Systematic discovery of novel prokaryotic defense systems: progress and prospects
Received date: 2018-03-21
Revised date: 2018-04-07
Online published: 2018-04-19
Supported by
Supported by the National Natural Science Foundation of China(31571283);Supported by the National Natural Science Foundation of China(31771381)
Microbial defense systems provide fundamental elements for biotechnology development. For example, molecular cloning techniques greatly depend on the discovery of the bacterial restriction-modification system, and similarly, deciphering the CRISPR adaptive immunity gives rise to the revolutionary genome editing technique CRISPR-Cas9. Therefore, exploring novel microbial defense systems has attracted world-wide attention, and new systems like prokaryotic Argonautes (pAgos) and the defense island system associated with restriction-modification (DISARM) were successively discovered and investigated. Recently, Sorek et al. reported a systematic strategy to predict novel defense systems within the vast microbial genomes and validated the antivirus or anti-plasmid capability of 10 candidates using synthetic biology procedures. Here, we introduce the systematic analysis pipeline developed by Sorek et al., summarize the characteristics of the novel microbial defense systems, and prospect the research trends and challenges in this rising field.
Key words： prokaryotic defense system; phage/virus; defense gene family
Ming Li,Feiyue Cheng,Luyao Gong,Hua Xiang . Systematic discovery of novel prokaryotic defense systems: progress and prospects[J]. Hereditas(Beijing), 2018 , 40(4) : 259 -265 . DOI: 10.16288/j.yczz.18-075
| [1] | Labrie SJ, Samson JE, Moineau S . Bacteriophage resistance mechanisms. Nat Rev Microbiol, 2010,8(5):317-327. |
| [2] | Stern A, Sorek R . The phage-host arms race: shaping the evolution of microbes. Bioessays, 2011,33(1):43-51. |
| [3] | Dy RL, Richter C, Salmond GPC, Fineran PC . Remarkable mechanisms in microbes to resist phage infections. Annu Rev Virol, 2014,1(1):307-331. |
| [4] | Tock MR, Dryden DT . The biology of restriction and anti-restriction. Curr Opin Microbiol, 2005,8(4):466-472. |
| [5] | Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P . CRISPR provides acquired resistance against viruses in prokaryotes. Science, 2007,315(5819):1709-1712. |
| [6] | Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS , Koonin EV, van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science, 2008,321(5891):960-964. |
| [7] | Anba J, Bidnenko E, Hillier A, Ehrlich D, Chopin MC . Characterization of the lactococcal abid1 gene coding for phage abortive infection. J Bacteriol, 1995,177(13):3818-3823. |
| [8] | Fineran PC, Blower TR, Foulds IJ, Humphreys DP, Lilley KS, Salmond GPC . The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc Natl Acad Sci USA, 2009,106(3):894-899. |
| [9] | Jinek M, East A, Cheng A, Lin S, Ma EB, Doudna J . RNA-programmed genome editing in human cells. eLife, 2013,2:e00471. |
| [10] | Cong L, Ran FA, Cox D, Lin SL, Barretto R, Habib N, Hsu PD, Wu XB, Jiang WY, Marraffini LA, Zhang F . Multiplex genome engineering using CRISPR/Cas systems. Science, 2013,339(6121):819-823. |
| [11] | Mali P, Yang LH, Esvelt KM, Aach J, Guell M , DiCarlo JE, Norville JE, Church GM. RNA-Guided human genome engineering via Cas9. Science, 2013,339(6121):823-826. |
| [12] | Ofir G, Melamed S, Sberro H, Mukamel Z, Silverman S, Yaakov G, Doron S, Sorek R . DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat Microbiol, 2018,3(1):90-98. |
| [13] | Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G , Sorek R. Systematic discovery of antiphage defense systems in the microbial pangenome. Science, 2018, 359(6379): eaar4120. |
| [14] | Makarova KS, Wolf YI, Snir S, Koonin EV . Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol, 2011,193(21):6039-6056. |
| [15] | Makarova KS, Wolf YI, Koonin EV . Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res, 2013,41(8):4360-4377. |