Bacterial structural biology articles within Nature Communications

Featured

• Article
  15 April 2024 | Open Access

  Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation

  Said et al. used cryoEM, biochemistry and bioinformatics to uncover how the Sm-like protein Rof regulates transcription termination. Rof binds termination factor ρ, inhibiting ρ ring closure and its association with RNA or transcription complexes.

  • Nelly Said
  • , Mark Finazzo
  •  & Markus C. Wahl

• Article
  08 April 2024 | Open Access

  The assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili

  Type 1 pili are crucial cell surface bacterial virulence factors. Here, the authors show that FimD is required to assemble the most stable quaternary pilus structure by ensuring that the resulting protein polymer is free of structural defects.

  • Dawid S. Zyla
  • , Thomas Wiegand
  •  & Rudi Glockshuber

• Article
  29 March 2024 | Open Access

  Structural basis of Acinetobacter type IV pili targeting by an RNA virus

  Here, the authors structurally characterise the interaction between Acinetobacter phage AP205 and the type IV Acinetobacter pili using cryo-electron microscopy, uncovering the mechanistic determinants of this interaction.

  • Ran Meng
  • , Zhongliang Xing
  •  & Junjie Zhang

• Article
  29 February 2024 | Open Access

  A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa

  The second messenger c-di-GMP regulates various processes in bacteria, including biofilm formation and motility. Here, the authors show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein and a diguanylate cyclase.

  • Xueliang Zhan
  • , Kuo Zhang
  •  & Haihua Liang

• Article
  13 February 2024 | Open Access

  A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria

  The cell-wall peptidoglycan in model bacteria typically includes 4,3- and 3,3-crosslinks, catalysed by DD- and LD-transpeptidases, respectively. Here, the authors identify and characterise the activity and structure of an LD-transpeptidase that generates a new type of crosslink (1,3).

  • Akbar Espaillat
  • , Laura Alvarez
  •  & Felipe Cava

• Article
  07 February 2024 | Open Access

  Hormonal steroids induce multidrug resistance and stress response genes in Neisseria gonorrhoeae by binding to MtrR

  Transcriptional regulator MtrR inhibits the expression of the multidrug efflux pump operon mtrCDE in Neisseria gonorrhoeae. Here, Hooks et al. show that hormonal steroids bind to MtrR and decrease its affinity for cognate promoters, thus leading to increased mtrCDE expression and enhanced antimicrobial resistance.

  • Grace M. Hooks
  • , Julio C. Ayala
  •  & Richard G. Brennan

• Article
  20 January 2024 | Open Access

  Structure-guided discovery of anti-CRISPR and anti-phage defense proteins

  Bacteria use various defense systems to protect themselves from phage infection, and phages have evolved diverse counter-defense measures to overcome host defenses. Here, the authors use protein structural similarity and gene co-occurrence analyses for identification of new anti-phage and counter-defense systems.

  • Ning Duan
  • , Emily Hand
  •  & Akintunde Emiola

• Article
  21 December 2023 | Open Access

  Structural insights into the regulation, ligand recognition, and oligomerization of bacterial STING

  Here the authors present the crystal structure of a bacterial STING. The structure shows that bacterial STING can modulate immune responses by forming anti-parallel dimers or, in certain species, through the presence of a long lid.

  • Mei-Hui Hou
  • , Yu-Chuan Wang
  •  & Yeh Chen

• Article
  19 December 2023 | Open Access

  Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa

  Filamentous phages can assemble into mesoscale structures termed tactoids that protect bacteria in biofilms from antibiotics. Here, the authors dissect the biophysical factors influencing this protection using two model phages, Pf4 and fd.

  • Jan Böhning
  • , Miles Graham
  •  & Tanmay A. M. Bharat

• Article
  04 December 2023 | Open Access

  A structure of the relict phycobilisome from a thylakoid-free cyanobacterium

  Phycobilisomes are megacomplexes in cyanobacteria that capture light. Here, authors characterize a relict paddle-shaped phycobilisome structure, revealing phycobilisome diversity prior to the development of thylakoids.

  • Han-Wei Jiang
  • , Hsiang-Yi Wu
  •  & Ming-Yang Ho

• Article
  28 November 2023 | Open Access

  Structural and functional insights into the delivery of a bacterial Rhs pore-forming toxin to the membrane

  Bacterial Rhs proteins constitute a diverse family of secreted toxins. Here, the authors present a cryo-electron microscopy structure of an Rhs protein from Pseudomonas aeruginosa and provide insights into the mechanisms by which the protein delivers its encapsulated pore-forming toxin fragment to the bacterial membrane.

  • Amaia González-Magaña
  • , Igor Tascón
  •  & David Albesa-Jové

• Article
  24 November 2023 | Open Access

  Stochastic chain termination in bacterial pilus assembly

  Adhesive type-1 pili from Escherichia coli are filamentous protein complexes consisting of a short tip and a long rod formed by up to several thousand copies of a major subunit. Here, Giese et al. reconstitute the entire type-1 pilus rod assembly reaction in vitro, using all constituent protein subunits, and identify a subunit that acts as an irreversible assembly terminator.

  • Christoph Giese
  • , Chasper Puorger
  •  & Rudi Glockshuber

• Article
  18 November 2023 | Open Access

  Serine peptidase Vpr forms enzymatically active fibrils outside Bacillus bacteria revealed by cryo-EM

  Here, cryo-EM is used to identify an unreported fibril species derived from lab-cultured Bacillus amyloiquefaciens composed of the extracellular serine peptidase Vpr. Fibrillar Vpr is shown to be enzymatically active, suggesting the fibril form represents a strategy of enriching Vpr extracellular activity.

  • Yijia Cheng
  • , Jianting Han
  •  & Qin Cao

• Article
  06 November 2023 | Open Access

  Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes

  Outer membrane tethering is important for cell envelope integrity in diderm bacteria. Here, the authors present structures and functional analyses of the stalked porin OmpM, which is the main outer membrane tethering system within the Terrabacteria.

  • Augustinas Silale
  • , Yiling Zhu
  •  & Bert van den Berg

• Article
  03 November 2023 | Open Access

  Structure and function of the EA1 surface layer of Bacillus anthracis

  S-layers form continuous protein lattices on the surface of bacteria. Here, authors use S-layer depolymerizing nanobodies to solve the structure of the EA1 S-layer in the pathogen Bacillus anthracis and show its role as cell wall supportive structure”

  • Adrià Sogues
  • , Antonella Fioravanti
  •  & Han Remaut

• Article
  03 November 2023 | Open Access

  Structure of a membrane-bound menaquinol:organohalide oxidoreductase

  The structure of a bacterial membrane protein complex involved in the bioremediation of tetrachloroethene, a major chlorinated organic pollutant, was determined. It elucidates the path of electrons from menaquinol to the active site of the enzyme.

  • Lorenzo Cimmino
  • , Américo G. Duarte
  •  & Julien Maillard

• Article
  31 October 2023 | Open Access

  The structure of a hibernating ribosome in a Lyme disease pathogen

  Ribosomes are prime targets for antibiotics in pathogenic bacteria. Here, cryo-electron microscopy reveals features in the Borrelia burgdorferi ribosome that provide insights into ribosome evolution, dormancy, and antibiotic binding.

  • Manjuli R. Sharma
  • , Swati R. Manjari
  •  & Nilesh K. Banavali

• Article
  25 August 2023 | Open Access

  Architecture of the Heme-translocating CcmABCD/E complex required for Cytochrome c maturation

  The covalent linkage of hemes to cytochromes c requires a maturation machinery. Here, the authors provide mechanistic insights into how the heme translocase complex CcmABCD flops a heme group, driven by ATP hydrolysis, and delivers it to the chaperone CcmE.

  • Lorena Ilcu
  • , Lukas Denkhaus
  •  & Oliver Einsle

• Article
  21 August 2023 | Open Access

  Crystal structure and functional implications of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases

  Here, the authors present structural and functional characterization of bacterial CD-NTases that synthesize cyclic dipyrimidines for phage resistance, revealing a (R/Q)xW motif dictating pyrimidine selection which suggests a sequential pathway for synthesizing 2’3’-cyclic di-UMP.

  • Chia-Shin Yang
  • , Tzu-Ping Ko
  •  & Yeh Chen

• Article
  10 August 2023 | Open Access

  High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase

  The 2-oxoglutarate dehydrogenase complex (ODH) is a textbook example of multienzymatic machinery. Here, the authors report the structural and regulatory properties of the Actinobacterial enzyme OdhA, a fusion of two ODH components acting in a supercomplex with pyruvate dehydrogenase.

  • Lu Yang
  • , Tristan Wagner
  •  & Marco Bellinzoni

• Article
  05 August 2023 | Open Access

  BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B₁₂ uptake in gut Bacteroides

  Uptake of vitamin B₁₂ is important for colonisation of the gut by Bacteroides species. Here the authors characterise B₁₂ uptake in Bacteroides thetaiotaomicron, mediated by outer membrane protein complexes consisting of surface-exposed BtuG lipoproteins and BtuB TonB-dependent transporters.

  • Javier Abellon-Ruiz
  • , Kalyanashis Jana
  •  & Bert van den Berg

• Article
  31 July 2023 | Open Access

  Conformational changes in the essential E. coli septal cell wall synthesis complex suggest an activation mechanism

  The divisome is a macromolecular machine composed of more than 30 proteins that controls cell wall constriction during bacterial cell division. Here, the authors provide insights into the structure and dynamics of the divisome core complex using a combination of structure prediction, molecular dynamics simulation, single-molecule imaging, and mutagenesis.

  • Brooke M. Britton
  • , Remy A. Yovanno
  •  & Zach Hensel

• Article
  27 July 2023 | Open Access

  Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unit

  In this work, the authors provide mechanistic insights for understanding the sodium-dependent, bacterial flagellar stator unit PomAB ion selectivity, directional rotation, and rotor incorporation in Vibrio spp.

  • Haidai Hu
  • , Philipp F. Popp
  •  & Nicholas M. I. Taylor

• Article
  17 July 2023 | Open Access

  Molecular basis of β-lactam antibiotic resistance of ESKAPE bacterium E. faecium Penicillin Binding Protein PBP5

  Penicillin Binding Proteins (PBPs) are the main targets of β-lactam antibiotics. Here the authors use NMR spectroscopy, crystallography and microbiology to define the dynamics of E. faecium PBP5 in solution and show that increased acyl-enzyme hydrolysis correlates with increased resistance.

  • Yamanappa Hunashal
  • , Ganesan Senthil Kumar
  •  & Wolfgang Peti

• Article
  11 July 2023 | Open Access

  DipM controls multiple autolysins and mediates a regulatory feedback loop promoting cell constriction in Caulobacter crescentus

  Proteins with a catalytically inactive LytM-type endopeptidase domain regulate cell wall-degrading enzymes in bacteria. Here, Izquierdo-Martinez et al. show that one such protein, DipM, coordinates different peptidoglycan-remodeling pathways to ensure proper cell constriction and daughter cell separation in the model bacterium Caulobacter crescentus.

  • Adrian Izquierdo-Martinez
  • , Maria Billini
  •  & Martin Thanbichler

• Article
  07 July 2023 | Open Access

  Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics

  Bacterial resistance to sulfonamide antibiotics (sulfas) is mediated by acquisition of sul genes, which encode sulfa-insensitive versions of the target enzyme, dihydropteroate synthase. Here, Venkatesan et al. study Sul enzymes using biochemical, structural, mutational and functional analyses, revealing the molecular basis for Sul-mediated drug resistance.

  • Meenakshi Venkatesan
  • , Michael Fruci
  •  & Alexei Savchenko

• Article
  17 May 2023 | Open Access

  Structural analysis and architectural principles of the bacterial amyloid curli

  Using Alpha fold modelling and cryo-EM reconstruction the authors reveal the structural and architectural principles of the bacterial functional amyloid curli, encompassing the continuous stacking of β-solenoid pseudo repeats within and across subunits.

  • Mike Sleutel
  • , Brajabandhu Pradhan
  •  & Han Remaut

• Article
  20 April 2023 | Open Access

  Structural insights into RNase J that plays an essential role in Mycobacterium tuberculosis RNA metabolism

  Here the authors report the crystal structures of RNase J from Mycobacterium tuberculosis in apo-state and complex with single strand RNA, revealing its physiological function in RNA metabolism.

  • Luyao Bao
  • , Juan Hu
  •  & Jixi Li

• Article
  19 April 2023 | Open Access

  Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b

  During infection, the Legionella effector Lem3 removes a phosphocholine moiety from the human protein Rab1. Here, the authors present the crystal structure of the stabilised Lem3:Rab1b complex, revealing the catalytic mechanism and substrate recognition of PPM phosphatases shaped Lem3.

  • Marietta S. Kaspers
  • , Vivian Pogenberg
  •  & Aymelt Itzen

• Article
  15 April 2023 | Open Access

  Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins

  Using cryo-EM, the authors identified 42 MIPs, including outer junction protein CFAP77 and outer dense fibers, in native doublet microtubules of Tetrahymena thermophila. Knockout of CFAP77 reduced ciliary beat frequency and led to outer junction damage.

  • Shintaroh Kubo
  • , Corbin S. Black
  •  & Khanh Huy Bui

• Article
  03 April 2023 | Open Access

  Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

  In our gut, oxalate-degrading bacteria absorb oxalate, a causative substance for kidney stone formation, and reduce our health risk. In this work, the authors report the structure of the oxalate transporter responsible for this process and how the protein works.

  • Titouan Jaunet-Lahary
  • , Tatsuro Shimamura
  •  & Atsuko Yamashita

• Article
  01 March 2023 | Open Access

  Crystal structure of a subtilisin-like autotransporter passenger domain reveals insights into its cytotoxic function

  Autotransporters are bacterial proteins that possess multiple activities associated with pathogenesis. Here the authors present the structure of the autotransporter subtilase Ssp from Serratia marcescens and show that its distinctive structural features are required for its cytotoxic function.

  • Lilian Hor
  • , Akila Pilapitiya
  •  & Begoña Heras

• Article
  27 February 2023 | Open Access

  Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter

  Bacteria and archaea use tripartite ATP-independent periplasmic (TRAP) transporters to import essential nutrients. Davies et al. report a high resolution structure of a TRAP and show that it uses an ‘elevator-with-an operator’ mechanism.

  • James S. Davies
  • , Michael J. Currie
  •  & Renwick C. J. Dobson

• Article
  22 February 2023 | Open Access

  Structural remodelling of the carbon–phosphorus lyase machinery by a dual ABC ATPase

  Here, authors analyse the structural organisation of the large carbon-phosphorus lyase enzyme from bacteria using electron microscopy and discover that it contains two ATP-binding cassette dimers of PhnK and PhnL and opens upon ATP hydrolysis.

  • Søren K. Amstrup
  • , Sui Ching Ong
  •  & Ditlev E. Brodersen

• Article
  07 February 2023 | Open Access

  Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

  Bacteria can exchange DNA through extracellular appendages (‘mating pili’) in a process known as conjugation. Here, Beltran et al. determine atomic structures by cryo-electron microscopy of a bacterial conjugative pilus and two archaeal pili, showing that the archaeal pili are homologous to bacterial mating pili.

  • Leticia C. Beltran
  • , Virginija Cvirkaite-Krupovic
  •  & Mart Krupovic

• Article
  06 January 2023 | Open Access

  Brucella effectors NyxA and NyxB target SENP3 to modulate the subcellular localisation of nucleolar proteins

  The bacterium Brucella abortus is an intracellular pathogen that modulates autophagy in host cells. Here, the authors identify two B. abortus effectors that interact with host protease SENP3, thus promoting cytoplasmic accumulation of nucleolar proteins associated with ribosomal biogenesis and facilitating intracellular replication of the pathogen

  • Arthur Louche
  • , Amandine Blanco
  •  & Suzana P. Salcedo

• Article
  16 December 2022 | Open Access

  A secreted effector with a dual role as a toxin and as a transcriptional factor

  Bacteria can deliver toxic effector proteins into the cytosol of neighboring cells. Here, the authors show that Yersinia pseudotuberculosis secretes an effector that modulates gene expression in neighboring cells of the same species and inhibits the growth of other competitors.

  • Dandan Wang
  • , Lingfang Zhu
  •  & Xihui Shen

• Article
  13 December 2022 | Open Access

  Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria

  ComEA is a DNA-binding protein required for DNA uptake during bacterial transformation. Here, Ahmed et al. determine X-ray crystal structures of ComEA from Gram-positive bacteria, identifying a domain that is absent in Gram-negative bacteria and drives ComEA oligomerization, which is required for transformation.

  • Ishtiyaq Ahmed
  • , Jeanette Hahn
  •  & Matthew B. Neiditch

• Article
  05 December 2022 | Open Access

  SepN is a septal junction component required for gated cell–cell communication in the filamentous cyanobacterium Nostoc

  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
  26 November 2022 | Open Access

  Structural basis for lipid and copper regulation of the ABC transporter MsbA

  The bacterial ABC transporter MsbA is essential for lipopolysaccharide biogenesis. Here, the authors apply native mass spectrometry, X-ray crystallography, cryo-EM and biochemical approaches to characterize the structural basis and functional roles of MsbA binding to copper and specific lipids.

  • Jixing Lyu
  • , Chang Liu
  •  & Arthur Laganowsky

• Article
  20 October 2022 | Open Access

  Promiscuity of response regulators for thioredoxin steers bacterial virulence

  The response regulator SsrB, a master activator of the Salmonella pathogenicity island-2 gene cluster, is under allosteric control of thioredoxin. Authors utilise in vitro and in vivo models to investigate if other members of the response regulator family might have adopted thioredoxin as a regulator.

  • Ju-Sim Kim
  • , Alexandra Born
  •  & Andrés Vázquez-Torres

• Article
  13 October 2022 | Open Access

  Structural and functional analysis of EntV reveals a 12 amino acid fragment protective against fungal infections

  Enterococcus faecalis has been reported to inhibit Candida albicans virulence via secretion of the bacteriocin EntV. Here, the authors present the crystal structure and characterise the antifungal properties of this peptide in numerous in vitro and in vivo assays.

  • Melissa R. Cruz
  • , Shane Cristy
  •  & Danielle A. Garsin

• Article
  14 September 2022 | Open Access

  Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli

  New cryo-EM structures of the formate hydrogenlyase complex from the model bacterium E. coli clarify how electrons and protons move through the complex and are combined to make H2 gas. The complex shows important similarities and differences to related bioenergetic complexes across the tree of life.

  • Ralf Steinhilper
  • , Gabriele Höff
  •  & Bonnie J. Murphy

• Article
  29 August 2022 | Open Access

  Proteolytic processing induces a conformational switch required for antibacterial toxin delivery

  Contact-dependent growth inhibition (CDI) is an important mechanism of bacterial competition. Here, Bartelli et al. show that proteolytic processing of a CDI toxin induces a conformational switch required for translocation into target bacteria.

  • Nicholas L. Bartelli
  • , Victor J. Passanisi
  •  & Christopher S. Hayes

• Article
  26 August 2022 | Open Access

  Water-organizing motif continuity is critical for potent ice nucleation protein activity

  Ice nucleation proteins have the same tandemly arrayed water-organizing motifs seen in some antifreeze proteins, but on a larger scale. The authors show that mutation, interruption, and truncation of these arrays reduce ice nucleation activity indicating that the two protein types share a common mechanism.

  • Jordan Forbes
  • , Akalabya Bissoyi
  •  & Peter L. Davies

• Article
  20 July 2022 | Open Access

  Kinesin-8-specific loop-2 controls the dual activities of the motor domain according to tubulin protofilament shape

  Kinesin-8s are dual-activity motor proteins that can move processively on microtubules and depolymerize microtubule plus-ends. This study shows how kinesin-8s alternate between a promotility and a pro-microtubule-depolymerization state via their tubulin shape-sensing loop-2 region.

  • Byron Hunter
  • , Matthieu P. M. H. Benoit
  •  & John S. Allingham

• Article
  27 May 2022 | Open Access

  Structural basis for broad anti-phage immunity by DISARM

  DISARM (Defense Island System Associated with Restriction Modification) systems can provide bacteria with protection against a wide range of phage. Here, Bravo et al. determine cryo-EM structures of the core DISARM complex that shed light onto phage DNA recognition and activation of this widespread defense system.

  • Jack P. K. Bravo
  • , Cristian Aparicio-Maldonado
  •  & David W. Taylor

• Article
  26 April 2022 | Open Access

  A periplasmic cinched protein is required for siderophore secretion and virulence of Mycobacterium tuberculosis

  The pathogen Mycobacterium tuberculosis uses the siderophores called mycobactins and carboxymycobactins to acquire iron from the host. Here, Zhang et al. identify a protein that is important for siderophore secretion and for the pathogen’s growth in low-iron medium.

  • Lei Zhang
  • , James E. Kent
  •  & Michael Niederweis

• Article
  12 April 2022 | Open Access

  ComFC mediates transport and handling of single-stranded DNA during natural transformation

  The ComFC protein is essential for natural transformation, a process that plays a major role in the spread of antibiotic resistance genes. Here the authors show that ComFC is a membrane-associated protein that participates in the transport of DNA through the cell membrane and the handling of the single-stranded DNA once delivered into the cytoplasm.

  • Prashant P. Damke
  • , Louisa Celma
  •  & J. Pablo Radicella

• Article
  05 April 2022 | Open Access

  Cryo-EM structures of a LptDE transporter in complex with Pro-macrobodies offer insight into lipopolysaccharide translocation

  Lateral opening of the LptDE transporter in the outer membrane of Gram-negative bacteria is necessary for insertion of lipopolysaccharides. Here, Botte et al. report a cryo-EM structure of a partially opened LptDE transporter, in complex with rigid chaperones derived from nanobodies.

  • Mathieu Botte
  • , Dongchun Ni
  •  & Michael Hennig