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Invasion by diverse fungal pathogens in Arabidopsis thaliana commonly activates both tryptophan-dependent and independent defense pathways exhibiting distinct sensitivity to the bak1-5 mutation

ABSTRACT: Invasion by diverse fungal pathogens in Arabidopsis thaliana commonly activates both tryptophan-dependent and independent defense pathways exhibiting distinct sensitivity to the bak1-5 mutation

PROVIDER: PRJNA514314 | ENA |

REPOSITORIES: ENA

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Invasion by diverse fungal pathogens in Arabidopsis thaliana commonly activates both tryptophan-dependent and independent defense pathways exhibiting distinct sensitivity to the bak1-5 mutation

Project description:Transcriptome analysis to identify genes up- and down-regulated genes in pen2 bak1-5 plants compared with pen2 plants in the case of Alternaria brassicicola (Ab) inoculation .

2020-01-31 | GSE124921 | GEO

Codon-dependent transcriptional changes in response to tryptophan limitation in the tryptophan auxotrophic pathogens Chlamydia trachomatis and Streptococcus pyogenes

Project description:RNAseq analysis was performed for C. trachomatis serovar L2 and S. pyogenes NZ131 in the presence and absence of tryptophan to monitor transcriptional changes.

2021-11-23 | GSE174036 | GEO

Post-epidemic eosinophilia myalgia syndrome associated with L-Tryptophan

Project description:Eosinophilia–myalgia syndrome (EMS) is characterized by subacute onset of myalgias and peripheral eosinophilia, followed by chronic neuropathy and skin induration. The EMS epidemic in 1989 was linked to L-tryptophan consumption originating from a single source. Following the Food and Drug Administration (FDA) ban on the sale of L-tryptophan, the incidence of EMS declined rapidly. Moreover, no new cases have been published since the FDA ban was lifted in 2005. We report the clinical, histopathological and immunogenetic features of a new case of L-tryptophan-associated EMS along with evidence of activated transforming growth factor-ß and interleukin-4 signaling in the lesional skin. 6 samples were analyzed to include EMS patient and two replicates along with three normal controls

2012-01-28 | E-GEOD-26934 | biostudies-arrayexpress

Tryptophan metabolism response in E. coli

Project description:DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. We investigated the global changes in mRNA abundance in Escherichia coli elicited by various perturbations of tryptophan metabolism. To do so we printed DNA microarrays containing 95% of all annotated E. coli ORFs. We determined the expression profile that is predominantly dictated by the activity of the tryptophan repressor. Only three operons, trp, mtr, and aroH, exhibited appreciable expression changes consistent with this profile. The quantitative changes we observed in mRNA levels for the five genes of the trp operon were consistent within a factor of 2, with expectations based on established Trp protein levels. Several operons known to be regulated by the TyrR protein, aroF-tyrA, aroL, aroP, and aroG, were down-regulated on addition of tryptophan. TyrR can be activated by any one of the three aromatic amino acids. Only one operon, tnaAB, was significantly activated by the presence of tryptophan in the medium. We uncovered a plethora of likely indirect effects of changes in tryptophan metabolism on intracellular mRNA pools, most prominent of which was the sensitivity of arginine biosynthetic operons to tryptophan starvation. This study is detailed in Khodursky AB et al.(2000) Proc Natl Acad Sci U S A 97:12170-5 Keywords: other

2001-07-30 | GSE7 | GEO

Dietary tryptophan and circadian rhythms

Project description:Mice were fed a normal chow diet or a tryptophan depleted diet for two weeks under normal 12-hr light/dark cycles (LD) or in constant darkness (DD). Mice were sacrificed every 4th hour over the 24-hr circadian cycle. The suprachiasmatic nucleus (SCN) was harvested and RNA was isolated using a standard TRIZOL protocol. The data suggest that dietary tryptophan is an important component of the diet regulating circadian homeostsis.

2023-05-30 | GSE186242 | GEO

Atorvastatin improved ulcerative colitis in association with gut microbiota-derived tryptophan metabolism

Project description:Aims: Atorvastatin is a commonly used cholesterol-lowering drug that possesses non-canonical anti-inflammatory properties. However, the precise mechanism underlying its anti-inflammatory effects remains unclear. Materials and methods: The acute phase of ulcerative colitis (UC) was induced using a 5 % dextran sulfate sodium (DSS) solution for 7 consecutive days and administrated with atorvastatin (10 mg/kg) from day 3 to day 7. mRNA-seq, histological pathology, and inflammatory response were determined. Intestinal microbiota alteration, tryptophan, and its metabolites were analyzed through 16S rRNA sequencing and untargeted metabolomics. Key findings: Atorvastatin relieved the DSS-induced UC in mice, as evidenced by colon length, body weight, disease activity index score and pathological staining. Atorvastatin treatment reduced the level of pro_x0002_inflammatory cytokines interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α). Atorvastatin also relieved the intestinal microbiota disorder caused by UC and decreased the proliferation of pernicious microbiota such as Akkermansia and Bacteroides. Atorvastatin dramatically altered tryptophan metabolism and increased the fecal contents of tryptophan, indolelactic acid (ILA), and indole-3-acetic acid (IAA). Furthermore, atorvastatin enhanced the expression level of aryl hydrocarbon receptor (AhR) and interleukin-22 (IL-22) and further promoted the expression level of intestinal tight junction proteins, such as ZO-1 and occludin, in colitis mice. Significance: These findings indicated that atorvastatin could alleviate UC by regulating intestinal flora disorders, promoting microbial tryptophan metabolism, and repairing the intestinal barrier.

2024-11-04 | GSE280960 | GEO

Tryptophan plays a central role in yeast’s tolerance to isobutanol

Project description:Isobutanol is considered a potential biofuel and can be produced by genetically modified microorganisms. Saccharomyces cerevisiae inherently produces isobutanol through valine intermediate(s), so it serves as a good host. However, isobutanol's toxicity remains a key obstacle for bioproduction. In our study, we first used image recognition to screen the colony growth of a yeast gene deletion library and inferred that genes involved in tryptophan biosynthesis, ubiquitination, and the pentose phosphate pathway (PPP) contribute to isobutanol tolerance. The importance of tryptophan in yeast's tolerance to isobutanol was confirmed by the recovery of isobutanol tolerance in a tryptophan biosynthesis defective strain by adding exogenous tryptophan. Transcriptomic analysis revealed that amino acid biosynthesis- and transportation-related genes in a tryptophan biosynthesis defective host were up regulated under conditions such as nitrogen starvation. This may explain why ubiquitination for protein degradation was involved for the protein turnover. PPP metabolites and vitamin B1/B6 may serve as precursors and cofactors in tryptophan biosynthesis to enhance isobutanol tolerance. Furthermore, the tolerance mechanism may also be linked to tryptophan metabolism, including the kynurenine pathway and nicotinamide adenine dinucleotide biosynthesis. Both pathways are responsible for cellular redox balance and antioxidative ability and figured out that tryptophan may play a crucial role on isobutanol tolerance. Our study highlights the central role of tryptophan in yeast's isobutanol tolerance and offers new clues for engineering a yeast host with strong isobutanol tolerance.

2021-10-20 | GSE175794 | GEO

Codon-dependent transcriptional changes in response to tryptophan limitation in the tryptophan auxotrophic pathogens Chlamydia trachomatis and Streptococcus pyogenes

Project description:Codon-dependent transcriptional changes in response to tryptophan limitation in the tryptophan auxotrophic pathogens Chlamydia trachomatis and Streptococcus pyogenes

| PRJNA728014 | ENA

Tryptophan as a miR team organizer prevents colon cancer liver metastasis [colon]

Project description:Tryptophan treatment play a significant role in miR expression. We have characterized the miR expression network through miR-on-chip profiling of the mouse treated with or without tryptophan. In this dataset, we include the expression data from mouse small intestine and colon tissue treated with or without tryptophan.

2023-09-03 | GSE212633 | GEO

Triazolinedione protein modification: from an overlooked off-target effect to a tryptophan-based bioconjugation strategy

Project description:Labelling of tyrosine residues in peptides and proteins has been reported to selectively occur via a 'tyrosine-click' reaction with triazolinedione reagents (TAD). However, we here demonstrate that TAD reagents are actually not selective for tyrosine and that tryptophan residues are in fact also labelled with these reagents. This off-target labelling remained under the radar as it is challenging to detect these physiologically stable but thermally labile modifications with the commonly used HCD and CID MS/MS techniques. We show that selectivity of tryptophan over tyrosine can be achieved by lowering the pH of the aqueous buffer to effect selective Trp-labelling. Given the low relative abundance of tryptophan compared to tyrosine in natural proteins, this results in a new site-selective bioconjugation method that does not rely on enzymes nor unnatural amino acids and is demonstrated for peptides and recombinant proteins.

2022-06-09 | PXD031607 | Pride

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