TFAM organizes DNA into compact higher order structures

Abstract

TFAM (Transcription Factor A, Mitochondrial) is an essential human protein that plays two key roles in mitochondrial DNA (mtDNA) homeostasis. TFAM acts as a transcription factor that specifically binds to promoter regions, but it is also solely responsible for organizing mtDNA into nucleoids by nonspecifically covering the entire genome. Many studies have addressed TFAM in transcription regulation, but its role as a genome organizing entity is not well characterized. The current understanding of how TFAM compacts DNA into nucleoids is based on crystal structures of a TFAM monomer bound to short fragments of DNA (22-28 bp). However, this does not adequately reflect the biological role of TFAM in organizing the nucleoid where multiple TFAM molecules oligomerize on the 16.5 kb genome to form the nucleoid. Here, we present a biochemical and structural analysis of TFAM oligomerization on longer DNA. Our results show that TFAM compacts longer segments of DNA into higher order complexes that are homogenous yet exhibit continuous conformational dynamics. Significance statementMutations or damage to mitochondrial DNA (mtDNA) severely impairs cellular respiration and is implicated in many human diseases and aging. Transcription Factor A, Mitochondrial (TFAM) is an essential protein that is solely responsible for packaging mtDNA into nucleoids thereby shielding it from DNA damage. Despite its importance, the mechanism by which this is accomplished is poorly understood. Here, we use biochemistry to show that TFAM oligomerizes on DNA to form compact, homogenous higher order structures in solution. We also examined these complexes at a low resolution using cryo-EM, suggesting an organizational unit of mtDNA. This work reveals there may be a regular organization to mitochondrial nucleoids, providing the basis for further understanding mtDNA compaction by TFAM.