Phylogeny derived from homodimeric endonuclease correlates with its pre-RNA substrates

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DOI: 10.4236/abb.2011.23018   PDF   HTML   XML   4,627 Downloads   9,546 Views  

Abstract

Amongst endonuclease, the homodimeric variety is found in many prokaryotes for processing of the introns out from pre-RNAs. But as the variety and the complexity of introns rise with evolution, do the homodimeric endonuclease adapt to the changes? The correlations between evolving pre-RNAs and adapting homodimeric endonuclease in lower prokaryotes is investigated in this paper. First, we construct and observe the appearance of a long branch in the phylogeny based on homodimeric endonuclease. To appreciate the finer aspects of accelerating evolution near this long branch, we delve deeper into the pre-RNA substrates of the endonuclease. Computational evidence of an as-yet-unreported noncoding RNA gene then emerges from this study. The capabilities of homodimeric endonuclease and the complexities of its pre-RNA substrates appear to evolve in steps together.

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Mitra, S. , Das, S. , Sahoo, S. , Sinha, C. and Chakrabarti, J. (2011) Phylogeny derived from homodimeric endonuclease correlates with its pre-RNA substrates. Advances in Bioscience and Biotechnology, 2, 117-122. doi: 10.4236/abb.2011.23018.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] Chen, K., Eargle, J., Sarkar, K., Gruebele, M. and Luthey-Schulten, Z. (2010) Functional role of ribosomal signatures. Biophysical Journal, 99, 3930-3940. doi:10.1016/j.bpj.2010.09.062
[2] Sachidanandam, R. (2005) RNAi as a bioinformatic con- sumer. Briefings in Bioinformatics, 6, 146-162. doi:10.1093/bib/6.2.146
[3] Srinivasan, G., James,C. and Krzycki, J. (2002) Pyrroly- sine encoded by UAG in archaea: charging of a UAG- decoding specialized tRNA. Science, 296, 1459-1462. doi:10.1126/science.1069588
[4] Kohrer, C., Srinivasan, G., Mandal, D., Mallick, B., Ghosh, Z., Chakrabarti, J. and RajBhandary, U. (2008) Identification and characterization of a tRNA decoding the rare AUA codon in Haloarcula marismortui. RNA, 14, 1-10.
[5] Das, S., Mitra, S., Sahoo, S. and Chakrabarti, J. (2011) Novel hybrid encodes both continuous and split tRNA genes. Journal of Biomolecular Structure and Dynamics, 28, 827-831.
[6] Mallick, B., Chakrabarti, J., Sahoo, S., Ghosh, Z. and Das, S. (2005) Identity Elements of Archaeal tRNA. DNA Research, 12, 235-246. doi:10.1093/dnares/dsi008
[7] Abelson, J., Trotta, C.R. and Li, H. (1998) tRNA splicing. Journal of Biological Chemistry, 273, 12685-12688. doi:10.1074/jbc.273.21.12685
[8] Wolf, Y.I., Rogozin, I.B., Grishin, N.V. and Koonin, E.V. (2002) Genome trees and the tree of life. Trends in Genetics, 18, 472-479. doi:10.1016/S0168-9525(02)02744-0
[9] Woese, C.R. (1987) Bacterial evolution. Microbiology and Molecular Biology Reviews, 51, 221-271.
[10] Aravind, L., Tatusov, R.L., Wolf, Y.I., Walker, D.R. and Koonin, E.V. (1998) Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends in Genetics, 14, 442-444. doi:10.1016/S0168-9525(98)01553-4
[11] Nelson, K.E., Clayton, R.A., Gill, S.R., et al. (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritime. Nature, 399, 323-329. doi:10.1038/20601
[12] Ochman, H., Lawrence, J.G. and Groisman, E.A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299-304. doi:10.1038/35012500
[13] Gogarten, J.P., Doolittle, W.F. and Lawrence, J.G. (2002) Prokaryotic evolution in light of gene transfer. Molecular Biology and Evolution, 19, 2226-2238.
[14] Jain, R., Rivera, M.C., Moore, J.E. and Lake, J.A. (2002) Horizontal gene transfer in microbial genome evolution. Theoretical Population Biology, 61, 489-495. doi:10.1006/tpbi.2002.1596
[15] Zhaxybayeva, O., Swithers, K.S., Lapierre, P., Fournier, G.P., Bickhart, D.M., DeBoy, R.T., Nelson, K.E., Nesbo, C. L., Ford Doolittle, W.J., Gogarten, P. and Noll, K.M. (2009) On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proceedings of the National Academy of Sciences, 106, 5865-5870. doi:10.1073/pnas.0901260106
[16] Garrity, G. (2001) Bergey’s manual of systematic bac- teriology. Springer-Verlag, Berlin.
[17] Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., et al. (1997) Complete genome sequence of Methanobac- terium thermoautotrophicum DH, functional analysis and comparative genomics. Journal of Bacteriology, 179, 7135-7155.
[18] Slesare, A.I., Mezhevaya, K.V., Makarova, K.S., et al. (2002) The complete genome of hyperthermophile Me- thanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proceedings of the National Academy of Sciences, 99, 4644-4649. doi:10.1073/pnas.032671499
[19] Kjems, J., Leffers, H., Olsen,T. and Garrett, R.A. (1989) A unique tRNA intron in the variable loop of the extreme thermophile Thermophilum pendens and its possible evo- lutionary implications. Journal of Biological Chemistry, 264, 17834-17837.
[20] Li, H. and Abelson, J. (2000) Crystal structure of a dimeric archaeal splicing Endonuclease. Journal of Molecular Biology, 302, 639-648. doi:10.1006/jmbi.2000.3941
[21] Tocchini-Valentini, G.D., Fruscoloni, P. and Tocchini- Valentini, G.P. (2005) Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea. Proceedings of the National Academy of Sciences, 102, 15418-15422.
[22] Mittal, A. and Jayaram, B. (2011) Backbones of folded proteins reveal novel invariant amino acid neighborhoods. Journal of Biomolecular Structure and Dynamics, 28, 443-454.
[23] Ghosh, Z., Mallick, B. and Chakrabarti, J. (2009) Cellular versus microRNAs in host-virus interaction. Nucleic Acids Research, 37, 1035-1048. doi:10.1093/nar/gkn1004
[24] Giulio, M.D. (1999) The non-monophyletic origin of the tRNA molecule. Journal of Theoretical Biology, 197, 403-414. doi:10.1006/jtbi.1998.0882

  
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