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| Open AccessDefining the biogeographical map and potential bacterial translocation of microbiome in human ‘surface organs’
Given that the human body is composed of many microbial niches, and there have been few reports on the biogeography of the microbiome, the authors analyse the intra-individual inter-organ and intra-organ microbiome of seven surface organs of deceased individuals.
- Jun-Jun She
- , Wei-Xin Liu
- & Jun Yu
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Article
| Open AccessGenomic and panproteomic analysis of the development of infant immune responses to antigenically-diverse pneumococci
By combining genome sequencing and antibody binding (to all common pneumococcal proteins) data, Croucher et al. present a high-resolution analysis of the emergence of immune responses in children that can protect against pneumonia.
- Nicholas J. Croucher
- , Joseph J. Campo
- & David Goldblatt
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Article
| Open AccessFunctional host-specific adaptation of the intestinal microbiome in hominids
Here, Rühlemann et al. analyze the gut microbiome of wild-living African great apes (Gorillas, Bonobos, Chimpanzees) in comparison to that of humans, identifying host specific patterns and shared evolutionary conserved traits disrupted in humans.
- M. C. Rühlemann
- , C. Bang
- & A. Franke
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Article
| Open AccessThe virulence regulator VirB from Shigella flexneri uses a CTP-dependent switch mechanism to activate gene expression
Protein VirB regulates the expression of virulence genes in the pathogen Shigella flexneri by binding to DNA sequences far upstream of their promoters. Here, Jakob et al. show that VirB acts as a CTP-dependent molecular switch that uses a loading-and-sliding mechanism to control transcription of its target genes.
- Sara Jakob
- , Wieland Steinchen
- & Martin Thanbichler
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Article
| Open AccessConvergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China
Bacteria in the same environment can share genetic material but the extent to which this influences development of antimicrobial resistance is unclear. Here, the authors investigate the evidence for co-evolution of antimicrobial resistance in bacteria found coexisting in animals and the environment in chicken farms and slaughterhouses in China.
- Michelle Baker
- , Xibin Zhang
- & Tania Dottorini
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Article
| Open AccessIncrease in antioxidant capacity associated with the successful subclone of hypervirulent carbapenem-resistant Klebsiella pneumoniae ST11-KL64
Plasmid acquisition imposes an adaptive burden, which can be ameliorated by host-plasmid coevolution. Here, the authors characterise virulence plasmids of carbapenem-resistant Klebsiella pneumoniae, and show the discard of certain sequences to enhance survival, conferring an evolutionary advantage.
- Ruobing Wang
- , Anru Zhang
- & Hui Wang
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Article
| Open AccessSpatial structure, chemotaxis and quorum sensing shape bacterial biomass accumulation in complex porous media
Pores and channels within complex porous structures, such as the soil or the human gut, influence fluid flow and thus bacterial colonization. Here, Scheidweiler et al. study bacterial colonization of a model complex porous structure and show how the interactions between fluid flow, microscale structure, chemotaxis, and gradients of a quorum-sensing signaling molecule control the heterogenous accumulation of bacterial biomass.
- David Scheidweiler
- , Ankur Deep Bordoloi
- & Pietro de Anna
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Article
| Open AccessA genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand
Previous reports of microbial endemism have been restricted to sub-genus level taxa. Here, Power et al. present evidence supporting that a bacterial genus, Venenivibrio, is endemic to Aotearoa-New Zealand.
- Jean F. Power
- , Carlo R. Carere
- & Matthew B. Stott
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Article
| Open AccessCRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei
Human milk oligosaccharides (HMOs) utilization by Bacteroides species remains poorly understood. Here, the authors describe a single specific gene cluster responsible for sialylated HMOs utilization in a B. dorei natural isolate and prove its functionality in vivo using CRISPR-Cas12a.
- Sivan Kijner
- , Dena Ennis
- & Moran Yassour
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Article
| Open AccessPhage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication
Bacteriophages have primarily been studied using fast-growing laboratory cultures of their bacterial hosts. Here, Maffei et al. show that diverse phages can infect deep-dormant bacteria and suspend their replication until the host resuscitates; however, a particular phage can directly replicate and induce the lysis of deep-dormant hosts.
- Enea Maffei
- , Anne-Kathrin Woischnig
- & Alexander Harms
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Article
| Open AccessDifferential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults
Knowledge on how the gut microbiome and resistome responds to antibiotics across age remains limited. Here, using metagenomics data from Danish infants and young adults, the authors show that antibiotics have a more lasting impact on adults compared to infants.
- Xuanji Li
- , Asker Brejnrod
- & Søren Johannes Sørensen
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Article
| Open AccessMicrobial interactions shape cheese flavour formation
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
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Article
| Open AccessStructural 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
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Article
| Open AccessA unique sigma/anti-sigma system in the actinomycete Actinoplanes missouriensis
Bacteria of the genus Actinoplanes form sporangia which, upon contact with water, release motile spores. Here, the authors study the mechanisms behind sporangium dehiscence and discover a sigma/anti-sigma system with unique features.
- Takeaki Tezuka
- , Kyota Mitsuyama
- & Yasuo Ohnishi
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Article
| Open AccessA type VII-secreted lipase toxin with reverse domain arrangement
Here Garrett et al. describe a toxin, TslA, secreted by type VII secretion system that has a reverse domain arrangement compared to other previously characterised substrates. The authors show that TslA is a lipase with antibacterial activity.
- Stephen R. Garrett
- , Nicole Mietrach
- & Tracy Palmer
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Article
| Open AccessStructural dynamics of the CROPs domain control stability and toxicity of Paeniclostridium sordellii lethal toxin
Paeniclostridium sordellii lethal toxin (TcsL) is a potent toxin that can cause toxic shock syndrome. TcsL contains a unique CROPs domain with unclear functions. Here, the authors provide evidence of the CROPs domain’s role in stability and toxicity of TcsL.
- Yao Zhou
- , Xiechao Zhan
- & Liang Tao
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Article
| Open AccessBiophysical 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
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Article
| Open AccessThe Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
The bacterium Helicobacter pylori, often found in the human stomach, can be classified into distinct subpopulations associated with the geographic origin of the host. Here, the authors provide insights into H. pylori population structure by collecting over 1,000 clinical strains from 50 countries and generating and analyzing high-quality bacterial genome sequences.
- Kaisa Thorell
- , Zilia Y. Muñoz-Ramírez
- & Charles S. Rabkin
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Article
| Open AccessGeometric constraint-triggered collagen expression mediates bacterial-host adhesion
Cells in the body live in geometrically constrained microenvironments. Here, Feng at al report that these constraints induce collagen IV expression which is responsible for location dependent bacterial adhesion.
- Yuting Feng
- , Shuyi Wang
- & Jianyong Huang
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Article
| Open AccessResin acids play key roles in shaping microbial communities during degradation of spruce bark
The bark is the outermost defense of trees against microbial attack, largely due to toxicity of extractive compounds. Here, Ristinmaa et al. study microbial community dynamics and chemical changes during degradation of spruce bark over six months, showing that the microbial degradation of extractive compounds, such as resin acids, has a major role in shaping the microbial community.
- Amanda Sörensen Ristinmaa
- , Albert Tafur Rangel
- & Johan Larsbrink
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Article
| Open AccessThe distinct translational landscapes of gram-negative Salmonella and gram-positive Listeria
In this work, Bryant and Lastovka et al. utilise advanced ribosome profiling and transcriptomics techniques, to reveal distinct translation control mechanisms in Salmonella and Listeria, two highly divergent bacterial species.
- Owain J. Bryant
- , Filip Lastovka
- & Betty Y. -W. Chung
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Article
| Open AccessAirway environment drives the selection of quorum sensing mutants and promote Staphylococcus aureus chronic lifestyle
This study by Ding et al reveals that the quorum-sensing dysfunction typically encountered in lung-adapted Staphylococcus aureus isolates could be selected by an enhanced ability to consume sialic acid released from airway mucins by the microbiota.
- Xiongqi Ding
- , Catherine Robbe-Masselot
- & Anne Jamet
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Article
| Open AccessStrong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP
The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. Here, Clerc et al. show that marine bacteria are strongly attracted to algal polysaccharides, and this chemotactic behaviour is enhanced by dimethylsulfoniopropionate (DMSP), a ubiquitous algal metabolite.
- Estelle E. Clerc
- , Jean-Baptiste Raina
- & Roman Stocker
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Article
| Open AccessMachine learning-based motion tracking reveals an inverse correlation between adhesivity and surface motility of the leptospirosis spirochete
A common approach to study bacterial motility is fluorescent labelling, but this can be hampered by protein expression instability and/or interference with bacterial physiology. Here, Abe et al. describe a machine learning-based method for motion tracking of spirochetes on cultured animal cells, which does not require labelling and might be applied to study motility of other bacterial species.
- Keigo Abe
- , Nobuo Koizumi
- & Shuichi Nakamura
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Article
| Open AccessFunctional divergence of a bacterial enzyme promotes healthy or acneic skin
Cutibacterium acnes phylotypes can be catalogued based on their association with acneic or healthy skin. Here, Hajam et al show that the functional divergence of a hyaluronidase enzyme expressed by the phylotypes is a major determinant of acne severity.
- Irshad A. Hajam
- , Madhusudhanarao Katiki
- & George Y. Liu
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Article
| Open AccessNational genomic surveillance integrating standardized quantitative susceptibility testing clarifies antimicrobial resistance in Enterobacterales
Kayama et al. present a blueprint for a national genomic surveillance study that conducts genome sequencing of thousands of strains, integrates standardized quantitative antimicrobial susceptibility testing, and characterizes antimicrobial resistance determinants.
- Shizuo Kayama
- , Koji Yahara
- & Motoyuki Sugai
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Article
| Open AccessA 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
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Article
| Open AccessDiversification of division mechanisms in endospore-forming bacteria revealed by analyses of peptidoglycan synthesis in Clostridioides difficile
The enzymes FtsW and FtsI are thought to be essential for the synthesis of septal peptidoglycan (PG) during bacterial cell division. Here, Shrestha et al. show that the pathogen Clostridioides difficile lacks a canonical FtsW/FtsI pair, with its homologs fulfilling sporulation-specific roles including the synthesis of septal PG during sporulation-specific cell division.
- Shailab Shrestha
- , Najwa Taib
- & Aimee Shen
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Article
| Open AccessKlebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence
Convergent strains, those containing characteristics of both multidrug-resistant & hypervirulent Klebsiella pneumoniae, are a global threat to public health. In this work, authors analyse convergent isolates from the United States and reveal unexpectantly low virulence.
- Travis J. Kochan
- , Sophia H. Nozick
- & Alan R. Hauser
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Article
| Open AccessResurrecting ancestral antibiotics: unveiling the origins of modern lipid II targeting glycopeptides
Glycopeptide antibiotics (GPAs) are microbial natural products synthesized by multiple enzymes, including a nonribosomal peptide synthetase for assembly of the peptide core. Here, the authors use computational techniques to infer a gene set for biosynthesis of an ancestral GPA, produce the peptide in a microbial host, and provide insights into the evolution of key enzymatic domains.
- Mathias H. Hansen
- , Martina Adamek
- & Nadine Ziemert
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Article
| Open AccessThe protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus
Research on the biology and pathogenicity of ‘Candidatus Liberibacter asiaticus’ (CLas), the bacterium that causes citrus Huanglongbing disease, is hampered by our inability to cultivate it in artificial media. Here, Carter et al. use a high-throughput yeast-two-hybrid screen to identify thousands of interactions between CLas proteins, thus providing insights into their potential functions.
- Erica W. Carter
- , Orlene Guerra Peraza
- & Nian Wang
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Article
| Open AccessStructural 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
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Article
| Open AccessMetagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface
The authors study microbial communities in hydrothermally heated, subseafloor sediment layers. They find that microbial abundance and diversity decrease with sediment depth and temperature, and provide evidence for the existence of a specialized deep, hot biosphere.
- Paraskevi Mara
- , David Geller-McGrath
- & Andreas Teske
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Article
| Open AccessRNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms
The roles of extracellular RNAs present in bacterial biofilms are poorly understood. Here, Mugunthan et al. show that specific mRNAs associate with extracellular DNA in the matrix of bacterial biofilms, facilitating the formation of viscoelastic networks.
- Sudarsan Mugunthan
- , Lan Li Wong
- & Thomas Seviour
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Article
| Open AccessParabacteroides distasonis ameliorates insulin resistance via activation of intestinal GPR109a
Here, the authors show that the gut commensal Parabacteroides distasonis alleviates insulin resistance via nicotinic acid-intestinal GPR109a axis activation, a process promoted by Dendrobium officinale polysaccharide.
- Yonggan Sun
- , Qixing Nie
- & Shaoping Nie
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Article
| Open AccessDistributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century
Core genome multilocus sequence typing (cgMLST) is used to classify bacterial strains for epidemiological applications. Here, the authors describe a distributed cgMLST scheme that does not require a central database of allelic sequences, and apply it to study evolutionary patterns of epidemic and endemic strains of the genus Neisseria.
- Ling Zhong
- , Menghan Zhang
- & Zhemin Zhou
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Article
| Open AccessThe genomic epidemiology of shigellosis in South Africa
As a leading cause of diarrhoeal mortality and morbidity, authors examine the epidemiology and genome dynamics of shigellosis in South Africa, utilising whole genome sequence analysis.
- George E. Stenhouse
- , Karen H. Keddy
- & Kate S. Baker
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Article
| Open AccessStochastic 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
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Article
| Open AccessThe Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope bridge for phospholipid trafficking
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
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Article
| Open AccessHigh-resolution temporal profiling of E. coli transcriptional response
Understanding how cells dynamically adapt to their environment is important, but temporal information about cellular behaviour is often limited. Here, Miano et al. apply unsupervised machine learning to a dataset describing the activity of over 1,800 promoters in E. coli, measured every 10 minutes, defining three primary stages of promoter activation in response to heavy metal stress.
- Arianna Miano
- , Kevin Rychel
- & Jeff Hasty
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Article
| Open AccessTaxonomic and environmental distribution of bacterial amino acid auxotrophies
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
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Article
| Open AccessDirect comparison of spatial transcriptional heterogeneity across diverse Bacillus subtilis biofilm communities
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
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Article
| Open AccessSerine 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
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Article
| Open AccessA smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex
The Mycobacterium tuberculosis complex (MTBC) includes several pathogens thought to have originated in East Africa from an ancestor closely related to Mycobacterium canettii. Here, the authors describe a clinical tuberculosis strain isolated in Ethiopia that has typical M. canettii features but is phylogenetically much closer to the MTBC clade, supporting that the emergence of MTBC pathogens is a recent evolutionary event.
- Bazezew Yenew
- , Arash Ghodousi
- & Daniela Maria Cirillo
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Article
| Open Accessc-di-GMP inhibits the DNA binding activity of H-NS in Salmonella
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
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Article
| Open AccessMid-cell migration of the chromosomal terminus is coupled to origin segregation in Escherichia coli
In slow-growing Escherichia coli, the chromosomal terminus is initially located at the new pole and must therefore migrate to midcell during replication to reproduce the same pattern in the daughter cells. Here, Sadhir & Murray use high-throughput time-lapse microscopy to quantify this transition, its timing and its relationship to chromosome segregation, identifying an unexplored connection between the origin of replication locus and the terminus.
- Ismath Sadhir
- & Seán M. Murray
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Article
| Open AccessThe environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli
Here, the authors use the proVWXoperon of Escherichia coli as a model system to show how the nucleoid associated protein H-NS regulates gene expression in vivo by local chromatin remodelling.
- Fatema-Zahra M. Rashid
- , Frédéric G. E. Crémazy
- & Remus T. Dame
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Article
| Open AccessBacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient
Bacterial functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, Wang et al. investigate bacterial communities along a natural pH gradient in forest soils, and find that average genome size and functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral.
- Cong Wang
- , Qing-Yi Yu
- & Cheng Gao
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Article
| Open AccessATP synthase evolution on a cross-braced dated tree of life
The timing of cellular evolution is poorly constrained. Here, the authors used improved molecular dating approaches to study the evolution of the ATP synthase in light of a dated tree of life thereby providing an absolute timescale for cellular evolution including eukaryotic origins.
- Tara A. Mahendrarajah
- , Edmund R. R. Moody
- & Anja Spang
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