Bacteria articles within Nature

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  • Letter |

    The structure of the bacterial 70S ribosome in complex with ArfA, the release factor RF2, a short non-stop mRNA and a cognate P-site tRNA is presented, revealing how ArfA and RF2 facilitate alternative translation termination of the non-stop ribosomal complex using a stop-codon surrogate mechanism.

    • Chengying Ma
    • , Daisuke Kurita
    •  & Ning Gao

  • Article |

    The mystery of how bacteria that lack motile structures such as pili or flagella can ‘glide’ along surfaces is solved by a detailed description of the bacterial focal adhesion complex and its associated protein machinery.

    • Laura M. Faure
    • , Jean-Bernard Fiche
    •  & Tâm Mignot

  • 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

  • Letter |

    The structure of a bacterial ribosome–RelA complex reveals that RelA, a protein recruited to the ribosome in the case of scarce amino acids, binds in a different location to translation factors, and that this binding event suppresses auto-inhibition to activate synthesis of the (p)ppGpp secondary messenger, thus initiating stringent control.

    • Alan Brown
    • , Israel S. Fernández
    •  & V. Ramakrishnan

  • Letter |

    The crystal structure of monomeric Lachnospiraceae bacterium Cpf1 protein bound to CRISPR RNA is presented, establishing a framework for engineering LbCpf1 to improve its efficiency and specificity for genome editing.

    • De Dong
    • , Kuan Ren
    •  & Zhiwei Huang

  • Article |

    A combination of X-ray crystallography, electron microscopy, functional assays and time-lapse fluorescence microscopy shows that a protein of previously unknown function, TssA, forms a dodecameric complex that interacts with components of the tube and sheath of the type VI secretion system of bacteria, and that it primes and coordinates biogenesis of both the tail tube and the sheath.

    • Abdelrahim Zoued
    • , Eric Durand
    •  & Eric Cascales

  • Article |

    Two crystal structures of the Escherichia coli β-barrel assembly machinery (BAM complex) are presented, one of which includes all five subunits (BamA–BamE), in two distinct conformational states; together with functional assays and molecular dynamics stimulations, these structures help to generate a model for outer membrane protein insertion.

    • Yinghong Gu
    • , Huanyu Li
    •  & Changjiang Dong

  • Letter |

    The structure of E. coli Cascade bound to foreign target DNA is presented, revealing the basis of the relaxed Cascade PAM recognition specificity, which results from its interaction with the minor groove, and demonstrating how a wedge in Cascade forces the directional pairing of the target strand with CRISPR RNA while stabilizing the non-target displaced strand.

    • Robert P. Hayes
    • , Yibei Xiao
    •  & Ailong Ke

  • Letter |

    Until now, the oxidation steps necessary for complete nitrification had always been observed to occur in two separate microorganisms in a cross-feeding interaction; here, together with the study by Daims et al., van Kessel et al. report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as ‘comammox’ (for complete ammonia oxidation).

    • Maartje A. H. J. van Kessel
    • , Daan R. Speth
    •  & Sebastian Lücker

  • Article |

    Antibiotic-resistant strains of Staphylococcus aureus, such as MRSA, are proving increasingly difficult to treat; here, one reason for this is confirmed to be the fact that S. aureus bacteria can reside in intracellular reservoirs where they are protected from antibiotics, but a new strategy—based on an antibody–antibiotic conjugate—can specifically target these reservoirs.

    • Sophie M. Lehar
    • , Thomas Pillow
    •  & Sanjeev Mariathasan

  • Letter |

    The structure of the Cas1–Cas2 complex bound to a protospacer sequence illustrates how foreign DNA is captured and measured by bacterial proteins in preparation for integration into CRISPR loci.

    • James K. Nuñez
    • , Lucas B. Harrington
    •  & Jennifer A. Doudna

  • Article |

    Ion channels in bacterial biofilms are shown to conduct long-range electrical signals within the biofilm community through the propagation of potassium ions; as predicted by a simple mathematical model, potassium channel gating is shown to coordinate metabolic states between distant cells via electrical communication.

    • Arthur Prindle
    • , Jintao Liu
    •  & Gürol M. Süel

  • Letter |

    The authors develop a mouse model of Enterococcus faecalis colonization to show that enterococci harbouring the bacteriocin-expressing plasmid pPD1 replace indigenous enterococci and have the ability to transfer the plasmid to other enterococci, which enhances the stability of the bacteriocin-expressing bacteria in the gut; this result suggests a therapeutic approach that leverages niche-specificity to eliminate antibiotic-resistant bacteria from infected individuals.

    • Sushma Kommineni
    • , Daniel J. Bretl
    •  & Nita H. Salzman

  • 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

  • Article |

    A novel drug, ribocil, is shown to mimic the binding of a natural ligand to a bacterial riboflavin riboswitch (a non-coding stretch of messenger RNA whose structure is affected by a ligand—usually one related to the function of the protein encoded by the messenger RNA) to cause inhibition of bacterial growth; the ability to target an RNA structural element with a synthetic small molecule may expand our view of the target space susceptible to therapeutic intervention.

    • John A. Howe
    • , Hao Wang
    •  & Terry Roemer

  • Letter |

    More than 15% of the bacterial domain consists of a radiation of phyla about which very little is known; here, metagenomics is used to reconstruct 8 complete and 789 draft genomes from more than 35 of these phyla, revealing a shared evolutionary history, metabolic limitations, and unusual ribosome compositions.

    • Christopher T. Brown
    • , Laura A. Hug
    •  & Jillian F. Banfield

  • Letter |

    Fluorescent labelling is used to show that in E. coli, outer membrane protein (OMP) turnover is passive and binary in nature, and OMPs cluster to form islands in which diffusion of individual proteins is restricted owing to lateral interactions with other OMPs; new OMPs are inserted mostly at mid-cell, meaning that old OMP islands are displaced to the poles of growing cells.

    • Patrice Rassam
    • , Nikki A. Copeland
    •  & Colin Kleanthous

  • Letter |

    A single particle cryo-EM structure of the 70S ribosome in complex with the elongation factor Tu breaks the 3 Å resolution barrier of the technique and locally exceeds the resolution of previous crystallographic studies, revealing all modifications in rRNA and explaining their roles in ribosome function and antibiotic binding.

    • Niels Fischer
    • , Piotr Neumann
    •  & Holger Stark

  • Letter |

    A new mechanism is identified for correct placement of the division machinery in Streptococcus pneumoniae that relies on the novel factor MapZ to form ring structures at the cell equator; these structures move apart as the cell elongates, acting as permanent markers of division sites.

    • Aurore Fleurie
    • , Christian Lesterlin
    •  & Christophe Grangeasse

  • Article |

    Non-caloric artificial sweeteners (NAS), widely used food additives considered to be safe and beneficial alternatives to sugars, are shown here to lead to the development of glucose intolerance through compositional and functional changes in the gut microbiota of mice, and the deleterious metabolic effects are transferred to germ-free mice by faecal transplant; NAS-induced dysbiosis and glucose intolerance are also demonstrated in healthy human subjects.

    • Jotham Suez
    • , Tal Korem
    •  & Eran Elinav

  • Letter |

    The inherent stochasticity in metabolic reactions is a potent source of phenotypic heterogeneity in cell populations, with potentially fundamental implications for cancer research.

    • Daniel J. Kiviet
    • , Philippe Nghe
    •  & Sander J. Tans

  • Letter |

    Functional metagenomic selections for resistance to 18 antibiotics in 18 different soils reveal that bacterial community composition is the primary determinant of soil antibiotic resistance gene content.

    • Kevin J. Forsberg
    • , Sanket Patel
    •  & Gautam Dantas

  • Article |

    This study shows that Bacillus subtilis switches from a solitary, motile lifestyle to a multicellular, sessile state in a random, memoryless fashion, but that the underlying gene network is buffered against its own stochastic variation to tightly time the reverse transition; thus bacteria keep track of time to force their progeny to cooperate during the earliest stage of multicellular growth.

    • Thomas M. Norman
    • , Nathan D. Lord
    •  & Richard Losick

  • Letter |

    Growth of a flagellum outside the bacterial cell proceeds by successive subunit acquisition from the cell export machinery to form a chain that is pulled to the flagellum tip, where subunit crystallization provides the entropic force to drive the process.

    • Lewis D. B. Evans
    • , Simon Poulter
    •  & Gillian M. Fraser

  • Article |

    The crystal structure of BamA, the central component of the β-barrel assembly machinery (BAM) complex, from N. gonorrhoeae and H. ducreyi is determined; the structure consists of an interior cavity capped by extracellular loops, an exterior rim with a narrowed hydrophobic surface and a lateral opening of the barrel domain, providing insight into a possible route for the insertion of β-barrel membrane proteins into the bacterial outer membrane.

    • Nicholas Noinaj
    • , Adam J. Kuszak
    •  & Susan K. Buchanan

  • Letter |

    An X-ray structure of bacterial type VI secretion system components reveals that PAAR family proteins bind at the tip of the VgrG spike, providing new insights into the mechanisms of type VI secretion; experiments using bacteria confirmed the importance of PAAR proteins.

    • Mikhail M. Shneider
    • , Sergey A. Buth
    •  & Petr G. Leiman

  • Article |

    Mycobacterium tuberculosis has the ability to survive within the host for months to decades in an asymptomatic state, and adaptations to hypoxia are thought to have an important role in pathogenesis; here a systems-wide reconstruction of the regulatory network provides a framework for understanding mycobacterial persistence in the host.

    • James E. Galagan
    • , Kyle Minch
    •  & Gary K. Schoolnik

  • Letter |

    A diamond chip with nitrogen–vacancy centres is used for magnetic imaging of living magnetotactic bacteria with sub-cellular spatial resolution.

    • D. Le Sage
    • , K. Arai
    •  & R. L. Walsworth

  • Article |

    A Staphylococcus aureus leukotoxin targets cells expressing the chemokine receptor CCR5, a mechanism for the specificity of leukotoxins towards different immune cells.

    • Francis Alonzo III
    • , Lina Kozhaya
    •  & Victor J. Torres

  • Article |

    The twin-arginine translocation (Tat) pathway transports folded proteins across membranes in bacteria and plant chloroplasts; the crystal structure of TatC, an integral membrane protein and core component of this complex, is now presented.

    • Sarah E. Rollauer
    • , Michael J. Tarry
    •  & Susan M. Lea

  • Letter |

    FusKR, a fucose-sensing two-component system, has been identified in enterohaemorrhagic E. coli, linking fucose utilization and virulence factor gene expression and providing insight into how sensing of a host signal can facilitate bacterial colonization.

    • Alline R. Pacheco
    • , Meredith M. Curtis
    •  & Vanessa Sperandio

  • News & Views |

    The identification of a sea-floor microorganism that single-handedly conducts anaerobic oxidation of methane changes our picture of how the flux of this greenhouse gas from the ocean to the atmosphere is regulated. See Article p.541

    • Samantha B. Joye

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