TABLE 1.
Host genes regulated in expression by APV infectiona
| Accession no.b | Gene or gene product | Fold change in transcription (SD)c at the following time P.i.:
|
|||
|---|---|---|---|---|---|
| 2.5 h | 24 h | 48 h | 96 h | ||
| Avian pneumovirus gene transcripts | |||||
| EMB, Q9QF48 | Nucleocapsid protein | NC | 19.57 (2.50) | 50.40 (1.87) | 67.56 (5.18) |
| EMB, Q9QF47 | Phosphoprotein | NC | 28.33 (3.16) | 25.99 (2.07) | 58.73 (4.07) |
| EMB, Q90244 | Matrix protein | NC | 14.54 (2.22) | 21.14 (2.66) | 44.93 (2.68) |
| EMB, Q9QD13 | Fusion glycoprotein | NC | 23.72 (2.09) | 35.42 (2.87) | 65.62 (7.10) |
| EMB, Q9QF45 | Matrix glycoprotein M2 ORF2 | 3.04 (0.28) | 24.87 (0.92) | 21.44 (1.55) | 70.08 (6.94) |
| EMB, Q9QF46 | Matrix glycoprotein M2 ORF1 | NC | 20.62 (1.57) | 30.83 (2.92) | 65.66 (3.89) |
| EMB, P87509 | RNA-dependent RNA polymerase | NC | 14.20 (1.08) | 22.73 (1.68) | 37.29 (2.73) |
| IFN-induced transcripts | |||||
| SWP, MX_CHICKd | IFN-induced GTP-binding protein Mx | NC | 14.20 (2.41) | 38.63 (2.09) | 61.38 (6.06) |
| SWP, INI2_PANTRd | IFN-induced protein 6-16 precursor | NC | 17.39 (1.95) | 13.87 (1.84) | 30.64 (2.40) |
| SWP, IFT1_HUMANd | IFN-induced 56-kDa protein | 6.89 (1.87) | 32.28 (3.58) | 19.70 (2.90) | 20.90 (4.13) |
| EMB, AAH04977d | IFN-induced protein with TPR 4 | 4.38 (1.28) | 12.60 (3.12) | 18.67 (3.21) | 6.63 (0.64) |
| SWP, STA1_HUMANd | Signal transducer and activator of transcription 1-α/β | NC | 16.36 (1.98) | 33.77 (3.41) | 54.86 (2.13) |
| EMB, AAH02704 | Similar to signal transducer and activator of transcription 1 | NC | 11.32 (1.37) | 7.89 (1.10) | 9.54 (0.80) |
| SWP, IFT5_HUMAN | Retinoic acid- and IFN-inducible 58-kDa protein (RI58) | 2.80 (0.72) | 31.19 (3.80) | 28.30 (3.12) | 22.23 (3.07) |
| EMB, Q9QXH3d | IFNα-inducible protein P27-H | NC | 15.28 (1.96) | 12.19 (1.26) | 23.67 (4.16) |
| Proinflammatory chemoattractants and adhesion molecules | |||||
| SWP, EMF1_CHICKd | CXC chemokine 9E3 (human IL-8 homologue) | 2.39 (0.57) | 7.30 (1.39) | 39.32 (5.46) | 53.84 (5.30) |
| EMB, O73912 | CXC chemokine K60 | 2.01 (0.57) | 2.43 (0.61) | 18.64 (2.94) | 18.33 (2.84) |
| EMB, O35131d | Complement C3F | NC | 2.24 (0.15) | 10.03 (0.77) | 12.91 (1.20) |
| EMB, O42402d | Ornithokinin receptor | NC | NC | 2.32 (0.36) | 2.98 (0.41) |
| Ubiquitin-proteasome system | |||||
| SWP, PRSX_SPETR | 26S protease regulatory subunit S10B | NC | NC | 2.37 (0.21) | 2.21 (0.35) |
| SWP, UBPI_HUMANd | Ubiquitin carboxyl-terminal hydrolase 18 (Ubp) | 2.13 (0.41) | 11.94 (1.31) | 6.23 (1.32) | 11.83 (2.51) |
| EMB, AAH01874d | Similar to sequestosome 1 | 2.01 (0.24) | NC | 2.29 (0.26) | 7.78 (1.04) |
| SWP, CUL1_MOUSEd | Cullin homologue 1 (CUL-1) | NC | NC | NC | 2.13 (0.56) |
| EMB, O88544 | COP9 complex subunit 4 | NC | NC | 2.00 (0.21) | 2.20 (0.20) |
| Vesicular protein trafficking and fusion | |||||
| EMB, Q9Y4Z6 | Vacuolar protein sorting (Vps45) | NC | NC | 5.18 (1.11) | 4.44 (1.57) |
| EMB, Q9D872 | Signal recognition particle receptor B subunit | NC | NC | NC | 2.30 (0.50) |
| EMB, Q98932 | Rab5C-like protein | NC | 9.45 (0.88) | 30.34 (1.62) | 50.68 (2.39) |
| EMB, Q9JMJ6 | Syntaxin 7 | NC | NC | 2.04 (0.37) | 3.42 (0.74) |
| EMB, Q9Y5P9 | Endocytic receptor Endo180 | NC | 2.38 (0.14) | 3.06 (0.34) | 4.33 (0.15) |
| SWP, CLH1_HUMAN | Clathrin heavy chain 1 (CLH-17) | NC | NC | NC | 2.82 (0.85) |
| Antigen presentation | |||||
| EMB, O42404d | CD80-like protein precursor | NC | NC | 2.68 (0.32) | 4.67 (0.56) |
| Transcription regulation | |||||
| SWP, TMF1_HUMANd | TATA element modulatory factor (TMF) | NC | NC | 3.24 (0.28) | 4.83 (0.53) |
| SWP, PTB_PIG | Polypyrimidine tract-binding protein (PTB) | NC | NC | NC | 2.48 (0.38) |
| EMB, O95320 | U5 snRNP-specific 40-kDa protein | NC | NC | 4.58 (0.53) | 7.16 (1.88) |
| EMB, Q9WVG7 | Odd-skipped related 1 protein | NC | −1.89 (0.06) | −2.15 (0.08) | −2.02 (0.11) |
| Translation | |||||
| SWP, IF37_MOUSE | Translation initiation factor 3 subunit (eIF-3) | NC | 2.03 (0.29) | 5.18 (0.65) | 6.45 (0.78) |
| SWP, RL3_BOVIN | 60S ribosomal protein L3 | NC | NC | 9.22 (0.60) | 11.15 (0.98) |
| SWP, PDI_CHICK | Protein disulfide isomerase (PDI) | NC | NC | −2.32 (0.03) | −2.11 (0.01) |
| SWP, IF2P_HUMAN | Translation initiation factor 2 (IF-2) | NC | −2.20 (0.06) | −3.20 (0.03) | NC |
| EMB, Q9PTD6 | Ribosomal protein S6 | NC | NC | −3.00 (0.01) | −1.87 (0.04) |
| SWP, RL5B_XENLA | 60S ribosomal protein L5B | NC | NC | −2.67 (0.02) | −2.54 (0.05) |
| SWP, EF1A_CHICKd | Elongation factor 1-alpha 1 | NC | NC | −2.46 (0.03) | NC |
| SWP, NPM_CHICK | Nucleophosmin (NPM) (nucleolar phosphoprotein B23) | NC | NC | −2.18 (0.06) | NC |
| Cell growth and proliferation | |||||
| SWP, QSP_CHICK | Quiescence-specific protein precursor (P20K) | NC | 3.97 (0.81) | 5.02 (0.33) | 7.92 (0.64) |
| SWP, DIA_DROME | Diaphanous protein | NC | NC | −2.06 (0.03) | NC |
| Signal transduction | |||||
| EMB, Q9U9S7 | Adenylyl cyclase | 2.18 (0.16) | 8.91 (0.61) | 9.47 (0.23) | 16.52 (2.03) |
| EMB, Q08623 | PKC-zeta-interacting protein (ZIP) | NC | NC | 2.41 (0.18) | 6.76 (0.89) |
| RNA regulation | |||||
| SWP, RSFR_CHICK | RNase homologue precursor (RSFR) | NC | NC | NC | 2.54 (0.59) |
| Plasma/nuclear membrane proteins | |||||
| SWP, SSGP_VOLCA | Sulfated surface glycoprotein 185 (SSG 185) | 2.22 (0.28) | 20.78 (1.73) | 16.18 (0.89) | 40.35 (4.27) |
| SWP, N107_HUMAN | Nuclear pore complex protein NUP107 | NC | NC | 2.23 (0.28) | 2.08 (0.33) |
| Heat shock and stress response | |||||
| EMB, Q9JII7 | Arsenite-inducible RNA-associated protein | NC | NC | 2.95 (0.27) | 4.77 (0.70) |
| SWP, HS47_CHICK | 47-kDa heat shock protein precursor | NC | NC | −2.33 (0.03) | −2.05 (0.02) |
| SWP, ENPL_CHICK | Heat shock 108-kDa protein | NC | NC | −2.31 (0.04) | NC |
| EMB, O60884 | DNAJ protein | NC | NC | −1.98 (0.03) | NC |
| Cell cycle | |||||
| SWP, CGA2_CHICK | Cyclin A2 | NC | NC | 2.91 (0.56) | 3.95 (1.22) |
| SWP, CCT2_HUMAN | Cyclin T2 | NC | NC | 3.18 (0.54) | 4.82 (0.82) |
| Transporter proteins | |||||
| SWP, ABF2_HUMAN | Iron-inhibited ABC transporter 2 (ABCF2) | NC | NC | NC | 3.29 (0.59) |
| SWP, ATCP_HUMAN | Calcium-transporting ATPase 1 plasma membrane | NC | NC | NC | 2.22 (0.44) |
| Tumor-associated proteins | |||||
| EMB, Q9H3G6 | Melanoma differentiation associated protein-5 | NC | NC | 2.15 (0.20) | 2.56 (0.32) |
| EMB, O95140 | CPRP1 | NC | NC | 2.41 (0.57) | 3.37 (0.90) |
| SWP, CSR2_CHICK | Cysteine-rich protein 2 (CRP2) | NC | NC | −1.71 (0.04) | −3.22 (0.03) |
| EMB, O00199 | Integral membrane serine protease seprase | NC | −1.75 (0.06) | −3.32 (0.02) | −4.05 (0.04) |
| EMB, Q9JJK2 | Testis-specific adriamycin sensitivity protein | NC | NC | NC | −2.00 (0.10) |
| Cytoskeleton and motor proteins | |||||
| SWP, ACT2_XENTR | Actin alpha 2 | NC | NC | −2.79 (0.03) | −4.12 (0.01) |
| EMB, Q61852 | Actin gamma 2 | NC | NC | −2.98 (0.02) | −3.84 (0.02) |
| SWP, ACT2_HALRO | Actin 2/4/4A | NC | NC | −2.56 (0.04) | −3.68 (0.02) |
| SWP, ACT1_ORYLA | Actin (MA1) | NC | NC | −2.64 (0.03) | −4.08 (0.02) |
| EMB, Q9QZ83 | Gamma actin-like protein | NC | NC | −2.13 (0.02) | NC |
| PIR, S06117 | Myosin heavy chain | NC | NC | −3.64 (0.03) | −2.97 (0.05) |
| EMB, Q9NU67 | Retinitis pigmentosa 2 (RP2) | NC | NC | 5.97 (0.59) | 8.67 (1.61) |
| SWP, KIF2_HUMAN | Kinesin-like protein KIF2 | NC | NC | 3.75 (0.56) | 6.63 (0.87) |
| Protein degradation/lysosomal | |||||
| SWP, FUCO_HUMAN | Tissue alpha-l-fucosidase precursor | NC | NC | −2.44 (0.03) | −3.62 (0.02) |
| Mitochondrial protein | |||||
| SWP, COX1_CHICK | Cytochrome c oxidase polypeptide 1 | NC | NC | −1.69 (0.04) | −1.73 (0.03) |
| Extracellular matrix and cell adhesion | |||||
| SWP, HAS2_CHICK | Hyaluronan synthase 2 | NC | NC | 2.00 (0.25) | 4.60 (0.95) |
| EMB, O35103 | Osteomodulin | NC | NC | 3.13 (0.43) | 4.08 (0.96) |
| SWP, ITB1_CHICK | Integrin beta-1 precursor (CSAT antigen) | NC | NC | −1.83 (0.08) | −3.42 (0.05) |
| SWP, TSP2_CHICKd | Thrombospondin 2 precursor | NC | NC | −3.39 (0.04) | −8.24 (0.01) |
| EMB, Q91002 | Thrombospondin-4 | NC | NC | NC | −3.35 (0.10) |
| SWP, CA11_CHICK | Collagen alpha 1 (I) chain precursor | NC | NC | −2.28 (0.05) | −2.74 (0.03) |
| SWP, CA13_CHICK | Collagen alpha 1 (III) chain | NC | NC | −1.77 (0.03) | −2.65 (0.02) |
| SWP, CA18_HUMAN | Collagen alpha 1(VIII) chain precursor | NC | NC | NC | −1.82 (0.19) |
| SWP, CA21_CHICKd | Collagen alpha 2 (I) chain precursor | NC | NC | −2.34 (0.02) | −4.32 (0.01) |
| SWP, CA25_HUMAN | Collagen alpha 2(V) chain precursor | NC | NC | −2.12 (0.02) | −3.41 (0.02) |
| EMB, Q9DE68 | Dermatan sulfate proteoglycan decorin | NC | NC | NC | −2.15 (0.03) |
| EMB, O94769 | Extracellular matrix protein | NC | NC | −2.68 (0.02) | −2.26 (0.03) |
| SWP, LUM_CHICKd | Lumican precursor (keratan sulfate proteoglycan) | NC | NC | −2.09 (0.02) | −4.93 (0.02) |
| SWP, PEDF_MOUSE | Pigment epithelium-derived factor precursor | NC | NC | −2.09 (0.03) | −2.67 (0.05) |
| SWP, LYOX_CHICK | Protein-lysine 6-oxidase precursor | NC | NC | −1.71 (0.07) | NC |
| Metabolism | |||||
| SWP, RPIA_MOUSE | Ribose 5-phosphate isomerase | NC | NC | 4.55 (0.50) | 8.80 (0.66) |
| EMB, AAH02559 | High-glucose-regulated protein 8 | NC | 3.27 (0.24) | 13.94 (1.50) | 19.51 (2.20) |
| SWP, PKBS_BOVIN | Peripheral-type benzodiazepine receptor (PBR) | NC | 3.04 (0.20) | 9.07 (0.86) | 14.11 (0.86) |
| SWP, PWP2_HUMAN | Periodic tryptophan protein 2 homologue (PWP2) | NC | NC | 3.05 (0.64) | 4.02 (0.40) |
| SWP, P5CS_HUMAN | Delta 1-pyrroline-5-carboxylate synthetase (P5CS) | NC | NC | −3.24 (0.02) | −2.55 (0.03) |
| SWP, GNA1_DROME | Probable glucosamine-phosphate N-acetyltransferase | NC | NC | 2.35 (0.30) | 3.17 (0.58) |
| EMB, O15460 | Prolyl 4-hydroxylase alpha (ii) subunit | NC | NC | NC | 2.12 (0.49) |
| SWP, PNAD_PIG | Protein N-terminal asparagine amidohydrolase | NC | NC | 3.39 (0.41) | 2.92 (0.36) |
| EMB, AAB34334 | Protein phosphatase 1 gamma 1 | NC | NC | NC | 2.04 (0.44) |
| SWP, ADRO_MOUSE | NADPH: adrenodoxin oxidoreductase | NC | NC | 2.12 (0.31) | 2.73 (0.27) |
| SWP, AT5C_HUMAN | Potential phospholipid-transporting ATPase VC | NC | NC | −2.04 (0.01) | −2.63 (0.06) |
| EMB, AAH01741 | Similar to glyoxalase I | NC | NC | −2.91 (0.06) | −2.67 (0.04) |
| EMB, AAD02474 | Glyceraldehyde-3-phosphate dehydrogenase | NC | NC | −2.23 (0.01) | NC |
| SWP, ENOA_CHICK | Alpha enolase (2-phospho-D-glycerate hydrolyase) | NC | NC | −2.11 (0.03) | NC |
| SWP, APA1_CHICK | Apolipoprotein A-1 precursor | NC | NC | NC | −1.93(0.02) |
| SWP, FTDH_RAT | 10-Formyltetrahydrofolate dehydrogenase | NC | −1.77 (0.07) | NC | NC |
| SWP, ATP6_CHICK | ATP synthase A chain | NC | NC | −1.93 (0.03) | NC |
| Cell physiology and development | |||||
| SWP, FKBB_HUMAN | 12.6-kDa FK506-binding protein | NC | NC | −1.99 (0.05) | NC |
| SWP, FM14_MOUSE | Formin 1 isoform IV | NC | NC | NC | 2.69 (0.69) |
| SWP, GRP1_PETHY | Glycine-rich cell wall structural protein 1 | NC | NC | −3.44 (0.02) | −3.83 (0.04) |
| EMB, P97487 | Hippocampal amyloid protein | NC | NC | −1.82 (0.04) | −1.86 (0.06) |
| Unknown function | |||||
| EMB, Q9D0V1 | 1110067L12RIK protein | NC | NC | NC | 2.11 (0.37) |
| EMB, Q9D9V7 | 1700027J05RIK protein | NC | NC | NC | 2.28 (0.31) |
| EMB, Q9D9D0 | 1700101G24RIK protein | NC | NC | 2.44 (0.38) | 3.45 (0.69) |
| EMB, Q9CY20 | 2510027N19RIK protein | NC | NC | 2.67 (0.38) | 5.26 (1.03) |
| EMB, Q9D0E4 | 2610021K23RIK protein | NC | NC | NC | 2.82 (0.38) |
| EMB, Q9D2N6 | 4631426J05RIK protein | NC | NC | 2.92 (0.41) | 7.45 (1.23) |
| EMB, Q9D5P8 | 4930402H24RIK protein | NC | NC | 2.43 (0.36) | 4.78 (0.95) |
| EMB, Q9NUM1 | CDNA FLJ11277 fis, clone PLACE1009404 | 2.19 (0.32) | 3.67 (0.44) | 2.37 (0.24) | 5.29 (0.61) |
| EMB, Q9H8V6 | CDNA FLJ13201 fis, clone NT2RP3004498 | NC | NC | NC | 3.15 (0.39) |
| EMB, Q9H812 | CDNA FLJ14005 fis, clone Y79AA1002361 | NC | NC | 2.61 (0.49) | 3.08 (0.47) |
| EMB, Q9H7T5 | CDNA FLJ14273 fis, clone PLACE1004913 | NC | NC | −2.16 (0.05) | NC |
| EMB, Q9NXP3 | CDNA FLJ20129 fis, clone COL06190 | NC | NC | NC | −3.59 (0.10) |
| EMB, Q9NWV4 | CDNA FLJ20580 fis, clone REC00516 | NC | NC | −2.07 (0.07) | −3.18 (0.03) |
| EMB, Q9VKV8 | CG5343 protein | NC | NC | 2.21 (0.36) | 2.70 (0.52) |
| EMB, Q9VLT1 | CG8683 protein | NC | NC | NC | −3.31 (0.10) |
| IGI, RRN01291 | KIAA0613 protein | NC | NC | NC | 2.31 (0.45) |
| EMB, AAH02380 | Unknown (protein for IMAGE:2961244) | NC | NC | −2.05 (0.02) | −2.28 (0.03) |
| GEN, CAC35438 | Unnamed protein product | NC | 2.98 (0.39) | 2.94 (0.28) | 7.72 (1.05) |
| EMB, AAH05857 | Unknown (protein for MGC:2910). | NC | 2.89 (0.48) | 3.64 (0.51) | 8.65 (0.94) |
| EMB, AAH02575 | Unknown (protein for IMAGE:3161568) | NC | NC | 3.58 (0.60) | 6.57 (0.92) |
| GEN, CAC22485 | Unnamed protein product | NC | 2.28 (0.49) | 3.56 (0.60) | 5.59 (1.38) |
| EMB, CAB66533 | Hypothetical 22.5-kDa protein | NC | NC | 2.69 (0.65) | 4.74 (0.83) |
| EMB, Q9Y2J9 | KIAA0995 protein | NC | NC | 3.17 (0.52) | 4.31 (0.39) |
| EMB, Q9ULD7 | KIAA1283 protein | NC | NC | −2.15 (0.06) | −2.38 (0.06) |
| EMB, Q9P2H7 | KIAA1370 protein | NC | NC | 2.38 (0.32) | 3.31 (0.51) |
| EMB, Q9H3F0 | MSTP034 | NC | NC | NC | 2.41 (0.51) |
| EMB, Q9JM62 | Polyposis locus protein 1-like 1 | NC | NC | −1.74 (0.04) | −1.76 (0.05) |
| EMB, Q9D0Z1 | Q9D0Z1 1110039P19RIK protein | NC | NC | −2.64 (0.03) | −3.10 (0.05) |
| EMB, Q9H8C3 | Q9H8C3 CDNA FLJ13770 FIS, CLONE PLACE4000269 | NC | NC | 2.42 (0.30) | 4.10 (0.55) |
| IGI, RCHU01422 | RCHU01422 hypothetical protein | NC | NC | 2.45 (0.17) | 3.01 (0.40) |
| SWP, RNF6_HUMANd | Ring finger protein 6 | NC | NC | NC | 4.38 (1.38) |
| EMB, AAH06414 | Similar to KIAA0952 protein | NC | NC | 3.78 (0.48) | 6.86 (0.99) |
| EMB, Q9LGZ9 | Genomic DNA, chromosome 3, BAC clone:F1D9 | NC | 17.78 (1.60) | 30.55 (1.67) | 65.98 (3.70) |
| Hypothetical proteins | |||||
| EMB, Q9Y520 | Hypothetical 295.8-kDa protein | NC | NC | NC | 3.74 (0.55) |
| EMB, Q9H0P6 | Hypothetical 38.9-kDa protein | NC | NC | NC | 2.73 (0.33) |
| SWP, YG1W_YEAST | Hypothetical 44.2-kDa protein in RME1-TFC4 intergenic region | NC | NC | 4.83 (0.61) | 12.00 (1.17) |
| EMB, Q9Y3V7 | Hypothetical 63.3-kDa protein | NC | NC | NC | −2.04 (0.09) |
| SWP, Y052_HUMAN | Hypothetical protein KIAA0052 | NC | 2.57 (0.47) | 2.57 (0.15) | 11.54 (2.65) |
| EMB, AAH02877 | Similar to hypothetical protein FLJ1158 | NC | NC | NC | 4.33 (1.47) |
| EMB, AAH06213 | Similar to RIKEN cDNA 1200013A08 gene | NC | NC | 2.20 (0.50) | 2.04 (0.36) |
a
The APV infection time course experiment was repeated twice, and hybridization of SSH cDNA chips with fluorescent labeled probes was repeated twice per experiment. The table lists clones isolated by SSH and validated to be differentially expressed by microarray analysis. Only genes with twofold or greater changes in transcription in APV-infected cells relative to that in uninoculated controls are shown. Differentially expressed genes with no homologues in databases, which are designated “unknown,” are not shown.
b
From the Swiss Prot (SWP) and EMBL (EMB) databases. Regulated transcripts are classified according to functional groups.
c
Values are average Cy5-to-Cy3 ratios from four replicate experiments, along with their standard deviations which are given (in parentheses) only for transcripts showing twofold or greater changes in expression. NC, no change. SD, standard deviation.
d
Results were confirmed by real-time RT-PCR.