Expression and maintenance of mitochondrial DNA: new insights into human disease pathology

Abstract

Mitochondria are central players in cellular energy metabolism and, consequently, defects in their function result in many characterized metabolic diseases. Critical for their function is mitochondrial DNA (mtDNA), which encodes subunits of the oxidative phosphorylation complexes essential for cellular respiration and ATP production. Expression, replication, and maintenance of mtDNA require factors encoded by nuclear genes. These include not only the primary machinery involved (eg, transcription and replication components) but also those in signaling pathways that mediate or sense alterations in mitochondrial function in accord with changing cellular needs or environmental conditions. Mutations in these contribute to human disease pathology by mechanisms that are being revealed at an unprecedented rate. As I will discuss herein, the basic protein machinery required for transcription initiation in human mitochondria has been elucidated after the discovery of two multifunctional mitochondrial transcription factors, h-mtTFB1 and h-mtTFB2, that are also rRNA methyltransferases. In addition, involvement of the ataxia-telangiectasia mutated (ATM) and target of rapamycin (TOR) signaling pathways in regulating mitochondrial homeostasis and gene expression has also recently been uncovered. These advancements embody the current mitochondrial research landscape, which can be described as exploding with discoveries of previously unanticipated roles for mitochondria in human disease and aging.

Figure 1

The human mitochondrial transcription machinery and potential mechanism through which the human mitochondrial transcription factor/rRNA methyltransferase, h-mtTFB1, influences the A1555G deafness-associated mtDNA mutation. The minimal protein requirements for transcription initiation from human mtDNA promoters in vitro (bottom right) are shown associated with a segment of mtDNA (gray helix). POLRMT, the bacteriophage-related RNA polymerase (largest blue shape) is shown initiating RNA synthesis from an unwound promoter (RNA is represented by the black line exiting the bubble in the mtDNA strands). Formation of this open promoter complex requires promoter-bound h-mtTFA (dark blue L-shape), a dual high-mobility group-box protein, and either h-mtTFB1 or h-mtTFB2 (light blue shape) shown bridging an interaction between the C-terminal tail of h-mtTFA and POLRMT. The two mitochondrial ribosomal RNAs (12S and 16S) are mtDNA encoded and produced by processing of primary transcripts synthesized by POLRMT. Both h-mtTFB1 and h-mtTFB2 are also rRNA methyltransferases that can methylate a conserved stem-loop in the mitochondrial 12S rRNA, based on studies in bacteria. At the top left, h-mtTFB1 (blue shape) is shown methylating the 12S rRNA stem-loop before the eventual assembly of the RNA into mitochondrial ribosomes (green ovals). Each small red oval represents a methyl group added to one of two tandem adenines in the loop of the stem-loop (each of the adenines is dimethylated at ring position N6). The A1555G deafness-associated mtDNA point mutation (X) is in close proximity to the methylated stem-loop, and the structure of this region of the ribosome is affected by this mutation, as well as by the h-mtTFB1-mediated methylation events. It is through these structural perturbations (attributable to alterations in methylation status of the 12S rRNA) that h-mtTFB1 most likely influences the pathogenicity of the maternally inherited A1555G deafness mutation.

Figure 2

Speculative model of A-T pathology that incorporates recently uncovered roles for ATM in mitochondrial homeostasis. Three key proteins in the proposed pathogenic pathway (blue rounded rectangles) are ATM, p53, and ribonucleotide reductase (RNR). RNR comprises a large R1 subunit and one of two small subunits, R2 and p53R2. Solid blue lines represent known or well-accepted relationships between these factors and normal downstream cellular processes (top, white half of the figure) or pathogenic features of A-T (bottom, shaded half of the figure). For example, the role of ATM in nuclear DNA damage sensing is well established, as is the nuclear genomic instability that contributes to A-T pathology because of loss of this function. Bold black arrows indicate newly identified roles for ATM and RNR in the regulation of mitochondrial function described in the text. Dashed arrows represent speculative pathogenic consequences of disrupted mtDNA metabolism and mitochondrial respiration because of loss of ATM signaling in A-T patient cells. These include increased mitochondrial ROS production that would cause or contribute to the known oxidative stress associated with the disease and other consequences of loss of mitochondrial function that are also common to mitochondrial diseases (eg, neurodegeneration, ataxia, and diabetes). As depicted in the top, white half, these mitochondrial defects in A-T patient cells could be precipitated from the loss of ATM acting directly on mitochondria, through the alteration of p53 function (which can influence mitochondria directly or via RNR) or through direct (ie, non-p53-mediated) influence on RNR expression.