Codon usage bias in radioresistant bacteria

Maddalena Dilucca; Athanasia Pavlopoulou; Alexandros G Georgakilas; Andrea Giansanti

doi:10.1016/j.gene.2020.144554

Codon usage bias in radioresistant bacteria

Gene. 2020 Jun 5:742:144554. doi: 10.1016/j.gene.2020.144554. Epub 2020 Mar 13.

Authors

Maddalena Dilucca¹, Athanasia Pavlopoulou², Alexandros G Georgakilas³, Andrea Giansanti⁴

Affiliations

¹ Physics Department, Sapienza University of Rome, Rome, Italy. Electronic address: maddalena.dilucca@gmail.com.
² Izmir International Biomedicine and Genome Institute (iBG-Izmir), Dokuz Eyll University, 35340, Turkey.
³ Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Athens, Greece.
⁴ Physics Department, Sapienza University of Rome, Rome, Italy; INFN Roma1 Unit, Rome, Italy.

PMID: 32173539
DOI: 10.1016/j.gene.2020.144554

Abstract

The relationship between patterns of codon usage bias (CUB), the preferential usage of synonimous nucleotide triplets encoding the same amino acid, and radioresistance was investigated int he genomes of 16 taxonomically distinct radioresistant prokaryotic organisms and in a control set of 11 non-radioresistant bacteria. The radioresistant species were found to be strongly biased towards G and C in the third synonimous codon position. ENC and neutrality plots also sugest that CUB in radioresistant bacteria is mainly affected by mutational bias. Furthermore, the availability of tRNA gene copy number was analyzed and it was found that nine radioresistant species have the sam number of tRNA gene copies for each codon. This suggests that tRNA gene copies and codon bias co-evolved in a specific way in radioresistant species.

Keywords: Bacteria; Codon bias; Gene; Protein interaction network; Radioresistance.

MeSH terms

Bacteria / genetics*
Bacteria / radiation effects
Codon Usage / radiation effects*
Genome, Bacterial / radiation effects*
Mutation / radiation effects
RNA, Transfer / genetics
Radiation Tolerance / genetics*
Selection, Genetic / radiation effects*

Substances

RNA, Transfer