Bacterial genetics articles within Nature Communications

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  • Article
    | Open Access

    The Nus factor complex regulates rRNA folding and prevents Rho-dependent transcription termination in bacteria. Here, Baniulyte et al. show that it also inhibits translation of one of the Nus factor-encoding genes, suhB, and probably regulates the expression of other genes in diverse bacterial species.

    • Gabriele Baniulyte
    • , Navjot Singh
    •  & Joseph T. Wade

  • Article
    | Open Access

    The RNA-binding protein CsrA regulates the expression of hundreds of bacterial genes. Here, Potts et al. use several approaches to assess the contribution of CsrA to global gene expression in E. coli, revealing new binding targets and physiological roles such as in envelope function and iron homeostasis.

    • Anastasia H. Potts
    • , Christopher A. Vakulskas
    •  & Tony Romeo

  • Article
    | Open Access

    Transcription factors MarR and MarA confer multidrug resistance in enteric bacteria by modulating efflux pump and porin expression. Here, Sharma et al. show that MarA also upregulates genes required for lipid trafficking and DNA repair, thus reducing antibiotic entry and quinolone-induced DNA damage.

    • Prateek Sharma
    • , James R. J. Haycocks
    •  & David C. Grainger

  • Article
    | Open Access

    Some antibiotic resistance genes found in pathogenic bacteria might derive from antibiotic-producing actinobacteria. Here, Jianget al. provide bioinformatic and experimental evidence supporting this hypothesis, and propose a specific mechanism for the transfer of these genes between bacterial phyla.

    • Xinglin Jiang
    • , Mostafa M. Hashim Ellabaan
    •  & Sang Yup Lee

  • Article
    | Open Access

    Elizabethkingia anophelis is an emerging pathogen of high antimicrobial resistance. Perrin and colleagues sequenced isolates of a 2015/2016 E. anophelis outbreak in Wisconsin and found substantial genetic diversity, accelerated evolutionary rate and a disruptive mutation in the DNA repair gene mutY.

    • Amandine Perrin
    • , Elise Larsonneur
    •  & Sylvain Brisse

  • Article
    | Open Access

    Several unusual features have been reported for bacteria of the phylum Planctomycetes, such as cytosolic compartmentalization and an endocytosis-like process. Here, Boedekeret al. provide evidence supporting a Gram-negative cell plan and the absence of endocytosis-like processes in these organisms.

    • Christian Boedeker
    • , Margarete Schüler
    •  & Christian Jogler

  • Article
    | Open Access

    Bacteria may respond to a change in environment by using alternative transcriptional start sites. Here, the authors use a novel genome-wide capture and reverse transcription method to find substrate-specific start sites for hundreds of genes at single base resolution inClostridium phytofermentans.

    • Magali Boutard
    • , Laurence Ettwiller
    •  & Andrew C. Tolonen

  • Article
    | Open Access

    Some bacterial toxin-antitoxin systems consist of a labile antitoxin that inhibits a toxin, and a chaperone that stabilizes the antitoxin. Here, Bordes et al. identify a sequence within the antitoxin to which the chaperone binds and which can be transferred to other proteins to make them chaperone-dependent.

    • Patricia Bordes
    • , Ambre Julie Sala
    •  & Pierre Genevaux

  • Article
    | Open Access

    Colistin is an antibiotic used in the treatment of Pseudomonas aeruginosa infections in cystic fibrosis patients. Here, Jochumsen et al. reconstruct the pathways for the molecular evolution of colistin resistance in P. aeruginosaand show that the number of pathways is highly constrained by interactions among genes.

    • Nicholas Jochumsen
    • , Rasmus L. Marvig
    •  & Anders Folkesson

  • Article
    | Open Access

    Plasticity and clonal population structure in bacterial genomes can hinder traditional SNP-based genetic association studies. Here, Corander and colleagues present a method to identify variable-length sequence elements enriched in a phenotype of interest, and demonstrate its use in human pathogens.

    • John A. Lees
    • , Minna Vehkala
    •  & Jukka Corander

  • Article
    | Open Access

    The transcription factor Zur controls the zinc deprivation response in Bacillus subtilis. Here, Shin and Helmann show that Zur-regulated genes are derepressed in three waves in response to zinc deprivation, and this is linked to the biochemistry of zinc sensing by Zur.

    • Jung-Ho Shin
    •  & John D. Helmann

  • Article
    | Open Access

    Microbes survive in dynamic environments by modulating their intracellular metabolism. Here, the authors reveal that mycobacteria employ a rheostat-like mechanism to regulate carbon flux between the oxidative TCA cycle and the glyoxylate shunt during glucose-acetate diauxic shift.

    • Paul Murima
    • , Michael Zimmermann
    •  & John D. McKinney

  • Article
    | Open Access

    The CsrA protein binds to and represses translation of certain bacterial mRNAs. Here, Dugar et al. show for the human pathogen Campylobacter jejunithat the major flagellin mRNA acts as both a target and a regulatory 'sponge' for CsrA, and is localized at the cell poles in a translation-dependent manner.

    • Gaurav Dugar
    • , Sarah L. Svensson
    •  & Cynthia M. Sharma

  • Article
    | Open Access

    The interactions between gut bacteria and enteric pathogens are poorly understood. Here, Yoon et al. show that subinhibitory antibiotic treatment in a mouse model leads to overgrowth of an E. coli strain carrying a catalase-encoding gene that enhances infection with the human pathogen Vibrio cholerae.

    • Mi Young Yoon
    • , Kyung Bae Min
    •  & Sang Sun Yoon

  • Article
    | Open Access

    Chlamydia trachomatis isolates causing a blinding disease (trachoma) form a single lineage that is different from the lineages causing urogenital infections. Here, Andersson et al. show however that trachoma isolates from Australia are more closely related to urogenital strains than to other trachoma isolates.

    • Patiyan Andersson
    • , Simon R. Harris
    •  & Philip M. Giffard

  • Article
    | Open Access

    Expression of transcription factors to alter gene regulation can cause substantial changes to expression across a genome. Here the authors ‘rewire’ E. coliand analyse the global transcriptome alterations to identify novel network interactions.

    • Rebecca Baumstark
    • , Sonja Hänzelmann
    •  & Mark Isalan

  • Article
    | Open Access

    Lactobacillus is a lactic acid bacteria and has a wide range of application from use in probiotic food production to biotherapeutics. Here, the authors sequence and compare the genomes of 213 different Lactobacillusstrains and related genera, and provide new insight into phylogenomic organization and adaptive immunity elements in this bacteria family.

    • Zhihong Sun
    • , Hugh M. B. Harris
    •  & Paul W. O’Toole

  • Article
    | Open Access

    GadEWX regulons play a critical role in transcription regulation in response to acid stress. By reconstructing genome-wide GadEWX transcriptional network, here the authors show how GadEWX simultaneously coordinates many other cellular processes to produce the overall response of E. colito acid stress.

    • Sang Woo Seo
    • , Donghyuk Kim
    •  & Bernhard O. Palsson

  • Article
    | Open Access

    Non-typeable Haemophilus influenzae, which causes ear and lung infections, has a DNA methyltransferase encoded by alternative alleles that are subject to random ON/OFF switching. Here, Atack et al.show that this epigenetic switch controls the expression of key proteins involved in virulence.

    • John M. Atack
    • , Yogitha N. Srikhanta
    •  & Michael P. Jennings

  • Article
    | Open Access

    Bacterial DNA methylation is involved in many processes, from host defense to antibiotic resistance, however current methods for examining methylated genomes lack single-cell resolution. Here Beaulaurier et al. present Single Molecule Modification Analysis of Long Reads, a new tool for de novodetection of epigenetic heterogeneity.

    • John Beaulaurier
    • , Xue-Song Zhang
    •  & Gang Fang

  • Article
    | Open Access

    DNA phasing information — the determination of which specific sequences belong to the same DNA molecule—is not easily obtained from sequencing applications that rely on short reads. Here the authors develop a phasing method based on massively parallel barcoding of single DNA molecules.

    • Erik Borgström
    • , David Redin
    •  & Afshin Ahmadian

  • Article
    | Open Access

    Horizontal gene transfer is important for bacterial evolution but the molecular basis of its fitness costs remain unclear. Here the authors show that fitness costs produced by a plasmid in P. aeruginosaare alleviated by mutations in recently acquired genes encoded in mobile genetic elements.

    • Alvaro San Millan
    • , Macarena Toll-Riera
    •  & R. Craig MacLean

  • Article
    | Open Access

    Adaptation of Mycobacterium tuberculosis to the host environment is principally mediated through its transcription factors. Here, the authors report the DNA binding and transcriptional profile of ~80% of all predicted M. tuberculosistranscription factors, and find wide-spread dormant DNA binding.

    • Kyle J. Minch
    • , Tige R. Rustad
    •  & David R. Sherman

  • Article
    | Open Access

    Genetic variation in Mycobacterium tuberculosiscomplex (MTBC) bacteria is responsible for differences in factors such as virulence and transmissibility. Here, the authors analyse the genomes of 1,601 MTBC isolates from diverse geographic locations and identify 62 SNPs that may be used to resolve lineages and sublineages of these strains.

    • Francesc Coll
    • , Ruth McNerney
    •  & Taane G. Clark

  • Article |

    The bacterial ‘adaptive’ immune system known as CRISPR-Cas destroys foreign DNA molecules, such as viral genomes, to which the cells have previously been exposed. Here, Hynes et al.show that this gain of immunity is favoured by exposure to defective viruses, a result reminiscent of vaccination.

    • Alexander P. Hynes
    • , Manuela Villion
    •  & Sylvain Moineau

  • Article |

    Cre recombinase is widely used to precisely manipulate genes and chromosomes, but it often displays off-target activity. Here, the authors improve the accuracy of Cre-mediated recombination by introducing specific mutations in the enzyme’s dimerization surface.

    • Nikolai Eroshenko
    •  & George M. Church

  • Article
    | Open Access

    DNA double-strand breaks commonly occur in all replicating cells. Wimberly and colleagues show that in non-replicating cells, aborted transcription/translation forms RNA/DNA hybrid R-loops that prime origin-independent replication, leading to DNA breakage, point mutations and chromosomal rearrangements.

    • Hallie Wimberly
    • , Chandan Shee
    •  & P. J. Hastings

  • 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

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