Genome Organization of Escherichia Phage YD-2008.s: A New Entry to Siphoviridae Family
Main Article Content
Abstract
Malaysia is one of the countries that are loaded with mega biodiversity which includes microbial communities. Phages constitute the major component in the microbial communities and yet the numbers of discovered phages are just a minute fraction of its population in the biosphere. Taking into account of a huge numbers of waiting to be discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD- 2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae family under the order of Caudovirales. Genomic sequence analyses revealed phage YD-2008.s genome as linear dsDNA of 44,613 base pairs with 54.6% G+C content. Sixty-two open reading frames (ORFs) were identified on phage YD-2008.s full genome, using bioinformatics annotation software; Rapid Annotation using Subsystem Technology (RAST). Among the ORFs, twenty-eight of them code for functional proteins. Thirty two are classified as hypothetical proteins and there are two unidentified proteins. Even though majority of the coded putative proteins have high amino acids similarities to phages from the genus Hk578likevirus of the Siphoviridae family, yet phage YD-2008.s stands with its’ own distinctiveness. Therefore, this is another new finding to Siphoviridae family as well as to the growing list of viruses in International Committee on Taxonomy of Viruses (ICTV) database.
Malaysia merupakan salah sebuah negara yang kaya dengan kepelbagaian biologi, termasuk komuniti mikrob. Faj adalah komponen utama di dalam komuniti mikrob tetapi bilangan faj yang ditemui sehingga kini hanyalah sebahagian kecil dari keseluruhan populasi faj dalam biosfera. Memandangkan jumlah faj yang belum diemui adalah banyak, satu faj baharu telah berjaya dipencilkan dengan menggunakan Eschrichia coli ATCC 11303 sebagai perumah. Faj baru ini dinamakan Eschrichia phage YD-2008.s. Faj ini mempunyai kepala berbentuk ikosahedra berukuran 57nm diameter dengan struktur ekor yang fleksibel dengan panjang berukuran 107nm diameter; membuktikan ia adalah dari Siphoviridae family dibawah Caudovirales order. Analisis jujukan genomik menunjukkan phage YD-2008.s mempunyai genom dsDNA yang linear bersaiz 44,613bp dengan kandungan 54.6% G+C. Dengan menggunakan perisian anotasi bioinformatik (RAST), sebanyak enam puluh dua kerangka bacaan (ORFs) telah dikenal pasti dalam genom phage YD-2008.s. Diantara ORFs yang dikenalpasti, dua puluh lapan dikodkan mempunyai protein berfungsi. Malah, 32 ORFs diklasifikasi sebagai protein hipotetikal dan dua lagi ORF baru belum dikenal pasti. Walaupun, majoriti protein berkod yang diduga menunjukkan persamaan asid amino yang tinggi dengan faj dari genus ‘HK578likevirus’ dari Siphoviridae family, tetapi phage YD-2008.s mempunyai keunikan tersendiri. Oleh itu, faj ini merupakan satu lagi penemuan baharu dalam Siphoviridae family serta tambahan virus baru di dalam pangkalan data Jawatankuasa Antarabangsa Taksonomi Virus (ICTV).
Article Details
This work is licensed under a Creative Commons Attribution 4.0 International License.
References
Abeles S R and Pride D T. (2014). Molecular bases and role of viruses in the human microbiome. Journal of Molecular Biology 426: 3892–3906. https://doi.org/10.1016/j.jmb.2014.07.002
Ackermann H W. (1998). Tailed bacteriophage: The order Caudovirales. Advances in Virus Research 51: 135–201. https://doi.org/10.1016/S0065-3527(08)60785-X
Ackermann H W. (2007). 5500 Phages examined in the electron microscope. Archives of Virology 152: 277–243. https://doi.org/10.1007/s00705-006-0849-1
Ackermann H W and Prangishvili D. (2012). Prokaryote viruses studied by electron microscope. Archives of Virology 157: 1843–1849. https://doi.org/10.1007/s00705-012-1383-y
Adriaenssens E M, Edwards R, Nash J H E, Mahadevan P, Seto D, Ackermann H W, Lavigne R and Kropinski A M. (2014). Integration of genomic and proteomic analyses in the classification of the Siphoviridae family. Virology 477 (March): 144–154. https://doi.org/10.1016/j.virol.2014.10.016
Cannon J F, Thurn N A and Richardson P E. (2013). The effect of salinity, pH, temperature and dissolved oxygen on sensitivity of PCR identification of T4 bacteriophage. Journal of the South Carolina Academy of Sciences 11(2): 17–20.
Chang H W and Kim K H. (2011). Comparative genomic analysis of bacteriophage EP23 infecting Shigella sonnei and Escherichia coli. Journal of Microbiology 49(6): 927–934. https://doi.org/10.1007/s12275-011-1577-0
Chang K C, Lin N T, Hu A, Lin Y S, Chen L K and Lai M J. (2011). Genomic analysis of bacteriophage ?AB1, a ?KMV-like virus infecting multidrug resistant Acinetobacter baumannii. Genomics 97: 249–255. https://doi.org/10.1016/j.ygeno.2011.01.002
Chumby N, Edwards A M, Davidson A R, Maxwell K L. (2012). The bacteriophage HK97 gp15 moron element encodes a novel superinfection exclusion protein. Journal of Bacteriology 194(18): 5012–5019. https://doi.org/10.1128/JB.00843-12
Dessel W V, Mellaert V, Liesegang H, Raasch C, Keersmaeker D, Geukens N, Lammertyn E, Streit W and Anne J. ( 2005). Complete genomic nucleotide sequence and analysis of the temperate bacteriophage VWB. Virology 331: 325–337. https://doi.org/10.1016/j.virol.2004.10.028
Duck L Y and Park J H. (2012) Genome organization of temperate phage 11143 from Emetic Bacillus cereus NCTC 11143. Journal of Microbiology Biotechnology 22(5):649– 653. https://doi.org/10.4014/jmb.1110.10065
Forrester S J and Hall N. (2014). The revolution of whole genome sequencing to study parasites. Molecular and Biochemical Parasitology 195: 77–81. https://doi.org/10.1016/j.molbiopara.2014.07.008
Gan H M, Sieo C C, Tang S G H, Omar A R and Ho Y W. (2013) The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli 078:K80. Virology 10: 308. https://doi.org/10.1186/1743-422X-10-308
Jones S and Portnoy D A. (1994). Small plaques mutant. Methods in Enzymology 236: 526–531. https://doi.org/10.1016/0076-6879(94)36040-5
Klumpp J and Loessner M J. (2013). Listeria phages: Genomes, evolution and application. Bacteriophage 3: e2686. https://doi.org/10.4161/bact.26861
King A M Q, Adams M J, Carstens E B and Lefkowitz E J. (2012). Virus taxonomy: Classification and nomenclature of viruses. Nineth report of the International Committee on Taxonomy of Viruses. San Diego: Elsevier Academy Press.
Lee J H, Shin H and Son B. (2013). Characterization and complete genome sequence of a virulent bacteriophage B4 infecting food-borne pathogenic Bacillus cereus. Archives of Virology. 158: 2101–2108. https://doi.org/10.1007/s00705-013-1719-2
Li S, Lina L, Zhu J, Zou L, Li M, Cong Y, Rao X, Hu X, Zhou Y, Chen Z and Hu F. (2010). Characterization and genome sequencing of a novel coliphage isolated from engineered Escherichia coli. Intervirology 53: 211–220. https://doi.org/10.1159/000299063
Matsuzaki S, Uchiyama M R J, Sakurai S, Kuroda T U M, Ikeuchi M, Fujieda T T M, Wakiguchi H and Imai S. (2005). Bacteriophage therapy: A revitalized therapy against bacterial infections disease. Journal of Infection and Chemoteraphy 11: 211–219. https://doi.org/10.1007/s10156-005-0408-9
McNair K, Bailey B A and Edwards R A. (2012). PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics 28: 614–618. https://doi.org/10.1093/bioinformatics/bts014
Pan F G, Wu H, Liu J H, Ai Y X, Meng X M, Meng R Z and Meng Q F. (2013). Complete genome sequence of Escherichia coli 0157:H7 lytic phage JL1. Archives of Virology 158: 2429–2432. https://doi.org/10.1007/s00705-013-1727-2
Pearson W R. (2013). An introduction to sequence similarity (homology) searching. Current Protocol of Bioinformatics 42: 3.1.1–3.1.8. https://doi.org/10.1002/0471250953.bi0301s42
Savalia D, Westblade L F, Goel M, Florens L, Kemp P, Akulenko N, Pavlova, Padovan J C, Chait BT, Washburn M P, Ackermann H W, Mushegian A, Gabisonia T, Molineux I and Severinov K. (2008). Genomic and proteomic analysis of phiEco32, a novel Escherichia coli bacteriophage. Journal of Molecular Biology 377: 774–789. https://doi.org/10.1016/j.jmb.2007.12.077
Sellvam D and Arip Y M. (2012) Partial genomic characterization on potentially new bacteriophage: New addition to ICTV database? Proceedings of AIC Unsyiah (E-journal) 2(1): 296–301.
Valera F R, Mizuno C M and Ghai R. (2014). Tales from a thousand and one phages. Bacteriophage 4: e28265. https://doi.org/10.4161/bact.28265
Yu J G, Lim J A, Song Y R, Huu S, Kim G H, Koh Y J and Chang S O. (2016). Isolation and characterization of bacteriophage against Psedumonas syringe pv. Actinidae causing bacterial canker disease in kiwifruit. Journal of Microbiology and Biotechnology 26(2): 385–393. https://doi.org/10.4014/jmb.1509.09012