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Extensive functional divergence of the RosR transcription factor across haloarchaea

ABSTRACT: Extensive functional divergence of the RosR transcription factor across haloarchaea

PROVIDER: PRJNA1169916 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30916272_1.fastq.gz	Fastqsanger.gz
	SRR30916272_2.fastq.gz	Fastqsanger.gz
	SRR30916274_1.fastq.gz	Fastqsanger.gz
	SRR30916274_2.fastq.gz	Fastqsanger.gz
	SRR30916278_1.fastq.gz	Fastqsanger.gz

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Extensive functional divergence of the RosR transcription factor across haloarchaea [ChIP-Seq]

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Project description:For microbial cells, an appropriate response to changing environmental conditions is critical for viability. Transcription regulatory proteins, or transcription factors (TFs) sense environmental signals to change gene expression. However, it remains unclear how TFs and their corresponding gene regulatory networks are selected for over evolutionary time scales. The function of TFs and how they evolve are particularly understudied in archaeal organisms. Here we identified, characterized, and compared the function of the RosR transcription factor across three related species of hypersaline adapted model archaea. RosR was previously characterized as a global regulator of gene expression during oxidative stress in the species Halobacterium salinarum (HsRosR). Here we use functional genomics and quantitative phenotyping to demonstrate that, despite strong conservation of HsRosR across species, its function diverges substantially. Surprisingly, RosR in Haloferax volcanii and Haloferax mediterranei regulates genes whose products function in motility and the outer membrane, leading to significant defects in motility when rosR is deleted. Given weak conservation and degeneration in the RosR cis-regulatory sequence across species, we hypothesize that the RosR regulatory network is easily rewired during evolution across related species of archaea.

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Project description:To better characterize how variation in regulatory sequences drives divergence in gene expression, we undertook a systematic study of transcription factor binding and gene expression in blastoderm embryos of four species, which sample much of the diversity in the 40 million-year old genus Drosophila: D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. We compared gene expression, measured by mRNA-seq, to the genome-wide binding, measured by ChIP-seq, of four transcription factors involved in early anterior-posterior patterning. We found that mRNA levels are much better conserved than individual transcription factor binding events, and that changes in a gene’s expression were poorly explained by changes in adjacent transcription factor binding. However highly bound sites, sites in regions bound by multiple factors and sites near genes are conserved more frequently than other binding, suggesting that a considerable amount of transcription factor binding is weakly or non-functional and not subject to purifying selection

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