Subedi Dinesh, Barr Jeremy J
School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
School of Biological Sciences, Monash University, Clayton, Victoria, Australia
mSystems. 2021 Feb 16;6(1):e00990-20. doi: 10.1128/mSystems.00990-20.
T-series phages have been model organisms for molecular biology since the 1940s. Given that these phages have been stocked, distributed, and propagated for decades across the globe, there exists the potential for genetic drift to accumulate between stocks over time. Here, we compared the temporal stability and genetic relatedness of laboratory-maintained phage stocks with a T-series collection from 1972. Only the T-even phages produced viable virions. We obtained complete genomes of these T-even phages, along with two contemporary T4 stocks. Performing comparative genomics, we found 12 and 16 nucleotide variations, respectively, in the genomes of T2 and T6, whereas there were ∼172 nucleotide variations between T4 sublines compared with the NCBI RefSeq genome. To account for the possibility of artifacts in NCBI RefSeq, we used the 1972 T4 stock as a reference and compared genetic and phenotypic variations between T4 sublines. Genomic analysis predicted nucleotide variations in genes associated with DNA metabolism and structural proteins. We did not, however, observe any differences in growth characteristics or host range between the T4 sublines. Our study highlights the potential for genetic drift between individually maintained T-series phage stocks, yet after 48 years, this has not resulted in phenotypic alterations in these important model organisms. T-series bacteriophages have been used throughout the world for various molecular biology researches, which were critical for establishing the fundamentals of molecular biology, from the structure of DNA to advanced gene-editing tools. These model bacteriophages help keep research data consistent and comparable between laboratories. However, we observed genetic variability when we compared contemporary sublines of T4 phages to a 48-year-old stock of T4. This may have effects on the comparability of results obtained using T4 phage. Here, we highlight the genomic differences between T4 sublines and examined phenotypic differences in phage replication parameters. We observed limited genomic changes but no phenotypic variations between T4 sublines. Our research highlights the possibility of genetic drift in model bacteriophages.
自20世纪40年代以来,T系噬菌体一直是分子生物学的模式生物。鉴于这些噬菌体在全球范围内已被储存、分发和传代培养了数十年,随着时间的推移,不同菌株之间存在积累遗传漂变的可能性。在这里,我们将实验室保存的噬菌体菌株与1972年的一个T系噬菌体文库进行了时间稳定性和遗传相关性的比较。只有T偶数噬菌体产生了有活力的病毒粒子。我们获得了这些T偶数噬菌体以及两个当代T4菌株的完整基因组。通过进行比较基因组学研究,我们在T2和T6的基因组中分别发现了12个和16个核苷酸变异,而与NCBI RefSeq基因组相比,T4亚系之间有大约172个核苷酸变异。为了考虑NCBI RefSeq中人为错误的可能性,我们以1972年的T4菌株作为参考,并比较了T4亚系之间的遗传和表型变异。基因组分析预测了与DNA代谢和结构蛋白相关的基因中的核苷酸变异。然而,我们没有观察到T4亚系之间在生长特性或宿主范围上有任何差异。我们的研究突出了单独保存的T系噬菌体菌株之间发生遗传漂变的可能性,然而48年后,这并未导致这些重要模式生物出现表型改变。T系噬菌体在世界各地被用于各种分子生物学研究,这些研究对于奠定分子生物学基础至关重要,从DNA结构到先进的基因编辑工具。这些模式噬菌体有助于保持各实验室间研究数据的一致性和可比性。然而,当我们将当代T4噬菌体亚系与一个保存了48年的T4菌株进行比较时,我们观察到了遗传变异性。这可能会对使用T4噬菌体获得的结果的可比性产生影响。在这里,我们突出了T4亚系之间的基因组差异,并研究了噬菌体复制参数中的表型差异。我们观察到T4亚系之间基因组变化有限,但没有表型变异。我们的研究突出了模式噬菌体发生遗传漂变的可能性。