Related Experiment Video
Updated: Jul 30, 2026
Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
Published on: August 2, 2015
Genes targeted by protein kinase CK2: a genome-wide expression array analysis in yeast
K Ackermann1, A Waxmann, C V Glover
1Biochemische Zellphysiologie, Deutsches Krebsforschungszentrum, Heidelberg, Germany. k.ackermann@dkfz-heidelberg.de
Abstract:
Protein kinase CK2, a tetramer composed of two catalytically active (CK2alpha isoforms) and two regulatory (CK2beta isoforms) subunits, is suspected to have, among others, a role in gene transcription. To identify the genes targeted by CK2, the transcriptional effect of silencing the CK2 subunit genes in Saccharomyces cerevisiae (CK2alpha isoform genes: CKA1 and CKA2; CK2beta isoform genes: CKB1 and CKB2) was examined using genome-wide expression array analysis (oligonucleotide array chips). Silencing did not influence the overwhelming majority (5801) of the over six thousand open reading frames composing the yeast genome. Cells knocked-out for both CKA1 and CKA2 and plasmid-rescued by Cka1 affected specifically at 2-fold discrimination level the transcription of 57 genes, and when rescued by Cka2, the transcription of 118 genes. In CKB1/CKB2 double knock-outs, transcription of 54 genes was specifically altered. Interestingly, aside overlaps between the gene spectra affected by CKA1 and CKA2 silencing, there were overlaps also between those influenced by CK2alpha and CK2beta isoform silencing. The data indicate a distinct role of CK2 in gene transcription control, identify specific functional differences between the two catalytic subunits in gene targeting, and reveal independent effects by the regulatory subunits.
Insights
Protein kinase CK2 (CK2) plays a role in gene transcription. Silencing CK2 subunits in yeast revealed specific gene targets, highlighting distinct roles for catalytic and regulatory subunits in gene regulation.
Area of Science:
- Molecular Biology
- Yeast Genetics
- Gene Regulation
Background:
- Protein kinase CK2 (CK2) is a crucial enzyme involved in various cellular processes.
- CK2 is a heterotetrameric complex comprising catalytic (CK2alpha) and regulatory (CK2beta) subunits.
- CK2 is implicated in gene transcription, but its specific gene targets remain largely uncharacterized.
Purpose of the Study:
- To identify genes transcriptionally regulated by Protein Kinase CK2 (CK2) in Saccharomyces cerevisiae.
- To elucidate the distinct roles of CK2alpha and CK2beta subunits in targeting specific genes.
- To investigate the impact of CK2 subunit silencing on genome-wide gene expression.
Main Methods:
- Genome-wide expression analysis using oligonucleotide microarrays in Saccharomyces cerevisiae.
- Systematic silencing of CK2 alpha subunit genes (CKA1, CKA2) and beta subunit genes (CKB1, CKB2).
- Differential gene expression analysis to identify genes with at least a 2-fold change in transcription.
Main Results:
- Silencing of CK2 subunits affected a small fraction of the yeast genome (57-118 genes).
- Specific gene sets were identified for CK2alpha (Cka1, Cka2) and CK2beta (Ckb1, Ckb2) subunit silencing.
- Overlapping gene targets were observed between CK2alpha isoforms and between CK2alpha and CK2beta subunits, suggesting complex regulatory interactions.
Conclusions:
- Protein kinase CK2 plays a distinct role in controlling gene transcription in yeast.
- Specific functional differences exist between CK2alpha catalytic subunits in gene targeting.
- CK2beta regulatory subunits exert independent effects on gene transcription, distinct from catalytic subunits.
