Bacterial structural biology articles within Nature Communications

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  • Article
    | Open Access

    Upon target RNA recognition, type III CRISPR-Cas systems produce cyclic oligoadenylates that activate effectors such as Csm6 ribonucleases. Here, Garcia-Doval et al. show that Enteroccocus italicus Csm6 degrades its cyclic hexa-AMP activator, and report the crystal structure of the protein bound to an activator mimic.

    • Carmela Garcia-Doval
    • , Frank Schwede
    •  & Martin Jinek

  • Article
    | Open Access

    The actin homolog MreB directs cell-wall insertion and maintains cell shape in many rod-shaped bacteria. Here, Shi et al. perform molecular dynamics simulations for MreB to extract mechanical parameters for inputs into a coarse-grained biophysical polymer model that predicts MreB filament properties.

    • Handuo Shi
    • , David A. Quint
    •  & Kerwyn Casey Huang

  • Article
    | Open Access

    KUP transporters facilitate potassium uptake by the co-transport of protons and are key players in potassium homeostasis. Here authors identify the potassium importer KimA from Bacillus subtilis as a new member of the KUP transporter family and show the cryo-EM structure of KimA in an inward-occluded, trans-inhibited conformation.

    • Igor Tascón
    • , Joana S. Sousa
    •  & Inga Hänelt

  • Article
    | Open Access

    Large Clostridial toxins infiltrate host cells using a translocation domain (LCT-T). Here, using a genomics-driven approach and functional assays, the authors uncover the presence of distant LCT-T homologs in bacteria outside clostridia and provide evidence for a toxic effector function in the gammaproteobacterium Serratia marcescens.

    • Kathleen E. Orrell
    • , Michael J. Mansfield
    •  & Roman A. Melnyk

  • Article
    | Open Access

    Bacterial microcompartments (BMCs) consist of a protein shell and an encapsulated enzymatic core. Here, Kalnins et al. study a BMC from Klebsiella pneumoniae, show that the enzymatic core is encapsulated in a hierarchical manner, and solve the cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle.

    • Gints Kalnins
    • , Eva-Emilija Cesle
    •  & Kaspars Tars

  • Article
    | Open Access

    SPOR domains are present in bacterial proteins that recognize cell-wall peptidoglycan strands stripped of the peptide stems. Here, Alcorlo et al. show that, indeed, the presence of peptide stems abrogates binding to a SPOR domain, and provide insights into the molecular basis for recognition.

    • Martín Alcorlo
    • , David A. Dik
    •  & Juan A. Hermoso

  • Article
    | Open Access

    Bacterial type II secretion systems (T2SSs) translocate virulence factors, toxins and enzymes across the cell outer membrane. Here, Chernyatina and Low use negative stain and cryo-electron microscopy to reveal the core architecture of an assembled T2SS from the pathogen Klebsiella pneumoniae.

    • Anastasia A. Chernyatina
    •  & Harry H. Low

  • Article
    | Open Access

    Iron is essential for growth of Mycobacterium tuberculosis, but most of the iron in the human body is stored in heme within hemoglobin. Here, Mitra et al. identify two heme uptake mechanisms in M. tuberculosis, one dependent on the inner-membrane Dpp importer and the other dependent on host albumin.

    • Avishek Mitra
    • , Ying-Hui Ko
    •  & Michael Niederweis

  • Article
    | Open Access

    The bacterial enzyme PaaZ is involved in the breakdown of environmental pollutants via the aerobic-anaerobic hybrid pathway but its substrate transfer mechanism is not fully understood. Here, the authors present cryoEM structures of free and ligand-bound PaaZ that suggest a mechanism for internal substrate channeling.

    • Nitish Sathyanarayanan
    • , Giuseppe Cannone
    •  & Kutti R. Vinothkumar

  • Article
    | Open Access

    Bacteria produce small iron-binding molecules called siderophores, which are recognised by outer-membrane transporters. Here, the authors show that a Pseudomonas transporter recognises the siderophore enterobactin using extracellular loops distant from the pore, and propose that there is a second binding site deeper inside the structure.

    • Lucile Moynié
    • , Stefan Milenkovic
    •  & James H. Naismith

  • Article
    | Open Access

    WalKR is an essential two-component regulator that controls peptidoglycan synthesis in the human pathogen Staphylococcus aureus. Here, the authors provide biochemical, structural, and functional evidence supporting that the binding of a zinc ion inhibits autophosphorylation and thus alters WalKR regulatory activity.

    • Ian R. Monk
    • , Nausad Shaikh
    •  & Timothy P. Stinear

  • Article
    | Open Access

    Chlamydia trachomatis forms membrane-bound inclusions inside the host cell that are decorated with IncA, a SNARE-like protein that promotes the fusion of inclusions. Here, Cingolani et al. show that the protein folds into a non-canonical four-helix bundle and identify an intramolecular clamp required for membrane fusion.

    • Gino Cingolani
    • , Michael McCauley
    •  & Fabienne Paumet

  • Article
    | Open Access

    Multidrug efflux pumps actively expel a wide range of toxic substrates from bacteria and play a major role in drug resistance. Here authors show the in situ structure of the efflux pump AcrAB-TolC obtained by electron cryo-tomography and subtomogram averaging.

    • Xiaodong Shi
    • , Muyuan Chen
    •  & Zhao Wang

  • Article
    | Open Access

    GpsB is a cytosolic protein that modulates bacterial cell wall synthesis by interacting with cytoplasmic domains of peptidoglycan synthases. Here, Cleverley et al. describe structural features that are important for these interactions, and identify new interacting partners of GpsB in three bacterial species.

    • Robert M. Cleverley
    • , Zoe J. Rutter
    •  & Richard J. Lewis

  • Article
    | Open Access

    SH2 domains bind to tyrosine-phosphorylated proteins and play crucial roles in signal transduction in mammalian cells. Here, Kaneko et al. identify a large family of SH2 domains in the bacterial pathogen Legionella that bind to mammalian phosphorylated proteins, in some cases with very high affinity.

    • Tomonori Kaneko
    • , Peter J. Stogios
    •  & Shawn S.-C. Li

  • Article
    | Open Access

    Gram-positive bacterial envelopes comprise proteinaceous surface layers (S-layers) important for survival and virulence that are often anchored to the cell wall through secondary cell wall polymers. Here the authors use a structural and biophysical approach to define the molecular mechanism of this important interaction.

    • Ryan J. Blackler
    • , Arturo López-Guzmán
    •  & Stephen V. Evans

  • Article
    | Open Access

    LpxB is a membrane-associated glycosyltransferase required for bacterial lipopolysaccharide biosynthesis. Here, Bohl et al. solve the crystal structure of a soluble LpxB variant, showing an intertwined C-terminally swapped dimer, and residues likely mediating association with lipidic substrates or the membrane.

    • Heather O. Bohl
    • , Ke Shi
    •  & Hideki Aihara

  • Article
    | Open Access

    Chitin degrading bacteria are important for marine ecosystems. Here the authors structurally and functionally characterize the Vibrio harveyi outer membrane diffusion channel chitoporin and give mechanistic insights into chito-oligosaccharide uptake.

    • Anuwat Aunkham
    • , Michael Zahn
    •  & Bert van den Berg

  • Article
    | Open Access

    Many Gram-negative bacteria secrete exopolysaccharides via functionally homologous synthase-dependent systems. Here the authors use electron microscopy to reveal that biofilm-promoting cellulose in E. coli is secreted by a conserved multi-component secretion system with a megadalton-sized asymmetric architecture.

    • Petya Violinova Krasteva
    • , Joaquin Bernal-Bayard
    •  & Jean-Marc Ghigo

  • Article
    | Open Access

    The bacterial zinc transporter ZntB is important for maintaining zinc homeostasis and is mechanistically not well understood. Here, the authors present the cryo-EM structure of ZntB at 4.2 Å resolution, perform transport assays and propose a model for its Zn2+ transport mechanism.

    • Cornelius Gati
    • , Artem Stetsenko
    •  & Albert Guskov

  • Article
    | Open Access

    The Bam complex promotes the insertion of β-barrel proteins (such as UpaG, a trimeric autotransporter adhesin) into the bacterial outer membrane. Here, Sikdar et al. show that UpaG β-barrel segments fold into a trimeric structure in the periplasm before they interact with the Bam complex.

    • Rakesh Sikdar
    • , Janine H. Peterson
    •  & Harris D. Bernstein

  • Article
    | Open Access

    Bacterial flagellar filaments are composed almost entirely of a single protein—flagellin—which can switch between different supercoiled states in a highly cooperative manner. Here the authors present near-atomic resolution cryo-EM structures of nine flagellar filaments, and begin to shed light on the molecular basis of filament switching.

    • Fengbin Wang
    • , Andrew M. Burrage
    •  & Edward H. Egelman

  • Article
    | Open Access

    Bacterial wall biosynthesis is a complex process that requires the coordination of multiple enzymes. Here, the authors structurally characterize the PBP2:MreC complex involved in peptidoglycan elongation and cross-linking, and demonstrate that its disruption leads to loss of H. pylori shape and inability to sustain growth.

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

  • Article
    | Open Access

    Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.

    • Donna Matzov
    • , Shintaro Aibara
    •  & Ada E. Yonath

  • Article
    | Open Access

    Bacterial disulfide isomerases shuffle incorrect disulfide bonds. Here, the authors structurally characterize the disulfide isomerase ScsC fromProteus mirabilisand identify a functionally important shape-shifting motif that allows ScsC to adopt a diverse range of conformations and enable swarming in the presence of copper stress.

    • Emily J. Furlong
    • , Alvin W. Lo
    •  & Jennifer L. Martin

  • Article
    | Open Access

    Bacterial outer membrane TonB-dependent transporters (TBDTs) mediate the influx of several nutrients. Here the authors use single-molecule force spectroscopy to show that the interaction between TonB andEscherichia coliTBDT BtuB is mechanically resistant to the pulling that gates the BtuB channel.

    • Samuel J. Hickman
    • , Rachael E. M. Cooper
    •  & David J. Brockwell

  • Article
    | Open Access

    The bacterial flagellum is a motile organelle that enables bacterial movement. Here the authors explain how the structurally similar flagellum components FlgG and FlgE can give rise to distinct macrostructures—the rod and hook—through subtle differences in domain orientation attributable to a short N-terminal insertion in FlgG.

    • Takashi Fujii
    • , Takayuki Kato
    •  & Keiichi Namba

  • Article
    | Open Access

    Many bacteria use TonB-dependent outer membrane receptors to scavenge iron from their host during infection. Here, the authors report on the structure and function of FusA, which is a bacterial receptor that is used to obtain iron from plants.

    • Rhys Grinter
    • , Inokentijs Josts
    •  & Daniel Walker

  • Article
    | Open Access

    Type IV pili are present on a wide range of bacterial pathogens and mediate diverse functions. Here the authors report a high resolution crystal structure of the pilin subunit PilE, and a cryoEM reconstruction of the Type IV pilus filament from N. meningitidisthat offer insight into pilus assembly and functions.

    • Subramania Kolappan
    • , Mathieu Coureuil
    •  & Lisa Craig

  • Article
    | Open Access

    Cyclic-di-GMP is a bacterial second messenger that binds to the regulatory domain of ATPases of some bacteria. Here, the authors report the crystal structure of this interaction, identify a cyclic-di-GMP binding mode, and show that this interaction might be important for bacterial biofilm formation.

    • Yu-Chuan Wang
    • , Ko-Hsin Chin
    •  & Shan-Ho Chou

  • Article
    | Open Access

    Haemophilus influenzae requires haem, and acquires it from host haemoproteins including haemopexin. Here, the authors examine the haem transport system consisting of HxuA, HxuB and HxuC via the structures of HxuA in complex with haemopexin.

    • Silvia Zambolin
    • , Bernard Clantin
    •  & Philippe Delepelaire

  • Article
    | Open Access

    Antibiotic resistance is a major clinical problem that threatens to undermine our ability to control infectious diseases. Here the authors present detailed structural analysis of Rifampin phosphotransferase from Listeria monocytogenes, yielding insight on how this class of enzyme inactivates its target antibiotics.

    • Peter J. Stogios
    • , Georgina Cox
    •  & Gerard D. Wright

  • Article
    | Open Access

    Bacterial DNA primarily exists in a negatively supercoiled or under-wound state. Here, by mapping the supercoiling state, the authors show that there is a gradient of supercoiling across the bacterial chromosome with the terminus being more negatively supercoiled than the origin.

    • Avantika Lal
    • , Amlanjyoti Dhar
    •  & Sankar Adhya

  • Article
    | Open Access

    The regulation of iron levels is an important physiological process as excess cellular iron is highly toxic. Here the authors present several structures of a bacterial ferric uptake regulator (Fur) in complex with the Fe2+transport protein operator and Fur box, shedding light on how iron promotes DNA recognition by Fur.

    • Zengqin Deng
    • , Qing Wang
    •  & Zhongzhou Chen

  • Article
    | Open Access

    Planctomycetes are unusual bacteria with complex intracellular compartments and an apparent lack of peptidoglycan in their cell walls. Here, van Teeseling et al. show that the cell wall of an anammox planctomycete does contain peptidoglycan, and propose to redefine planctomycetes as Gram-negative bacteria.

    • Muriel C.F. van Teeseling
    • , Rob J. Mesman
    •  & Laura van Niftrik

  • Article
    | Open Access

    The densely crosslinked protein coats of bacterial spores are among the most durable static structures in biology. Wu et al.reconstitute the basement layer of a bacterial spore coat on membrane-coated beads, and generate covalently-modified spore-like particles with therapeutic potential.

    • I-Lin Wu
    • , Kedar Narayan
    •  & Kumaran S. Ramamurthi

  • Article
    | Open Access

    During the initiation of bacterial DNA replication, loader proteins transfer the hexameric helicase ring onto replication origin DNA. Liu et al.report the crystal structure of a 570-kDa prepriming complex and suggest that the release of loader proteins is associated with the transition of the helicase ring to a spiral configuration.

    • Bin Liu
    • , William K. Eliason
    •  & Thomas A. Steitz

  • Article
    | Open Access

    Bacterial cell wall peptidoglycan is essential for viability and shape determination. Using high-resolution microscopy, Foster and colleagues elucidate the peptidoglycan architecture and insertion pattern in Escherichia coliand other Gram-negative bacteria, and propose a new model for cell wall elongation.

    • Robert D. Turner
    • , Alexander F. Hurd
    •  & Simon J. Foster

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