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Gene expression-based assessment of the effect of PQQ

ABSTRACT: Pyrroloquinoline quinone (PQQ) is a naturally occurring compound and known to improve growth and reproductive performance when added to diets of PQQ-deprived rodents. To understand its mechanism of action, changes in hepatic gene expression were measured in rats fed diets with or without added PQQ. Of the ~10,000 genes and ESTs analyzed, 4.7% of the transcripts were sensitive to changes in PQQ dietary status. PQQ deprivation generally caused downregulation of genes associated with mitochondriogenesis, cell differentiation, and immune function. These gene expression changes provide the basis for most of the previously published functional observations associated with PQQ deficiency and PQQ administered in pharmacological amounts. To assess PQQ’s potential functions, we used gene expression profiling through microarray technology as part of a comprehensive approach to identify potential pathways and mechanisms. Given that the systemic effects of PQQ deprivation are influenced at levels of dietary intake in the micromolar range, highly purified diets were used to reduce expression from other bioactive factors and xenobiotics, such as those found in typical rodent chow diets. Dietary conditions were also chosen to clarify the response to PQQ deprivation. A goal was to determine if specific changes in dietary protocol or patterns could be used to identify genes important to the function of PQQ. Because it has been observed that mitochondrial-related functions are influenced by PQQ, we hypothesized that changes in genes important to fatty acid and amino acid metabolism and mitochondrial function would be likewise affected by dietary levels of PQQ. The overall study was carried out using two experiments. In this specific experiment, PQQ depletion and repletion was studied to understand the effect of PQQ on gene expression.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE17811 | GEO | 2009/08/26

SECONDARY ACCESSION(S): PRJNA120033

REPOSITORIES: GEO

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Project description:Pyrroloquinoline quinone (PQQ) is a naturally occurring compound and known to improve growth and reproductive performance when added to diets of PQQ-deprived rodents. To understand its mechanism action, changes in hepatic gene expression were measured in rats fed diets with or without added PQQ. Gene expression changes for PQQ supplemented (EC50 ~ 3 nmol PQQ/Kg diet) or deficient rats were assayed by expression microarray analysis and compared to those for known transcriptional regulators (epicatechin; Epi; dexamethasone, Dex; clofibrate, Clo; phenobarbital, Pb). Two principal expression clusters were observed; one for Dex and another for Pb, Epi, Clo, and PQQ. Within the latter, a PQQ subcluster containing a unique group of genes for cell signaling and transport functions. Next, short and long term PQQ depletion and repletion protocols (48 or 36 h, respectively) were performed, leading to changes in hepatic gene expression for both time periods. Of the ~10,000 genes and ESTs analyzed, 4.7% of the transcripts were sensitive to changes in PQQ dietary status. PQQ deprivation generally caused down regulation of genes associated with mitochondriogenesis, cell differentiation, and immune function. These gene expression changes provide the basis for most of the previously published functional observations associated with PQQ deficiency and PQQ administered in pharmacological amounts. To assess PQQ’s potential functions, we used gene expression profiling through microarray technology as part of a comprehensive approach to identify potential pathways and mechanisms. Given that the systemic effects of PQQ deprivation are influenced at levels of dietary intake in the micromolar range, highly purified diets were used to reduce expression from other bioactive factors and xenobiotics, such as those found in typical rodent chow diets. To establish if the changes in gene expression in response to PQQ exposure will follow a similar pattern as other xenobiotics, the responses to PQQ exposure were contrasted with those from exposure to epicatechin (Epi), dexamethasone (Dex), clofibrate (Clo), or phenobarbital (Pb). Dietary conditions were also chosen to clarify the response to short- and longer-term PQQ deprivation. A goal was to determine if specific changes in dietary protocol or patterns could be used to identify genes important to the function of PQQ. Because it has been observed that mitochondrial-related functions are influenced by PQQ, we hypothesized that changes in genes important to fatty acid and amino acid metabolism and mitochondrial function would be likewise affected by dietary levels of PQQ. The overall study was carried out using two experiments. In this specific experiment, the gene expression profiles of Sprague Dawley (SD) rats treated with different xenobiotics were compared to the gene expression profile of PQQ treated SD rats.

Project description:This bacterial genome encodes pyrroloquinoline quinone (PQQ) synthase enzyme required for the synthesis of PQQ in bacteria. The gene pqqE encoding PQQ synthase was annotated in Deinococcus radiodurans R1 genome and synthesis of PQQ was shown in this bacterium. PQQ roles as an antioxidant and as an inducer of protein kinase in bacterial system was shown. The pqqE disuption mutant showed several folds decrease in gamma radiation tolerance of wild type cells and strong impairment of DSB repair. Homology search analysis of PQQ binding domains showed the presence of multiple PQQ binding domains in proteins encoded by five uncharacterized ORFs of this bacterial genome. Many of these proteins are having STK domain of proteins kinases. The effect of pqqE mutation on gene expression under normal and post irradiation conditions was monitored by transcriptome analysis of mutant and compared with wild type cells. All the genes subjected to microarray analysis are as described in the genome sequence of bacterium available at ftp://ftp.ncbi.nih.gov/genomes/bacteria/Deinococcus_radiodurans. Oligonucleotides designed to represent the respective predicted ORFs of Deinococcus radiodurans ((NC_001263, NC_001264, NC_000958, NC_000959) are synthesized and purified by hydrophobic column on HPLC. The oligonucleotides are deposited on to poly-L-Lysine slide in triplicate. Microarrays were scanned using Gene Pix 4000B and hybridization signals were quantified using GenePix Pro 5.1. Prior to channel normalization, microarray outputs were filtered to remove spots of poor signal quality by excluding those data points with a mean intensity by less that 2 standard deviation above background in both channels. Normalization of data and its statistical analysis were carried out in the R computing environment using linear models for microarray data package (Limma). Using this tool, the global LOESS normalization was carried out for each microarray. The 3- replicate spots per gene in each array were used to maximize the robustness of differential expression measurements of each gene via the âlmFitâ function within Limma. Two biological replicates were carried out for transcriptome analysis of pqqE mutant strain against wild type cells.

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Gene expression-based assessment of the effect of PQQ

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