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35 results for “peptidoglycan”
Source data for publication "Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation"
<p><strong>This dataset contains the source data for the figures in the following publication: </strong></p> <p><strong>Title: </strong>Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation</p> <p><strong>Authors: </strong>Sanika Vaidya, Dibya Saha, Daniel K.H. Rode, Gabriel Torrens, Mads F. Hansen, Praveen K. Singh, Eric Jelli, Kazuki Nosho, Hannah Jeckel, Stephan Göttig, Felipe Cava, Knut Drescher</p> <p><strong>Journal: </strong>Nature Microbiology, 2025</p> <p> </p> <p><strong>Description of the dataset: </strong></p> <p>The data is organized by figures in the publication receferenced above. For each figure, there is a XLSX-file that contains the processed data and a ZIP-archive that contains the raw image data. The ZIP-archive also contains readme documents with more detailed descriptions for every set of raw image data. </p> <p>Example: For Figure 1 in the main text of the publication, there following data are available:</p> <ul> <li>raw data: Figure_01.zip</li> <li>processed data: Processed_Source_Data_Figure1.xlsx</li> </ul> <p>Similarly, XLSX-files and ZIP-archives are available for the main text Figures 1-6. For the Extended Data (ED) Figures 1-10, there are XLSX-files available that present the data shown in each figure. Only some of the Extended Data Figures present results based on image data - therefore raw image data ZIP-archives are only available for ED Figures 3, 6, 7, 8, 9, 10.</p>
Comparative genomics of eight aphid subfamilies reveals variable relationships between host horizontally-transferred genes and symbiont peptidoglycan metabolism.
<p>Genome assemblies, annotations, and orthologs of aphids (<em>Geopemphigus sp.</em>, <em>Stegophylla sp.</em>, <em>Chaitophorus viminalis</em>, and<em> Pemphigus obesinymphae</em>) and their symbionts. </p> <p>step1_final_assemblies_and_annotations.tar.gz: Aphid genomes and annotations</p> <p>step2_protein_evidence_used_for_genome_annotation.tar.gz: Protein evidence used for aphid genome annotation</p> <p>step3_amino_acid_inputs_for_aphid_orthologs: amino acid inputs for aphid ortholog assignmentt</p> <p>step5_buchnera_genomes_and_annotations.tar.gz: Buchnera genomes and annotations</p>
Figure 2 in Peptidoglycan from Immunobiotic Lactobacillus rhamnosus Improves Resistance of Infant Mice to Respiratory Syncytial Viral Infection and Secondary Pneumococcal Pneumonia
Figure 2. – Photography of a juvenile lemon shark identified as Negaprion acutidens with an estimated total length of 70 cm (Photo MI).
Figure 1 in Peptidoglycan from Immunobiotic Lactobacillus rhamnosus Improves Resistance of Infant Mice to Respiratory Syncytial Viral Infection and Secondary Pneumococcal Pneumonia
Figure 1. – The Chesterfield islands (A) lie in the Coral Sea with New Caledonia (NC) to the east and Australia (AUS) to the west. The atoll structure of the Chesterfield (B) includes a V shaped barrier reef in the South (C) where the juvenile lemon sharks were observed (arrow).
Confocal Microscopy Imaging of Peptidoglycan Uptake in the Mouse Intestine
<p>Confocal imaging data set accompanying Fig.5 and Fig.6 for the article: Wheeler R, Dias Bastos PA, Disson O, Rifflet A, Gabanyi I, Spielbauer J, Bérard M, Lecuit M, Gomperts Boneca I. Microbiota-induced active translocation of peptidoglycan across the intestinal barrier dictates its within-host dissemination (2023) PNAS; doi: 10.1073/pnas.2209936120<br> <br> Stainings are described in detail in the the PNAS article methodology.<br> Files names beginning Fig 5A-1; DAPI, WGA, anti-E-cadherin, MDP-rhodamine<br> Files names beginning Fig 5A-2, Fig 5A-3 & Fig S5; DAPI, Phalloidin, anti-Siglec-F, MDP-rhodamine<br> Files names beginning Fig 5B; DAPI, Phalloidin, <em>E.coli </em>peptidoglycan-Alexa Fluor 647 conjugate<br> Files names beginning Fig 6B; DAPI, Phalloidin, anti-Siglec-F, MDP-rhodamine (also corresponds to Supplementary data Figure 5)<br> Files names beginning Fig S5-1; DAPI, Phalloidin, anti-CgA, MDP-rhodamine<br> Files names beginning Fig S5-2; DAPI, Phalloidin, anti-NKM-16-4-2, MDP-rhodamine</p>
Data from: Peptidoglycan-tethered and free forms of the Braun lipoprotein are in dynamic equilibrium in Escherichia coli
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Physiological roles of peptidoglycan carboxypeptidases DacC and DacA in Escherichia coli
<p><span>Peptidoglycan (PG) is an essential bacterial architecture pivotal for shape maintenance and adaptation to osmotic stress. Although PG synthesis and modification are tightly regulated under harsh environmental stresses, few related mechanisms have been investigated. In this study, we aimed to investigate the coordinated and distinct roles of the PG carboxypeptidases DacC and DacA, in adaptation to alkaline and salt stresses and shape maintenance </span><span>in <em>Escherichia coli</em>. We found that DacC is an alkaline PG carboxypeptidase, whose enzyme activity and protein stability are significantly enhanced under alkaline stress. Both DacC and DacA were required for bacterial growth under alkaline stress, whereas only DacA was required for the adaptation to salt stress. Under normal growth conditions, only DacA was necessary for cell shape maintenance, while under alkaline stress conditions, both DacA and DacC were necessary for cell shape maintenance, but their roles were distinct. Notably, all these roles of DacC and DacA were independent of ld-transpeptidases, which are necessary for the formation of PG 3-3 crosslinks and covalent bonds between PG and the outer membrane lipoprotein Lpp. Instead, DacC and DacA interacted with penicillin-binding proteins (PBPs), dd-transpeptidases, mostly in a C-terminal domain-dependent manner, and these interactions were necessary for most of their roles. Collectively, our results demonstrate the coordinated and distinct novel roles of PG carboxypeptidases in stress adaptation and shape maintenance and provide novel insights into the cellular functions of PG carboxypeptidases associated with PBPs.</span></p>
Fig. 2 in Peptidoglycan in eukaryotes: Unanswered questions
Fig. 2. Evolution of plastids from cyanobacteria. Algae and plants have been formed by fusion of an archaeon, a alphaproteobacterium that has evolved to mitochondria, and a cyanobacterium that has evolved to chloroplasts, and brought with it its peptidoglycan-containing cell wall. The three grey rectangles show loss of peptidoglycan. Based in part on Takano and Takechi (2010).
Fig. 1. The D in Peptidoglycan in eukaryotes: Unanswered questions
Fig. 1. The D-alanyl-D-alanine motif of the bacterial cell wall compared to a penicillin. Solid triangle means that the group at this bond is pointing towards the viewer. Broken triangular bonds are pointing away from the viewer. The R groups vary, and there may be CH3 instead of H to the far right in penicillin.
Physiological roles of peptidoglycan carboxypeptidases DacC and DacA in Escherichia coli
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Data from: Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli
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MtrA regulation of essential peptidoglycan cleavage in Mycobacterium tuberculosis during infection [mtrA_knockdown]
GEO Series GSE166805. Mycolicibacterium smegmatis; Mycobacterium tuberculosis. 24 samples. Type: Expression profiling by high throughput sequencing.
MtrA regulation of essential peptidoglycan cleavage in Mycobacterium tuberculosis during infection [MtrA_OE_pH]
GEO Series GSE166804. Mycobacterium tuberculosis. 24 samples. Type: Expression profiling by high throughput sequencing.
KhpA and KhpB Regulate Peptidoglycan Synthesis and Cell Division in the “Superbug” Streptococcus pneumoniae
GEO Series GSE101583. Streptococcus pneumoniae. 6 samples. Type: Expression profiling by high throughput sequencing.
Targeting pH-responsive Transcriptional Regulation of Peptidoglycan Cleavage Potentiates Fast Clearance of Mycobacterium tuberculosis with Frontline Antibiotics
GEO Series GSE166806. Mycobacterium tuberculosis; Mycolicibacterium smegmatis. 60 samples. Type: Expression profiling by high throughput sequencing.
MtrA regulation of essential peptidoglycan cleavage in Mycobacterium tuberculosis during infection [pH]
GEO Series GSE165514. Mycobacterium tuberculosis. 12 samples. Type: Expression profiling by high throughput sequencing.
SpxB regulates O-acetylation dependent resistance of Lactococcus lactis peptidoglycan to hydrolysis
GEO Series GSE7386. Lactococcus cremoris subsp. cremoris MG1363. 3 samples. Type: Expression profiling by array.
PGLYRP-1 mediated intracellular peptidoglycan detection promotes mucosal protection
GEO Series GSE279626. Homo sapiens; Mus musculus. 82 samples. Type: Expression profiling by high throughput sequencing.
A Cross-sectional Study on the Association of Peptidoglycan Fragments Derived From Gut Microbiota With Colorectal Cancer
ClinicalTrials.gov study NCT06379412. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Cross-sectional Study on the Association of Peptidoglycan Fragments Derived From Gut Microbiota With Alcohol Liver Disease
ClinicalTrials.gov study NCT07284862. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.