Relative roles of Stp1 and Stp2 in amino acid and peptide utilization in Candida albicans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA607573 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11116124.fastq.gz | Fastqsanger.gz | |||
| SRR11116125.fastq.gz | Fastqsanger.gz | |||
| SRR11116126.fastq.gz | Fastqsanger.gz | |||
| SRR11116127.fastq.gz | Fastqsanger.gz | |||
| SRR11116128.fastq.gz | Fastqsanger.gz |
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Project description:Candida albicans is a member of the normal commensal flora with the ability to cause disease in susceptible individuals. Nutrient acquisition is of central importance for C. albicans to colonize and thrive in the host. We have previously assessed the role of amino acid utilization for growth and manipulation of pH, triggering the filamentation program and promoting immune evasion. While the role of amino acids has been largely studied, protein utilization has remained less well understood. We investigated the utilization of peptides as a source of carbon and to support the neutralization phenomena. We found that both transcription factors Stp1 and Stp2 are required for proper peptide utilization in a manner dependent of amino acid sensing signaling involving the SPS system. However, we found that Stp2 is the major contributor for this process. Epistasis experiments shown that Stp1 partially restores the ability to utilize peptides in the absence of amino acid signaling, whilst Stp2 is sufficient to fully restore this phenotype. Transcriptomic analysis revealed that the response to amino acids and peptides is very similar, but peptides represent a more difficult carbon source to utilize. It is known that the Stp1/Stp2 duet has divergent roles in C. albicans, however the specific set of genes controlled by each TF remained unclear. We showed that the Stp1 regulon is limited to two oligopeptide transporters (OPT1, OPT9), and iron-acquisition oxidoreductase (CFL2), a nucleoside transporter (NUP) and a leucine aminopeptidase (APE2), whereas Stp2 is responsible for the regulation of amino acid uptake and catabolic genes, in a manner dependent of amino acid sensing. Surprisingly, Stp2 affects expression of genes involved in the filamentation response (e.g. UME6, SFL2) that have been associated with host colonization. In a GI tract competition experiment, mutants lacking the amino acid sensor Ssy1 or the TF Stp2 exhibited decreased colonization, while an stp1Δ/Δ mutant showed increase colonization. Taken together, these results highlight the importance of peptide and amino acid utilization for colonization of the host, a prerequisite for disseminated disease.
2020-02-20 | GSE145576 | GEO
Project description:Lantibiotics are highly modified peptides that are part of the bacteriocin family of antimicrobial peptides. We have identified a Phr peptide quorum sensing system (TprA/PhrA) that controls the expression of a lantibiotic gene cluster in the Gram-positive human pathogen, Streptococcus pneumoniae. We have characterized the basic mechanism for a Phr peptide signaling system in S. pneumoniae D39 and found that it induces expression of the lantibiotic genes when pneumococcal cells are at high density in the presence of galactose, a main sugar of the human nasopharynx, a highly competitive microbial environment. In this study we used RNA-seq analysis to examine the changes in relative transcript amounts caused by ∆tprA and ∆phrA mutations or the addition of the 10-residue synthetic PhrA peptide. These analyses reveal that PhrA peptide addition induces the transcription of a cluster of lantibiotic gene that appear to process and provide immunity to a lantibiotic peptide. In addition, TprA, a transcriptional factor regulated by a Phr peptide, autoregulates its own transcription.
2015-10-20 | GSE68598 | GEO
Project description:We investigated the transcriptome profile of HEK293T cells transfected with a plasmid encoding 9J10, a peptide isolated in a phenotypic screen from a library of peptides derived from bacterial and archaeal genomes. The peptide was identified in a screen for FOXO3a reactivation and has been shown to interact with 14-3-3 proteins and induce relocalisation of FOXO3a from the cytoplasm to the nucleus. A peptide with a single amino acid mutation does not interact with 14-3-3 and was included as a control. A constitutively active FOXO3a mutant was also included as a control.
2021-05-28 | E-MTAB-10161 | biostudies-arrayexpress
Project description:phytoplankton exudate utilization by bacteria
| PRJEB44710 | ENA
Project description:D-Glutamate (D-Glu), an essential component of peptidoglycans, can be utilized as carbon and nitrogen source by Pseudomonas aeruginosa. DNA microarrays were employed to identify genes involved in D-Glu catabolism. Through gene knockout and growth phenotype analysis, the divergent dguR-dguABC (D-glutamate utilization) gene cluster was shown to participate in D-Glu catabolism and regulation. The dguA gene encodes a FAD-dependent D-amino acid dehydrogenase with D-Glu as its preferred substrate, and its promoter was specifically induced by exogenous D-Glu and D-Gln. The function of DguR as transcriptional activator of the dguABC operon was demonstrated by promoter activity measurements in vivo and by mobility shift assays with purified His-tagged DguR in vitro. Although the DNA-binding activity of DguR did not require D-Glu, the presence of D-Glu in the binding reaction was found to stabilize a preferred nucleoprotein complex. The dguB gene encodes a putative enamine/imine deaminase of the RidA family, but its role in D-Glu catabolism remained to be determined. While a lesion in dguC encoding a periplasmic solute binding protein did not affect growth on D-Glu, the AatJMQP transporter for acidic amino acid uptake was found essential for D-Glu and L-Glu utilization. Expression of this uptake system was subjected to induction by exogenous DL-Glu, most likely via the AauSR two-component system. In summary, DguA was identified in this study as a new member of the FAD-dependent amino acid dehydrogenase family for D-amino acid catabolism. DguR serves as a D-Glu sensor and transcriptional activator of the dguA promoter. Pseudomonas aeruginosa PAO1 was chosen as model to study gene response with different D-amino acids.
2013-05-03 | E-GEOD-46603 | biostudies-arrayexpress
Project description:D-Glutamate (D-Glu), an essential component of peptidoglycans, can be utilized as carbon and nitrogen source by Pseudomonas aeruginosa. DNA microarrays were employed to identify genes involved in D-Glu catabolism. Through gene knockout and growth phenotype analysis, the divergent dguR-dguABC (D-glutamate utilization) gene cluster was shown to participate in D-Glu catabolism and regulation. The dguA gene encodes a FAD-dependent D-amino acid dehydrogenase with D-Glu as its preferred substrate, and its promoter was specifically induced by exogenous D-Glu and D-Gln. The function of DguR as transcriptional activator of the dguABC operon was demonstrated by promoter activity measurements in vivo and by mobility shift assays with purified His-tagged DguR in vitro. Although the DNA-binding activity of DguR did not require D-Glu, the presence of D-Glu in the binding reaction was found to stabilize a preferred nucleoprotein complex. The dguB gene encodes a putative enamine/imine deaminase of the RidA family, but its role in D-Glu catabolism remained to be determined. While a lesion in dguC encoding a periplasmic solute binding protein did not affect growth on D-Glu, the AatJMQP transporter for acidic amino acid uptake was found essential for D-Glu and L-Glu utilization. Expression of this uptake system was subjected to induction by exogenous DL-Glu, most likely via the AauSR two-component system. In summary, DguA was identified in this study as a new member of the FAD-dependent amino acid dehydrogenase family for D-amino acid catabolism. DguR serves as a D-Glu sensor and transcriptional activator of the dguA promoter.
2013-05-03 | GSE46603 | GEO
Project description:We are studying new ways to look for abnormal areas/tissues of the colon during a colonoscopy. The current scopes used for colonoscopies are very good. But if the area doesn’t look different to the naked eye, then the scope can’t improve on that. We are using special stains or dyes and special scopes to see abnormal areas that are hard to see with the naked eye. The stain or dye is "fluorescent", meaning it glows when special light is used in the colonoscopy scope.
You are being asked to let us spray a peptide with a fluorescent tag onto your colon. Peptides are small chains of amino acids (the building blocks that make up proteins) linked together. The peptide we use has 7 amino acids attached to a fluorescent tag ("FIT C" or Fluoresceinisothiocyanate). FITC is used by eye doctors to examine your eyes (the yellow eye drops).
We are testing this "fluorescent peptide" to see if it will stick if there are any abnormal areas. If the peptide "sticks", it will "glow" when a special light in the scope is used. In this study, we will apply the fluorescent peptide to your colon by using a spray tube that fits in the colonoscope.
This is a phase IB study. This means that although we have applied the peptide to 25 people in our first research study, we still need to learn more about "fluorescent peptide" in people. The Food and Drug Administration (FDA) has not approved this agent, but is allowing us to test it in this study. The main goal of this study is to see if the peptide "glows" well and if we can take pictures of areas that do glow.
This is a research study of the peptide and our ability to see it "glow or fluoresce". Being in this study and applying the peptide won’t change how our biopsies are taken or how your colonoscopy is done.
| 2167986 | ecrin-mdr-crc
Project description:The loading of high affinity peptides onto nascent class I MHC (MHC-I) molecules is facilitated by chaperones, including the class I-specific chaperone TAP-binding protein-related (TAPBPR). TAPBPR features a loop (amino acids 24-35) that projects towards the empty MHC-I peptide binding groove and rests above the F pocket. The 24-35 loop is much shorter in the closely related homologue tapasin, and therefore may be partly responsible for the unique antigen editing properties of TAPBPR. Previously we reported a deep mutational scan of human TAPBPR focused on the 24-35 loop, and determined the relative effects of single amino acid mutations on binding and peptide-mediated release of the murine H2-Dd MHC-I allomorph. Here, we extend our studies to determine the mutational landscape of the 24-35 loop when TAPBPR binds a human MHC-I allomorph, HLA-A*02:01. The data highlights how TAPBPR affinity can be increased or decreased for different MHC-I allomorphs by tuning the electrostatic complementarity of the 24-35 loop for surfaces on the rim of the peptide-binding groove. By changing the selection pressure from HLA-A2 binding to HLA-A2 loading and processing, we find that TAPBPR is reasonably tolerant of mutations in the 24-35 loop for efficient peptide-MHC-I processing and surface trafficking.
2019-09-01 | GSE126206 | GEO
Project description:Aberrant protein aggregation jeopardize cellular functionality and underlies the development of a myriad of late-onset maladies including Alzheimer’s disease (AD) and Huntington’s disease (HD). Accordingly, molecules that mitigate the toxicity of hazardous protein aggregates are of great interest as potential future therapeutics. Here we asked whether a small peptide, composed of five amino acids (5MER peptide) that was derived from the human pro-inflammatory CD44, could protect model nematodes from the toxicity of aggregative proteins that underlie the development of neurodegenerative disorders in humans. We found that the 5MER peptide mitigates the toxicity that stems from both, the AD-causing Aβ peptide and a stretch of poly-glutamine that is accountable to the development of several disorders including HD, without affecting lifespan. This protection was dependent on the activity of the aging-regulating transcription factors and associated with enhanced Aβ and polyQ35-YFP aggregation. A transcriptomic analysis unveiled that the peptide modulates the expression of various genes including these which are known as protein homeostasis (proteostasis) regulators such as txt-13, and modifiers of proteasome activity. The knockdown of txt-13 protects worms from proteotoxicity to the same extent as the 5MER peptide, suggesting that the peptide activates the transcellular chaperone signaling to promote proteostasis. Together, our results propose that the 5MER peptide should be considered as a component of future therapeutic cocktails for the treatment of neurodegenerative maladies.
2023-12-27 | GSE230640 | GEO
Project description:We have identified a novel xylose-utilization phenotype controlled by a single gene, and we sought to characterize how both the presence and absence of xylose in the presence or absence of the trait affected the S. cerevisiae transcriptional program over time. To do so, we measured global steady state mRNA levels on three pairs of sister spores from a Simi White strain that was backcrossed twice to S288c. Each pair of spores was from an independent tetrad, and contained one xylose utilizing ("positive", GSY2465, 2466, 2469) and one xylose non-utilizing spore ("negative", GSY2464, 2467, 2470). We grew each of the six spores in the presence or absence of xylose for 72 hours with samples taken every 8 hours. We then assayed relative RNA abundance versus a pooled reference, containing equimolar amounts of each sample, using Agilent yeast catalog arrays.
2010-04-09 | GSE19116 | GEO