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Structure and function predictions of hypothetical proteins in Vibrio Phages
Swapnil G. Sanmukh, Waman Narayan Paunikar, Tarun Kanti Ghosh, Tapan Chakrabarti
Pages - 161 - 175     |    Revised - 30-11-2010     |    Published - 20-12-2010
Volume - 4   Issue - 5    |    Publication Date - December 2010  Table of Contents
Bioinformatics web tools, conserved domains, Protein structure prediction, uncharacterized proteins, pathogenicity
The Vibriophages are the potential agents for the transfer of the virulence factor to their host through lateral gene transfer. The complete genome sequencing of various known vibriophages has been done which deciphered the presence of various gene sequences for hypothetical proteins whose function is not yet understood. We analyzed complete genome of 21such Vibriophages for hypothetical proteins from which 13 phages were sorted for our studies. Our attempt is to predict the structure and function of these hypothetical proteins by the application of computational methods and Bioinformatics. The probable function prediction of the hypothetical protein was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching sequence databases for the presence of orthologous enzymatic conserved domains in the hypothetical sequences. While tertiary structures were constructed using PS2 Server (Protein Structure Prediction server). These study revealed presences of enzymatic functional domain in 92 uncharacterized proteins, their roles are yet to be discovered in Vibriophages. These deciphered enzymatic data for hypothetical proteins can be used for the understanding of functional, structural, evolutionary and metabolic development of Vibriophages and its life cycle along with their role in host evolution and pathogenicity.
CITED BY (13)  
1 Thakare, H. S., Meshram, D. B., Jangam, C. M., Labhasetwar, P., Roychoudhary, K., & Ingle, A. B. (2016). Comparative genomics for understanding the structure, function and sub-cellular localization of hypothetical proteins in Thermanerovibrio acidaminovorans DSM 6589 (tai). Computational biology and chemistry, 61, 226-228.
2 Sanmukh, S. G., Khairnar, K., Khairnar, S., & Paunikar, W. N. Novel Applications of Bacterial and Algal Viruses in Advancement of Molecular Biology and for Enhancement of Bio-fuel Production.
3 Siddiqui, A., Ahmad, M., Pandya, A., Sanmukh, S., & Khairnar, K. (2014). Genome Annotation and Structure Predictions for Hypothetical Proteins in Agrobacterium Fabrum Str. C58 Plasmid At. International Journal of Computer Applications, 85(1).
4 Sanmukh, S. G., & Paunikar, W. N. (2012). Unique features of Plasmids among different Citrobacter species.
5 Sanmukh, S. G., & Paunikar, W. N. (2012). Understanding Mycobacteriophages through their unrevealed proteins. Fuzzy Systems, 4(6), 195-231.
6 Sanmukh, S. G., & Paunikar, W. N. (2012). Yersinia Phages and their Novel Proteins. Data Mining and Knowledge Engineering, 4(5), 205-209.
7 Sanmukh, S., & Paunikar, W. (2012). Study of Prophages from Lactobacillus Species. Automation and Autonomous System, 4(5), 166-179.
8 Sanmukh, S. G., Rahman, M., & Paunikar, W. N. (2012). Comparative Genomic Studies of hypothetical proteins in Cyanophages. evolution, 20, 33.
9 Sanmukh, S. G., Paunikar, W. N., Meshram, D. B., & Ghosh, T. K. (2011). Insilico function prediction for hypothetical proteins in Vibrio parahaemolyticus Chromosome II. Data Mining and Knowledge Engineering, 3(7), 404-432.
10 Sanmukh, S. G., Meshram, D. B., Paunikar, W. N., & Ghosh, T. K. (2011). Computational characterizations for structure and function of unclassified proteins in Ictalurus punctatus. Artificial Intelligent Systems and Machine Learning, 3(5), 260-280.
11 Paunikar, W. N., Sanmukh, S. G., & Ghosh, T. K. (2011). Exploring the hypothetical proteins in Rizhophages and their role in influencing Rhizobium species in soil. Artificial Intelligent Systems and Machine Learning, 3(4), 186-194.
12 Sanmukh, S. G., Paunikar, W. N., & Ghosh, T. K. (2011). Study of Hypothetical Proteins in Salmonella Phages and Predicting their Structural and Functional Relationship. Biometrics and Bioinformatics, 3(2), 70-73.
13 Sanmukh, S. G., Paunikar, W. N., Meshram, D. B., & Ghosh, T. K. (2011). Functionality Search in Hypothetical Proteins of Halobacterium Salinarum. Fuzzy Systems, 3(5), 164-187.
1 Google Scholar
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1 A. Guidolin and P.A.Manning: Genetics of Vibrio cholerae and its bacteriophages. Microbiol Rev (1987), 51:2858298.
2 Alex, B., Lachlan, C., Richard, D., Robert, D. F., Volker, H., Sam, G.J., Ajay, K., Mhairi, M., Simon, M., Erik, L. L. S., David, J. S., Corin Y., Sean, R. E., (2004). The Pfam families’ database. Nucleic Acids Research, Vol. 32, D1388D141.
3 Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., Lipman, D. J., (1997). Gapped BLAST and PSI8BLAST: “a new generation of protein database search programs”. Nucleic Acids Res. 25 (17), 33898402.
4 Aron, M. Bauer., John, B. A., Myra, K. D., Carol, D. S., Noreen, R. G., Marc, G., Luning, H., Siqian, H., David, I. H., John, D. J., Zhaoxi, K., Dmitri, K., Christopher, J. L.,Cynthia A. L., Chunlei, L., Fu, L., Shennan, L., Gabriele, H. M., Mikhail, M., James, S. S., Narmada, T., Roxanne, A. Y., Jodie, J. Y., Dachuan, Z., Stephen, H. B., (2006). CDD: “a conserved domain database for interactive domain family analysis. “Nucleic Acids Research, Vol. 35, D237– D240.
5 Azaro, M.A., and Landy, A. (2002) l integrase and the l Int family. In: Mobile DNA II. Craig, N.L. (ed.). Washington, DC: American Society for Microbiology Press, pp. 118–148
6 B. M. Davis and M. K. Waldor. “Filamentous phages linked to virulence of Vibrio cholera”. Curr. Opin. Microbiol. (2003), 6:35–42.
7 Basu,N., Kar,S. and Ghosh,R.K. “Molecular analysis of filamentous phage VSK of Vibrio cholerae 0139: “A possible clue to genetic transmission Unpublished
8 C. A. Kellogg, J.B. Rose, S.C. Jiang, J.M. Thurmond and J.H. Paul,” Genetic diversity of vibriophages isolated from marine environments around Florida and Hawaii,” USA. Mar Ecol Prog Ser (1995), 120: 89–98.
9 Campos, J., Martinez, E., Izquierdo, Y. and Fando, R. VEJ {phi}, “A novel filamentous phage of Vibrio cholerae able to transduce the cholera toxin genes.” Microbiology (Reading, Engl.) 156 (PT 1), 1088115 (2010)
10 Campos,J., Martinez,E., Suzarte,E., Rodriguez,B.L., Marrero,K., Silva,Y.K., Ledon,T.Y., Del Sol,R.E. and Fando,R.A. VGJphi: “A Novel Lysogenic Filamentous Phage of Vibrio cholerae which Shares the Same Integration Site with CTXphi “ Unpublished
11 Cédric, N., Desmond, G. H., Jaap, H., (2000). T8coffee: “a novel method for fast and accurate multiple sequence alignment.” J. Mol. Biol. 302, 2058217
12 Chih8Chieh, C., Jenn8Kang, H., Jinn8Moon, Y., (2006). (PS) 2 : “protein structure prediction server Nucl.” Acids Res. 34, W1528W157.
13 Das,M., Bhowmick,T.S., Sarkar,B.L., Nair,G.B., Yamasaki,S. and Nandy,R.K. “Complete genome sequence of lytic vibriophage N4 indicates close relativeness of T7 viral supergroup Unpublished
14 Davis, B.M., and Waldor, M.K. “(2000) CTXf contains a hybrid genome derived from tandemly integrated elements.” Proc Natl Acad Sci USA 97: 8572–8577
15 Davis, B.M., and Waldor, M.K. (2002) ‘”Mobile genetic elements and bacterial pathogenesis”. In: Mobile DNA II. Craig, N.L. (ed.). Washington, DC: American Society for Microbiology Press, pp. 1040–1059.
16 Dilip, G., Alankar, R., (2009). “Computational Function and Structural Annotations for Hypothetical Proteins Bacillus anthracis. Biofrontiers”, 1, 27836.
17 E. A. Jouravleva, G. A. McDonald, C. F. Garon, M. B. Finkelstein, and R. A. Finkelstein. “Characterization and possible function of a new filamentous bacteriophage from Vibrio cholera”. Microbiology (1998), 144:315–324.
18 Edward, E., Gary, L. G., Osnat, H., John, M., John, O., Roberto, J. P., Linda, B., Delwood, R., Andrew, J. H., (2000). “Biological function made crystal clear- annotation of hypothetical proteins via structural genomics.” Current Opinion in Biotechnology 11, 25830.
19 . Ehara, M., Nguyen, M.B., Nguyen,T.D., Ngo,C.T., Le,H.T., Nguyen,T.H. and Iwami,M. Integrated kappa phage genome Unpublished
20 Faruque,S.M., Bin Naser., Fujihara., Diraphat., Chowdhury., Kamruzzaman., Qadri., Yamasaki,S., Ghosh,R.K. and Mekalanos,J.J. Genomic sequence and receptor for the Vibrio cholerae phage KSF81phi: “evolutionary divergence among filamentous vibriophages mediating lateral gene transfer.” J. Bacteriol. 187 (12), 409584103 (2005)
21 H. Nakanishi, Y. Iida, K. Maeshima, T. Teramoto, Y. Hosaka and M. Ozaki. “Isolation and properties of bacteriophages of Vibrio parahaemolyticus. “Biken J (1966), 9: 149– 157.
22 Hardies, S.C., Comeau, A.M., Serwer, P. and Suttle, C.A. “The complete sequence of marine bacteriophage VpV262 infecting vibrio parahaemolyticus indicates that an ancestral component of a T7 viral supergroup is widespread in the marine environment”; Virology 310 (2), 3598371 (2003)
23 Honma, Y., Ikema, M., Toma, C., Ehara, M. and Iwanaga, M.” Molecular analysis of a filamentous phage (fsl) of Vibrio cholerae O139;” Biochim. Biophys. Acta 1362 (283), 1098115 (1997)
24 J. Campos, E. Martinez, E. Suzarte, B. L. Rodriguez, K. Marrero, Y. Silva, T. Ledo´n, R. del Sol, and R. Fando. VGJ_, “a novel filamentous phage of Vibrio cholerae, integrates into the same chromosomal site as CTX”_. J. Bacteriol. (2003), 185:5685–5696.
25 J. Campos, E. Martinez, K. Marrero, Y. Silva, B. L. Rodriguez, E. Suzarte, T. Ledon, and R. Fando.’ Novel type of specialized transduction for CTX_ or its satellite phage RS1 mediated by filamentous phage VGJ_ in Vibrio cholera”. J. Bacteriol. (2003), 185:7231–7240.
26 J.A. Baross, J. Liston, and R.Y. Morita. “Some implications of genetic exchange among marine vibrios, including Vibrio parahaemolyticus, naturally occurring in the Pacific oyster”. In International Symposium on Vibrio parahaemolyticus. Fujino, T., Sakaguchi, G., Sakazaki, R., and Takeda, Y. (eds). Tokyo, Japan: Saikon Publishing, (1974), pp. 129–137.
27 K. Moebus and H. Nattkemper. ‘Bacteriophage sensitivity patterns among bacteria isolated from marine waters. Helgolander Meeresunters.“(1981), 34: 3758385
28 . K. Moebus. Ecology of manne bacteriophages. In: Goyal, S. M., Gerba. C. P, Bitton, G. (eds.) Phage ecology. John Wiley & Sons. New York, (1987), p. 1378156
29 Kapfhammer, D., Blass, J., Evers, S. and Reidl, J. Vibrio cholerae phage K139: “complete genome sequence and comparative genomics of related phages”; J. Bacteriol. 184 (23), 659286601 (2002)
30 M. Ikema and Y. Honma. “A novel filamentous phage, fs2, of Vibriocholerae O139.” Microbiology (1998), 144:1901–1906.
31 M. K. Waldor and J. J. Mekalanos”. Lysogenic conversion by a filamentous phage encoding cholera toxin”. Science (1996), 272:1910–1914.
32 Miller,E.S., Heidelberg,J.F., Eisen,J.A., Nelson,W.C., Durkin,A.S., Ciecko,A., Feldblyum,T.V., White,O., Paulsen,I.T., Nierman,W.C., Lee,J., Szczypinski,B. and Fraser,C.M. “Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage” J. Bacteriol. 185 (17), 522085233 (2003)
33 Moyer, K.E., Kimsey, H.H., and Waldor, M.K. (2001) “Evidence for a rolling-circle mechanism of phage DNA synthesis from both replicative and integrated forms of CTXf. Mol Microbiol 41:” 311–323.
34 Ochman, H., Lawrence, J.G., and Groisman, E.A. (2000)” Lateral gene transfer and the nature of bacterial innovation.” Nature 405: 299–304.
35 Roman, L. T., Michael, Y., Galperin, Darren A. Natale, Eugene V. Koonin (2000). ”The COG database: a tool for genome –scale analysis of protein functions and evolution. Nucleic Acid Research.” 28, 33836.
36 S. Kar, R. K. Ghosh, A. N. Ghosh, and A. Ghosh.” Integration of the DNA of a novel filamentous bacteriophage VSK from Vibrio cholerae O139 into the host chromosomal DNA. FEMS Microbiol.” Lett. (1996), 145:17–22.
37 S. M. Faruque, I. Bin Naser, K. Fujihara, P. Diraphat, N. Chowdhury, M. Kamruzzaman, F. Qadri, S. Yamasaki, A. N. Ghosh, and J. J. Mekalanos. “Genomic sequence and receptor for the Vibrio cholerae phage KSF-1_: evolutionary divergence among filamentous vibriophages mediating lateral gene transfer”. J. Bacteriol. (2005), 187:4095–4103.
38 S. Matsuzaki, S. Tanaka, T. Koga, and T. Kawata. “A broad-host-range vibriophage, KVP40, isolated from sea water”. Microbiol. Immunol. (1992), 36:93–97.
39 S. Matsuzaki, T. Inoue, M. Kuroda, S. Kimura and S. Tanaka. “Cloning and sequencing of major capsid protein (mcp) gene of a vibriophage, KVP20, possibly related to Teven coliphages” Gene (1998), 222: 25–30.
40 . Schaffer, A. A., Aravind, L., Madden, T. L., Shavirin, S. Spouge, J. L., Wolf, Y. I., Koonin, E. V., Altschul, S. F., (2001).” Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements”. Nucleic Acids Res. 29(14), 29948 3005.
41 T. Koga, S. Toyoshima and T. Kawata. “Morphological varieties and host ranges of Vibrio parahaemolyticus bacteriophages isolated from seawater”. Appl Environ Microbiol (1982), 44: 466–470.
42 W.I. Lencer and B. Tsai. “The intracellular voyage of cholera toxin: going retro. “Trends Biochem Sci (2003), 28: 639– 645.
43 Wang,D., Kan,B., Li,Y., Liu,Z., Gao,S., Liu,Y., Liang,W., Zhang,L., Yan,M., Li,W., Liu,G., Liu,Y., Li,J., Diao,B., Zhu,Z. and Qiu,H. Vibrio cholerae phage VP2 complete genome Unpublished
44 Wendy, B. et al., (2000). “The EMBL Nucleotide Sequence Database”. Nucleic Acid Research. 28, 19823
45 Zafer, A., Yucel, A., Mark, B., (2006). “Protein secondary structure prediction for a singlesequence using hidden semi-Markov models, BMC Bioinformatics, “7, 178.
46 Zdobnov, E. M., Rolf, A., (2001).” Interproscan- an integration platform for the signatures recognition methods in InterPro. Bioinformatics “17, 8478848
Dr. Swapnil G. Sanmukh
Mr. Waman Narayan Paunikar
National Environmental Engineering Research Institute, NEERI, Nagpur, India - India
Mr. Tarun Kanti Ghosh
National Environmental Engineering Research Institute, NEERI, Nagpur, India - India
Dr. Tapan Chakrabarti