Microbial genetics articles within Nature

Featured

  • Letter |

    The CRISPR/Cas system known to aid bacterial defences by targeting invading DNA can also act to evade eukaryotic defences through a different class of small RNAs downregulating an endogenous immunogenic bacterial lipoprotein.

    • Timothy R. Sampson
    • , Sunil D. Saroj
    •  & David S. Weiss

  • Article |

    Daily oxidation–reduction cycles of peroxiredoxin proteins are shown to be conserved in all domains of life, including Bacteria, Archaea and Eukaryota.

    • Rachel S. Edgar
    • , Edward W. Green
    •  & Akhilesh B. Reddy

  • Article |

    The human gut microbiome from a large cohort of more than 500 indivduals living on three continents with three distinct cultures is analysed, emphasizing the effect of host age, diet and environment on the composition and functional repertoire of fecal microbiota.

    • Tanya Yatsunenko
    • , Federico E. Rey
    •  & Jeffrey I. Gordon

  • News & Views |

    Epigenetics is a hot new research field, but it seems that the influenza virus already has it figured out. By mimicking epigenetic regulation in human cells, one flu strain suppresses the expression of antiviral genes. See Article p.428

    • Alexei L. Krasnoselsky
    •  & Michael G. Katze

  • Outlook |

    Some people get horribly sick from the flu, and even die. Others just rest for a few days. What's behind this fateful variation?

    • Christine Junge

  • News & Views |

    A newly discovered variation in the process by which bacteria resist invasion by foreign nucleic acids provides an intriguing parallel between the defence mechanisms of the different domains of life. See Article p.602

    • Susan Gottesman

  • Letter |

    Pyrrolysine is the twenty-second naturally occurring amino acid, and it is required for the formation of methane from methylamines. Pyrrolysine is the last remaining natural amino acid with a poorly characterized biosynthetic pathway. Here it is shown that the radical SAM protein PylB converts lysine to 3-methylornithine, which then undergoes a PylC-catalysed condensation with another lysine to generate a product that is oxidized by PylD to generate pyrrolysine.

    • Marsha A. Gaston
    • , Liwen Zhang
    •  & Joseph A. Krzycki

  • News & Views |

    Protein folding is a high-stakes process, with cell dysfunction and death being the unforgiving penalties for failure. Work in bacteria hints that organisms manage this process beyond the boundaries of the cytoplasm — and even the cell.

    • Evan T. Powers
    •  & William E. Balch

  • Letter |

    During replication, topological stress builds ahead of the polymerase. Current models propose that linear eukaryotic chromosomes are divided into topological domains, and that stress is relieved by the activity of a topoisomerase. Here, it is found that replication stress seems to be present throughout the chromosome, rather than in domains, and that the relief of stress in longer chromosomes is facilitated by the activity of the cohesin/condensin-like Smc5/6 complex as well as by topoisomerase. They propose that the Smc5/6 complex prevent formation of topological tension ahead of the replication fork by promoting fork rotation, leading to the formation of sister chromatin intertwinings behind.

    • Andreas Kegel
    • , Hanna Betts-Lindroos
    •  & Camilla Sjögren

  • Letter |

    As the rates of replication and transcription are different, the machineries that carry out these processes are bound to clash on DNA. In contrast to results from head-on collisions, co-directional encounters have been shown to have mild effects in vitro, requiring no additional replication restart factors. It is now shown that in bacterial cells, both types of events require the activities of restart proteins to resume replication when a transcription complex is encountered.

    • Houra Merrikh
    • , Cristina Machón
    •  & Panos Soultanas

  • News & Views |

    The Lassa virus nucleoprotein coats the viral genome to make a template for RNA synthesis. A study shows that it also binds the 'cap' structure of cellular messenger RNAs and directs immune evasion using a novel mechanism. See Article p.779

    • Félix A. Rey

  • 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

  • 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 |

    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 |

    The Escherichia coli isocitrate dehydrogenase kinase/phosphatase (AceK) is a bifunctional enzyme that can phosphorylate or dephosphorylate isocitrate dehydrogenase (ICDH) to either inactivate or activate it in response to environmental changes. Now the structures of AceK and the AceK–ICDH complex have been solved, revealing the conformational changes that occur when AceK changes from a kinase to a phosphatase and vice versa.

    • Jimin Zheng
    •  & Zongchao Jia

  • Article
    | Open Access

    Deep metagenomic sequencing and characterization of the human gut microbiome from healthy and obese individuals, as well as those suffering from inflammatory bowel disease, provide the first insights into this gene set and how much of it is shared among individuals. The minimal gut metagenome as well as the minimal gut bacterial genome is also described.

    • Junjie Qin
    • , Ruiqiang Li
    •  & Jun Wang

  • Article |

    The integrase protein of retroviruses such as HIV-1 catalyses insertion of the viral genome into that of the host. Here, the long-awaited structure of the full-length integrase complex is predicted, revealing not only details of the biochemistry of the integration reaction, but also the means by which current inhibitors affect this process.

    • Stephen Hare
    • , Saumya Shree Gupta
    •  & Peter Cherepanov

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