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| Status |
Public on Aug 25, 2009 |
| Title |
Microarray studies of pqqE disruption mutant vs wild type |
| Platform organism |
Deinococcus radiodurans |
| Sample organism |
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 |
| Experiment type |
Expression profiling by array
|
| Summary |
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.
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| Overall design |
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 “lmFit” function within Limma. Two biological replicates were carried out for transcriptome analysis of pqqE mutant strain against wild type cells.
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| Contributor(s) |
Rajpurohit YS, Wang L, Yin L, Hua Y, Misra HS |
| Citation(s) |
22961447 |
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| Submission date |
Aug 19, 2009 |
| Last update date |
Oct 20, 2017 |
| Contact name |
Hari S Misra |
| E-mail(s) |
[email protected]
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| Phone |
91-22-25595417
|
| Fax |
91-22-25505151
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| Organization name |
Bhabha Atomic Research Centre
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| Department |
Molecular Biology Division
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| Lab |
Molecular Genetics
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| Street address |
2-46 S, Moldular Laboratories, Central Avenue, Bhabha Atomic Research Centre
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| City |
Mumbai |
| State/province |
MS |
| ZIP/Postal code |
400085 |
| Country |
India |
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| Platforms (1) |
| GPL8947 |
Bhabha Atomic Research Centre Deinococcus radiodurans 3166 array [condensed version] |
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| Samples (2) |
| GSM442567 |
The pqqE disruption mutant vs wild type under normal growth conditions_Rep1 |
| GSM442568 |
The pqqE disruption mutant vs wild type under gamma irradiated conditions_Rep 2 |
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| Relations |
| BioProject |
PRJNA118441 |
