Identification of ASB7 as ER stress responsive gene through a genome wide in silico screening for genes with ERSE.

Vivek Vishnu Anasa,Palaniyandi Ravanan,Priti Talwar,Madhumathi Manickam,Salvatore V Pizzo

doi:10.1371/journal.pone.0194310

Vivek Vishnu Anasa, Palaniyandi Ravanan + Show 3 more

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https://doi.org/10.1371/journal.pone.0194310

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Journal: PloS one	Publication Date: Apr 9, 2018
Citations: 6	License type: CC BY 4.0

Affiliation: Vellore Institute of Technology University

Abstract

The endoplasmic reticulum (ER) not only performs its basic function of regulating calcium homeostasis, lipid biosynthesis, folding, modifying and transporting proteins but also plays a decisive role in regulating multiple cellular processes ranging from cell growth and differentiation to apoptosis and autophagy. Disturbances in ER homeostasis initiate the unfolded protein response (UPR) implicated in the pathogenesis of many human diseases. Drugging the UPR components for therapeutic interventions has received considerable attention. The purpose of this study is to identify genes that are previously unsuspected to be regulated under ER stress. Because ER stress-inducible gene expression is majorly regulated under ERSE elements, we screened human genome by adopting an in silico approach using ERSE elements (I, II, III) as probes and identified 337 candidate genes. Having knowledge of the importance of E3 ubiquitin ligase in the ERAD machinery; we validated our preliminary search by focusing on one of the hits i.e. ASB7 gene that encodes E3 ubiquitin ligase. In HeLa cells, we found that pharmacological induction of ER stress led to an increase in the expression of ASB7 with simultaneous activation of UPR pathways. Although knockdown of ASB7 expression leads to significant reduction in GRP78 and CHOP mRNA levels, it did not protect cells from ER stress-induced cell death. Also, an up-regulation in the expression of pro-inflammatory genes like TNF-α and IL-1β in ASB7 knockdown cells was observed under ER stress. Collectively, our findings suggest that ASB7 is regulated under ER stress and this study also identifies several other genes that could apparently be regulated under ER stress.

Highlights

endoplasmic reticulum (ER) is an essential organelle involved in various cellular processes including protein folding, sorting and transportation [1, 2]
As a starting point to identify genes unknown to be regulated under ER stress, we used a computational approach to search for Endoplasmic reticulum stress element (ERSE) motifs within human Genome Reference Consortium (GRC) (GRCh37.p13) (Fig 1)
Python program was written to scan the human genome using ERSE elements: ERSE-I (CCAAT-N9-CCACG), ERSE-II (ATTGG-N-CCACG) and ERSE-III (CCAAT-N26-CCACG) as probes and found 535 ERSE-I, 362 ERSE-II and 411 ERSE-III elements with their locations summarized in S1 Table

Summary

Introduction

ER is an essential organelle involved in various cellular processes including protein folding, sorting and transportation [1, 2]. Inefficient clearance of misfolded proteins or change in the Ca2+ homeostasis leads to accumulation of unfolded. The ER responds by increasing its protein folding capacity through specialized signaling pathways that are collectively known as the UPR which restores the ER protein homeostasis and further regulates cell survival [4, 5]. UPR increases transcription of genes encoding enzymes and chaperones involved in protein folding, secretion and degradation of misfolded proteins, and thereby constituting a coordinated regulatory mechanism that restores protein-folding in the ER and re-establishes normal cellular function [6, 7]

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