Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA.
G3 (Bethesda). 2024 May 7;14(5). doi: 10.1093/g3journal/jkae049.
Over the past decade, thousands of bacteriophage genomes have been sequenced and annotated. A striking observation from this work is that known structural features and functions cannot be assigned for >65% of the encoded proteins. One approach to begin experimentally elucidating the function of these uncharacterized gene products is genome-wide screening to identify phage genes that confer phenotypes of interest like inhibition of host growth. This study describes the results of a screen evaluating the effects of overexpressing each gene encoded by the temperate Cluster F1 mycobacteriophage Girr on the growth of the host bacterium Mycobacterium smegmatis. Overexpression of 29 of the 102 Girr genes (~28% of the genome) resulted in mild to severe cytotoxicity. Of the 29 toxic genes described, 12 have no known function and are predominately small proteins of <125 amino acids. Overexpression of the majority of these 12 cytotoxic no known functions proteins resulted in moderate to severe growth reduction and represent novel antimicrobial products. The remaining 17 toxic genes have predicted functions, encoding products involved in phage structure, DNA replication/modification, DNA binding/gene regulation, or other enzymatic activity. Comparison of this dataset with prior genome-wide cytotoxicity screens of mycobacteriophages Waterfoul and Hammy reveals some common functional themes, though several of the predicted Girr functions associated with cytotoxicity in our report, including genes involved in lysogeny, have not been described previously. This study, completed as part of the HHMI-supported SEA-GENES project, highlights the power of parallel, genome-wide overexpression screens to identify novel interactions between phages and their hosts.
在过去的十年中,已经对数千种噬菌体基因组进行了测序和注释。从这项工作中可以明显看出,已知的结构特征和功能无法分配给> 65%的编码蛋白。开始通过实验阐明这些未鉴定的基因产物的功能的一种方法是进行全基因组筛选,以鉴定赋予感兴趣表型(例如抑制宿主生长)的噬菌体基因。本研究描述了评估过度表达温和噬菌体 F1 簇 Girr 编码的每个基因对宿主细菌耻垢分枝杆菌生长的影响的筛选结果。102 个 Girr 基因中的 29 个(约占基因组的 28%)的过表达导致轻度至重度细胞毒性。在所描述的 29 个有毒基因中,有 12 个没有已知功能,并且主要是小于 125 个氨基酸的小蛋白。这些 12 种具有细胞毒性的未知功能蛋白中的大多数的过表达导致中度至重度生长减少,代表了新型抗菌产物。其余 17 个有毒基因具有预测的功能,编码与噬菌体结构、DNA 复制/修饰、DNA 结合/基因调控或其他酶活性相关的产物。将该数据集与先前对分枝杆菌噬菌体 Waterfoul 和 Hammy 的全基因组细胞毒性筛选进行比较,揭示了一些共同的功能主题,尽管与我们的报告中的细胞毒性相关的一些预测的 Girr 功能,包括与溶原性相关的基因,以前尚未描述。本研究是 HHMI 支持的 SEA-GENES 项目的一部分,强调了平行的、全基因组过表达筛选在识别噬菌体与其宿主之间的新型相互作用方面的强大功能。