International Journal of Molecular Sciences

Research

22 pages, 3515 KiB

Open AccessArticle

From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel

by Filipe Cortes-Figueiredo, Filipa S. Carvalho, Ana Catarina Fonseca, Friedemann Paul, José M. Ferro, Sebastian Schönherr, Hansi Weissensteiner and Vanessa A. Morais

Int. J. Mol. Sci. 2021, 22(21), 12031; https://doi.org/10.3390/ijms222112031 - 6 Nov 2021

Cited by 3 | Viewed by 4136

Abstract

Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) [...] Read more.

Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS’s variants (TSS found 57.92% of PCP’s variants), with a significant correlation between the variant levels of variants found with both pipelines. Full article

(This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization)

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15 pages, 2253 KiB

Open AccessArticle

Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe

by Tomasz Mamos, Michał Grabowski, Tomasz Rewicz, Jamie Bojko, Dominik Strapagiel and Artur Burzyński

Int. J. Mol. Sci. 2021, 22(19), 10300; https://doi.org/10.3390/ijms221910300 - 24 Sep 2021

Cited by 9 | Viewed by 2666

Abstract

The Ponto-Caspian region is the main donor of invasive amphipods to freshwater ecosystems, with at least 13 species successfully established in European inland waters. Dikerogammarus spp. and Pontogammarus robustoides are among the most successful, due to their strong invasive impact on local biota. [...] Read more.

The Ponto-Caspian region is the main donor of invasive amphipods to freshwater ecosystems, with at least 13 species successfully established in European inland waters. Dikerogammarus spp. and Pontogammarus robustoides are among the most successful, due to their strong invasive impact on local biota. However, genomic knowledge about these invaders is scarce, while phylogeography and population genetics have been based on short fragments of mitochondrial markers or nuclear microsatellites. In this study, we provide: (i) a reconstruction of six mitogenomes for four invasive gammarids (D. villosus, D. haemobaphes, D. bispinosus, and P. robustoides); (ii) a comparison between the structure of the newly obtained mitogenomes and those from the literature; (iii) SNP calling rates for individual D. villosus and D. haemobaphes from different invasion sites across Europe; and (iv) the first time-calibrated full mitogenome phylogeny reconstruction of several Ponto-Caspian taxa. We found that, in comparison to other gammarids, the mitogenomes of Ponto-Caspian species show a translocation between the tRNA-E and tRNA-R positions. Phylogenetic reconstruction using the mitogenomes identified that Ponto-Caspian gammarids form a well-supported group that originated in the Miocene. Our study supports paraphyly in the family Gammaridae. These provided mitogenomes will serve as vital genetic resources for the development of new markers for PCR-based identification methods and demographic studies. Full article

(This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization)

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15 pages, 4680 KiB

Open AccessArticle

Hearing Impairment in a Mouse Model of Diabetes Is Associated with Mitochondrial Dysfunction, Synaptopathy, and Activation of the Intrinsic Apoptosis Pathway

by Ah-Ra Lyu, Tae-Hwan Kim, Sun-Ae Shin, Eung-Hyub Kim, Yang Yu, Akanksha Gajbhiye, Hyuk-Chan Kwon, A Reum Je, Yang Hoon Huh, Min Jung Park and Yong-Ho Park

Int. J. Mol. Sci. 2021, 22(16), 8807; https://doi.org/10.3390/ijms22168807 - 16 Aug 2021

Cited by 8 | Viewed by 2624

Abstract

Although previous studies continuously report an increased risk of hearing loss in diabetes patients, the impact of the disease on the inner ear remains unexplored. Herein, we examine the pathophysiology of diabetes-associated hearing impairment and cochlear synaptopathy in a mouse model of diabetes. [...] Read more.

Although previous studies continuously report an increased risk of hearing loss in diabetes patients, the impact of the disease on the inner ear remains unexplored. Herein, we examine the pathophysiology of diabetes-associated hearing impairment and cochlear synaptopathy in a mouse model of diabetes. Male B6.BKS(D)-Lepr^db/J (db/db, diabetes) and heterozygote (db/+, control) mice were assigned into each experimental group (control vs. diabetes) based on the genotype and tested for hearing sensitivity every week from 6 weeks of age. Each cochlea was collected for histological and biological assays at 14 weeks of age. The diabetic mice exerted impaired hearing and a reduction in cochlear blood flow and C-terminal-binding protein 2 (CtBP2, a presynaptic ribbon marker) expression. Ultrastructural images revealed severely damaged mitochondria from diabetic cochlea accompanied by a reduction in Cytochrome c oxidase subunit 4 (COX4) and CR6-interacting factor 1 (CRIF1). The diabetic mice presented significantly decreased levels of platelet endothelial cell adhesion molecule (PECAM-1), B-cell lymphoma 2 (BCL-2), and procaspase-9, but not procaspase-8. Importantly, significant changes were not found in necroptotic programmed cell death markers (receptor-interacting serine/threonine-protein kinase 1, RIPK1; RIPK3; and mixed lineage kinase domain-like pseudokinase, MLKL) between the groups. Taken together, diabetic hearing loss is accompanied by synaptopathy, microangiopathy, damage to the mitochondrial structure/function, and activation of the intrinsic apoptosis pathway. Our results imply that mitochondrial dysfunction is deeply involved in diabetic hearing loss, and further suggests the potential benefits of therapeutic strategies targeting mitochondria. Full article

(This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization)

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21 pages, 4789 KiB

Open AccessArticle

Mitocryptide-2: Identification of Its Minimum Structure for Specific Activation of FPR2–Possible Receptor Switching from FPR2 to FPR1 by Its Physiological C-terminal Cleavages

by Takayuki Marutani, Kodai Nishino, Tomoyuki Miyaji, Keisuke Kamada, Koji Ohura, Yoshiaki Kiso and Hidehito Mukai

Int. J. Mol. Sci. 2021, 22(8), 4084; https://doi.org/10.3390/ijms22084084 - 15 Apr 2021

Cited by 5 | Viewed by 2576

Abstract

Mitocryptides are a novel family of endogenous neutrophil-activating peptides originating from various mitochondrial proteins. Mitocryptide-2 (MCT-2) is one of such neutrophil-activating peptides, and is produced as an N-formylated pentadecapeptide from mitochondrial cytochrome b. Although MCT-2 is a specific endogenous ligand for formyl [...] Read more.

Mitocryptides are a novel family of endogenous neutrophil-activating peptides originating from various mitochondrial proteins. Mitocryptide-2 (MCT-2) is one of such neutrophil-activating peptides, and is produced as an N-formylated pentadecapeptide from mitochondrial cytochrome b. Although MCT-2 is a specific endogenous ligand for formyl peptide receptor 2 (FPR2), the chemical structure within MCT-2 that is responsible for FPR2 activation is still obscure. Here, we demonstrate that the N-terminal heptapeptide structure of MCT-2 with an N-formyl group is the minimum structure that specifically activates FPR2. Moreover, the receptor molecule for MCT-2 is suggested to be shifted from FPR2 to its homolog formyl peptide receptor 1 (FPR1) by the physiological cleavages of its C-terminus. Indeed, N-terminal derivatives of MCT-2 with seven amino acid residues or longer caused an increase of intracellular free Ca²⁺ concentration in HEK-293 cells expressing FPR2, but not in those expressing FPR1. Those MCT-2 derivatives also induced β-hexosaminidase secretion in neutrophilic/granulocytic differentiated HL-60 cells via FPR2 activation. In contrast, MCT-2(1–4), an N-terminal tetrapeptide of MCT-2, specifically activated FPR1 to promote those functions. Moreover, MCT-2 was degraded in serum to produce MCT-2(1–4) over time. These findings suggest that MCT-2 is a novel critical factor that not only initiates innate immunity via the specific activation of FPR2, but also promotes delayed responses by the activation of FPR1, which may include resolution and tissue regeneration. The present results also strongly support the necessity of considering the exact chemical structures of activating factors for the investigation of innate immune responses. Full article

(This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization)

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10 pages, 1663 KiB

Open AccessArticle

Ordered Clusters of the Complete Oxidative Phosphorylation System in Cardiac Mitochondria

by Semen Nesterov, Yury Chesnokov, Roman Kamyshinsky, Alisa Panteleeva, Konstantin Lyamzaev, Raif Vasilov and Lev Yaguzhinsky

Int. J. Mol. Sci. 2021, 22(3), 1462; https://doi.org/10.3390/ijms22031462 - 2 Feb 2021

Cited by 23 | Viewed by 2728

Abstract

The existence of a complete oxidative phosphorylation system (OXPHOS) supercomplex including both electron transport system and ATP synthases has long been assumed based on functional evidence. However, no structural confirmation of the docking between ATP synthase and proton pumps has been obtained. In [...] Read more.

The existence of a complete oxidative phosphorylation system (OXPHOS) supercomplex including both electron transport system and ATP synthases has long been assumed based on functional evidence. However, no structural confirmation of the docking between ATP synthase and proton pumps has been obtained. In this study, cryo-electron tomography was used to reveal the supramolecular architecture of the rat heart mitochondria cristae during ATP synthesis. Respirasome and ATP synthase structure in situ were determined using subtomogram averaging. The obtained reconstructions of the inner mitochondrial membrane demonstrated that rows of respiratory chain supercomplexes can dock with rows of ATP synthases forming oligomeric ordered clusters. These ordered clusters indicate a new type of OXPHOS structural organization. It should ensure the quickness, efficiency, and damage resistance of OXPHOS, providing a direct proton transfer from pumps to ATP synthase along the lateral pH gradient without energy dissipation. Full article

(This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization)

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Review

Jump to: Research, Other

23 pages, 1348 KiB

Open AccessReview

Synapses: The Brain’s Energy-Demanding Sites

by Andreia Faria-Pereira and Vanessa A. Morais

Int. J. Mol. Sci. 2022, 23(7), 3627; https://doi.org/10.3390/ijms23073627 - 26 Mar 2022

Cited by 25 | Viewed by 3964

Abstract

The brain is one of the most energy-consuming organs in the mammalian body, and synaptic transmission is one of the major contributors. To meet these energetic requirements, the brain primarily uses glucose, which can be metabolized through glycolysis and/or mitochondrial oxidative phosphorylation. The [...] Read more.

The brain is one of the most energy-consuming organs in the mammalian body, and synaptic transmission is one of the major contributors. To meet these energetic requirements, the brain primarily uses glucose, which can be metabolized through glycolysis and/or mitochondrial oxidative phosphorylation. The relevance of these two energy production pathways in fulfilling energy at presynaptic terminals has been the subject of recent studies. In this review, we dissect the balance of glycolysis and oxidative phosphorylation to meet synaptic energy demands in both resting and stimulation conditions. Besides ATP output needs, mitochondria at synapse are also important for calcium buffering and regulation of reactive oxygen species. These two mitochondrial-associated pathways, once hampered, impact negatively on neuronal homeostasis and synaptic activity. Therefore, as mitochondria assume a critical role in synaptic homeostasis, it is becoming evident that the synaptic mitochondria population possesses a distinct functional fingerprint compared to other brain mitochondria. Ultimately, dysregulation of synaptic bioenergetics through glycolytic and mitochondrial dysfunctions is increasingly implicated in neurodegenerative disorders, as one of the first hallmarks in several of these diseases are synaptic energy deficits, followed by synapse degeneration. Full article

(This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization)

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Graphical abstract

14 pages, 2943 KiB

Open AccessReview

Analysis of Mitochondrial Function, Structure, and Intracellular Organization In Situ in Cardiomyocytes and Skeletal Muscles

by Andrey V. Kuznetsov, Sabzali Javadov, Raimund Margreiter, Judith Hagenbuchner and Michael J. Ausserlechner

Int. J. Mol. Sci. 2022, 23(4), 2252; https://doi.org/10.3390/ijms23042252 - 18 Feb 2022

Cited by 9 | Viewed by 4434

Abstract

Analysis of the function, structure, and intracellular organization of mitochondria is important for elucidating energy metabolism and intracellular energy transfer. In addition, basic and clinically oriented studies that investigate organ/tissue/cell dysfunction in various human diseases, including myopathies, cardiac/brain ischemia-reperfusion injuries, neurodegenerative diseases, cancer, [...] Read more.

Analysis of the function, structure, and intracellular organization of mitochondria is important for elucidating energy metabolism and intracellular energy transfer. In addition, basic and clinically oriented studies that investigate organ/tissue/cell dysfunction in various human diseases, including myopathies, cardiac/brain ischemia-reperfusion injuries, neurodegenerative diseases, cancer, and aging, require precise estimation of mitochondrial function. It should be noted that the main metabolic and functional characteristics of mitochondria obtained in situ (in permeabilized cells and tissue samples) and in vitro (in isolated organelles) are quite different, thereby compromising interpretations of experimental and clinical data. These differences are explained by the existence of the mitochondrial network, which possesses multiple interactions between the cytoplasm and other subcellular organelles. Metabolic and functional crosstalk between mitochondria and extra-mitochondrial cellular environments plays a crucial role in the regulation of mitochondrial metabolism and physiology. Therefore, it is important to analyze mitochondria in vivo or in situ without their isolation from the natural cellular environment. This review summarizes previous studies and discusses existing approaches and methods for the analysis of mitochondrial function, structure, and intracellular organization in situ. Full article

(This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization)

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18 pages, 929 KiB

Open AccessReview

Mitochondrial Oxidative Stress—A Causative Factor and Therapeutic Target in Many Diseases

by Paweł Kowalczyk, Dorota Sulejczak, Patrycja Kleczkowska, Iwona Bukowska-Ośko, Marzena Kucia, Marta Popiel, Ewa Wietrak, Karol Kramkowski, Karol Wrzosek and Katarzyna Kaczyńska

Int. J. Mol. Sci. 2021, 22(24), 13384; https://doi.org/10.3390/ijms222413384 - 13 Dec 2021

Cited by 98 | Viewed by 5211

Abstract

The excessive formation of reactive oxygen species (ROS) and impairment of defensive antioxidant systems leads to a condition known as oxidative stress. The main source of free radicals responsible for oxidative stress is mitochondrial respiration. The deleterious effects of ROS on cellular biomolecules, [...] Read more.

The excessive formation of reactive oxygen species (ROS) and impairment of defensive antioxidant systems leads to a condition known as oxidative stress. The main source of free radicals responsible for oxidative stress is mitochondrial respiration. The deleterious effects of ROS on cellular biomolecules, including DNA, is a well-known phenomenon that can disrupt mitochondrial function and contribute to cellular damage and death, and the subsequent development of various disease processes. In this review, we summarize the most important findings that implicated mitochondrial oxidative stress in a wide variety of pathologies from Alzheimer disease (AD) to autoimmune type 1 diabetes. This review also discusses attempts to affect oxidative stress as a therapeutic avenue. Full article

(This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization)

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26 pages, 4200 KiB

Open AccessReview

Diverse Functions of Tim50, a Component of the Mitochondrial Inner Membrane Protein Translocase

by Minu Chaudhuri, Anuj Tripathi and Fidel Soto Gonzalez

Int. J. Mol. Sci. 2021, 22(15), 7779; https://doi.org/10.3390/ijms22157779 - 21 Jul 2021

Cited by 5 | Viewed by 3840 | Correction

Abstract

Mitochondria are essential in eukaryotes. Besides producing 80% of total cellular ATP, mitochondria are involved in various cellular functions such as apoptosis, inflammation, innate immunity, stress tolerance, and Ca²⁺ homeostasis. Mitochondria are also the site for many critical metabolic pathways and are [...] Read more.

Mitochondria are essential in eukaryotes. Besides producing 80% of total cellular ATP, mitochondria are involved in various cellular functions such as apoptosis, inflammation, innate immunity, stress tolerance, and Ca²⁺ homeostasis. Mitochondria are also the site for many critical metabolic pathways and are integrated into the signaling network to maintain cellular homeostasis under stress. Mitochondria require hundreds of proteins to perform all these functions. Since the mitochondrial genome only encodes a handful of proteins, most mitochondrial proteins are imported from the cytosol via receptor/translocase complexes on the mitochondrial outer and inner membranes known as TOMs and TIMs. Many of the subunits of these protein complexes are essential for cell survival in model yeast and other unicellular eukaryotes. Defects in the mitochondrial import machineries are also associated with various metabolic, developmental, and neurodegenerative disorders in multicellular organisms. In addition to their canonical functions, these protein translocases also help maintain mitochondrial structure and dynamics, lipid metabolism, and stress response. This review focuses on the role of Tim50, the receptor component of one of the TIM complexes, in different cellular functions, with an emphasis on the Tim50 homologue in parasitic protozoan Trypanosoma brucei. Full article

(This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization)

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14 pages, 1921 KiB

Open AccessReview

Impact of Sodium–Glucose Co-Transporter 2 Inhibitors on Cardiac Protection

by Victor Chien-Chia Wu, Yan-Rong Li and Chao-Yung Wang

Int. J. Mol. Sci. 2021, 22(13), 7170; https://doi.org/10.3390/ijms22137170 - 2 Jul 2021

Cited by 8 | Viewed by 2932

Abstract

Sodium–glucose co-transporter 2 (SGLT2) inhibitors have been approved as a new class of anti-diabetic drugs for type 2 diabetes mellitus (T2DM). The SGLT2 inhibitors reduce glucose reabsorption through renal systems, thus improving glycemic control in all stages of diabetes mellitus, independent of insulin. [...] Read more.

Sodium–glucose co-transporter 2 (SGLT2) inhibitors have been approved as a new class of anti-diabetic drugs for type 2 diabetes mellitus (T2DM). The SGLT2 inhibitors reduce glucose reabsorption through renal systems, thus improving glycemic control in all stages of diabetes mellitus, independent of insulin. This class of drugs has the advantages of no clinically relevant hypoglycemia and working in synergy when combined with currently available anti-diabetic drugs. While improving sugar level control in these patients, SGLT2 inhibitors also have the advantages of blood-pressure improvement and bodyweight reduction, with potential cardiac and renal protection. In randomized control trials for patients with diabetes, SGLT2 inhibitors not only improved cardiovascular and renal outcomes, but also hospitalization for heart failure, with this effect extending to those without diabetes mellitus. Recently, dynamic communication between autophagy and the innate immune system with Beclin 1-TLR9-SIRT3 complexes in response to SGLT2 inhibitors that may serve as a potential treatment strategy for heart failure was discovered. In this review, the background molecular pathways leading to the clinical benefits are examined in this new class of anti-diabetic drugs, the SGLT2 inhibitors. Full article

(This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization)

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