A conditional knockout rat resource of mitochondrial protein-coding genes via a DdCBE-induced premature stop codon

Hundreds of pathogenic variants of mitochondrial DNA (mtDNA) have been reported to cause mitochondrial diseases, which still lack effective treatments. It is a huge challenge to install these mutations one by one. We repurposed the DddA-derived cytosine base editor to incorporate a premature stop codon in the mtProtein-coding genes to ablate mitochondrial proteins encoded in the mtDNA (mtProteins) instead of installing pathogenic variants and generated a library of both cell and rat resources with mtProtein depletion. In vitro, we depleted 12 of 13 mtProtein-coding genes with high efficiency and specificity, resulting in decreased mtProtein levels and impaired oxidative phosphorylation. Moreover, we generated six conditional knockout rat strains to ablate mtProteins using Cre/loxP system. Mitochondrially encoded ATP synthase membrane subunit 8 and NADH:ubiquinone oxidoreductase core subunit 1 were specifically depleted in heart cells or neurons, resulting in heart failure or abnormal brain development. Our work provides cell and rat resources for studying the function of mtProtein-coding genes and therapeutic strategies.

Kinetic Mathematical Modeling of Oxidative Phosphorylation in Cardiomyocyte Mitochondria

Oxidative phosphorylation (OXPHOS) is an oxygen-dependent process that consumes catabolized nutrients to produce adenosine triphosphate (ATP) to drive energy-dependent biological processes such as excitation-contraction coupling in cardiomyocytes. In addition to in vivo and in vitro experiments, in silico models are valuable for investigating the underlying mechanisms of OXPHOS and predicting its consequences in both physiological and pathological conditions. Here, we compare several prominent kinetic models of OXPHOS in cardiomyocytes. We examine how their mathematical expressions were derived, how their parameters were obtained, the conditions of their experimental counterparts, and the predictions they generated. We aim to explore the general landscape of energy production mechanisms in cardiomyocytes for future in silico models.

Understanding mitochondria and the utility of optimization as a canonical framework for identifying and modeling mitochondrial pathways

The goal of this paper is to provide an overview of our current understanding of mitochondrial function as a framework to motivate the hypothesis that mitochondrial behavior is governed by optimization principles that are constrained by the laws of the physical and biological sciences. Then, mathematical optimization tools can generally be useful to model some of these processes under reasonable assumptions and limitations. We are specifically interested in optimizations via variational methods, which are briefly summarized. Within such an optimization framework, we suggest that the numerous mechanical instigators of cell and intracellular functioning can be modeled utilizing some of the principles of mechanics that govern engineered systems, as well as by the frequently observed feedback and feedforward mechanisms that coordinate the multitude of processes within cells. These mechanical aspects would need to be coupled to governing biochemical rules. Of course, biological systems are significantly more complex than engineered systems, and require considerably more experimentation to ascertain and characterize parameters and subsequent behavior. That complexity requires well-defined limitations and assumptions for any derived models. Optimality is being motivated as a framework to help us understand how cellular decisions are made, especially those that transition between physiological behaviors and dysfunctions along pathophysiological pathways. We elaborate on our interpretation of optimality and cellular decision making within the body of this paper, as we revisit these ideas in the numerous different contexts of mitochondrial functions.

Physiological and Pathophysiological Roles of Mitochondrial Na+-Ca2+ Exchanger, NCLX, in Hearts

It has been over 10 years since SLC24A6/SLC8B1, coding the Na⁺/Ca²⁺/Li⁺ exchanger (NCLX), was identified as the gene responsible for mitochondrial Na⁺-Ca²⁺ exchange, a major Ca²⁺ efflux system in cardiac mitochondria. This molecular identification enabled us to determine structure–function relationships, as well as physiological/pathophysiological contributions, and our understandings have dramatically increased. In this review, we provide an overview of the recent achievements in relation to NCLX, focusing especially on its heart-specific characteristics, biophysical properties, and spatial distribution in cardiomyocytes, as well as in cardiac mitochondria. In addition, we discuss the roles of NCLX in cardiac functions under physiological and pathophysiological conditions—the generation of rhythmicity, the energy metabolism, the production of reactive oxygen species, and the opening of mitochondrial permeability transition pores.

A simple model of cardiac mitochondrial respiration with experimental validation

Cardiac mitochondria are intracellular organelles that play an important role in energy metabolism and cellular calcium regulation. In particular, they influence the excitation-contraction cycle of the heart cell. A large number of mathematical models have been proposed to better understand the mitochondrial dynamics, but they generally show a high level of complexity, and their parameters are very hard to fit to experimental data. We derived a model based on historical free energy-transduction principles, and results from the literature. We proposed simple expressions that allow to reduce the number of parameters to a minimum with respect to the mitochondrial behavior of interest for us. The resulting model has thirty-two parameters, which are reduced to twenty-three after a global sensitivity analysis of its expressions based on Sobol indices. We calibrated our model to experimental data that consists of measurements of mitochondrial respiration rates controlled by external ADP additions. A sensitivity analysis of the respiration rates showed that only seven parameters can be identified using these observations. We calibrated them using a genetic algorithm, with five experimental data sets. At last, we used the calibration results to verify the ability of the model to accurately predict the values of a sixth dataset. Results show that our model is able to reproduce both respiration rates of mitochondria and transitions between those states, with very low variability of the parameters between each experiment. The same methodology may apply to recover all the parameters of the model, if corresponding experimental data were available.

Minor contribution of NCX to Na+-Ca2+ exchange activity in brain mitochondria

NCLX was identified as a mitochondrial Na⁺-Ca²⁺ exchanger. However, contribution of NCLX to overall mitochondrial Na⁺-Ca²⁺ exchange activity remains unclear, especially in brain mitochondria where plasma membrane Na⁺-Ca²⁺ exchanger NCX also exists. We studied the issue using isolated mouse brain mitochondria. The Na⁺- as well as Li⁺-dependent Ca²⁺ efflux from mitochondria was significantly inhibited by a NCLX blocker, but was insensitive to NCX blockers, suggesting that NCLX comprises a major part in forward mode of mitochondrial Na⁺-Ca²⁺ exchange activity. On the other hand, the Na⁺-dependent Ca²⁺ influx into mitochondria, the reverse mode, was insensitive to all the blockers tested, suggesting unidentified Ca²⁺ transport systems.

Membrane current evoked by mitochondrial Na+-Ca2+ exchange in mouse heart

The electrogenicity of mitochondrial Na+-Ca2+ exchange (NCXm) had been controversial and no membrane current through it had been reported. We succeeded for the first time in recording NCXm-mediated currents using mitoplasts derived from mouse ventricle. Under conditions that K+, Cl-, and Ca2+ uniporter currents were inhibited, extra-mitochondrial Na+ induced inward currents with 1 μM Ca2+ in the pipette. The half-maximum concentration of Na+ was 35.6 mM. The inward current was diminished without Ca2+ in the pipette, and was augmented with 10 μM Ca2+. The Na+-induced inward currents were largely inhibited by CGP-37157, an NCXm blocker. However, the reverse mode of NCXm, which should be detected as an outward current, was hardly induced by extra-mitochondrial application of Ca2+ with Na+ in the pipette. It was concluded that NCXm is electrogenic. This property may be advantageous for facilitating Ca2+ extrusion from mitochondria, which has large negative membrane potential.