compound from intestinal gas that it can utilize as an energy source. See Article p. 426

    • Samuel I. Miller

  • Letter |

    The oxidation of formate and water to bicarbonate and H2 is relatively common in microorganisms under anaerobic conditions. But can this reaction sustain growth in an isolated species? Here it is shown that several individual Thermococcus species can use formate oxidation for growth. Moreover, the biochemical basis of this ability is delineated.

    • Yun Jae Kim
    • , Hyun Sook Lee
    •  & Sung Gyun Kang

  • Letter |

    Clostridium difficile, an important nosocomial pathogen, produces two toxins. Studies with purified toxins have indicated that only toxin A is important for pathogenesis, but recently it has been suggested that toxin B causes the majority of the disease symptoms in the context of a bacterial infection. These authors demonstrate that both toxins are important for disease and will need to be considered for diagnosis and treatment.

    • Sarah A. Kuehne
    • , Stephen T. Cartman
    •  & Nigel P. Minton

  • Letter |

    Experimental determination of the secondary structure of RNA molecules has usually been carried out on a case-by-case basis. Now, however, a deep-sequencing approach has been used to profile the secondary structure of 3,000 distinct messenger RNA transcripts from Saccharomyces cerevisiae. The results provide interesting hints about the role of secondary structure in protein translation, and set the stage for the examination of how such structures can change in response to environmental conditions.

    • Michael Kertesz
    • , Yue Wan
    •  & Eran Segal

  • Letter |

    Bacteria regularly evolve antibiotic resistance, but little is known about this process at the population level. Here, a continuous culture of Escherichia coli facing increasing antibiotic levels is followed. Most isolates taken from this population are less antibiotic resistant than the population as a whole. A few highly resistant mutants provide protection to the less resistant constituents, in part by producing the signalling molecule indole, which serves to turn on drug efflux pumps and oxidative-stress protective mechanisms.

    • Henry H. Lee
    • , Michael N. Molla
    •  & James J. Collins

  • News & Views |

    A charitable deed by a few cells in a bacterial culture can help the rest of that population survive in the presence of antibiotics. This finding can aid further research into a major problem in public health.

    • Hyun Youk
    •  & Alexander van Oudenaarden

  • News & Views |

    Tumour viruses can cause cancer by altering gene expression and protein activity in the host cell. Tumour adenoviruses, however, seem to go to great lengths to ensure that one particular host cell protein, p53, is suppressed.

    • Kevin M. Ryan

  • News & Views |

    An aggressive and unpredictable fungal pathogen is devastating larch plantations in Britain. Its remarkably broad host range, and the possibility of further geographical spread, give heightened cause for concern.

    • Clive Brasier
    •  & Joan Webber

  • Letter |

    A central hub of carbon metabolism is the tricarboxylic acid (TCA) cycle, which serves to connect the processes of glycolysis, gluconeogenesis, respiration, amino acid synthesis and other biosynthetic pathways. These authors show that TCA metabolism in the human malaria parasite Plasmodium falciparum is largely disconnected from glycolysis and is organized along a fundamentally different architecture — not cyclic, but branched — from the canonical textbook pathway.

    • Kellen L. Olszewski
    • , Michael W. Mather
    •  & Manuel Llinás

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