Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria

Proceedings of the National Academy of Sciences of the United States of America

Volumn 115, Issue 3, 2018, Pages 567-572

  Kilcher, Samuel ^a   Studer, Patrick ^a   Muessner, Christina ^a   Klumpp, Jochen ^a   Loessner, Martin J ^a   Adhya, Sankar ^b  

^a ETH ZURICH   (Switzerland)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Bacteriophage engineering; Biotechnology; L form bacteria; Listeria monocytogenes; Synthetic biology

Indexed keywords

BACTERIOPHAGE DNA; SYNTHETIC DNA;

ARTICLE; BACILLUS; BACTERIAL CELL; BACTERIAL CELL WALL; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIOPHAGE; BYSTANDER EFFECT; CELL KILLING; CONTROLLED STUDY; DNA FRAGMENTATION; DNA REPLICATION; DNA TRANSFECTION; GENE SYNTHESIS; GENE TECHNOLOGY; GENETIC CROSS; GENETIC ENGINEERING; GRAM POSITIVE BACTERIUM; IN VITRO STUDY; INFECTIOUS AGENT; LISTERIA MONOCYTOGENES; MICROBIAL ACTIVITY; NONHUMAN; PHAGE THERAPY; PRIORITY JOURNAL; STAPHYLOCOCCUS; SYNTHETIC BIOLOGY; TARGET CELL; VIRUS GENOME; VIRUS PARTICLE; VIRUS REACTIVATION; CLASSIFICATION; GENETICS; PHYSIOLOGY; VIROLOGY;

BACTERIOPHAGES; GENOME, VIRAL; GRAM-POSITIVE BACTERIA; LISTERIA MONOCYTOGENES; SYNTHETIC BIOLOGY;

EID: 85042004438     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1714658115     Document Type: Article

References (42)

1. Schmelcher M, Loessner MJ (2014) Application of bacteriophages for detection of foodborne pathogens. Bacteriophage 4:e28137.
2. Endersen L, et al (2014) Phage therapy in the food industry. Annu Rev Food Sci Technol 5:327-349.
3. Knoll BM, Mylonakis E (2014) Antibacterial bioagents based on principles of bacteriophage biology: An overview. Clin Infect Dis 58:528-534.
4. Reardon S (2014) Phage therapy gets revitalized. Nature 510:15-16.
5. Wright A, Hawkins CH, Anggård EE, Harper DR (2009) A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy. Clin Otolaryngol 34: 349-357.
6. Loc-Carrillo C, Abedon ST (2011) Pros and cons of phage therapy. Bacteriophage 1: 111-114.
7. Cooper CJ, Khan Mirzaei M, Nilsson AS (2016) Adapting drug approval pathways for bacteriophage-based therapeutics. Front Microbiol 7:1209.
8. Nobrega FL, Costa AR, Kluskens LD, Azeredo J (2015) Revisiting phage therapy: New applications for old resources. Trends Microbiol 23:185-191.
9. Shousha A, et al (2015) Bacteriophages isolated from chicken meat and the horizontal transfer of antimicrobial resistance genes. Appl Environ Microbiol 81:4600-4606.
10. Abedon ST, Kuhl SJ, Blasdel BG, Kutter EM (2011) Phage treatment of human infections. Bacteriophage 1:66-85.
11. Labrie SJ, Samson JE, Moineau S (2010) Bacteriophage resistance mechanisms. Nat Rev Microbiol 8:317-327.
12. Pires DP, Cleto S, Sillankorva S, Azeredo J, Lu TK (2016) Genetically engineered phages: A review of advances over the last decade. Microbiol Mol Biol Rev 80:523-543.
13. Lu TK, Collins JJ (2007) Dispersing biofilms with engineered enzymatic bacteriophage. Proc Natl Acad Sci USA 104:11197-11202.
14. Bikard D, et al (2014) Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol 32:1146-1150.
15. Citorik RJ, Mimee M, Lu TK (2014) Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat Biotechnol 32:1141-1145.
16. Kiro R, Shitrit D, Qimron U (2014) Efficient engineering of a bacteriophage genome using the type I-E CRISPR-Cas system. RNA Biol 11:42-44.
17. Lemay ML, Tremblay DM, Moineau S (2017) Genome engineering of virulent lactococcal phages using CRISPR-Cas9. ACS Synth Biol 6:1351-1358.
18. Martel B, Moineau S (2014) CRISPR-Cas: An efficient tool for genome engineering of virulent bacteriophages. Nucleic Acids Res 42:9504-9513.
19. Tao P, Wu X, Tang WC, Zhu J, Rao V (2017) Engineering of bacteriophage T4 genome using CRISPR-Cas9. ACS Synth Biol 6:1952-1961.
20. Bundy BC, Franciszkowicz MJ, Swartz JR (2008) Escherichia coli-based cell-free synthesis of virus-like particles. Biotechnol Bioeng 100:28-37.
21. Shin J, Jardine P, Noireaux V (2012) Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. ACS Synth Biol 1:408-413.
22. Ando H, Lemire S, Pires DP, Lu TK (2015) Engineering modular viral scaffolds for targeted bacterial population editing. Cell Syst 1:187-196.
23. Jaschke PR, Lieberman EK, Rodriguez J, Sierra A, Endy D (2012) A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast. Virology 434:278-284.
24. Dell'Era S, et al. (2009) Listeria monocytogenes L-forms respond to cell wall deficiency by modifying gene expression and the mode of division. Mol Microbiol 73:306-322.
25. Allan EJ, Hoischen C, Gumpert J (2009) Bacterial L-forms. Adv Appl Microbiol 68:1-39.
26. White TB, Doyle RJ, Streips UN (1981) Transformation of a Bacillus subtilis L-form with bacteriophage deoxyribonucleic acid. J Bacteriol 145:878-883.
27. Studer P, et al (2016) Proliferation of Listeria monocytogenes L-form cells by formation of internal and external vesicles. Nat Commun 7:13631.
28. Dorscht J, et al (2009) Comparative genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site. J Bacteriol 191:7206-7215.
29. Monk IR, Gahan CG, Hill C (2008) Tools for functional postgenomic analysis of listeria monocytogenes. Appl Environ Microbiol 74:3921-3934.
30. Klumpp J, Loessner MJ (2013) Listeria phages: Genomes, evolution, and application. Bacteriophage 3:e26861.
31. Klumpp J, Calendar R, Loessner MJ (2010) Complete nucleotide sequence and molecular characterization of Bacillus phage TP21 and its relatedness to other phages with the same name. Viruses 2:961-971.
32. Klumpp J, et al (2014) The odd one out: Bacillus ACT bacteriophage CP-51 exhibits unusual properties compared to related Spounavirinae W.Ph. and Bastille. Virology 462-463:299-308.
33. Kwan T, Liu J, DuBow M, Gros P, Pelletier J (2005) The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc Natl Acad Sci USA 102: 5174-5179.
34. Gill JJ (2014) Revised genome sequence of Staphylococcus aureus bacteriophage K. Genome Announc 2:e01173-13.
35. Gibson DG, et al (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343-345.
36. Weigel C, Seitz H (2006) Bacteriophage replication modules. FEMS Microbiol Rev 30: 321-381.
37. Zimmer M, Sattelberger E, Inman RB, Calendar R, Loessner MJ (2003) Genome and proteome of Listeria monocytogenes phage PSA: An unusual case for programmed + 1 translational frameshifting in structural protein synthesis. Mol Microbiol 50:303-317.
38. Farber JM, Peterkin PI (1991) Listeria monocytogenes, a food-borne pathogen. Microbiol Rev 55:476-511.
39. Lauer P, Chow MY, Loessner MJ, Portnoy DA, Calendar R (2002) Construction, characterization, and use of two Listeria monocytogenes site-specific phage integration vectors. J Bacteriol 184:4177-4186.
40. Loessner MJ, Wendlinger G, Scherer S (1995) Heterogeneous endolysins in Listeria monocytogenes bacteriophages: A new class of enzymes and evidence for conserved holin genes within the siphoviral lysis cassettes. Mol Microbiol 16:1231-1241.
41. Chang S, Cohen SN (1979) High frequency transformation of Bacillus subtilis protoplasts by plasmid DNA. Mol Gen Genet 168:111-115.
42. Sambrook J, Russell DW (2001) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY).