Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii

Waleed M M El-Sayed; Alli L Gombolay; Penghao Xu; Taehwan Yang; Youngkyu Jeon; Sathya Balachander; Gary Newnam; Sijia Tao; Nicole E Bowen; Tomáš Brůna; Mark Borodovsky; Raymond F Schinazi; Baek Kim; Yongsheng Chen; Francesca Storici

doi:10.1016/j.isci.2020.102005

Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii

iScience. 2020 Dec 29;24(1):102005. doi: 10.1016/j.isci.2020.102005. eCollection 2021 Jan 22.

Authors

Waleed M M El-Sayed^{1

2

3}, Alli L Gombolay¹, Penghao Xu¹, Taehwan Yang¹, Youngkyu Jeon¹, Sathya Balachander¹, Gary Newnam¹, Sijia Tao⁴, Nicole E Bowen⁴, Tomáš Brůna¹, Mark Borodovsky^{1

5

6}, Raymond F Schinazi⁴, Baek Kim⁴, Yongsheng Chen², Francesca Storici¹

Affiliations

¹ School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
² School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
³ Marine Microbiology Department, National Institute of Oceanography and Fisheries, Red Sea, 84517, Egypt.
⁴ Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA.
⁵ Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
⁶ School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Abstract

Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genome of cells. The distribution of rNMPs in DNA has been studied only in limited genomes. Using the ribose-seq protocol and the Ribose-Map bioinformatics toolkit, we reveal the distribution of rNMPs incorporated into the whole genome of a photosynthetic unicellular green alga, Chlamydomonas reinhardtii. We discovered a disproportionate incorporation of adenosine in the mitochondrial and chloroplast DNA, in contrast to the nuclear DNA, relative to the corresponding nucleotide content of these C. reinhardtii organelle genomes. Our results demonstrate that the rNMP content in the DNA of the algal organelles reflects an elevated ATP level present in the algal cells. We reveal specific biases and patterns in rNMP distributions in the algal mitochondrial, chloroplast, and nuclear DNA. Moreover, we identified the C. reinhardtii orthologous genes for all three subunits of the RNase H2 enzyme using GeneMark-EP + gene finder.

Keywords: Genomics; Molecular Biology.

Abstract

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