Name: “phyloquant” to study the evolutionary relationships of organisms based on large scale quantitative protein expression
Keywords: Phyloquant

Dataset Information

“phyloquant” to study the evolutionary relationships of organisms based on large scale quantitative protein expression

ABSTRACT: “phyloquant” to study the evolutionary relationships of organisms based on large scale quantitative protein expression

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Trypanosoma Rangeli Sc58 Trypanosoma Cruzi Marinkellei Trypanosoma Dionisii Trypanosoma Cruzi Trypanosoma Erneyi

TISSUE(S): Cell Culture

DISEASE(S): Chagas Disease

SUBMITTER: Livia Rosa-Fernandes

LAB HEAD: Giuseppe Palmisano

PROVIDER: PXD017228 | Pride | 2021-09-09

REPOSITORIES: Pride

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Publications

PhyloQuant approach provides insights into Trypanosoma cruzi evolution using a systems-wide mass spectrometry-based quantitative protein profile.

Mule Simon Ngao SN Costa-Martins André Guilherme AG Rosa-Fernandes Livia L de Oliveira Gilberto Santos GS Rodrigues Carla Monadeli F CMF Quina Daniel D Rosein Graziella E GE Teixeira Marta Maria Geraldes MMG Palmisano Giuseppe G

Communications biology 20210311 1

The etiological agent of Chagas disease, Trypanosoma cruzi, is a complex of seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance of T. cruzi genetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution requires understanding the parasite origin and population structure. In this study, we introduce the PhyloQuant approach to infer the evolutionary relationsh ...[more]

PMID: 33707618

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Project description:In mammals, increasing evidence supports the generality of cotranscriptional gene regulation and the idea that genetic control often occurs subsequent to RNA polymerase II (Pol II) recruitment. In our recent experiments, we have used Pol II Chromatin Immunoprecipitation (ChIP) to investigate relationships between the mechanistic events that control acute stress response (ASR) gene activation following stimulation of the alpha1a-Adrenergic Receptor expressed in rat-1 fibroblasts. We validate the temporal accuracy of our Pol II ChIP assay by comparison to major transcriptional events assessable by microarray and PCR analysis of precursor and mature mRNA. Initial temporal microarray analysis of gene activation following agonist addition identified genes that were upregulated and provided a temporal profile of changes in polyadenylated mRNA levels. Combined with PCR analysis of pre-mRNA, total RNA, polyadenylated RNA and the Pol II ChIP data, we demonstrate complex multilevel gene regulation including a diverse set of cotranscriptional mechanisms. Given our data, we propose that analysis of a genes regulation must begin with global assessement of changes in transcriptional behavior to identify events that are actually rate limiting if reductionist mechanistic dissection is to distinguish events that are regulated from the larger set of mechanisms available to most genes. This microarray analysis reports on the temporal changes in polyadenylated mRNA levels in proliferating rat-1 fibroblasts following stimulation of the alpha-1a Adrenergic Receptor with filter sterilized 10 uM phenylephrine (PE). Cells were treated and harvested at 70 to 80% confluence. Rat-1 cells under these conditions are still mid-log phase and continue to proliferate for at least another replicative cycle. Message levels in untreated cells were determined for 3 biological replicates, but all other time points are single replicates as sufficiently detailed dissection made replicates expensive and unnecessary, given that clear trending behavior in the expression profiles demonstrates profile accuracy.

Project description:The experiment is aiming to analyze the effect of overexpression of the Arabidopsis At1g06160 AP2/ERF-domain transcription factor on gene expression and the involvement of the At1g06160-regulated genes in the jasmonic acid or jasmonic acid/ethylene signal transduction pathways. The experiment was performed with 12 hybridizations, using 24 samples of species [Arabidopsis thaliana], using 12 arrays of array design [Agilent Arabidopsis 3 Oligo Microarray [G4142A]], producing 12 raw data files and 0 transformed and/or normalized data files. In the first two hybridizations (#1 and #2), two independent transgenic Arabidopsis lines containing a construct carrying the Arabidopsis gene At1g06160 fused to an inducible promoter were used. This promoter is activated after the addition of the chemical estradiol to the plant medium. Addition of estradiol results in overexpression of At1g06160. For each independent line, total RNA from estradiol-treated and -untreated plants were collected and labeled with Cy3 and Cy5, respectively, and hybridization was performed for each At1g06160-inducible line. Two other hybridizations (#3 and #4) were performed using two independent transgenic Arabidopsis control lines containing a construct carrying the GUS gene fused to an inducible promoter. For each independent line, total RNA from estradiol-treated and -untreated plants were collected and labeled with Cy3 and Cy5, respectively and hybridization was performed for each GUS-inducible line. The last 8 hybridizations were performed using wild-type Arabidopsis plants. The aim was analyze the effect of the jasmonic acid hormone or the effect of a combination of the jasmonic acid and ethylene hormones on gene expression in wild-type. Hybridizations #5 and #6: wild-type Arabidopsis seedlings were treated with jasmonic acid (JA) or with the control DMSO and total RNA was collected after 8 hours. Total RNA from JA-treated and DMSO-treated plants were collected and labeled with Cy3 and Cy5, respectively, and hybridization was performed. A second hybridization was performed using independent biological samples that were treated and labeled similarly. Hybridizations #7 and #8: wild-type Arabidopsis seedlings were treated with jasmonic acid (JA) or with the control DMSO and total RNA was collected after 24 hours. Total RNA from JA-treated and DMSO-treated plants were collected and labeled with Cy3 and Cy5, respectively, and hybridization was performed. A second hybridization was performed using independent biological samples that were treated and labeled similarly. Hybridizations #9 and #10: wild-type Arabidopsis seedlings were treated with jasmonic acid (JA) and ethylene or with the control DMSO/Na-phosphate and total RNA was collected after 8 hours. Total RNA from JA/ethylene-treated and DMSO/Na-phosphate-treated plants were collected and labeled with Cy3 and Cy5, respectively, and hybridization was performed. A second hybridization was performed using independent biological samples that were treated and labeled similarly. Hybridizations #11 and #12: wild-type Arabidopsis seedlings were treated with jasmonic acid (JA) and ethylene or with the control DMSO/Na-phosphate and total RNA was collected after 24 hours. Total RNA from JA/ethylene-treated and DMSO/Na-phosphate-treated plants were collected and labeled with Cy3 and Cy5, respectively, and hybridization was performed. A second hybridization was performed using independent biological samples that were treated and labeled similarly.

Dataset Information

“phyloquant” to study the evolutionary relationships of organisms based on large scale quantitative protein expression

Publications

PhyloQuant approach provides insights into Trypanosoma cruzi evolution using a systems-wide mass spectrometry-based quantitative protein profile.

Similar Datasets

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