AiM  Vol.6 No.13 , November 2016
Identification of Prophages within the Mycobacterium avium 104 Genome and the Link of Their Function Regarding to Environment Survival
Mycobacterium avium is an opportunistic bacterium associated with pathogenic behavior in both humans and animals. M. avium has evolved as a pathogen by having an environmental component in its life . Prophages are the integrated viral forms in bacterium genome. They constitute about 10% - 20% of genome of many bacteria and they contribute to pathogenicity of microbes. We investigated whether the M. avium 104 genome contained prophages and evaluated the genes/proteins for putative functions. Three prophage genes were identified in the M. avium 104 database, and sequences were analyzed for specific motifs. The prophage sequences were then cloned in Mycobacterium smegmatis and the bacterial phenotype was evaluated in gain of function assays for environmental stresses, such as tolerance to extreme temperatures, UV light, biofilm formation and resistance to acid as well as macrophage survival. The results indicate that two of the prophage genes, MAV_0696 and MAV_2265, confer M. smegmatis with enhanced ability to produce biofilm. Using a Real-Time PCR, it was determined that MAV_0696 and MAV_2265 transcripts were upregulated upon biofilm formation by M. avium. The expression of MAV_2265 gene was significantly higher at all selected time points. In addition, the expression of MAV_2265 in M. smegmatis also led to significantly greater survival rate at pH 5.0 compared to the wild-type control. None of the other physical abilities were altered by overexpressing the prophage genes in M. smegmatis. In summary, we identified three prophage sequences in M. avium 104, from which two of them were found to be associated with biofilm formation and one with resistance to the acidic environment. Future studies will identify the mechanisms involved in the prophages function.
Cite this paper: Zhao, M. , Gilbert, K. , Danelishvili, L. , Jeffrey, B. and Bermudez, L. (2016) Identification of Prophages within the Mycobacterium avium 104 Genome and the Link of Their Function Regarding to Environment Survival. Advances in Microbiology, 6, 927-941. doi: 10.4236/aim.2016.613087.

[1]   Falkinham 3rd, J.O. (1996) Epidemiology of Infection by Nontuberculous Mycobacteria. Clinical Microbiology Reviews, 9, 177-215.

[2]   Ohta, H. (2003) Disseminated Mycobacterium avium Complex (MAC) in a Patient with Acquired Immunodeficiency Syndrome (AIDS). Annals of Nuclear Medicine, 17, Front Cover, 114.

[3]   Inderlied, C.B., Kemper, C.A. and Bermudez, L.E. (1993) The Mycobacterium avium Complex. Clinical Microbiology Reviews, 6, 266-310.

[4]   von Reyn, C.F., Maslow, J.N., Barber, T.W., Falkinham, J.O. and Arbeit, R.D. (1994) Persistent Colonisation of Potable Water as a Source of Mycobacterium avium Infection in AIDS. Lancet, 343, 1137-1141.

[5]   Johansen, T.B., Olsen, I., Jensen, M.R., Dahle, U.R., Holstad, G. and Djonne, B. (2007) New Probes Used for IS1245 and IS1311 Restriction Fragment Length Polymorphism of Mycobacterium avium subsp. avium and Mycobacterium avium subsp. hominissuis Isolates of Human and Animal Origin in Norway. BMC Microbiology, 7, 14.

[6]   Canchaya, C., Fournous, G., Chibani-Chennoufi, S., Dillmann, M.L. and Brussow, H. (2003) Phage as Agents of Lateral Gene Transfer. Current Opinion in Microbiology, 6, 417-424.

[7]   Canchaya, C., Proux, C., Fournous, G., Bruttin, A. and Brussow, H. (2003) Prophage Genomics. Microbiology and Molecular Biology Reviews, 67, 238-276.

[8]   Schuch, R. and Fischetti, V.A. (2006) Detailed Genomic Analysis of the W Beta and Gamma Phages Infecting Bacillus anthracis: Implications for Evolution of Environmental Fitness and Antibiotic Resistance. Journal of Bacteriology, 188, 3037-3051.

[9]   Wagner, P.L., Livny, J., Neely, M.N., Acheson, D.W., Friedman, D.I. and Waldor, M.K. (2002) Bacteriophage Control of Shiga Toxin 1 Production and Release by Escherichia coli. Molecular Microbiology, 44, 957-970.

[10]   Brussow, H., Canchaya, C. and Hardt, W.D. (2004) Phages and the Evolution of Bacterial Pathogens: From Genomic Rearrangements to Lysogenic Conversion. Microbiology and Molecular Biology Reviews, 68, 560-602.

[11]   Bae, T., Baba, T., Hiramatsu, K. and Schneewind, O. (2006) Prophages of Staphylococcus aureus Newman and Their Contribution to Virulence. Molecular Microbiology, 62, 1035-1047.

[12]   Boyd, E.F. and Brussow, H. (2002) Common Themes among Bacteriophage-Encoded Virulence Factors and Diversity among the Bacteriophages Involved. Trends in Microbiology, 10, 521-529.

[13]   Sumby, P., Barbian, K.D., Gardner, D.J., Whitney, A.R., Welty, D.M., Long, R.D., Bailey, J.R., Parnell, M.J., Hoe, N.P., Adams, G.G., et al. (2005) Extracellular Deoxyribonuclease made by Group A Streptococcus Assists Pathogenesis by Enhancing Evasion of the Innate Immune Response. Proceedings of the National Academy of Sciences of the United States of America, 102, 1679-1684.

[14]   Hatfull, G.F., Cresawn, S.G. and Hendrix, R.W. (2008) Comparative Genomics of the Mycobacteriophages: Insights into Bacteriophage Evolution. Research in Microbiology, 159, 332-339.

[15]   Zhou, Y., Liang, Y., Lynch, K.H., Dennis, J.J. and Wishart, D.S. (2011) PHAST: A Fast Phage Search Tool. Nucleic Acids Research, 39, W347-W352.

[16]   Carter, G., Wu, M., Drummond, D.C. and Bermudez, L.E. (2003) Characterization of Biofilm Formation by Clinical Isolates of Mycobacterium avium. Journal of Medical Microbiology, 52, 747-752.

[17]   Yamazaki, Y., Danelishvili, L., Wu, M., MacNab, M. and Bermudez, L.E. (2006) Mycobacterium avium Genes Associated with the Ability to Form a Biofilm. Applied and Environmental Microbiology, 72, 819-825.

[18]   Danelishvili, L., Wu, M., Stang, B., Harriff, M., Cirillo, S.L., Cirillo, J.D., Bildfell, R., Arbogast, B. and Bermudez, L.E. (2007) Identification of Mycobacterium avium Pathogenicity Island Important for Macrophage and Amoeba Infection. Proceedings of the National Academy of Sciences of the United States of America, 104, 11038-11043.

[19]   Olivier, K.N., Weber, D.J., Wallace Jr., R.J., Faiz, A.R., Lee, J.H., Zhang, Y., Brown-Elliot, B.A., Handler, A., Wilson, R.W., Schechter, M.S., et al. (2003) Nontuberculous Mycobacteria. I: Multicenter Prevalence Study in Cystic Fibrosis. American Journal of Respiratory and Critical Care Medicine, 167, 828-834.

[20]   Yamazaki, Y., Danelishvili, L., Wu, M., Hidaka, E., Katsuyama, T., Stang, B., Petrofsky, M., Bildfell, R. and Bermudez, L.E. (2006) The Ability to form Biofilm Influences Mycobacterium avium Invasion and Translocation of Bronchial Epithelial Cells. Cellular Microbiology, 8, 806-814.

[21]   Holden, M.T., Feil, E.J., Lindsay, J.A., Peacock, S.J., Day, N.P., Enright, M.C., Foster, T.J., Moore, C.E., Hurst, L., Atkin, R., et al. (2004) Complete Genomes of Two Clinical Staphylococcus aureus Strains: Evidence for the Rapid Evolution of Virulence and Drug Resistance. Proceedings of the National Academy of Sciences of the United States of America, 101, 9786-9791.

[22]   Aziz, R.K., Edwards, R.A., Taylor, W.W., Low, D.E., McGeer, A. and Kotb, M. (2005) Mosaic Prophages with Horizontally Acquired Genes Account for the Emergence and Diversification of the Globally Disseminated M1T1 Clone of Streptococcus pyogenes. Journal of Bacteriology, 187, 3311-3318.

[23]   Banks, D.J., Lei, B. and Musser, J.M. (2003) Prophage Induction and Expression of Prophage-Encoded Virulence Factors in Group A Streptococcus Serotype M3 Strain MGAS315. Infection and Immunity, 71, 7079-7086.

[24]   Betley, M.J. and Mekalanos, J.J. (1985) Staphylococcal Enterotoxin A Is Encoded by Phage. Science, 229, 185-187.

[25]   Reidl, J. and Mekalanos, J.J. (1995) Characterization of Vibrio cholerae Bacteriophage K139 and Use of a Novel Mini-Transposon to Identify a Phage-Encoded Virulence Factor. Molecular Microbiology, 18, 685-701.

[26]   Allison, G.E. and Verma, N.K. (2000) Serotype-Converting Bacteriophages and O-Antigen Modification in Shigella flexneri. Trends in Microbiology, 8, 17-23.

[27]   Nakayama, K., Kanaya, S., Ohnishi, M., Terawaki, Y. and Hayashi, T. (1999) The Complete Nucleotide Sequence of phi CTX, a Cytotoxin-Converting Phage of Pseudomonas aeruginosa: Implications for Phage Evolution and Horizontal Gene Transfer via Bacteriophages. Molecular Microbiology, 31, 399-419.

[28]   Figueroa-Bossi, N., Uzzau, S., Maloriol, D. and Bossi, L. (2001) Variable Assortment of Prophages Provides a Transferable Repertoire of Pathogenic Determinants in Salmonella. Molecular Microbiology, 39, 260-271.

[29]   Boyd, E.F. and Brussow, H. (2002) Common Themes among Bacteriophage-Encoded Virulence Factors and Diversity among the Bacteriophages Involved. Trends in Microbiology, 10, 521-529.

[30]   Mirold, S., Rabsch, W., Tschape, H. and Hardt, W.D. (2001) Transfer of the Salmonella Type III Effector sopE between Unrelated Phage Families. Journal of Molecular Biology, 312, 7-16.