CDK12 Activity-Dependent Phosphorylation Events in Human Cells
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Growth
2.2. Proteomic Analyses
2.2.1. Sample Preparation
2.2.2. Phospho-Peptide Enrichment
2.2.3. Quantitative Analysis of HeLa Phosphoproteome
2.2.4. Assessment of Variability
3. Results
3.1. Phosphorylation Events Altered by Inhibitory Analog in CDK12as
3.2. Sites Directly Phosphorylated by CDK12
3.3. Control for Off-Target Effects of Inhibitory Analog 1-NM-PP1
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Protein Name | Protein Description | Gene Name | Fold Change | Functional “Keywords” | Comments |
---|---|---|---|---|---|
MK03_HUMAN | Mitogen-activated protein kinase 3 | MAPK3 | −6.3 | signaling; Txn-regulation | |
SOS1_HUMAN | Son of sevenless homolog 1 | SOS1 | −6.1 | signaling | |
RHG35_HUMAN | Rho GTPase-activating protein 35 | ARHGAP35 | −5.6 | Txn-regulation; signaling | |
LIMD1_HUMAN | LIM domain-containing protein 1 | LIMD1 | −5.4 | Txn-regulation; scaffold prot; cell fate | |
ANS1A_HUMAN | Ankyrin repeat and SAM domain-containing protein 1A | ANKS1A | −4.2 | signaling; cell migration | |
KANK2_HUMAN | KN motif and ankyrin repeat domain-containing protein 2 | KANK2 | −4.0 | Txn-regulation; steroid co-activators | |
MK01_HUMAN | Mitogen-activated protein kinase 1 | MAPK1 | −3.7 | signaling; Txn-regulation | |
BCAR3_HUMAN | Breast cancer anti-estrogen resistance protein 3 | BCAR3 | −3.1 | signaling; reg. DNA synthesis | |
NU214_HUMAN | Nuclear pore complex protein Nup214 | NUP214 | −5.3 | mRNA maturation: nuclear export | |
TPR_HUMAN | Nucleoprotein TPR | TPR | −5.1 | mRNA maturation: nuclear export | TPR, pep 1 |
AHNK_HUMAN | Neuroblast differentiation-associated protein AHNAK | AHNAK | −4.9 | mRNA maturation: poly A binding; splicing | AHNK, pep 1 |
DDX20 / Gemin 3 | Probable ATP-dependent RNA helicase DDX20 | DDX20 | −4.2 | mRNA maturation: splicing; snRNP | |
AHNK_HUMAN | Neuroblast differentiation-associated protein AHNAK | AHNAK | −3.6 | mRNA maturation: poly A binding; splicing | AHNK, pep 2 |
AHNK_HUMAN | Neuroblast differentiation-associated protein AHNAK | AHNAK | −3.5 | mRNA maturation: poly A binding; splicing | AHNK, pep 3 |
TPR_HUMAN | Nucleoprotein TPR | TPR | −3.2 | mRNA maturation: nuclear export | TPR, pep 2 |
PARD3_HUMAN | Partitioning defective 3 homolog | PARD3 | −11.1 | cell division; signaling | |
SEPT7_HUMAN | Septin-7 | SEPT7 | −6.3 | mitosis; kinetochore; ciliogenesis | |
ADA17_HUMAN | ADAM 17 | ADAM17 | −5.3 | mitosis; signaling; spindle | |
CLAP2_HUMAN | CLIP-associating protein 2 | CLASP2 | −3.4 | microtubule-binding; kinetochore | |
XPC_HUMAN | DNA repair protein complementing XP-C | XPC | >−12 | DNA repair; Txn | |
DPOLA_HUMAN | DNA polymerase alpha catalytic subunit | POLA1 | −3.0 | DNA synthesis | |
CTNA1_HUMAN | Catenin alpha-1 | CTNNA1 | −6.1 | other… cell adhesion | |
ARFP1_HUMAN | Arfaptin-1 | ARFIP1 | −5.2 | other… Golgi; vessicles; phospholipase D |
Protein | Peptide | Fold Change | Potential Protein Kinase | |
---|---|---|---|---|
‘as’ | ‘WT’ | |||
HDAC4 | SSPLLR (S266) | −2.7 | −5.8 | PIM1; PRKG1; PIM3 |
AHNK | VSMPDVELNLKSPK (S3426) | −3 | −2.7 | JNK1/3; P38d (MAPK13) |
ANLN | TQSLPVTEK (S485) | −4.3 | −2.5 | ANPa; COT; ANPb; |
RAB34 | INSDDSNLYLTASK (S241) | −2.5 | −2.4 | MAPKAPK3; ANPa; PRKG2 |
NF1 | SFDHLISDTK (S2543) | −4.1 | −2.2 | PIM1/3; MSK1 |
WDCP | DSFSHSPGAVSSLK (S690) | −2.6 | −2 | ERK1/2/5 |
AFAP1 | LSSERPSSDGEGVVE… (S283) | (+)2.1 | (+) 3.4 | CK2a2 (CSNK2A2); CK2a1 (CSNK2A1); MAPKAPK3 |
Potential Kinase | # Sites |
---|---|
PIM 1, 2 or 3 | 5 |
PRKG1 or 2 | 5 |
CDK2 or 3 | 3 |
JNK1 or 3 | 3 |
MAPKAPK3 or 2 | 3 |
mTOR/FRAP | 2 |
PLK3 | 2 |
BARK2/1 | 1 |
CAMK4 | 1 |
CDK7 | 1 |
CDK9 | 1 |
CHK2 | 1 |
GSK2B | 1 |
GSK3A | 1 |
IKKb | 1 |
PFTAIRE2 | 1 |
RHOK | 1 |
ROCK1 | 1 |
SCYL2 | 1 |
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Bartkowiak, B.; Yan, C.M.; Soderblom, E.J.; Greenleaf, A.L. CDK12 Activity-Dependent Phosphorylation Events in Human Cells. Biomolecules 2019, 9, 634. https://doi.org/10.3390/biom9100634
Bartkowiak B, Yan CM, Soderblom EJ, Greenleaf AL. CDK12 Activity-Dependent Phosphorylation Events in Human Cells. Biomolecules. 2019; 9(10):634. https://doi.org/10.3390/biom9100634
Chicago/Turabian StyleBartkowiak, Bartlomiej, Christopher M. Yan, Erik J. Soderblom, and Arno L. Greenleaf. 2019. "CDK12 Activity-Dependent Phosphorylation Events in Human Cells" Biomolecules 9, no. 10: 634. https://doi.org/10.3390/biom9100634
APA StyleBartkowiak, B., Yan, C. M., Soderblom, E. J., & Greenleaf, A. L. (2019). CDK12 Activity-Dependent Phosphorylation Events in Human Cells. Biomolecules, 9(10), 634. https://doi.org/10.3390/biom9100634