A novel chimeric prophage vB_LdeS-phiJB from commercial Lactobacillus delbrueckii subsp. bulgaricus

Journal of Industrial Microbiology and Biotechnology

Volumn 43, Issue 5, 2016, Pages 681-689

  Guo, Tingting ^a   Zhang, Chenchen ^a   Xin, Yongping ^a   Xin, Min ^a   Kong, Jian ^a  

^a SHANDONG UNIVERSITY   (China)

Author keywords

Chimeric phage; Comparative genomic; Lactobacillusdelbrueckii subsp. bulgaricus

Indexed keywords

CHIMERA; DAIRY INDUSTRY; DNA REPLICATION; GENE CLUSTER; LACTOBACILLUS DELBRUECKII; LYSOGENIZATION; OPEN READING FRAME; PROPHAGE; BIODIVERSITY; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MULTIGENE FAMILY; PHENOTYPE; VIROLOGY; VIRUS DNA CELL DNA INTERACTION; VIRUS GENE;

YOGHURT;

BIODIVERSITY; DNA REPLICATION; GENES, VIRAL; LACTOBACILLUS DELBRUECKII; LYSOGENY; MULTIGENE FAMILY; OPEN READING FRAMES; PHENOTYPE; PROPHAGES; VIRUS INTEGRATION; YOGURT;

EID: 84957110242     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-016-1739-5     Document Type: Article

References (48)

1. Akhter S, Aziz RK, Edwards RA (2012) PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res 40:e126. doi:10.1093/nar/gks406
2. Aleksandrova V, Ishlimova D, Urshev Z (2013) Classification of Lactobacillus delbrueckii ssp. bulgaricus phage Gb1 into group “b” Lactobacillus delbrueckii bacteriophages based on its partial genome sequencing. Bulg J Agric Sci 19(Supplement 2):90–93
3. Auad L, Räisänen L, Raya RR, Alatossava T (1999) Physical mapping and partial genetic characterization of the Lactobacillus delbrueckii subsp. bulgaricus bacteriophage lb539. Arch Virol 144:1503–1512
4. Aziz RK, Edwards RA, Taylor WW, Low DE, McGeer A, Kotb M (2005) Mosaic prophages with horizontally acquired genes account for the emergence and diversification of the globally disseminated M1T1 clone of Streptococcus pyogenes. J Bacteriol 187:3311–3318. doi:10.1128/JB.187.10.3311-3318.2005
5. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero D, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712. doi:10.1126/science.1138140
6. Baugher JL, Durmaz E, Klaenhammer TR (2014) Spontaneously induced prophage in Lactobacillus gasseri contribute to horizontal gene transfer. Appl Environ Microbiol 80:3508–3517. doi:10.1128/AEM.04092-13
7. Brüssow H, Desiere F (2001) Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol Microbiol 39(2):213–222. doi:10.1046/j.1365-2958.2001.02228.x
8. Canchaya C, Proux C, Fournous G, Bruttin A, Brüssow H (2003) Prophage genomics. Microbiol Mol Biol Rev 67:238–276. doi:10.1128/MMBR.67.2.238-276.2003
9. Casey E, Mahony J, O’Connell-Motherway M, Bottacini F, Cornelissen A, Neve H, Heller KJ, Noben J-P, Bello FD, van Sinderen D (2014) Molecular characterization of three Lactobacillus delbrueckii subsp. bulgaricus phages. Appl Environ Microbiol 80:5623–5635. doi:10.1128/AEM.01268-14
10. Casey E, Mahony J, Neve H, Noben JP, Bello FD, van Sinderen D (2015) Novel phage group infecting Lactobacillus delbrueckii subsp. lactis, as revealed by genomic and proteomic analysis of bacteriophage Ldl1. Appl Environ Microbiol 81:1319–1326. doi:10.1128/AEM.03413-14
11. Casjens S (2003) Prophages and bacterial genomics: what have we learned so far? Mol Microbiol 49:277–300. doi:10.1046/j.1365-2958.2003.03580.x
12. Darling ACE, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394–1403. doi:10.1101/gr.2289704
13. Dupont L, Boizet-Bonhoure B, Coddeville M, Auvray F, Ritzenthaler P (1995) Characterization of genetic elements required for site-specific integration of Lactobacillus delbrueckii subsp. bulgaricus bacteriophage mv4 and construction of an integration-proficient vector for Lactobacillus plantarum. J Bacteriol 177:586–595
14. Durmaz E, Miller MJ, Azcarate-Peril MA, Toon SP, Klaenhammer TR (2008) Genome sequence and characteristics of Lrm1, a prophage from industrial Lactobacillus rhamnosus strain M1. Appl Environ Microbiol 74:4601–4609. doi:10.1128/AEM.00010-08
15. García P, Ladero V, Alonso JC, Suárez JE (1999) Cooperative interaction of CI protein regulated lysogeny of Lactobacillus casei by bacteriophage A2. J Virol 73:3920–3929
16. Garneau JE, Moineau S (2011) Bacteriophages of lactic acid bacteria and their impact on milk fermentations. Microb Cell Fact 10(Suppl 1):S20. doi:10.1186/1475-2859-10-S1-S20
17. Guglielmotti D, Marcó MB, Vinderola C, de Los Reyes Gavilán C, Reinheimer J, Quiberoni A (2007) Spontaneous Lactobacillus delbrueckii phage-resistant mutants with acquired bile tolerance. Int J Food Microbiol 119:236–242. doi:10.1016/j.ijfoodmicro.2007.08.010
18. Labrie SJ, Moineau S (2007) Abortive infection mechanisms and prophage sequences significantly influence the genetic makeup of emerging lytic lactococcal phages. J Bacteriol 189:1482–1487. doi:10.1128/JB.01111-06
19. Lahbib-Mansais Y, Boizet B, Dupont L, Mata M, Ritzenthaler P (1992) Characterization of a temperate bacteriophage of Lactobacillus delbrueckii subsp. bulgaricus and its interactions with the host cell chromosome. Microbiology 138:1139–1146
20. Liu YG, Whittier RF (1995) Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25:674–681
21. Lunde M, Blatny JM, Lillehaug D, Aastveit AH, Nes IF (2003) Use of real-time quantitative PCR for the analysis of φLC3 prophage stability in lactococci. Appl Environ Microbiol 69:41–48. doi:10.1128/AEM.69.1.41-48.2003
22. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A et al (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 103:15611–15616. doi:10.1073/pnas.0607117103
23. Matthews REF (1982) Classification and nomenclature of viruses. Fourth report of the international committee on taxonomy of viruses. Intervirology 17:1–200
24. Mercanti DJ, Carminati D, Reinheimer JA, Quiberoni A (2011) Widely distributed lysogeny in probiotic lactobacilli represents a potentially high risk for the fermentative dairy industry. Int J Food Microbiol 144:503–510. doi:10.1016/j.ijfoodmicro
25. Mikkonen M, Alatossava T (1994) Characterization of the genome region encoding structural proteins of Lactobacillus delbrueckii subsp. lactis lacteriophage LL-H. Gene 151:53–59
26. Mikkonen M, Räisänen L, Alatossava T (1996) The early gene region completes the nucleotide sequence of Lactobacillus delbrueckii subsp. lactis phage LL-H. Gene 175:49–57
27. Paez-Espino D, Sharon I, Morovic W, Stahl B, Thomas B, Barrangou R, Banfield J (2015) CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus. mBio 6(2):e00262-15. doi:10.1128/mBio.00262-15
28. Piotr J, Podleśny M, Pawelec J, Malinowska A, Kowalczyk S, Targński Z (2013) Spontaneous release of bacteriophage particles by Lactobacillus rhamnosus Pen. J Microbiol Biotechnol 23:357–363. doi:10.4014/jmb.1207.07037
29. Quiberoni A, Guglielmotti D, Reinheimer JA (2003) Inactivation of Lactobacillus delbrueckii bacteriophages by heat and biocides. Int J Food Microbiol 84:51–62. doi:10.1016/S0168-1605(02)00394-X
30. Quiberoni A, Guglielmotti D, Binetti A, Reinheimer J (2004) Characterization of three Lactobacillus delbrueckii subsp. bulgaricus phages and the physicochemical analysis of phage adsorption. J Appl Microbiol 96:340–351. doi:10.1046/j.1365-2672.2003.02147.x
31. Räisänen L, Schubert K, Jaakonsaari T, Alatossava T (2004) Characterization of lipoteichoic acids as Lactobacillus delbrueckii phage receptor components. J Bacteriol 186:5529–5532
32. Räisänen L, Draing C, Pfitzenmaier M, Schubert K, Jaakonsaari T, von Aulock S, Hartung T, Alatossava T (2007) Molecular interaction between lipoteichoic acids and Lactobacillus delbrueckii phages depends on d-Alanyl and alpha-glucose substitution of poly(glycerophosphate) backbones. J Bacteriol 189:4135–4140
33. Ravin V, Räisänen L, Alatossava T (2002) A conserved C-terminal region in Gp71 of the small isometric-head phage LL-H and ORF474 of the prolate-head phage JCL1032 is implicated in specificity of adsorption to its host, Lactobacillus delbrueckii. J Bacteriol 184:2455–2459
34. Riipinen K-A, Forsma P, Alatossava T (2011) The genomes and comparative genomics of Lactobacillus delbrueckii phages. Arch Virol 156:1217–1233. doi:10.1007/s00705-011-0980-5
35. Saxelin M, Tynkkynen S, Matilla-Sandholm T, de Vos WM (2005) Probiotic and other functional microbes: from markets to mechanisms. Curr Opin Biotechnol 16:204–211. doi:10.1016/j.copbio.2005.02.003
36. Suárez V, Zago M, Quiberoni A, Carminati D, Giraffa G, Reinheimer J (2008) Lysogeny in Lactobacillus delbrueckii strains and characterization of two new temperate prolate-headed bacteriophages. J Appl Microbiol 105:1402–1411. doi:10.1111/j.1365-2672.2008.03876.x
37. Suárez VB, Maciel N, Guqiielmotti D, Zago M, Giraffa G, Reinheimer J (2008) Phage-resistance linked to cell heterogeneity in the commercial strain Lactobacillus delbrueckii subsp. lactis Ab1. Int J Food Microbiol 128:401–405
38. Trucco V, Reinheimer J, Quiberoni A, Suárez VB (2011) Adsorption of temperate phages of Lactobacillus delbrueckii strains and phage resistance linked to their cell diversity. J Appl Microbiol 110:935–942
39. Urshev Z, Ishlimova D (2015) Distribution of clustered regularly interspaced palindrome repeats CRISPR2 and CRISPR3 in Lactobacillus delbrueckii ssp. bulgaricus strains. Biotechnol Biotec Eq 29:541–546
40. van de Guchte M, Penaud S, Grimaldi C, Barbe V, Bryson K, Nicolas P et al (2006) The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc Natl Acad Sci USA 103:9274–9278. doi:10.1073/pnas.0603024103
41. Vinderola G, Marcó MB, Guglielmotti DM, Perdigón G, Giraffa G, Reinheimer J, Quiberoni A (2007) Phage-resistant mutants of Lactobacillus delbrueckii may have functional properties that differ from those of parent strains. Int J Food Microbiol 116:96–102
42. Wang S, Kong J, Gao C, Guo T, Liu X (2010) Isolation and characterization of a novel virulent phage (phiLdb) of Lactobacillus delbrueckii. Int J Food Microbiol 137:22–27. doi:10.1016/j.ijfoodmicro.2009.10.024
43. Weigel C, Seitz H (2006) Bacteriophage replication modules. FEMS Microbiol Rev 30:321–381. doi:10.1111/j.1574-6976.2006.00015.x
44. Williams KP (2002) Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res 30:866–875. doi:10.1093/nar/30.4.866
45. Xu J, Hendrix RW, Duda RL (2004) Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol Cell 16:11–21. doi:10.1016/j.molcel.2004.09.006
46. Zago M, Scaltriti E, Rossetti L, Guffanti A, Armiento A, Fornasari ME, Grolli S, Carminati D, Brini E, Pavan P, Felsani A, D’Urzo A, Moles A, Claude J-B, Grandori R, Ramoni R, Giraffa G (2013) Characterization of the genome of the dairy Lactobacillus helveticus bacteriophage φAQ113. Appl Environ Microbiol 79:4712–4718. doi:10.1128/AEM.00620-13
47. Zhang X, Kong J, Qu Y (2006) Isolation and characterization of a Lactobacillus fermentum temperate bacteriophage from Chinese yogurt. J Appl Microbiol 101:857–863. doi:10.1111/j.1365-2672.2006.03007.x
48. Zhang X, Wang S, Guo T, Kong J (2011) Genome analysis of Lactobacillus fermentum temperate bacteriophage φPYB5. Int J Food Microbiol 144:400–405. doi:10.1016/j.ijfoodmicro.2010.10.026