CFP last date
20 January 2025
Call for Paper
February Edition
IJCA solicits high quality original research papers for the upcoming February edition of the journal. The last date of research paper submission is 20 January 2025

Submit your paper
Know more
The week's pick
Responsive image
SFLA-Based Line Balancing and Task Optimization in Master-Slave Controlled Hanger Transportation Systems for Garment Production

Duc Hoang Nguyen
Random Articles
Reseach Article

Comparative Genomic Studies of hypothetical proteins in Cyanophages

by S. G. Sanmukh, M. Rahman, W. N. Paunikar
journal cover thumbnail

International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 45 - Number 15
Year of Publication: 2012
Authors: S. G. Sanmukh, M. Rahman, W. N. Paunikar
10.5120/6855-9405

S. G. Sanmukh, M. Rahman, W. N. Paunikar . Comparative Genomic Studies of hypothetical proteins in Cyanophages. International Journal of Computer Applications. 45, 15 ( May 2012), 16-33. DOI=10.5120/6855-9405

@article{ 10.5120/6855-9405,
author = { S. G. Sanmukh, M. Rahman, W. N. Paunikar },
title = { Comparative Genomic Studies of hypothetical proteins in Cyanophages },
journal = { International Journal of Computer Applications },
issue_date = { May 2012 },
volume = { 45 },
number = { 15 },
month = { May },
year = { 2012 },
issn = { 0975-8887 },
pages = { 16-33 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume45/number15/6855-9405/ },
doi = { 10.5120/6855-9405 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T20:37:39.852525+05:30
%A S. G. Sanmukh
%A M. Rahman
%A W. N. Paunikar
%T Comparative Genomic Studies of hypothetical proteins in Cyanophages
%J International Journal of Computer Applications
%@ 0975-8887
%V 45
%N 15
%P 16-33
%D 2012
%I Foundation of Computer Science (FCS), NY, USA
Abstract

The Cyanophages are the phages infecting cyanobacteria. They are potential agents for the horizontal gene transfer. The complete genome of 10 known Cyanophages deciphered the presence of various gene sequences for hypothetical proteins whose functions are not yet understood. 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 for the hypothetical proteins was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching protein databases for the presence of conserved domains. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed presences of functional domain in 258 uncharacterized proteins. These deciphered enzymatic data for hypothetical proteins can be used for the understanding of functional, structural and evolutionary development of cyanophages and its life cycle along with their role in host evolution.

References
  1. 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. The Pfam families' database. Nucleic Acids Research, Vol. 32, D138-D141, 2004.
  2. Altschul, S. , F. , Madden, T. , L. , Schaffer, A. , A. , Zhang, J. , Zhang, Z. , Miller, W. , Lipman, D. , J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (17), 3389-402, 1997.
  3. 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. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Research, Vol. 35, D237–D240, 20
  4. Baba, T. , Takeuchi, F. , Kuroda, M. , Yuzawa, H. , Aoki, K. , Oguchi, A. , et al. Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 359: 1819–1827, 2002.
  5. Barre, F. X. , and Sherratt, D. J. Xer site-specific recombination: promoting chromosome segregation. In Mobile DNA II, 2002.
  6. Breitbart, M. , Thompson, L. R. , Suttle, C. A. , Sullivan, M. B. Exploring the Vast Diversity of Marine Viruses. Oceanogr 20: 135–139, 2007.
  7. Canchaya, C. , Proux, C. , Fournous, G. , Bruttin, A. , and Brussow, H. Prophage genomics. Microbiol Mol Biol Rev 67: 238–276, 2003.
  8. Casjens, S. Prophages and bacterial genomics: what have we learned so far? Mol Microbiol 49: 277–300, 2003.
  9. Cédric, N. , Desmond, G. H. , Jaap, H. T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217, 2000.
  10. Chen, F. and Lu, J. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl. Environ. Microbiol. 68 (5), 2589-2594,2002.
  11. Chih-Chieh, C. , Jenn-Kang, H. , Jinn-Moon, Y. (PS)2: protein structure prediction server Nucl. Acids Res. 34, W152-W157, 2006.
  12. Edward, E. , Gary, L. G. , Osnat, H. , John, M. , John, O. , Roberto, J. P. , Linda, B. , Delwood, R. , Andrew, J. H. Biological function made crystal clear- annotation of hypothetical proteins via structural genomics. Current Opinion in Biotechnology 11, 25-30, 2000.
  13. Fuhrman, J. A. Marine viruses and their biogeochemical and ecological effects. Nature 399: 541–8,1999.
  14. Mann, N. H. , Clokie, M. R. , Millard, A. , Cook, A. , Wilson, W. H. , Wheatley, P. J. , Letarov, A. and Krisch, H. M. The genome of S-PM2, a 'photosynthetic' T4-type bacteriophage that infects marine Synechococcus strains. J. Bacteriol. 187 (9), 3188-3200, 2005.
  15. Millard, A. D. , Zwirglmaier, K. , Downey, M. J. , Mann, N. H. H. and Scanlan, D. J. Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution. Environ. Microbiol. 11 (9), 2370-2387, 2009.
  16. Paul, J. H. and Sullivan, M. B. Marine phage genomics: what have we learned? Curr Opin Biotechnol 16: 299–307, 2005.
  17. Pope,W. H. , Weigele,P. R. , Chang,J. , Pedulla,M. L. , Ford,M. E. , Houtz,J. M. , Jiang,W. , Chiu,W. , Hatfull,G. F. , Hendrix,R. W. and King, J. Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a 'horned' bacteriophage of marine Synechococcus. J. Mol. Biol. 368 (4), 966-981, 2007.
  18. Roman, L. T. , Michael, Y. , Galperin, Darren A. Natale, Eugene V. Koonin. The COG database: a tool for genome –scale analysis of protein functions and evolution. Nucleic Acid Research. 28, 33-36, 2000.
  19. Schaffer, A. A. , Aravind, L. , Madden, T. L. , Shavirin, S. Spouge, J. L. , Wolf, Y. I. , Koonin, E. V. , Altschul, S. F. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29(14), 2994-3005, 2001.
  20. Simpson, A. J. , Reinach, F. C. , Arruda, P. , Abreu, F. A. , Acencio, M. , Alvarenga, R. , et al. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature 406: 151–157, 2002.
  21. Smoot, J. C. , Barbian, K. D. , Van Gompel, J. J. , Smoot, L. M. , Chaussee, M. S. , Sylva, G. L. , et al. Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Proc Natl Acad Sci USA 99: 4668–4673, (2002).
  22. Smoot, L. M. , Smoot, J. C. , Graham, M. R. , Somerville, G. A. , Sturdevant, D. E. , Migliaccio, C. A. , et al. Global differential gene expression in response to growth temperature alteration in group A Streptococcus. Proc Natl Acad Sci USA 98: 10416–10421, 2001.
  23. Sullivan, M. B. , Huang, K. H. , Ignacio-Espinoza, J. C. , Berlin, A. M. , Kelly, L. , Weigele, P. R. , Defrancesco, A. S. , Kern, S. E. , Thompson, L. R. , Young, S. , Yandava, C. , Fu, R. , Krastins, B. , Chase, M. , Sarracino, D. , Osburne, M. S. , Henn, M. R. and Chisholm, S. W. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environ. Microbiol. 12 (11), 3035-3056, 2010.
  24. Sullivan, M. B. , Krastins, B. , Hughes, J. L. , Kelly, L. , Chase, M. , Sarracino, D. and Chisholm, S. W. The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial 'mobilome'. Environ. Microbiol. 11 (11), 2935-2951, 2009.
  25. Suttle, C. A. Viruses in the sea. Nature 437: 356–61, 2005.
  26. Swapnil, G. S. , Dilip, B. M. , Waman, N. P. , Tarun, K. G. Computational characterizations for structure and function of unclassified proteins in Ictalurus punctatus. CiiT International Journal of Artificial Intelligent Systems and Machine Learning DOI: AIML052011001 , 2011.
  27. Swapnil, G. S. , Waman, N. P. Study of hypothetical proteins in Shigella phages. CiiT International Journal of fuzzy Systems 2011.
  28. Swapnil, G. S. , Waman, N. P. , Dilip, B. M. , Tarun, K. G. Functionality search in hypothetical proteins of Halobacterium salinarum CiiT International Journal of fuzzy Systems 2011.
  29. Swapnil, G. S. , Waman, N. P. , Dilip, B. M. , Tarun, K. G. Insilico function prediction for hypothetical proteins in Vibrio parahaemolyticus Chromosome II. CiiT International Journal of Data Mining and Knowledge Engineering. DOI: DMKE052011003, 2011.
  30. Swapnil, G. S. , Waman, N. P. , Tarun, K. G. Computational approach for structure and functionality search for hypothetical proteins in Mycobacterium leprae CiiT International Journal of Data Mining and Knowledge Engineering DOI: DMKE032011014, 2011.
  31. Swapnil, G S. , Waman, N. P. , Tarun, K G. Study of Hypothetical Proteins in Salmonella Phages and Predicting their Structural and Functional Relationship CiiT International Journal of Biometrics and Bioinformatics. DOI: BB022011001, 2011.
  32. Swapnil, G. S. , Waman, N. P. , Tarun, K. G. & Tapan, C. Structure and Function Predictions of Hypothetical Proteins in Vibrio Phages. International Journal of Biometrics and Bioinformatics. 4, 161-175, 2010.
  33. Waman, N. P. , Swapnil, G. S. and Tarun, K. G. . Exploring the hypothetical proteins in Rizhophages and their role in influencing Rhizobium species in soil. CiiT International Journal of Artificial Intelligent systems and Machine Learning DOI: AIML042011002, 2011.
  34. Weigele,P. R. , Pope,W. H. , Pedulla,M. L. , Houtz,J. M. , Smith, A. L. , Conway, J. F. , King,J. , Hatfull,G. F. , Lawrence, J. G. and Hendrix,R. W. Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus. Environ. Microbiol. 9 (7), 1675-1695, 2007.
  35. Whiteley, M. , Bangera, M. G. , Bumgarner, R. E. , Parsek, M. R. , Teitzel, G. M. , Lory, S. , and Greenberg, E. P. Gene expression in Pseudomonas aeruginosa biofilms. Nature 413: 860–864, 2001.
  36. Yoshida,T. , Nagasaki,K. , Takashima,Y. , Shirai,Y. , Tomaru,Y. , Takao,Y. , Sakamoto,S. , Hiroishi,S. and Ogata,H. Ma-LMM01 infecting toxic Microcystis aeruginosa illuminates diverse cyanophage genome strategies. J. Bacteriol. 190 (5), 1762-1772, 2008.
  37. Zafer, A. , Yucel, A. , Mark, B. Protein secondary structure prediction for a single-sequence using hidden semi-Markov models, BMC Bioinformatics ,7, 178, 2006.
  38. Zdobnov, E. M. , Rolf, A. Interproscan- an integration platform for the signatures recognition methods in InterPro. Bioinformatics 17,847-848, 2001.
Index Terms

Computer Science
Information Sciences

Keywords

Bioinformatics Web Tools Conserved Domains Protein Structure Prediction Uncharacterized Proteins Life Cycle

Powered by PhDFocusTM