Please wait a minute...

中国生物工程杂志

China Biotechnology
China Biotechnology  2020, Vol. 40 Issue (1-2): 140-145    DOI: 10.13523/j.cb.1905022
Orginal Article     
Advances in Bacteria-Phage Antagonistic Coevolution
CUI Zi-hong,JI Xiu-ling()
Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
Download: HTML   PDF(385KB) HTML
Export: BibTeX | EndNote (RIS)      

Abstract  

Coevolution is ubiquitous in nature. The natural enemies of bacteria and bacteria are a constant battle.Bacteria-phage system is a model material for studying coevolution. Bacteriophages, currently, there are two recognized models for the mechanism of bacteria-phage antagonistic coevolution: GFG model and MA model;corresponding to two models: ARD model and FSD model.The antagonistic coevolutionary kinetic model of bacteriophage was determined by time-shift assays. Long-tailed phages are the largest family of tailed phages. At present, the studies on bacteria-phage system coevolution mainly focus on the short tail and myotail phage and their hosts, while the bacteria-long tail phage coevolution has not been reported.



Key wordsAntagonistic coevolution      Defense mechanism      Coevolutionary dynamics     
Received: 15 May 2019      Published: 27 March 2020
ZTFLH:  Q815  
Corresponding Authors: Xiu-ling JI     E-mail: jixiuling1023@126.com
Cite this article:

CUI Zi-hong,JI Xiu-ling. Advances in Bacteria-Phage Antagonistic Coevolution. China Biotechnology, 2020, 40(1-2): 140-145.

URL:

https://manu60.magtech.com.cn/biotech/10.13523/j.cb.1905022     OR     https://manu60.magtech.com.cn/biotech/Y2020/V40/I1-2/140

[1]   Dennehy J J . What can phages tell us about host-pathogen coevolution. International Journal of Evolutionary Biology, 2012,2012(3):1-12.
[2]   Dong C, Hao G F, Hua H L , et al. Anti-CRISPRdb: a comprehensive online resource for anti-CRISPR proteins. Nucleic Acids Res, 2018,46(D1):D393-D398.
[3]   Gómez P, Buckling A . Bacteria-phage antagonistic coevolution in soil. Science, 2011,332(6025):106-109.
[4]   Zhang Q G, Buckling A . Antagonistic coevolution limits population persistence of a virus in a thermally deteriorating environment. Ecol Lett, 2011,14(3):282-288.
[5]   Thompson J N . The role of coevolution. Science, 2012,335(6067):410-411
[6]   Woolhouse M, Webster J, Domingo E , et al. Biological and biomedical implications of the coevolution of pathogens and their hosts. Nat Genet, 2002,32(4):569-577.
[7]   Scanlan P D . Bacteria-bacteriophage coevolution in the human gut: implications for microbial diversity and functionality. Trends in Microbiology, 2017,25(8):614-623.
[8]   Koskella1 B, Brockhurst M . Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev, 2014,38(5):916-931.
[9]   Gomez P, Ashby B, Buckling A . Population mixing promotes arm race host-parasite coevolution. Pro R Soc B, 2014,282(1798):20142297.
[10]   Gómez P, Paterson S, Meester L D , et al. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community. Nature Communications, 2016,7:12453.
[11]   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.
[11]   Li T M, Du P . CRISPR-Cas system and coevolution of bacteria and phages. Hereditas, 2011,33(3):213-218.
[12]   Shabbir M A, Hao H, Shabbir M Z , et al. Bacteria vs. bacteriophages: parallel evolution of immune arsenals. Front Microbiol, 2016,7:1292.
[13]   Makarova K S, Wolf Y I, Alkhnbashi O S , et al. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol, 2015,13(11):722-736.
[14]   Koonin E V, Makarova K S, Zhang F . Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol, 2017,37:67-78.
[15]   Common J, Morley D, Westra E R , et al. CRISPR-Cas immunity leads to a coevolutionary arms race between Streptococcus thermophilus and lytic phage374. Biological Sciences, 2019,74(1772):20180098.
[16]   Chopin M C, Chopin A, Bidnenko E . Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol, 2005,8(4):473-479.
[17]   Ofir G, Melamed S, Sberro H , et al. DISARM is a widespread bacterial defence system with broad anti-phage activities. Nature Microbiology, 2017,3(1):90-98.
[18]   张庆, 商延, 朱见深 . 噬菌体与宿主细菌的攻防机制. 山东农业科学, 2018,50(7):48-54.
[18]   Zhang Q, Shang Y, Zhu J S . Defense and anti-defense mechanisms of bacteriophages and host bacteria. Shandong Agricultural Sciences, 2018,50(7):48-54.
[19]   Sun X, Gohler A, Heller K , et al. The ltp gene of temperate Streptococcus thermophilus phage TP-J34 confers superinfection exclusion to Streptococcus thermophilus and Lactococcus lactis. Virology, 2006,350(1):146-157.
[20]   Doermann A H . Lysis inhibition with Escherichia coli bacteriophages. J Bacteriol, 1948,55(2):57-75.
[21]   Bondy-Denomy J, Pawluk A, Maxwell K L , et al. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature, 2012,493(7432):429-432.
[22]   Smargon A A, Cox D B T, Pyzocha N K , et al. Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol Cell, 2017,65(4):618-630.
[23]   Pawluk A, Bondy-Denomy J, Cheung V H , et al. A new group of phage anti[1]-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. MBio, 2014,5(2): e00896.
[24]   Rauch B J, Silvis M R, Hultquist J F , et al. Inhibition of CRISPR-Cas9 with bacteriophage proteins. Cell, 2016,168(1-2):150-158.
[25]   Fineran P C, Blower T R, Foulds I J , et al. The phage abortive infection system ToxIN,functions as a protein-RNA toxin-antitoxin pair. Proc Natl Acad Sci USA, 2009,106(3):894-899.
[26]   Molineux I J . Host-parasite interactions: recent developments in the genetics of abortive phage infections. New Biol, 1991,3(3):230-236.
[27]   Snyder L . Phage‐exclusion enzymes: a bonanza of biochemical and cell biology reagents. Molecular Microbiology, 1995,15(3):415-420.
[28]   Slavcev R A, Hayes S . Stationary phase-like properties of the bacteriophage lambda Rex exclusion phenotype. Molecular Genetics & Genomics, 2003,269(1):40-48.
[29]   Snyder L . Phage-exclusion enzymes: a bonanza of biochemical and cell biology reagents. Molecular Microbiology, 2010,15(3):415-420.
[30]   Bergsland K J, Kao C, Yu Y T , et al. A site in the T4 bacteriophage major head protein gene that can promote the inhibition of all translation in Escherichia coli. Journal of Molecular Biology, 1990,213(3):477-494.
[31]   Yu Y T, Snyder L . Translation elongation factor Tu cleaved by a phage-exclusion system. Proceedings of the National Academy of Sciences of the United States of America, 1994,91(2):802-806.
[32]   Lacks S A, Greenberg B . A deoxyribonuclease of Diplococcus pneumoniae specific for methylated DNA. Journal of Biological Chemistry, 1975,250(11):4060-4066.
[33]   Zabeau M, Friedman S, Montagu M V , et al. The ral gene of phage lambda. I. Identification of a non-essential gene that modulates restriction and modification in E. coli. Mol Gen Genet, 1980,179(1):63-73.
[34]   King G, Murray N E . Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12. Molecular Microbiology, 1995,16(4):769-777.
[35]   Moldovan R, Chapman-Mcquiston E, Wu X L . On kinetics of phage adsorption. Biophysical Journal, 2007,93(1):303-315.
[36]   Bertin A, De F M, Letellier L . Bacteriophage-host interactions leading to genome internalization. Current Opinion in Microbiology, 2011,14(4):492-496.
[37]   Chatterjee S, Rothenberg E . Interaction of bacteriophage l with its E. coli receptor, LamB. Viruses, 2012,4(11):3162-3178.
[38]   Meyer J R, Dobias D T, Weitz J S , et al. Repeatability and contingency in the evolution of a key innovation in phage lambda. Science, 2012,335(6067):428-432.
[39]   František Golais, Jaroslav Hollý, Jana Vítkovská . Coevolution of bacteria and their viruses. Folia Microbiol. 2013,58(3):177-186.
[40]   Thrall P H, Barrett L G, Dodds P N , et al. Epidemiological and evolutionary outcomes in gene-for-gene and matching allele models. Frontiers in Plant Science, 2016,6(761):1084.
[41]   Frickel J, Sieber M, Becks L . Eco-evolutionary dynamics in a coevolving host-virus system. Ecology Letters, 2016,19(4):450.
[42]   Vorburger C, Perlman S J . The role of defensive symbionts in host-parasite coevolution. Biol Rev, 2018,93(4):1747-1764.
[43]   Paterson S, Vogwill T, Buckling A , et al. Antagonistic coevolution accelerates molecular evolution. Nature. 2010,464(7286):275-278.
[44]   Murphy J, Bottacini F, Mahony J , et al. Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages. Sci Rep, 2016,6:21345.
[45]   Hall A R, Scanlan P D, Morgan A D , et al. Host-parasite coevolutionary arms races give way to fluctuating selection. Ecology Letters, 2011,14(7):635-642.
[46]   Vos M, Birkett P J, Birch E , et al. Local adaptation of bacteriophages to their bacterial hosts in soil. Science. 2009,325(5942):833.
[47]   Tadmor A D, Ottesen E A, Leadbetter J R , et al. Probing individual environmental bacteria for viruses by using microfluidic digital PCR. Science, 2011,333(6038):58-62.
[48]   Kimura S, Sakoa Y, Yoshida T . Rapid microcystis cyanophage gene diversification revealed by longand short-term genetic analyses of the tail sheath gene in a natural pond. Appl Environ Micro, 2013,79(8):2789-2795.
[49]   Koskella B, Parr N . The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Philos Trans R Soc Lond B Biol Sci, 2015,370(1675):20140297.
[50]   Retel C, Märkle H, Becks L , et al. Ecological and evolutionary processes shaping viral genetic diversity. Viruses, 2019; 11(3):220.
[1] ZHAI Jun-ye,CHENG Xu,SUN Ze-min,LI Chun,LV Bo. Current Advances in Biosynthesis of Acteoside[J]. China Biotechnology, 2021, 41(5): 94-104.
[2] LI Bo,WANG Ze-jian,LIANG Jian-guang,LIU Ai-jun,LI Hai-dong. Breeding of High-yield Rifamycin SV Strain by Plasma Action Combined with Oxygen Restriction Model[J]. China Biotechnology, 2021, 41(2/3): 38-44.
[3] WANG You-bei,GUO Si-yu,CHANG Bi-bo,YE Rui-fang,HUA Qiang. Establishment of Conjugation System for the Spiramycin Producer Streptomyces spiramyceticus[J]. China Biotechnology, 2021, 41(2/3): 45-52.
[4] ZHOU Hui-ying,ZHOU Cui-xia,ZHANG Ting,WANG Xue-yu,ZHANG Hui-tu,JI Yi-zhi,LU Fu-ping. Enhancing the Expression of the Substrate by the Extracellular Secreted Enzymes and Improving the Alkaline Protease Production in Bacillus licheniformis[J]. China Biotechnology, 2021, 41(2/3): 53-62.
[5] ZHU Ya-xin, DUAN Yan-ting, GAO Yu-hao, WANG Ji-yue, ZHANG Xiao-mei, ZHANG Xiao-juan, XU Guo-qiang, SHI Jin-song, XU Zheng-hong. Synthesis and Regulation of Poly-γ-glutamic Acid with Different D/L Monomer Ratios[J]. China Biotechnology, 2021, 41(1): 1-11.
[6] WANG Zhen,LI Xia,YUAN Ying-jin. Advances in Production of Caffeic Acid and Its Ester Derivatives in Heterologous Microbes[J]. China Biotechnology, 2020, 40(7): 91-99.
[7] FAN Bin,CHEN Huan,SONG Wan-ying,CHEN Guang,WANG Gang. Advances in Lactic Acid Bacteria Gene Modification[J]. China Biotechnology, 2020, 40(6): 84-92.
[8] MEI Yu-wei,YANG Zi-yun,YU Fan,LONG Xu-wei. Recent Progress on Fermentation and Antibacterial Applications of Surfactin[J]. China Biotechnology, 2020, 40(5): 105-116.
[9] CEN Qian-hong,GAO Tong,REN Yi,LEI Han. Recombinant Saccharomyces cerevisiae Expressing Helicobacter pylori VacA Protein and Its Immunogenicity Analysis[J]. China Biotechnology, 2020, 40(5): 15-21.
[10] TONG Mei,CHENG Yong-qing,LIU Jin-yi,XU Chen. Construction of a Strain for Promoting Production of Small Molecule Antibodies in Periplasmic Space of Escherichia coli[J]. China Biotechnology, 2020, 40(5): 48-56.
[11] QIN Xu-ying,YANG Hong-jiang. Research Progress on Techniques for Separation, Purification of Bacteriophages[J]. China Biotechnology, 2020, 40(5): 78-83.
[12] WANG Ze-jian,LI Bo,WANG Ping,ZHANG Qin,HANG Hai-feng,LIANG Jian-guang,ZHUANG Ying-ping. Effects of Glucose and Maltose Substrates on the Intracellular Metabolic Flux Distribution of Curdlan Polysaccharides Biosynthesis by Alcaligenes faecalis[J]. China Biotechnology, 2020, 40(5): 30-39.
[13] WANG Meng,ZHANG Quan,GAO Hui-peng,GUAN Hao,CAO Chang-hai. Research Progress on the Biological Fermentation of Xylitol[J]. China Biotechnology, 2020, 40(3): 144-153.
[14] CHEN Zi-han,ZHOU Hai-sheng,YIN Xin-jian,WU Jian-ping,YANG Li-rong. Optimizing the Culture Conditions for Amphibacillus xylanus Glutamate Dehydrogenase Gene Engineering Bacteria[J]. China Biotechnology, 2019, 39(10): 58-66.
[15] AN Ming-hui,TIAN Wen,HAN Xiao-xu,SHANG Hong. Construction and Phenotypic Analyses of Recombinant Lactobacillus Expressing Single-Chain Antibody of HIV[J]. China Biotechnology, 2019, 39(10): 1-8.