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
Affiliations
Waleed M.M. El-Sayed
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Marine Microbiology Department, National Institute of Oceanography and Fisheries, Red Sea, 84517, Egypt
Alli L. Gombolay
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Penghao Xu
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Taehwan Yang
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Youngkyu Jeon
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Sathya Balachander
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Gary Newnam
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Sijia Tao
Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
Nicole E. Bowen
Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
Tomáš Brůna
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Mark Borodovsky
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
Raymond F. Schinazi
Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
Baek Kim
Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
Yongsheng Chen
School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
Francesca Storici
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Corresponding author
Summary: 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.
