El-Sayed Waleed M M, Gombolay Alli L, Xu Penghao, Yang Taehwan, Jeon Youngkyu, Balachander Sathya, Newnam Gary, Tao Sijia, Bowen Nicole E, Brůna Tomáš, Borodovsky Mark, Schinazi Raymond F, Kim Baek, Chen Yongsheng, Storici Francesca
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.
iScience. 2020 Dec 29;24(1):102005. doi: 10.1016/j.isci.2020.102005. eCollection 2021 Jan 22.
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, . 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 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 orthologous genes for all three subunits of the RNase H2 enzyme using GeneMark-EP + gene finder.
核糖核苷单磷酸（rNMPs）是细胞基因组中最常见的非标准核苷酸。rNMPs在DNA中的分布仅在有限的基因组中得到研究。利用核糖测序协议和核糖图谱生物信息学工具包，我们揭示了光合单细胞绿藻全基因组中掺入的rNMPs的分布情况。我们发现，与核DNA相比，线粒体和叶绿体DNA中腺苷的掺入比例不成比例，这与这些细胞器基因组的相应核苷酸含量有关。我们的结果表明，藻类细胞器DNA中的rNMP含量反映了藻类细胞中升高的ATP水平。我们揭示了藻类线粒体、叶绿体和核DNA中rNMP分布的特定偏差和模式。此外，我们使用GeneMark-EP +基因查找器鉴定了核糖核酸酶H2酶所有三个亚基的直系同源基因。
