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Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.

ABSTRACT: Protein expression is regulated by the production and degradation of messenger RNAs (mRNAs) and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics so as to build a quantitative genomic model of the differential regulation of gene expression in lipopolysaccharide-stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for more than half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction for newly activated cellular functions and by protein life-cycle changes for remodeling of preexisting functions.

SUBMITTER: Jovanovic M

PROVIDER: S-EPMC4506746 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

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Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.

Jovanovic Marko M Rooney Michael S MS Mertins Philipp P Przybylski Dariusz D Chevrier Nicolas N Satija Rahul R Rodriguez Edwin H EH Fields Alexander P AP Schwartz Schraga S Raychowdhury Raktima R Mumbach Maxwell R MR Eisenhaure Thomas T Rabani Michal M Gennert Dave D Lu Diana D Delorey Toni T Weissman Jonathan S JS Carr Steven A SA Hacohen Nir N Regev Aviv A

Science (New York, N.Y.) 20150212 6226

Protein expression is regulated by the production and degradation of messenger RNAs (mRNAs) and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics so as to build a quantitative genomic model of the differential regulation of gene expression in lipopolysaccharide-stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Converse ...[more]

PMID: 25745177

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Project description:BackgroundThe moon jellyfish Aurelia aurita is a widespread scyphozoan species that forms large seasonal blooms. Here we provide the first comprehensive view of the entire complex life of the Aurelia Red Sea strain by employing transcriptomic profiling of each stage from planula to mature medusa.ResultsA de novo transcriptome was assembled from Illumina RNA-Seq data generated from six stages throughout the Aurelia life cycle. Transcript expression profiling yielded clusters of annotated transcripts with functions related to each specific life-cycle stage. Free-swimming planulae were found highly enriched for functions related to cilia and microtubules, and the drastic morphogenetic process undergone by the planula while establishing the future body of the polyp may be mediated by specifically expressed Wnt ligands. Specific transcripts related to sensory functions were found in the strobila and the ephyra, whereas extracellular matrix functions were enriched in the medusa due to high expression of transcripts such as collagen, fibrillin and laminin, presumably involved in mesoglea development. The CL390-like gene, suggested to act as a strobilation hormone, was also highly expressed in the advanced strobila of the Red Sea species, and in the medusa stage we identified betaine-homocysteine methyltransferase, an enzyme that may play an important part in maintaining equilibrium of the medusa's bell. Finally, we identified the transcription factors participating in the Aurelia life-cycle and found that 70% of these 487 identified transcription factors were expressed in a developmental-stage-specific manner.ConclusionsThis study provides the first scyphozoan transcriptome covering the entire developmental trajectory of the life cycle of Aurelia. It highlights the importance of numerous stage-specific transcription factors in driving morphological and functional changes throughout this complex metamorphosis, and is expected to be a valuable resource to the community.

Dataset Information

Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.

Publications

Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.

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