Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis

Nelson Martínez-Matías,José R Rodríguez-Medina,Abiel Roche-Lima,Loyda M Melendez-Aponte,Ingrid Montes-Rodríguez,Igor Stagljar,Brian C Rymond,Lilliam Villanueva,Ednalise Santiago-Cartagena,Kelvin Carrasquillo-Carrión,Mohan Babu,Sahily González-Crespo,Nataliya Chorna

doi:10.1038/s41598-021-86671-8

Abstract

Functional analysis of the Mtl1 protein in Saccharomyces cerevisiae has revealed that this transmembrane sensor endows yeast cells with resistance to oxidative stress through a signaling mechanism called the cell wall integrity pathway (CWI). We observed upregulation of multiple heat shock proteins (HSPs), proteins associated with the formation of stress granules, and the phosphatase subunit of trehalose 6-phosphate synthase which suggests that mtl1Δ strains undergo intrinsic activation of a non-lethal heat stress response. Furthermore, quantitative global proteomic analysis conducted on TMT-labeled proteins combined with metabolome analysis revealed that mtl1Δ strains exhibit decreased levels of metabolites of carboxylic acid metabolism, decreased expression of anabolic enzymes and increased expression of catabolic enzymes involved in the metabolism of amino acids, with enhanced expression of mitochondrial respirasome proteins. These observations support the idea that Mtl1 protein controls the suppression of a non-lethal heat stress response under normal conditions while it plays an important role in metabolic regulatory mechanisms linked to TORC1 signaling that are required to maintain cellular homeostasis and optimal mitochondrial function.

Highlights

Materials and methodsThree mRNA samples each from wild-type and mtl1Δ strains (6 different biological samples in total) were analyzed by Next Generation Sequencing (NGS) ( Generation Sequencing)
Functional analysis of the Mtl[1] protein in Saccharomyces cerevisiae has revealed that this transmembrane sensor endows yeast cells with resistance to oxidative stress through a signaling mechanism called the cell wall integrity pathway (CWI)
To assess the effect of Mtl1p in the regulation of stress genes, we measured the mRNA levels in the mtl1Δ strain compared to a WT using Generation Sequencing (NGS) and quantitative proteomic analysis by tandem mass tag (TMT) labelling of tryptic peptides generated from total proteins followed by tandem mass spectrometry (MS–MS)

Summary

Materials and methods

Three mRNA samples each from wild-type and mtl1Δ strains (6 different biological samples in total) were analyzed by NGS ( Generation Sequencing). Five each of WT control and mtl1Δ experimental total protein samples (250 μg per sample) were delivered for quantitative proteomics analysis (Supplementary Table S3). Similar to our analysis of differently expressed mRNAs, the datasets were pre-processed with tailored P ython[42] and R [www.R-project.org] scriptings for missing values, as well as identification and processing of outliers using the Interquantile (IQR) mean imputation method. To understand the cellular regulatory mechanisms in mtl1Δ strain, we applied an integrative multi-omics analysis of mtl1Δ proteome, and metabolome using Cytoscape and the ClueGO plugin in the Cytoscape which integrates Gene Ontology (GO) terms and creates a functionally organized GO/pathway term network corrected by kappa statistics[49] using two-sided (Enrichment/ Depletion) tests based on the hypergeometric distribution (Supplementary Table S2). Pathways visualizations have been carried out using ClueGO plugin for Cytoscape 3.7.2 and ChemDraw 15 (PerkinElmer)

Results and discussions

46 Glucose

Conclusions