Page 111 - Read Online
P. 111
Ambros et al. Microbiome Res Rep 2023;2:34 https://dx.doi.org/10.20517/mrr.2023.18 Page 19 of 19
Cell 2006;127:721-33. DOI
47. Bobay LM, Rocha EP, Touchon M. The adaptation of temperate bacteriophages to their host genomes. Mol Biol Evol 2013;30:737-51.
DOI PubMed PMC
48. Hotopp JCD, Grifantini R, Kumar N, et al. Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal
transfer and pathogen-specific genes. Microbiology 2006;152:3733-49. DOI
49. Bobay LM, Touchon M, Rocha EP. Pervasive domestication of defective prophages by bacteria. Proc Natl Acad Sci U S A
2014;111:12127-32. DOI PubMed PMC
50. Yang JY, Fang W, Miranda-Sanchez F, et al. Degradation of host translational machinery drives tRNA acquisition in viruses. Cell Syst
2021;12:771-9.e5. DOI PubMed PMC
51. Bailly-Bechet M, Vergassola M, Rocha E. Causes for the intriguing presence of tRNAs in phages. Genome Res 2007;17:1486-95. DOI
PubMed PMC
52. Yoshikawa G, Askora A, Blanc-Mathieu R, et al. Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high
complement of tRNA genes. Sci Rep 2018;8:4486. DOI PubMed PMC
Ile
53. Tomikawa C, Auxilien S, Guérineau V, et al. Characterization of redundant tRNA s with CAU and UAU anticodons in Lactobacillus
plantarum. J Biochem 2018;163:233-41. DOI
54. McDonald MJ, Chou CH, Swamy KB, Huang HD, Leu JY. The evolutionary dynamics of tRNA-gene copy number and codon-use in
E. coli. BMC Evol Biol 2015;15:163. DOI PubMed PMC
55. Murphy J, Mahony J, Ainsworth S, Nauta A, van Sinderen D. Bacteriophage orphan DNA methyltransferases: insights from their
bacterial origin, function, and occurrence. Appl Environ Microbiol 2013;79:7547-55. DOI PubMed PMC
56. Pingoud A, Fuxreiter M, Pingoud V, Wende W. Type II restriction endonucleases: structure and mechanism. Cell Mol Life Sci
2005;62:685-707. DOI PubMed
57. Bickle TA, Krüger DH. Biology of DNA restriction. Microbiol Rev 1993;57:434-50. DOI PubMed PMC
58. Sternberg N, Coulby J. Cleavage of the bacteriophage P1 packaging site (pac) is regulated by adenine methylation. Proc Natl Acad Sci
U S A 1990;87:8070-4. DOI PubMed PMC
59. Jensen TØ, Tellgren-Roth C, Redl S, et al. Genome-wide systematic identification of methyltransferase recognition and modification
patterns. Nat Commun 2019;10:3311. DOI PubMed PMC
60. Marinus MG, Morris NR. Biological function for 6-methyladenine residues in the DNA of Escherichia coli K12. J Mol Biol
1974;85:309-22. DOI PubMed
61. Lahue RS, Au KG, Modrich P. DNA mismatch correction in a defined system. Science 1989;245:160-4. DOI
62. Smith MJ, Jeddeloh JA. DNA methylation in lysogens of pathogenic Burkholderia spp. Requires prophage induction and is restricted
to excised phage DNA. J Bacteriol 2005;187:1196-200. DOI PubMed PMC
63. Kenyon CJ, Walker GC. DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli. Proc Natl Acad Sci U S
A 1980;77:2819-23. DOI PubMed PMC

