The fungal CCAAT-binding complex and HapX display highly variable but evolutionary conserved synergetic promoter-specific DNA recognition
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ABSTRACT:
PROVIDER: PRJNA533305 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11040534_1.fastq.gz | Fastqsanger.gz | |||
| SRR11040534_2.fastq.gz | Fastqsanger.gz | |||
| SRR11040535_1.fastq.gz | Fastqsanger.gz | |||
| SRR11040535_2.fastq.gz | Fastqsanger.gz | |||
| SRR11040536_1.fastq.gz | Fastqsanger.gz |
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Project description:To sustain iron homeostasis, microorganisms have evolved fine-tuned mechanisms for uptake, storage and detoxification of the essential metal iron. In the human pathogen Aspergillus fumigatus, the fungal-specific bZIP-type transcription factor HapX coordinates adaption to both iron starvation and iron excess and is thereby crucial for virulence. Previous studies indicated that a HapX homodimer interacts with the CCAAT-binding complex (CBC) to cooperatively bind bipartite DNA motifs; however, the significance of the HapX and CBC interaction and the mode of HapX-DNA recognition had not been resolved. In this study, we characterized the genome-wide binding profiles of HapX using the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). Our ChIP-seq results, in combination with in vitro surface plasmon resonance analysis, phylogenetic comparison, and genetic analysis, revealed an astonishing plasticity of the CBC:HapX DNA-recognition mode.
2019-12-31 | GSE129969 | GEO
Project description:To sustain iron homeostasis, microorganisms have evolved fine-tuned mechanisms for uptake, storage and detoxification of the essential metal iron. In the human pathogen Aspergillus fumigatus, the fungal-specific bZIP-type transcription factor HapX coordinates adaption to both iron starvation and iron excess and is thereby crucial for virulence. Previous studies indicated that a HapX homodimer interacts with the CCAAT-binding complex (CBC) to cooperatively bind bipartite DNA motifs; however, the mode of HapX-DNA recognition had not been resolved. Here, combination of in vivo (genetics and ChIP-seq), in vitro (surface plasmon resonance) and phylogenetic analyses identified an astonishing plasticity of CBC:HapX:DNA interaction. DNA motifs recognized by the CBC:HapX protein complex comprise a bipartite DNA binding site 5'-CSAATN12RWT-3' and an additional 5'-TKAN-3' motif positioned 11-23 bp downstream of the CCAAT motif, i.e. occasionally overlapping the 3'-end of the bipartite binding site. Phylogenetic comparison taking advantage of 20 resolved Aspergillus species genomes revealed that DNA recognition by the CBC:HapX complex shows promoter-specific cross-species conservation rather than regulon-specific conservation. Moreover, we show that CBC:HapX interaction is absolutely required for all known functions of HapX. The plasticity of the CBC:HapX:DNA interaction permits fine tuning of CBC:HapX binding specificities that could support adaptation of pathogens to their host niches.
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Project description:We conducted a network-based analysis of the Hap5 transcription factor belonging to the CCAAT-Binding Complex in Candida glabrata.
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Project description:Iron is an essential cofactor for a wide range of cellular processes. Previous studies have shown that siderophore-mediated uptake and intracellular handling of iron are crucial for virulence of Aspergillus fumigatus. Here we show that the bzip-type transcription factor HapX plays a crucial role in the transcriptional remodeling required for adaption to iron starvation in this opportunistic fungal pathogen. HapX was found to be interconnected in a negative feed-back loop with the previously identified iron regulator SreA: SreA repressed expression of hapX during iron sufficiency and HapX repressed sreA during iron starvation. Genome-wide transcriptional profiling and analysis of selected metabolites (protophorphyrine IX, siderophores and amino acids) indicated extensive metabolic remodeling in response to iron starvation. HapX was found to participate in both, repression and activation of genes during iron starvation. HapX was in particular required for repression of iron-dependent and mitochondrial-localized activities including respiration, TCA cycle, amino acid metabolism, iron-sulfur-cluster biosynthesis and heme biosynthesis. Pathways positively affected by HapX included production of siderophores and the ribotoxin and major allergen AspF1. Analysis of the free amino acid pool revealed HapX-dependent coordination of the production of siderophores with the supply of its precursor ornithine. Consistent with the hapX expression pattern, HapX-deficiency was deleterious with respect to growth rate and conidiation during iron depleted but not iron-replete conditions. HapX-deficiency caused significant attenuation of virulence in a murine model aspergillosis underlining that A. fumigatus faces iron starvation in the host and that the HapX-dependent metabolic reprogramming is therefore crucial for virulence.
2010-07-01 | GSE22052 | GEO
Project description:Iron is an essential cofactor for a wide range of cellular processes. Previous studies have shown that siderophore-mediated uptake and intracellular handling of iron are crucial for virulence of Aspergillus fumigatus. Here we show that the bzip-type transcription factor HapX plays a crucial role in the transcriptional remodeling required for adaption to iron starvation in this opportunistic fungal pathogen. HapX was found to be interconnected in a negative feed-back loop with the previously identified iron regulator SreA: SreA repressed expression of hapX during iron sufficiency and HapX repressed sreA during iron starvation. Genome-wide transcriptional profiling and analysis of selected metabolites (protophorphyrine IX, siderophores and amino acids) indicated extensive metabolic remodeling in response to iron starvation. HapX was found to participate in both, repression and activation of genes during iron starvation. HapX was in particular required for repression of iron-dependent and mitochondrial-localized activities including respiration, TCA cycle, amino acid metabolism, iron-sulfur-cluster biosynthesis and heme biosynthesis. Pathways positively affected by HapX included production of siderophores and the ribotoxin and major allergen AspF1. Analysis of the free amino acid pool revealed HapX-dependent coordination of the production of siderophores with the supply of its precursor ornithine. Consistent with the hapX expression pattern, HapX-deficiency was deleterious with respect to growth rate and conidiation during iron depleted but not iron-replete conditions. HapX-deficiency caused significant attenuation of virulence in a murine model aspergillosis underlining that A. fumigatus faces iron starvation in the host and that the HapX-dependent metabolic reprogramming is therefore crucial for virulence. A. fumigatus 293 and hapX mutants were grown in the presence and absence of iron and in cultures shifted from no iron to iron-containing conditions after 1 h incubation. Hybridizations were performed with biological replicates for wt vs hapX +/- iron. For the iron-shift experiments, there were biological replicates for wt in both conditions and for hapX in -iron but there was only a single biological sample for hapX iron-shift sample. All hybs were performed with flip-dye pairs.
2010-07-01 | E-GEOD-22052 | biostudies-arrayexpress
Project description:The CCAAT-binding complex (CBC) is a heterotrimetric transcription factor conserved in all eukaryotes. The CBC specifically interacts with the pentanucleotide motif known as the CCAAT box, which is one of the most ubiquitous cis-acting elements on the eukaryotic promoters. In Aspergillus fumigatus, the CBC consists of three subunits HapB, HapC, and HapE, which are all required for specific binding to the target sequences. This regulatory complex has been shown to be involved in the regulation of a wide range of cellular processes, including primary and secondary metabolism, iron homeostasis, as well as azole drug resistance and virulence in mammalian hosts. In this study, we investigated the genome-wide binding profile of the CBC using the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). We identified over 1,000 peak regions, which showed more than 5-fold enrichment compared to the input control in steady-state iron-replete (+Fe) and iron-starvation (-Fe) conditions. Bioinformatic analysis of the peak regions revealed the 5’-CSAATVR-3’ sequence as the most enriched nucleotide motif, suggesting that this motif acts as the consensus binding sequence for the CBC in vivo.
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Project description:CCAAT/enhancer-binding protein alpha (C/EBPα) is a lineage-specific transcription factor that directs development of granulocytes. To obtain insights into the genome-wide transcriptome of wild type C/EBPα, we have performed chromatin immunoprecipitation on DNA promoter microarrays (ChIP-chip) in the murine 32D myeloid progenitor cell line. These cells expressed an estradiol-inducible form of wild-type C/EBPα.
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