STREPTOCOCCUS THERMOPHILUS 231-X10 FAJININ KISMİ GENOMİK KARAKTERİZASYONU

Yıl 2017, Cilt: 42 Sayı: 2, 136 - 144, 15.04.2017

Esra Acar-soykut

Öz

Bu çalışmada, daha önce yapılmış çalışmalarla morfolojik olarak tanımlanmış,
konakçı spektrumu ve yapısal proteinleri belirlenmiş, restriksiyon fragment
analizleri yapılmış 231-X10 fajının belirli bir genom bölgesinin dizi analizi
yapılmıştır. Dizi analizi yapılmış olan bu bölgede 13 adet açık okuma
çerçevesinin yani 13 farklı fonksiyonu kodlayan gen bölgesinin olabileceği
ortaya çıkarılmıştır. Bu gen bölgelerinin faj DNA’sının replikasyonu, DNA’nın
paketlenmesi, kapsid ve kuyruk yapısının oluşumundan sorumlu proteinleri
kodladığı belirlenmiştir.  231-X10 fajına
ait bu genom bölgesi tarafından kodlanan proteinlerin aminoasit bazında
cos-tipi DNA paketleme mekanizmasına sahip fajlarla yüksek benzerlik gösterdiği
tespit edilmiş ve dolayısıyla bu fajın da cos-tipi olabileceği sonucuna
varılmıştır. Yapılan bu incelemeler sonucunda S. thermophilus fajlarının ortak bir atadan geldiği, nokta
mutasyonlar, küçük eklemeler ve kayıplar ile evrimleştikleri düşüncesi
desteklenmiştir.

Anahtar Kelimeler

S. thermophilus fajı, dizi analizi, genomik organizasyon

PARTIAL GENOMIC CHARACTERIZATION OF STREPTOCOCCUS THERMOPHILUS PHAGE 231-X10

Öz

In this study,
the partial genomic sequencing of S.
thermophilus 231-X10 phage was carried out. 231-X10 was identified
morphologically, and its host spectrum, structural proteins and restriction
analysis have also been completed in previous studies. Thirteen different open
reading frames that was coded by thirteen genes were detected in that partial
genome. These genes are responsible for DNA replication, DNA packaging and the
formation of capsid and tail structure. The proteins that are encoded by the
genomic region of 231-X10 phage have been found to show high similarities
between the phages which have cos-type DNA packaging mechanism on the basis of
amino acids. Thus, it is concluded that the 231-X10 phage might also be
cos-type. As a result of these investigations, it is supported the idea that S. thermophilus phages come from a
common ancestor and evolved with point mutations, small additions and
deletions.

Anahtar Kelimeler

S. thermophilus phage, sequence analysis, genomic organisation

Kaynakça

• 1. Tunail N, Ayhan K, Akçelik M, Durlu-Özkaya F, Doğan HB, Kaleli D, Tükel Ç, Acar E. 2002. Yoğurt fabrikalarında faj probleminin çözümüne yönelik araştırmalar. TÜBİTAK/TARP-2106 Nolu Proje Raporu.
• 2. Ackermann HW. 2006. Classification of bacteriophage. In: The Bacteriophage 2nd. Calendar R. (Ed), Oxford University Press, USA, pp. 8-16.
• 3. Paez-Espino D, Sharon I, Morovic W, Stahl B, Thomas BC, Barrangou R, Banfield JF. 2015. CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus. mBio, mbio.asm.org, 6 (2), e00262-15.
• 4. Lamothe G, Levesque C, Bissonnette F, Cochu A, Vadeboncoeur C, Frenette M, Duplessis M, Tremblay D, Moineau S. 2005. Characterization of the cro-ori region of the Streptococcus thermophilus virulent bacteriophage DT1. Appl Environ Microbiol, 71 (3), 1237-1246.
• 5. Brüssow H, Desiere F. 2006. Evolution of Tailed Phages: Insights from Comparative Phage Genomics. In: The Bacteriophage 2nd. Calendar R. (Ed), Oxford University Press, USA, pp. 26-36.
• 6. Brüssow H, Suarez JE. 2006. Lactobacillus phages. In: The Bacteriophage 2nd. Calendar R. (Ed), Oxford University Press, USA, pp. 653-657.
• 7. Quiberoni A, Moineau S, Rousseau GM, Reinheimer J, Ackermann HW. 2010. Streptococcus thermophilus bacteriophages. Int Dairy J, 20, 657–664.
• 8. Ali YHM, Yousef NMH. 2014. Detection and characterization bacteriophages attacking dairy Streptococcus thermophilus starter cultures. African J Microbiol Res, 8 (27), 2598-2603.
• 9. McDonnell B, Mahonya J, Neve H, Hanemaaijer L, Nobend J-P, Kouwen T, van Sinderen D. 2016. Identification and analysis of a novel group of bacteriophages infecting the lactic acid bacterium Streptococcus thermophilus. Appl Environ Microbiol, 82 (17), 5153-5165.
• 10. Prevots F, Relano P, Mata M, Ritzenthaler P. 1989. Close relationship of virulent bacteriophages of Streptococcus salivarius subsp. thermophilus at both the protein and the DNA level, J Gen Microbiol, 135, 3337-3344.
• 11. Le Marrec C, Sinderen D, Walsh L, Stanley E, Vlegels E, Moineau S, Heinze P, Fitzgerald G, Fayard B. 1997. Two groups of bacteriophages Streptococcus thermophilus can be distinguished on the basis of mode of packaging and genetic determinants for major structural proteins. Appl Environ Microbiol, 63, 3246–3253.
• 12. Tremblay DM, Moineau S. 1999. Complete genomic sequence of the lytic bacteriophage DT1 of Streptococcus thermophilus. Virology, 255, 63–76.
• 13. Suárez VB, Quiberoni A, Binetti AG, Reinheimer JA. 2002. Thermophilic lactic acid bacteria phages isolated from Argentinian dairy industries. J Food Prot, 65 (10), 1597-1604.
• 14. Quiberoni A, Auad L, Binetti AG, Suarez VB, Reinheimer JA, Raya RR. 2003. Comparative analysis of Streptococcus thermophilus bacteriophages isolated from a yoghurt industrial plant. Food Microbiol, 20, 461-469.
• 15. Stanley E, Fitzgerald GF, Le Marrec C, Fayard B, van Sinderen D. 1997. Sequence analysis and characterization of phiO1205, a temperate bacteriophage infecting Streptococcus thermophilus CNRZ1205. Microbiology, 143, 3417–3429.
• 16. Lucchini S, Desiere F, Brüssow H. 1998.The structural gene module in Streptococcus thermophilus bacteriophage phiSfi11 shows a hierarchy of relatedness to Siphoviridae from a wide range of bacterial hosts. Virology, 246, 63–73.
• 17. Desiere F, Lucchini S, Brussow H. 1999. Comparative sequence analysis of the DNA packaging, head, and tail morphogenesis modules in the temperate cos-site Streptococcus thermophilus bacteriophage Sfi21. Virology, 260, 244–253.
• 18. Levesque C, Duplessis M, Labonte J, Labrie S, Fremaux C, Tremblay D. 2005. Genomic organization and molecular analysis of virulent bacteriophage 2972 infecting an exopolysaccharide-producing Streptococcus thermophilus strain. Appl Environ Microbiol, 71, 4057–4068.
• 19. Deveau, H., Barrangou, R., Garneau, J.E., Labonte, J., Fremaux, C., Boyaval, P., Romero, D.A., Horvath, P. and Moineau, S. 2008. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol, 190, 1390–1400.
• 20. Guglielmotti DM, Deveau H, Binetti AG, Reinheimer JA, Moineau S, Quiberoni A. 2009. Genome analysis of two virulent Streptococcus thermophilus phages isolated in Argentina. Int J Food Microbiol, 136, 101–109.
• 21. Milles S, Griffin C, O’Sullivan O, Coffey A, Mcauliffe OE, Meijer WC, Serrano LM, Ross RP. 2011. A new phage on the "Mozzarella" block: Bacteriophage 5093 shares a low level of homology with other Streptococcus thermophilus phages. Int Dairy J, 21, 963–969.
• 22. Ali Y, Koberg S, Heßner S, Sun X, Rabe B, Back A, Neve H, Heller KJ. 2014. Temperate Streptococcus thermophilus phages expressing superinfection exclusion proteins of the Ltp type. Front Microbiol, 5: 98.
• 23. Brüssow H. 2001. Phages of dairy bacteria. Annu Rev Microbiol, 55, 283-303.
• 24. Acar Soykut E, Tunail N. 2010. Morphological Characterization of Streptococcus salivarius subp. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus virulent phages, GIDA (FOOD), 35 (5), 317-323.
• 25. Acar-Soykut E, Tunail N. 2016. Classification of Streptococcus thermophilus phages originating from Turkey, J Food Saf, 36, 186-194.
• 26. ORFfinder, Open Reading Frame finder, https://www.ncbi.nlm.nih.gov/orffinder/ (Accessed 01 August 2016).
• 27. NCBI, National Centre for Biotechnology Information, www.ncbi.nlm.nih.gov (Accessed 01 August 2016).
• 28. Acar-Soykut E, Diker S. K. 2011. Süt Endüstrisinde Sorun Yaratan Termofilik Fajların Genomik Karakterizasyonları TÜBİTAK 110O035 nolu proje.
• 29. Krusch U, Neve H, Luschei B, Teuber M. 1987. Characterization of virulent bacteriophages of Streptococcus salivarius subsp. thermophilus by host specifity and electron microscopy. Kieler Milchwirtschaftliche Forschungsberichte, 39 (3), 155-167.
• 30. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1626 p.
• 31. 454 De Novo Genome Sequence, http://454.com/downloads/454SystemsBrochureSpread_Fin Final.pdf (Accessed 30 August 2016).
• 32. BLAST, Basic Local Alignment Search Tool, http://blast.ncbi.nlm.nih.gov/Blast.cgi (Accessed 01 August 2016).
• 33. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH 2015. CDD: NCBI’s conserved domain database. Nucleic Acids Res, 43 (Database issue), D222–D226.
• 34. Desiere F, Lucchini S, Brussow H. 1998. Evolution of Streptococcus thermophilus bacteriophage genomes by modular exchanges followed by point mutations and small deletions and insertions. J Virol, 241 (2), 345-356.
• 35. Hsia K-C, Chak K-F, Liang P-H, Cheng Y-C, Ku W-Y, Yuan H-S. 2004. DNA binding and degradation by the HNH Protein ColE7. Struct, 12 (2), 205-214.
• 36. Williams LS, Levdikov VM, Minakhin L, Severinov K, Antson, AA. 2013. 12-fold symmetry of the putative portal protein from the Thermus thermophilus bacteriophage G20C determined by X-ray analysis. Acta Crystallogr F, 69 (11), 1239-1241.
• 37. Gan L, Speir JA, Conway JF, Lander G, Cheng N, Firek BA, Hendrix RW, Duda RL, Liljas L, Johnson JE. 2006. Capsid conformational sampling in HK97 maturation visualized by X-Ray crystallography and cryo-EM. Struct, 14, 1655–1665.
• 38. Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM, Chirgadze NY, Davidson AR, Maxwell KLA. 2013. Conserved spiral structure for highly diverged phage tail assembly chaperones. J Mol Biol, 425 (14), 2436–2449.
• 39. Belcaid M, Bergeron A, Poisson G. 2011. The evolution of the tape measure protein: units, duplications and losses. BMC Bioinformatics, 12 (Suppl 9): S10.
• 40. Katsura I, Hendrix RW. 1984. Length determination in bacteriophage lambda tails. Cell, 39, 691-698.
• 41. Abuladze NK, Gingery M, Tsai J, Eiserling FA. 1994. Tail Length Determination in Bacteriophage T4, Virology, 199 (2), 301-310.
• 42. Brüssow H, Desiere F. 2001. Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol Microbiol, 39 (2), 213-222.