Yin Zhimin, Pawełkowicz Magdalena, Michalak Krystyna, Chrzanowska Mirosława, Zimnoch-Guzowska Ewa
Młochów Research Center, Plant Breeding and Acclimatization Institute - National Research Institute, Platanowa Street 19, 05-831, Młochów, Poland,
Arch Virol. 2014 Nov;159(11):3119-23. doi: 10.1007/s00705-014-2128-x. Epub 2014 Jun 18.
Two previously sequenced tobacco rattle virus (TRV) isolates, Slu24 and Deb57, from Polish potato fields have recombinant RNA2 species. The 3'-proximal region of the Slu24 RNA2 is derived from the 3' terminus of its supporting RNA1, while that of the Deb57 RNA2 is derived from the 3' terminus of the unrelated RNA1 from the isolate SYM or PpK20. Gene structure annotation revealed open reading frames encoding truncated 16-kDa proteins in the recombinant regions of the RNA2 of Deb57 and Slu24. Reading frame shifts, single nucleotide substitutions and deletions occurred during recombination, including shifts from a stop codon or replacements of an internal stop codon. In the recombinant region of the Deb57 RNA2, the first reading frameshift event starts from the AUG start codon of the truncated 16-kDa protein. The second frameshift event, caused by a single nucleotide deletion upstream of the stop codon, leads to the splitting of the stop codon into two amino acid codons and the continuation of translation. In addition, a U-to-A substitution changes a potential internal stop codon UAA, which is caused by recombination-related frame shifts, into the codon AAA, encoding lysine. The replacement of this internal stop codon with an amino acid codon prevented the premature translation termination of the truncated 16-kDa protein. These recombination-related reading frame shifts are the driving force underlying the major differences in the translated amino acids, consequently leading to their translation into distinct polypeptides. Conversely, single nucleotide substitutions in the recombinant regions of the RNA2 of Deb57 or Slu24 resulted in only minor changes in the translated amino acids.
从波兰马铃薯田分离出的两个先前已测序的烟草脆裂病毒（TRV）分离株Slu24和Deb57具有重组RNA2种类。Slu24 RNA2的3'近端区域源自其支持性RNA1的3'末端，而Deb57 RNA2的3'近端区域则源自分离株SYM或PpK20中不相关RNA1的3'末端。基因结构注释显示，在Deb57和Slu24的RNA2重组区域中存在编码截短的16 kDa蛋白的开放阅读框。重组过程中发生了读框移位、单核苷酸替换和缺失，包括从终止密码子的移位或内部终止密码子的替换。在Deb57 RNA2的重组区域中，第一个读框移位事件从截短的16 kDa蛋白的AUG起始密码子开始。第二个读框移位事件是由终止密码子上游的单核苷酸缺失引起的，导致终止密码子分裂为两个氨基酸密码子并继续翻译。此外，U到A的替换将由重组相关读框移位引起的潜在内部终止密码子UAA变为编码赖氨酸的密码子AAA。用氨基酸密码子替换这个内部终止密码子可防止截短的16 kDa蛋白过早终止翻译。这些与重组相关的读框移位是翻译氨基酸主要差异的驱动力，从而导致它们翻译成不同的多肽。相反，Deb57或Slu24的RNA2重组区域中的单核苷酸替换仅导致翻译氨基酸的微小变化。
