Whole-genome synthesis and characterization of viable S13-like bacteriophages

• Published in: PloS one 2012-07, Vol.7 (7), p.e41124-e41124
• Main Authors: Liu, Yuchen, Han, Yonghua, Huang, Weiren, Duan, Yonggang, Mou, Lisha, Jiang, Zhimao, Fa, Pingping, Xie, Jun, Diao, Ruiying, Chen, Yuanbin, Ye, Yiwang, Yang, Ruilin, Chen, Jing, Sun, Xiaojuan, Li, Zesong, Tang, Aifa, Gui, Yaoting, Cai, Zhiming
• Format: Article
• Language: English
• Subjects: Adsorption; Bacteria; Bacteriophages - genetics; Biology; Biotechnology; Calcium; Calcium - chemistry; Calcium chloride; Capsid protein; Chemical synthesis; Chimeras; Chlamydia; Deoxyribonucleic acid; DNA; DNA polymerase; DNA sequencing; E coli; Electroporation; Environmental conditions; Escherichia coli - metabolism; Escherichia coli - virology; Evolution; Gene sequencing; Gene Transfer, Horizontal; Genes; Genetic aspects; Genetic Engineering - methods; Genetic Markers; Genetically modified organisms; Genetics; Genome, Bacterial; Genome, Viral; Genomes; Genomics; Homologous recombination; Homology; Hospitals; Hydrogen-Ion Concentration; Laboratories; Life cycle engineering; Life cycles; Medicine; Models, Genetic; Morphogenesis; Mutation; Nucleotide sequence; Oligonucleotides; Open Reading Frames; Phages; Phylogeny; Plaques; Proteins; Reproductive health; Sequence Analysis, DNA; Synthesis; Temperature; Ultraviolet Rays; Urology; Viral proteins
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0041124

Unprecedented progresses in high-throughput DNA sequencing and de novo gene synthesis technologies have allowed us to create living organisms in the absence of natural template. The sequence of wild-type S13 phage genome was downloaded from GenBank. Two synonymous mutations were introduced into wt-S13 genome to generate m1-S13 genome. Another mutant, m2-S13 genome, was obtained by engineering two nonsynonymous mutations in the capsid protein coding region of wt-S13 genome. A chimeric phage genome was designed by replacing the F capsid protein open reading frame (ORF) from phage S13 with the F capsid protein ORF from phage G4. The whole genomes of all four phages were assembled from a series of chemically synthesized short overlapping oligonucleotides. The linear synthesized genomes were circularized and electroporated into E.coli C, the standard laboratory host of S13 phage. All four phages were recovered and plaques were visualized. The results of sequencing showed the accuracy of these synthetic genomes. The synthetic phages were capable of lysing their bacterial host and tolerating general environmental conditions. While no phenotypic differences among the variant strains were observed when grown in LB medium with CaCl(2), the S13/G4 chimera was found to be much more sensitive to the absence of calcium and to have a lower adsorption rate under calcium free condition. The bacteriophage S13 and its variants can be chemically synthesized. The major capsid gene of phage G4 is functional in the phage S13 life cycle. These results support an evolutional hypothesis which has been proposed that a homologous recombination event involving gene F of quite divergent ancestral lineages should be included in the history of the microvirid family.