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Proteome labeled by a cuprous ion-responsive protein labeling reagent in the ATP7A WT and ATP7A KO living cells

ABSTRACT: We have developed a new molecular probe called CuR. This probe is selectively activated by labile Cu(I), hence enabling labeling of the proteins in Cu(I)-rich cellular environments. We applied CuR to ATP7A-WT and ATP7A-KO cells that were pretreated with or without Cu(gtsm). Next, we enriched the labeled proteins by immunoprecipitation, digested them with trypsin, and analyzed them using liquid chromatography-tandem mass spectrometry. We used label-free quantification in the mass spectrometry analysis to detect changes in labeled proteins caused by exogenous copper compared to the non-copper-treated condition.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Itaru Hamachi

PROVIDER: PXD048267 | JPOST Repository | Sun Jan 05 00:00:00 GMT 2025

REPOSITORIES: jPOST

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Project description:Background: With lower manufacturing cost, high spot density, and flexible probe design, genomic tiling microarrays are ideal for comprehensive transcriptome studies. Typically, transcriptome profiling using microarrays involves reverse transcription, which converts RNA to cDNA. The cDNA is then labeled and hybridized to the probes on the arrays, thus the RNA signals are detected indirectly. Reverse transcription is known to generate artifactual cDNA, in particular the synthesis of second-strand cDNA, leading to false discovery of antisense RNA. To address this issue, we have developed an effective method using RNA that is directly labeled, thus by-passing the cDNA generation. This paper describes the development of this method and its application to mapping transcriptome profiles. Results: RNA extracted from laboratory cultures of Porphyromonas gingivalis was fluorescently labeled with an alkylation reagent and hybridized directly to probes on genomic tiling microarrays specifically designed for this periodontal pathogen. The generated transcriptome profile was strand-specific and produced signals close to background level in most antisense regions of the genome. In contrast, high levels of signal were detected in the antisense regions when the hybridization was done with cDNA. In addition, five antisense areas were tested with independent strand-specific RT-PCR and none to negligible amplification was detected, indicating that the strong antisense cDNA signals were artifacts. Conclusions: An efficient method was developed for mapping transcriptome profiles specific to both coding strands of a bacterial genome. This method chemically labels and uses extracted RNA directly in microarray hybridization. The generated transcriptome profile was free of cDNA artifactual signals. In addition, this method requires fewer processing steps and is more sensitive in detecting small amount of RNA compared to end-labeling methods due to the incorporation of more fluorescent molecules per RNA fragment.

			Action	DRS
	20230627_sample1a-t1.raw	Raw
	20230627_sample1a-t2.raw	Raw
	20230627_sample1b-t1.raw	Raw
	20230627_sample1b-t2.raw	Raw
	20230627_sample1c-t1.raw	Raw

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Proteome labeled by a cuprous ion-responsive protein labeling reagent in the ATP7A WT and ATP7A KO living cells

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