Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton
Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton
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DOI：
10.3389/fmicb.2019.00134
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发表时间：
2018-11
影响因子：
5.2
通讯作者：
Amelia O. Harrison;Ryan M. Moore;Shawn W. Polson;K. E. Wommack
中科院分区：
文献类型：
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作者：
Amelia O. Harrison;Ryan M. Moore;Shawn W. Polson;K. E. Wommack
核糖核苷酸还原酶(RNRs)是一种古老的催化核糖核苷酸还原为脱氧核糖核苷酸的酶。它们几乎是所有细胞生命所必需的，在病毒基因组中也很突出。RNRs有着共同的祖先，必须产生蛋白质自由基才能直接进行核糖核苷酸还原。RNRs产生自由基的机制是多种多样的，RNRs分为三大类和几个亚类。自由基产生方法的多样性意味着细胞生物和病毒通常含有最适合DNA复制周围环境条件的RNR。然而，这种多样性也导致了主题序列数据库中RNR的高误注率。这些错误的注释导致了对RNR生物化学的错误翻译假设，并降低了该标记基因在病毒生态学研究中的作用。我们在原氯球菌噬菌体P-SSP7基因组中发现了RNR基因的错误注释，这导致了通常从海洋浮游病毒群落中观察到的RNR基因的一系列错误注释。这些RNRs在海洋蓝鳍金枪鱼病毒和氰基鸟病毒中被发现，目前被错误地注释为II类RNRs，它不依赖O2，需要辅因子B12。事实上，这些氰基病毒RNRs是依赖O2的I类酶，可能需要由铁、锰或这两种金属的组合组成的双金属辅因子。在P-SSP7基因组中发现了一个被忽视的I类β亚基，并对α和β亚基进行了系统发育分析，证实了P-SSP7的RNR1类。系统发育和保守残基分析也表明，P-SSP7 RNR可能构成一个新的I类亚类。以P-SSP7为代表的RNR分支的重新注释意味着大多数裂解噬菌体含有I类RNRs，而它们的宿主B12产生的聚球藻和原氯球菌含有II类RNRs。通过使用I类RNR，噬藻体避免了对宿主产生的B12的依赖，这是一种更有效的裂解病毒策略。氰尿症病毒中一个新的RnRβ亚基的发现也意味着一些未知的病毒基因可能是熟悉的细胞基因，对于基于同源性的注释方法来说太过分化而无法识别。
Ribonucleotide reductases (RNRs) are ancient enzymes that catalyze the reduction of ribonucleotides to deoxyribonucleotides. They are required for virtually all cellular life and are prominent within viral genomes. RNRs share a common ancestor and must generate a protein radical for direct ribonucleotide reduction. The mechanisms by which RNRs produce radicals are diverse and divide RNRs into three major classes and several subclasses. The diversity of radical generation methods means that cellular organisms and viruses typically contain the RNR best-suited to the environmental conditions surrounding DNA replication. However, such diversity has also fostered high rates of RNR misannotation within subject sequence databases. These misannotations have resulted in incorrect translative presumptions of RNR biochemistry and have diminished the utility of this marker gene for ecological studies of viruses. We discovered a misannotation of the RNR gene within the Prochlorococcus phage P-SSP7 genome, which caused a chain of misannotations within commonly observed RNR genes from marine virioplankton communities. These RNRs are found in marine cyanopodo- and cyanosiphoviruses and are currently misannotated as Class II RNRs, which are O2-independent and require cofactor B12. In fact, these cyanoviral RNRs are Class I enzymes that are O2-dependent and may require a di-metal cofactor made of Fe, Mn, or a combination of the two metals. The discovery of an overlooked Class I β subunit in the P-SSP7 genome, together with phylogenetic analysis of the α and β subunits confirms that the RNR from P-SSP7 is a Class I RNR. Phylogenetic and conserved residue analyses also suggest that the P-SSP7 RNR may constitute a novel Class I subclass. The reannotation of the RNR clade represented by P-SSP7 means that most lytic cyanophage contain Class I RNRs, while their hosts, B12-producing Synechococcus and Prochlorococcus, contain Class II RNRs. By using a Class I RNR, cyanophage avoid a dependence on host-produced B12, a more effective strategy for a lytic virus. The discovery of a novel RNR β subunit within cyanopodoviruses also implies that some unknown viral genes may be familiar cellular genes that are too divergent for homology-based annotation methods to identify.