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A Quantitative Method for Proteome Reallocation Using Minimal Regulatory Interventions

ABSTRACT: A Quantitative Method for Proteome Reallocation Using Minimal Regulatory Interventions

PROVIDER: PRJNA554797 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9692052_1.fastq.gz	Fastqsanger.gz
	SRR9692052_2.fastq.gz	Fastqsanger.gz
	SRR9692053.fastq.gz	Fastqsanger.gz
	SRR9692053_1.fastq.gz	Fastqsanger.gz
	SRR9692053_2.fastq.gz	Fastqsanger.gz

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A Quantitative Method for Proteome Reallocation Using Minimal Regulatory Interventions

Project description:A Quantitative Method for Proteome Reallocation Using Minimal Regulatory Interventions

| PRJNA554797 | ENA

A Quantitative Method for Proteome Reallocation Using Minimal Regulatory Interventions

Project description:Engineering resource allocation in biological systems is an ongoing challenge. Organisms allocate resources for ensuring survival, reducing the productivity of synthetic biology functions. Here we present a novel approach for engineering the resource allocation of Escherichia coli by rationally modifying its transcriptional regulatory network. Our method (ReProMin) identifies the minimal set of genetic interventions that maximises the savings in cell resources. To this end, we categorized Transcription Factors according to the essentiality of its targets and we used proteomic data to rank them. We designed the combinatorial removal of TFs that maximise the release of resources. Our resulting strain containing only three mutations, theoretically releasing 0.5% of its proteome, had higher proteome budget, increased production of an engineered metabolic pathway and showed that the regulatory interventions are highly specific. This approach shows that combining proteomic and regulatory data is an effective way of optimizing strains using conventional molecular methods.

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Quantitative proteome dynamics across embryogenesis in a model chordate

Project description:The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ~7k translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.

2023-11-27 | GSE237005 | GEO

A Quantitative Sequencing Method for 5-Formylcytosine in RNA

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Proteome-scale tagging and functional screening in mammalian cells by ORFtag [ORFtag]

Project description:Determining protein function in a systematic and comprehensive manner is a key goal in modern molecular biology research but is challenging with current approaches. Here, we introduce ORFtag, a versatile method for the massively parallel protein tagging and interrogation of protein function at the proteome scale with minimal effort and expense. We demonstrate the versatility of ORFtag in mouse and human cells with a series of functional screens for transcriptional activators, repressors and post-transcriptional gene regulatory proteins.

2024-05-10 | GSE240282 | GEO

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Project description:Cellular communication is a fundamental process in biology. We developed an in vitro procedure for quantitatively analyzing proteome-wide changes triggered by interaction of different cell types. Using an adipocyte-macrophage bilayer co-culture model we detected thousands of proteins and deciphered regulatory pathways involved in low-grade inflammation leading to insulin resistance. The method can be applied for multiple cell-cell combinations to gain understanding in cellular interaction.

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2023-04-17 | GSE227689 | GEO

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