Control of mitochondrial DNA ( mt DNA ) replication and expression contributes to energy conversion through oxidative phosphorylation. Mitochondrial transcription elongation factor (TEFM) was the candidate for controlling the transition from termination of transcription for replication primer production to processive, near-genome length transcription for the expression of mt DNA genes. Genes in the promoter-proximal region transcripts are greatly enhanced in Tefm knockout mice but mostly stop before the transcription to replication switch, so de novo mt DNA replication is markedly diminished. Proximity labeling (Bio ID) measurements indicate that TEFM acts on multiple RNA processing factors. Our results show that TEFM is a general transcription elongation factor involved in gene transcription and primer formation and that the absence of TEFM changes the process of RNA within mammalian mitochondria.
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TEFM Required for Embryonic Survival
TEFM is a protein that's found in cell mitochondria, and the baby's survival depends on it. It also mediates the transcriptional lengthening of mitochondrial DNA, and hence the genes that control the mitochondria's expression, affecting the way that the cell uses and processes energy. Its gene codes for a mitochondrial transcription elongation factor that improves the processivity of the mitochondrial RNA polymerase POLRMT. TEFM controls mitochondrial transcriptional elongation and defects cause various tissue-specific neurological and neuromuscular symptoms. It's because mitochondria are the primary source of ATP from oxidative phosphorylation (OXPHOS) and they have many biosynthetic mechanisms, that regulate cellular homeostasis. Those 13 main subunits of the OXPHOS system are built in the organelle. Mitochondria store and encode the mitochondrial DNA (mtDNA) coding for these polypeptides, as well as a whole host of mitochondrial (mt-) tRNAs and two mt-rRNAs. Every molecule of remaining mitochondrial protein is coded by the nuclear genome and transported into the mitochondria from the cytoplasm.
TEFM Interacts with RNA Processing Factors
Deletion of TEFM impacts RNA processing. In the absence of TEFM, we observed, using several independent methods (RNA-Seq, northern blot, RT-qPCR), highly enriched unprocessed transcripts where strong secondary structure (e.g., mt-tRNA gene cluster) was used. Qualitative proteomics stripped of the labels revealed that many of the proteins responsible for processing RNA were upregulated without TEFM. TEFM could act on mammalian mitochondrial RNA-processing machinery, but the molecular mechanisms will have to be revealed with more research. The transcription elongation and RNA processing could interact to make pre-RNA maturation more accurate and efficient and to open up new regulatory pathways for the regulation of gene expression in mitochondrial DNA.
Fig. 1 TEFM provides primers for mitochondrial DNA replication (Jiang, S., et al. 2019).
TEFM Deficits Result in Mitochondrial Degeneration
The deficiency in TEFM can cause extreme mitochondrial dysfunction. Because TEFM regulates transcriptional elongation of mitochondrial DNA, its loss could have effects on mitochondrial gene expression and therefore mitochondrial function. Mitochondria are essential cell energy producers that are vital for cellular metabolism and function.
So TEFM missing means that mitochondrial genes get suppressed mitochondrial function gets disrupted, cell energy sources become compromised, and cells are killed. This radical mitochondrial malfunction can compromise the physiology of the whole body, especially high-energy-demanding tissues, and organs like the heart, muscle, etc. Thus, TEFM is involved in the survival of the mitochondria and cells.
TEFM Knockout Mmitochondrial Proteome
Manual classification of differentially expressed proteins suggested that many mitochondrial processes such as oxidative phosphorylation, fatty acid, and amino acid metabolism, protein translation (ribosome formation), mitochondrial structure/morphology, apoptosis, and RNA metabolism were severely disrupted by TEFM depletion. Loss of TEFM changes the architecture of mitochondrial ribosomes, which can disrupt mitochondrial protein translation. Processing of transcription and pre-mRNA also occurs in tandem in the nucleus, which has consequences for transcript maturation and gene regulation. In the nucleus, the carboxyl-terminal domain (CTD) of the largest RNA polymerase II subunit is phosphorylated at transcription start, recruiting proteins involved in processing RNA, such as those for 5′ capping, splicing, and polyadenylation. As a landing strip to pull processing factors into contact with active transcribing RNA polymerase II, pre-mRNAs are processed quickly during active transcriptional elongation.
Neurological Pathologies Arise as TEFM Lost
The mitochondrial or nuclear genomes are affected by many different human diseases that result in dysfunctional mitochondrial respiratory functions. More and more mutations have been found in nuclear genes encoding for mitochondrial RNA biology. The TEFM gene encodes a mitochondrial transcription elongation factor that facilitates the processivity of the mitochondrial RNA polymerase POLRMT. TEFM variants cause mitochondrial respiratory chain defects and various clinical manifestations such as treatable mitochondrial myopathy with impaired neuromuscular transmission. Levels of promoter-distal mitochondrial RNA transcripts are diminished in muscle and primary fibroblasts of patients with affected conditions. TEFM controls the length of mitochondrial transcription and defective versions produce multiple tissue-specific neurological and neuromuscular symptoms.
Conclusion
Most mitochondrial diseases are caused by malfunctions in the mtDNA replication machinery, but pathogenic variations in mitochondrial transcriptional machinery are just emerging. In recent years, POLRMT variants have been linked to mitochondrial disease and a variety of neurological symptoms. TEFM is part of the mitochondrial transcriptional machinery. Without TEFM, transcription elongation suffers, mitochondrial DNA expression drops and the bioenergetic crisis ensues. TEFM does not make DNA replication-relevant RNA primers more likely to be formed. We have also discovered that TEFM is needed for replication primers and near-genome-length transcription of mitochondrial DNA.
References
- Jiang, S., et al. TEFM regulates both transcription elongation and RNA processing in mitochondria. EMBO reports. 2019, 20(6): e48101.
- Yu, H., et al. TEFM enhances transcription elongation by modifying mtRNAP pausing dynamics. Biophysical Journal. 2018, 115(12): 2295-2300.
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