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Journal of Cosmology, 2010, Vol 13, 3625-3627.
JournalofCosmology.com, December, 2010

Extending Genomic Limits Through Metagenomic Exploration

Vipin Chandra Kalia, Ph.D.,
Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi-110007, India.

Commentary

Organismal evolution is a continuous process, which is manifested in the diversity of living beings. Microbes being smaller and have much shorter life span than most eukaryotes, undergo rapid transformation. Exposure to extremely stressed conditions obliges microbes to respond and survive through rapid genetic modifications. Our excitement and surprises spring from our ignorance about the abilities of Nature. Nature has evolved every possible combination of life and its processes. It is only for us to discover each one of them from time to time. To illustrate the point, the molecular techniques of metagenomics have made us realize the quantum of information, which is yet to be explored especially in the microbial world (Handelsman, 2004, Tringe, et al., 2005) It has been aided by the fast and massive gene sequencing techniques – providing us with a vast quantum of data and soon it may be even difficult to analyze what will be generated through this exploration. Nature seems to have in its reservoir all that is needed for its survival and existence (Medhekar and Miller, 2007) Now it is only a matter of putting in efforts to reveal what bacteria can do? Bacteria acquire novel properties for its survival through horizontal gene transfer or modify their internal reservoirs of genetic material to suit the needs (Lal et al., 2008). Classical cases of antibiotic resistance either acquired or developing it from within are now an established fact (Cotter and Stibitz, 2007). So much so that pharmaceutical companies are no longer interested in investing in developing novel antibiotics (Kalia et al., 2007). Man made chemical entities used for crop protection appeared non-biodegradable at some stage in the last century are no longer so. Many microbes such as Stenotrophomonas, Sphingomonas, Citrobacter are known to degrade xenobiotics. (Selvakumar et al., 2008, Lal et al., 2010, Verma et al., 2010a,b,). The next in the queue are the organisms with ability to degrade the “non”-biodegradable lingo-cellulosic materials for generating bioenergy. Man made plastics appear non-biodegradable but nature has its equivalent – the polyhydroxyalkanoates (Kalia et al., 2003, Singh et al., 2009).

Although, the six major elements of the Periodic Table carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus have not been reported to be substituted for major biological functions, theoretically it is possible for other elements to serve similar functions. Most of the research has been limited to substitution of molybdenum by tungsten (W), zinc by cadmium in certain enzymes (Hille, 2002, Lane et al., 2005). Since Arsenic (As) as arsenate is analogous to phosphate, the possibility of its existence as a background element in the DNA, without getting expressed or manifested in other compounds such as proteins, lipids, or other cellular components is quite high (Wolfe-Simon, et al., 2010). The absence of arsenic from these molecules may be because of the instability of arsenic. Conditions which may provide stability to Arsenic may allow its incorporation in other compounds. Here, the likely protector to metals may be the polyhydroxyalkanoates, which themselves are produced under physiological stress conditions of excess of carbon and limitation of nutrients (Kalia et al., 2003, Singh et al., 2009).

What appears unbelievable today may turn out to hold good for quite a few other elements as well. It is only a matter of time and effort, which many may not like to put in and feel surprised and shaken when others (the more daring and innovative types) chance upon such findings “by chance”. Extremophiles have shown the route map for most physiological conditions and finally it is the passion and faith which drives us to the unknown, unexplored and unreported (Morimoto et al., 2008, Picataggio, 2009). Complete change in the chemical stability may allow bacteria to allow incorporation of elements. Constant exposure to a host of “harsh” environmental conditions is likely to evolve the genetic machinery in a newer direction. It is an example of courage and innovation to bring out information in public (Wolfe-Simon, et al., 2010), which many will take long to accept.





References

Cotter, P.A., and Stibitz, S. (2007). c-di-GMP-mediated regulation of virulence and biofilm formation. Curr. Opin. Microbiol., 10, 17-23.

Handelsman, J. (2004). Metagenomics: Application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Reviews, 68, 669-685.    

Hille, R. (2002). Molybdenum and tungsten in biology. Trends Biochem. Sci., 27, 360-367.

Kalia, V.C., Chauhan, A., Bhattacharyya, G., and Rashmi (2003). Genomic databases yield novel bioplastic producers. Nat. Biotechnol. 21, 845-846.

Kalia, V.C., Rani, A., Lal, S., Cheema, S., and Raut, C.P. (2007). Combing databases reveals potential antibiotic producers. Expert Opin. Drug Discov., 2, 211-224.

Lal, R., Pandey, G., Sharma, P., Kumari, K., Malhotra, S., Pandey, R., Raina, V., Kohler, H-P. E., Holliger, C., Jackson, C., Oakeshott, J.G. (2010). Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. Microbiol. Mol. Biol. Revs., 74, 1-21.

Lal, S., Cheema, S., and Kalia, V.C. (2008). Phylogeny vs genome reshuffling: Horizontal gene transfer. Ind. J. Microbiol., 48, 228-242.

Lane, T.W., Saito, M.A., George, G.N., Pickering I.J., Prince, R.C., Morel, F.M.M. (2005). A cadmium enzyme from a marine diatoms. Nature 435, 42.

Medhekar, B., Miller, J.F. (2007). Diversity-generating retroelements Curr. Opin. Micriobiol., 10, 388-395.

Ogasawara, N. (2008). Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis. DNA Res., 15, 73-81.

Picataggio, S. (2009). Potential impact of synthetic biology on the development of microbial systems for the production of renewable fuels and chemicals. Curr. Opin. Biotechnol., 19, 325-329.

Selvakumaran, S., Kapley, A., Kalia, V.C., and Purohit, H.J. (2008). Phenotypic and phylogenetic groups to evaluate the diversity of Citrobacter isolates from activated biomass of effluent treatment plants. Bioresour. Technol., 99, 1189-1195.

Singh, M., Patel, S.K.S., and Kalia, V.C. (2009). HYPERLINK "http://www.microbialcellfactories.com/content/8/1/38/abstract"Bacillus subtilis as potential producer for polyhydroxyalkanoates. Microbial Cell Factories, 8, 38.

Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C., Bork, P., Hugenholtz, P., and Rubin, E.M. (2005). Comparative metagenomics of microbial communities. Science, 308, 554-557.

Verma, V., Raju, S.C., Kapley, A., Kalia, V.C., Daginawala, H.F., and Purohit, H.J. (2010a). Evaluation of genetic and functional diversity of Stenotrophomonas isolates from diverse effluent treatment plants. Bioresour. Technol., 101, 7744-7753.

Verma, V., Raju, S.C., Kapley, A., Kalia, V.C., Gajanan, S.K., Daginawala, H.F., and Purohit, H.J. (2010b). Degradative potential of Stenotrophomonas strain HPC383 having genes homologous to dmp operon. Bioresour. Technol., doi: doi:10.1016/j.biortech.2010.11.016

Wolfe-Simon, Felisa; Blum, Jodi Switizer; Kulp, Thomas R.; Gordon, Gwyneth W.; Hoeft, Shelley E.; Pett-Ridge, Jennifer; Stolz, John F.; Webb, Samuel M.; Weber, Peter K.; Davies, Paul C.W.; Anbar, Ariel D.; Oremland, Ronald S. (2010). A bacterium that can grow by using arsenic instead of phosphorous. Science doi: 10.1126/science.1197258




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