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Cellulose perturbation has broad impacts on resource allocation in Arabidopsis thaliana putatively mediated by glycine rich peptides

ABSTRACT: Cellulose perturbation has broad impacts on resource allocation in Arabidopsis thaliana putatively mediated by glycine rich peptides

PROVIDER: PRJNA431443 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6508050_1.fastq.gz	Fastqsanger.gz
	SRR6508050_2.fastq.gz	Fastqsanger.gz
	SRR6508060_1.fastq.gz	Fastqsanger.gz
	SRR6508060_2.fastq.gz	Fastqsanger.gz
	SRR6508070_1.fastq.gz	Fastqsanger.gz

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Cellulose perturbation has broad impacts on resource allocation in Arabidopsis thaliana putatively mediated by glycine rich peptides

Project description:The interplay between plant chemistry and architecture was investigated using a pharmacological approach combined with mutant analysis. Due to the high abundance and essential role of cellulose in plant development and function, it was hypothesized that perturbation of cellulose biosynthesis would have far-reaching effects on plant chemistry and resource allocation. The impact of cellulose disruption was studied through comprehensive multiphase-NMR (CMP-NMR) using the Arabidopsis thaliana cellulose synthase mutant ectopic lignification1 (eli1). CMP-NMR confirmed several known metabolic impacts of cellulose disruption including increased lignification, increased starch production, and a shift from crystalline to amorphous cellulose. It also revealed unexpected metabolic impacts such as increased methanol production, increased seed-derived lipid content, and the presence of the peptide pentaglycine, which had not been previously observed in plants. It was further hypothesized that the metabolic impacts of cellulose disruption are mediated by one or more signal molecules that would be elevated in cellulose synthase mutants such as eli1. The presence of one or more signal molecules in eli1 that induce a lignification response was confirmed by exposing wild-type seedlings to ground tissue from eli1. Treatment of wild-type seedlings with pentaglycine suggested that the peptide may be at least partially responsible for mediating this response. A case is made for glycine rich proteins (GRPs) as the source of pentaglycine in vivo, and for wall associated kinases (WAKs) as receptors that trigger either developmental or defence responses through differential binding of intact GRPs and oligoglycine peptides.

2018-09-01 | GSE109595 | GEO

Proteome resource allocation in bacteria

Project description:A central aim of cell biology is 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.

2015-02-12 | PXD001467 | Pride

Specific growth rate-dependent proteome resource allocation dynamics in Escherichia coli

Project description:Cells usually respond to changing growth conditions with a change in the specific growth rate (μ) and adjustment of their proteome to adapt and maintain metabolic efficiency. Description of the principles behind proteome resource allocation is thus important for understanding metabolic regulation in responce to changing specific growth rate. We analysed the allocation dynamics of Escherichia coli proteome resources into different metabolic processes in response to changing μ. E. coli was grown on minimal and defined rich media in steady state continuous cultures at different μ and characterised by absolute quantitative LC-MS/MS based proteomics. We detected slowly growing cells investing more proteome resources in energy generation and carbohydrate transport and metabolism whereas for achieving faster growth cells needed to devote most resources to translation and processes closely related to the protein synthesis pipeline. Furthermore, down-regulation of energy generation and carbohydrate metabolism proteins with faster growth displayed very similar expression dynamics with the global transcriptional regulator CRP (cyclic AMP receptor protein), pointing to a dominant protein resource allocating role for this protein. Our data also suggest that acetate overflow may be the result of global proteome resource optimisation as cells saved proteome resources by switching from fully respiratory to respiro-fermentative growth. The presented results give a quantitative overview how E. coli adjusts its proteome to achieve faster growthin response to perturbations in μ. Quantitative understanding of proteome resource allocation could contribute to the design of more efficient cell factories through proteome optimisation towards proteins related to target molecule synthesis.

2015-02-27 | PXD001594 | Pride

Different resource allocation in a Bacillus subtilis population displaying bimodal motility

Project description:Different resource allocation in a Bacillus subtilis population displaying bimodal motility

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Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens

Project description:Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens

| PRJEB23255 | ENA

Cysteine-rich peptides promote interspecific genetic isolation in Arabidopsis

Project description:Cysteine-rich peptides promote interspecific genetic isolation in Arabidopsis

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Growth Rate Dependent and Nutrient-specific Gene Expression Resource Allocation in Fission Yeast

Project description:Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Quantitative studies using various growth conditions have singled out growth rate as a major physiological variable explaining relative protein abundances. Here, we used the simple eukaryote Schizosaccharomyces pombe to determine the importance of growth rate in explaining relative changes in protein and mRNA levels during growth on a series of non-limiting nitrogen sources. Although half of fission yeast genes were significantly correlated with the growth rate, this came alongside widespread nutrient-specific regulation. Proteome and transcriptome often showed coordinated regulation but with notable exceptions, such as metabolic enzymes. Genes positively correlated with growth rate participated in every level of protein production with the notable exception of RNA polymerase II, whereas those negatively correlated mainly belonged to the environmental stress response programme. Critically, metabolic enzymes, which represent ~55-70% of the proteome by mass, showed mainly condition-specific regulation. Specifically, many enzymes involved in glycolysis and NAD-dependent metabolism as well as the fermentative and respiratory pathways were condition-dependent and not consistently correlated with growth. In summary, we provide a rich account of resource allocation to gene expression in a simple eukaryote, advancing our basic understanding of the interplay between growth-rate dependent and nutrient-specific gene expression.

2022-02-24 | PXD027835 | Pride

Nonuniformity of Whole-Cerebral Neural Resource Allocation, a Neuromarker of the Broad-Task Attention.

Project description:The neural basis of attention is thought to involve the allocation of limited neural resources. However, the quantitative validation of this hypothesis remains challenging. Here, we provide quantitative evidence that the nonuniform allocation of neural resources across the whole cerebral gray matter reflects the broad-task process of sustained attention. We propose a neural measure for the nonuniformity of whole-cerebral allocation using functional magnetic resonance imaging. We found that this measure was significantly correlated with conventional indicators of attention level, such as task difficulty and pupil dilation. We further found that the broad-task neural correlates of the measure belong to frontoparietal and dorsal attention networks. Finally, we found that patients with attention-deficit/hyperactivity disorder showed abnormal decreases in the level of the proposed measure, reflecting the executive dysfunction. This study proposes a neuromarker suggesting that the nonuniform allocation of neural resources may be the broad-task neural basis of sustained attention.

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