Evidence of a pathway of reduction in bacteria: Reduced quantities of restriction sites impact tRNA activity in a trial set

Oliver Bonham-Carter, Lotfollah Najjar, Dhundy Bastola

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

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 au- Toimmune defenses to end pathogen threats. These motifs may also appear in the host's genome where they are methy-lated 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 sub-tilis, Escherichia coli, Haemophilus inuenzae, 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 ex- Tends from palindromes to tRNAs which may follow from evolutionary pressures concerning restriction site handling.

Original languageEnglish (US)
Title of host publication2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
Pages926-932
Number of pages7
DOIs
StatePublished - 2013
Event2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 - Wshington, DC, United States
Duration: Sep 22 2013Sep 25 2013

Publication series

Name2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013

Conference

Conference2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
CountryUnited States
CityWshington, DC
Period9/22/139/25/13

Keywords

  • Palindromic avoidance
  • Pathway of reduction
  • TRNA

ASJC Scopus subject areas

  • Bioengineering
  • Biomedical Engineering
  • Health Informatics

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    Bonham-Carter, O., Najjar, L., & Bastola, D. (2013). Evidence of a pathway of reduction in bacteria: Reduced quantities of restriction sites impact tRNA activity in a trial set. In 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 (pp. 926-932). (2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013). https://doi.org/10.1145/2506583.2512365