Kang Seung Yi, Ahn Dog Gn, Lee Chan, Lee Yong Sup, Shin Cha-Gyun
Department of Biotechnology, Chung-Ang University, Ansung, Korea.
J Microbiol Biotechnol. 2008 Jun;18(6):1044-9.
In order to study functional nucleotides in prototype foamy virus (PFV) DNA on specific recognition by PFV integrase (IN), we designed chimeric U5 long terminal repeat (LTR) DNA substrates by exchanging comparative sequences between human immunodeficiency virus type-1 (HIV-1) and PFV U5 LTRs, and investigated the 3'-end processing reactivity using HIV-1 and PFV INs, respectively. HIV-1 IN recognized the nucleotides present in the fifth and sixth positions at the 3'-end of the substrates more specifically than any other nucleotides in the viral DNA. However, PFV IN recognized the eighth and ninth nucleotides as distinctively as the fifth and sixth nucleotides in the reactions. In addition, none of the nucleotides present in the twelfth, sixteenth, seventeenth, eighteenth, nineteenth, and twentieth positions were not differentially recognized by HIV-1 and PFV INs, respectively. Therefore, our results suggest that the functional nucleotides that are specifically recognized by its own IN in the PFV U5 LTR are different from those in the HIV-1 U5 LTR in aspects of the positions and nucleotide sequences. Furthermore, it is proposed that the functional nucleotides related to the specific recognition by retroviral INs are present inside ten nucleotides from the 3'-end of the U5 LTR.
为了研究原型泡沫病毒（PFV）DNA中的功能性核苷酸被PFV整合酶（IN）特异性识别的情况，我们通过交换人类免疫缺陷病毒1型（HIV-1）和PFV U5长末端重复序列（LTR）之间的比较序列，设计了嵌合U5 LTR DNA底物，并分别使用HIV-1和PFV INs研究了3'-末端加工反应活性。HIV-1 IN比病毒DNA中的任何其他核苷酸更特异性地识别底物3'-末端第五和第六位的核苷酸。然而，在反应中，PFV IN对第八和第九位核苷酸的识别与对第五和第六位核苷酸的识别一样明显。此外，HIV-1和PFV INs分别对第十二、十六、十七、十八、十九和二十位的核苷酸没有差异识别。因此，我们的结果表明，PFV U5 LTR中被其自身IN特异性识别的功能性核苷酸在位置和核苷酸序列方面与HIV-1 U5 LTR中的不同。此外，有人提出，与逆转录病毒INs特异性识别相关的功能性核苷酸存在于U5 LTR 3'-末端的十个核苷酸内。
