Bacterial genetics articles within Nature

Featured

  • Article
    | Open Access

    Reconstruction of four Treponema pallidum genomes associated with human remains from around 2,000 years ago suggests that T. pallidum existed in the Americas and diverged to its modern subspecies before the fifteenth century European contact with the Americas.

    • Kerttu Majander
    • , Marta Pla-Díaz
    •  & Verena J. Schuenemann

  • Article
    | Open Access

    The prokaryotic non-enzymatic effector protein Cam1 mediates CRISPR immunity by binding tetra-adenylate second messengers and forming a pore in the membrane that induces membrane depolarization and growth arrest.

    • Christian F. Baca
    • , You Yu
    •  & Luciano A. Marraffini

  • Article
    | Open Access

    A study examining bacterial gene expression in human-derived samples identifies a gene encoding a small RNA and describes how it orchestrates the transition between chronic and acute infection in Pseudomonas aeruginosa.

    • Pengbo Cao
    • , Derek Fleming
    •  & Marvin Whiteley

  • Article
    | Open Access

    A study demonstrates that specific interactions between the two committed enzymes for the synthesis of lipopolysaccharide and peptidoglycan enable coordinated assembly of the outer membrane and cell wall in the Gram-negative pathogen Pseudomonas aeruginosa.

    • Katherine R. Hummels
    • , Samuel P. Berry
    •  & Thomas G. Bernhardt

  • Article
    | Open Access

    Data from more than 9,700 human stool and oral metagenomes has been used to decipher the strain transmission patterns of the human microbiome from mother to infant, within households and within populations.

    • Mireia Valles-Colomer
    • , Aitor Blanco-Míguez
    •  & Nicola Segata

  • Article
    | Open Access

    RNA targeting by the Sulfuricurvum type V single-effector nuclease SuCas12a2 drives abortive infection through non-specific cleavage of double-stranded DNA—after recognition of an RNA target through an activating protospacer-flanking sequence, SuCas12a2 efficiently degrades ssRNA, ssDNA and dsDNA.

    • Oleg Dmytrenko
    • , Gina C. Neumann
    •  & Chase L. Beisel

  • Article |

    Retron-Sen2 of Salmonella Typhimurium encodes a toxin and a reverse transcriptase, which, together with the Sen2 multi-copy single-stranded DNA synthesized by the reverse transcriptase make up a tripartite toxin–antitoxin system that functions in anti-phage defence.

    • Jacob Bobonis
    • , Karin Mitosch
    •  & Athanasios Typas

  • Article |

    The mechanism of Thoeris—a bacterial anti-phage defence system—is described in detail, revealing that bacterial TIR-domain proteins recognize infection and produce signalling molecules to execute cell death, akin to the roles of these proteins in plants.

    • Gal Ofir
    • , Ehud Herbst
    •  & Rotem Sorek

  • Article |

    The authors systematically characterize structural variation in the genomes of gut microbiota and show that they are associated with bacterial fitness and with host risk factors, and that examining genes coded in these regions facilitates investigation of mechanisms that may underlie these associations.

    • David Zeevi
    • , Tal Korem
    •  & Eran Segal

  • Letter |

    Isolates of the Vibrio cholerae O1 serotype Ogawa from Yemen are from a single sublineage of the seventh pandemic El Tor (7PET) lineage and are susceptible to several commonly used antibiotics as well as to polymyxins.

    • François-Xavier Weill
    • , Daryl Domman
    •  & Marie-Laure Quilici

  • Letter |

    Finely tuned control of strain engraftment and abundance in the mouse gut microbiota was achieved using the marine polysaccharide porphyran, which could exclusively be used by an introduced subset of wild-type or genetically modified Bacteroides strains.

    • Elizabeth Stanley Shepherd
    • , William C. DeLoache
    •  & Justin L. Sonnenburg

  • Article |

    Whole-genome sequencing of 264 clones sampled from 12 Escherichia coli populations evolved over 50,000 generations under identical culture conditions is used to characterize the patterns and dynamics of genome evolution over time.

    • Olivier Tenaillon
    • , Jeffrey E. Barrick
    •  & Richard E. Lenski

  • Letter |

    When transcription and replication machineries collide on DNA, they can cause mutations to occur in the area near the collision; these mutations are now shown to include two types—duplications/deletions within the transcription unit and base substitutions in the cis-regulatory element of gene expression.

    • T. Sabari Sankar
    • , Brigitta D. Wastuwidyaningtyas
    •  & Jue D. Wang

  • Letter |

    Maximum-depth sequencing (MDS), a new method of detecting extremely rare variants within a bacterial population, is used to show that mutation rates in Escherichia coli vary across the genome by at least an order of magnitude, and also to uncover mechanisms of antibiotic-induced mutagenesis.

    • Justin Jee
    • , Aviram Rasouly
    •  & Evgeny Nudler

  • Review Article |

    The CRISPR-Cas systems of bacteria and archaea provide adaptive immunity against invading mobile genetic elements such as phages and plasmids; this Review describes the discovery of these systems and the mechanisms of immunity, including recent progress in establishing the molecular basis of host immunization.

    • Luciano A. Marraffini

  • 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

  • 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

  • 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 |

    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

  • 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

  • Article |

    In bacteria, the lack of compartmentalization within membrane-enclosed compartments has made it difficult to determine how mature messenger RNAs are spatially distributed. Here the authors use fluorescence experiments in bacteria to follow mRNA dispersal after transcription. They find, surprisingly, that the newly transcribed mRNAs show limited diffusion, and speculate that the packed chromosomal material may itself act as a partition to separate translation from mRNA degradation.

    • Paula Montero Llopis
    • , Audrey F. Jackson
    •  & Christine Jacobs-Wagner

  • 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

  • Letter |

    Staphylococcal superantigens can lead to toxic shock syndrome. They are encoded on pathogenicity islands and with the aid of helper phages can be excised and packaged into highly transmissable phage particles. Here it is shown that a specific, non-essential helper phage protein is responsible for derepression of the pathogenicity island, thereby providing the mechanism for the first step of its mobilization.

    • María Ángeles Tormo-Más
    • , Ignacio Mir
    •  & José R. Penadés

Browse broader subjects

Browse Bacterial genetics across other nature.com journals