Mitochondrial Nucleoid: Shield and Switch of the Mitochondrial Genome

Table 1

Mitochondrial nucleoid-associated proteins with known functions.

Nucleoid protein	Location/shape	Function in mtDNA metabolism and/or nucleoid	Reference
Mitochondrial transcription factor A (TFAM)	Core region/homodimerization	(i) Transcription initiation	[66, 89, 90]
		(ii) mtDNA binding, bending, and packaging
		(iii) mtDNA copy number regulation and segregation
Mitochondrial single-stranded DNA-binding; protein (mtSSB)	Core region	(i) Single-stranded mtDNA binding	[66, 89, 90, 122]
		(ii) Coating of single strands of mtDNA
ATP-dependent Lon protease (LONP1)	Core region/homo-oligomeric; ring	(i) Binding to G-rich single-stranded mtDNA	[63, 66, 96, 123]
		(ii) Interaction with POLG and Twinkle
		(iii) mtDNA quality control
		(iv) TFAM degradation
Twinkle	Core region/hexamer	(i) mtDNA replication	[66]
mtDNA polymerase γ (POLG/POLG2)	Core region	(i) mtDNA replication and repair	[66, 89, 90, 122]
Mitochondrial transcription factor B1/B2; (TFB2M/TFB1M)	Core region	(i) Transcription	[66]
Mitochondrial RNA polymerase (POLRMT)	Core region	(i) Transcription	[66]
Mitochondrial transcription termination factor (mTERF)	Core region	(i) Transcription and replication	[94]
Mitochondrial topoisomerase I (TOP1M)	Core region	(i) Replication	[62]
ATPase AAA-domain-containing protein 3 (ATAD3)	Peripheral region/hexamer	(i) Binding to the D-loop region of mtDNA	[62, 66]
		(ii) Molecular scaffolding for mitochondrial translation; via association with both the mitochondrial inner; membrane and the ribosome
		(iii) Organization and segregation of nucleoids
Prohibitins 1 and 2 (PHB1 and PHB2)	Peripheral region/oligomeric; ring	(i) Stabilizing TFAM in mitochondrial nucleoids	[62]
		(ii) Maintenance of mitochondrial morphology
		(iii) Regulation of mtDNA copy number
Mitochondrial nucleoid factor 1 (MNF1 or M19)	Peripheral zone	(i) Linking between mtDNA and mitochondrial; ATP production	[76]
		(ii) mtDNA translation
		(iii) Assembly of respiratory complexes
Mitochondrial AAA protein ClpX	Peripheral region (?)	(i) mtDNA distribution	[66]
		(ii) TFAM quality control
Leucine-rich pentatricopeptide-repeat motif-containing; protein 130 (LRP130)	Peripheral region (?)	(i) Increased mtDNA transcription and RNA stability	[124]