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• Mitochondria-mediated energy homeostasis is crucial for brain functions and cognition. • Aberrant mitophagy, respiratory chain deficits, and oxidative stress resulting from mitochondrial dysfunction could lead to aberrant neurodevelopment. • Detailed studies are required to effectively answer the long-standing of whether mitochondrial dysfunction is a cause or a consequence of neurodevelopmental disorders. • Mitochondria are considered as potential therapeutic targets for neurodevelopmental disorders. Mitochondria have a crucial role in brain development and neurogenesis, both in embryonic and adult brains. Since the brain is the highest energy consuming organ, it is highly vulnerable to mitochondrial dysfunction. This has been implicated in a range of brain disorders including, neurodevelopmental conditions, psychiatric illnesses, and neurodegenerative diseases. Genetic variations in mitochondrial DNA (mtDNA), and nuclear DNA encoding mitochondrial proteins, have been associated with several cognitive disorders. However, it is not yet clear whether mitochondrial dysfunction is a primary cause of these conditions or a secondary effect. Our review article deals with this topic, and brings out recent advances in mitochondria-oriented therapies. Mitochondrial dysfunction could be involved in the pathogenesis of a subset of disorders involving cognitive impairment. In these patients, mitochondrial dysfunction could be the cause of the condition, rather than the consequence. There are vast areas in this topic that remains to be explored and elucidated. [ABSTRACT FROM AUTHOR]

• Mitochondrially targeted compounds using the triphenylphosphonium (TPP+) moiety are widely used for research and therapeutic purposes. • Previous studies have shown significant functional effects of the targeting moiety itself, without any targeted substance. • This study significantly extends the knowledge about these effects on mitochondrial membrane protein levels and tests several hypotheses about the mechanism. • Triphenylphosphonium-based lipophilic cations exert profound but reversible effects on a mitochondrial ETC proteins, which cannot be explained only by a loss of membrane potential. Triphenylphosphonium (TPP) derivatives are commonly used to target chemical into mitochondria. We show that alkyl-TPP cause reversible, dose- and hydrophobicity-dependent alterations of mitochondrial morphology and function and a selective decrease of mitochondrial inner membrane proteins including subunits of the respiratory chain complexes, as well as components of the mitochondrial calcium uniporter complex. The treatment with alkyl-TPP resulted in the cleavage of the pro-fusion and cristae organisation regulator Optic atrophy-1. The structural and functional effects of alkyl-TPP were found to be reversible and not merely due to loss of membrane potential. A similar effect was observed with the mitochondria-targeted antioxidant MitoQ. [ABSTRACT FROM AUTHOR]

• Transplanting low efficiency mitochondria reduces AGS malignancy. • Exogenous mitochondria are more preserved. • Mesenchymal form of AGS was reduced. Mitochondria are essential for energy supplementation and metabolic homeostasis of cancer cells. Using mitochondria transplantation to reduce the malignancy of gastric cancer (GC) cells is herein proposed. In our study normal human gastric mucous epithelium cell line (GES-1) showed a lower mitochondrial membrane potential (MMP) compared to immortalized human vascular endothelial cell line (EAhy 926) and human gastric adenocarcinoma cell line (AGS). The transplantation of GES-1 mitochondria to AGS were confirmed both by confocal microscopy and flow cytometry. After transplanting GES-1 mitochondria, the AGS showed a reduced cell migration, and invasion without affecting cell viability and apoptosis. Investigating the expression of proteins involved in epithelial-mesenchymal-transition (EMT), transplanted GES-1 mitochondria reduced the expression of mesenchymal markers α-SMA, MMP-9, snail, vimentin and N-cadherin, whereas the epithelial markers E-cadherin and clauding-1 were not changed. The proteins implicated in the cell cycle such as cyclin B1 and D1 were decreased. In mice, inoculation with AGS carrying the transplanted GES-1 mitochondria resulted in smaller sized tumors. Further investigating the mitochondrial balance, the transplanted GES-1 mitochondria were more stably preserved compared to endogenous AGS mitochondria. The MMP, ATP production and mitochondrial mass decreased in GES-1 mitochondria and the mitophagic proteins LC3 II and PINK1 were up-regulated. In conclusion the decreased malignancy of AGS was a result of exogenous GES-1 mitochondria transplantation. This suggests for a therapy with low efficiency mitochondria transplantation in the treatment of cancer cells. [ABSTRACT FROM AUTHOR]

• Development of a new Python algorithm/program (Python Charge Cluster Detection, PCCD) to detect charge clusters (CCs). • Comparative study showed that green algae's mitochondrial proteins contain more CCs than other green plants. • CCs are mainly located in the N-terminal and C-terminal regions of the proteins in green algae and the other green plants. • The pentatricopeptide repeat-containing proteins carry CC that are involved in correct and specific RNA editing. Protein function is dependent on charge interactions and charge biased regions, which are involved in a wide range of cellular and biochemical processes. We report the development of a new algorithm implemented in Python and its use to identify charge clusters CC (NegativeCC: NCC, PositiveCC: PCC and MixedCC: MCC) and compare their presence in mitochondrial proteins of plant groups. To characterize the resulting CC, statistical, structural and functional analyses were conducted. The screening of 105 399 protein sequences showed that 2.6 %, 0.48 % and 0.03 % of the proteins contain NCC, PCC and MCC, respectively. Mitochondrial proteins encoded by the nuclear genome of green algae have the biggest proportion of both PCC (1.6 %) and MCC (0.4 %) and mitochondrial proteins coded by the nuclear genome of other plants group have the highest portion of NCC (7.5 %). The mapping of the identified CC showed that they are mainly located in the terminal regions of the protein. Annotation showed that proteins with CC are classified as binding proteins, are included in the transmembrane transport processes, and are mainly located in the membrane. The CC scanning revealed the presence of 2373 and 784 sites and 192 and 149 motif profiles within NCC and PCC, respectively. The investigation of CC within pentatricopeptide repeat-containing proteins revealed that they are involved in correct and specific RNA editing. CC were proven to play a key role in providing insightful structural and functional information of complex protein assemblies which could be useful in biotechnological applications. [ABSTRACT FROM AUTHOR]

• Mitochondrial optic atrophy-1 (OPA1) adapts mitochondrial structure to bioenergetic function: long (L-OPA1) isoforms mediate organellar fusion, but when transmembrane potential (Δψ m) is lost, L-OPA1 is cleaved to short, inactive S-OPA1. • L-OPA1 of H9c2, L6.C11, and C2C12 myoblasts are insensitive to loss of Δψ m , but OPA1 processing is restored following differentiation. • OPA1 knockdown indicates that intact OPA1 is necessary for effective myoblast differentiation. • OMA1-mediated OPA1 processing is a key mechanism of mitochondrial stress sensing, and is necessary for myoblast differentiation. Mitochondrial optic atrophy-1 (OPA1) plays key roles in adapting mitochondrial structure to bioenergetic function. When transmembrane potential across the inner membrane (Δψ m) is intact, long (L-OPA1) isoforms shape the inner membrane through membrane fusion and the formation of cristal junctions. When Δψ m is lost, however, OPA1 is cleaved to short, inactive S-OPA1 isoforms by the OMA1 metalloprotease, disrupting mitochondrial structure and priming cellular stress responses such as apoptosis. Previously, we demonstrated that L-OPA1 of H9c2 cardiomyoblasts is insensitive to loss of Δψ m via challenge with the protonophore carbonyl cyanide chlorophenyl hydrazone (CCCP), but that CCCP-induced OPA1 processing is activated upon differentiation in media with low serum supplemented with all- trans retinoic acid (ATRA). Here, we show that this developmental induction of OPA1 processing in H9c2 cells is independent of ATRA; moreover, pretreatment of undifferentiated H9c2s with chloramphenicol (CAP), an inhibitor of mitochondrial protein synthesis, recapitulates the Δψ m -sensitive OPA1 processing observed in differentiated H9c2s. L6.C11 and C2C12 myoblast lines display the same developmental and CAP-sensitive induction of OPA1 processing, demonstrating a general mechanism of OPA1 regulation in mammalian myoblast cell settings. Restoration of CCCP-induced OPA1 processing correlates with increased apoptotic sensitivity. Moreover, OPA1 knockdown indicates that intact OPA1 is necessary for effective myoblast differentiation. Taken together, our results indicate that a novel developmental mechanism acts to regulate OMA1-mediated OPA1 processing in myoblast cell lines, in which differentiation engages mitochondrial stress sensing. [ABSTRACT FROM AUTHOR]

• The mitoPADdb stores mutations and qualitative expression variations of mitochondrial protein-encoding (MPE) genes associated with diseases. • It groups the diseases into 15 standard categories and links pathways, genes, and diseases. • The mitoPADdb compares quantitative transcript expression of MPE genes across diseases. • It can be a valuable resource for investigating mitochondrial dysfunction-related diseases and developing targeted therapy. Mitochondrial protein/gene mutations and expression variations contribute to the pathogenesis of various diseases, such as neurodegenerative and metabolic diseases. Detailed studies on mitochondrial protein-encoding (MPE) genes across diseases can provide clues for novel therapeutic strategies. Here, we collected, compiled, and manually curated the MPE gene mutation and expression variations data and their association with diseases in a single platform named mitoPADdb. The database contains 810 genes with 18,356 mutations and 1284 qualitative expression variations associated with 1793 diseases, grouped into 15 categories. It allows users to perform a comparative quantitative gene expression analysis for 317 transcriptomic studies across disease categories. Further, it provides information on MPE genes-associated molecular pathways. The mitoPADdb is a valuable resource for investigating mitochondrial dysfunction-related diseases. It can be accessed via http://bicresources.jcbose.ac.in/ssaha4/mitopaddb/index.html. [ABSTRACT FROM AUTHOR]

Mitochondria are one of the central organelles involved in cellular energy metabolism and play a regulatory role in various human pathologies ranging from inborn errors of metabolism, cancer, inflammation, and infections. Mitochondrial DNA encodes limited number of genes that is not sufficient for its optimal functioning. Hence, mitochondria import ∼1500 of proteins and ncRNAs from the nucleus depending on energy requirement of cell, tissue size, complexity and diversity of functions. Mitochondrial outer membrane can serve as a platform for regulation of local translation of nuclear-encoded mRNAs of mitochondrial proteins (nmRNAmp); however, underlying molecular mechanism for translational regulation of nmRNAmp at mitochondria is unexplored. Emerging evidence now suggest that mitochondria are enriched with specific miRNAs known as mitomiRs, which may be nuclear or mitochondrial DNA encoded. MitomiRs may modulate mitochondrial function and metabolism by fine-tuning protein levels related to mitochondria. The discovery of mitomiRs raised the questions of elucidating molecular pathways for their biogenesis, translocation, action sites and mechanism of action. Here, we have reviewed the existing reports describing the role of mitomiRs in sub mitochondrial compartments and discussed possible molecular mechanisms of mitomiRs in the regulation of nmRNAmp and mitogenome encoded transcripts. Further understanding of mitomiRs will uncover their implication in various pathophysiological conditions associated with mitochondria. [ABSTRACT FROM AUTHOR]

• Mitochondria are place of vitamin D metabolism and the target of its activities. • Vitamin D influences the activity of membrane and mitochondrial ion channels. • Genomic pathways regulated by vitamin D directly or indirectly regulate genes encoding mitochondrial ion channels. • Vitamin D might have direct impact on conductivity of mitochondrial channel proteins. Recent studies revealed that mitochondria are not only a place of vitamin D 3 metabolism but also direct or indirect targets of its activities. This review summarizes current knowledge on the regulation of ion channels from plasma and mitochondrial membranes by the active form of vitamin D 3 (1,25(OH) 2 D 3). 1,25(OH) 2 D 3 , is a naturally occurring hormone with pleiotropic activities; implicated in the modulation of cell differentiation, and proliferation and in the prevention of various diseases, including cancer. Many experimental data indicate that 1,25(OH) 2 D 3 deficiency induces ionic remodeling and 1,25(OH) 2 D 3 regulates the activity of multiple ion channels. There are two main theories on how 1,25(OH) 2 D 3 can modify the function of ion channels. First, describes the involvement of genomic pathways of response to 1,25(OH) 2 D 3 in the regulation of the expression of the genes encoding channels, their auxiliary subunits, or additional regulators. Interestingly, intracellular ion channels, like mitochondrial, are encoded by the same genes as plasma membrane channels. Therefore, the comprehensive genomic regulation of the channels from these two different cellular compartments we analyzed using a bioinformatic approach. The second theory explores non-genomic pathways of vitamin D 3 activities. It was shown, that 1,25(OH) 2 D 3 indirectly regulates enzymes that impact ion channels, change membrane physical properties, or directly bind to channel proteins. In this article, the involvement of genomic and non-genomic pathways regulated by 1,25(OH) 2 D 3 in the modulation of the levels and activity of plasma membrane and mitochondrial ion channels was investigated by an extensive review of the literature and analysis of the transcriptomic data using bioinformatics. [ABSTRACT FROM AUTHOR]

• Mitochondria are pivotal players in the survival of central nervous system function. • "Mitochondrial dysfunction" is central to the pathogenesis of AD. • There is contrasting data regarding extracellular mitochondria concentration in AD. • Early studies on mitochondrial transplant have shown to strike back against AD. Alzheimer's disease (AD) is a leading neurodegenerative pathology associated with aging worldwide. It is estimated that AD prevalence will increase from 5.8 million people today to 13.8 million by 2050 in the United States alone. AD effects in the brain are well known; however, there is still a lack of knowledge about the cellular mechanisms behind the origin of AD. It is known that AD induces cellular stress affecting the energy metabolism in brain cells. During the pathophysiological advancement of AD, damaged mitochondria enter a vicious cycle, producing reactive oxygen species (ROS), harming mitochondrial DNA and proteins, leading to more ROS and cellular death. Additionally, mitochondria are interconnected with the plaques formed by amyloid-β in AD and have underlying roles in the progression of the disease and severity. For years, the biomedical field struggled to develop new therapeutic options for AD without a significant advancement. However, mitochondria are striking back existing outside cells in a new mechanism of intercellular communication. Extracellular mitochondria are exchanged from healthy to damaged cells to rescue those with a perturbed metabolism in a process that could be applied as a new therapeutic option to repair those brain cells affected by AD. In this review we highlight key aspects of mitochondria's role in CNS' physiology and neurodegenerative disorders, focusing on AD. We also suggest how mitochondria strikes back as a therapeutic target and as a potential agent to be transplanted to repair neurons affected by AD. [ABSTRACT FROM AUTHOR]

Mitochondrial diseases are a group of genetic disorders characterized by dysfunctional mitochondria. Within eukaryotic cells, mitochondria contain their own ribosomes, which synthesize small amounts of proteins, all of which are essential for the biogenesis of the oxidative phosphorylation system. The ribosome is an evolutionarily conserved macromolecular machine in nature both from a structural and functional point of view, universally responsible for the synthesis of proteins. Among the diseases afflicting humans, those of ribosomal origin – either cytoplasmic ribosomes (80S) or mitochondrial ribosomes (70S) – are relevant. These are inherited or acquired diseases most commonly caused by either ribosomal protein haploinsufficiency or defects in ribosome biogenesis. Here we review the scientific literature about the recent advances on changes in mitochondrial ribosomal structural and assembly proteins that are implicated in primary mitochondrial diseases and neurodegenerative disorders, and their possible connection with metalloid pollution and toxicity, with a focus on MRPL44, NAM9 (MNA6) and GEP3 (MTG3), whose lack or defect was associated with resistance to tellurite. Finally, we illustrate the suitability of yeast Saccharomyces cerevisiae (S. cerevisiae) and the nematode Caenorhabditis elegans (C. elegans) as model organisms for studying mitochondrial ribosome dysfunctions including those involved in human diseases. [ABSTRACT FROM AUTHOR]

[Display omitted] Sigmar1 is a widely expressed molecular chaperone protein in mammalian cell systems. Accumulating research demonstrated the cardioprotective roles of pharmacologic Sigmar1 activation by ligands in preclinical rodent models of cardiac injury. Extensive biochemical and immuno-electron microscopic research demonstrated Sigmar1′s sub-cellular localization largely depends on cell and organ types. Despite comprehensive studies, Sigmar1′s direct molecular role in cardiomyocytes remains elusive. In the present study, we determined Sigmar1′s subcellular localization, transmembrane topology, and function using complementary microscopy, biochemical, and functional assays in cardiomyocytes. Quantum dots in transmission electron microscopy showed Sigmar1 labeled quantum dots on the mitochondrial membranes, lysosomes, and sarcoplasmic reticulum-mitochondrial interface. Subcellular fractionation of heart cell lysates confirmed Sigmar1′s localization in purified mitochondria fraction and lysosome fraction. Immunocytochemistry confirmed Sigmar1 colocalization with mitochondrial proteins in isolated adult mouse cardiomyocytes. Sigmar1′s mitochondrial localization was further confirmed by Sigmar1 colocalization with Mito-Tracker in isolated mouse heart mitochondria. A series of biochemical experiments, including alkaline extraction and proteinase K treatment of purified heart mitochondria, demonstrated Sigmar1 as an integral mitochondrial membrane protein. Sigmar1′s structural requirement for mitochondrial localization was determined by expressing FLAG-tagged Sigmar1 fragments in cells. Full-length Sigmar1 and Sigmar1′s C terminal-deletion fragments were able to localize to the mitochondrial membrane, whereas N-terminal deletion fragment was unable to incorporate into the mitochondria. Finally, functional assays using extracellular flux analyzer and high-resolution respirometry showed Sigmar1 siRNA knockdown significantly altered mitochondrial respiration in cardiomyocytes. Overall, we found that Sigmar1 localizes to mitochondrial membranes and is indispensable for maintaining mitochondrial respiratory homeostasis in cardiomyocytes. [ABSTRACT FROM AUTHOR]

• RMND1 pathogenic variants cause a generalized mitochondrial translation defect. • SHL, neurological phenotype, renal impairment and POI in females is known as Perrault syndrome. • This report reinforces the evidence for the link between mitochondrial and ovarian functions. RMND1 (Required for Meiotic Nuclear Division 1 homolog) is a nuclear encoded mitochondrial protein. Biallelic variants in RMND1 are described in patients with white matter encephalopathy, hearing loss and renal dysfunction. In addition to this phenotype, two independent families (3 patients) have been reported with ovarian failure. We report on a 17-year-old girl with RMND1 related mitochondrial disorder including white matter encephalopathy, hearing loss and renal insufficiency who presented primary ovarian insufficiency in whom a homozygous variant c.713 A > G (p.Asn238Ser) in the RMND1 gene was found. We report the fourth patient with RMND1 biallelic pathogenic variants and primary ovarian insufficiency. [ABSTRACT FROM AUTHOR]

• ATPAF1 is an essential factor of ATP synthase biogenesis in mammals. • ATPAF1 related ATP synthase defect leads to mitochondrial dysfunctions and cell death. • TPAF1 related ATP synthase defect in mice results in cardiac remodeling and dysfunction. ATP11p and ATP12p are two nuclear-encoded mitochondrial chaperone proteins required for assembling the F1Fo-ATP synthase F1 sector. ATPAF1 and ATPAF2 are the mammalian homologs of ATP11p and ATP12p. However, the biochemical and physiological relevance of ATPAF1 and ATPAF2 in animal tissues with high energy-dependence remains unclear. To explore the in vivo role of ATP assembly and the effects of ATP synthase deficiency in animals, we have generated knockout (KO) mouse models of these assembly factors using CRISPR/Cas9 technology. While the Atpaf2 -KO mice were embryonically lethal, Atpaf1 -KO mice grew to adulthood but with smaller body sizes and elevated blood lactate later in life. We specifically investigated how ATPAF1 deficiency may affect ATP synthase biogenesis and mitochondrial respiration in the mouse heart, an organ highly energy-dependent. Western blots and Blue-Native electrophoresis (BN-PAGE) demonstrated a decreased F1 content and ATP synthase dimers in the Atpaf1 -KO heart. Mitochondria from ATPAF1-deficient hearts showed ultrastructural abnormalities with condensed degenerated mitochondria, loss of cristae, and impaired respiratory capacity. ATP synthase deficiency also leads to impaired autophagy and mitochondrial dynamic. Consequently, decreased cardiac function was exhibited in adult Atpaf1 -KO mice. The results provide strong support that ATPAF1 is essential for ATP synthase assembly and mitochondrial oxidative phosphorylation, thus playing a crucial role in maintaining cardiac structure and function in animals. [ABSTRACT FROM AUTHOR]

• Acetylation of mitochondrial proteins were decreased in hepatocellular carcinoma. • Histones were highly acetylated, which claims large demands of nuclear acetyl-CoA. • Metabolism was reprogrammed on aspect of acetyl-CoA utility and localization in HCC. • Regulation of acetylation may attribute to acetyl-CoA utility of cellular organelles. As an essential post-translational modification, acetylation participates in various cellular processes and shows aberrances during tumorigenesis. Owing to its modification substrate, acetyl-CoA, acetylation is postulated as a depot for acetyl groups and evolve to build a connection between epigenetics and metabolism. Here we depict a distinct acetylome atlas of hepatocellular carcinoma from the perspectives of both protein acetylation and acetyl-CoA metabolism. We found that tumor acetylome demonstrated a compartment-dependent alteration that the acetylation level of mitochondrial proteins tended to be decreased while nuclear proteins were highly acetylated. In addition, elevated expression of ATP-citrate synthase (ACLY) was observed in tumors, which would facilitate histone acetylation by transporting mitochondrial acetyl coenzyme A to the nucleus. A hypothetical model of the oncogenic acetylome was proposed that growing demands for histone acetylation in tumor cells would drive the relocalization of acetyl-CoA to the nucleus, which may contribute to the global deacetylation of mitochondrial proteins to support the nuclear acetyl-CoA pool in an ACLY-dependent manner. Our findings are thought-provoking on the potential linkage between epigenetics and metabolism in the progression of tumorigenesis. [ABSTRACT FROM AUTHOR]

• Drp1 is an essential protein required for mitochondrial dynamics. • Mutations in Drp1 result in debilitating disease conditions in patients. • We investigated four middle domain mutations of Drp1 by mimicking them in yeast Dnm1. • Alterations in mitochondrial structure, Dnm1 localization, dynamics and function are reported. The dynamin-related protein 1 (Drp1) and its homologs in various eukaryotes are essential to maintain mitochondrial morphology and regulate mitochondrial division. Several mutations in different domains of Drp1 have been reported, which result in debilitating conditions. Four such disease-causing mutations of the middle domain of Drp1 were mimicked in the yeast dynamin-related GTPase (Dnm1) and were characterized in this study. Mitochondrial morphology and protein function were observed to be altered to a variable extent in cells expressing the mutated variants of Dnm1. Several aspects related to the protein such as punctate formation, localization to mitochondria, dynamic behavior and structure were analyzed by microscopy, biochemical studies and molecular dynamics simulations. Significant effects on the protein structure and function were observed in cells expressing A430D and G397D mutations. Overall, our data provide insight into the molecular and cellular alterations resulting from middle domain mutations in Dnm1. [ABSTRACT FROM AUTHOR]

• Altered synovial microvasculature in Rheumatoid arthritis (RA) holds a significant association with mitochondrial functioning. • Sexual biasness exists in the onset of RA which essentially modulates the path of inflammatory milieu. • Estrogenic regulation of cellular metabolism may extend to the functioning of mitochondria in RA. • In silico analysis revealed the mitochondrial proteins associated with RA pathogenesis were also gene targets of estradiol. • Mitochondrial functioning modulated by estrogen in RA could potentially form a targeted therapeutic approach. Alteration of immune response and synovium microvasculature in Rheumatoid arthritis (RA) progression has been suggested to be associated with mitochondrial functioning. Mitochondria, with maternally inherited DNA, exhibit differential response to the female hormone estrogen. Various epidemiological evidence has also shown the prominence of RA in the female population, depicting the role of estrogen in modulating the pathogenesis of RA. As estrogen regulates the expression of differential proteins and associated signaling pathways of RA, its influence on mitochondrial functioning seems evident. Thus, in this review, the studies related to mitochondria and their relation with estrogen and Rheumatoid arthritis were retrieved. We analyzed the different mitochondrial activities that are altered in RA and the possibility of their estrogenic control. The study expands to in silico analysis, revealing the differential mitochondrial proteins expressed in RA and examining these proteins as potential estrogenic targets. It was found that ALDH2, CASP3, and SOD2 are the major mitochondrial proteins involved in RA progression and are also potent estradiol targets. The analysis establishes the role of mitochondrial proteins in RA progression, which were found to be direct or indirect targets of estrogen, depicting its potential for regulating mitochondrial functions in RA. [ABSTRACT FROM AUTHOR]

• We report a novel m.10197G > C variant in MT-ND3 with Leigh syndrome. • Newly discovered m.10197G > C was confirmed to be pathogenic by functional analysis. • We imported allotopically expressed wild-type MT-ND3 into mitochondria. • We imported codon-optimized MT-ND3 in three patients with m.10197G > C and m.10191 T > C missense variants in the MT-ND3. • Allotopically expressed MT-ND3 increases ATP production, partial restoration of Complex I (CI) assembly, and cell proliferation. Mitochondrial diseases are caused by nuclear, or mitochondrial DNA (mtDNA) variants and related co-factors. Here, we report a novel m.10197G > C variant in MT-ND3 in a patient, and two other patients with m.10191 T > C. MT-ND3 variants are known to cause Leigh syndrome or mitochondrial complex I deficiency. We performed the functional analyses of the novel m.10197G > C variant that significantly lowered MT-ND3 protein levels, causing complex I assembly and activity deficiency, and reduction of ATP synthesis. We adapted a previously described re-engineering technique of delivering mitochondrial genes into mitochondria through codon optimization for nuclear expression and translation by cytoplasmic ribosomes to rescue defects arising from the MT-ND3 variants. We constructed mitochondrial targeting sequences along with the codon-optimized MT-ND3 and imported them into the mitochondria. To achieve the goal, we imported codon-optimized MT-ND3 into mitochondria in three patients with m.10197G > C and m.10191 T > C missense variants in the MT-ND3. Nuclear expression of the MT-ND3 gene partially restored protein levels, complex I deficiency, and significant improvement of ATP production indicating a functional rescue of the mutant phenotype. The codon-optimized nuclear expression of mitochondrial protein and import inside the mitochondria can supplement the requirements for ATP in energy-deficient mitochondrial disease patients. [ABSTRACT FROM AUTHOR]

• Mitochondrial matrix-localized p53 with an intrinsic 3′→5′ exoribonuclease activity participates in mtRNA degradation. • The substrates targeted by p53 in mitochondria includes polyA- and non-polyA containing ssRNAs, and RNA/DNA hybrid. • p53 harbors a general 3′-end mRNA degradation feature. • The accumulation of p53 in mitochondrial matrix leads to decrease in the level of various mitochondrial RNAs, and in decline in the amount of mitochondrial DNA-encoded proteins. Mitochondrial RNA degradation plays an important role in maintenance of the mitochondria genetic integrity. Mitochondrial localization of p53 was observed in non-stressed and stressed cells. p53, as an RNA-binding protein, exerts 3′→5′ exoribonuclease activity. The data suggest that in non-stressed cells, mitochondrial matrix-localized p53, with exoribonuclease activity, may play a housekeeping positive role. p53, through restriction the formation of new RNA/DNA hybrid and processing R-loop, might serve as mitochondrial R-loop suppressor. Conversely, stress-induced matrix-p53 decreases the amount of mitochondrial single-stranded RNA transcripts (including polyA- and non-polyA RNAs), thereby leading to the decline in the amount of mitochondria-encoded oxidative phosphorylation components. [ABSTRACT FROM AUTHOR]

• In epilepsy increased production of ROS leading to neuronal death. • Oxidative stress has important role to play in seizure generation. • The mitochondrial dysfunctioning increasing the excitatory postsynaptic potential. • Calcium influx promotes neuronal death via mitochondrial apoptotic pathways. Epileptogenesis is most commonly associated with neurodegeneration and a bioenergetic defect attributing to the fact that mitochondrial dysfunction plays a key precursor for neuronal death. Mitochondria are the essential organelle of neuronal cells necessary for certain neurophysiological processes like neuronal action potential activity and synaptic transmission. The mitochondrial dysfunction disrupts calcium homeostasis leading to inhibitory interneuron dysfunction and increasing the excitatory postsynaptic potential. In epilepsy, the prolonged repetitive neuronal activity increases the excessive demand for energy and acidosis in the brain further increasing the intracellular calcium causing neuronal death. Similarly, the mitochondrial damage also leads to the decline of energy by dysfunction of the electron transport chain and abnormal production of the ROS triggering the apoptotic neuronal death. Thus, the elevated level of cytosolic calcium causes the mitochondria DNA damage coinciding with mtROS and releasing the cytochrome c binding to Apaf protein further initiating the apoptosis resulting in epileptic encephalopathies. The various genetic and mRNA studies of epilepsy have explored the various pathogenic mutations of genes affecting the mitochondria functioning further initiating the neuronal excitotoxicity. Based on the results of previous studies, the recent therapeutic approaches are targeting basic mitochondrial processes, such as energy metabolism or free-radical generation, or specific interactions of disease-related proteins with mitochondria and hold great promise to attenuate epileptogenesis. Therefore, the current review emphasizes the emerging insights to uncover the relation between mitochondrial dysfunction and ROS generation contributing to mechanisms underlying epileptic seizures. [ABSTRACT FROM AUTHOR]

Complex I is the largest and most intricate of the protein complexes of mitochondrial electron transport chain (ETC). This L-shaped enzyme consists of a peripheral hydrophilic matrix domain and a membrane-bound orthogonal hydrophobic domain. The interfacial region between these two arms is known to be critical for binding of ubiquinone moieties and has also been shown to be the binding site of Complex I inhibitors. Knowledge on specific roles of the ETC interfacial region proteins is scarce due to lack of knockout cell lines and animal models. Here we mutated nuclear encoded NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 (NDUFS2), one of three protein subunits of the interfacial region, in a human embryonic kidney cell line 293 using a CRISPR/Cas9 procedure. Disruption of NDUFS2 significantly decreased cell growth in medium, Complex I specific respiration, glycolytic capacity, ATP pool and cell-membrane integrity, but significantly increased Complex II respiration, ROS generation, apoptosis, and necrosis. Treatment with idebenone, a clinical benzoquinone currently being investigated in other indications, partially restored growth, ATP pool, and oxygen consumption of the mutant. Overall, our results suggest that NDUFS2 is vital for growth and metabolism of mammalian cells, and respiratory defects of NDUFS2 dysfunction can be partially corrected with treatment of an established mitochondrial therapeutic candidate. This is the first report to use CRISPR/Cas9 approach to construct a knockout NDUFS2 cell line and use the constructed mutant to evaluate the efficacy of a known mitochondrial therapeutic to enhance bioenergetic capacity. [ABSTRACT FROM AUTHOR]

• Mitochondrial proteins are differentially expressed in EE patient's skeletal muscle. • Most of the proteins are down-regulated in the OXPHOS complex IV. • Altered proteins are involved predominantly in oxidoreductase activity. Ethylmalonic encephalopathy (EE) is a rare autosomal recessive inborn error of metabolism. To study the molecular effects of ETHE1 p. D165H mutation, we employed mass spectrometry-based mitochondrial proteome and phosphoproteome profiling in the human skeletal muscle. Eighty-six differentially altered proteins were identified, of which thirty-seven mitochondrial proteins were differentially expressed, and most of the proteins (37%) were down-regulated in the OXPHOS complex-IV. Also, nine phosphopeptides that correspond to eight mitochondrial proteins were significantly affected in EE patient. These altered proteins recognized are involved in several pathways and molecular functions, predominantly in oxidoreductase activity. This is the first study that has integrated proteome and phosphoproteome of skeletal muscle and identified multiple proteins associated in the pathogenesis of EE. [ABSTRACT FROM AUTHOR]

• We provide a list of yeast mitochondrial protein kinases and phosphatases • 972 (~70%) of proteins in yeast mitochondria contain a total of >9,400 phospho-sites. • Phosphorylation affects a large repertoire of mitochondrial functions. • Phosphorylation of mitochondrial DNA encoded proteins is rare. • Many proteins are phosphorylated prior to their import into the organelle. Protein phosphorylation is one of the best-known post-translational modifications occurring in all domains of life. In eukaryotes, protein phosphorylation affects all cellular compartments including mitochondria. High-throughput techniques of mass spectrometry combined with cell fractionation and biochemical methods yielded thousands of phospho-sites on hundreds of mitochondrial proteins. We have compiled the information on mitochondrial protein kinases and phosphatases and their substrates in Saccharomyces cerevisiae and provide the current state-of-the-art overview of mitochondrial protein phosphorylation in this model eukaryote. Using several examples, we describe emerging features of the yeast mitochondrial phosphoproteome and present challenges lying ahead in this exciting field. [ABSTRACT FROM AUTHOR]

• The interactome of c-Src inside the mitochondrial matrix was examined using proximity-dependent biotin identification (BioID) • We identified 51 mitochondrial proteins potentially interacting with c-Src. • In silico analyses suggest that c-Src targets 24 phosphorylation sites among 17 mitochondrial proteins. • Coimmunoprecipitation assays confirmed interaction of c-Src with SLP2 and ATP5β. C-Src kinase is localized in several subcellular compartments, including mitochondria where it is involved in the regulation of organelle functions and overall metabolism. Surprisingly, the characterization of the intramitochondrial Src interactome has never been fully determined. Using in vitro proximity-dependent biotin identification (BioID) coupled to mass spectrometry, we identified 51 candidate proteins that may interact directly or indirectly with c-Src within the mitochondrial matrix. Pathway analysis suggests that these proteins are involved in a large array of mitochondrial functions such as protein folding and import, mitochondrial organization and transport, oxidative phosphorylation, tricarboxylic acid cycle and metabolism of amino and fatty acids. Among these proteins, we identified 24 tyrosine phosphorylation sites in 17 mitochondrial proteins (AKAP1, VDAC1, VDAC2, VDAC3, LonP1, Hsp90, SLP2, PHB2, MIC60, UBA1, EF-Tu, LRPPRC, ACO2, OAT, ACAT1, ETFβ and ATP5β) as potential substrates for intramitochondrial Src using in silico prediction of tyrosine phospho-sites. Interaction of c-Src with SLP2 and ATP5β was confirmed using coimmunoprecipitation. This study suggests that the intramitochondrial Src could target several proteins and regulate different mitochondrial functions. [ABSTRACT FROM AUTHOR]

• Alzheimer disease is a neurodegenerative disorder with dementia and progressive impairment. • Aβ is chief factor intricated in oxidative damage, radical formation and mitochondrial damage. • ROS production leads to AD. • Hyperphopshorylated tau is responsible for destabilizing microtubules. Brain is a fully differentiated organ and is sensitive towards oxidative damage of various compounds including lipids, proteins, and DNA that occurs during process of normal aging and is mainly due to its high energy metabolism and reduced activity of anti-oxidative defense mechanism. Mitochondria are dynamic ATP-generating organelles which constitutes cellular functions such as regulation of intracellular calcium, bio-energetic processes, and reduction–oxidation of cells. Such functioning is negatively affected due to the presence of amyloid β peptide (Aβ) which is involved in pathogenesis of Alzheimer disease (AD). Aβ interacts with mitochondria and leads to mitochondrial dysfunction. Mitochondrial dysfunction, abnormal interactions, oxidative stress, and mis-folding of synaptic proteins inside nervous system are explored and regarded as primary or initial features in insurgence of pathology (AD and other neurological disease). The major histopathological hallmarks of AD are characterized by presence of these hallmarks intracellularly, its further progression and exacerbation which leads to excessive accumulation of oligomeric as well as fibrillar-β-amyloid peptides (present extracellularly) and accumulation of neurofibrillary tangles intracellularly. The current review will focus on alterations and variation in mitochondria/mitochondrial DNA (mtDNA) and the rationale for involvement of related abnormalities in pathogenesis of AD. [ABSTRACT FROM AUTHOR]

Considering the versatile functions attributed to uncoupling protein 2 (UCP2) in health and disease, a profound understanding of the protein's molecular actions under physiological and pathophysiological conditions is indispensable. This review aims to revisit and shed light on the fundamental molecular functions of UCP2 in mitochondria, with particular emphasis on its intricate role in regulating mitochondrial calcium (Ca2+) uptake. UCP2′s modulating effect on various vital processes in mitochondria makes it a crucial regulator of mitochondrial homeostasis in health and disease. [ABSTRACT FROM AUTHOR]

• Mitochondrial proteins are differentially expressed in RA PBMCs as compared to healthy controls. • Differentially expressed proteins are part of OXPHOS and mitochondrial dysfunction. • Mitochondrial membrane potential, superoxide levels and total cellular ATP are reduced in RA PBMCs. The autoimmune inflammatory disease, Rheumatoid arthritis (RA), has known imbalances in energy metabolism and superoxide levels thus may have an etiology associated with mitochondrial dysfunction. We thus evaluated the presence of a differential mitochondrial proteome as well as other characteristics including mitochondrial mass, membrane potential (Ψm), total cellular ATP and superoxide levels. Eighteen mitochondrial proteins were down-regulated while four were up-regulated in RA patients in comparison to the healthy controls (HC). A significant decrease in mitochondrial Ψm, superoxides and cellular ATP levels was observed in RA with constant mitochondrial mass suggesting mitochondrial dysfunction responsible for functional disparity in RA. [ABSTRACT FROM AUTHOR]

• Protein gene and intron content is compared among mitogenomes from 46 diverse land plants. • Protein gene content varies substantially among most land plant lineages, except liverworts and mosses. • Intron content is highly variable among the major land plant lineages, but relatively stable within each major lineage. • Ancestrally cis -spliced introns have shifted to trans -splicing dozens of times in lycophytes and seed plants. • Convergent evolution is a recurrent theme in mitogenomic evolution. The functional content of the mitochondrial genome (mitogenome) is highly diverse across eukaryotes. Among land plants, our understanding of the variation in mitochondrial gene and intron content is improving from concerted efforts to densely sample mitogenomes from diverse land plants. Here I review the current state of knowledge regarding the diversity in content of protein genes and introns in the mitogenomes of all major land plant lineages. Mitochondrial protein gene content is largely conserved among mosses and liverworts, but it varies substantially among and within other land plant lineages due to convergent losses of genes encoding ribosomal proteins and, to a lesser extent, genes for proteins involved in cytochrome c maturation and oxidative phosphorylation. Mitochondrial intron content is fairly stable within each major land plant lineage, but highly variable among lineages, resulting from occasional gains and many convergent losses over time. Trans- splicing has evolved dozens of times in various vascular plant lineages, particularly those with relatively higher rates of mitogenomic rearrangement. Across eukaryotes, mitochondrial protein gene and intron content has been shaped massive convergent evolution. [ABSTRACT FROM AUTHOR]

Chemical acetylation is postulated to occur in mitochondria. Mitochondrial transcription factor A (TFAM or mtTFA), a mitochondrial transcription initiation factor as well as the major mitochondrial nucleoid protein coating the entire mitochondrial genome, is proposed to be acetylated in animals and cultured cells. This study investigated the properties of human TFAM, in conjunction with the mechanism and effects of TFAM acetylation in vitro. Using highly purified recombinant human TFAM and 3 kb circular DNA as a downsized mtDNA model, we studied how the global TFAM–DNA interaction is affected/regulated by the quantitative TFAM–DNA relationship and TFAM acetylation. Results showed that the TFAM–DNA ratio strictly affects the TFAM property to unwind circular DNA in the presence of topoisomerase I. Mass spectrometry analysis showed that in vitro chemical acetylation of TFAM with acetyl-coenzyme A occurs preferentially on specific lysine residues, including those reported to be acetylated in exogenously expressed TFAM in cultured human cells, indicating that chemical acetylation plays a crucial role in TFAM acetylation in mitochondria. Intriguingly, the modification significantly decreased TFAM's DNA-unwinding ability, while its DNA-binding ability was largely unaffected. Altogether, we propose TFAM is chemically acetylated in vivo , which could change mitochondrial DNA topology, leading to copy number and gene expression modulation. [ABSTRACT FROM AUTHOR]

• Each kingdom has apparently developed its specific UPRmt regulators. • However, UPRmt activation induces nuclear gene expression of many similar genes. • Strategies to resolve mitochondrial dysfunctions are thus partially conserved. • We identified conserved genes across kingdoms as candidates for future research. Mitochondria are key components of eukaryotic cells, so their proper functioning is monitored via different mitochondrial signalling responses. One of these mitochondria-to-nuclear 'retrograde' responses to maintain mitochondrial homeostasis is the mitochondrial unfolded protein response (UPRmt), which can be activated by a variety of defects including blocking mitochondrial translation, respiration, protein import or transmembrane potential. Although UPRmt was first reported in cultured mammalian cells, this signalling pathway has also been extensively studied in the nematode Caenorhabditis elegans. In yeast, there are no published studies focusing on UPRmt in a strict sense, but other unfolded protein responses (UPR) that appear related to UPRmt have been described, such as the UPR activated by protein mistargeting (UPRam) and mitochondrial compromised protein import response (mitoCPR). In plants, very little is known about UPRmt and only recently some of the regulators have been identified. In this paper, we summarise and compare the current knowledge of the UPRmt and related responses across eukaryotic kingdoms: animals, fungi and plants. Our comparison suggests that each kingdom has evolved its own specific set of regulators, however, the functional categories represented among UPRmt–related target genes appear to be largely overlapping. This indicates that the strategies for preserving proper mitochondrial functions are partially conserved, targeting mitochondrial chaperones, proteases, import components, dynamics and stress response, but likely also non-mitochondrial functions including growth regulators/hormone balance and amino acid metabolism. We also identify homologs of known UPRmt regulators and responsive genes across kingdoms, which may be interesting targets for future research. [ABSTRACT FROM AUTHOR]

• Stable isotope labelling can be used to measure the turnover rate of specific mitochondrial proteins in vivo. • Mitochondrial protein turnover rates vary >100 fold. • Degradation studies are revealing the rate of assembly and maintenance of mitochondrial protein complexes in vivo. Plant mitochondria operate as the powerhouses for cellular energy production by using the combined functions of both imported and organelle-synthesised proteins. Homeostasis of mitochondrial proteins is controlled by both synthesis and degradation processes which together define protein turnover in this organelle. Better understanding of plant mitochondrial protein turnover will provide information on protein quality control inside these organelles and its importance for proper function and regulation of mitochondrial machinery. This review discusses methods used for measurement of turnover rates of plant mitochondrial proteins and presents our current understanding of these rates for key mitochondrial proteins and protein complexes. The assembly and maintenance of mitochondrial OXPHOS complexes, in particular Complexes I and V, will be discussed in detail based on the evidence for differential protein turnover rates of the same protein subunits in different mitochondrial fractions. The impact of the loss of specific plant mitochondrial proteases on proteolysis events and rates of mitochondrial protein turnover will be highlighted. The challenges and future directions for investigation of plant mitochondrial protein turnover are also discussed. [ABSTRACT FROM AUTHOR]

The mitochondrial respiratory chain (MRC) is comprised of ~92 nuclear and mitochondrial DNA-encoded protein subunits that are organized into five different multi-subunit respiratory complexes. These complexes produce 90% of the ATP required for cell sustenance. Specific sets of subunits are assembled in a modular or non-modular fashion to construct the MRC complexes. The complete assembly process is gradually chaperoned by a myriad of assembly factors that must coordinate with several other prosthetic groups to reach maturity, making the entire process extensively complicated. Further, the individual respiratory complexes can be integrated into various giant super-complexes whose functional roles have yet to be explored. Mutations in the MRC subunits and in the related assembly factors often give rise to defects in the proper assembly of the respiratory chain, which then manifests as a group of disorders called mitochondrial diseases, the most common inborn errors of metabolism. This review summarizes the current understanding of the biogenesis of individual MRC complexes and super-complexes, and explores how mutations in the different subunits and assembly factors contribute to mitochondrial disease pathology. [ABSTRACT FROM AUTHOR]

• Plant UCPs biochemical properties, 3D structure, and physiological role are reviewed. • UCPs transcriptional regulation and co-expression networks across species is revisited. • Plant UCPs play a major role in cell signaling towards cellular bioenergetics and stress response. The biological function of plant mitochondrial uncoupling proteins (pUCPs) has been a matter of considerable controversy. For example, the pUCP capacity to uncouple respiration from ATP synthesis in vivo has never been fully acknowledged, in contrast to the mammalian UCP1 (mUCP1) role in uncoupling respiration-mediated thermogenesis. Interestingly, both pUCPs and mUCPs have been associated with stress response and metabolic perturbations. Some central questions that remain are how pUCPs and mUCPs compare in biochemical properties, molecular structure and cell biology under physiological and metabolically perturbed conditions. This review takes advantage of the large amount of data available for mUCPs to review the biochemical properties, 3D structure models and potential physiological roles of pUCPs during plant development and response to stress. The biochemical properties and structure of pUCPs are revisited in light of the recent findings that pUCPs catalyse the transport of metabolites across the mitochondrial inner membrane and the resolved mUCP2 protein structure. Additionally, transcriptional regulation and co-expression networks of UCP orthologues across species are analysed, taking advantage of publicly available curated experimental datasets. Taking these together, the biological roles of pUCPs are analysed in the context of their potential roles in thermogenesis, ROS production, cell signalling and the regulation of plant cellular bioenergetics. Finally, pUCPs biological function is discussed in the context of their potential role in protecting against environmental stresses. [ABSTRACT FROM AUTHOR]

We report a patient carrying a novel pathogenic variant p.(Tyr101Cys) in ISCA1 leading to MMDS type 5. He initially presented a psychomotor regression with loss of gait and language skills and a tetrapyramidal spastic syndrome. Biochemical analysis of patient fibroblasts revealed impaired lipoic acid synthesis and decreased activities of complex I and II of respiratory chain. While ISCA1 is involved in the mitochondrial machinery for iron-sulfur cluster biogenesis, these dysfunctions are secondary to impaired maturation of mitochondrial proteins containing the [4Fe-4S] clusters. Expression and purification of the human ISCA1 showed a decreased stability of the [2Fe-2S] cluster in the mutated protein. [ABSTRACT FROM AUTHOR]

• Remodeling of mitochondria and mitochondrial functionality is an eminent factor in cellular life and death. • Dysfunctions of mitochondrial functions and apoptosis pathway are associated with pathological process in cancer. • We investigated a prognostic significance of Drp1 in a clinic-pathological study. • ROS mediated up-regulated mitochondrial mass and shift in mitochondrial fission. • Bcl-2 mediated mitochondrial fission promoting up-regulation of cell cycle marker CyclinD1 in cancer cells. Dysregulation in mitochondrial dynamics has been associated with several diseases including cancer. Present study assessed the alteration in mitochondrial fission protein (Drp1) in oral epithelial cells collected from clinically confirmed pre-cancer and cancer patients and further correlates it with the cellular apoptosis signaling. Results indicate the ROS accumulation in OSCC patients is accompanied by several changes including increase in mitochondrial mass, expression of mitochondrial fission protein (Drp1) and alteration in apoptotic signaling. The positive co-relation has been observed between the expressions of anti-apoptotic Bcl-2proteinswith mitochondrial fission protein Drp1. Higher mitochondrial fission in oral cancer cells was also correlated with the increased expression of cell cycle marker CyclinD1 indicating highly proliferative stage of oral cancer cells. The clinical correlation can be extended to develop biomarker for diagram and program in oral cancer management. [ABSTRACT FROM AUTHOR]

• In this study, we performed the comparative analysis of the experimentally-characterized mitochondrial proteomes of four bilaterian animals (human, mouse, Caenorhabditis elegans, and Drosophila melanogaster). • Of several factors affecting the size of the mitochondrial proteome in animals, evolution of novel mitochondrial proteins in mammals and loss of ancestral mitochondrial proteins in protostomes were the main contributors. • Interestingly, gain/loss of N-terminus mitochondrial targeting signals was not a significant factor in the evolution of the size of the animal mitochondrial proteome. Despite a conserved set of core mitochondrial functions, animal mitochondrial proteomes show a large variation in size. We analyzed putative mechanisms behind and functional significance of this variation by performing comparative analysis of the experimentally-verified mitochondrial proteomes of four bilaterian animals (human, mouse, Caenorhabditis elegans , and Drosophila melanogaster) and two non-animal outgroups (Acanthamoeba castellanii and Saccharomyces cerevisiae). We found that of several factors affecting mitochondrial proteome size, evolution of novel mitochondrial proteins in mammals and loss of ancestral proteins in protostomes were the main contributors. Interestingly, the gain and loss of the N-terminal mitochondrial targeting signal was not a major factor in the proteome size evolution. [ABSTRACT FROM AUTHOR]

• We developed two tools for comparative analysis of animal mitochondrial proteomes. • MMPdb helps analyze and download mitochondrial proteomes of model animals. • MitoPredictor uses machine-learning to predict mitochondrial proteins in animals. • MMPdb is publicly available at http://mmpdb.eeob.iastate.edu/. Data on experimentally-characterized animal mitochondrial proteomes (mt-proteomes) are limited to a few model organisms and are scattered across multiple databases, impeding a comparative analysis. We developed two resources to address these problems. First, we re-analyzed proteomic data from six species with experimentally characterized mt-proteomes: animals (Homo sapiens , Mus musculus , Caenorhabditis elegans , and Drosophila melanogaster), and outgroups (Acanthamoeba castellanii and Saccharomyces cerevisiae) and created the Metazoan Mitochondrial Proteome Database (MMPdb) to host the results. Second, we developed a novel pipeline, "MitoPredictor" that uses a Random Forest classifier to infer mitochondrial localization of proteins based on orthology, mitochondrial targeting signal prediction, and protein domain analyses. Both tools generate an R Shiny applet that can be used to visualize and interact with the results and can be used on a personal computer. MMPdb is also available online at https://mmpdb.eeob.iastate.edu/. [ABSTRACT FROM AUTHOR]

Mitochondria play pivotal roles in cellular energy metabolism, the synthesis of essential biomolecules and the regulation of cell death and aging. The proper folding, unfolding and degradation of the many proteins active within mitochondria is surveyed by the mitochondrial quality control machineries. Here, we describe the principal components of the mitochondrial quality control system and recent developments in the elucidation of the molecular mechanisms maintaining a functional mitochondrial proteome. [ABSTRACT FROM AUTHOR]

Mitochondrial protein quality control requires the action of proteases to remove damaged or unnecessary proteins and perform key regulatory cleavage events. Important components of the quality control network are the mitochondrial AAA proteases, which capture energy from ATP hydrolysis to destabilize and degrade protein substrates on both sides of the inner membrane. Dysfunction of these proteases leads to the breakdown of mitochondrial proteostasis and is linked to the development of severe human diseases. In this review, we will describe recent insights into the structure and motions of the mitochondrial AAA proteases and related enzymes. Together, these studies have revealed the mechanics of ATP-driven protein destruction and significantly advanced our understanding of how these proteases maintain mitochondrial health. [ABSTRACT FROM AUTHOR]

The PGC-1 transcriptional coactivators have been proposed as master regulators of mitochondrial biogenesis and energy metabolism. Here we show that the single member of the family in Drosophila , spargel (srl) has an essential role in early development. Female germline-specific RNAi knockdown resulted in embryonic semilethality. Embryos were small, with most suffering a catastrophic derangement of cellularization and gastrulation, although genes dependent on localized determinants were expressed normally. The abundance of mtDNA, representative mitochondrial proteins and mRNAs were not decreased in knockdown ovaries or embryos, indicating that srl has a more general role in early development than specifically promoting mitochondrial biogenesis. • The Drosophila PGC-1 transcriptional coactivator spargel was knocked down in the female germline. • As a result, embryonic development suffered a catastrophic failure. • However, RNA and protein analysis found no evidence of specific effects on mitochondrial gene expression. • Spargel thus plays some other or more general role in early development. [ABSTRACT FROM AUTHOR]

Mitochondrial dynamics and mitophagy are important aspects of mitochondrial quality control, and are linked to neurodegenerative diseases and muscular diseases. Fis1, a protein on the mitochondrial outer membrane, is thought to mediate mitochondrial fission. However, Fis1 null worms and mammalian cells only display mild fission defects but show aberrant mitophagy. To assess Fis1 function in vivo , we generated conditional knock-out Fis1 mice to allow for specific Fis1 deletion in adult skeletal muscle. In the absence of Fis1 in Type I muscle, mitochondrial hyperfusion, respiratory chain deficiency, and increased mitophagy were found. Moreover, abnormal mitophagy was aggravated by endurance exhaustive exercise stress (EEE), suggesting that Fis1 is involved in maintaining normal mitophagy in mitochondria-rich Type I muscle during exercise. Additionally, Fis1 loss induced delayed onset muscle ultrastructure change (DOMUC) in Type I muscle and strong inflammation in response to acute exhaustive exercise (EE). Thus, we identify a role for Fis1 in maintaining normal mitochondrial structure and function at rest and under exercise stress. [ABSTRACT FROM AUTHOR]

This study aimed to determine the role of mitochondria-associated proteins (HtrA2, α-synuclein, and Park7) in attention deficit/hyperactivity disorder (ADHD). A total of 125 patients with ADHD (77.6% were males) and 66 healthy controls (66.7% were males) were recruited. We found that girls with ADHD demonstrated higher plasma HtrA2 level than control girls, and their HtrA2 levels were positively correlated with verbal comprehensive ability, and negatively correlated to behavior symptoms. Among boys, we observed no correlations between these mitochondrial proteins, neuropsychological findings, and clinical symptoms. Our findings suggest that an underlying gender-specific mitochondria pathway may influence with the pathophysiology of ADHD. • The role of mitochondria-associated proteins (HtrA2, α-synuclein, and Park7) in ADHD was investigated. • Girls with ADHD demonstrated higher plasma HtrA2 level than control girls. • No correlations between these mitochondrial proteins and clinical symptoms were observed in ADHD boys. • An underlying gender-specific mitochondria pathway may influence with the pathophysiology of ADHD. [ABSTRACT FROM AUTHOR]

Mitochondria, the double membrane-walled powerhouses of the eukaryotic cell, are also the seats of synthesis of two critical yet prevalent nonbilayer-prone phospholipids, namely phosphatidylethanolamine (PE) and cardiolipin (CL). Besides their established biochemical roles in the regulation of partner protein function, PE and CL are also key protagonists in the biophysics of mitochondrial membrane remodeling and dynamics. In this review, we address lipid geometry and behavior at the single-molecule level as well as their intimate coupling to whole organelle morphology and remodeling during the concerted events of mitochondrial fission. We present evidence from recent experimental measurements ably supported and validated by computational modeling studies to support our notion that conical lipids play a catalytic as well as a structural role in mitochondrial fission. • Mitochondria are enriched in nonbilayer-prone conical lipids, particularly PE and CL. • Redistribution of conical lipids by proteins facilitate membrane superconstriction. • Conical lipids likely also play a catalytic role in mitochondrial membrane fission. • CL breakdown to PA and DAG may regulate mitochondrial fission. • Studies of membrane mechanics by computational modeling can sort the roles of lipids and proteins in mitochondrial dynamics. [ABSTRACT FROM AUTHOR]

Proteins embedded in the inner mitochondrial membrane (IMM) perform essential cellular functions. Maintaining the folding state of these proteins is therefore of the utmost importance, and this is ensured by IMM chaperones and proteases that refold and degrade unassembled and misfolded proteins. However, the physiological consequences specific to IMM protein misfolding remain obscure because deletion of these chaperones/proteases (the typical experimental strategy) often affects many mitochondrial processes other than protein folding and turnover. Thus, novel experimental systems are needed to evaluate the direct effects of misfolded protein on the membrane. Such a system has been developed in recent years. Studies suggest that numerous pathogenic mutations in isoform 1 of adenine nucleotide translocase (Ant1) cause its misfolding on the IMM. In this review, we first discuss potential mechanisms by which dominant Ant1 mutations may cause disease, highlighting IMM protein misfolding, per se, as a likely pathological factor. Then we discuss the intramitochondrial effects of Ant1 misfolding such as IMM proteostatic stress, respiratory chain dysfunction, and mtDNA instability. Finally, we summarize the mounting evidence that IMM proteostatic stress can perturb mitochondrial protein import to cause the toxic accumulation of mitochondrial proteins in the cytosol: a cell stress mechanism termed mitochondrial Precursor Overaccumulation Stress (mPOS). • Misfolded variants of adenine nucleotide translocase 1 (Ant1) were recently identified that cause dominant human diseases. • Ant1 misfolding on the inner mitochondrial membrane (IMM) destabilizes protein complexes assembly and mtDNA. • IMM stress induces cell death by mitochondrial Precursor Overaccumulation Stress (mPOS) independent of bioenergetics. • Anti-mPOS therapy may offer a potential treatment for diseases caused by mitochondria-induced proteostatic stress. [ABSTRACT FROM AUTHOR]

Mitochondrial trifunctional protein (MTP) deficiency is a rare autosomal recessive disorder with several phenotypes. Neuromyopathic form of MTP deficiency is characterized by infantile or juvenile-onset, progressive peripheral neuropathy and rhabdomyolysis. To date, only one Chinese patient harboring homozygous c. 739C>T (p.R247C) in HADHB has been reported. Here, using whole exome sequencing (WES), we identified a compound heterozygote of c.407T>C (p.M136T) and c.421G>A (p.A141T) within HADHB in a Chinese MTP deficiency patient of neuromyopathic form. In vitro cell functional studies were performed to evaluate the effect of mutations on MTP complex expression and subcellular location, which revealed that p.M136T and p.A141T mutations compromised MTP complex stability but not altered subcellular localization, resulting in lower protein level at 37 °C but higher at 30 °C. These results indicated that both mutations were pathogenic through a loss-of-function mechanism and temperature-sensitive leading to their correlation with the mild phenotype. The current study broadens the genetic spectrum of HADHB and highlights the importance of screening fatty acid oxidation deficiency-related gene mutations among patients with intermittent rhabdomyolysis, as in the patient reported here, although extremely rare. • Broaden the genetic spectrum of HADHB. • Temperature-sensitive HADHB mutations correlate with mild neuromyopathic phenotype. • Fatty acid oxidation deficiency should be a suspected etiology in patients with intermittent rhabdomyolysis. [ABSTRACT FROM AUTHOR]

Mitochondria are essential organelles required for cellular processes ranging from energy production to cellular differentiation. To perform these functions, mitochondria physically and functionally interact with other organelles such as the endoplasmic reticulum (ER) and endosomes. While the role of ER-mitochondria contact sites is well established, the interaction between mitochondria and endosomes has only recently been reported. These interactions are involved in lipid and ion transfer and potentially play a crucial role in mitochondria quality control and the release of mitochondrial components within extracellular vesicles. Here, we will discuss the current view of mitochondria-endosome interaction, both physically and functionally. • Mitochondria physically and functionally interact with the endoplasmic reticulum (ER) and endosomes. • These interactions are emerging as part of a larger array of intracellular transport mechanisms. • Mitochondria-endosomes interactions regulate metabolism, quality control mechanisms and innate immunity. • Mitochondrial proteins are exported in extracellular vesicle as quality control mechanism and/or for cell-cell communication. [ABSTRACT FROM AUTHOR]

Chronic progressive external ophthalmoplegia (CPEO) is a common presentation of mitochondrial disease. We performed a retrospective evaluation of the molecular genetic testing and genotype-phenotype correlations in a large cohort of adult-onset CPEO patients (N = 111). One hundred percent of patients tested had at least one mitochondrial DNA (mtDNA) deletion. Genetic testing of nuclear genes encoding mitochondrial proteins identified pathogenic/likely pathogenic variants likely to be associated with CPEO in 7.6% of patients. As expected, the nuclear gene most associated with DNA variation was POLG. A single likely pathogenic mitochondrial DNA variant (m.12278T>C) was identified in two unrelated patients. No significant differences were noted in the clinical phenotypes of patients with pathogenic or likely pathogenic nuclear variants in comparison to those with negative nuclear gene testing. Analysis of deletion size and heteroplasmy in muscle-derived mtDNA showed significant correlations with age of symptom onset but not disease severity (number of canonical CPEO features). Results suggest that smaller mtDNA deletions (p = 0.0127, r2 = 0.1201) and higher heteroplasmy of single mtDNA deletions (p = 0.0112, r2 = 0.2483) are associated with an earlier age of onset in CPEO patients. • Higher heteroplasmy of mtDNA deletions associated with earlier age of onset. • Hereditary nuclear cause of CPEO identified in 7.6% of patients. • LRPCR/NGS can be discrepant in number of deletions in muscle-derived mtDNA. [ABSTRACT FROM AUTHOR]

Mitochondria are involved in a variety of cellular metabolic processes and their functions are regulated by intrinsic and extrinsic stimuli. Recent studies have revealed functional diversity and importance of mitochondria in many cellular processes, including the innate immune response. This study evaluated the specific response and proteomic changes in host Caenorhabditis elegans mitochondria during Pseudomonas aeruginosa PAO1 infection. We performed an inclusive approach to determine the C. elegans mitochondria proteome. The protein fractions of mitochondria were analysed by tandem LC-MS/MS, 129 differentially regulated proteins were identified, indicating an involvement of various mitochondrial processes. The several known components of the oxidative phosphorylation (OXPHOS) machinery, the tricarboxylic acid (TCA) cycle, mitochondrial unfolded protein response (UPRmt) and stable mitochondria-encoded proteins were found to be differentially expressed. Our results in-depth provide new horizons for mitochondria-associated protein functions and the classification of mitochondrial diseases during host-pathogen interaction. [ABSTRACT FROM AUTHOR]

Mancozeb (Manganese ethylene bis-dithiocarbamate with zinc salt) is a dithiocarbamate fungicide used to control fungal disease in many fruit plants, flowers and the maintenance of field crops. The effect of mancozeb on cell viability of human gastric adenocarcinoma AGS, SNU-1 cells and human normal FHs 74 Int cells were investigated. This study demonstrated that mancozeb was able to inhibit cell proliferation by 56–82% at 5–10 μM concentrations after 48 h. Mancozeb treatment for 48 h resulted in 33% (P < 0.05) and 61% (P < 0.001) increase in apoptotic cells at 5 and 10 μM concentrations in AGS cells, respectively. Treatment with mancozeb did not cause cell cycle arrest, while modulated the expression level of cleaved caspase-3, and cleavage of poly-(ADP-ribose) polymerase. Furthermore, treatment with mancozeb caused a rapid stimulation of reactive oxygen species (ROS) and loss of mitochondrial transmembrane potential. The results also showed that mancozeb-induced apoptosis was accompanied by up-regulation of Bax and down-regulation of Bcl-2 and Bcl-xL. Overall, our data suggested that mancozeb caused ROS generation which induced significant (P < 0.05) apoptosis in AGS cells that was attenuated with pretreatment of NAC. More importantly, same concentration of mancozeb did not show any considerable effect on cell growth, death, cell cycle arrest and ROS generation in normal FHs 74 Int cells. Overall, for the first time these results suggest that mancozeb has selective anticancer activity at lower concentrations against gastric cancer cells. • Mancozeb showed anticancer activity against cancer cells at very low concentrations • Mancozeb modulated mitochondrial protein expression to induce apoptosis • It induced ROS and mitochondrial membrane depolarization in gastric cancer cells • NAC pretreatment attenuated cell death caused by mancozeb • Mancozeb induced cyto-toxicity was selective and did not affect the normal cells [ABSTRACT FROM AUTHOR]

Withaferin A (WA), a steroidal lactone derived from a medicinal plant (Withania somnifera), inhibits cancer development in transgenic and chemically-induced rodent models of breast cancer but the underlying mechanism is not fully grasped. We have shown previously that WA treatment causes apoptotic cell death in human breast cancer cells that is preceded by inhibition of complex III of the mitochondrial electron transport chain. This study extends these observations to now demonstrate alterations in mitochondrial dynamics in WA-induced apoptosis. Assembly of complex III was decreased in MCF-7 and SUM159 cells but not in MDA-MB-231 as determined by native blue gel electrophoresis. Because WA is a Michael acceptor (electrophile), we explored the possibility of whether it covalently modifies cysteine residue(s) in ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 (UQCRFS1). Covalent modification of cysteine in UQCRFS1 was not observed after WA treatment. Instead, WA treatment inhibited chemically-induced mitochondrial fusion and decreased the mitochondrial volume, and this effect was accompanied by a decrease in the expression of proteins involved in fusion process, including mitofusin1, mitofusin2, and full-length optic atrophy protein 1 (OPA1). A loss of volume in fragmented mitochondria also occurred in WA-exposed cells when compared to vehicle-treated control. WA treatment also caused a decrease in protein level of mitochondrial fission-regulating protein dynamin-related protein 1 (DRP1). Functional studies revealed that DRP1 deficiency and OPA1 knockdown attenuated apoptotic potential of WA. Taken together, these results indicate that WA not only alters Complex III assembly but also inhibits mitochondrial dynamics in breast cancer cells. [ABSTRACT FROM AUTHOR]