Polymerase and Proofreading Exonuclease Domains of the Nuclear-encoded DNA-dependent RNA Polymerase of Plant Mitochondria
Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai – 625 021, India.
Research Article
World Journal of Advanced Research and Reviews, 2023, 19(02), 989–1004
Article DOI: 10.30574/wjarr.2023.19.2.1670
Publication history:
Received on 08 July 2023; revised on 18 August 2023; accepted on 21 August 2023
Abstract:
Mitochondria, found in all eukaryotic cells, play a crucial role in generating much needed biological energy for the cells in the form of adenosine triphosphates (ATPs). It is a semi-autonomous organelle and is partly controlled by its own genome and mostly by the nuclear imports. To replicate its own genome, it uses two DNA polymerases, viz. polymerases IA and IB which are essentially similar to the E. coli DNA polymerase I. The nuclear-encoded RNA polymerase (NEP) (EC 2.7.7.6) is imported from the nucleus and involves in the transcription of all mitochondrial genes. In Arabidopsis thaliana, the mitochondrial NEP showed 59.05% identity to the NEP of the chloroplasts, but only 28.24% identity to the T7 RNA polymerase, suggesting the NEPs of mitochondria and chloroplasts are distinctly different. However, in both the plant NEPs, the polymerase catalytic core and proofreading (PR) exonuclease domains are completely conserved. The mitochondrial NEP’s catalytic core from different plant sources is remarkably conserved and is in close agreement with other RNA polymerases reported already and possesses a typical template-binding pair (-YG-), a basic catalytic amino acid (K) to initiate catalysis and a basic nucleotide selection amino acid R at -4, from the catalytic K. The catalytic metal-binding motifs are identified based on sequence similarity and site-directed mutagenesis (SDM) experiments. The PR exonuclease of the mitochondrial NEP belongs to the DEDD-superfamily of exonucleases.
Keywords:
Mitochondrial transcription; Nuclear-encoded RNA polymerase; RNA polymerase active site; Proofreading exonuclease; Exonuclease active site; Mechanism of action
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