Bacterial physiology articles within Nature Communications

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  • Article
    | Open Access

    Some cyanobacteria excrete nitrite when the supply of inorganic carbon is limiting, but the underlying mechanisms are unclear. Here, Kraus et al. identify a conserved protein that interacts with nitrite reductase, thus regulating nitrogen metabolism and promoting nitrite excretion.

    • Alexander Kraus
    • , Philipp Spät
    •  & Wolfgang R. Hess

  • Article
    | Open Access

    Cheese fermentation and flavour formation are the result of complex biochemical reactions driven by the activity of multiple microorganisms. Here, the authors identify microbial interactions as a mechanism underlying flavour formation in Cheddar cheese.

    • Chrats Melkonian
    • , Francisco Zorrilla
    •  & Ahmad A. Zeidan

  • Article
    | Open Access

    E. coli maintains membrane lipid asymmetry by transferring glycerophospholipids from the outer membrane to the inner membrane; this requires outer membrane protein MlaA, periplasmic chaperone MlaC, and inner-membrane complex MlaBDEF. Here, the authors show that in some bacteria that lack MlaA and MlaC, MlaD forms a transenvelope bridge comprising a typical inner-membrane domain and, in addition, an outer-membrane domain.

    • Kyrie P. Grasekamp
    • , Basile Beaud Benyahia
    •  & Christophe Beloin

  • Article
    | Open Access

    Many microorganisms are auxotrophic, that is, unable to synthesize the compounds they require for growth. Here, Ramoneda et al. predict amino acid biosynthetic capabilities of over 26,000 bacterial genomes using a metabolic pathway model validated with empirical data, and identify ecological contexts in which auxotrophy can be a successful strategy.

    • Josep Ramoneda
    • , Thomas B. N. Jensen
    •  & Noah Fierer

  • Article
    | Open Access

    The bacterium Bacillus subtilis can form various types of surface-associated communities, such as colonies, pellicles and submerged biofilms. Here, Dergham et al. provide a direct comparison of spatial transcriptional heterogeneity across the three types of surface-associated communities, revealing mosaic expression patterns for genes involved in various pathways.

    • Yasmine Dergham
    • , Dominique Le Coq
    •  & Romain Briandet

  • Article
    | Open Access

    H-NS is a global regulatory protein that represses expression of many genes in bacteria. Here, Li et al. show that a second messenger, cyclic di-GMP, binds to H-NS and inhibits its binding to DNA, thus relieving H-NS-mediated transcriptional silencing.

    • Shuyu Li
    • , Qinmeng Liu
    •  & Lei Zhang

  • Article
    | Open Access

    This paper reports on two mycobacterial glycerolipid acyltransferases capable of transferring acyl chains to position 1 or position 2 of both glycerol-3-phosphate and lysophosphatidic acid.

    • Shiva Kumar Angala
    • , Ana Carreras-Gonzalez
    •  & Mary Jackson

  • Article
    | Open Access

    Sulfate-reducing microorganisms are common in anoxic environments and represent an important link between the sulfur and carbon cycles. Here, Dyksma & Pester show that microbial sulfate reduction and aerobic respiration are not mutually exclusive in the same organism, sulfate reducers can mineralize organic polymers, and anaerobic mineralization of complex organic matter is not necessarily a multi-step process.

    • Stefan Dyksma
    •  & Michael Pester

  • Article
    | Open Access

    TerC family membrane proteins associate with the general protein secretion complex to facilitate the co-translocational loading of Mn(II) into nascent metalloenzymes. Here, the authors show that Bacillus subtilis mutants lacking TerC proteins are defective in production of the membrane-embedded lipoteichoic acid synthase and secreted proteases.

    • Bixi He
    • , Ankita J. Sachla
    •  & John D. Helmann

  • Article
    | Open Access

    In bacteria such as E. coli, Min proteins ensure proper localization of the septum at the mid-zone of the cell before cell division. Here, the authors study the effects of changes in relative expression of Min proteins on cell size, providing evidence that Min proteins contribute to the regulation of cell size and the timing of septum formation.

    • Harsh Vashistha
    • , Joanna Jammal-Touma
    •  & Hanna Salman

  • Article
    | Open Access

    Bacterial growth rate depends on the number of active ribosomes and translation elongation rate. Matamouros et al. show that Corynebacterium glutamicum, a gram-positive model species, uses a different strategy than Escherichia coli during slow growth by strongly reducing the translation elongation rate while keeping a high number of active ribosomes.

    • Susana Matamouros
    • , Thomas Gensch
    •  & Michael Bott

  • Article
    | Open Access

    Bacteria of the SAR202 clade are ubiquitously distributed in the ocean, but their biology is poorly understood due to the lack of cultivated isolates. Here, Lim et al. report the cultivation of marine SAR202 bacteria and provide insights into the physiology of these enigmatic microorganisms.

    • Yeonjung Lim
    • , Ji-Hui Seo
    •  & Jang-Cheon Cho

  • Article
    | Open Access

    Broad-spectrum antibiotics can kill harmless bacteria in our intestine, thus facilitating invasion by antibiotic-resistant bacteria such as carbapenem-resistant Enterobacteriaceae (CRE). Here, Yip et al. show that killing gut bacteria with antibiotics leads to enrichment of nutrients and depletion of inhibitory microbial metabolites, which overall potentiates CRE growth.

    • Alexander Y. G. Yip
    • , Olivia G. King
    •  & Julie A. K. McDonald

  • Article
    | Open Access

    Thermophilic microorganisms can live at high temperatures, but the origin and evolution of this ability are unclear. Here, the authors isolate a thermophilic bacterium from a deep-sea hydrothermal vent, and show it belongs to a major early-diverging lineage whose ancestor was likely also a thermophilic bacterium.

    • Hao Leng
    • , Yinzhao Wang
    •  & Xiang Xiao

  • Article
    | Open Access

    Inhibition of bacterial cell wall synthesis by β-lactam antibiotics results in a loss of cell wall integrity, but cells die via a combination of downstream events involving metabolic perturbations and oxidative damage. Here, Kawai et al. identify key enzymatic steps that stimulate the generation of reactive oxygen species and highlight the role of iron homeostasis in the lethal effects mediated by oxidative damage.

    • Yoshikazu Kawai
    • , Maki Kawai
    •  & Jeff Errington

  • Article
    | Open Access

    Aerobic methanotrophic bacteria oxidize methane in sulfide-rich environments, even though hydrogen sulfide (H2S) inhibits methane oxidation and aerobic respiration. Here, Schmitz et al. show that a single microorganism can oxidize methane and H2S simultaneously, and this is associated with upregulation of a sulfide-insensitive terminal oxidase.

    • Rob A. Schmitz
    • , Stijn H. Peeters
    •  & Arjan Pol

  • Article
    | Open Access

    Microbes often produce molecules (termed siderophores) that bind iron and then are taken up using specific receptors for iron acquisition. Here, the authors show that a compound produced by Bacillus subtilis plays a more complex role, by modulating iron availability and conferring protection against oxidative stress during inter-species competition.

    • Vincent Charron-Lamoureux
    • , Lounès Haroune
    •  & Pascale B. Beauregard

  • Article
    | Open Access

    Serine/threonine kinases (STKs) regulate the synthesis of capsular polysaccharide in bacteria through unclear mechanisms. Here, Tang et al. identify a protein that is phosphorylated by an STK and modulates the activity of a phosphoregulatory system in Streptococcus suis, thus linking STKs to capsular polysaccharide synthesis.

    • Jinsheng Tang
    • , Mengru Guo
    •  & Hongjie Fan

  • Article
    | Open Access

    Pathogenic Brucella abortus, containing a mix of lipopolysaccharides with or without O-antigen, grows its envelope in a unipolar manner. Here, Servais et al, localize the LPS translocation machinery and identify the main O-antigen ligase in Brucella species, shedding light on the basic biology of this organism.

    • Caroline Servais
    • , Victoria Vassen
    •  & Xavier De Bolle

  • Article
    | Open Access

    Bacteria undergo nutrient fluctuations during repeated feast and famine cycles and need to metabolically adapt to these changes. Using quantitative proteomics, Zhu & Dai show that the stringent response of (p)ppGpp is crucial for the timely adaption of bacterial growth to both amino acid and carbon downshift.

    • Manlu Zhu
    •  & Xiongfeng Dai

  • Article
    | Open Access

    Deep mutational scanning can be used to investigate protein function and stability. Here, Dewachter et al. use deep mutational scanning on three essential bacterial proteins to study the mutations’ effects in their original genomic context, providing insight into the proteins’ function and their potential as targets for new antibiotic development.

    • Liselot Dewachter
    • , Aaron N. Brooks
    •  & Jan Michiels

  • Article
    | Open Access

    Some bacteria use the muropeptide transporter AmpG for uptake and recycling of cell wall fragments that are released during cell growth and division. Here, Gilmore & Cava show that the plant pathogen Agrobacterium tumefaciens, which lacks an AmpG homologue, uses a different type of transporter for the same function, which is essential for normal growth in this organism.

    • Michael C. Gilmore
    •  & Felipe Cava

  • Article
    | Open Access

    Small regulatory RNAs (sRNAs) often act in concert with the RNA-chaperone Hfq to regulate the expression of multiple target transcripts in bacteria. Here, the authors identify Hfq-interacting sRNAs and their targets in the pathogen Vibrio cholerae, including an RNA sponge that binds and inactivates four sRNAs that modulate the quorum sensing pathway.

    • Michaela Huber
    • , Anne Lippegaus
    •  & Kai Papenfort

  • Article
    | Open Access

    The filamentous cyanobacterium Nostoc regulates communication between sister cells via a conformational change in septal junctions. Here, the authors identify and characterize protein SepN as a component of septal junctions, and highlight the importance of controlling molecular diffusion between cells to ensure the survival of a multicellular organism.

    • Ann-Katrin Kieninger
    • , Piotr Tokarz
    •  & Iris Maldener

  • Article
    | Open Access

    The cell wall and cytoplasmic MreB polymers are important for bacterial cell shape. However, Spiroplasma cells lack a cell wall and still display a helical shape and kink-based motility, which is thought to rely on five MreB isoforms and a fibril protein. Here, Lartigue et al. show that heterologous expression of a single Spiroplasma MreB isoform confers helical shape and kinking ability to Mycoplasma cells, which are naturally spherical and non-motile.

    • Carole Lartigue
    • , Bastien Lambert
    •  & Laure Béven

  • Article
    | Open Access

    Lytic polysaccharide monooxygenases contribute to microbial degradation of chitin, but how the resulting oxidized chitooligosaccharides are utilized by microbes is unclear. Here, the authors describe a complete pathway for oxidative chitin utilization in marine bacteria.

    • Wen-Xin Jiang
    • , Ping-Yi Li
    •  & Yu-Zhong Zhang

  • Article
    | Open Access

    The transfer of electronic energy through a photosystem can harm the photosynthetic apparatus when not balanced with CO2 fixation. Here, the authors show that CO2 modulates electronic energy transfer in cyanobacteria by binding to and enhancing the activity of the light-harvesting complex.

    • Alejandra Guillén-García
    • , Savannah E. R. Gibson
    •  & Martin J. Cann

  • Article
    | Open Access

    Nucleotide second messengers, such as cAMP and c-di-GMP, regulate many physiological processes in bacteria, including biofilm formation. Here, the authors provide evidence of cross-talk between cAMP and c-di-GMP pathways through direct interaction of their effectors, showing that the cAMP receptor protein (CRP) can play regulatory roles at the post-translational level.

    • Cong Liu
    • , Di Sun
    •  & Weijie Liu

  • Article
    | Open Access

    Orthologs of natural competence genes are conserved in non-competent bacterial species, suggesting they have a role other than in transformation. Here, the authors show that competence induction in Staphylococcus aureus occurs in response to reactive oxygen species and host defenses that compromise bacterial respiration during infection, leading to increased DNA and glucose uptake and glycolytic flux.

    • Mar Cordero
    • , Julia García-Fernández
    •  & Daniel Lopez

  • Article
    | Open Access

    Cells of the predatory bacterium Bdellovibrio bacteriovorus, which invades and replicates within the periplasm of other bacteria, have a characteristic curved rod shape. Here, Banks et al. show that a peptidoglycan hydrolase is required for the curved shape, and this facilitates invasion of prey cells.

    • Emma J. Banks
    • , Mauricio Valdivia-Delgado
    •  & R. Elizabeth Sockett

  • Article
    | Open Access

    Many bacteria can take up exogenous DNA, in a process that often requires surface appendages composed of thousands of protein subunits called pilins. Here, Braus et al. show that a minor pilin binds directly to DNA and is important for DNA uptake in the pathogen Legionella pneumophila.

    • Sebastian A. G. Braus
    • , Francesca L. Short
    •  & Manuela K. Hospenthal

  • Article
    | Open Access

    Bacterial responses to nutrient limitation and other stress conditions are often modulated by the nucleotide-based second messenger (p)ppGpp. Here, the authors show that (p)ppGpp inhibits the SRP membrane-protein insertion and secretion pathway by binding to GTPases Ffh and FtsY.

    • Laura Czech
    • , Christopher-Nils Mais
    •  & Gert Bange

  • Article
    | Open Access

    Antibiotic persisters are phenotypic variants within an isogenic bacterial population that are transiently tolerant to antibiotic treatment. Here, the authors provide evidence that cytoplasmic acidification, amplified by a compromised respiratory complex I, can act as a signaling hub for perturbed metabolic homeostasis in antibiotic persisters.

    • Bram Van den Bergh
    • , Hannah Schramke
    •  & Matthias Heinemann

  • Article
    | Open Access

    The pathogen Mycobacterium tuberculosis depends on host fatty acids and cholesterol as carbon sources. Here, Beites et al. identify a protein complex that is essential for fatty acid and cholesterol utilization and thus for survival of M. tuberculosis during infection, supporting this pathway as a potential target for tuberculosis drug development.

    • Tiago Beites
    • , Robert S. Jansen
    •  & Sabine Ehrt

  • Article
    | Open Access

    It is unclear how bacterial cells adapt the reversible switching of flagellar motor rotation to environments of different viscosities. Here, Antani et al. show that flagellar mechanosensors allosterically control the motor’s binding affinity for the chemotaxis response regulator, CheY-P, to adapt flagellar switching over varying viscous loads.

    • Jyot D. Antani
    • , Rachit Gupta
    •  & Pushkar P. Lele

  • Article
    | Open Access

    Bacterial surface adhesion proteins are characterized by unusual mechanical properties. Here, the authors use atomic force microscopy-based technique to study a surface-anchoring protein Cpe0147 from Clostridium perfringens and show that an ester bond can withstand considerable mechanical forces and prevent complete protein unfolding.

    • Hai Lei
    • , Quan Ma
    •  & Yi Cao

  • Article
    | Open Access

    Xyloglucans are polysaccharides found in plant cell walls. Here, the authors describe the xyloglucan depolymerization machinery of phytopathogenic Xanthomonas bacteria, and show that sugars released by this system induce the expression of key virulence factors driving pathogenesis.

    • Plinio S. Vieira
    • , Isabela M. Bonfim
    •  & Mario T. Murakami

  • Article
    | Open Access

    Type IV pili (T4P) are retractile appendages used by bacteria for DNA uptake and other purposes. T4P extension is thought to occur through the action of a single motor protein, PilB. Here, Ellison et al. show that T4P synthesis in Acinetobacter baylyi depends not only on PilB but also on an additional, distinct motor, TfpB.

    • Courtney K. Ellison
    • , Triana N. Dalia
    •  & Ankur B. Dalia

  • Article
    | Open Access

    Here the authors use microfluidics and single-cell microscopy to quantify the growth dynamics of individual E. coli cells exposed to nutrient fluctuations with periods as short as 30 seconds, finding that nutrient fluctuations reduce growth rates up to 50% compared to a steady nutrient delivery of equal average concentration, implying that temporal variability is an important parameter in bacterial growth.

    • Jen Nguyen
    • , Vicente Fernandez
    •  & Roman Stocker

  • Article
    | Open Access

    Bacterial stress responses are potential targets for new antimicrobials. Here, Avican et al. present global transcriptomes for 32 bacterial pathogens grown under 11 stress conditions, and identify common and unique regulatory responses, as well as processes participating in different stress responses.

    • Kemal Avican
    • , Jehad Aldahdooh
    •  & Maria Fällman

  • Article
    | Open Access

    Bacterial cell division by cell wall synthesis proteins is guided by treadmilling filaments of the cytoskeleton protein FtsZ. Here authors use nanofabrication, advanced microscopy, and microfluidics to resolve the function of FtsZ treadmilling in the Gram-positive model organism Bacillus subtilis.

    • Kevin D. Whitley
    • , Calum Jukes
    •  & Séamus Holden

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