病毒辅助代谢基因的研究进展
作者:
基金项目:

国家自然科学基金(32160294,31860147)


Advances in viral auxiliary metabolic genes
Author:
  • 摘要
  • | |
  • 访问统计
  • |
  • 参考文献 [42]
  • |
  • 相似文献 [20]
  • | | |
  • 文章评论
    摘要:

    病毒通过影响微生物的营养循环、生物多样性和遗传信息传递等,在全球海洋的生物地球化学循环中发挥关键作用。病毒还可以控制微生物的群落组成、关键代谢过程等,这些依赖于病毒基因组上的辅助代谢基因(auxiliary metabolic genes,AMGs)。AMGs在病毒感染宿主的过程中表达并参与调控宿主的代谢过程。病毒基因组中的AMGs包括中央碳代谢、氮代谢、磷和硫循环、核苷酸代谢以及与氧化应激反应相关的基因。AMGs有利于子代病毒更高效地组装和释放,对于病毒种群的繁衍具有重要意义,同时对病毒-宿主相互作用机制的研究产生重要影响。本文针对病毒辅助代谢基因的起源、类别及其重要的生态作用进行简要综述,以期为进一步阐明病毒在不同生态系统中的功能提供依据。

    Abstract:

    Viruses play a key role in the biogeochemical cycle of global ocean by influencing the nutrient cycling, biodiversity, and genetic information transfer of microorganisms. Virus-encoded auxiliary metabolic genes (AMGs) can modulate the community composition and key metabolic pathways of microorganisms. Through the expression of AMGs, viruses reprogram the host metabolic pathways. Virus-encoded AMGs are known to include the genes associated with central carbon metabolism, nitrogen, phosphorus, and sulfur cycling, nucleotide metabolism, and oxidative stress response. AMGs are beneficial to the assembly and release of progeny virus, which is of great significance for virus reproduction and the research on virus-host interaction mechanism. In this paper, we briefly reviewed the origin, classification, and ecological roles of virus-encoded AMGs, aiming to provide reference for illuminating the roles of viruses in different ecosystems.

    参考文献
    [1] Pascelli C, Laffy PW, Botté E, Kupresanin M, Rattei T, Lurgi M, Ravasi T, Webster NS. Viral ecogenomics across the Porifera. Microbiome, 2020, 8(1):144.
    [2] Li Z, Pan D, Wei G, Pi W, Zhang C, Wang JH, Peng Y, Zhang L, Wang Y, Hubert CRJ, Dong X. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. The ISME Journal, 2021, 15(8):2366-2378.
    [3] Cobián Güemes AG, Youle M, Cantú VA, Felts B, Nulton J, Rohwer F. Viruses as winners in the game of life. Annual Review of Virology, 2016, 3(1):197-214.
    [4] Suttle CA. Marine viruses-major players in the global ecosystem. Nature Reviews Microbiology, 2007, 5(10):801-812.
    [5] Gao EB, Huang YH, Ning DG. Metabolic genes within cyanophage genomes:implications for diversity and evolution. Genes, 2016, 7(10):80.
    [6] Coutinho FH, Gregoracci GB, Walter JM, Thompson CC, Thompson FL. Metagenomics sheds light on the ecology of marine microbes and their viruses. Trends in Microbiology, 2018, 26(11):955-965.
    [7] Thompson LR, Zeng QL, Kelly L, Huang KH, Singer AU, Stubbe J, Chisholm SW. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. PNAS, 2011, 108(39):E757-E764.
    [8] Huang XY, Jiao NZ, Zhang R. The genomic content and context of auxiliary metabolic genes in roseophages. Environmental Microbiology, 2021, 23(7):3743-3757.
    [9] 高恶斌,宁德刚.噬藻体辅助代谢基因(AMGs)研究进展.微生物学通报, 2014, 41(8):1667-1674. Gao EB, Ning DG. Advances in researches on cyanophage auxiliary metabolic genes. Microbiology China, 2014, 41(8):1667-1674.(in Chinese)
    [10] Warwick-Dugdale J, Buchholz HH, Allen MJ, Temperton B. Host-hijacking and planktonic piracy:how phages command the microbial high seas. Virology Journal, 2019, 16(1):15.
    [11] Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, Singleton CM, Solden LM, Naas AE, Boyd JA, Hodgkins SB, Wilson RM, Trubl G, Li C, Frolking S, Pope PB, Wrighton KC, Crill PM, Chanton JP, Saleska SR, Tyson GW, Rich VI, Sullivan MB. Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology, 2018, 3(8):870-880.
    [12] Focardi A, Ostrowski M, Goossen K, Brown MV, Paulsen I. Investigating the diversity of marine bacteriophage in contrasting water masses associated with the east Australian Current (EAC) system. Viruses, 2020, 12(3):317.
    [13] Crummett LT, Puxty RJ, Weihe C, Marston MF, Martiny JBH. The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses. Virology, 2016, 499:219-229.
    [14] Weynberg KD, Laffy PW, Wood-Charlson EM, Turaev D, Rattei T, Webster NS, Van Oppen MJH. Coral-associated viral communities show high levels of diversity and host auxiliary functions. PeerJ, 2017, 5:e4054.
    [15] Harrison E, Brockhurst MA. Ecological and evolutionary benefits of temperate phage:what does or doesn't kill you makes you stronger. BioEssays, 2017, 39(12):1700112.
    [16] Laanto E, Hoikkala V, Ravantti J, Sundberg LR. Long-term genomic coevolution of host-parasite interaction in the natural environment. Nature Communications, 2017, 8:111.
    [17] Scanlan PD. Bacteria-bacteriophage coevolution in the human gut:implications for microbial diversity and functionality. Trends in Microbiology, 2017, 25(8):614-623.
    [18] Jiang T, Guo C, Wang M, Wang MW, You SY, Liu YD, Zhang XR, Liu HB, Jiang Y, Shao HB, Liang YT, McMinn A. Isolation and complete genome sequence of a novel cyanophage, S-B05, infecting an estuarine Synechococcus strain:insights into environmental adaptation. Archives of Virology, 2020, 165(6):1397-1407.
    [19] Gasper R, Schwach J, Hartmann J, Holtkamp A, Wiethaus J, Riedel N, Hofmann E, Frankenberg-Dinkel N. Distinct features of cyanophage-encoded t-type phycobiliprotein lyase φcpet:the role of auxiliary metabolic genes. The Journal of Biological Chemistry, 2017, 292(8):3089-3098.
    [20] 高恶斌,董一鸣.噬藻体遗传多样性及其分子生态学研究现状与展望.生态科学, 2016, 35(2):166-173. Gao EB, Dong YM. Advances in researches on cyanophage genetic diversity and molecular ecology. Ecological Science, 2016, 35(2):166-173.(in Chinese)
    [21] Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Shedding new light on viral photosynthesis. Photosynthesis Research, 2015, 126(1):71-97.
    [22] Hurwitz BL, U'Ren JM. Viral metabolic reprogramming in marine ecosystems. Current Opinion in Microbiology, 2016, 31:161-168.
    [23] Tsiola A, Michoud G, Fodelianakis S, Karakassis I, Kotoulas G, Pavlidou A, Pavloudi C, Pitta P, Simboura N, Daffonchio D, Tsapakis M. Viral metagenomic content reflects seawater ecological quality in the coastal zone. Viruses, 2020, 12(8):806.
    [24] Coutinho FH, Cabello-Yeves PJ, Gonzalez-Serrano R, Rosselli R, López-Pérez M, Zemskaya TI, Zakharenko AS, Ivanov VG, Rodriguez-Valera F. New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal. Microbiome, 2020, 8(1):163.
    [25] Anderson CL, Sullivan MB, Fernando SC. Dietary energy drives the dynamic response of bovine rumen viral communities. Microbiome, 2017, 5(1):155.
    [2cs. eLife, 2014, 3:e03125.
    [42] Kelly L, Ding H, Huang KH, Osburne MS, Chisholm SW. Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent. The ISME Journal, 2013, 7(9):1827-1841.
    [43] Zheng XW, Liu W, Dai X, Zhu YX, Wang JF, Zhu YQ, Zheng HJ, Huang Y, Dong ZY, Du WB, Zhao FQ, Huang L. Extraordinary diversity of viruses in deep-sea sediments as revealed by metagenomics without prior virion separation. Environmental Microbiology, 2021, 23(2):728-743.
    [44] Behrenfeld MJ, O'Malley RT, Siegel DA, McClain CR, Sarmiento JL, Feldman GC, Milligan AJ, Falkowski PG, Letelier RM, Boss ES. Climate-driven trends in contemporary ocean productivity. Nature, 2006, 444(7120):752-755.
    [45] Wegner CE, Gaspar M, Geesink P, Herrmann M, Marz M, Küsel K. Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of the elements nitrogen, sulfur, and carbon. Applied and Environmental Microbiology, 2019, 85(5):e02346-e02318.
    [46] Anantharaman K, Duhaime MB, Breier JA, Wendt KA, Toner BM, Dick GJ. Sulfur oxidation genes in diverse deep-sea viruses. Science, 2014, 344(6185):757-760.
    [47] Kieft K, Zhou Z, Anderson RE, Buchan A, Campbell BJ, Hallam SJ, Hess M, Sullivan MB, Walsh DA, Roux S, Anantharaman K. Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature Communications, 2021, 12:3503.
    [48] Hurwitz BL, Brum JR, Sullivan MB. Depth-stratified functional and taxonomic niche specialization in the'core'and'flexible'Pacific Ocean virome. The ISME Journal, 2015, 9(2):472-484.
    [49] Wasmund K, Mußmann M, Loy A. The life sulfuric:microbial ecology of sulfur cycling in mari嵮腥縠s来獤i祭塥豮t彳琮 鬼乩朾E啮其i孲祯獮m繥幮浴驡卬渠坍icrobiology造佒奥桰息割歴硳稼/坩嘾縬嬠串帰由男爬嬠9(4):323-344.
    [50] Yu ZC, Chen XL, Shen QT, Zhao DL, Tang BL, Su HN, Wu ZY, Qin QL, Xie BB, Zhang XY, Yu Y, Zhou BC, Chen B, Zhang YZ. Filamentous phages prevalent in Pseudoalteromonas spp. confer properties advantageous to host survival in Arctic Sea ice. The ISME Journal, 2015, 9(4):871-881.
    [51] Brum JR, Hurwitz BL, Schofield O, Ducklow HW, Sullivan MB. Seasonal time bombs:dominant temperate viruses affect Southern Ocean microbial dynamics. The ISME Journal, 2016, 10(2):437-449.
    [52] Chen Y, Golding I, Sawai S, Guo L, Cox EC. Population fitness and the regulation of Escherichia coli genes by bacterial viruses. PLoS Biology, 2005, 3(7):e229.
    [53] Mills DC, Jervis AJ, Abouelhadid S, Yates LE, Cuccui J, Linton D, Wren BW. Functional analysis of N-linking oligosaccharyl transferase enzymes encoded by deep-sea vent proteobacteria. Glycobiology, 2015, 26(4):398-409.
    [54] Mara P, Vik D, Pachiadaki MG, Suter EA, Poulos B, Taylor GT, Sullivan MB, Edgcomb VP. Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. The ISME Journal, 2020, 14(12):3079-3092.MB. Genome-resolved viral ecology in a marine oxygen minimum zone. Environmental Microbiology, 2021, 23(6):2858-2874.
    [39] Diamond S, Andeer PF, Li Z, Crits-Christoph A, Burstein D, Anantharaman K, Lane KR, Thomas BC, Pan C, Northen TR, Banfield JF. Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nature Microbiology, 2019, 4(8):1356-1367.
    [40] Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, Krastins B, Chase M, Sarracino D, Osburne MS, Henn MR, Chisholm SW. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environmental Microbiology, 2010, 12(11):3035-3056.
    [41] Roux S, Hawley AK, Torres Beltran M, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell-and meta-genomi
    引证文献
    网友评论
    网友评论
    分享到微博
    发 布
引用本文

于航,徐志伟,魏云林,季秀玲. 病毒辅助代谢基因的研究进展[J]. 微生物学报, 2022, 62(8): 2879-2892

复制
分享
文章指标
  • 点击次数:1399
  • 下载次数: 2471
  • HTML阅读次数: 2062
  • 引用次数: 0
历史
  • 收稿日期:2021-11-24
  • 最后修改日期:2022-02-17
  • 在线发布日期: 2022-08-16
文章二维码