title: DNA and RNA binding by the mitochondrial lon protease is regulated by nucleotide and protein substrate.
abstract: The ATP-dependent Lon protease belongs to a unique group of proteases that bind DNA. Eukaryotic Lon is a homo-oligomeric ring-shaped complex localized to the mitochondrial matrix. In vitro, human Lon binds specifically to a single-stranded GT-rich DNA sequence overlapping the light strand promoter of human mitochondrial DNA (mtDNA). We demonstrate that Lon binds GT-rich DNA sequences found throughout the heavy strand of mtDNA and that it also interacts specifically with GU-rich RNA. ATP inhibits the binding of Lon to DNA or RNA, whereas the presence of protein substrate increases the DNA binding affinity of Lon 3.5-fold. We show that nucleotide inhibition and protein substrate stimulation coordinately regulate DNA binding. In contrast to the wild type enzyme, a Lon mutant lacking both ATPase and protease activity binds nucleic acid; however, protein substrate fails to stimulate binding. These results suggest that conformational changes in the Lon holoenzyme induced by nucleotide and protein substrate modulate the binding affinity for single-stranded mtDNA and RNA in vivo. Co-immunoprecipitation experiments show that Lon interacts with mtDNA polymerase gamma and the Twinkle helicase, which are components of mitochondrial nucleoids. Taken together, these results suggest that Lon participates directly in the metabolism of mtDNA.
authors.affiliation: Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA.
authors.forename: Tong
authors.initials: T
authors.lastname: Liu
authors.forename: Bin
authors.initials: B
authors.lastname: Lu
authors.forename: Irene
authors.initials: I
authors.lastname: Lee
authors.forename: Gabriela
authors.initials: G
authors.lastname: Ondrovicová
authors.forename: Eva
authors.initials: E
authors.lastname: Kutejová
authors.forename: Carolyn K
authors.initials: CK
authors.lastname: Suzuki
mesh_terms: D049069:ATP-Dependent Proteases; D002412:Cations / Q000378:metabolism; D004265:DNA Helicases; D000074002:DNA Polymerase gamma; D019915:DNA Primase / Q000378:metabolism; D004272:DNA, Mitochondrial / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D006147:Guanine / Q000378:metabolism; D006360:Heat-Shock Proteins / Q000378:metabolism*; D006801:Humans; D066298:In Vitro Techniques; D008928:Mitochondria / Q000201:enzymology* / Q000235:genetics; D024101:Mitochondrial Proteins; D016601:RNA-Binding Proteins / Q000378:metabolism; D011994:Recombinant Proteins / Q000378:metabolism; D012697:Serine Endopeptidases / Q000378:metabolism*; D013379:Substrate Specificity; D014498:Uracil / Q000378:metabolism
chemical_list: D002412:Cations; D004272:DNA, Mitochondrial; D004268:DNA-Binding Proteins; D006360:Heat-Shock Proteins; D024101:Mitochondrial Proteins; D016601:RNA-Binding Proteins; D011994:Recombinant Proteins; D014498:Uracil; D006147:Guanine; D019915:DNA Primase; D000074002:DNA Polymerase gamma; D004259:DNA-Directed DNA Polymerase; D049069:ATP-Dependent Proteases; D012697:Serine Endopeptidases; D004265:DNA Helicases; C431576:TWNK protein, human