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The three-dimensional conformation of the genome also may plays an important role in transcriptional regulation and environmental adaptation. Here, using chromosome conformation capture, we investigate the high-order architecture of the Zymomonas mobilis chromosome in response to genomic mutant and ambient stimuli (acetic acid and furfural, derived from lignocellulosic hydrolysate). We find that genomic mutation only influences the local chromosome contacts, whereas stress of acetic acid and furfural restrict the long-range contacts and change the chromosome organization at domain scales significantly. Further deciphering the domain feature unveils the important transcription factors, Ferric uptake regulation (Fur) proteins, which act as nucleoid-associated proteins to promote long-range (> 200 kb) chromosomal communications and regulate the expression of genes involved in stress response. Our work suggests that ubiquitous transcription factors in prokaryotes mediate chromosome organization and regulate stress-resistance genes in bacterial adaptation. RNA-seq analysis to reveal the regulation process of Fur proteins. Overall design: The gene expression levels of different strains were compared under different growth conditions"],"tag":["xref:PubMed:38716861"],"repository":["ENA"],"description_synonyms":["F14P3.4, RNA polymerase II core promoter proximal region sequence-specific binding, Transcription, T-cell leukemia, Factors, Gene Expressions, conformation, AGL4, F14P3_4, F10N7_150, Gene, zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, homeobox 1, RNA-seq., Factor, SEPALLATA 2, metal ion regulated core promoter proximal region sequence-specific binding, metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity, copper ion regulated core promoter proximal region sequence-specific binding, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity, Transcription Factor, Expressions, Transcription factor, F10N7.150, transcription factor activity, zinc ion regulated core promoter proximal region sequence-specific DNA binding, RNA polymerase II proximal promoter sequence-specific DNA binding, copper ion regulated proximal promoter sequence-specific DNA binding, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, AGAMOUS-like 4, RNA polymerase II transcription factor activity, Whole Transcriptome Shotgun Sequencing, zinc ion regulated proximal promoter sequence-specific DNA binding, sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity, Expression, sequence-specific distal enhancer binding RNA polymerase II transcription factor activity, metal ion regulated sequence-specific DNA binding, metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, relational structural quality, KNOTTED1-like homeobox gene 5, metal ion regulated proximal promoter sequence-specific DNA binding, TRANSCRIPTION FACTOR, RNA polymerase II distal enhancer sequence-specific binding"],"name_synonyms":["F14P3.4, RNA polymerase II core promoter proximal region sequence-specific binding, Transcription, T-cell leukemia, Factors, Gene Expressions, conformation, AGL4, F14P3_4, F10N7_150, Gene, zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, homeobox 1, RNA-seq., Factor, SEPALLATA 2, metal ion regulated core promoter proximal region sequence-specific binding, metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity, copper ion regulated core promoter proximal region sequence-specific binding, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity, Transcription Factor, Expressions, Transcription factor, F10N7.150, transcription factor activity, zinc ion regulated core promoter proximal region sequence-specific DNA binding, RNA polymerase II proximal promoter sequence-specific DNA binding, copper ion regulated proximal promoter sequence-specific DNA binding, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, AGAMOUS-like 4, RNA polymerase II transcription factor activity, Whole Transcriptome Shotgun Sequencing, zinc ion regulated proximal promoter sequence-specific DNA binding, sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity, Expression, sequence-specific distal enhancer binding RNA polymerase II transcription factor activity, metal ion regulated sequence-specific DNA binding, metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, relational structural quality, KNOTTED1-like homeobox gene 5, metal ion regulated proximal promoter sequence-specific DNA binding, TRANSCRIPTION FACTOR, RNA polymerase II distal enhancer sequence-specific binding"],"additional_accession":[]},"is_claimable":false,"name":"Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [RNA-Seq]","description":"Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [RNA-Seq]","dates":{"last_updated":"2025-09-24","first_public":"2024-05-19"},"accession":"PRJNA914691","cross_references":{"GEO":["GSE221498"],"taxon":["542"],"PubMed":["38716861"]}}