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Article
| Open AccessBacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years
Bacteria usually have at least one rRNA operon on the chromosome, suggesting that the exclusive presence of rRNA operons on a plasmid is rare and unlikely to be stably maintained. Here, Anda et al. find that at least four bacterial clades in different phyla lost their chromosomal rRNA operons independently, and one of the clades has maintained this peculiar genome organization for hundreds of millions of years.
- Mizue Anda
- , Shun Yamanouchi
- & Wataru Iwasaki
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Article
| Open AccessFunctional annotation of enzyme-encoding genes using deep learning with transformer layers
Functional annotation of open reading frames in microbial genomes remains substantially incomplete. Here, Kim et al. present a deep learning model that utilizes transformer layers as a neural network architecture to predict specific catalytic functions for enzyme-encoding genes of unknown function.
- Gi Bae Kim
- , Ji Yeon Kim
- & Sang Yup Lee
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Article
| Open AccessFunctional and structural diversity in deubiquitinases of the Chlamydia-like bacterium Simkania negevensis
Intracellular bacteria use deubiquitinase effectors to avoid being targeted for autophagic clearance. The authors show that the Chlamydia-like bacterium Simkania negevensis encodes an unusually broad range of these enzymes, including members that specifically target linear and K6-linked ubiquitin chains.
- Vanessa Boll
- , Thomas Hermanns
- & Kay Hofmann
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Article
| Open AccessEssential gene complement of Planctopirus limnophila from the bacterial phylum Planctomycetes
Bacteria of the phylum Planctomycetes display unique cell biology features but are relatively understudied. Here, the authors report a genome-wide analysis of essential gene content in a planctomycete, providing insights into the divergent molecular and cell biology of these organisms.
- Elena Rivas-Marin
- , David Moyano-Palazuelo
- & Damien P. Devos
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Article
| Open AccessEnterohaemorrhagic E. coli utilizes host- and microbiota-derived L-malate as a signaling molecule for intestinal colonization
Here, Liu et al show that enterohaemorrhagic Escherichia coli utilizes host- and microbiota-derived L-malate as an essential nutrient and signalling molecule to promote its growth and colonization in the large intestine.
- Bin Liu
- , Lingyan Jiang
- & Bin Yang
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Article
| Open AccessSingle-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus
The authors use single-cell analysis to identify genes specifically expressed in plant root cells that respond to infection by nitrogen-fixing rhizobia. They show that one of these genes, SYMRKL1, is required for normal progression of infection.
- Manuel Frank
- , Lavinia Ioana Fechete
- & Stig Uggerhøj Andersen
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Article
| Open AccessDual 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
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Article
| Open AccessMicrobiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts
Gut microbiota play pivotal roles in IBD. Here, Ning et al. use a multi-omics approach to characterize gut microbiota and metabolites alterations, and potential pathogenic bacteria associated with IBD, with the aim to help develop more precise biomarkers for IBD diagnosis and drug targets
- Lijun Ning
- , Yi-Lu Zhou
- & Jie Hong
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Article
| Open AccessGreater wax moth control in apiaries can be improved by combining Bacillus thuringiensis and entrapments
The greater wax moth (GWM) is a major bee pest. Here, the authors show how a pest control method that combines a strain of Bacillus thuringiensis and a lure-based entrapment can help to control GWM using lab experiments and field beehives.
- Bo Han
- , Li Zhang
- & Pingli Dai
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Article
| Open AccessStructure 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
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Article
| Open AccessStructural basis for the toxicity of Legionella pneumophila effector SidH
Legionella pneumophila secretes hundreds of effectors to facilitate infection. Here, Sharma et al show that the virulence effector SidH adopts a unique α-helical conformation, leading to toxicity via tRNA binding site and resolve the structural basis of SidH regulation through ubiquitination.
- Rahul Sharma
- , Michael Adams
- & Sagar Bhogaraju
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Article
| Open AccessStructure 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
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Article
| Open AccessThe 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
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Article
| Open AccessPathogen-driven degradation of endogenous and therapeutic antibodies during streptococcal infections
Group A streptococcus causes a wide range of human diseases and significantly contributes to morbidity and mortality worldwide. Here, Toledo et al show how streptococcus alters the structure and function of endogenous and therapeutic antibodies during infection and how this is affected by the host microenvironment.
- Alejandro Gomez Toledo
- , Eleni Bratanis
- & Johan Malmström
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Article
| Open AccessAcylation of glycerolipids in mycobacteria
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
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Article
| Open AccessSIgA structures bound to Streptococcus pyogenes M4 and human CD89 provide insights into host-pathogen interactions
Here, the authors used cryo-EM to explore secretory Immunoglobulin A interactions with bacterial and host receptors, uncovering unexpected binding stoichiometry and unappreciated functional consequences relevant to understanding host-pathogen interactions.
- Qianqiao Liu
- & Beth M. Stadtmueller
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Article
| Open AccessMiniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale
The filarial worm Brugia malayi has evolved a mutualistic association with the endosymbiotic bacteria Wolbachia. Here, Sounart et al describe a spatial transcriptomic technique that can spatially resolve these miniature specimens.
- Hailey Sounart
- , Denis Voronin
- & Stefania Giacomello
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Article
| Open AccessCryptic susceptibility to penicillin/β-lactamase inhibitor combinations in emerging multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages
Staphylococcus epidermidis can cause invasive infections that are difficult to treat due to multi-resistance to most clinically relevant drugs, including methicillin and other β-lactam antibiotics, vancomycin, and rifampicin. In this work, the authors use in vitro assays and a mouse infection model to explore cryptic susceptibility and development of resistance to penicillin/β-lactamase combinations.
- Xiaoliang Ba
- , Claire L. Raisen
- & Jesper Larsen
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Article
| Open AccessGlobally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle
Photosynthesis is thought to be restricted to a few bacterial and eukaryotic phyla. Here, Li et al. provide evidence of photosynthetic abilities in uncultivated bacteria within the phylum Myxococcota, suggesting that some of these organisms may combine predatory and photosynthetic abilities.
- Liuyang Li
- , Danyue Huang
- & Yinzhao Wang
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Article
| Open AccessOxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium
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
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Article
| Open AccessTerC proteins function during protein secretion to metalate exoenzymes
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
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Article
| Open AccessRhs NADase effectors and their immunity proteins are exchangeable mediators of inter-bacterial competition in Serratia
Rhs proteins delivered by the Type VI secretion system play a key role in competition between rival bacteria. Here, the authors show that Rhs proteins with exchangeable NAD(P)+ glycohydrolase toxin domains and ‘orphan’ immunity proteins are flexible agents of intraspecies competition in Serratia.
- Martin Hagan
- , Genady Pankov
- & Sarah J. Coulthurst
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Article
| Open AccessThe leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes
The human pathogen Streptococcus pyogenes secretes a short peptide (LCP) that mediates intercellular communication and controls bacterial virulence. Here, the authors show that LCP homologues act as bacterial intercellular signals and regulate gene expression also in other bacteria.
- Shifu Aggarwal
- , Elaine Huang
- & Muthiah Kumaraswami
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Article
| Open AccessAuxin-producing bacteria promote barley rhizosheath formation
The rhizosheath, or the soil layer closely attached to roots, can help plants tolerate drought. Here, the authors show that rhizosheath formation in barley is promoted by soil bacteria that produce indole-3-acetic acid, a common auxin.
- Feiyun Xu
- , Hanpeng Liao
- & Weifeng Xu
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Article
| Open AccessGenome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli
Measuring gene expression responses for every transcription factor (TF)-gene pair in living prokaryotic cells is challenging. Here the authors report pooled promoter responses to TF perturbation sequencing (PPTP-seq) using CRISPRi, which they use to address this problem in E. coli.
- Yichao Han
- , Wanji Li
- & Fuzhong Zhang
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Article
| Open AccessA linear and circular dual-conformation noncoding RNA involved in oxidative stress tolerance in Bacillus altitudinis
The presence and/or biological functionality of circular RNAs in bacteria are unclear. Here, the authors identify a dual-conformation (linear and circular) noncoding RNA that promotes tolerance to oxidative stress in Bacillus altitutidinis, and provide evidence for the existence of other circular RNAs in diverse bacterial species.
- Ting-Ting He
- , Yun-Fan Xu
- & Hai-Yan Wang
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Article
| Open AccessBacterial cell-size changes resulting from altering the relative expression of Min proteins
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
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Article
| Open AccessAssembly mechanism of a Tad secretion system secretin-pilotin complex
The bacterial Tight adherence (Tad) secretion system assembles surface pili that drive cell adherence and biofilm formation. Here, authors show the mechanism of assembly for the outer membrane secretin RcpA and how it recruits its pilotin TadD.
- Matteo Tassinari
- , Marta Rudzite
- & Harry H. Low
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Article
| Open AccessGrowth-rate dependency of ribosome abundance and translation elongation rate in Corynebacterium glutamicum differs from that in Escherichia coli
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
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Article
| Open AccessPhage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety
Bacteriophages (phages) can modify the gut microbiome to benefit human health. Here, the authors report the results of a double blind, randomized, placebo-controlled trial, showing that faecal filtrate transplantation (FFT), containing phages from lean healthy donors, is safe and improves glycemic variability in patients with metabolic syndrome, while shifting the gut phage composition.
- Koen Wortelboer
- , Patrick A. de Jonge
- & Hilde Herrema
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Article
| Open AccessBacterial motility can govern the dynamics of antibiotic resistance evolution
In nature, bacteria experience gradients of antibiotics, but we know little about how such heterogeneity affects bacterial adaptation. Piskovsky and Oliveira develop quantitative models of bacterial adaptation in antibiotic landscapes and find that bacterial motility can govern the spatiotemporal dynamics of antibiotic resistance evolution.
- Vit Piskovsky
- & Nuno M. Oliveira
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Article
| Open AccessIntrinsically disordered CsoS2 acts as a general molecular thread for α-carboxysome shell assembly
Carboxysomes are bacterial proteinaceous organelle encapsulating enzymes and pathways to enhance carbon fixation. Here, authors engineer and determine cryoEM structure of minimal α-carboxysome shells to uncover the principle of shell assembly and encapsulation by CsoS2.
- Tao Ni
- , Qiuyao Jiang
- & Peijun Zhang
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Article
| Open AccessMolecular architecture and electron transfer pathway of the Stn family transhydrogenase
Acetogenic bacteria deploy electron-bifurcating transhydrogenase for electron carrier adjustments in the ancient Wood-Ljungdahl pathway. Here, the authors report a cryo-EM structure of the Stn class transhydrogenase from the Sporomusa ovata and dissect its electron transfer pathway.
- Anuj Kumar
- , Florian Kremp
- & Jan M. Schuller
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Article
| Open AccessAncient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains
The analysis of microbial genomes from human archaeological samples offers a snapshot of ancient pathogens. Here, Hodgins et al. analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, encoding tetanus neurotoxins.
- Harold P. Hodgins
- , Pengsheng Chen
- & Andrew C. Doxey
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Article
| Open AccessCoordinated peptidoglycan synthases and hydrolases stabilize the bacterial cell wall
The integrity and maintenance of cell-wall peptidoglycan is essential for growth and cell shape in bacteria. Here, the authors show how the coordinated actions of a synthase, which inserts new peptidoglycan strands, and a hydrolase, which generates openings to allow the insertion, determine the integrity of bacterial cell wall.
- Huan Zhang
- , Srutha Venkatesan
- & Beiyan Nan
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Article
| Open AccessUsing a synthetic machinery to improve carbon yield with acetylphosphate as the core
In metabolic engineering, releasing of carbon in the form of CO2 leads to significant decrease of atomic economy. Here, the authors construct a carbon-conserving pathway, which converts glucose into acetyl phosphate without carbon loss, with oscillatory system to improve production of multiple target compounds.
- Likun Guo
- , Min Liu
- & Guang Zhao
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Article
| Open AccessArchitecture 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
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Article
| Open AccessFiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential
Here, the authors show that fiber supplementation protects from antibiotic-induced gut microbiome damage by reducing the abundance of aerobic bacteria as well as metabolic pathways associated with oxidative metabolism.
- Swathi Penumutchu
- , Benjamin J. Korry
- & Peter Belenky
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Article
| Open AccessCultivation of marine bacteria of the SAR202 clade
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
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Article
| Open AccessAntibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites
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
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Article
| Open AccessCrystal 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
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Article
| Open AccessThe RIX domain defines a class of polymorphic T6SS effectors and secreted adaptors
Bacteria use the type VI secretion system (T6SS) to deliver toxic effectors into bacterial or eukaryotic cells. Here, Kanarek et al. identify a protein domain, RIX, that defines a class of polymorphic T6SS effectors with antibacterial and anti-eukaryotic toxic domains, and that enables T6SS-mediated delivery of other effectors.
- Katarzyna Kanarek
- , Chaya Mushka Fridman
- & Dor Salomon
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Article
| Open AccessHigh 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
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Matters Arising
| Open AccessReply to: Antibiotics and hexagonal order in the bacterial outer membrane
- Selen Manioglu
- , Seyed Majed Modaresi
- & Sebastian Hiller
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Article
| Open AccessProfiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium
The bacterial pathogen Burkholderia cenocepacia and related species are often multidrug resistant because their cell envelope restricts antibiotic penetration. Here, Hogan et al systematically identify genes associated with resistance and susceptibility to cell envelope-targeting antibiotics, providing insights into underlying mechanisms and suggesting avenues for development of improved antibacterial therapies.
- Andrew M. Hogan
- , A. S. M. Zisanur Rahman
- & Silvia T. Cardona
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Article
| Open AccessBtuB 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
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Article
| Open AccessConformational 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
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Article
| Open AccessIon 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
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Article
| Open AccessSequestration of histidine kinases by non-cognate response regulators establishes a threshold level of stimulation for bacterial two-component signaling
Bacterial two-component systems consist of a sensor histidine kinase (HK) that perceives a signal, and a cognate response regulator (RR) that modulates target gene expression. Here, the authors combine experiments and mathematical modelling to show that phosphorylated HKs can be sequestered by non-cognate RRs, which prevents responses to weak signals.
- Gaurav D. Sankhe
- , Rubesh Raja
- & Deepak Kumar Saini
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