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Mitochondrial DNA and RNA 2.0

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 13124

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Dr. Carlo Vascotto

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Guest Editor

Department of Medicine, University of Udine, 33100 Udine, Italy
Interests: DNA repair; mitochondrial RNA processing; protein trafficking; role of mitochondria in tumor biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue “Mitochondrial DNA and RNA”.

Mitochondria are the primary sites of ATP production and are also involved in several other important cellular processes, such as programmed cell death and cell signaling. Mitochondria are surrounded by a double-membrane system consisting of inner and outer mitochondrial membranes separated by an intermembrane space. The inner membrane delimitates the innermost compartment, the matrix, where mitochondrial DNA (mtDNA) resides. Human mtDNA is a circular, 16 kbp long molecule that encodes 13 proteins, 2 ribosomal RNAs, and 22 tRNAs. Once transcribed, mitochondrial RNA (mtRNA) is processed, mitoribosomes are assembled, and mtDNA-encoded proteins belonging to the respiratory chain are synthesized. All these processes require the coordinated spatiotemporal action of several enzymes, and many different factors are involved in the regulation and control of protein synthesis and in the stability and turnover of mitochondrial DNA and RNA.

The goal of this Special Issue is to present the current knowledge around mtDNA replication and repair mechanisms, processing of mitochondrial RNA transcripts, and how alteration of these processes may affect cell physiology in pathological conditions.

Original research reports, reviews, perspectives/opinions, and methodology articles are invited.

Dr. Carlo Vascotto
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

mitochondria
DNA repair and replication
RNA processing
mitochondrial transcription
nucleoids

Published Papers (5 papers)

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Research

Jump to: Review

18 pages, 1958 KiB

Open AccessArticle

Elucidating the Role of OXPHOS Variants in Asthenozoospermia: Insights from Whole Genome Sequencing and an In Silico Analysis

by Maria-Anna Kyrgiafini, Themistoklis Giannoulis, Alexia Chatziparasidou and Zissis Mamuris

Int. J. Mol. Sci. 2024, 25(7), 4121; https://doi.org/10.3390/ijms25074121 - 8 Apr 2024

Viewed by 482

Abstract

Infertility is a global health challenge that affects an estimated 72.4 million people worldwide. Between 30 and 50% of these cases involve male factors, showcasing the complex nature of male infertility, which can be attributed to both environmental and genetic determinants. Asthenozoospermia, a condition characterized by reduced sperm motility, stands out as a significant contributor to male infertility. This study explores the involvement of the mitochondrial oxidative phosphorylation (OXPHOS) system, crucial for ATP production and sperm motility, in asthenozoospermia. Through whole-genome sequencing and in silico analysis, our aim was to identify and characterize OXPHOS gene variants specific to individuals with asthenozoospermia. Our analysis identified 680,099 unique variants, with 309 located within OXPHOS genes. Nine of these variants were prioritized due to their significant implications, such as potential associations with diseases, effects on gene expression, protein function, etc. Interestingly, none of these variants had been previously associated with male infertility, opening up new avenues for research. Thus, through our comprehensive approach, we provide valuable insights into the genetic factors that influence sperm motility, laying the foundation for future research in the field of male infertility. Full article

(This article belongs to the Special Issue Mitochondrial DNA and RNA 2.0)

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22 pages, 2632 KiB

Open AccessArticle

Exploring the Mitogenomes of Mantodea: New Insights from Structural Diversity and Higher-Level Phylogenomic Analyses

by Qinpeng Liu, Yingqi Liu, Qiaoqiao Liu, Li Tian, Hu Li, Fan Song and Wanzhi Cai

Int. J. Mol. Sci. 2023, 24(13), 10570; https://doi.org/10.3390/ijms241310570 - 24 Jun 2023

Cited by 1 | Viewed by 1243

Abstract

The recently reorganized classification of Mantodea has made significant progress in resolving past homoplasy problems, although some relationships among higher taxa remain uncertain. In the present study, we utilized newly sequenced mitogenomes and nuclear gene sequences of 23 mantid species, along with published data of 53 mantises, to perform familial-sampling structural comparisons of mantodean mitogenomes and phylogenomic studies. Our rstructural analysis revealed generally conserved mitogenome organizations, with a few cases of tRNA gene rearrangements, including the detection of trnL₂ duplication for the first time. In our phylogenetic analysis, we found a high degree of compositional heterogeneity and lineage-specific evolutionary rates among mantodean mitogenomes, which frequently corresponded to several unexpected groupings in the topologies under site-homogeneous models. In contrast, the topologies obtained using the site-heterogeneous mixture model fit the currently accepted phylogeny of Mantodea better. Topology tests and four-cluster likelihood mapping analyses further determined the preferred topologies. Our phylogenetic results confirm the monophyly of superfamilial groups Schizomantodea, Amerimantodea, Heteromantodea, Promantidea, and Mantidea and recover the early-branching relationships as (Mantoidoidea + (Amerimantodea + (Metallyticoidea + Cernomantodea))). Additionally, the results suggest that the long-unresolved phylogenetic position of Majangidae should be placed within Mantidea, close to Mantoidea, rather than within Epaphroditoidea. Our findings contribute to understanding the compositional and structural diversity in mantodean mitogenomes, underscore the importance of evolutionary model selection in phylogenomic studies, and provide new insights into the high-level phylogeny of Mantodea. Full article

(This article belongs to the Special Issue Mitochondrial DNA and RNA 2.0)

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11 pages, 1352 KiB

Open AccessArticle

Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade

by Luísa Sá, Mafalda Almeida, Simon Azonbakin, Erica Matos, Ricardo Franco-Duarte, Alberto Gómez-Carballa, Antonio Salas, Anatóle Laleye, Alexandra Rosa, António Brehm, Martin B. Richards, Pedro Soares and Teresa Rito

Int. J. Mol. Sci. 2022, 23(16), 9219; https://doi.org/10.3390/ijms23169219 - 16 Aug 2022

Cited by 2 | Viewed by 5068

Abstract

Despite the importance of ancient DNA for understanding human prehistoric dispersals, poor survival means that data remain sparse for many areas in the tropics, including in Africa. In such instances, analysis of contemporary genomes remains invaluable. One promising approach is founder analysis, which identifies and dates migration events in non-recombining systems. However, it has yet to be fully exploited as its application remains controversial. Here, we test the approach by evaluating the age of sub-Saharan mitogenome lineages sampled outside Africa. The analysis confirms that such lineages in the Americas date to recent centuries—the time of the Atlantic slave trade—thereby validating the approach. By contrast, in North Africa, Southwestern Asia and Europe, roughly half of the dispersal signal dates to the early Holocene, during the “greening” of the Sahara. We elaborate these results by showing that the main source regions for the two main dispersal episodes are distinct. For the recent dispersal, the major source was West Africa, but with two exceptions: South America, where the fraction from Southern Africa was greater, and Southwest Asia, where Eastern Africa was the primary source. These observations show the potential of founder analysis as both a supplement and complement to ancient DNA studies. Full article

(This article belongs to the Special Issue Mitochondrial DNA and RNA 2.0)

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Review

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19 pages, 677 KiB

Open AccessReview

A Scoping Review Investigating the “Gene-Dosage Theory” of Mitochondrial DNA in the Healthy Skeletal Muscle

by Zandra Overgaard Pedersen, Britt Staevnsbo Pedersen, Steen Larsen and Tina Dysgaard

Int. J. Mol. Sci. 2023, 24(9), 8154; https://doi.org/10.3390/ijms24098154 - 2 May 2023

Cited by 1 | Viewed by 1734

Abstract

This review provides an overview of the evidence regarding mtDNA and valid biomarkers for assessing mitochondrial adaptions. Mitochondria are small organelles that exist in almost all cells throughout the human body. As the only organelle, mitochondria contain their own DNA, mitochondrial DNA (mtDNA). mtDNA-encoded polypeptides are subunits of the enzyme complexes in the electron transport chain (ETC) that are responsible for production of ATP to the cells. mtDNA is frequently used as a biomarker for mitochondrial content, since changes in mitochondrial volume are thought to induce similar changes in mtDNA. However, some exercise studies have challenged this “gene-dosage theory”, and have indicated that changes in mitochondrial content can adapt without changes in mtDNA. Thus, the aim of this scoping review was to summarize the studies that used mtDNA as a biomarker for mitochondrial adaptions and address the question as to whether changes in mitochondrial content, induce changes in mtDNA in response to aerobic exercise in the healthy skeletal muscle. The literature was searched in PubMed and Embase. Eligibility criteria included: interventional study design, aerobic exercise, mtDNA measurements reported pre- and postintervention for the healthy skeletal muscle and English language. Overall, 1585 studies were identified. Nine studies were included for analysis. Eight out of the nine studies showed proof of increased oxidative capacity, six found improvements in mitochondrial volume, content and/or improved mitochondrial enzyme activity and seven studies did not find evidence of change in mtDNA copy number. In conclusion, the findings imply that mitochondrial adaptions, as a response to aerobic exercise, can occur without a change in mtDNA copy number. Full article

(This article belongs to the Special Issue Mitochondrial DNA and RNA 2.0)

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22 pages, 1944 KiB

Open AccessReview

Mitochondrial DNA Repair in Neurodegenerative Diseases and Ageing

by Veronica Bazzani, Mara Equisoain Redin, Joshua McHale, Lorena Perrone and Carlo Vascotto

Int. J. Mol. Sci. 2022, 23(19), 11391; https://doi.org/10.3390/ijms231911391 - 27 Sep 2022

Cited by 17 | Viewed by 3444

Abstract

Mitochondria are the only organelles, along with the nucleus, that have their own DNA. Mitochondrial DNA (mtDNA) is a double-stranded circular molecule of ~16.5 kbp that can exist in multiple copies within the organelle. Both strands are translated and encode for 22 tRNAs, 2 rRNAs, and 13 proteins. mtDNA molecules are anchored to the inner mitochondrial membrane and, in association with proteins, form a structure called nucleoid, which exerts a structural and protective function. Indeed, mitochondria have evolved mechanisms necessary to protect their DNA from chemical and physical lesions such as DNA repair pathways similar to those present in the nucleus. However, there are mitochondria-specific mechanisms such as rapid mtDNA turnover, fission, fusion, and mitophagy. Nevertheless, mtDNA mutations may be abundant in somatic tissue due mainly to the proximity of the mtDNA to the oxidative phosphorylation (OXPHOS) system and, consequently, to the reactive oxygen species (ROS) formed during ATP production. In this review, we summarise the most common types of mtDNA lesions and mitochondria repair mechanisms. The second part of the review focuses on the physiological role of mtDNA damage in ageing and the effect of mtDNA mutations in neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease. Considering the central role of mitochondria in maintaining cellular homeostasis, the analysis of mitochondrial function is a central point for developing personalised medicine. Full article

(This article belongs to the Special Issue Mitochondrial DNA and RNA 2.0)

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