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1 The Korean Journal of Microbiology, Vol. 45, No. 3, September 009, p Copyright 009, The Microbiological Society of Korea s Semi-quantitative RT-PCR w v H9N y» ù» 1 Á Á 3 Á 4 Á x 5 Á 5 Á 5 Á 5 Á«x 5 Á 1 * w w w w w w œw w»z w v mrna. z s ü ƒ s w ƒ w ƒ» d w. v H9N k s UMNSAH/DF-1 z ¾ d w» w RNA semi-quantitative RT-PCR w d w. RNA w RNA z w» w mouse RNA RNA carrier wš sw mouse GAPDH RNA PCR ü RNA w. z ¾ 16~0. z 1 z s ü w 8 d w. 8 mrna PA w 7 mrna (HA, NA, PB1, PB, NP, M, NS yyw mrna) w s band, y d ùkû. d v RNA polymerase t w w w. Key words ý avian influenza virus, H9N, RT-PCR v Ax v, 8 negative strand RNA š. t w hemagglutinin (HA) neuraminidase (NA) x w, 16ƒ HA 9ƒ NAƒ wš ƒ w w 144 x w, w y š (8). x w š (). w x š w w w z. w w y v w š (1, 3, 6, 10), w w NA, RNA polymerase v œm» t w. x œm ƒ HA œm t w w w šƒ (9), NP y w w w w š (5). ƒ t w w ù 6 *To whom correspondence should be addressed. Tel: , Fax: mbkooyb@inje.ac.kr x v œm, ƒ r. p, RNA polymerase w w ww w t š w. s UMNSAH/DF-1 v H9N 8 l semi-quantitative reverse transcription polymerase chain reaction (semi-quantitative RT-PCR) w d w RNA polymerase y d y w. RNA polymerase t w w k. v H9N(A/Ck/kr/MS96/96) w, 9 w w w, w -70 C o w. s s UMNSAH/DF-1 (ATCC cat no. CRL 103) American Type Culture Collection (USA) l 10% FBSƒ ƒ w, 37 o C, 5% CO» 86

2 Vol. 45, No. 3 v mrna 87 DMEM w. 4 well 80% w, 1 ml PBS wš 10~100,000 PBS w 100 µl w. 37 o C, 5% CO» 1 z 1ml PBS 3z wš DMEM 1ml w w v d s z w RNA w. RNA semi-quantitative RT-PCR s s l QIAamp Viral RNA Mini kit (QIAGEN, USA) w RNA w. 140 µl mouse l w RNA 0.5 µg ƒw RNA w. w RNA 10 µl (1 µg) 50 µl universal primer (Uni 1, AGCAAAAGCAGG)(4) 0.5 µg, oligo(dt) 15 (Promega, WI, USA) 0.5 µg, 100 unit MMLV reverse transcriptase (Bioneer, Korea) 4 C 1 w o ww. s RNA Trizol (Invitrogen, USA) w w. s w RNA 10 µl (1 µg) oligo(dt) 15 v w w w. w 1µl 5 µl v PCR Table 1 t w oligonucleotide w sw. w Taq polymerase Genetbio (Korea) w w, s 94 o C 10 z, 94 o C 30, 57 o C 30, 7 o C 30 5 wš, 7 C 7 w o Table 1. List of synthetic oligonucleotides used in this study. wz 1.5% ƒ» w w. UMNSAH/DF-1 s H9N d z» s ü mrna. UMNSAH/DF-1 s H9N ( 100 w ) jš ù z 4 RNA semi-quantitative RT- PCR w d w. 8 RNA NP RNA sw. RNA w ƒw mouse RNA GAPDH sw, ƒ RNA z z w» w s GAPDH w z PCR ww. Semi-quantitative RT- PCR z 16~0 ùkû (Fig. 1). 1 mrna w. mrna d UMNSAH/DF-1 s 10~100,000 w H9N jš s 1 z z w. s RNA Name Sequence Use Size (bp) PBRTf ATT TGC CGC AGC CCC ACC PBRTr CTC TCA ATA CTG CGG ATT CCA CT RT-PCR for PB mrna 17 PB1RTf CGC AAA TTC AAA CGA GGA GAT C PB1RTr CTC AAT TTC CTT ATG ACT GAC AAA C RT-PCR for PB1 mrna 18 PARTf GAA CTT CTC CAG CCT TGA AAA C PARTr CTT TGA TCG TTG GGA GCA GG RT-PCR for PA mrna 181 NPRTf AGA GAG GGG AAA TGG ATG AGA G NPRTr CTG GGG TCC ATC CCA G RT-PCR for NP mrna 191 NSRTf GGC AGG TTC CCT TTG CAT CA NSRTr TCC GAT GAG AGG ACC CCA ATT G RT-PCR for NS mrna 17 MRTf CGA GGA CTG CAG CGT AGA C MRTr CCC ATC CTG TTG TAT ATG AG RT-PCR for M mrna 197 NARTf AGC ATT GAT TCC AGT TAT GTG TG NARTr CCT GAA AGT CTC ATA ACC TGA G RT-PCR for NA mrna 04 HARTf CAC CAC CCA CCT ACT GAT AC HARTr GAT CTC ACT CGC AGT GTC TG RT-PCR for HA mrna 194 GAPDHf GAG TCA ACG GAT TTG GCC GT GAPDHr CAC AAA CAT GGG GGC ATC AG RT-PCR for GAPDH mrna 309 Uni1 AGC AAA AGC AGG Reverse transcription ag GAPDHf and GAPDHr were used for amplification of chicken GAPDH mrna as well as mouse GAPDH mrna

3 88 Giyoun Na et al. Kor. J. Microbiol Fig. 1. Determination of interval of viral release after infection in UMNSAH/DF-1 cells. Cells were infected with 100-fold diluted H9N (allantoic fluid) as described in the 'Materials and Methods'. Culture medium was taken at indicated time pointes after infection and mixed with mouse total RNA as carrier used for viral RNA isolation. Isolated RNA was reverse transcribed using uni1 primer and oligo(dt). Polymerase chain reaction was carried out for NP RNA as well as mouse GAPDH (internal control). 15 하여 semi-quantitative RT-PCR를 사용하여 분석한 결과를 Fig. 에 나타내었다. 증폭 횟수는 5로 하였다. 그 결과 PA를 제외한 나머지 7종의 mrna의 수준은 해당 증폭 조건에서 뚜렷한 band 를 보여주었다. 요막액의 희석배수에 따른 증폭정도를 고려할 때, 10, 100, 1,000배 희석하여 접종하였을 때 증폭된 band를 관찰할 수 있었다. 토 론 본 연구와 유사한 연구 결과가 Uchide 등(11)에 의해 보고된 바 있다. 그들은 인플루엔자를 감염한 배양세포에서 HA 게놈 RNA 및 HA mrna의 수준을 semi-quantitative RT-PCR과 southern hybridization으로 측정하였다. 그 결과에 의하면 증식한 바이러스가 감염 후 1시간 후에 방출되기 시작하였으며, 그 시 기에 HA mrna의 수준이 최고였으며, 그 이후에는 점차 감소 Fig.. Reverse transcription-polymerase chain reaction (RT-PCR) of viral mrnas. Total RNA was isolated from cells infected with indicated dilutions of allantoic fluid stock of H9N influenza virus. After 1 h incubation cells were harvested and used for RNA isolation. RT-PCR was performed as described in the 'Materials and Methods'. 하였다. 반면에 HA 게놈 RNA는 48시간까지 계속 증가하는 것 으로 나타났다. 이러한 연구 결과에 따라서 본 연구에서는 증식 한 바이러스가 방출되는 시간을 semi-quantitative RT-PCR에 의 해 결정하고 그 직전에(mRNA가 최고 수준으로 존재할 때) mrna를 분리하여 실험에 사용하고자 하였다. 그러나 인플루엔 자 바이러스의 감염 후 전사되어지는 mrna는 유전자에 따라서 그 전사 시기가 서로 다르다는 보고가 있다. Shapiro 등(7)에 의 하면 NS1 mrna는 감염 초기에 발현되어지며, M mrna는 감 염 후기에 발현된다고 보고하였다. 따라서 감염 후 바이러스 mrna 분리의 최적 시기는 mrna에 따라 다를 수 있다. 본 연 구에서는 감염 후 1시간 후에 분리한 mrna를 대상으로 8종 mrna 모두를 대상으로 RT-PCR을 수행하였다. 그 중 PA mrna를 제외한 7종의 mrna에 대해서는 만족할 만한 PCR 산 물을 얻었다. PA mrna의 경우 감염 전반에 걸쳐 그 수준이 낮 은지 아니면 높은 수준으로 존재하는 시기가 있는지 더 연구해 야 할 것이다. 요막액에서 증식한 조류인플루엔자의 최적 희석 배수는 실험 적으로 결정하여야 한다. 본 연구에서는 요막액 원액과 10배 희 석한 것을 감염한 세포에서 방출되는 바이러스의 양을 NP 유전 자의 게놈을 semi-quantitative RT-PCR로 증폭하여 측정한 결과 큰 차이가 없었지만 10배 희석액과 100배 희석액을 비교하였을 때 감염 후 방출되는 바이러스의 양이 차이가 있는 것으로 나타 났다(자료 미제시). 따라서 포화 감염을 일으키는 희석배수는 10 배와 100배 사이일 것으로 보인다. 최적 바이러스 농도는 포화 감염을 시킬 수 있는 농도보다 조금 낮은 농도가 될 것으로 추 정된다. 본 연구에서는 100배 희석한 요막액을 배양세포에 감염 하고 1시간 후에 방출되는 바이러스 RNA 게놈의 semiquantitative RT-PCR을 수행하였다. 반면에 배양세포 내에서 전사 되어 지는 mrna의 semi-quantitative RT-PCR을 위해서는 감염 바이러스의 양에 따른 8종 유전자의 mrna의 수준을 보기 위하 여 요막액을 10~100,000배 희석한 것을 배양세포에 접종하였다. 바이러스 RNA polymerase에 의해 전사된 8종 mrna로부터 RT-PCR에 의해 증폭된 산물의 양의 차이가 반드시 세포 내의 바이러스 mrna 수준 차이를 나타내는 것은 아닐 것이다. 그 이유는 PCR에 사용된 주형 및 프라이머에 따라 증폭 효율에 차 이가 있을 수 있기 때문이다. 세포 내에 있는 바이러스 mrna 종류에 따른 양적 비교는 본 연구에서는 수행하지 않았으며, northern blot 분석이나 quantitative realtime RT-PCR에 의해 측 정할 수 있을 것이다. 본 연구에서 사용한 프라이머를 사용하였 을 때 PB1, PB, NS mrna의 semi-quantitative RT-PCR 산물 이 다른 유전자 mrna의 증폭 산물보다 많은 것으로 보였다. 따라서 이들 중 하나 혹은 그 이상의 mrna를 대상으로 semiquantitative RT-PCR을 실행하여 RNA polymerase 활성을 측정하 면 될 것이다. 새로운 항인플루엔자 제제의 개발 표적으로서 RNA polymerase가 대두되고 있다(3, 6). 실제로 RNA polymerase에 대한 RNAi 혹은 단일사슬 항체 등에 의한 인플루엔자 바이러스 의 RNA의 복제 억제에 관한 연구 결과가 보고되고 있다(1, 10).

4 Vol. 45, No. 3 v mrna 89 v mrna semi-quantitative RT-PCR d w RNA polymerase y š w. ù w w realtime RT-PCR w. w w s w s mrna y d œ wš. w RNA polymerase t w w. 1 ( y: ) 006 w w w. š x 1. Cheng, C., L. Yao, A. Chen, R. Jia, L. Huan, J. Guo, H. Bo, Y. Shu, and Z. Zhang Inhibitory effect of small interfering RNA specific for a novel candidate target in PB1 gene of influenza A virus. J. Drug Target. 17, Collin, N. and X. de Radigus Vaccine production capacity for seasonal and pandemic (H1N1) 009 influenza. Vaccine 7, Gong, J., H. Fang, M. Li, Y. Liu, K. Yang, Y. Liu, and W. Xu Potential targets and their relevant inhibitors in anti-influenza fields. Curr. Med. Chem. 16, Hoffmann, E., J. Stech, Y. Guan, R.G. Webster, and D.R. Perez Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 146, Mukhtar, M.M., S. Li, W. Li, T. Wan, Y. Mu, W. Wei, L. Kang, S.T. Rasool, Y. Xiao, Y. Zhu, and J. Wu Single-chain intracellular antibodies inhibit influenza virus replication by disrupting interaction of proteins involved in viral replication and transcription. Int. J. Biochem. Cell. Biol. 41, Nakazawa, M., S.E. Kadowaki, I. Watanabe, Y. Kadowaki, M. Takei, and H. Fukuda PA subunit of RNA polymerase as a promising target for anti-influenza virus agents. Antiviral Res. 78, Shapiro, G.I., T. Gurney, Jr., and R.M. Krug Influenza virus gene expression: control mechanisms at early and late times of infection and nuclear-cytoplasmic transport of virus-specific RNAs. J. Virol. 61, Spackman, E A brief introduction to the avian influenza virus. Methods Mol. Biol. 436, Sui, J., W.C. Hwang, S. Perez, G. Wei, D. Aird, L.M. Chen, E. Santelli, B. Stec, G. Cadwell, M. Ali, H. Wan, A. Murakami, A. Yammanuru, T. Han, N.J. Cox, L.A. Bankston, R.O. Donis, R.C. Liddington, and W.A. Marasco Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses. Nat. Struct. Mol. Biol. 16, Thathaisong, U., S. Maneewatch, K. Kulkeaw, K. Thueng-In, O. Poungpair, P. Srimanote, T. Songserm, P. Tongtawe, P. Tapchaisri, and W. Chaicumpa Human monoclonal single chain antibodies (HuScFv) that bind to the polymerase proteins of influenza A virus. Asian Pac. J. Allergy Immunol. 6, Uchide, N., K. Ohyama, T. Bessho, and T. Yamakawa. 00. Semi-quantitative RT-PCR-based assay, improved by Southern hybridization technique, for polarity-specific influenza virus RNAs in cultured cells. J. Virol. Methods 106, (Received September 7, 009/Accepted September 5, 009) ABSTRACT : Deterimination of an Optimal Time Point for Analyzing Transcriptional Activity and Analysis of Transcripts of Avian Influenza Virus H9N in Cultured Cell Giyoun Na 1, Young-Min Lee, Sung June Byun 3, Ik-Soo Jeon 4, Jong-Hyeon Park 5, In-Soo Cho 5, Yi-Seok Joo 5, Yun-Jung Lee 5, Jun-Hun Kwon 5, and Yongbum Koo 1 * ( 1 School of Biological Sciences, Inje University, Inje University, Gimhae , Republic of Korea, Department of Microbiology, College of Medicine, Chungbuk University, Chungju , Republic of Korea, 3 Animal Biotechnology Division, National Institute of Animal Science, Suwon , Republic of Korea, 4 Planning and Coordination Division, National Institute of Animal Science, Suwon , Republic of Korea 5 National Veterinary Research and Quarantine Services, Anyang , Republic of Korea) The transcription of mrna of avian influenza virus is regulated temporally during infection. Therefore, the measurement of transcript level in host cells should be performed before viral release from host cells because

5 90 Giyoun Na et al. Kor. J. Microbiol errors can occur in the analysis of the transcript levels if the viruses released from the infected cells re-infect cells. In this study, the timing of viral release was determined by measuring the level of viral RNA from viruses released from H9N-infected chicken fibroblast cell line UMNSAH/DF-1 by semi-quantitative RT-PCR. The viral genomic RNA was isolated together with mouse total RNA which was added to the collected medium as carrier to monitor the viral RNA recovery and to use its GAPDH as an internal control for normalizing reverse transcription reaction as well as PCR reaction. It was found that viral release of H9N in the chicken fibroblast cell line UMNSAH/DF-1 took between 16 and 0 h after infection. We measured all 8 viral mrna levels. Of the 8 transcripts, 7 species of viral mrnas (each encoding HA, NA, PB1, PB, NP, M, NS, respectively) except PA mrna showed robust amplification, indicating these mrna can be used as targets for amplification to measure transcript levels. These results altogether suggest that the method in this study can be used for screening antiviral materials against viral RNA polymerase as a therapeutic target.

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