Carpenter C D, Simon A E
Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003, USA.
J Virol. 1996 Jan;70(1):478-86. doi: 10.1128/JVI.70.1.478-486.1996.
Sequences at the 3' ends of plus-strand RNA viruses and their associated subviral RNAs are important cis elements for the synthesis of minus strands in vivo and in vitro. All RNAs associated with turnip crinkle virus (TCV), including the genomic RNA (4,054 bases) and satellite RNAs (sat-RNAs) such as sat-RNA D (194 bases), terminate with the motif CCUGCCC. While investigating the ability of in vivo-generated recombinants between sat-RNA D and TCV to be amplified in plants, we discovered that sat-RNA D, although truncated by as many as 15 bases in the chimeric molecules, was released from the chimeric transcripts and amplified to high levels. The "new" sat-RNA D molecules nearly all terminated with the motif (C1-2)UG(C1-3) (which may begin with 1 or 2 cytosines and end with 1, 2, or 3 cytosines), which was similar or identical to the natural sat-RNA D 3' end. The new sat-RNA D also contained between 1 and 22 bases of heterogeneous sequence upstream from the terminal motif, which, in some cases, was apparently derived from internal regions of either the plus or minus strand of the TCV genomic RNA. Since most of these internal genomic RNA sequences within TCV were not adjacent to (C1-2)UG(C1-3), at least two steps were required to produce new sat-RNA D 3' ends: nonhomologous recombination with the TCV genomic RNA followed by the addition or modification of the terminus to generate the (C1-2)UG(C1-3) motif.
正链RNA病毒及其相关亚病毒RNA 3'端的序列是体内和体外负链合成的重要顺式元件。与芜菁皱缩病毒（TCV）相关的所有RNA，包括基因组RNA（4054个碱基）和卫星RNA（sat-RNA）如sat-RNA D（194个碱基），均以基序CCUGCCC结尾。在研究植物中体内产生的sat-RNA D与TCV之间的重组体的扩增能力时，我们发现，虽然嵌合分子中的sat-RNA D被截短多达15个碱基，但它能从嵌合转录本中释放出来并扩增到高水平。“新”的sat-RNA D分子几乎都以基序（C1 - 2）UG（C1 - 3）（可能以1或2个胞嘧啶开头，以1、2或3个胞嘧啶结尾）结尾，这与天然sat-RNA D的3'端相似或相同。新的sat-RNA D在末端基序上游还含有1至22个碱基的异质序列，在某些情况下，这些序列显然源自TCV基因组RNA正链或负链的内部区域。由于TCV内的这些内部基因组RNA序列大多不与（C1 - 2）UG（C1 - 3）相邻，因此产生新的sat-RNA D 3'端至少需要两个步骤：与TCV基因组RNA进行非同源重组，然后对末端进行添加或修饰以产生（C1 - 2）UG（C1 - 3）基序。
