Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism

Abstract

YajL is the most closely related Escherichia coli homolog of Parkinsonism-associated protein DJ-1, a protein with a yet-undefined function in the oxidative-stress response. YajL protects cells against oxidative-stress-induced protein aggregation and functions as a covalent chaperone for the thiol proteome, including FeS proteins. To clarify the cellular responses to YajL deficiency, transcriptional profiling of the yajL mutant was performed. Compared to the parental strain, the yajL mutant overexpressed genes coding for chaperones, proteases, chemical chaperone transporters, superoxide dismutases, catalases, peroxidases, components of thioredoxin and glutaredoxin systems, iron transporters, ferritins and FeS cluster biogenesis enzymes, DNA repair proteins, RNA chaperones, and small regulatory RNAs. It also overexpressed the RNA polymerase stress sigma factors sigma S (multiple stresses) and sigma 32 (protein stress) and activated the OxyR and SoxRS oxidative-stress transcriptional regulators, which together trigger the global stress response. The yajL mutant also overexpressed genes involved in septation and adopted a shorter and rounder shape characteristic of stressed bacteria. Biochemical experiments showed that this upregulation of many stress genes resulted in increased expression of stress proteins and improved biochemical function. Thus, protein defects resulting from the yajL mutation trigger the onset of a robust and global stress response in a prokaryotic model of DJ-1-associated Parkinsonism.

Fermentation and alternative respiration compensate for NADH dehydrogenase deficiency in a prokaryotic model of DJ-1-associated Parkinsonism

“…After image quantification and global signal correction (following the manufacturer's instructions), the ratios between intensity values measured in the yajL mutant and its parent MG1655 were calculated and normalized using the standard LOWESS (locally weighted scatterplot smoothing) procedure (Messaoudi et al, 2013). This statistical correction has the advantage of removing intensity-dependent effects in the observed log 2 (ratio) values and is thus well adapted to correcting systematic bias related to low-intensity measures.…”

“…It contains yajL disrupted by l Red in the Escherichia coli strain BW25113 [lacI q rrnB3 DlacZ4787 hsdR514 D(araBAD)567 D(rhaBAD)568 rph-1 ], leading to strain JW5067 (Baba et al, 2006). We transduced the yajL mutation into strain MG1655 as described previously (Messaoudi et al, 2013). For complementation experiments, the yajL mutant was transformed by plasmid pCA24N-yajL as described previously .…”

“…Reproducibility between results obtained with different microarray replicates was verified and used to eliminate genes with artefactual signals. Finally, to assess whether any of the cellular functions associated with the genes identified as upregulated in the yajL mutant were observed at a frequency greater than that expected by chance, P values were calculated as described previously (Messaoudi et al, 2013) (hypergeometric distribution). Note that this approach was successfully applied previously (Messaoudi et al, 2013).…”

“…Finally, to assess whether any of the cellular functions associated with the genes identified as upregulated in the yajL mutant were observed at a frequency greater than that expected by chance, P values were calculated as described previously (Messaoudi et al, 2013) (hypergeometric distribution). Note that this approach was successfully applied previously (Messaoudi et al, 2013). The microarray data were deposited at the Gene Expression Omnibus (http://www.ncbi.…”

“…In contrast to NADH dehydrogenase 1, which contains many subunits and several FeS clusters, and is sensitive to dysregulated biogenesis and environmental stresses, the alternative dehydrogenases PoxB, GlpD and DadA each consist of a single protein devoid of FeS clusters. The overexpression of alternative dehydrogenases in the mutant could be induced by the stress regulator s S , which is a known inducer of pyruvate oxidase PoxB and alanine dehydrogenase DadA, and is overexpressed in the mutant in the exponential phase (Messaoudi et al, 2013).…”