The human mitochondrial genome contains a second light strand promoter

Tan, Benedict G.; Mutti, Christian Daniel; Shi, Yonghong; Xie, Xie; Zhu, Xuefeng; Silva-Pinheiro, Pedro; Menger, Katja E.; Díaz-Maldonado, Héctor; Wei, Wei; Nicholls, Thomas J.; Chinnery, Patrick F.; Minczuk, Michal; Falkenberg, Maria; Gustafsson, Claes M.

doi:10.1016/j.molcel.2022.08.011

Cited by 24 publications

(23 citation statements)

References 66 publications

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“…We found that the production rate of mt-mRNA is the same as for mt-rRNA, likely the most abundant transcript in mitochondria. These observations are naturally explained by our heavy-strand polycistronic transcription model that includes a single transcription start site 10 and rate.…”

Section: Discussionmentioning

confidence: 97%

A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis

McShane

Couvillion

Ietswaart

et al. 2023

Preprint

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Mitochondria play a critical role in cellular metabolism primarily through hosting the oxidative phosphorylation (OXPHOS) machinery that is encoded by mitochondrial DNA (mtDNA) and nuclear DNA, with each genome separately regulated in their respective compartments. To unravel how the two gene expression systems collaborate to produce the OXPHOS complexes, the regulatory principles controlling the production of mtDNA-encoded proteins need to be elucidated. Here, we performed a quantitative analysis of the mitochondrial messenger RNA (mt-mRNA) life cycle to gain insight into which steps of gene expression experience the most regulatory control. Our analysis revealed a unique balance between the rapid turnover and high accumulation of mt-mRNA, leading to a 700-fold higher transcriptional output than nuclear-encoded OXPHOS genes. Additionally, we observed that mt-mRNA processing and its association with the mitochondrial ribosome occur rapidly and that these processes are linked mechanistically. These data resulted in a model of mtDNA expression that is predictive across human cell lines, revealing that differential turnover and translation efficiencies are the major contributors to mitochondrial-encoded protein synthesis. Applying this framework to a disease model of Leigh syndrome, French-Canadian type, we found that disrupting the responsible nuclear-encoded gene, LRPPRC, perturbs OXPHOS biogenesis predominantly through altering mt-mRNA stability. Our findings provide a comprehensive view of the intricate regulatory mechanisms governing mtDNA-encoded protein synthesis, highlighting the importance of quantitatively analyzing the mitochondrial RNA life cycle for decoding the regulatory principles of mtDNA expression.

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Section: Discussionmentioning

confidence: 97%

A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis

McShane

Couvillion

Ietswaart

et al. 2023

Preprint

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“…This includes the presence of transcription units oriented in opposing directions, or by the existence of topologically-restricted domains created by attachment to a membrane. Human mtDNA promoters are responsible for polycistronic transcription of almost the whole genome in both directions ( 1 , 83 ). However, it remains unclear whether promoters are active simultaneously, as individual regulation of promoter firing could mitigate the effects of topological stress during transcription.…”

Section: Discussionmentioning

confidence: 99%

Two type I topoisomerases maintain DNA topology in human mitochondria

Menger

Chapman

Díaz-Maldonado

et al. 2022

Nucleic Acids Research

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Genetic processes require the activity of multiple topoisomerases, essential enzymes that remove topological tension and intermolecular linkages in DNA. We have investigated the subcellular localisation and activity of the six human topoisomerases with a view to understanding the topological maintenance of human mitochondrial DNA. Our results indicate that mitochondria contain two topoisomerases, TOP1MT and TOP3A. Using molecular, genomic and biochemical methods we find that both proteins contribute to mtDNA replication, in addition to the decatenation role of TOP3A, and that TOP1MT is stimulated by mtSSB. Loss of TOP3A or TOP1MT also dysregulates mitochondrial gene expression, and both proteins promote transcription elongation in vitro. We find no evidence for TOP2 localisation to mitochondria, and TOP2B knockout does not affect mtDNA maintenance or expression. Our results suggest a division of labour between TOP3A and TOP1MT in mtDNA topology control that is required for the proper maintenance and expression of human mtDNA.

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“…7a). The latter included a recently discovered light strand promoter 47 and two regions of unknown function, including one between m.16,400-16,450 previously reported to be depleted of heteroplasmic variation 19 , and another across the artificial chromosome break. These two regions also had a lower population frequency of variants (Extended Data Fig.…”

Section: Mainmentioning

confidence: 99%

“… (a) The MLC score of positions across the control region are shown; a schematic of annotated non-coding elements is displayed above. The five peaks from left to right overlap (1) a recently discovered second light strand promoter 47 , (2-3) regions of unknown function within the D-loop, (4) conserved sequence block 3, or (5) the light strand promoter. Base scores are provided in Supplementary Dataset 6.…”

Section: Extended Data Figuresmentioning

confidence: 99%

Quantifying constraint in the human mitochondrial genome

Lake

Liu

Battle

et al. 2022

Preprint

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Mitochondrial DNA (mtDNA) has an important, yet often overlooked, role in health and disease. Constraint models quantify depletion of genetic variation by negative selection, representing a powerful tool for identifying deleterious variation underlying human phenotypes1-4. However, a constraint model for the mtDNA had not been developed, due to the unique features of this genome. Here we describe the development of a mitochondrial constraint model and its application to the Genome Aggregation Database (gnomAD), a large-scale population dataset reporting mtDNA variation across 56,434 humans5. Our results demonstrate strong depletion of expected variation, showing most pathogenic mtDNA variants remain undiscovered. To aid their identification, we compute constraint metrics for every protein, transfer RNA, and ribosomal RNA gene in the human mtDNA, as well as for non-coding regions. This includes assessment of regional or positional constraint within every gene, and local constraint for every base position. We identify enrichment of pathogenic variation in the most constrained sites, which include loci typically overlooked in mtDNA analyses, and show that the most constrained gene regions and non-coding elements encode functionally-critical sites. Lastly, we demonstrate how these metrics can improve the discovery of mtDNA variation underlying rare and common human phenotypes.

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The human mitochondrial genome contains a second light strand promoter

Cited by 24 publications

References 66 publications

A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis

A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis

Two type I topoisomerases maintain DNA topology in human mitochondria

Quantifying constraint in the human mitochondrial genome

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