A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes.
A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes.
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DOI：
10.1186/1471-2148-13-33
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发表时间：
2013-02-07
影响因子：
3.4
通讯作者：
Breitbart M
中科院分区：
文献类型：
--
作者：
Dwivedi B;Xue B;Lundin D;Edwards RA;Breitbart M
核糖核苷酸还原酶（RNR）是一种负责从核糖核苷酸形成脱氧核糖核苷酸的酶，存在于生命的所有领域和许多病毒基因组中。RNR也是在环境宏基因组中鉴定的最丰富的基因之一。这项研究的重点是了解RNR在细菌（感染细菌的病毒）中的分布，多样性和进化。隐马尔可夫模型的配置文件被用来分析由685个完全测序的双链DNA序列和22个环境病毒宏基因组编码的蛋白质，以确定RNR同源物在培养的细菌和未培养的病毒社区，分别。在128个噬菌体基因组中鉴定出RNR，几乎是已知编码RNR的噬菌体数量的三倍。I类RNR是在EAE中观察到的最常见的RNR类别（70%），其次是II类（29%）和III类（28%）。28%的基因组含有属于多个RNR类别的基因。RNR类分布根据噬菌体类型、分离环境和宿主利用氧的能力而变化。大多数含有RNA的病毒是肌尾病毒科（65%），其次是虹吸病毒科（30%）和短尾病毒科（3%）。噬菌体和宿主RNR的遗传和基因组组织揭示了几种不同的进化情景，涉及水平基因转移，共同进化和差异选择压力。几个假定的分裂RNR基因中断的自我剪接内含子或内含肽被确定，提供了进一步的证据频繁的遗传交换的作用。最后，病毒宏基因组数据表明，RNR在未培养的病毒群落中普遍存在且高度动态，需要未来的研究来确定RNR提供选择性优势的环境条件。这项全面的研究描述了噬菌体基因组和环境病毒宏基因组中RNR的分布，多样性和进化。特定的RNR类之间的独特分布，结合从RNR基因预测的各种进化情景，建议多个遗传来源和不同的选择力的RNR中的RNR。这项研究显着提高了我们对噬菌体RNR的理解，提供了对这一重要的辅助代谢基因的多样性和进化的深入了解，以及噬菌体响应其细菌宿主和环境的进化。
Ribonucleotide reductase (RNR), the enzyme responsible for the formation of deoxyribonucleotides from ribonucleotides, is found in all domains of life and many viral genomes. RNRs are also amongst the most abundant genes identified in environmental metagenomes. This study focused on understanding the distribution, diversity, and evolution of RNRs in phages (viruses that infect bacteria). Hidden Markov Model profiles were used to analyze the proteins encoded by 685 completely sequenced double-stranded DNA phages and 22 environmental viral metagenomes to identify RNR homologs in cultured phages and uncultured viral communities, respectively. RNRs were identified in 128 phage genomes, nearly tripling the number of phages known to encode RNRs. Class I RNR was the most common RNR class observed in phages (70%), followed by class II (29%) and class III (28%). Twenty-eight percent of the phages contained genes belonging to multiple RNR classes. RNR class distribution varied according to phage type, isolation environment, and the host’s ability to utilize oxygen. The majority of the phages containing RNRs are Myoviridae (65%), followed by Siphoviridae (30%) and Podoviridae (3%). The phylogeny and genomic organization of phage and host RNRs reveal several distinct evolutionary scenarios involving horizontal gene transfer, co-evolution, and differential selection pressure. Several putative split RNR genes interrupted by self-splicing introns or inteins were identified, providing further evidence for the role of frequent genetic exchange. Finally, viral metagenomic data indicate that RNRs are prevalent and highly dynamic in uncultured viral communities, necessitating future research to determine the environmental conditions under which RNRs provide a selective advantage. This comprehensive study describes the distribution, diversity, and evolution of RNRs in phage genomes and environmental viral metagenomes. The distinct distributions of specific RNR classes amongst phages, combined with the various evolutionary scenarios predicted from RNR phylogenies suggest multiple inheritance sources and different selective forces for RNRs in phages. This study significantly improves our understanding of phage RNRs, providing insight into the diversity and evolution of this important auxiliary metabolic gene as well as the evolution of phages in response to their bacterial hosts and environments.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
4.2
作者：
Anderson, Rika E.;Brazelton, William J.;Baross, John A.
通讯作者：
Baross, John A.
影响因子：
3.7
作者：
Chen, Chang-Lin;Pan, Tzu-Ying;Hu, Hui-Yu
通讯作者：
Hu, Hui-Yu
DOI：
10.1073/pnas.0609915104
发表时间：
2007-04-10
影响因子：
11.1
作者：
Friedrich, Nancy C.;Torrents, Eduard;Edgell, David R.
通讯作者：
Edgell, David R.
影响因子：
10.5
作者：
Belle, A;Landthaler, M;Shub, DA
通讯作者：
Shub, DA