Phylogeny derived from homodimeric endonuclease correlates with its pre-RNA substrates
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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.
- 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
- Sachidanandam, R. (2005) RNAi as a bioinformatic con- sumer. Briefings in Bioinformatics, 6, 146-162. doi:10.1093/bib/6.2.146
- 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
- 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.
- 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.
- 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
- 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
- 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
- Woese, C.R. (1987) Bacterial evolution. Microbiology and Molecular Biology Reviews, 51, 221-271.
- 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
- 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
- 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
- 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.
- 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