一种新的噬菌体基因多样性分子标记基因phoH研究进展

doi:10.13560/j.cnki.biotech.bull.1985.2017-0725

生物技术通报 ›› 2017, Vol. 33 ›› Issue (10): 40-45.doi: 10.13560/j.cnki.biotech.bull.1985.2017-0725

一种新的噬菌体基因多样性分子标记基因phoH研究进展

李想^{1, 2}, 孙岩^{1, 2}, 王新珍³, 刘俊杰¹, 王光华¹

1. 中国科学院东北地理与农业生态研究所中国科学院黑土区农业生态重点实验室，哈尔滨 150081
2. 中国科学院大学，北京 100049
3. 中国科学院遗传与发育生物学研究所农业资源研究中心中国科学院农业水资源重点实验室，石家庄 050021

收稿日期:2017-09-01 出版日期:2017-10-29 发布日期:2017-10-29
作者简介:李想，女，硕士研究生，研究方向：微生物生态；E-mail：lixiang215@mails.ucas.edu.cn
基金资助:
国家自然科学基金项目（41571246）

Research Progress of New Biomarker Gene of phoH for Bacteriophage Genetic Diversity

LI Xiang^1，2, SUN Yan^1，2, WANG Xin-zhen³, LIU Jun-jie¹, WANG Guang-hua¹

1. Key Laboratory of Mollisols Agroecology，Northeast Institute of Geography and Agroecology，Chinese Academy of Sciences，Harbin 150081
2. University of Chinese Academy of Sciences，Beijing 100049
3. Key Laboratory of Agricultural Water Resources，Center for Agricultural Resources Research，Institute of Genetics and Developmental Biology，Chinese Academy of Sciences，Shijiazhuang 050021

Received:2017-09-01 Published:2017-10-29 Online:2017-10-29

摘要/Abstract

摘要： 噬菌体作为结构最简单的生命体，不仅在调节寄主群落结构、遗传物质的水平移动方面作用巨大，同时也被证明在元素生物地球化学循环中具有非常重要的地位。尽管噬菌体的重要性越来越引起研究者的关注，但遗憾的是目前对于噬菌体基因多样性的研究还存在很大的局限性，发现并验证一种适合于研究噬菌体基因多样性的分子标记基因是环境病毒生态学研究的热点之一。介绍了一种新的分子标记基因-噬菌体辅助代谢磷酸盐调节基因phoH，并综述了近年来利用该基因揭示海洋海水、稻田田面水和沙漠石下生物中噬菌体基因多样性的研究进展。结果表明，噬菌体phoH基因分布与其生存环境关系密切，按获取环境不同phoH基因被划分为多个类群。最后对噬菌体phoH基因未来研究方向给予展望。

关键词: 噬菌体, phoH基因, 多样性, 海洋, 稻田

Abstract: Bacteriophages（phages）are the simplest biological entities，which play important roles not only in the regulation of their host communities and horizontal transfer of genetic materials，but also in the element biogeochemical cycles. Although the importance of phages is increasingly being paid attentions by researchers，however there are still great limitations on the study of phage gene diversity until now. Therefore，the work of finding and verification of a suitable molecular marker gene for studying the genetic diversity of phage in natural environments is one of the hotspots of virus ecology. In this paper，a new molecular biomarker gene of phage auxiliary metabolic gene of phoH was introduced，and the recent advances in using this gene to reveal the phage genetic diversity in marine waters，paddy floodwaters and desert hypoliths are reviewed. Results showed that the distribution of phage phoH gene was closely related to its living environments，and phoH clones were divided into several groups according their obtained environments. In the end of the paper，the future research directions of phage phoH gene are also proposed.

Key words: bacteriophage, phoH gene, diversity, marine, paddy field

李想, 孙岩, 王新珍, 刘俊杰, 王光华. 一种新的噬菌体基因多样性分子标记基因phoH研究进展[J]. 生物技术通报, 2017, 33(10): 40-45.

LI Xiang, SUN Yan, WANG Xin-zhen, LIU Jun-jie, WANG Guang-hua. Research Progress of New Biomarker Gene of phoH for Bacteriophage Genetic Diversity[J]. Biotechnology Bulletin, 2017, 33(10): 40-45.

参考文献

[1] Fuhrman JA. Marine viruses and their biogeochemical and ecological effects[J]. Nature, 1999, 399(6736)：541.
[2] Sabehi G, Shaulov L, Silver DH, et al. A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans[J]. Proc Natl Academy of Sciences, 2012, 109(6)：2037-2042.
[3] Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes：the unseen majority[J]. Proc Natl Academy of Sciences, 1998, 95(12)：6578-6583.
[4] Breitbart M, Rohwer F. Here a virus, there a virus, everywhere the same virus?[J]. Trends in Microbiology, 2005, 13(6)：278-284.
[5] Suttle CA. Viruses in the sea[J]. Nature, 2005, 437(7057)：356.
[6] Weinbauer MG. Ecology of prokaryotic viruses[J]. FEMS MicroBiol Rev, 2004, 28(2)：127-181.
[7] Suttle CA. Marine viruses-major players in the global ecosystem[J]. Nature Reviews. Microbiology, 2007, 5(10)：801.
[8] Brüssow H. Bacteriophage-host interaction：from splendid isolation into a messy reality[J]. Current Opinion in Microbiology, 2013, 16(4)：500-506.
[9] Hambly E, Suttle CA. The viriosphere, diversity, and genetic exchange within phage communities[J]. Current Opinion in Microbiology, 2005, 8(4)：444-450.
[10] Mann NH. The third age of phage[J]. PLoS Biology, 2005, 3(5)：e182.
[11] Ward DM, Weller R, Bateson MM. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community[J]. Nature, 1990, 345(6270)：63-65.
[12] Edwards RA, Rohwer F. Opinion：viral metagenomics[J]. Nature Reviews. Microbiology, 2005, 3(6)：504.
[13] Rohwer F, Edwards R. The Phage Proteomic Tree：a genome-based taxonomy for phage[J]. Journal of Bacteriology, 2002, 184(16)：4529-4535.
[14] Fuller NJ, Wilson WH, Joint IR, et al. Occurrence of a sequence in marine cyanophages similar to that of T4 g20 and its application to PCR-based detection and quantification techniques[J]. Appl Environ Microbiol, 1998, 64(6)：2051-2060.
[15] Jameson E, Mann NH, Joint I, et al. The diversity of cyanomyovirus populations along a North-South Atlantic Ocean transect[J]. The ISME Journal, 2011, 5(11)：1713.
[16] Sullivan MB, Coleman ML, Quinlivan V, et al. Portal protein diversity and phage ecology[J]. Environ Microbiol, 2008, 10(10)：2810-2823.
[17] Filée J, Tétart F, Suttle CA, et al. Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere[J]. Proc Natl Acad Sci USA, 2005, 102(35)：12471-12476.
[18] Jia Z, Ishihara R, Nakajima Y, et al. Molecular characterization of T4-type bacteriophages in a rice field[J]. Environ Microbiol, 2007, 9(4)：1091-1096.
[19] Breitbart M, Miyake JH, Rohwer F. Global distribution of nearly identical phage-encoded DNA sequences[J]. FEMS Microbiology Letters, 2004, 236(2)：249-256.
[20] Chen F, Wang K, Huang S, et al. Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences[J]. Environ Microbiol, 2009, 11(11)：2884-2892.
[21] Mann NH, Cook A, Millard A, et al. Marine ecosystems：bacterial photosynthesis genes in a virus[J]. Nature, 2003, 424(6950)：741-741.
[22] Sullivan MB, Lindell D, Lee JA, et al. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts[J]. PLoS Biology, 2006, 4(8)：e234.
[23] Williamson SJ, Rusch DB, Yooseph S, et al. The Sorcerer II Global Ocean Sampling Expedition：metagenomic characterization of viruses within aquatic microbial samples[J]. PLoS One, 2008, 3(1)：e1456.
[24] Thompson L R, Zeng Q, Kelly L, et al. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism[J]. Proc Natl Academy of Sciences, 2011, 108(39)：E757-E764.
[25] Goldsmith DB, Crosti G, Dwivedi B, et al. Development of phoH as a novel signature gene for assessing marine phage diversity[J]. Appl Environ Microbiol, 2011, 77(21)：7730-7739.
[26] Dwivedi B, Xue BJ, Lundin D, et al. A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes[J]. BMC Evolutionary Biology, 2013, 13：33.
[27] 王光华, 刘俊杰. 自然环境中 T4 型噬菌体 g23 基因多样性研究进展[J]. 微生物学报, 2011, 51(6)：732-739.
[28] 荆瑞勇, 王光华. 不同自然环境下噬藻体 g20 基因多样性研究进展[J]. 微生物学报, 2013, 53(11)：1149-1157.
[29] Millard A, Clokie MRJ, Shub DA, et al. Genetic organization of the psbAD region in phages infecting marine Synechococcus strains[J]. Proc Natl Acad Sci USA, 2004, 101(30)：11007-11012.
[30] Bryan MJ, Burroughs NJ, Spence EM, et al. Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer[J]. PLoS One, 2008, 3(4)：e2048.
[31] Lindell D, Jaffe JD, Johnson ZI, et al. Photosynthesis genes in marine viruses yield proteins during host infection[J]. Nature, 2005, 438(7064)：86.
[32] Lindell D, Sullivan MB, Johnson ZI, et al. Transfer of photosynthesis genes to and from Prochlorococcus viruses[J]. Proc Natl Acad Sci USA, 2004, 101(30)：11013-11018.
[33] Hsieh YJ, Wanner BL. Global regulation by the seven-component Pi signaling system[J]. Current Opinion in Microbiology, 2010, 13(2)：198-203.
[34] Adriaenssens EM, Cowan DA. Using signature genes as tools to assess environmental viral ecology and diversity[J]. Appl Environ Microbiol, 2014, 80(15)：4470-4480.
[35] Goldsmith DB, Parsons RJ, Beyene D, et al. Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea[J]. Peer J, 2015, 3：e997.
[36] Wang X, Liu J, Yu Z, et al. Novel groups and unique distribution of phage phoH genes in paddy waters in northeast China[J]. Scientific Reports, 2016, 6：38428.
[37] Jing R, Liu J, Yu Z, et al. Phylogenetic distribution of the capsid assembly protein gene(g20)of cyanophages in paddy floodwaters in Northeast China[J]. PLoS One, 2014, 9(2)：e88634.
[38] Adriaenssens EM, Van Zyl L, De Maayer P, et al. Metagenomic analysis of the viral community in Namib Desert hypoliths[J]. Environ Microbiol, 2015, 17(2)：480-495.
[39] Twort FW. An investigation on the nature of ultramicroscopic viruses[J]. The Lancet, 1915, 186(4814)：1241-1243.
[40] Zhong Y, Chen F, Wilhelm SW, et al. Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g20[J]. Appl Environ Microbiol, 2002, 68(4)：1576-1584.
[41] Zeidner G, Preston CM, Delong EF, et al. Molecular diversity among marine picophytoplankton as revealed by psbA analyses[J].Environ Microbiol，2003，5(3)：212-216.

一种新的噬菌体基因多样性分子标记基因phoH研究进展

Research Progress of New Biomarker Gene of phoH for Bacteriophage Genetic Diversity

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