Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq analysis of HAstV1, HAstV4, MLB1, MLB2 and VA1 astrovirus infection in cell culture

ABSTRACT: The purpose of the study was to investigate the dynamics of viral RNA production during astrovirus infection. Caco-2 cells were infected at MOI 5 with HAstV1, HAstV4 or VA1; Huh7.5.1 cells were infected at MOI 5 with MLB1 or MLB2. Cells were harvested at 6, 12, 18, 24 (HAstV1) or 24 (HAstV4, MLB1, MLB2, VA1) hours post-infection, and total RNA was extracted, fragmented, depleted for rRNA and sequenced.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Andrew Firth

PROVIDER: E-MTAB-16460 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The cellular proteome is the set of expressed proteins at a given time and defines an organism's phenotype under specific conditions. The proteome is shaped and remodeled by both protein synthesis and degradation. In this study, we combined metabolic and chemical isobaric peptide labeling to simultaneously determine protein decay and de novo synthesis of intracellular Listeria monocytogenes, while focusing on the role of the AAA+ chaperone protein ClpC. ClpC associates with the peptidase ClpP to form an ATP-dependent protease complex and has been shown to play a role in virulence development in the human pathogen L. monocytogenes. However, the mechanism by which ClpC is involved in the survival and proliferation of intracellular L.monocytogenes remains elusive. We observed extensive proteome remodeling in L. monocytogenes upon interaction with the host, supporting the hypothesis that ClpC-dependent protein degradation is required to initiate bacterial adaptation mechanisms. We identified more than 100 putative ClpC target proteins through their stabilization in a clpC deletion strain. Beyond the identification of direct targets, we also observed indirect effects of the clpC deletion on the protein abundance in diverse cellular and metabolic pathways, such as iron acquisition and flagellar assembly. Overall, our data highlights the crucial role of ClpC for L. monocytogenes adaptation to the host environment through proteome remodeling. Importance Survival and proliferation of pathogenic bacteria inside the host depend on their ability to adapt to the changing environment. It is therefore important to profile the underlying changes on the bacterial proteome level during the infection process to understand pathogenesis and host-dependent adaptation processes. The interplay between protein synthesis and decay governs cellular protein abundance. SILAC pulse labeling enables direct readout of these events during infection. Combining this approach with tandem-mass-tag (TMT) labeling enabled multiplexed and time-resolved bacterial proteome quantification during infection. We applied this integrated approach to investigate protein turnover during the temporal progression of bacterial adaptation to the host on a system-wide scale. Our experimental approach can easily be transferred to probe the proteome remodeling in other bacteria under a variety of perturbations.

Dataset Information

RNA-seq analysis of HAstV1, HAstV4, MLB1, MLB2 and VA1 astrovirus infection in cell culture

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