Table 1.
Regulation of mRNAs encoding cell cycle-related proteins at 24 h postinfection in HRSV-infected primary airway epithelial cellsa
| Cell cycle phase or function and gene name | Proteinb | Function, interaction, and regulation in HRSV-infected cells | Fold change in mRNA level in HRSV-infected cells |
|---|---|---|---|
| G1 phase and G1/S transition | |||
| CCND2 | Cyclin D2 | Essential for the control of the cell cycle at the G1/S transition; interacts with CDK4 and CDK6 | −9.1 |
| CCNE1 | Cyclin E1 | Essential for the control of the cell cycle at the G1/S transition; interacts with CDK2; low levels reported in bronchial epithelial cells, consistent with terminal differentiation (40) | −2.17 |
| CDK4 | Cyclin-dependent kinase 4 | Interacts with cyclin D1 | −7.2 |
| CDKN1B | Cyclin-dependent kinase inhibitor 1B (p27, Kip1) | Involved in G1 arrest; inhibitor of cyclin E and cyclin A-CDK2 complexes | 2.11 |
| CDKN3 | Cyclin-dependent kinase inhibitor 3 | Dephosphorylates CDK2 | −6.72 |
| CUL3 | Cullin 3 | Involved in ubiquitinylation of cyclins D1 and E, and hence involved in regulation of the G1/S transition | −2.07 |
| SKP2 | S-phase kinase-associated protein 2 (p45) | Specifically recognizes phosphorylated CDKN1B/p27/Kip1; involved in regulation of the G1/S transition | −3.14 |
| S phase and DNA replication | |||
| MCM3 | Minichromosome maintenance complex component 3 | Allows DNA to undergo a single round of replication per cell cycle | −5.24 |
| MCM4 | Minichromosome maintenance complex component 4 | Involved in the control of DNA replication | −5.09 |
| MCM5 | Minichromosome maintenance complex component 5 | Involved in the control of DNA replication. Quantitative proteomics revealed 9- and 3-fold decreases in the relative abundance of this protein in the nuclei of A549 cells infected with HRSV subgroups A and B, respectively, but no change in the relative abundance in the cytoplasm (27, 28). | −3.45 |
| PCNA | Proliferating cell nuclear antigen | Involved in the control of DNA replication | −4.32 |
| G2 phase and G2/M transition | |||
| BCCIP | BRCA2- and CDKN1A-interacting protein | May promote cell cycle arrest by enhancing the inhibition of CDK2 activity by CDKN1A | −2.15 |
| BIRC5 | Baculoviral IAP repeat-containing 5 | Part of the chromosomal passenger complex that acts as a key regulator of mitosis | −8.88 |
| CCNB1 | Cyclin B1 | Control of the cell cycle at the G2/M transition | −4.83 |
| CDK7 | Cyclin-dependent kinase 7 | Cyclin-activating kinase; activates the cyclin-associated kinases CDK1, CDK2, CDK4, and CDK6 by threonine phosphorylation | 2.33 |
| DDX11 | DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (CHL1-like helicase homolog, Saccharomyces cerevisiae) | DNA helicase involved in cellular proliferation and expressed in dividing cells | −2.98 |
| GTSE1 | G2 and S-phase expressed 1 | mRNA expressed in the G2/M phase; protein overexpression delays the G2/M phase progression | −4.95 |
| KPNA2 | Karyopherin α2 (RAG cohort 1, importin α1) | Involved in nuclear import. Quantitative proteomics revealed a 7-fold decrease in the abundance of this protein in the nuclear fractions of A549 cells infected with HRSV subgroup A (27). | −4.48 |
| SERTAD1 | SERTA domain containing 1 | Stimulates E2F-1/DP-1 transcriptional activity | 3.08 |
| M phase | |||
| CCNB2 | Cyclin B2 | Control of the cell cycle at the G2/M transition | −5.49 |
| CDC20 | Cell division cycle 20 homolog (S. cerevisiae) | Required for full ubiquitin ligase activity of the anaphase-promoting complex/cyclosome (APC/C); synthesis is initiated at G1/S | −8.11 |
| MRE11A | Meiotic recombination 11 homolog A (S. cerevisiae) | Role in maintenance of telomere integrity | −7.01 |
| RAD51 | RAD51 homolog (S. cerevisiae) (RecA homolog, Escherichia coli) | Involved in the response to DNA damage; interacts with p53 | −3.81 |
| Cell cycle checkpoint and arrest | |||
| ATR | Ataxia telangiectasia and Rad3 related | Serine/threonine kinase that activates the checkpoint; promotion of DBA repair and apoptosis | −2.12 |
| CDC2 | Cell division cycle 2, G1 to S and G2 to M | Quantitative proteomics revealed a 5-fold decrease in the relative abundance of this protein in the nuclei of A549 cells infected with HRSV subgroups A and B (27, 28). | −4.22 |
| CDKN1A | Cyclin-dependent kinase inhibitor 1A (p21WAF1/CIP1) | Binds to and inhibits cyclin-dependent kinase activity, preventing phosphorylation of critical cyclin-dependent kinase substrates and blocking cell cycle progression | 3.07 |
| CDKN2B | Cyclin-dependent kinase inhibitor 2B (p15; inhibits CDK4) | Inhibitor of cyclins | 3.44 |
| GAD | Minichromosome maintenance complex component 2 (MCM) | Required for entry into S phase; allows DNA to undergo a single round of replication per cell cycle | −7.67 |
| GADD45A | Growth arrest and DNA damage inducible, alpha subunit | Binds to PCNA and can inhibit entry of cells into S phase | 5.35 |
| KNTC1 | Kinetochore associated 1 | Part of the mitotic checkpoint; prevents cells from prematurely exiting mitosis | −3.32 |
| MAD2L2 | Mitotic arrest deficient 2-like 2 (yeast) | Involved in mitosis | −3.06 |
| RAD1 | RAD1 homolog (Schizosaccharomyces pombe) | Involved in the cell cycle checkpoint response and DNA repair | −3.34 |
| RAD9A | RAD9 homolog A (S. pombe) | Involved in the cell cycle checkpoint response and DNA repair | 2.38 |
| TFDP1 | Transcription factor Dp-1 | Can stimulate E2F-dependent transcription. The DP2/E2F complex functions in the control of cell cycle progression from G1 to S phase. | −3.54 |
| Negative regulation of the cell cycle | |||
| ATM | Ataxia telangiectasia mutated | Serine/threonine kinase that activates checkpoint signaling upon double-strand breaks; phosphorylates p53 | −4.12 |
| BRCA1 | Breast cancer 1, early onset | DNA-dependent ATPase and 5′-to-3′ DNA helicase required for the maintenance of chromosomal stability | −7.33 |
| RBL1 | Retinoblastoma-like 1 (p107) | Regulates entry into cell division | −3.63 |
| RBL2 | Retinoblastoma-like 2 (p130) | Regulates entry into cell division | −2.03 |
| Other cell cycle regulators | |||
| DIRAS3 | DIRAS family, GTP-binding RAS-like 3 | Present in the cell membrane | 5.6 |
| CCNF | Cyclin F | Acts as an inhibitor of centrosome reduplication | −5.01 |
| CDK5R1 | Cyclin-dependent kinase 5, regulatory subunit 1 (p35) | Neuron-specific activator of CDK5 | 3.99 |
| CKS1B | CDC28 protein kinase regulatory subunit 1B | Binds to the catalytic subunit of the cyclin-dependent kinases and is essential for their biological function | −3.27 |
| CKS2 | CDC28 protein kinase regulatory subunit 2 | Binds to the catalytic subunit of the cyclin-dependent kinases and is essential for their biological function- | −3.03 |
| MKI67 | Antigen identified by monoclonal antibody Ki-67 | Maintains cell proliferation; expression occurs during late G1; cannot be detected in G0 | −5.86 |
| Control mRNAs for PCR | |||
| B2M | β2 microglobulin | PCR control. Quantitative proteomics revealed a 2-fold increase in abundance in the cytoplasm in HRSV subgroup A- and B-infected cells (27, 28). | 12.89 |
| HPRT1 | Hypoxanthine phosphoribosyltransferase 1 | PCR control. Quantitative proteomics revealed no change in the relative abundance of this protein in the nuclear fractions of A549 cells infected with HRSV subgroup A or B (27, 28). | −1.93 |
| RPL13A | Ribosomal protein L13a | PCR control.- | −5.08 |
| GAPDH | Glyceraldehyde-3-phosphate dehydrogenase | PCR control. Quantitative proteomics revealed no change in the relative abundance of this protein in the nuclear fractions of A549 cells infected with HRSV subgroup A or B, a finding also reflected in independent Western blot analysis (27, 28). | −1.2 |
| ACTB | Actin, beta | PCR control | −1.1 |
a
Protein functions are annotated based on previous work on HRSV. In cases where the relative abundance of the protein encoded by the mRNA has been shown by quantitative proteomics using stable isotope labeling with amino acids in cell culture (SILAC) (27, 28) to be changed in A549 cells infected with HRSV subgroups A and B, the row is shaded.
b
IAP, inhibitor of apoptosis proteins; RAG, recombinase-activating gene.