Dataset Information

LFQ Analysis of Differential Protein Regulation in Response to Tween-20 Exposure in TwnR mutant and Wild Type Myxococcus xanthus strains

ABSTRACT: This dataset compares the relative protein abundances between wild type Myxococcus xanthus and a detergent resistant mutant, in the presence or absence of 0.006% tween-20 detergent, after either 2 or 6 hours. Comparisons were made using MaxQuant and Label Free Quantitation (LFQ)

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Myxococcus Xanthus

SUBMITTER: Brandon Saiz

LAB HEAD: Daniel Wall

PROVIDER: PXD053718 | Pride | 2024-07-26

REPOSITORIES: Pride

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Publications

Cell-cell transfer of adaptation traits benefits kin and actor in a cooperative microbe.

Subedi Kalpana K Roy Pravas C PC Saiz Brandon B Basile Franco F Wall Daniel D

Proceedings of the National Academy of Sciences of the United States of America 20240716 30

Microbes face many physical, chemical, and biological insults from their environments. In response, cells adapt, but whether they do so cooperatively is poorly understood. Here, we use a model social bacterium, <i>Myxococcus xanthus</i>, to ask whether adapted traits are transferable to naïve kin. To do so we isolated cells adapted to detergent stresses and tested for trait transfer. In some cases, strain-mixing experiments increased sibling fitness by transferring adaptation traits. This cooper ...[more]

PMID: 39012831

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Project description:Polyethylene glycol sorbitan monoacylates (Tween) are detergents of widespread use in plant sciences. We show them, notably Tween 20, to cause a rapid and complex change in transcript abundance which bears all characteristics of a PAMP / elicitor-induced defense response, and they do so at concentrations which cause no detectable deleterious effects on plant cellular integrity. The activity does not reside in the intact Tween molecule itself, but is caused by medium-chain fatty acids, notably lauric acid (LA), which are efficiently released from the Tween-backbone by the plant. The Tween / LA-response is independent of the jasmonate signalling system. Medium-chain fatty acids are thus novel elicitors/regulators of plant pathogen defense. The results also have several practical implications: (i) The use of Tweens and, as we show, several other detergents, as solvating/wetting agents on intact plants causes profound physiological changes which may mask actual effects of test compounds; (ii) Tweens by themselves can be regarded (and probably used) as economical, non-toxic, and safe-to-apply elicitors of inducible plant immunity against pathogens. Experiment Overall Design: In preliminary Northern blot experiments using the Arabidopsis thaliana genes OPR1 / OPR2, strongest responses were observed between 1 h and 2.5 h after foliar treatment with 0.2 % Tween 20 solution (approx. 1.6 mM). These conditions were thus chosen for the microarray experiments. Three experiments were carried out, two 1 h after the onset of the Tween treatment (expt. IA and IB which are biological repetitions; GSM126247, GSM126248; GSM126990, GSM126991 files) and one after 2.5 h (expt. II; GSM126244, GSM126246 files, c and t respectively) to allow a distinction between fast, transient and slower, more permanent responses. Experiment Overall Design: All the experiments were conducted at the same day time in the morning. For every experiment a total of three independent replicas (33 Arabidopsis thaliana Col-0 plants per experiment) were done. The plants used were 28 days old, growing under sterile conditions in 0.5 L glass jars containing MS medium. The controls were sprayed with water and the samples with 0.2 % (w/v) Tween 20 detergent. The plant material was collected in a random way from the different glass jars, the samples were dried in tissue paper, weighted (1 g) and immediately frozen in liquid nitrogen. This complete procedure took place in less than 1 min. Total RNA extraction from every individual experiment was made with TRIzol. Once the RNA quality of every independent induction experiment was satisfactory, the RNA samples were mixed. Experiment Overall Design: RNA quality and quantity control, cRNA labeling, hybridizations, expression data normalization and analysis were performed in collaboration with Carsten MÃ¼ssig and Thomas Altmann (Max-Planck-Institute for Molecular Plant Physiology, Golm) according to the Affymetrix manual. Clustering was performed using the Access and the MAPMAN program. Experiment Overall Design: The levels of 118 transcripts were elevated (2-fold) after 1 h, i.e., in both, the IA and IB arrays, but only 12 levels were reduced (by 2-fold). In the 2.5 h array the corresponding numbers were 137 and 11. The transcript levels of 38 genes were found elevated in all three arrays. The validity of the array data was checked for 25 randomly-picked genes out of the 38 genes by RT-PCR.

Project description:Rationale There is a need for new and better biomarkers for hypertrophic cardiomyopathy (HCM) which correlate more closely with disease progression as determined by clinical imaging and biohumoral information. We have used a combination of heart tissue and plasma proteomics to identify potential biomarkers for HCM and developed them into an exploratory targeted proteomic assay. Objective To identify informative staging biomarkers for HCM and develop them into a blood test. The test using 10 µl of plasma, was developed into a 10 min liquid chromatography-tandem/mass spectrometry (LC-MS/MS) assay to analyze multiple candidate biomarkers and evaluate their association with clinical phenotypes in patients with HCM. Methods and Results Myocardial tissue and plasma samples from patients with HCM and healthy volunteers (controls) were screened using a combined gel- and nano-LC quadrupole time of flight MS approach. Twenty-six potential biomarkers were identified from the proteomics screens and developed into a multiplexed targeted proteomic assay. Their association with clinical phenotypes was tested in plasma samples collected from 207 prospectively recruited participants: 110 patients with HCM (50.1 ± 15.0 years, 70% male; 48 [44%] with identified genetic mutations) and 97 controls (49.6 ± 13.4 years, 58% male), randomly split into training (80 HCM, 67 controls) and validation datasets (30 HCM, 30 controls). Six markers (Aldolase Fructose-Bisphosphate A, Complement C3, Glutathione S-Transferase Omega 1, Ras Suppressor Protein 1, Talin 1, and Thrombospondin 1) were significantly increased (P<0.006) in the plasma of HCM patients compared to controls in the training dataset. These markers correlated with left ventricular (LV) wall thickness, LV mass and % myocardial scar on cardiovascular magnetic resonance imaging. Using supervized machine learning (ML) this panel differentiated HCM from controls (area under the curve: 0.89 in the training dataset, sensitivity 96%, 95% confidence interval [CI] 77–93; specificity 87%, 95%CI 77–94; and 0.87 in the validation dataset, sensitivity 97%, 95%CI 83–100; specificity 77%, 95%CI 58–90). Four of the biomarkers as well as the composite ML score of the plasma proteome correlated with the presence of nonsustained ventricular tachycardia and the estimated 5-year risk of sudden cardiac death. Conclusion By developing a high-throughput, multiplex, and targeted proteomic plasma assay we identified 6 biomarkers that correlate with the presence of disease and with clinical risk score for sudden cardiac death.

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	2422mut_A_2h_NoTween.raw	Raw
	2422mut_A_2h_Tween.raw	Raw
	2422mut_A_6h_NoTween.raw	Raw
	2422mut_A_6h_Tween.raw	Raw
	2422mut_B_2h_NoTween.raw	Raw