Bacterial structural biology articles within Nature Communications

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  • Article
    | Open Access

    Accurate descriptions of protein-protein interactions are essential for understanding biological systems. Here the authors present AF2Complex and show that application to the E. coli cytochrome biogenesis system I yields confident computational models for three sought-after assemblies.

    • Mu Gao
    • , Davi Nakajima An
    •  & Jeffrey Skolnick

  • 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

    EndoE is a multi-domain glycoside hydrolase of the human pathogen Enterococcus faecalis. Here, the authors present crystal structures of EndoE and provide biochemical insights into the molecular basis of EndoE’s substrate specificity and catalytic mechanism.

    • Mikel García-Alija
    • , Jonathan J. Du
    •  & Marcelo E. Guerin

  • Article
    | Open Access

    The S-layer is a two-dimensional protein array that covers the cell surface of many bacteria and archaea. Here, the authors use high-resolution X-ray crystallography and electron microscopy to provide detailed insights into S-layer organisation and assembly for the bacterial pathogen Clostridioides difficile.

    • Paola Lanzoni-Mangutchi
    • , Oishik Banerji
    •  & Paula S. Salgado

  • 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

    The cell wall of the bacterial pathogen Group A Streptococcus is decorated with a polysaccharide termed GAC, which is a target for vaccine development. Here, Rush et al. characterize the linkage between GAC and peptidoglycan, and identify a protein that deacetylates the linkage and thus protects the pathogen against host cationic antimicrobial proteins.

    • Jeffrey S. Rush
    • , Prakash Parajuli
    •  & Natalia Korotkova

  • Article
    | Open Access

    Pseudomonas aeruginosa employs lectins to bind to its host cells, and is known to be the major cause of lung infections. Lectin B (LecB) from Pseudomonas aeruginosa binds specifically to galactose and fucose and is important for pathogenicity, adhesion and biofilm formation. In this work, the neutron crystal structure (1.9 Å) of the deuterated LecB/Ca/fucose complex is reported. The structure, in combination with perdeuteration of the ligand and the receptor allowed the observation of hydrogen atoms, protonation states and hydrogen bonds involved in the interaction between pathogenic bacteria and host cells. Thus the study provides structural insights into the mechanism of high affinity binding of LecB to its targets.

    • Lukas Gajdos
    • , Matthew P. Blakeley
    •  & Anne Imberty

  • Article
    | Open Access

    Efflux transporters of the RND family confer resistance to multiple antibiotics in Gram-negative bacteria. Here, the authors identify pyridylpiperazine-based compounds that potentiate antibiotic activity in E. coli through allosteric inhibition of its primary RND transporter.

    • Coline Plé
    • , Heng-Keat Tam
    •  & Ruben C. Hartkoorn

  • Article
    | Open Access

    The bacterial Cyclic-oligonucleotide-Based Anti-phage Signaling System (CBASS) contains a CD-NTase that synthesizes cyclic di- and tri-nucleotides, and bacterial STING proteins recognize c-di-GMP generated by CD-NTase during phage infection and signal the infected bacteria to commit suicide. Here, the authors provide insights into the molecular basis for c-di-GMP recognition of bacterial STING proteins by determining two STING protein crystal structures with bound c-di-GMP from Prevotella corporis and Myroides sp. ZB35.

    • Tzu-Ping Ko
    • , Yu-Chuan Wang
    •  & Yeh Chen

  • Article
    | Open Access

    Germination of Bacillus subtilis spores in response to L-alanine requires a putative membrane receptor consisting of three proteins. Here, Artzi et al. use evolutionary co-variation analysis and functional assays of mutants to provide evidence that one of the proteins, GerAB, likely acts as the L-alanine sensor.

    • Lior Artzi
    • , Assaf Alon
    •  & David Z. Rudner

  • Article
    | Open Access

    Terminal bd oxidases endow bacterial pathogens with resistance to cellular stressors. The authors report the structure of E. coli bd-II type oxidase with the bound inhibitor aurachin D, providing a structural basis for the design of specifically binding antibiotics.

    • Antonia Grauel
    • , Jan Kägi
    •  & Thorsten Friedrich

  • Article
    | Open Access

    In C-glycosides the sugar moiety is linked through a carbon-carbon bond to the non-sugar moiety, which can be cleaved by intestinal microbes. Here, the authors use bioinformatics analysis to identify C-glycoside deglycosidase enzymes in intestinal and soil bacteria, biochemically characterise them and determine their structures and probe catalytic important residues in mutagenesis experiments.

    • Takahiro Mori
    • , Takuto Kumano
    •  & Michihiko Kobayashi

  • Article
    | Open Access

    Biofilm formation in Bacillus subtilis requires expression of matrix production genes, which are upregulated by transcriptional activator RemA. Here, the authors show that RemA forms octameric rings with the potential to form a 16-meric superstructure, suggesting that the protein can wrap DNA through a LytTR-related domain.

    • Tamara Hoffmann
    • , Devid Mrusek
    •  & Gert Bange

  • Article
    | Open Access

    M. tuberculosis cytochrome bd oxidase is of interest as a TB drug target. Here, the authors present the 2.5 Å cryo-EM structure of M. tuberculosis cytochrome bd oxidase and identify a disulfide bond within the canonical quinol binding and oxidation domain (Q-loop) and a menaquinone-9 binding site at heme b595.

    • Schara Safarian
    • , Helen K. Opel-Reading
    •  & Hartmut Michel

  • Article
    | Open Access

    ParA is an ATPase involved in the segregation of newly replicated DNA in bacteria. Here, structures of a ParA filament bound to DNA and of ParA in various nucleotide states offer insight into its conformational changes upon DNA binding and filament assembly, including the basis for ParA’s cooperative binding to DNA.

    • Alexandra V. Parker
    • , Daniel Mann
    •  & Julien R. C. Bergeron

  • Article
    | Open Access

    In Gram-negative bacteria, lipoproteins are transported from the inner membrane (IM) to the outer membrane (OM) by the ATP-binding cassette (ABC) transporter LolCDE. Here the authors present cryo-EM structures of nanodisc-embedded LolCDE in different states, providing mechanistic insight into the transport mechanism.

    • Stuti Sharma
    • , Ruoyu Zhou
    •  & Maofu Liao

  • Article
    | Open Access

    Bacteria can secrete diffusible protein toxins that kill competing bacteria. Here, the authors use biochemical, biophysical and structural analyses to show how one of these toxins exploits TolC (a major antibiotic efflux channel) to transport itself across the outer membrane of target cells.

    • Nicholas G. Housden
    • , Melissa N. Webby
    •  & Colin Kleanthous

  • Article
    | Open Access

    In the basal body of the bacterial flagellum, the LP ring acts as a bushing supporting the distal rod for its rapid and stable rotation. Here, Yamaguchi et al. present the electron cryomicroscopy structure of the LP ring around the rod, shedding light into potential mechanisms involved in stability and assembly of the structure.

    • Tomoko Yamaguchi
    • , Fumiaki Makino
    •  & Keiichi Namba

  • Article
    | Open Access

    The bacteriophytochrome DrBphP from Deinococcus radiodurans shows high sequence homology to the histidine kinase Agp1 from Agrobacterium fabrum but lacks kinase activity. Here, the authors structurally and biochemically analyse DrBphP and Agp1, showing that DrBphP is a light-activatable phosphatase.

    • Elina Multamäki
    • , Rahul Nanekar
    •  & Heikki Takala

  • 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

    Gram-negative bacteria can display intrinsic antibiotic resistance due to the action of tripartite efflux pumps, which include a H+/drug antiporter component. Here, the authors present a structure-function analysis of antiporter AcrB in intermediate states of the transport cycle, showing novel drug-binding sites and transport pathways.

    • Heng-Keat Tam
    • , Wuen Ee Foong
    •  & Klaas M. Pos

  • Article
    | Open Access

    Clostridioides difficile adenine methyltransferase A (CamA) is required for the sporulation and colonization of the pathogen that causes gastrointestinal infections. Here, the authors characterise CamA kinetically and present its crystal structure bound to the DNA recognition sequence, which reveals DNA distortions including bending and the flipping of the target adenine out of the DNA helix, as well as protein conformational changes upon cofactor binding.

    • Jujun Zhou
    • , John R. Horton
    •  & Xiaodong Cheng

  • Article
    | Open Access

    MreC is a membrane-associated protein that modulates the activity of the elongasome, a protein complex that controls cell wall formation in rod-shaped bacteria. Here, the authors use electron cryo-microscopy and X-ray crystallography to determine the structure of a self-associated form of MreC in atomic detail.

    • Alexandre Martins
    • , Carlos Contreras-Martel
    •  & Andréa Dessen

  • Article
    | Open Access

    The Multiple Peptide Resistance Factors (MprFs) utilize two separate domains to synthesize and translocate aminoacyl phospholipids to the outer leaflets of bacterial membranes. Here authors present cryo-electron microscopy structures of MprF homodimer from Rhizobium tropici (RtMprF) at two different states in complex with lysyl-phosphatidylglycerol (LysPG).

    • Danfeng Song
    • , Haizhan Jiao
    •  & Zhenfeng Liu

  • Article
    | Open Access

    As part of two-component systems, diguanylate cyclases (DGCs) are activated by phosphorylation. Structural and computational analyses of DgcR, a model DGC, reveal the phosphorylation-induced conformational changes and the activation mechanism likely shared by many DGCs with N-terminal coiled-coil linkers.

    • Raphael D. Teixeira
    • , Fabian Holzschuh
    •  & Tilman Schirmer

  • Article
    | Open Access

    The Legionella effector DrrA AMPylates the host protein Rab1 during infection, but the mechanism is still under debate. Here, the authors provide structural insights into the low-affinity DrrA:Rab1 interaction, showing that Rab1 allosterically activates DrrA through a non-conventional binding mechanism.

    • Jiqing Du
    • , Marie-Kristin von Wrisberg
    •  & Aymelt Itzen

  • Article
    | Open Access

    Tuberculosis necrotizing toxin (TNT) is secreted by Mycobacterium tuberculosis to kill host cells. Here, Tak, Dokland and Niederweis show that proteins EsxE and EsxF form membrane-spanning hetero-oligomeric pores that are important for TNT secretion.

    • Uday Tak
    • , Terje Dokland
    •  & Michael Niederweis

  • Article
    | Open Access

    Lipopolysaccharides, important components of the bacterial cell envelope, are synthesized at the inner membrane by the Wzx/Wzy-dependent assembly pathway. A cryo-EM structure of an intact E. coli WzzB, the polysaccharide co-polymerase component of this pathway, reveals details of the transmembrane, cytoplasmic domains and a conserved a proline-rich segment proximal to the C-terminal transmembrane helix.

    • Benjamin Wiseman
    • , Ram Gopal Nitharwal
    •  & Martin Högbom

  • Article
    | Open Access

    Pathogenic IgA1 metalloproteases block the initial host immune response by cleaving host IgA1. Using cryoEM, the authors here provide structural insights into the substrate recognition mechanism of Streptococcus pneumoniae IgA1 protease, and develop a protease-inhibiting antibody.

    • Zhiming Wang
    • , Jeremy Rahkola
    •  & Elan Eisenmesser

  • Article
    | Open Access

    Type IVa pili are bacterial surface filaments that undergo extension and retraction powered by a protein machine that spans the cell envelope. Here, Treuner-Lange et al. show that a complex formed by PilY1 and minor pilins is an integral part of this machine and is necessary for pilus extension, adhesion and retraction termination.

    • Anke Treuner-Lange
    • , Yi-Wei Chang
    •  & Lotte Søgaard-Andersen

  • Article
    | Open Access

    The bacterial periplasmic predator Bdellovibrio bacteriovorus deacetylates the peptidoglycan of the prey bacterium early upon invasion. Here, the authors identify and characterize a Bdellovibrio lysozyme that acts specifically on deacetylated peptidoglycan and is important for periplasmic exit.

    • Christopher J. Harding
    • , Simona G. Huwiler
    •  & Andrew L. Lovering

  • Article
    | Open Access

    Understanding bacterial adhesion is important in a number of different areas of study. Here using a range of simulations and experimental methods, the authors, report on the molecular mechanism behind the binding of bacteria to cellulose fibers at high shear force in the human gut.

    • Zhaowei Liu
    • , Haipei Liu
    •  & Michael A. Nash

  • Article
    | Open Access

    FliD forms a cap complex at the tip of bacterial flagella and is essential for flagellum filament assembly. Here, the authors present the cryo-EM structure of the Campylobacter jejuni cap complex, revealing a pentameric assembly of FliD and further show that the C. jejuni flagellum filament is 11-stranded.

    • Natalie S. Al-Otaibi
    • , Aidan J. Taylor
    •  & Julien R. C. Bergeron

  • Article
    | Open Access

    Many pathogens manipulate ubiquitin-mediated signaling to evade host cell defense. Here, the authors characterize the structure and enzymatic activity of a deubiquitylase domain from the causative pathogen of scrub typhus, providing evidence for a distinct mechanism of ubiquitin chain selectivity.

    • Jason M. Berk
    • , Christopher Lim
    •  & Mark Hochstrasser

  • Article
    | Open Access

    Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. Here, Neuhaus et al. show that the bacterium Thermus thermophilus produces two forms of type IV pilus, differing in structure, protein composition, and function.

    • Alexander Neuhaus
    • , Muniyandi Selvaraj
    •  & Vicki A. M. Gold

  • Article
    | Open Access

    The chaperone SurA is involved in outer membrane protein (OMP) biogenesis in Gram-negative bacteria, but its mechanism of action is not fully understood. Combining mass spectrometric, biophysical and computational approaches, the authors here show how the conformational dynamics of SurA facilitate OMP binding.

    • Antonio N. Calabrese
    • , Bob Schiffrin
    •  & Sheena E. Radford

  • Article
    | Open Access

    Gene rv3722c is essential for in vitro growth of Mycobacterium tuberculosis, but its function is unclear. Here, Jansen et al. show that Rv3722c is the primary aspartate aminotransferase of this pathogen, mediates nitrogen distribution, and is important for virulence during infection of macrophages and mice.

    • Robert S. Jansen
    • , Lungelo Mandyoli
    •  & Kyu Y. Rhee

  • Article
    | Open Access

    The second messenger c-di-GMP modulates multiple responses to environmental and cellular signals in bacteria. Here, Skotnicka et al. identify a protein that binds c-di-GMP and contributes to chromosome organization and segregation in Myxococcus xanthus, with DNA-binding activity regulated by c-di-GMP.

    • Dorota Skotnicka
    • , Wieland Steinchen
    •  & Lotte Søgaard-Andersen

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