Prospective isolation according to melanin pigment content of melanoma cells with heterogeneous potentials for disease propagation
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PROVIDER: PRJNA912648 | ENA |
REPOSITORIES: ENA
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2025-07-09 | GSE221039 | GEO
Project description:Melanin is an antioxidant polyphenol pigment, which is required for the pathogenicity of many human and plant fungal pathogens. Nevertheless, its comprehensive regulatory mechanism still remain elusive. In this study, we systematically analyzed melanin-regulating signaling pathways in Cryptococcus neoformans. Here we identified four core melanin-regulating TFs, Bzp4, Usv101, Mbs1, and Hob1, which are required for induction of the laccase gene (LAC1). Bzp4, Usv101 and Mbs1 independently regulate LAC1 induction while Hob1 controls Bzp4 and Usv101 expression. Both Bzp4 and Usv101 are translocated from the cytoplasm into the nucleus upon nutrient starved condition, while Mbs1 is constitutively localized in the nucleus. Notably, the cAMP pathway is not involved in regulation of the four TFs, while the HOG pathway negatively regulates induction of BZP4 and LAC1. As potential kinases upstream of the core TFs, we identified the nine core kinases, whose deletion leads to defective melanin production and LAC1 induction. Deletion of GSK3 or KIC1 abolishes induction of LAC1 and BZP4, and also perturbs nuclear translocation of Bzp4. Notably, Gsk3 also regulates the expression of HOB1, USV101, and MBS1, indicating that it is a critical melanin-regulating kinase. Finally, the RNA-sequencing based transcriptome analysis of the wild-type and bzp4Δ, usv101Δ, hob1Δ, and mbs1Δ strains under nutrient rich and starved conditions reveals that the core melanin-regulating TFs govern redundant and distinct classes of genes, which are involved in a variety of biological processes.
2019-05-30 | GSE131891 | GEO
Project description:Feather coloration is one of the most extraordinary examples of phenotypic diversity. This diversity results both from the variation in hue as well as from the presence/absence of pigment in distinct feather regions. The mechanisms that drive presence/absence of pigmentation in feathers are not yet fully understood. Here we characterize the gene expression profiles associated with differential melanin pigmentation in Dark-eyed junco (Junco hyemalis) tails, a social feather ornament used in courtship and male-male competition. Junco tail feathers contain both white apigmented regions as well as dark melanin-pigmented regions. We compared the transcriptome-wide gene expression in developing white and dark regions of tail feathers to understand the regulatory pathways that may regulate the development of this feather ornament. We show that both white and dark feathers express melanocyte markers, indicating that white feathers contain cells capable of producing pigment. However, only dark cells express genes associated with melanin synthesis. We identify differences in expression of genes that may regulate melanocyte activation in dark feathers. Future studies should experimentally test the role of these genes in driving differences in feather pigmentation.
2023-01-08 | GSE167085 | GEO
Project description:Alternaria brassicicola is a successful saprophyte and necrotrophic plant pathogen. Several A. brassicicola genes have been characterized as virulence factors affecting pathogenesis of Brassica species. To study regulatory mechanisms of pathogenesis, we mined 421 genes in silico encoding putative transcription factors in a machine-annotated, draft genome sequence of A. brassicicola. Targeted gene disruption mutants for 114 of the genes with proteins predicted to contain at least one putative zinc-finger domain were produced and functionally analyzed. Six of these genes were associated with pathogenesis. Disruption mutants corresponding to five of the genes were ≥50% less virulent than the wild type. Unexpectedly, the mutants of one gene (designated Amr1) were 100% more virulent. Amr1 is a homolog of Cmr1, a transcription factor previously found to regulate melanin biosynthesis in several fungi. Gene deletion mutants (Δamr1) were created and their phenotypes characterized. The Δamr1 mutants utilized pectin as a carbon source more efficiently than the wild type, were melanin-deficient, and more sensitive to UV light and glucanase digestion. The Amr1 protein was localized in the nuclei of hyphae and in highly melanized conidia during the late stage of plant pathogenesis. RNA-seq analysis revealed that three genes in the melanin biosynthesis pathway, along with the deleted Amr1 gene, were not expressed in the mutants. In contrast, many hydrolytic enzyme-coding genes were expressed at much higher levels in the mutants than in the wild type during pathogenesis. The results of this study suggested that only a small number of transcription factors with zinc finger domains are needed to maintain strong virulence. Furthermore, a gene important for survival in nature negatively affected virulence, probably by less efficient use of pectin. We speculate that the functions of the Amr1 gene are important to the success of A. brassicicola as a competitive saprophyte and plant parasite gene expression profile comparisons between wild type and a transcription factor mutant during the late stage of host infection
2013-02-19 | E-GEOD-36781 | biostudies-arrayexpress
Project description:Electrochemically active bacteria (EAB) receive considerable attention for their utility in bioelectrochemical processes. Although electrode potentials are known to affect the metabolic activity of EAB, it is unclear whether EAB are able to sense and respond to electrode potentials. Here, we show that, in the presence of a high-potential electrode, a model EAB Shewanella oneidensis MR-1 can utilize NADH-dependent catabolic pathways and a background formate-dependent pathway to achieve high growth yield. We also show that an Arc regulatory system is involved in sensing electrode potentials and regulating the expression of catabolic genes, including those for NADH dehydrogenase. We suggest that these findings may facilitate the use of EAB in biotechnological processes and offer the molecular bases for their ecological strategies in natural habitats.
2018-02-22 | GSE102264 | GEO
Project description:The aim of this study was to determine the transcriptomic response of Saccharomyces pastorianus to environmental change during brewery propagation. Utilization of amino acids and fermentable carbohydrates during full-scale brewery propagation was compared to the simultaneous changes occurring in the yeast transcriptome. Transcription profiles were observed to fall within one of four different groups and the greatest changes were observed to occur within the first eight hours following inoculation. Nutrient uptake was at its greatest during this period and many genes involved in the utilization of amino acids and carbohydrates were activated. There was also a significant derepression response following monosaccharide exhaustion. A number of stress response genes were activated following inoculation, indicating a possible osmotic stress response. Nutrient limitation did not appear to initiate a significant stress response, but did activate genes involved in pseudohyphal growth and meiosis, despite the fact that neither biological process occurs in the strain utilized. The first hours after inoculation into propagation wort are particularly active with respect to nutrient utilization and transcriptional change. It is likely that this period is particularly stressful for the yeast cells though there is no evidence of viability loss and it may be concluded that the yeast cell can cope with this level of stress, possibly aided by the dynamic response of the transcriptome. Keywords: amino acid, brewing, carbohydrate, microarray, propagation, transcription, yeast GeneChip analyses were performed to determine the transcriptomic response of Saccharomyces pastorianus to environmental change during brewery propagation. Triplicate samples were taken immediately after inoculation and at intervals 4h, 8h, and 30h.
2009-06-02 | E-GEOD-16376 | biostudies-arrayexpress
Project description:A. flavus keratitis is one of the predominant fungal infections affecting the tropical parts of the world. Melanin is a virulence factor in numerous pathogenic fungi and the melanin layer maintains the cell wall structure and provides chemical and physical protection to the organism. However, the molecular and biological mechanisms modulating melanin-mediated host-pathogen interaction in A. flavus keratitis are not well understood. This work aimed to compare the morphology, surface proteome profile and virulence of melanized and non-melanized conidia of A. flavus. An environmental isolate and two clinical isolates were included in this study. L-DOPA melanin pathway-specific inhibitor kojic acid (KA) as used to prepare non-melanized conidia. Conidial surface proteins were extracted using 100% formic acid at 0 ºC and the extracted proteins were analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS PAGE). Formic acid extracts were analyzed in an Orbitrap Velos pro-mass spectrometer. Conidial surface morphology difference was examined using scanning electron microscopy (SEM). Furthermore, lactophenol and calcofluor staining were performed to check the morphology and staining efficiency of melanized conidia (MC) and non-melanized conidia (NMC). A Galleria mellonella insect model was used to examine the virulence efficiency of MC and NMC. Kojic acid treatment inhibited melanin synthesis in A. flavus and the conidial surface protein profile was significantly different in kojic acid-treated non-melanized conidia. Several cell wall-associated proteins and proteins responsible for oxidative stress, carbohydrate, and chitin metabolic pathway were found only in the formic acid extracts of NMC. SEM analysis showed the conidial surface morphology difference between the NMC and MC indicating the role of melanin in the structural integrity of the conidial cell wall. The levels of calcofluor staining efficiency were different, but there was no microscopic morphology difference in lactophenol cotton blue staining of MC and NMC. Evaluation of virulence of MC and NMC in G. mellonella model showed NMC was less virulent compared to MC . Our results showed that the integrity of the conidial surface is controlled by the melanin layer. The alteration in the surface protein profile indicated that many surface proteins are masked by the melanin layer and hence melanin can modulate the host response by preventing the exposure of fungal proteins to the host immune defense system. G. mellonella in vivo virulence assay also confirmed that the non-melanized conidia were susceptible to host defense as in other Aspergillus pathogens.
2024-05-23 | PXD037707 | Pride
Project description:Transcriptomic profiles of melanin pigmentation in a plumage ornament
| PRJNA702979 | ENA
Project description:Melanin, as a pivotal antioxidant pigment, plays a critical role in the pathogenicity of Cryptococcus neoformans. However, the underlying signaling pathways responsible for melanin biosynthesis in C. neoformans are not yet fully elucidated. In this study, proteome and metabolomics analyses were conducted to investigate the response of C. neoformans to melanin substrate Niger seed or L-DOPA. The proteome analysis identified significant differential expression of proteins in cells treated with Niger seed compared to L-DOPA, with distinct functional enrichment patterns observed. Subcellular localization analysis showed unique protein distribution in cells treated with each substrate. Metabolomics analysis revealed distinct metabolic profiles in response to Niger seed or L-DOPA, with notable differences in metabolite regulation between the two treatments. KEGG classification highlighted specific metabolic pathways affected by each substrate. Overall, this study provides valuable insights into the complex regulatory mechanisms underlying C. neoformans response to melanin substrates.
2025-07-23 | PXD056054 | Pride