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Evidence of a Pathway of Reduction in Bacteria: Reduced Quantities of Restriction Sites Impact tRNA Activity in a Trial Set

Published: 22 September 2013 Publication History

Abstract

Occurring naturally along the genomes of many viruses and other pathogens, short palindromic restriction sites (<14bps) are often exploited by bacterial restriction enzymes as autoimmune defenses to end pathogen threats. These motifs may also appear in the host's genome where they are methylated so as not to attract restriction enzymes to the host's genetic material. Since these motifs in the host's genome may pose a significant danger, it is likely that their numbers have been reduced due to possible failures of methylation during evolutionary time.
These palindromes are composed of bases likely containing information relating to codons used for protein translation. If palindromes are reduced in the genome, then its sequence composition making up the codons may also be found in reduced quantities. Furthermore, during translation codons are associated with tRNAs for protein fabrication which may also occur in reduced numbers.
We suggest that a pathway of reduction that can be followed from the onset of these missing palindromes to the reduction (or absence) of specific tRNAs correlated to the codons from the palindromes. To create evidence for this pathway, we studied the bacterial genomes of Bacillus subtilis, Escherichia coli, Haemophilus influenzae, Methanococcus jannaschii, Mycoplasma genitalium, Synechocystis sp. and Marchantia polymorpha. Across these organisms, we applied statistical data from reduced palindromic populations (biological and non-relevant words) to regression models and performed an analysis of genomic tRNA presence from their compositions. We illustrate a pathway of reduction that extends from palindromes to tRNAs which may follow from evolutionary pressures concerning restriction site handling.

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  • (2014)Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organismsProceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2649387.2660848(774-781)Online publication date: 20-Sep-2014

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  1. Evidence of a Pathway of Reduction in Bacteria: Reduced Quantities of Restriction Sites Impact tRNA Activity in a Trial Set

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    cover image ACM Conferences
    BCB'13: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
    September 2013
    987 pages
    ISBN:9781450324342
    DOI:10.1145/2506583
    Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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    Published: 22 September 2013

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    Author Tags

    1. palindromic avoidance
    2. pathway of reduction
    3. tRNA

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    September 22 - 25, 2013
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    • (2014)Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organismsProceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2649387.2660848(774-781)Online publication date: 20-Sep-2014

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