Ethidium bromide as a marker of mtDNA replication in living cells

Approaches and challenges in identifying, quantifying, and manipulating dynamic mitochondrial genome variations

Mitochondria, the cellular powerhouses, possess their own unique genetic system, including replication, transcription, and translation. Studying these processes is crucial for comprehending mitochondrial disorders, energy production, and their related diseases. Over the past decades, various approaches have been applied in detecting and quantifying mitochondrial genome variations with also the purpose of manipulation of mitochondria or mitochondrial genome for therapeutics. Understanding the scope and limitations of above strategies is not only fundamental to the understanding of basic biology but also critical for exploring disease-related novel target(s), as well to develop innovative therapies. Here, this review provides an overview of different tools and techniques for accurate mitochondrial genome variations identification, quantification, and discuss novel strategies for the manipulation of mitochondria to develop innovative therapeutic interventions, through combining the insights gained from the study of mitochondrial genetics with ongoing single cell omics combined with advanced single molecular tools.

Hypoxia-induced mitochondrial stress granules

Perturbations of mitochondrial proteostasis have been associated with aging, neurodegenerative diseases, and recently with hypoxic injury. While examining hypoxia-induced mitochondrial protein aggregation in C. elegans, we found that sublethal hypoxia, sodium azide, or heat shock-induced abundant ethidium bromide staining mitochondrial granules that preceded evidence of protein aggregation. Genetic manipulations that reduce cellular and organismal hypoxic death block the formation of these mitochondrial stress granules (mitoSG). Knockdown of mitochondrial nucleoid proteins also blocked the formation of mitoSG by a mechanism distinct from the mitochondrial unfolded protein response. Lack of the major mitochondrial matrix protease LONP-1 resulted in the constitutive formation of mitoSG without external stress. Ethidium bromide-staining RNA-containing mitochondrial granules were also observed in rat cardiomyocytes treated with sodium azide, a hypoxia mimetic. Mitochondrial stress granules are an early mitochondrial pathology controlled by LONP and the nucleoid, preceding hypoxia-induced protein aggregation.

Anti-Salmonella mode of action of natural L-phenyl lactic acid purified from Lactobacillus plantarum ZJ316

Salmonella is a serious foodborne pathogen responsible for more than 90 million cases of gastroenteritis worldwide annually. Due to the gradual increase in antibiotic-resistant Salmonella strains, the identification of natural antibacterial substances is urgently needed. Herein, we purified natural L-phenyl lactic acid (L-PLA) from Lactobacillus plantarum ZJ316 and revealed its antimicrobial mode against Salmonella enterica subsp. enterica ATCC 14028. L-PLA (98.14% pure) was obtained using the macroporous resin XAD-16, solid-phase extraction (SPE), reverse-phase high-performance liquid chromatography (RP-HPLC), and chiral chromatography. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) results showed that the cell morphology was severely compromised. Transmembrane electrical potential (ΔΨ), transmembrane pH gradient (ΔpH), intracellular ATP level, extracellular electrical conductivity (EC), and genomic DNA analyses were employed to evaluate the antibacterial mode of action of L-PLA. The proton motive force (PMF) and ATP of Salmonella cells rapidly dissipated, and the EC markedly increased. The gel retardation assay demonstrated that L-PLA could bind to genomic DNA and intercalate into the nucleic acids. The anti-Salmonella mode of action of L-PLA was attributed to the destruction of the cell membrane and genomic DNA binding. This research suggests that L-PLA has potential applications as an antimicrobial agent in food, medicine, and other fields. KEY POINTS: • Natural L-PLA was purified from L. plantarum ZJ316 with a purity of 98.14%. • L-PLA effectively inhibited Salmonella strains by antibacterial activities and MICs. • Membrane destruction and binding with DNA are the anti-Salmonella modes of L-PLA.

Techniques for investigating mitochondrial gene expression

The mitochondrial genome encodes 13 proteins that are components of the oxidative phosphorylation system (OXPHOS), suggesting that precise regulation of these genes is crucial for maintaining OXPHOS functions, including ATP production, calcium buffering, cell signaling, ROS production, and apoptosis. Furthermore, heteroplasmy or mis-regulation of gene expression in mitochondria frequently is associated with human mitochondrial diseases. Thus, various approaches have been developed to investigate the roles of genes encoded by the mitochondrial genome. In this review, we will discuss a wide range of techniques available for investigating the mitochondrial genome, mitochondrial transcription, and mitochondrial translation, which provide a useful guide to understanding mitochondrial gene expression.

Association of 5-methylcytosine and 5-hydroxymethylcytosine with mitochondrial DNA content and clinical and biochemical parameters in hepatocellular carcinoma

Increasing epidemiological evidence has indicated that inherited variations of mitochondrial DNA (mtDNA) copy number affect the genetic susceptibility of many malignancies in a tumour-specific manner and that DNA methylation also plays an important role in controlling gene expression during the differentiation and development of hepatocellular carcinoma (HCC). Our previous study demonstrated that HCC tissues showed a lower 5-hydroxymethylcytosine (5-hmC) content when compared to tumour-adjacent tissues, but the relationship among 5-hmC, 5-methylcytosine (5-mC) and mtDNA content in HCC patients is still unknown. This study aimed to clarify the correlation among mtDNA content, 5-mC and 5-hmC by quantitative real-time PCR and liquid chromatography tandem mass spectrometry analysis. We demonstrated that 5-hmC correlated with tumour size [odds ratio (OR) 0.847, 95% confidence interval (CI) 0.746–0.962, P = 0.011], and HCC patients with a tumour size ≥5.0 cm showed a lower 5-hmC content and higher levels of fasting plasma aspartate aminotransferase, the ratio of alanine amiotransferase to aspartate aminotransferase, γ-glutamyltransferase, alpha-fetoprotein than those with a tumour size <5 cm (all P<0.05). We further revealed that the mtDNA content of HCC tumour tissues was 225.97(105.42, 430.54) [median (25th Percentile, 75th Percentile)] and was negatively correlated with 5-mC content (P = 0.035), but not 5-hmC content, in genomic DNA from HCC tumour tissues.