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Moisture Modulates Soil Reservoirs of Active DNA and RNA viruses

ABSTRACT: Global proteomics analyses to identify viral proteins in the soil microbiome. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Environmental Samples <bacteria> (ncbitaxon:48479)

SUBMITTER: Kristin E. Burnum-Johnson

PROVIDER: MSV000086144 | MassIVE |

REPOSITORIES: MassIVE

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Moisture modulates soil reservoirs of active DNA and RNA viruses.

Wu Ruonan R Davison Michelle R MR Gao Yuqian Y Nicora Carrie D CD Mcdermott Jason E JE Burnum-Johnson Kristin E KE Hofmockel Kirsten S KS Jansson Janet K JK

Communications biology 20210826 1

Soil is known to harbor viruses, but the majority are uncharacterized and their responses to environmental changes are unknown. Here, we used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to detect active DNA viruses and RNA viruses in a native prairie soil and to determine their responses to extremes in soil moisture. The majority of transcribed DNA viruses were bacteriophage, but some were assigned to eukaryotic hosts, mainly insects. We also demonstrated that h ...[more]

PMID: 34446837

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Moisture modulates soil reservoirs of active DNA and RNA viruses.

Project description:Soil is known to harbor viruses, but the majority are uncharacterized and their responses to environmental changes are unknown. Here, we used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to detect active DNA viruses and RNA viruses in a native prairie soil and to determine their responses to extremes in soil moisture. The majority of transcribed DNA viruses were bacteriophage, but some were assigned to eukaryotic hosts, mainly insects. We also demonstrated that higher soil moisture increased transcription of a subset of DNA viruses. Metaproteome data validated that the specific viral transcripts were translated into proteins, including chaperonins known to be essential for virion replication and assembly. The soil viral chaperonins were phylogenetically distinct from previously described marine viral chaperonins. The soil also had a high abundance of RNA viruses, with highest representation of Reoviridae. Leviviridae were the most diverse RNA viruses in the samples, with higher amounts in wet soil. This study demonstrates that extreme shifts in soil moisture have dramatic impacts on the composition, activity and potential functions of both DNA and RNA soil viruses.

| S-EPMC8390657 | biostudies-literature

Impact of Microbiome on Hepatic Drug Processing Genes in Mice during Pregnancy

Project description:While microbiome and pregnancy are known to alter drug disposition, the interplay of the two physiological factors to impact expression and/or activity of drug processing genes (DPGs) has yet to be elucidated. This study aimed to investigate the effects of microbiome on host hepatic DPGs during pregnancy using conventional (CV) and germ-free (GF) mice. Four groups of female mice were used, namely CV non-pregnant (CVNP), GF non-pregnant (GFNP), CV pregnant (CVP), and GF pregnant (GFP) mice. Pregnant mice examined were on gestation day 15. Transcriptomic and targeted proteomics of hepatic DPGs were profiled using a multi-omics approach. Plasma bile acid and steroid hormone levels were quantified using LC-MS/MS. Cyp3a activities were measured by mouse liver microsome incubations. While the overall trend in pregnancy-induced changes in the expression or activity of hepatic DPGs in CV and GF mice was similar, significant differences in the magnitude of changes were observed. For certain genes, we noticed opposite effects of pregnancy on mRNA and protein expression of DPGs in both CV and GF mice. For instance, the mRNA levels of Cyp3a11, the murine homolog of human CYP3A4, were decreased by 1.7-fold and 3.3-fold by pregnancy in CV and GF mice, respectively. However, the protein levels of Cyp3a11 were increased similarly ~2-fold by pregnancy in both CV and GF mice. Yet, microsome incubations revealed a marked induction of Cyp3a activity by pregnancy that was >5-fold greater in CV mice than that in GF mice. Plasma bile acid and steroid hormone levels were also significantly altered by microbiome and pregnancy, respectively, which may contribute to the differential effects of pregnancy in CV and GF mice. This is the first study to show that microbiome can alter hepatic DPGs in pregnancy.

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Multi-Omics interrogation of soil microcosms amended with condensed tannins

Project description:Investigating soil microbiome responses to polyphenols under anoxia

2021-03-02 | PXD019911 | Pride

Defining the dynamic regulation of O-GlcNAc proteome in the mouse cortex -- The O-GlcNAcylation of synaptic and trafficking proteins related to neurodegenerative diseases

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Phosphoproteomic Response of Cardiac Endothelial Cells to Ischemic Injury and Ultrasound

Project description:Global and phosphoproteomic data from mouse primary cardiac endothelial cells treated with oxygen deprivation and/or ultrasound. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.

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Regulation of hyperoxia-induced neonatal lung injury via posttranslational cysteine redox modifications

Project description:Lung tissue from normoxia- or hyperoxia-treated control or SCNN1B overexpression mice were processed with a redox proteomics workflow and analyzed by LC-MS/MS with TMT based quantification. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.

2022-08-18 | MSV000090157 | MassIVE

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Project description:Metaproteomic data for Rodriguez-Ramos, et al. interrogating microbial and viral communities of hyporheic river sediments within the Columbia River. Samples were digested with trypsin, and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.

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Proteomics of the developing human lung

Project description:Proteomic data from human lung collected from human donors spanning 10 timepoints between 1 day old and 8 years old. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.

2020-08-07 | MSV000085929 | MassIVE

Gut microbial communities enriched with quaternary amines

Project description:Human fecal communities were dosed with either choline, carnitine, butyrobetaine, or glycine betaine to measure the microbial response to quaternary amine addition. Samples were digested with trypsin, and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.

2021-03-04 | MSV000087004 | MassIVE

Hepatic SerpinA1 Improves Energy and Glucose Metabolism through Regulation of Preadipocyte Proliferation and UCP1 Expression

Project description:Fat tissue inducible specific IGF1R and IR (insulin receptor) KO mouse model to investigate the effect of insulin resistance on mature adipocytes. Mouse serum proteomics performed using TMT-10 analyses. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.

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