Microbiology articles within Nature Communications

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  • Article |

    Lamivudine treatment of hepatitis B is associated with drug-resistance mutations in the virus’ DNA polymerase. In this study, 11 patients with drug resistance are investigated and the primary mutation in the DNA polymerase shown to be essential but not sufficient for establishing drug resistance.

    • Hong Thai
    • , David S. Campo
    •  & Yury Khudyakov

  • Article |

    Microbial metabolism is usually considered to be phototrophic or chemotrophic. By showing that light-induced photoelectrons from metal oxide and metal sulfides can stimulate the growth of chemoautotrophic and heterotrophic bacteria, this study indicates that light may be involved in non-phototrophic microbial activity.

    • Anhuai Lu
    • , Yan Li
    •  & Hailiang Dong

  • Article |

    Graphene is characterized by unique physical properties that offer substantial promise, most notably for electronic applications. Mannooret al. present a wireless graphene-based sensor for detecting bacteria on a range of biological tissues.

    • Manu S. Mannoor
    • , Hu Tao
    •  & Michael C. McAlpine

  • Article |

    The treatment ofMycobacterium tuberculosis with drugs such as isoniazid often results in drug resistance, but the mechanisms leading to the resistance are not fully known. In this study, an M. tuberculosisstrain lacking the sigma factor I is shown to be resistant to isoniazid.

    • Jong-Hee Lee
    • , Nicole C. Ammerman
    •  & William R. Bishai

  • Article |

    It is unclear whether pathogens can advantageously exploit the host's immune response. UsingCandida albicans, the authors show that host IL-17A binds to the fungi and induces nutrient starvation and autophagy, which eventually leads to enhanced biofilm formation and resistance to the hosts' defence.

    • Teresa Zelante
    • , Rossana G. Iannitti
    •  & Luigina Romani

  • Article
    | Open Access

    GALgenes enhance their own transcription via the transcription factor Gal4p, and the number of Galp4 sites in a promoter is expected to strengthen the feedback. In this study, Hsuet al. show that instead the feedback loops are activated by genes that have frequent bursts of expression and fast RNA decay kinetics.

    • Chieh Hsu
    • , Simone Scherrer
    •  & Attila Becskei

  • Article
    | Open Access

    Myeloid cells are important in the response to severe infection by invasiveStreptococcusGroup A. In this study, a distinct population of immature myeloid cells with ring shaped nuclei that produce interferon-γ are shown to be important for protection of mice against the early stages of invasive infection.

    • Takayuki Matsumura
    • , Manabu Ato
    •  & Kazuo Kobayashi

  • Article
    | Open Access

    Epitopes presented by MHC-II molecules bind to T-cell receptors to activate CD4+ T cells. In this study, changes in the carboxy-terminal region of the influenza hemagglutinin epitope HA305-320alters the strength of binding to the T-cell receptor, thus modulating T-cell receptor usage and activation.

    • David K. Cole
    • , Kathleen Gallagher
    •  & Andrew Godkin

  • Article
    | Open Access

    The influenza A virus genome consists of eight RNA segments, which permits genetic reassortment and contributes to the emergence of novel strains with pandemic potential. Here, electron tomography is used to study the three-dimensional structure of ribonucleoprotein complexes within progeny virions.

    • Takeshi Noda
    • , Yukihiko Sugita
    •  & Yoshihiro Kawaoka

  • Article |

    Genome-scale metabolic models for bacterial species allow a systematic study of inter-species interactions. Here, competitive and cooperative potential is predicted between 6,903 pairs of species, to explore the role of these interactions in shaping coexistence patterns in natural communities.

    • Shiri Freilich
    • , Raphy Zarecki
    •  & Eytan Ruppin

  • Article |

    Herpesvirus glycoprotein D binds to nectin 1 and the herpes virus entry mediator protein on the surface of host cells. In this study, Zhanget al. report the crystal structure of glycoprotein D in complex with the immunoglobulin-like domains of nectin 1, which suggests that binding of glycoprotein D to nectin 1 prevents nectin 1 dimerization.

    • Na Zhang
    • , Jinghua Yan
    •  & George F Gao

  • Article
    | Open Access

    New approaches are required to combatPlasmodium falciparuminfection. In this proteome-wide study, 1305 phosphorylation sites are identified and 36 kinases are shown to have crucial roles in parasite survival, providing new insights into parasite biology and potential new drug targets for anti-malarial chemotherapy.

    • Lev Solyakov
    • , Jean Halbert
    •  & Christian Doerig

  • Article |

    The 30S ribosomal subunit ofEscherichia coliinhibits the RNA-degrading enzyme Ribonuclease T2. Using mutational studies and hybrid ribosomes, Kitahara and Miyazaki show that helix 41 of the 30S ribosomal subunit blocks the enzyme activity, suggesting that helix 41 is required for preventing RNase T2 toxicity.

    • Kei Kitahara
    •  & Kentaro Miyazaki

  • Article |

    Parasites such as malaria elicit an immune response in their host, causing cytokine levels to increase. In this study, a parasite housekeeping gene, tyrosyl-tRNA synthetase, is shown to bind to host macrophages and, once inside the cells, enhance the levels of proinflammatory cytokines.

    • Tarun Kumar Bhatt
    • , Sameena Khan
    •  & Amit Sharma

  • Article
    | Open Access

    The risk factors associated with both ischemic and haemorrhagic stroke are not fully understood. Here a certain strain of the bacteria,Streptococcus mutans, which expresses a collagen-binding protein, is shown to be associated with haemorrhagic stroke in both animal models and human patients.

    • Kazuhiko Nakano
    • , Kazuya Hokamura
    •  & Takashi Ooshima

  • Article
    | Open Access

    A bacterial export gate complex transports flagellar proteins across the cytoplasmic membrane, but the mechanism of this process is unclear. Here, the export gate complex is revealed as a proton–protein antiporter that uses separate components of the proton motive force for different steps of the export process.

    • Tohru Minamino
    • , Yusuke V. Morimoto
    •  & Keiichi Namba

  • Article
    | Open Access

    Group BStreptococcuscauses meningitis in newborn infants but how the bacterium crosses the blood-brain barrier is unknown. Here, the bacterial pili adhesion molecule, PilA, is shown to bind to collagen and promote binding of the bacteria to integrins expressed on the blood-brain endothelium.

    • Anirban Banerjee
    • , Brandon J. Kim
    •  & Kelly S. Doran

  • Article
    | Open Access

    The chronic disease schistosomiasis is caused by the blood flukeSchistosoma mansoni. By studying DNA modifications throughout the lifecycle of the pathogen, the authors identify DNA methylation as a factor in egg development and suggest that the epigenetic machinery responsible may be a therapeutic target.

    • Kathrin K. Geyer
    • , Carlos M. Rodríguez López
    •  & Karl F. Hoffmann

  • Article
    | Open Access

    Dissolved organic matter, the main form of aquatic organic carbon, supports the aquatic food web and regulates light penetration in lakes. This study probes the main influences on the optical properties of dissolved organic matter in a global dataset of alpine and remote lakes revealing latitudinal trends.

    • N. Mladenov
    • , R. Sommaruga
    •  & I. Reche

  • Article
    | Open Access

    Group-1 influenza A neuramidase proteins have a 150-cavity that can be targeted by drugs, but the 2009 H1N1 virus neuramidase is not thought to have a 150-cavity. Here, biophysical simulations show that the 2009 H1N1 neuramidase exists in solution with an open 150-cavity, which is stabilized by a salt bridge.

    • Rommie E. Amaro
    • , Robert V. Swift
    •  & Robin M. Bush

  • Article |

    Studying how pathogens enter polarized epithelial cells is important for understanding infection. Here, activation of chemokine receptors on the apical membrane of epithelial cells, is shown to engage Src family tyrosine signalling, resulting in relocation of the viral co-receptor αvβ3 to the apical membrane and adenovirus entry.

    • Verena Lütschg
    • , Karin Boucke
    •  & Urs F. Greber

  • Article |

    Phylogenetic analysis is used to identify transmission chains, but no software is available for the automated partition of large phylogenies. Prosperiet al. apply a new search algorithm to identify transmission clusters within the phylogeny of HIV-1gene sequences linking molecular and epidemiological data.

    • Mattia C.F. Prosperi
    • , Massimo Ciccozzi
    •  & Andrea De Luca

  • Article
    | Open Access

    Secondary metabolites are widely used in human health and nutrition, but extraction yields from plants are often low. Nakagawaet al. have engineered the metabolism of Escherichia colito develop a fermentation system that produces plant alkaloids from simple carbon sources.

    • Akira Nakagawa
    • , Hiromichi Minami
    •  & Hidehiko Kumagai

  • Article
    | Open Access

    Saccharomycesyeasts can produce ethanol from sugars in the presence of oxygen. In this study, the authors demonstrate thatDekkera bruxellensis, a distantly related yeast, can also produce and consume ethanol due to the loss of a cis-regulatory element from the promoters of genes crucial for respiration.

    • Elżbieta Rozpędowska
    • , Linda Hellborg
    •  & Jure Piškur

  • Article
    | Open Access

    Plasmids are present in many bacteria and are often transferred between different species causing horizontal gene transfer. By comparing the sequences of 25 plasmid DNA backbones, the authors show that homologous recombination is prevalent in plasmids and that the plasmids have adapted to persist in different host bacteria.

    • Peter Norberg
    • , Maria Bergström
    •  & Malte Hermansson

  • Article
    | Open Access

    The infectious prion diseases affect numerous hoofed animal species, and it has been suggested that the properties of the local soil affect transmission of these diseases. Here, the authors studied two North American locations and demonstrate that soil clay content can influence the infection rate in deer.

    • W. David Walter
    • , Daniel P. Walsh
    •  & Michael W. Miller

  • Article
    | Open Access

    Leptosphaeria maculans is a plant pathogen that causes stem canker of oilseed rape. Rouxel et al. sequence and describe the key features of the L. maculansgenome, including partitioning into AT-rich blocks that are enriched in effector genes and transposable elements affected by repeat-induced point mutation.

    • Thierry Rouxel
    • , Jonathan Grandaubert
    •  & Barbara J. Howlett

  • Article |

    Proteorhodopsin is used by prokaryotes to generate energy from light. In this study, the authors describe a prokaryote-to-eukaryote horizontal gene transfer of a bacterial proteorhodopsin gene to dinoflagellates, suggesting that these eukaryotes can also use proteorhodopsin to obtain light and produce energy.

    • Claudio H. Slamovits
    • , Noriko Okamoto
    •  & Patrick J. Keeling

  • Article
    | Open Access

    HrpR and HrpS enhancer-binding proteins ofPseudomonas syringae activate σ54-dependent transcription of the HrpL promoter and are required for type-three secretion pathogenicity. Here, the authors demonstrate that, despite being co-regulated, HrpR and HrpS each have distinct functions for activating σ54.

    • Milija Jovanovic
    • , Ellen H. James
    •  & Jörg Schumacher

  • Article
    | Open Access

    Microorganisms are abundant in many environments and understanding their dispersal between ecosystems is important for ecology and conservation. These authors demonstrate that cyanobacterial populations are specific to hot or cold deserts and that gene flow between different populations does not occur.

    • Justin Bahl
    • , Maggie C. Y. Lau
    •  & Stephen B. Pointing

  • Article |

    Insertion sequences are transposable elements that are found in the genomes of many bacteria. Here, the authors identify an enhancer element that results in a high frequency of excision of insertion elements, and suggest that the excision enhancer element coevolved with the insertion sequences.

    • Masahiro Kusumoto
    • , Tadasuke Ooka
    •  & Tetsuya Hayashi

  • Article
    | Open Access

    Up to 20% of bacterial genomes are made up of cryptic prophages, but their function is relatively unknown. In this study, the authors demonstrate that prophages influence the response of the host cell to stress and provide a competitive growth advantage in the presence of antibiotics.

    • Xiaoxue Wang
    • , Younghoon Kim
    •  & Thomas K. Wood

  • Article
    | Open Access

    Identifying the transcripts and proteins that fluctuate in response to stimuli provides important information for understanding cell physiology. In this study, 52% of theBacillus subtilispredicted proteome is identified following glucose starvation, revealing further insight into protein dynamics at a global scale.

    • Andreas Otto
    • , Jörg Bernhardt
    •  & Dörte Becher

  • Article |

    Hydrogen production using photosynthetic bacteria is an appealing energy source, but typically the bacteria require anaerobic conditions. Here, the authors report a wild-type cyanobacterium strain that shows very high rates of hydrogen production under aerobic environmental conditions.

    • Anindita Bandyopadhyay
    • , Jana Stöckel
    •  & Himadri B. Pakrasi

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