Microbial genetics articles within Nature Communications

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  • Article
    | Open Access

    Sequence composition is thought to be a major factor governing the functionality of horizontally transferred genes. In contrast, Porse et al. show that phylogenetic origin, and the type of resistance mechanism, are major factors affecting the functionality of horizontally transferred antibiotic resistance genes.

    • Andreas Porse
    • , Thea S. Schou
    •  & Morten O. A. Sommer

  • Article
    | Open Access

    Bacteria use two-component systems (TCSs) to sense and respond to environmental changes. Here, the authors show that Staphylococcus aureus can survive in the absence of all its 16 TCSs under growth arrest conditions, and each TCS seems to be sufficient to sense and respond to specific environmental clues.

    • Maite Villanueva
    • , Begoña García
    •  & Iñigo Lasa

  • 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

    Arms races between phage and bacteria are well known from lab experiments, but insight from field systems is limited. Here, the authors show changes in the resistance and CRISPR loci of bacteria and the infectivity, host range and genome size of phage over multiple years in an aquaculture environment.

    • Elina Laanto
    • , Ville Hoikkala
    •  & Lotta-Riina Sundberg

  • Article
    | Open Access

    Zinc homeostasis in most bacteria is achieved by a set of regulators, each responding to a certain level of intracellular zinc. Here the authors show that, inStreptomyces coelicolor, the Zur regulator modulates the expression of genes for zinc import and export over a large range of zinc concentrations.

    • Seung-Hwan Choi
    • , Kang-Lok Lee
    •  & Jung-Hye Roe

  • 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

    The use of anammox microbiomes to treat wastewater is an escalating biotechnology, yet the functional role heterotrophic bacteria play in these systems remains poorly understood. Here, Lawsonet al. use metagenomics and metatranscriptomics to reveal that heterotrophs degrade free peptides, while recycling nitrate to nitrite.

    • Christopher E. Lawson
    • , Sha Wu
    •  & Daniel R. Noguera

  • 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

    Despite the importance of mismatch repair for genome stability, many Archaea and almost all Actinobacteria lack MutS and MutL proteins. Here the authors, usingMycobacterium smegmatisas a model, report that NucS/EndoMS endonuclease acts in a distinct mismatch repair pathway.

    • A. Castañeda-García
    • , A. I. Prieto
    •  & J. Blázquez

  • 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

    Fungi of the order Mucorales can cause life-threatening infections. Here, Chibucos et al. present genomic and transcriptomic analyses of a diverse set of Mucorales fungi, shedding light on their evolution and identifying potential therapeutic targets in the pathogens and the host.

    • Marcus C. Chibucos
    • , Sameh Soliman
    •  & Vincent M. Bruno

  • Article
    | Open Access

    Bacteria of the genus Streptomyces produce a great variety of natural products, the biosynthesis of which is subject to complex regulatory networks. Here the authors present a high-resolution, genome-wide analysis of the transcriptome and translatome of Streptomyces coelicolorunder various growth conditions.

    • Yujin Jeong
    • , Ji-Nu Kim
    •  & Byung-Kwan Cho

  • Article
    | Open Access

    The transcription factor Hsf1 and the molecular chaperone Hsp90 modulate the heat shock response in the pathogen Candida albicans. Here, Leach et al. reveal a complex interplay between the two factors that regulates the expression of genes involved in the heat shock response and virulence.

    • Michelle D. Leach
    • , Rhys A. Farrer
    •  & Leah E. Cowen

  • Article
    | Open Access

    Maintenance of cooperation in multicellular organisms is hypothesized to depend on high relatedness among cells. Here, Bastiaans et al. provide empirical support for this hypothesis by directly comparing the evolutionary stability of multicellular cooperation in experimental lines of a fungus kept at either high or low relatedness.

    • Eric Bastiaans
    • , Alfons J. M. Debets
    •  & Duur K. Aanen

  • Article
    | Open Access

    ANaerobic AMMonium OXidation (ANAMMOX) combined with partial nitritation has been adopted for removal of ammonium from wastewater. Here, Speth et al. describe the bacterial metagenome of a partial-nitritation/anammox (PNA) reactor, and provide 23 draft genomes, 19 of which were previously uncharacterized/sequenced/cultivated.

    • Daan R. Speth
    • , Michiel H. in ’t Zandt
    •  & Mike S. M. Jetten

  • Article
    | Open Access

    The fungal pathogen Candida glabrata readily acquires resistance to multiple types of antifungal drugs. Here, Healey et al. show that C. glabrataclinical isolates often carry mutations in a gene involved in DNA mismatch repair, and this is associated with increased propensity to develop antifungal resistance.

    • Kelley R. Healey
    • , Yanan Zhao
    •  & David S. Perlin

  • Article
    | Open Access

    It is thought that CRISPR-Cas systems, which confer acquired immunity to phage and archaeal viruses, are widespread among bacteria and archaea. Here, Burstein et al.show that entire lineages of uncultivated microorganisms are essentially devoid of CRISPR-Cas systems.

    • David Burstein
    • , Christine L. Sun
    •  & Jillian F. Banfield

  • Article
    | Open Access

    The clinical application of new sequencing techniques is expected to accelerate pathogen identification. Here, Bradley et al. present a clinician-friendly software package that uses sequencing data for quick and accurate prediction of antibiotic resistance profiles for S. aureus and M. tuberculosis.

    • Phelim Bradley
    • , N. Claire Gordon
    •  & Zamin Iqbal

  • Article
    | Open Access

    This study uses a large number of crosses between a common lab strain and vineyard-isolated strain of yeast, and estimates the phenotypic variance for various quantitative traits. Using this data set, the authors show additive quantitative trait loci (QTL) and QTL–QTL interactions to be on average 43% and 9%, respectively.

    • Joshua S. Bloom
    • , Iulia Kotenko
    •  & Leonid Kruglyak

  • Article
    | Open Access

    One of the key aspects for controlling infectious diseases is understanding how pathogens cross host species. Here the authors conduct a genome-wide analysis of Salmonella and show a high degree of variation, enabling host-adapted colonization among Salmonellaintestinal and systemic serovars.

    • Min Yue
    • , Xiangan Han
    •  & Dieter M. Schifferli

  • Article
    | Open Access

    Mutations allow RNA virus to adapt fast but also entail fitness costs. Geller et al. show that, in HIV-1, mutations occur three times less often in the most external domains of the envelope, and that this is due to changes in RNA sequence context and structure, which control viral and host-encoded mutational mechanisms.

    • Ron Geller
    • , Pilar Domingo-Calap
    •  & Rafael Sanjuán

  • Article
    | Open Access

    The Ljungan virus is a picornavirus that lacks the internal coat protein VP4, and the packaging of its RNA genome is poorly understood. Here, the authors use cryo-electron microscopy to visualize this virus and suggest that it uses a different mechanism to other viruses for encapsidation of its genome.

    • Ling Zhu
    • , Xiangxi Wang
    •  & David I. Stuart

  • 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

    Horizontal gene transfer from retroviruses to mammals is rare between unrelated viruses. Here the authors show the convergent acquisition by herpesviruses of a virulence gene of ancient retroviruses, which occurred at least twice from different donor lineages, to distinct herpesviruses that infect mammals.

    • Amr Aswad
    •  & Aris Katzourakis

  • 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 |

    Toxin–antitoxin systems of the Vap class regulate the growth of several bacterial pathogens including Mycobacterium tuberculosis. Here, the authors show that toxin VapC-mt4 arrests M. tuberculosis growth by specifically cleaving three tRNAs at a single site in their anticodon stem loop, leading to translation inhibition.

    • Jonathan W. Cruz
    • , Jared D. Sharp
    •  & Nancy A. Woychik

  • Article
    | Open Access

    Understanding the factors that enable some bird flu viruses to infect humans is important for the identification of circulating viruses with higher potential to infect us. Here, Taft et al.identify novel mutations in the polymerase of an avian H5N1 virus that help the virus to replicate in human cells and in mice

    • Andrew S. Taft
    • , Makoto Ozawa
    •  & Yoshihiro Kawaoka

  • 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

    Several pathogenic fungi such as Candida albicans undergo transitions between single-celled forms and multicellular filaments. Here the authors perform a genome-scale analysis of C. albicansand show that, contrary to common belief, filamentation is not required for escape from host immune cells.

    • Teresa R. O’Meara
    • , Amanda O. Veri
    •  & Leah E. Cowen

  • Article
    | Open Access

    Diversity-generating retroelements (DGRs) are genetic elements that introduce sequence variation within target genes in bacteria and their viruses. Here, Paul et al. report the discovery of DGRs in an archaeal virus and in two archaea from marine and terrestrial subsurface environments, respectively.

    • Blair G. Paul
    • , Sarah C. Bagby
    •  & David L. Valentine

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