Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Accurate transcription is required for the faithful expression of genetic information. Surprisingly though, little is known about the mechanisms that ...

Children's Hospital of Philadelphia

Transcription errors occur in all living cells; however, it is unknown how these errors affect cellular health. To answer this question, we monitor yeast cells that are genetically engineered to display error-prone transcription. We discover that these cells suffer from a profound loss in proteostasis, which sensitizes them to the expression of genes that are associated with protein-folding diseases in humans; thus, transcription errors represent a new molecular mechanism by which cells can acquire disease phenotypes. We further find that the error rate of transcription increases as cells age, suggesting that transcription errors affect proteostasis particularly in aging cells. Accordingly, transcription errors accelerate the aggregation of a peptide that is implicated in Alzheimer's disease, and shorten the lifespan of cells. These experiments reveal a previously unappreciated role for transcriptional fidelity in cellular health and aging. 

Transcription errors induce proteotoxic stress and shorten cellular lifespan.

Over the last decade, countless discoveries have been made that have expanded our knowledge of mitochondrial biology, and more often than not, these discoveries provided fascinating new insights into the etiology of human disease. For example, advances in mitochondrial genetics exposed the role of mitochondrial mutations in cancer progression, and the discovery of mitophagy highlighted the role of mitochondrial quality control in Parkinson's disease. Additional discoveries underscored the importance of the mTor pathway in aging and disease, and more recently, the mitochondrial unfolded protein response was implicated in the regulation of mammalian lifespan. Some of the most fundamental discoveries though, were made in the context of mitochondrial fusion and fission. The balance between these two opposing forces shapes the mitochondrial population in our cells, and influences mitochondrial function at every level. Here, we highlight the basic biology that underlies mitochondrial fusion and fission, explain how these processes promote human health by solving a problem that is innate to multifarious organelles, and make a novel prediction: that fusion and fission are intimately linked to mitochondrial protein quality control.

Linking mitochondrial dynamics to mitochondrial protein quality control.

Accurate transcription is required for the faithful expression of genetic information. To understand the molecular mechanisms that control the fidelity of transcription, we used novel sequencing technology to provide the first comprehensive analysis of the fidelity of transcription in eukaryotic cells. Our results demonstrate that transcription errors can occur in any gene, at any location, and affect every aspect of protein structure and function. In addition, we show that multiple proteins safeguard the fidelity of transcription and provide evidence suggesting that errors that evade these layers of RNA quality control profoundly affect the physiology of living cells. Together, these observations demonstrate that there is an inherent limit to the faithful expression of the genome and suggest that the impact of mutagenesis on cellular health and fitness is substantially greater than currently appreciated.

The landscape of transcription errors in eukaryotic cells.

Genetic instability of the mitochondrial genome (mtDNA) plays an important role in human aging and disease. Thus far, it has proven difficult to develop successful treatment strategies for diseases that are caused by mtDNA instability. To address this issue, we developed a model of mtDNA disease in the nematode C. elegans, an animal model that can rapidly be screened for genes and biological pathways that reduce mitochondrial pathology. These worms recapitulate all the major hallmarks of mtDNA disease in humans, including increased mtDNA instability, loss of respiration, reduced neuromuscular function, and a shortened lifespan. We found that these phenotypes could be rescued by intervening in numerous biological pathways, including IGF-1/insulin signaling, mitophagy, and the mitochondrial unfolded protein response, suggesting that it may be possible to ameliorate mtDNA disease through multiple molecular mechanisms.

Multiple Molecular Mechanisms Rescue mtDNA Disease in C. elegans.

The nervous system is composed of a large variety of neurons with a diverse array of morphological and functional properties. This heterogeneity is essential for the construction and maintenance of a distinct set of neural networks with unique characteristics. Accumulating evidence now indicates that neurons do not only differ at a functional level, but also at the genomic level. These genomic discrepancies seem to be the result of somatic mutations that emerge in nervous tissue during development and aging. Ultimately, these mutations bring about a genetically heterogeneous population of neurons, a phenomenon that is commonly referred to as "somatic brain mosaicism". Improved understanding of the development and consequences of somatic brain mosaicism is crucial to understand the impact of somatic mutations on neuronal function in human aging and disease. Here, we highlight a number of topics related to somatic brain mosaicism, including some early experimental evidence for somatic mutations in post-mitotic neurons of the hypothalamo-neurohypophyseal system. We propose that age-related somatic mutations are particularly interesting, because aging is a major risk factor for a variety of neuronal diseases, including Alzheimer's disease. We highlight potential links between somatic mutations and the development of these diseases and argue that recent advances in single-cell genomics and in vivo physiology have now finally made it possible to dissect the origins and consequences of neuronal mutations in unprecedented detail.

Somatic mutations in neurons during aging and neurodegeneration.

Nuclear-encoded mutations causing metabolic and degenerative diseases have highly variable expressivity. Patients sharing the homozygous mutation (c.523delC) in the adenine nucleotide translocator 1 gene (SLC25A4, ANT1) develop cardiomyopathy that varies from slowly progressive to fulminant. This variability correlates with the mitochondrial DNA (mtDNA) lineage. To confirm that mtDNA variants can modulate the expressivity of nuclear DNA (nDNA)-encoded diseases, we combined in mice the nDNA Slc25a4 null mutation with a homoplasmic mtDNA ND6 or COI variant. The ND6 variant significantly increased the severity of cardiomyopathy while the COI variant was phenotypically neutral. The adverse Slc25a4 and ND6 combination was associated with impaired mitochondrial complex I activity, increased oxidative damage, decreased l-Opa1, altered mitochondrial morphology, sensitization of the mitochondrial permeability transition pore, augmented somatic mtDNA mutation levels, and shortened lifespan. The strikingly different phenotypic effects of these mild mtDNA variants demonstrate that mtDNA can be an important modulator of autosomal disease.

Marc Vermulst

Center for Mitochondrial and Epigenomic Medicine

Children's Hospital of Philadelphia

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Marc Vermulst

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Children's Hospital of Philadelphia

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Center for Mitochondrial and Epigenomic Medicine