Mitochondrial DNA

• Copy number
  • a- mtDNA can be found in different copy numbers depending on the cell and tissue type, rendering mtDNA as polyplasmic.
  • i) ranging from ~1 × 10⁵ mtDNA copies in oocytes [[35]], ~4–6 × 10³ in heart to 0.5–2 × 10³ in lungs, liver and kidney [[36]].
  • b- yet still only representing 1% of the total cellular DNA [1].
• Structure
  • a- Mammalian mtDNA is a circular double-stranded molecule of approximately 16.6 kb in size [1] that
  • i) The heavy strand is rich in guanine and encodes 12 subunits of the oxidative phosphorylation system, two ribosomal RNAs (12S and 16S), and 14 tRNAs.
  • ii) The light strand encodes one subunit, and 8 tRNAs.
  • iii) So, altogether mtDNA encodes for 37 molecules : 2 rRNAs, 22 tRNAs, and 13 proteins subunits, all of which are involved in the oxidative phosphorylation process
  • iv) mtDNA is devoid of intronic regions, and the only noncoding sequence is known as the control region or D-loop, which regulates mitochondrial transcription and replication.11
  • v) a displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA.

Mitochondrial genes

[The 37 genes of the Cambridge Reference Sequence for human mitochondrial DNA and their locations[30]]

Gene	Type	Product	Positions in the mitogenome	Strand
MT-ATP8	protein coding	ATP synthase, Fo subunit 8 (complex V)	08,366–08,572 (overlap with MT-ATP6)	H
MT-ATP6	protein coding	ATP synthase, Fo subunit 6 (complex V)	08,527–09,207 (overlap with MT-ATP8)	H
MT-CO1	protein coding	Cytochrome c oxidase, subunit 1 (complex IV)	05,904–07,445	H
MT-CO2	protein coding	Cytochrome c oxidase, subunit 2 (complex IV)	07,586–08,269	H
MT-CO3	protein coding	Cytochrome c oxidase, subunit 3 (complex IV)	09,207–09,990	H
MT-CYB	protein coding	Cytochrome b (complex III)	14,747–15,887	H
MT-ND1	protein coding	NADH dehydrogenase, subunit 1 (complex I)	03,307–04,262	H
MT-ND2	protein coding	NADH dehydrogenase, subunit 2 (complex I)	04,470–05,511	H
MT-ND3	protein coding	NADH dehydrogenase, subunit 3 (complex I)	10,059–10,404	H
MT-ND4L	protein coding	NADH dehydrogenase, subunit 4L (complex I)	10,470–10,766 (overlap with MT-ND4)	H
MT-ND4	protein coding	NADH dehydrogenase, subunit 4 (complex I)	10,760–12,137 (overlap with MT-ND4L)	H
MT-ND5	protein coding	NADH dehydrogenase, subunit 5 (complex I)	12,337–14,148	H
MT-ND6	protein coding	NADH dehydrogenase, subunit 6 (complex I)	14,149–14,673	L
MT-RNR2	protein coding	Humanin	—	—
MT-TA	transfer RNA	tRNA-Alanine (Ala or A)	05,587–05,655	L
MT-TR	transfer RNA	tRNA-Arginine (Arg or R)	10,405–10,469	H
MT-TN	transfer RNA	tRNA-Asparagine (Asn or N)	05,657–05,729	L
MT-TD	transfer RNA	tRNA-Aspartic acid (Asp or D)	07,518–07,585	H
MT-TC	transfer RNA	tRNA-Cysteine (Cys or C)	05,761–05,826	L
MT-TE	transfer RNA	tRNA-Glutamic acid (Glu or E)	14,674–14,742	L
MT-TQ	transfer RNA	tRNA-Glutamine (Gln or Q)	04,329–04,400	L
MT-TG	transfer RNA	tRNA-Glycine (Gly or G)	09,991–10,058	H
MT-TH	transfer RNA	tRNA-Histidine (His or H)	12,138–12,206	H
MT-TI	transfer RNA	tRNA-Isoleucine (Ile or I)	04,263–04,331	H
MT-TL1	transfer RNA	tRNA-Leucine (Leu-UUR or L)	03,230–03,304	H
MT-TL2	transfer RNA	tRNA-Leucine (Leu-CUN or L)	12,266–12,336	H
MT-TK	transfer RNA	tRNA-Lysine (Lys or K)	08,295–08,364	H
MT-TM	transfer RNA	tRNA-Methionine (Met or M)	04,402–04,469	H
MT-TF	transfer RNA	tRNA-Phenylalanine (Phe or F)	00,577–00,647	H
MT-TP	transfer RNA	tRNA-Proline (Pro or P)	15,956–16,023	L
MT-TS1	transfer RNA	tRNA-Serine (Ser-UCN or S)	07,446–07,514	L
MT-TS2	transfer RNA	tRNA-Serine (Ser-AGY or S)	12,207–12,265	H
MT-TT	transfer RNA	tRNA-Threonine (Thr or T)	15,888–15,953	H
MT-TW	transfer RNA	tRNA-Tryptophan (Trp or W)	05,512–05,579	H
MT-TY	transfer RNA	tRNA-Tyrosine (Tyr or Y)	05,826–05,891	L
MT-TV	transfer RNA	tRNA-Valine (Val or V)	01,602–01,670	H
MT-RNR1	ribosomal RNA	Small subunit : SSU (12S)	00,648–01,601	H
MT-RNR2	ribosomal RNA	Large subunit : LSU (16S)	01,671–03,229	H

Methylation of mt DNA

• a- MtDNA methylation approximations to range from 1 to 20% [44].
• b- MtDNA methylation occurs only in non-CpG sites {F. C. Lopes, 2020 #1538}2nd
• c- LIMitation
  • Functional roles of mtDNA methylation remain unknown.
  • Current detection methods are too biased to be reliable
  • mtDNA involves fragmentation via sonication, causing loss of information

Mitochondrial turnover

• Defective mitochondria have to be eliminated to maintain cellular homeostasis
• Menzies and Gold [97] estimated that the turnover of mitochondria in rats in liver, heart and brain is 9.3, 17.5 and 24.4 days respectively [97]
• (Vincow, 2013 #929) drosophilia: mito proteins (RESpiratory chain proteins) showed an extensive range of half-lives, with mitochondrial proteins generally longer-lived than nonmitochondrial proteins (Fig. S1 and Dataset S1). The broad range of mitochondrial protein half-lives is consistent with the fact that, although autophagy degrades mitochondria as units, mitochondrial protein turnover also occurs through mitochondrial proteases (24) and the ubiquitin-proteasome system (25, 26)
• {Grünewald, 2016 #935} has half life of each MC subunits

Mitochondrial transcription (biogenesis)

TFAM (transcription factor A, mitochondrial)

a major transcriptional factor genetic removal of TFAM → neurodegeneration in mice [71]. This mouse model is known as MitoPark and exhibit clinical features. (2019 Raza 2nd). a conditional knock-out mouse with a disruption in a gene fundamental for mtDNA maintenance, the mitochondrial transcription factor A (Tfam), specifically in midbrain dopaminergic neurons, has been developed: the MitoPark mouse. Tfam is involved in mitochondrial biogenesis and mtDNA maintenance; it stabilizes mtDNA and regulates copy number; in the absence of Tfam a progressive deficiency in mitochondrial respiratory chain is observed followed by cell death. To generate the MitoPark mouse model, knock-in mice expressing Cre recombinase under the control of the dopamine transporter (DAT) were crossed with mice bearing loxP recombination sites flanking the Tfam gene (TfamloxP). In this way Tfam deletion is directed only in cells expressing DAT

Mitochondrial DYNAMICS (fusion/fission and transportation)

fusion		GTPases Optic Atrophy 1 (OPA1)
		MFN1
		MFN2
fission		Dynamin-Related Protein 1 (Drp1),

Mitochondrial Regulators

gene	protein	function	Pipeline
TRAP1
HTRA2 (, PARK13)	HTRA serine peptidase 2	Cause YOPD (Fitzgerald, 2017 #1289), we identified TRAP1 as an interactor of HTRA2 using an unbiased mass spectrometry approach

Circulating cell-free mitochondria in blood

(Amir Dache, 2020 #?)

between 200,000 and 3.7 million cell-free, intact mitochondria per milliliter of blood plasma. Whole functional mitochondria Normal oxygen consumption

Uncertain Spans

location	transcription	uncertainty
Top genome figures	two reference-figure schematics with many gene labels around concentric arcs; gene labels are transcribed where legible from the high-resolution crop.	partial label legibility for some tRNA boxes (e.g. SUCN, MGY positions on the inner arc).
Mitochondrial genes table / Strand column for MT-RNR2 humanin row	reads Humanin in Product column with no Position or Strand columns visible (likely a parenthetical note rather than a normal gene-position row).	source layout truncation.
Methylation of mt DNA / sub-bullet a	reads MtDNA methylation approximations to range from 1 to 20% [44]. (the leading article is missing in source).	source typography preserved including missing article.
Circulating cell-free mitochondria in blood / Amir Dache citation	reads Amir Dache, 2020 with the citation key #? not legible in this slice.	citation key cut at column edge.