The three faces of riboviral spontaneous mutation: spectrum, mode of genome replication, and mutation rate.
The three faces of riboviral spontaneous mutation: spectrum, mode of genome replication, and mutation rate.
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核武器自发突变的三个面：光谱，基因组复制模式和突变速率。
DOI：
10.1371/journal.pgen.1002832
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Drake JW
中科院分区：
文献类型：
--
作者：
García-Villada L;Drake JW
核糖病毒（没有DNA复制中间体的RNA病毒）是感染动物和植物的最丰富的病原体。只有少数核糖病毒感染可以用抗病毒药物控制，主要是因为耐药性突变的快速出现。关于i）突变的种类和相对频率（突变谱），ii）基因组复制和突变积累的模式，iii）自发突变的速率，几乎没有可靠的信息。为了阐明这些问题，我们开发了一个模型，在体内系统的基础上，噬菌体感染其天然宿主，大肠杆菌。将编码Read-Through蛋白的QRT-RT基因用作突变报告基因。为了减少突变频率的不确定性，由于选择，实验的QRQs人口建立后，一个单一的周期的感染和选择对RT-突变体在噬菌体生长过程中得到改善的质粒为基础的RT互补反式。QRQs基因组复制的动力学被证实，以反映线性过程的迭代复制（冲压机模式）。在7,517株QC 17菌株中共检测到32株RT突变株。对45个RT突变的测序分析揭示了由39个转换、4个颠换和2个插入缺失主导的谱。观察到明显的模板·引物错配偏倚：A·C>C·A>U·G>G·U>颠换错配。每个碱基复制的平均突变率为碱基替换的10.91 ×10−6和插入缺失的10.23 ×10−7。每个基因组复制的估计突变率（μg）为10.04（或每代噬菌体为10.08），尽管在一些RT突变体的生长过程中以约7倍的速度出现继发性RT突变，表明可能存在短暂的超突变。这些结果与之前报道的其他核糖病毒的结果进行了对比，以描述核糖病毒诱变的当前技术水平。病毒性疾病是公共卫生中一个主要关注的问题。由核糖病毒（严格意义上的RNA病毒）产生的疾病代表了一种特殊的紧迫性，因为这些病毒显示出对抗病毒药物产生抗性突变的特殊能力。不幸的是，人们对核糖病毒自发突变的速率和性质知之甚少。因此，其突变过程的表征可能有助于开发对抗核糖病毒疾病的改进方法。在这项研究中，我们研究了一种模型核糖病毒，噬菌体的体内突变过程，集中在三个关键方面：i）突变的种类和相对频率，ii）基因组复制的模式，和iii）自发突变的速率。我们的研究结果，结合其他有关核糖病毒诱变的信息，描绘了核糖病毒突变谱主要由过渡，主要是线性模式的基因组复制，和突变率每基因组复制的顺序为0.04噬菌体和植物病毒，但也许是一个数量级更高的哺乳动物核糖病毒。
Riboviruses (RNA viruses without DNA replication intermediates) are the most abundant pathogens infecting animals and plants. Only a few riboviral infections can be controlled with antiviral drugs, mainly because of the rapid appearance of resistance mutations. Little reliable information is available concerning i) kinds and relative frequencies of mutations (the mutational spectrum), ii) mode of genome replication and mutation accumulation, and iii) rates of spontaneous mutation. To illuminate these issues, we developed a model in vivo system based on phage Qß infecting its natural host, Escherichia coli. The Qß RT gene encoding the Read-Through protein was used as a mutation reporter. To reduce uncertainties in mutation frequencies due to selection, the experimental Qß populations were established after a single cycle of infection and selection against RT − mutants during phage growth was ameliorated by plasmid-based RT complementation in trans. The dynamics of Qß genome replication were confirmed to reflect the linear process of iterative copying (the stamping-machine mode). A total of 32 RT mutants were detected among 7,517 Qß isolates. Sequencing analysis of 45 RT mutations revealed a spectrum dominated by 39 transitions, plus 4 transversions and 2 indels. A clear template•primer mismatch bias was observed: A•C>C•A>U•G>G•U> transversion mismatches. The average mutation rate per base replication was ≈9.1×10−6 for base substitutions and ≈2.3×10−7 for indels. The estimated mutation rate per genome replication, μg, was ≈0.04 (or, per phage generation, ≈0.08), although secondary RT mutations arose during the growth of some RT mutants at a rate about 7-fold higher, signaling the possible impact of transitory bouts of hypermutation. These results are contrasted with those previously reported for other riboviruses to depict the current state of the art in riboviral mutagenesis. Viral disease is a subject of major concern in public health. Diseases produced by riboviruses (RNA viruses sensu stricto) represent a special urgency, because these viruses display an exceptional capability to generate resistance mutations against antiviral drugs. Unfortunately, little is known about the rate and nature of spontaneous mutation in riboviruses. Thus, characterization of their mutation process may be helpful in the development of improved ways to counteract riboviral diseases. In this study, we investigated the mutation process in vivo of a model ribovirus, the bacteriophage Qß, focusing on three key aspects: i) the kinds and relative frequencies of mutations, ii) the mode of genome replication, and iii) the rate of spontaneous mutation. Our results, combined with other information about riboviral mutagenesis, depict a ribovirus mutation spectrum largely dominated by transitions, a predominantly linear mode of genome replication, and a mutation rate per genome replication on the order of 0.04 for bacteriophages and plant viruses but perhaps an order of magnitude higher for mammalian riboviruses.
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影响因子：
4.5
作者：
Drake JW
通讯作者：
Drake JW
影响因子：
3.3
作者：
Burch, Christina L.;Guyader, Sebastien;Shen, Haipeng
通讯作者：
Shen, Haipeng
DOI：
10.1101/sqb.2000.65.81
发表时间：
2000-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
Bebenek, K;Kunkel, TA
通讯作者：
Kunkel, TA
DOI：
10.1073/pnas.96.24.13910
发表时间：
1999-11-23
影响因子：
11.1
作者：
Drake, JW;Holland, JJ
通讯作者：
Holland, JJ
DOI：
10.1073/pnas.0503009102
发表时间：
2005-09-06
影响因子：
11.1
作者：
Drake, JW;Bebenek, A;Peddada, S
通讯作者：
Peddada, S