Novel interaction interfaces mediate the interaction between the NEIL1 DNA glycosylase and mitochondrial transcription factor A

Abstract

The maintenance of human mitochondrial DNA (mtDNA) is critical for proper cellular function as damage to mtDNA, if left unrepaired, can lead to a diverse array of pathologies. Of the pathways identified to participate in DNA repair within the mitochondria, base excision repair (BER) is the most extensively studied. Protein-protein interactions drive the step-by-step coordination required for the successful completion of this pathway and are important for crosstalk with other mitochondrial factors involved in genome maintenance. Human NEIL1 is one of seven DNA glycosylases that initiates BER in both the nuclear and mitochondrial compartments. In the current work, we scrutinized the interaction between NEIL1 and mitochondrial transcription factor A (TFAM), a protein that is essential for various aspects of mtDNA metabolism. We note, for the first time, that both the N- and C- terminal domains of NEIL1 interact with TFAM revealing a unique NEIL1 protein-binding interface. The interaction between the two proteins, as observed biochemically, appears to be transient and is most apparent at concentrations of low salt. The presence of DNA (or RNA) also positively influences the interaction between the two proteins, and molar mass estimates indicate that duplex DNA is required for complex formation at higher salt concentrations. Hydrogen deuterium exchange mass spectrometry data reveal that both proteins exchange less deuterium upon DNA binding, indicative of an interaction, and the addition of NEIL1 to the TFAM-DNA complex alters the interaction landscape. The transcriptional activity of TFAM appears to be independent of NEIL1 expression under normal cellular conditions, however, in the presence of DNA damage, we observe a significant reduction in the mRNA expression of TFAM-transcribed mitochondrial genes in the absence of NEIL1. Overall, our data indicate that the interaction between NEIL1 and TFAM can be modulated by local environment such as salt concentrations, protein availability, the presence of nucleic acids, as well as the presence of DNA damage.

Frequencies and spectra of aflatoxin B1-induced mutations in liver genomes of NEIL1-deficient mice as revealed by duplex sequencing

“…Given the increased burden for elevated base damages within the mitochondria, especially those arising from the generation of reactive oxygen species, mitochondrial BER can be initiated by multiple DNA glycosylases including UNG1, MUTYH, OGG1, NEIL1, and NTH1 ( 83 , 84 ). The biological significance of mitochondrial BER in limiting the development of obesity and metabolic syndrome has been demonstrated through analyses of C57Bl6 mice deficient in Ogg1 ( 85–87 ).…”

Complex Roles of NEIL1 and OGG1: Insights Gained from Murine Knockouts and Human Polymorphic Variants

“…mtNEIL1 binds to the tetrameric form of mitochondrial single-stranded binding protein (mtSSB) in the presence of duplex DNA, but in the absence of DNA the complex is reduced to a NEIL1-mtSSB complex [102]. Furthermore, mtNEIL1 also interacts with mitochondrial transcription factor A (TFAM) [103]. A proposed biological role for this interaction is that in the absence of NEIL1, TFAM-transcribed mitochondrial genes are significantly downregulated.…”

Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase

“…NEIL1 is one of 11 mammalian DNA glycosylases that catalyzes the first step of BER (Prakash & Doublie ´, 2015;Prakash et al, 2012). The full-length mature NEIL1 enzyme comprises 390 amino-acid residues; over a quarter of the protein (100 residues at the C-terminus) is disordered and participates in various protein-protein interactions involving replication and repair factors (Sharma et al, 2018(Sharma et al, , 2022Hegde et al, 2012). The crystal structure of NEIL1 alone, lacking 56 amino-acid residues at the C-terminal end (NEIL1-�56), has previously been obtained (Doublie ´et al, 2004), as well as several DNA-bound structures of NEIL1 lacking 95 aminoacid residues at the C-terminal region (NEIL1-�95; Zhu et al, 2016;Liu et al, 2021).…”