Dataset Information

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria.

ABSTRACT: A central aim of cell biology was to understand the strategy of gene expression in response to the environment. Here, we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlying regulatory network, we find that the proteome partitions into several coarse-grained sectors, with each sector's total mass abundance exhibiting positive or negative linear relations with the growth rate. The growth rate-dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual dependencies can be characterized by a simple flux model involving only two effective parameters. The success and apparent generality of this model arises from tight coordination between proteome partition and metabolism, suggesting a principle for resource allocation in proteome economy of the cell. This strategy of global gene regulation should serve as a basis for future studies on gene expression and constructing synthetic biological circuits. Coarse graining may be an effective approach to derive predictive phenomenological models for other 'omics' studies.

SUBMITTER: Hui S

PROVIDER: S-EPMC4358657 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria.

Hui Sheng S Silverman Josh M JM Chen Stephen S SS Erickson David W DW Basan Markus M Wang Jilong J Hwa Terence T Williamson James R JR

Molecular systems biology 20150212 1

A central aim of cell biology was to understand the strategy of gene expression in response to the environment. Here, we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlying regulatory network, we find that the proteome partitions into several coarse-grained sectors, with each sector's total mass abundance exhibiting positive or negative linear relations with the grow ...[more]

PMID: 25678603

Similar Datasets

Project description:International institutions provide well over US$10 billion in development assistance for health (DAH) annually and between 1990 and 2014, DAH disbursements totaled $458 billion but how do they decide who gets what, and for what purpose? In this article, we explore how allocation decisions were made by the nine convening agencies of the Equitable Access Initiative. We provide clear, plain language descriptions of the complete process from resource mobilization to allocation for the nine multilateral agencies with prominent agendas in global health. Then, through a comparative analysis we illuminate the choices and strategies employed in the nine international institutions. We find that resource allocation in all reviewed institutions follow a similar pattern, which we categorized in a framework of five steps: strategy definition, resource mobilization, eligibility of countries, support type and funds allocation. All the reviewed institutions generate resource allocation decisions through well-structured and fairly complex processes. Variations in those processes seem to reflect differences in institutional principles and goals. However, these processes have serious shortcomings. Technical problems include inadequate flexibility to account for or meet country needs. Although aid effectiveness and value for money are commonly referenced, we find that neither performance nor impact is a major criterion for allocating resources. We found very little formal consideration of the incentives generated by allocation choices. Political issues include non-transparent influence on allocation processes by donors and bureaucrats, and the common practice of earmarking funds to bypass the normal allocation process entirely. Ethical deficiencies include low accountability and transparency at international institutions, and limited participation by affected citizens or their representatives. We find that recipient countries have low influence on allocation processes themselves, although within these processes they have some influence in relatively narrow areas.

Dataset Information

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria.

Publications

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets