Structure Dictates Nucleotide Conservation in 16S Ribosomal RNA

Ashwin Murali1,2, Maxim Imakaev3, Geoffrey Fudenberg4 and Leonid Mirny3,4,5 1Massachusetts Institute of Technology, MIT PRIMES program, Cambridge, MA, USA 2Andover High School, Andover, MA, 01810, USA 3Department of Physics, MIT, Cambridge, MA, USA 4Harvard University, Program in Biophysics, Cambridge, MA, USA 5Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA The 16s region of rRNA (ribosomal RNA) in bacteria is well known to essential to the identification and definition of various bacterial species. The RDP (Ribosomal Database Project) provides an extensive catalog of over a million sequences of the 16s region. Analyzing these sequences, one obtains the nucleotide contents of the 16s rRNA. Upon further investigation into the contents of these sequences, we conclude purine content is more conserved than any other pair of nucleotides. This conservation is in contrast to the stark variation present in the GC (guanine+cytosine content) for the same 16s regions. It does not escape our attention that in addition to purine conservation, there is also a relative GU (guanine+uracil content) conservation though it is not as strong as the conservation present in purine content. The conservation to a lesser degree of the GU content may be due to an artifact of both purine conservation and variation present in GC content. This purine content and GU content conservation is fascinating because the conservation of these nucleotide pairs is far greater than the conservation of any individual nucleotide (adenine, uracil, cytosine, or guanine content). In addition to these overall trends, we observe this conservation being present in smaller phyla and classes. In particular, in Firmicutes, this trend appears to be reversed with GT conservation being far greater than purine conservation as the standard deviation of GT content is a fourth that of the purine content for the same phyla. Further investigation must be conducted to figure out the cause of this specific abnormality in addition to the overall trend of purine conservation. We are currently investigating biophysical models and strongly suspect mass, spatial, and volumetric constraints play a strong role in the conservation of purine and GT content as opposed to GC content in the bacterial 16s rRNA.

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