bims-midmar 2021-09-19 papers

bims-midmar

Biomed News

on Mitochondrial DNA maintenance and replication

Issue of 2021–09–19
sixteen papers selected by
Flavia Söllner, Ludwig-Maximilians University

A role for mitochondrial DNA in cellular proteostasis.
Repeated mild traumatic brain injuries perturb the mitochondrial biogenesis via DNA methylation in the hippocampus of rat.
Plant Mitochondria - Past, present and future.
Role of Mitochondria in Neurodegenerative Diseases: From an Epigenetic Perspective.
Targeting Adaptive Cellular Responses To Mitochondrial Bioenergetic Deficiencies In Human Disease.
Sirtuin 3 regulates mitochondrial protein acetylation and metabolism in tubular epithelial cells during renal fibrosis.
Single-Molecule Insights Into the Dynamics of Replicative Helicases.
Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions.
Mitochondrial-derived peptides and exercise.
Mitochondrial Abnormalities and Synaptic Damage in Huntington's Disease: a Focus on Defective Mitophagy and Mitochondria-Targeted Therapeutics.
Mitochondrial disease: Replace or edit?
Mitochondrial A-kinase anchoring proteins in cardiac ventricular myocytes.
MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation.
Mito-Bomb: Targeting Mitochondria for Cancer Therapy.
The emerging role of mitochondria derived peptide humanin in the testis.
Targeting DNA topoisomerases: past & future.

Nat Rev Genet. 2021 Sep 13.

A role for mitochondrial DNA in cellular proteostasis.

Caroline Barranco.

DOI: https://doi.org/10.1038/s41576-021-00418-9
Mitochondrion. 2021 Sep 08. pii: S1567-7249(21)00119-7. [Epub ahead of print]

Repeated mild traumatic brain injuries perturb the mitochondrial biogenesis via DNA methylation in the hippocampus of rat.

Nagalakshmi Balasubramanian, Gouri Jadhav, Amul J Sakharkar.

  Mitochondrial biogenesis in the brain is impaired in various neurological disorders including traumatic brain injury (TBI). The long-lasting effects of TBI may be, in part, attributed to epigenetic mechanisms such as DNA methylation. However, the role of DNA methylation on regulatory elements of nuclear and mitochondrial genome in mitochondrial biogenesis is not known. We examined the epigenetic regulation of mitochondrial transcription factor A (TFAM), and further probed its implications in mitochondrial dysfunction in the hippocampus of rats subjected to repeated mild TBI (rMTBI) using weight drop injury paradigm. rMTBI-induced hypermethylation at TFAM promoter resulted in deficits in its protein levels in mitochondria after immediate (48 h) and protracted (30 d) time points. Further, rMTBI also caused hypomethylation of mitochondrial DNA (mtDNA) promoters (HSP1 and HSP2), which further culminated into low binding of TFAM. rMTBI-induced changes weakened mitochondrial biogenesis in terms of reduced mtDNA-encoded rRNA, mRNA, and protein levels leading to shortages of ATP. To verify the potential role of mtDNA methylation in rMTBI-induced persistent mitochondrial dysfunction, rMTBI-induced rats were treated with methionine, a methyl donor. Methionine treatment restored the methylation levels on HSP1 and HSP2 resulting in efficient binding of TFAM and normalized the rRNA, mRNA, and protein levels. These findings suggest the crucial role of DNA methylation at nuclear and mitochondrial promoter regions in mitochondrial gene expression and ATP activity in the hippocampus after rMTBI.

Keywords:  DNA methylation; Heavy strand promoter; Mild traumatic brain injury; Mitochondrial biogenesis; Mitochondrial transcription factor A; mitochondrial DNA

DOI:  https://doi.org/10.1016/j.mito.2021.09.001
Plant J. 2021 Sep 16.

Plant Mitochondria - Past, present and future.

Ian Max Møller, Allan G Rasmusson, Olivier Van Aken.

The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) The ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates. (ii) The partial insensitivity to rotenone, which turned out to be due to the presence of a second NADH dehydrogenase on the inner surface of the inner mitochondrial membrane in addition to the classical complex I NADH dehydrogenase. (iii) The partial insensitivity to cyanide, which turned out to be due to an alternative oxidase, which is also located on the inner surface of the inner mitochondrial membrane, in addition to the classical complex IV, cytochrome oxidase. With the appearance of molecular biology methods around 1985, followed by genomics, further unique properties were discovered: (iv) Plant mitochondrial DNA (mtDNA) is 10-600 times larger than the mammalian mtDNA, yet it only contains ca 50% more genes. (v) Plant mtDNA has kept the standard genetic code, and it has a low divergence rate with respect to point mutations, but a high recombinatorial activity. (vi) Mitochondrial mRNA maturation includes a uniquely complex set of activities for processing, splicing and editing (at hundreds of sites). (vii) Recombination in mtDNA creates novel reading frames that can produce male sterility. (viii) A large proteome of 2000-3000 different proteins containing many unique proteins such as 200-300 pentatricopeptide repeat proteins. We describe the present and fairly detailed picture of the structure and function of plant mitochondria and how the unique properties make their metabolism more flexible allowing them to be involved in many diverse processes in the plant cell, such as photosynthesis, photorespiration, CAM and C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death and genomic evolution. However, it is still a challenge to understand how the regulation of metabolism and mtDNA expression works at the cellular level and how retrograde signaling from the mitochondria coordinates all those processes.

DOI: https://doi.org/10.1111/tpj.15495
Front Cell Dev Biol. 2021 ;9 688789

Role of Mitochondria in Neurodegenerative Diseases: From an Epigenetic Perspective.

Sutong Xu, Xi Zhang, Chenming Liu, Qiulu Liu, Huazhen Chai, Yuping Luo, Siguang Li.

  Mitochondria, the centers of energy metabolism, have been shown to participate in epigenetic regulation of neurodegenerative diseases. Epigenetic modification of nuclear genes encoding mitochondrial proteins has an impact on mitochondria homeostasis, including mitochondrial biogenesis, and quality, which plays role in the pathogenesis of neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. On the other hand, intermediate metabolites regulated by mitochondria such as acetyl-CoA and NAD+, in turn, may regulate nuclear epigenome as the substrate for acetylation and a cofactor of deacetylation, respectively. Thus, mitochondria are involved in epigenetic regulation through bidirectional communication between mitochondria and nuclear, which may provide a new strategy for neurodegenerative diseases treatment. In addition, emerging evidence has suggested that the abnormal modification of mitochondria DNA contributes to disease development through mitochondria dysfunction. In this review, we provide an overview of how mitochondria are involved in epigenetic regulation and discuss the mechanisms of mitochondria in regulation of neurodegenerative diseases from epigenetic perspective.

Keywords:  epigenetics; metabolism; mitochondria; mtDNA; neurodegenerative diseases

DOI:  https://doi.org/10.3389/fcell.2021.688789
FEBS J. 2021 Sep 12.

Targeting Adaptive Cellular Responses To Mitochondrial Bioenergetic Deficiencies In Human Disease.

Christopher F Bennett, Conor T Ronayne, Pere Puigserver.

  Mitochondrial dysfunction is increasingly appreciated as a central contributor to human disease. Oxidative metabolism at the mitochondrial respiratory chain produces ATP and is intricately tied to redox homeostasis and biosynthetic pathways. Metabolic stress arising from genetic mutations in mitochondrial genes and environmental factors such as malnutrition or overnutrition is perceived by the cell and leads to adaptive and maladaptive responses that can underlie pathology. Here, we will outline cellular sensors that react to alterations in energy production, organellar redox, and metabolites stemming from mitochondrial disease (MD) mutations. MD is a heterogenous group of disorders primarily defined by defects in mitochondrial oxidative phosphorylation from nuclear or mitochondrial-encoded gene mutations. Pre-clinical therapies that improve fitness of MD mouse models have been recently identified. Targeting metabolic/energetic deficiencies, maladaptive signaling processes, and hyper-oxygenation of tissues are all strategies aside from direct genetic approaches that hold therapeutic promise. A further mechanistic understanding of these curative processes as well as the identification of novel targets will significantly impact mitochondrial biology and disease research.

Keywords:  Mitochondrial dysfunction; hypoxia; mTORC1; metabolism; mitochondrial disease; mitochondrial signaling; oxidative stress; reactive oxygen species; redox homeostasis

DOI:  https://doi.org/10.1111/febs.16195
Cell Death Dis. 2021 Sep 13. 12(9): 847

Sirtuin 3 regulates mitochondrial protein acetylation and metabolism in tubular epithelial cells during renal fibrosis.

Yu Zhang, Ping Wen, Jing Luo, Hao Ding, Hongdi Cao, Weichun He, Ke Zen, Yang Zhou, Junwei Yang, Lei Jiang.

Proximal tubular epithelial cells (TECs) demand high energy and rely on mitochondrial oxidative phosphorylation as the main energy source. However, this is disturbed in renal fibrosis. Acetylation is an important post-translational modification for mitochondrial metabolism. The mitochondrial protein NAD+-dependent deacetylase sirtuin 3 (SIRT3) regulates mitochondrial metabolic function. Therefore, we aimed to identify the changes in the acetylome in tubules from fibrotic kidneys and determine their association with mitochondria. We found that decreased SIRT3 expression was accompanied by increased acetylation in mitochondria that have separated from TECs during the early phase of renal fibrosis. Sirt3 knockout mice were susceptible to hyper-acetylated mitochondrial proteins and to severe renal fibrosis. The activation of SIRT3 by honokiol ameliorated acetylation and prevented renal fibrosis. Analysis of the acetylome in separated tubules using LC-MS/MS showed that most kidney proteins were hyper-acetylated after unilateral ureteral obstruction. The increased acetylated proteins with 26.76% were mitochondrial proteins which were mapped to a broad range of mitochondrial pathways including fatty acid β-oxidation, the tricarboxylic acid cycle (TCA cycle), and oxidative phosphorylation. Pyruvate dehydrogenase E1α (PDHE1α), which is the primary link between glycolysis and the TCA cycle, was hyper-acetylated at lysine 385 in TECs after TGF-β1 stimulation and was regulated by SIRT3. Our findings showed that mitochondrial proteins involved in regulating energy metabolism were acetylated and targeted by SIRT3 in TECs. The deacetylation of PDHE1α by SIRT3 at lysine 385 plays a key role in metabolic reprogramming associated with renal fibrosis.

DOI: https://doi.org/10.1038/s41419-021-04134-4
Front Mol Biosci. 2021 ;8 741718

Single-Molecule Insights Into the Dynamics of Replicative Helicases.

Richard R Spinks, Lisanne M Spenkelink, Nicholas E Dixon, Antoine M van Oijen.

  Helicases are molecular motors that translocate along single-stranded DNA and unwind duplex DNA. They rely on the consumption of chemical energy from nucleotide hydrolysis to drive their translocation. Specialized helicases play a critically important role in DNA replication by unwinding DNA at the front of the replication fork. The replicative helicases of the model systems bacteriophages T4 and T7, Escherichia coli and Saccharomyces cerevisiae have been extensively studied and characterized using biochemical methods. While powerful, their averaging over ensembles of molecules and reactions makes it challenging to uncover information related to intermediate states in the unwinding process and the dynamic helicase interactions within the replisome. Here, we describe single-molecule methods that have been developed in the last few decades and discuss the new details that these methods have revealed about replicative helicases. Applying methods such as FRET and optical and magnetic tweezers to individual helicases have made it possible to access the mechanistic aspects of unwinding. It is from these methods that we understand that the replicative helicases studied so far actively translocate and then passively unwind DNA, and that these hexameric enzymes must efficiently coordinate the stepping action of their subunits to achieve unwinding, where the size of each step is prone to variation. Single-molecule fluorescence microscopy methods have made it possible to visualize replicative helicases acting at replication forks and quantify their dynamics using multi-color colocalization, FRAP and FLIP. These fluorescence methods have made it possible to visualize helicases in replication initiation and dissect this intricate protein-assembly process. In a similar manner, single-molecule visualization of fluorescent replicative helicases acting in replication identified that, in contrast to the replicative polymerases, the helicase does not exchange. Instead, the replicative helicase acts as the stable component that serves to anchor the other replication factors to the replisome.

Keywords:  DNA replication; dynamics; fluorescence; helicases; multi-protein complexes; replisome; single-molecule

DOI:  https://doi.org/10.3389/fmolb.2021.741718
J Vis Exp. 2021 Aug 26.

Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions.

Meredith G Chambers, Ryan P McNamara, Dirk P Dittmer.

Extracellular vesicles (EVs) are released by all cell types and play an important role in cell signaling and homeostasis. The visualization of EVs often require indirect methods due to their small diameter (40-250 nm), which is beneath the diffraction limit of typical light microscopy. We have developed a super-resolution microscopy-based visualization of EVs to bypass the diffraction limit in both two and three dimensions. Using this approach, we can resolve the three-dimensional shape of EVs to within +/- 20 nm resolution on the XY-axis and +/- 50 nm resolution along the Z-axis. In conclusion, we propose that super-resolution microscopy be considered as a characterization method of EVs, including exosomes, as well as enveloped viruses.

DOI: https://doi.org/10.3791/62845
Biochim Biophys Acta Gen Subj. 2021 Sep 11. pii: S0304-4165(21)00170-7. [Epub ahead of print] 130011

Mitochondrial-derived peptides and exercise.

Jonathan S T Woodhead, Troy L Merry.

  Acute exercise, and in particular aerobic exercise, increases skeletal muscle energy demand causing mitochondrial stress, and mitochondrial-related adaptations which are a hallmark of exercise training. Given that mitochondria are central players in the exercise response, it is imperative that they have networks that can communicate their status both intra- and inter-cellularly. Peptides encoded by short open-reading frames within mitochondrial DNA, mitochondrial-derived peptides (MDPs), have been suggested to form a newly recognised branch of this retrograde signalling cascade that contribute to coordinating the adaptive response to regular exercise. Here we summarise the recent evidence that acute high intensity exercise in humans can increase concentrations of the MDPs humanin and MOTS-c in skeletal muscle and plasma, and speculate on the mechanisms controlling MDP responses to exercise stress. Evidence that exercise training results in chronic changes in MDP expression within tissues and the circulation is conflicting and may depend on the mode, duration, intensity of training plan and participant characteristics. Further research is required to define the effect of these variables on MDPs and to determine whether MDPs other than MOTS-c have exercise mimetic properties. MOTS-c treatment of young and aged mice improves exercise capacity/performance and leads to adaptions that are similar to that of being physically active (weight loss, increased antioxidant capacity and improved insulin sensitivity), however, studies utilising a MOTS-c inactivating genetic variant or combination of exercise + MOTS-c treatment in mice suggest that there are distinct and overlapping pathways through which exercise and MOTS-c evoke metabolic benefits. Overall, MOTS-c, and potentially other MDPs, may be exercise-sensitive myokines and further work is required to define inter- and intra-tissue targets in an exercise context.

Keywords:  Cellular signalling; Hormesis; Mitochondria; Muscle; Physical activity; ROS

DOI:  https://doi.org/10.1016/j.bbagen.2021.130011
Mol Neurobiol. 2021 Sep 14.

Mitochondrial Abnormalities and Synaptic Damage in Huntington's Disease: a Focus on Defective Mitophagy and Mitochondria-Targeted Therapeutics.

Neha Sawant, Hallie Morton, Sudhir Kshirsagar, Arubala P Reddy, P Hemachandra Reddy.

  Huntington's disease (HD) is a fatal and pure genetic disease with a progressive loss of medium spiny neurons (MSN). HD is caused by expanded polyglutamine repeats in the exon 1 of HD gene. Clinically, HD is characterized by chorea, seizures, involuntary movements, dystonia, cognitive decline, intellectual impairment, and emotional disturbances. Several years of intense research revealed that multiple cellular changes, including defective axonal transport, protein-protein interactions, defective bioenergetics, calcium dyshomeostasis, NMDAR activation, synaptic damage, mitochondrial abnormalities, and selective loss of medium spiny neurons are implicated in HD. Recent research on mutant huntingtin (mHtt) and mitochondria has found that mHtt interacts with the mitochondrial division protein, dynamin-related protein 1 (DRP1), enhances GTPase DRP1 enzymatic activity, and causes excessive mitochondrial fragmentation and abnormal distribution, leading to defective axonal transport of mitochondria and selective synaptic degeneration. Recent research also revealed that failure to remove dead and/or dying mitochondria is an early event in the disease progression. Currently, efforts are being made to reduce abnormal protein interactions and enhance synaptic mitophagy as therapeutic strategies for HD. The purpose of this article is to discuss recent research in HD progression. This article also discusses recent developments of cell and mouse models, cellular changes, mitochondrial abnormalities, DNA damage, bioenergetics, oxidative stress, mitophagy, and therapeutics strategies in HD.

Keywords:  Huntington’s disease; Mitochondria-targeted therapies; Mitochondrial abnormalities; Mitophagy; Mutant huntingtin; Polyglutamine repeat expansion

DOI:  https://doi.org/10.1007/s12035-021-02556-x
Science. 2021 Sep 10. 373(6560): 1200-1201

Mitochondrial disease: Replace or edit?

Eli Y Adashi, Donald S Rubenstein, Jim A Mossman, Eric A Schon, I Glenn Cohen.

[Figure: see text].

DOI: https://doi.org/10.1126/science.abg0491
Physiol Rep. 2021 Sep;9(17): e15015

Mitochondrial A-kinase anchoring proteins in cardiac ventricular myocytes.

Rinzhin T Sherpa, Chase Fiore, Karni S Moshal, Adam Wadsworth, Michael W Rudokas, Shailesh R Agarwal, Robert D Harvey.

  Compartmentation of cAMP signaling is a critical factor for maintaining the integrity of receptor-specific responses in cardiac myocytes. This phenomenon relies on various factors limiting cAMP diffusion. Our previous work in adult rat ventricular myocytes (ARVMs) indicates that PKA regulatory subunits anchored to the outer membrane of mitochondria play a key role in buffering the movement of cytosolic cAMP. PKA can be targeted to discrete subcellular locations through the interaction of both type I and type II regulatory subunits with A-kinase anchoring proteins (AKAPs). The purpose of this study is to identify which AKAPs and PKA regulatory subunit isoforms are associated with mitochondria in ARVMs. Quantitative PCR data demonstrate that mRNA for dual specific AKAP1 and 2 (D-AKAP1 & D-AKAP2), acyl-CoA-binding domain-containing 3 (ACBD3), optic atrophy 1 (OPA1) are most abundant, while Rab32, WAVE-1, and sphingosine kinase type 1 interacting protein (SPHKAP) were barely detectable. Biochemical and immunocytochemical analysis suggests that D-AKAP1, D-AKAP2, and ACBD3 are the predominant mitochondrial AKAPs exposed to the cytosolic compartment in these cells. Furthermore, we show that both type I and type II regulatory subunits of PKA are associated with mitochondria. Taken together, these data suggest that D-AKAP1, D-AKAP2, and ACBD3 may be responsible for tethering both type I and type II PKA regulatory subunits to the outer mitochondrial membrane in ARVMs. In addition to regulating PKA-dependent mitochondrial function, these AKAPs may play an important role by buffering the movement of cAMP necessary for compartmentation.

Keywords:  A kinase anchoring proteins; cAMP; mitochondria; ventricular myocytes

DOI:  https://doi.org/10.14814/phy2.15015
Comput Struct Biotechnol J. 2021 ;19 4825-4839

MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation.

Yuexu Jiang, Duolin Wang, Yifu Yao, Holger Eubel, Patrick Künzler, Ian Max Møller, Dong Xu.

  Prediction of protein localization plays an important role in understanding protein function and mechanisms. In this paper, we propose a general deep learning-based localization prediction framework, MULocDeep, which can predict multiple localizations of a protein at both subcellular and suborganellar levels. We collected a dataset with 44 suborganellar localization annotations in 10 major subcellular compartments-the most comprehensive suborganelle localization dataset to date. We also experimentally generated an independent dataset of mitochondrial proteins in Arabidopsis thaliana cell cultures, Solanum tuberosum tubers, and Vicia faba roots and made this dataset publicly available. Evaluations using the above datasets show that overall, MULocDeep outperforms other major methods at both subcellular and suborganellar levels. Furthermore, MULocDeep assesses each amino acid's contribution to localization, which provides insights into the mechanism of protein sorting and localization motifs. A web server can be accessed at http://mu-loc.org.

Keywords:  Deep learning; Experimental benchmark datasets; Mechanism study; Protein localization; Web server

DOI:  https://doi.org/10.1016/j.csbj.2021.08.027
Adv Mater. 2021 Sep 12. e2007778

Mito-Bomb: Targeting Mitochondria for Cancer Therapy.

Xiaolu Guo, Naidi Yang, Wenhui Ji, Hang Zhang, Xiao Dong, Zhiqiang Zhou, Lin Li, Han-Ming Shen, Shao Q Yao, Wei Huang.

  Cancer has been one of the most common life-threatening diseases for a long time. Traditional cancer therapies such as surgery, chemotherapy (CT), and radiotherapy (RT) have limited effects due to drug resistance, unsatisfactory treatment efficiency, and side effects. In recent years, photodynamic therapy (PDT), photothermal therapy (PTT), and chemodynamic therapy (CDT) have been utilized for cancer treatment owing to their high selectivity, minor resistance, and minimal toxicity. Accumulating evidence has demonstrated that selective delivery of drugs to specific subcellular organelles can significantly enhance the efficiency of cancer therapy. Mitochondria-targeting therapeutic strategies are promising for cancer therapy, which is attributed to the essential role of mitochondria in the regulation of cancer cell apoptosis, metabolism, and more vulnerable to hyperthermia and oxidative damage. Herein, the rational design, functionalization, and applications of diverse mitochondria-targeting units, involving organic phosphine/sulfur salts, quaternary ammonium (QA) salts, peptides, transition-metal complexes, guanidinium or bisguanidinium, as well as mitochondria-targeting cancer therapies including PDT, PTT, CDT, and others are summarized. This review aims to furnish researchers with deep insights and hints in the design and applications of novel mitochondria-targeting agents for cancer therapy.

Keywords:  cancer therapy; chemodynamic therapy; mitochondria; photodynamic therapy; photothermal therapy

DOI:  https://doi.org/10.1002/adma.202007778
Biochim Biophys Acta Gen Subj. 2021 Sep 14. pii: S0304-4165(21)00168-9. [Epub ahead of print] 130009

The emerging role of mitochondria derived peptide humanin in the testis.

Yanhe Lue, Ronald Swerdloff, Yue Jia, Christina Wang.

  The discovery of mitochondrial derive peptides (MDPs) has spotlighted mitochondria as central hubs in control and regulation of cell viability and metabolism in the testis in response to intracellular and extracellular stresses. MDPs (Humanin, MOTS-c and SHLP-2) are present in testes. Humanin, the first MDP, is predominantly expressed in Leydig cells, and moderately in germ cells and seminal plasma. The administration of synthetic humanin peptide agonist HNG protects male germ cells against apoptosis induced by intratesticular hormonal deprivation, testicular hyperthermia, and chemotherapeutic agents in rodent testes. Humanin interacting with IGFBP-3 and/or Bax (pro-apoptotic proteins) prevents the activation of germ cell apoptosis. Humanin participates in the network of IL-12/IL-27 family of cytokines to exert the immune-modulation of the testicular environment. Humanin and other MDPs may be important in the amelioration of testicular stress and prevention of cell injury with possible implications for male infertility, fertility preservation and contraceptive development.

Keywords:  Apoptosis; Germ cells; Humanin; Male infertility; Testis

DOI:  https://doi.org/10.1016/j.bbagen.2021.130009
Cancer Drug Resist. 2021 ;4 758-761

Targeting DNA topoisomerases: past & future.

William H Gmeiner, Robert C A M van Waardenburg.

DOI: https://doi.org/10.20517/cdr.2021.65