Progress on phage genomics of Pseudomonas spp.
Received date: 2020-04-26
Revised date: 2020-07-10
Online published: 2020-07-29
Supported by
Supported by the National Natural Science Foundation of China Nos(31860147);Supported by the National Natural Science Foundation of China Nos(31700324)
Pseudomonas spp. are one of the most important ecological flora on the earth, widely distributed in freshwater, soil and other ecological environments. Pseudomonas phages are viruses hosted by Pseudomonas spp., which not only affect the survival and evolution of the hosts, but also play important roles in biomass circulation and energy flow. With the rapid development of genome sequencing technologies, the whole genome sequences of many Pseudomonas phages have been completed. As of July 2020, 247 Pseudomonas phage genomes were deposited in GenBank, accounting for 2.45% of the total 10,069 viral genomes. The genome sizes of Pseudomonas bacteriophages and the genetic contents are different, and the similarity between genomes is low, so the study on Pseudomonas bacteriophage genomes is relatively less. In this review, we summarize the characteristics, genetic diversity, and functional genes of Pseudomonas bacteriophages genomes in order to provide a reference for understanding the antagonistic coevolution of bacteria and phages and the genetic evolution of phages.
Key words： Pseudomonas phage; genome; genetic diversity; functional gene
Zhiwei Xu, Yunlin Wei, Xiuling Ji . Progress on phage genomics of Pseudomonas spp.[J]. Hereditas(Beijing), 2020 , 42(8) : 752 -759 . DOI: 10.16288/j.yczz.19-272
| [1] | Silby MW, Winstanley C, Godfrey SA, Levy SB, Jackson RW . Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev, 2011,35(4):652-680. |
| [2] | Czajkowski R, Ozymko Z, de Jager V, Siwinska J, Smolarska A, Ossowicki A, Narajczyk M, Lojkowska E. Genomic, proteomic and morphological characterization of two novel broad host lytic bacteriophages ΦPD10.3 and ΦPD23.1 infecting pectinolytic Pectobacterium spp. and Dickeya spp. PLoS ONE, 2015,10(3):1-23. |
| [3] | Olszak T, Latka A, Roszniowski B, Valvano MA, Drulis- Kawa Z . Phage life cycles behind bacterial biodiversity. Curr Med Chem, 2017,24(36):3987-4001. |
| [4] | Alseth EO, Pursey E, Luján AM, McLeod I, Rollie C, Westra ER. Bacterial biodiversity drives the evolution of CRISPR-based phage resistance. Nature, 2019,574(7779):549-552. |
| [5] | Li TM, Du B . CRISPR-Cas system and coevolution of bacteria and phages. Hereditas(Beijing), 2011,33(3):213-218. |
| [5] | 李铁民, 杜波 . CRISPR-Cas系统与细菌和噬菌体的共进化. 遗传, 2011,33(3):213-218. |
| [6] | Ceyssens PJ, Hertveldt K, Ackermann HW, Noben JP, Demeke M, Volckaert G, Lavigne R . The intron-containing genome of the lytic Pseudomonas phage LUZ24 resembles the temperate phage PaP3. Virology, 2008,377(2):233-238. |
| [7] | Ceyssens PJ, Mesyanzhinov V, Sykilinda N, Briers Y, Roucourt B, Lavigne R, Robben J, Domashin A, Miroshnikov K, Volckaert G, Hertveldt K . The genome and structural proteome of YuA, a new Pseudomonas aeruginosa phage resembling M6. Journal of bacteriology, 2007,190(4):1429-1435. |
| [8] | Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA, Namburi S, Pajcini KV, Popovich MG, Schleicher DT, Simanek BZ, Smith AL, Zdanowicz GM, Kumar V, Peebles CL, Jacobs WR Jr, Lawrence JG, Hendrix RW . Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet, 2006,2(6):e92. |
| [9] | Amgarten D, Martins LF, Lombardi KC, Antunes LP, de Souza APS, Nicastro GG, Kitajima EW, Quaggio RB, Upton C, Setubal JC, da Silva AM. Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC Genomics, 2017,18(1):346-363. |
| [10] | Wang PW, Chu LD, Guttman DS . Complete sequence and evolutionary genomic analysis of the pseudomonas aeruginosa transposable bacteriophage D3112. J Bacteriol, 2004,186(2):400-410. |
| [11] | Ha AD, Denver DR . Comparative genomic analysis of 130 bacteriophages Infecting bacteria in the genus Pseudomonas. Front Microbiol, 2018,9:1456. |
| [12] | Wittmann J, Dreiseikelmann B, Rohde M, Meier-Kolthoff JP, Bunk B, Rohde C . First genome sequences of achromobacter phages reveal new members of the N4 family. Virol J, 2014,11(1):2-15. |
| [13] | Sillankorva S, Kluskens LD, Lingohr EJ, Kropinski AM, Neubauer P, Azeredo J . Complete genome sequence of the lytic Pseudomonas fluorescens phage ?IBB-PF7A. Virol J, 2011,8:142. |
| [14] | Lu SG, Le S, Tan YL, Zhu JM, Li M, Rao XC, Zou LY, Li S, Wang J, Jin XL, Huang GT, Zhang L, Zhao X, Hu FQ . Genomic and proteomic analyses of the terminally redundant genome of the Pseudomonas aeruginosa phage PaP1: establishment of genus PaP1-like phages. PLoS One, 2013,8(5):e62933. |
| [15] | Kwan T, Liu J, Dubow M, Gros P, Pelletier J . Comparative genomic analysis of 18 Pseudomonas aeruginosa bacteriophages. J Bacteriol, 2006,188(3):1184-1187. |
| [16] | Watkins SC, Sible E, Putonti C . Pseudomonas PB1-Like phages: whole genomes from metagenomes offer insight into an abundant group of bacteriophages. Viruses, 2018,10(1):331-344. |
| [17] | Li M, Chen XR, Ma YS, Li ZB, Zhao QC . Complete genome sequence of PFP1, a novel T7-like Pseudomonas fluorescens bacteriophage. Arch Virol, 2018,163(1):3423-3426. |
| [18] | Lu SG, Le S, Tan YL, Li M, Liu C, Zhang KB, Huang JJ, Chen HM, Rao XC, Zhu JM, Zou LY, Ni QS, Li S, Wang J, Jin XL, Hu QW, Yao XY, Zhao X, Zhang L, Huang GT, Hu FQ . Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity. BMC Genomics, 2014,15(1):803-815. |
| [19] | Aparicio T, de Lorenzo V, Martínez-García E . Improved thermotolerance of genome-reduced Pseudomonas putida EM42 enables effective functioning of the PL/cI857 system. Biotechnol J, 2019,14(1):1800483. |
| [20] | Zhang FJ, Huang KC, Yang XJ, Sun L, You JJ, Pan XW, Cui XL, Yang HJ . Characterization of a novel lytic podovirus O4 of Pseudomonas aeruginosa. Arch Virol, 2018,163(1):2377-2383. |
| [21] | Carson S, Bruff E, DeFoor W, Dums J, Groth A, Hatfield T, Iyer A, Joshi K, McAdams S, Miles D, Miller D, Oufkir A, Raynor B, Riley S, Roland S, Rozier H, Talley S, Miller ES. Genome sequences of six paenibacillus larvae Siphoviridae Phages. Genome Announc, 2015,3(3):101-115. |
| [22] | Tang CF, Deng CJ, Zhang Y, Xiao C, Wang J, Rao XC, Hu FQ, Lu SG . Characterization and genomic analyses of Pseudomonas aeruginosa podovirus TC6: establishment of genus Pa11virus. Front Microbiol, 2018,9:2561. |
| [23] | Xu B, GAO J, GUO XK, Qin JH . Study on the biological and genomic characteristics of Pseudomonas aeruginosa phage D204. J Shanghai Jiaotong Univ, 2016,36(1):1-5. |
| [23] | 徐彬, 高晶, 郭晓奎, 秦金红 . 铜绿假单胞菌噬菌体D204的生物学特性和基因组学研究. 上海交通大学学报, 2016,36(1):1-5. |
| [24] | Cui XL . Screening of genes related to pseudomonas aeruginosa response to multiple strains of phage infection and functional annotation of phage C11 genome [Dissertation]. Sc i Tech of Tianjin Univ, 2016. |
| [24] | 崔晓莉 . 铜绿假单胞菌应答多株噬菌体感染相关基因的筛选及噬菌体C11基因组的功能注释[学位论文]. 天津科技大学, 2016. |
| [25] | Sharma S, Chatterjee S, Datta S, Prasad R, Dubey D, Prasad RK, Vairale MG . Bacteriophages and its applications: an overview. Folia Microbiol (Praha), 2017,62(1):17-55. |
| [26] | Cao HL, Lai Y, Bougouffa S, Xu ZL, Yan AX . Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853. BMC Genomics, 2017,18(1):459-475. |
| [27] | De Smet J, Hendrix H, Blasdel BG, Danis-Wlodarczyk K, Lavigne R . Pseudomonas predators: understanding and exploiting phage-host interactions. Nat Rev Microbiol, 2017,15(9):517-530. |
| [28] | Liang CJ, Meng FM, Ai YC . CRISPR/Cas systems in genome engineering of bacteriophages. Hereditas(Beijing), 2018,40(5):378-389. |
| [28] | 梁彩娇, 孟繁梅, 艾云灿 . 基于CRISPR/Cas系统的噬菌体基因组编辑. 遗传, 2018,40(5):378-389. |
| [29] | Pawluk A, Bondy-Denomy J, Cheung VH, Maxwell KL, Davidson AR . A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. mBio, 2014,5(2):e00896. |
| [30] | Habusha M, Tzipilevich E, Fiyaksel O, Ben-Yehuda S . A mutant bacteriophage evolved to infect resistant bacteria gained a broader host range. Mol Microbiol, 2019,111(6):1463-1475. |
| [31] | Holguín AV, Cárdenas P, Prada-Pe?aranda C, Rabelo Leite L, Buitrago C, Clavijo V, Oliveira G, Leekitcharoenphon P, M?ller Aarestrup F, Vives MJ . Host resistance, genomics and population dynamics in a salmonella Eenteritidis and phage system. Viruses, 2019,11(2):188. |
| [32] | Li M, Cheng FY, Gong LY, Xiang H . Systematic discovery of novel prokaryotic defense systems: progress and prospects. Hereditas(Beijing), 2018,40(4):259-265. |
| [32] | 李明, 程飞跃, 龚路遥, 向华 . 微生物新型防御系统的系统性发现与展望. 遗传, 2018,40(4):259-265. |
| [33] | Gao SH, Yu HY, Wu SY, Wang S, Geng JN, Luo YF, Hu SN . Advances of sequencing and assembling technologies for complex genomes. Hereditas(Beijing), 2018,40(11):944-963. |
| [33] | 高胜寒, 禹海英, 吴双阳, 王森, 耿佳宁, 骆迎峰, 胡松年 . 复杂基因组测序技术研究进展. 遗传, 2018,40(11):944-963. |
| [34] | Sternberg SH, Richter H, Charpentier E, Qimron U . Adaptation in CRISPR-Cas systems. Mol Cell, 2016,61(6):797-808. |
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