We are witnessing a period of renewed interest in the biology of the mitochondrion. The mitochondrion serves a critical function in the maintenance of cellular energy stores, thermogenesis, and apoptosis. Moreover, alterations in mitochondrial function contribute to several inherited and acquired human diseases and the aging process. This review summarizes our understanding of the transcriptional regulatory mechanisms involved in the biogenesis and energy metabolic function of mitochondria in higher organisms.

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Transcriptional regulatory circuits controlling mitochondrial biogenesis and function

The mitochondrion was originally a free-living prokaryotic organism, which explains the presence of a compact mammalian mitochondrial DNA (mtDNA) in contempory mammalian cells. The genome encodes for key subunits of the electron transport chain and RNA components needed for mitochondrial translation. Nuclear genes encode the enzyme systems responsible for mtDNA replication and transcription. Several of the key components of these systems are related to proteins replicating and transcribing DNA in bacteriophages. This observation has led to the proposition that some genes required for DNA replication and transcription were acquired together from a phage early in the evolution of the eukaryotic cell, already at the time of the mitochondrial endosymbiosis. Recent years have seen a rapid development in our molecular understanding of these machineries, but many aspects still remain unknown.

DNA Replication and Transcription in Mammalian Mitochondria

This Perspective illustrates the defining characteristics of free radical chemistry, beginning with its rich and storied history. Studies from our laboratory are discussed along with recent developments emanating from others in this burgeoning area. The practicality and chemoselectivity of radical reactions enable rapid access to molecules of relevance to drug discovery, agrochemistry, material science, and other disciplines. Thus, these reactive intermediates possess inherent translational potential, as they can be widely used to expedite scientific endeavors for the betterment of humankind.

Radicals: Reactive Intermediates with Translational Potential

Autophagy is a highly conserved process that maintains homeostasis by clearing damaged organelles and long-lived proteins. The consequences of deficiency in autophagy manifest in a variety of pathological states including neurodegenerative diseases, inflammatory disorders, and cancer. Here, we studied the role of autophagy in the homeostatic regulation of innate antiviral defense. Single-stranded RNA viruses are recognized by the members of the RIG-I-like receptors (RLRs) in the cytosol. RLRs signal through IPS-1, resulting in the production of the key antiviral cytokines, type I IFNs. Autophagy-defective Atg5−/− cells exhibited enhanced RLR signaling, increased IFN secretion, and resistance to infection by vesicular stomatitis virus. In the absence of autophagy, cells accumulated dysfunctional mitochondria, as well as mitochondria-associated IPS-1. Reactive oxygen species (ROS) associated with the dysfunctional mitochondria were largely responsible for the enhanced RLR signaling in Atg5−/− cells, as antioxidant treatment blocked the excess RLR signaling. In addition, autophagy-independent increase in mitochondrial ROS by treatment of cells with rotenone was sufficient to amplify RLR signaling in WT cells. These data indicate that autophagy contributes to homeostatic regulation of innate antiviral defense through the clearance of dysfunctional mitochondria, and revealed that ROS associated with mitochondria play a key role in potentiating RLR signaling.

https://www.pnas.org/content/pnas/106/8/2770.full.pdf

Absence of autophagy results in reactive oxygen species-dependent amplification of RLR signaling

Mammalian mitochondrial DNA (mtDNA) encodes 13 proteins that are essential for the function of the oxidative phosphorylation system, which is composed of four respiratory-chain complexes and adenosine triphosphate (ATP) synthase. Remarkably, the maintenance and expression of mtDNA depend on the mitochondrial import of hundreds of nuclear-encoded proteins that control genome maintenance, replication, transcription, RNA maturation, and mitochondrial translation. The importance of this complex regulatory system is underscored by the identification of numerous mutations of nuclear genes that impair mtDNA maintenance and expression at different levels, causing human mitochondrial diseases with pleiotropic clinical manifestations. The basic scientific understanding of the mechanisms controlling mtDNA function has progressed considerably during the past few years, thanks to advances in biochemistry, genetics, and structural biology. The challenges for the future will be to understand how mtDNA maintenance and expression are regulated and to what extent direct intramitochondrial cross talk between different processes, such as transcription and translation, is important.

Maintenance and Expression of Mammalian Mitochondrial DNA

Although cellular mitochondrial DNA (mtDNA) copy number varies widely among cell lines and tissues, little is known about the mechanism of mtDNA copy number control. Most nascent replication strands from the leading, heavy-strand origin (OH) are prematurely terminated, defining the 3′ boundary of the displacement loop (D-loop). We have depleted mouse LA9 cell mtDNA to ∼20% of normal levels by treating with 2′,3′-dideoxycytidine (ddC) and subsequently allowed recovery to normal levels of mtDNA. A quantitative ligation-mediated PCR assay was used to determine the levels of both terminated and extended nascent OH strands during mtDNA depletion and repopulation. Depleting mtDNA leads to a release of replication termination until mtDNA copy number approaches a normal level. Detectable total nascent strands per mtDNA genome remain below normal. Therefore, it is likely that the level of replication termination plays a significant role in copy number regulation in this system. However, termination of D-loop strand synthesis is persistent, indicating formation of the D-loop structure has a purpose that is required under conditions of rapid recovery of depleted mtDNA.

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Release of replication termination controls mitochondrial DNA copy number after depletion with 2′,3′-dideoxycytidine

We report a new method for the mass spectrometric detection of fleeting reaction intermediates in electrochemical reactions utilizing a "waterwheel" working electrode setup. This setup takes inspiration from desorption electrospray ionization (DESI) mass spectrometry, where the sampling time is on the order of milliseconds, to sample directly from the surface of a working electrode for mass spectrometric analysis. We present data that show the formation of a diimine intermediate of the electrochemical oxidation of uric acid that has a lifetime in solution of 23 ms as well as data that provide evidence for the formation of a similar diimine species from the electrooxidation of xanthine, which has not been previously observed.

Identification of fleeting electrochemical reaction intermediates using desorption electrospray ionization mass spectrometry.

The N,N-dimethylaniline (DMA) radical cation DMA(.+) , a long-sought transient intermediate, was detected by mass spectrometry (MS) during the electrochemical oxidation of DMA. This was accomplished by coupling desorption electrospray ionization (DESI) MS with a waterwheel working electrode setup to sample the surface of the working electrode during electrochemical analysis. This study clearly shows that DESI-based electrochemical MS is capable of capturing electrochemically generated intermediates with half-lives on the order of microseconds, which is 4-5 orders of magnitude faster than previously reported electrochemical mass spectrometry techniques.

Detection of the Short‐Lived Radical Cation Intermediate in the Electrooxidation of N,N‐Dimethylaniline by Mass Spectrometry

We report the observation of the electrochemically generated nitrenium ions of 4,4′-dimethyoxydiphenylamine and di-p-tolylamine in solution by mass spectrometry. This setup takes inspiration from desorption electrospray ionization mass spectrometry to sample directly from the surface of a rotating waterwheel working electrode for mass spectrometric analysis. Detection of the 4,4′-dimethyoxydiphenylamine nitrenium ion was expected based upon para-methoxy resonance stabilization, whereas observation of the di-p-tolylamine nitrenium ion might be unexpected because resonance stabilization from the para-substituted position is unavailable. However, the short timescale analysis of the setup allows for the isolation of the di-p-tolylamine nitrenium ion, which is electrogenerated in solution and detected mass spectrometrically.

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Observation of electrochemically generated nitrenium ions by desorption electrospray ionization mass spectrometry

Kinetic, spectroscopic, and computational studies of radical C–H arylations highlight the interplay between chemical and physical rate processes in these multiphase reactions. Anomalous concentration dependences observed here may be reconciled by considering the role of phase transfer processes that mediate concentrations in each phase. In addition, understanding interactions through phase boundaries enables their use in optimization of reaction performance.

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Timothy A. Brown

Papers

Release of replication termination controls mitochondrial DNA copy number after depletion with 2′,3′-dideoxycytidine

Identification of fleeting electrochemical reaction intermediates using desorption electrospray ionization mass spectrometry.

Detection of the Short‐Lived Radical Cation Intermediate in the Electrooxidation of N,N‐Dimethylaniline by Mass Spectrometry

Observation of electrochemically generated nitrenium ions by desorption electrospray ionization mass spectrometry

Mechanistic Insights into Two-Phase Radical C-H Arylations.