Characterization of long living yeast deletion mutants that lack mitochondrial metabolism genes DSS1, PPA2 and AFG3

Recurrent Implantation Failure: Bioinformatic Discovery of Biomarkers and Identification of Metabolic Subtypes

Recurrent implantation failure (RIF) is a challenging scenario from different standpoints. This study aimed to investigate its correlation with the endometrial metabolic characteristics. Transcriptomics data of 70 RIF and 99 normal endometrium tissues were retrieved from the Gene Expression Omnibus database. Common differentially expressed metabolism-related genes were extracted and various enrichment analyses were applied. Then, RIF was classified using a consensus clustering approach. Three machine learning methods were employed for screening key genes, and they were validated through the RT-qPCR experiment in the endometrium of 10 RIF and 10 healthy individuals. Receiver operator characteristic (ROC) curves were generated and validated by 20 RIF and 20 healthy individuals from Peking University People's Hospital. We uncovered 109 RIF-related metabolic genes and proposed a novel two-subtype RIF classification according to their metabolic features. Eight characteristic genes (SRD5A1, POLR3E, PPA2, PAPSS1, PRUNE, CA12, PDE6D, and RBKS) were identified, and the area under curve (AUC) was 0.902 and the external validated AUC was 0.867. Higher immune cell infiltration levels were found in RIF patients and a metabolism-related regulatory network was constructed. Our work has explored the metabolic and immune characteristics of RIF, which paves a new road to future investigation of the related pathogenic mechanisms.

Yeast UPS1 deficiency leads to UVC radiation sensitivity and shortened lifespan

UPS1/YLR193C of Saccharomyces cerevisiae (S. cerevisiae) encodes a mitochondrial intermembrane space protein. A previous study found that Ups1p is needed for normal mitochondrial morphology and that UPS1 deficiency disrupts the intramitochondrial transport of phosphatidic acid in yeast cells and leads to an altered unfolded protein response and mTORC1 signaling activation. In this paper, we first provide evidence showing that the UPS1 gene is involved in the UVC-induced DNA damage response and aging. We show that UPS1 deficiency leads to sensitivity to ultraviolet C (UVC) radiation and that this effect is accompanied by elevated DNA damage, increased intracellular ROS levels, abnormal mitochondrial respiratory function, an increased early apoptosis rate, and shortened replicative lifespan and chronological lifespan. Moreover, we show that overexpression of the DNA damage-induced checkpoint gene RAD9 effectively eliminates the senescence-related defects observed in the UPS1-deficient strain. Collectively, these results suggest a novel role for UPS1 in the UVC-induced DNA damage response and aging.

Hereditary Basis of Coat Color and Excellent Feed Conversion Rate of Red Angus Cattle by Next-Generation Sequencing Data

Angus cattle have made remarkable contributions to the livestock industry worldwide as a commercial meat-type breed. Some evidence supported that Angus cattle with different coat colors have different feed-to-meat ratios, and the genetic basis of their coat color is inconclusive. Here, genome-wide association study was performed to investigate the genetic divergence of black and red Angus cattle with 63 public genome sequencing data. General linear model analysis was used to identify genomic regions with potential candidate variant/genes that contribute to coat color and feed conversion rate. Results showed that six single nucleotide polymorphisms (SNPs) and two insertion−deletions, which were annotated in five genes (ZCCHC14, ANKRD11, FANCA, MC1R, and LOC532875 [AFG3-like protein 1]), considerably diverged between black and red Angus cattle. The strongest associated loci, namely, missense mutation CHIR18_14705671 (c.296T > C) and frameshift mutation CHIR18_12999497 (c.310G>-), were located in MC1R. Three consecutive strongly associated SNPs were also identified and located in FANCA, which is widely involved in the Fanconi anemia pathway. Several SNPs of highly associated SNPs was notably enriched in ZCCHC14 and ANKRD11, which are related to myofiber growth and muscle development. This study provides a basis for the use of potential genetic markers to be used in future breeding programs to improve cattle selection in terms of coat color and meat phenotype. This study is also helpful to understand the hereditary basis of different coat colors and meat phenotypes. However, the putative candidate genes or markers identified in this study require further investigation to confirm their phenotypic causality and potential effective genetic relationships.

How RNases Shape Mitochondrial Transcriptomes

Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.

Integrated Multi-Omics Analysis of Mechanisms Underlying Yeast Ethanol Tolerance

For yeast cells, tolerance to high levels of ethanol is vital both in their natural environment and in industrially relevant conditions. We recently genotyped experimentally evolved yeast strains adapted to high levels of ethanol and identified mutations linked to ethanol tolerance. In this study, by integrating genomic sequencing data with quantitative proteomics profiles from six evolved strains (data set identifier PXD006631) and construction of protein interaction networks, we elucidate exactly how the genotype and phenotype are related at the molecular level. Our multi-omics approach points to the rewiring of numerous metabolic pathways affected by genomic and proteomic level changes, from energy-producing and lipid pathways to differential regulation of transposons and proteins involved in cell cycle progression. One of the key differences is found in the energy-producing metabolism, where the ancestral yeast strain responds to ethanol by switching to respiration and employing the mitochondrial electron transport chain. In contrast, the ethanol-adapted strains appear to have returned back to energy production mainly via glycolysis and ethanol fermentation, as supported by genomic and proteomic level changes. This work is relevant for synthetic biology where systems need to function under stressful conditions, as well as for industry and in cancer biology, where it is important to understand how the genotype relates to the phenotype.

Mitochondrial dysfunction and apoptosis are attenuated through activation of AMPK/GSK-3β/PP2A pathway in Parkinson's disease

Parkinson's disease (PD) is a common neurological disorder worldwide, characterized by loss of dopaminergic neurons and decrease of dopamine content. Mitochondria plays an important role in the development of PD. Adenosine 5'-monophosphate-activated protein kinase (AMPK), glycogen synthase kinase 3 (GSK-3β) and protein phosphatase 2A (PP2A) are all key proteins that regulate mitochondrial metabolism and apoptosis, and they are involved in a variety of neurodegenerative diseases. Here, we aimed to explore the involvement of mitochondrial dysfunction and apoptosis in 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine hydrochloride (MPTP)-induced PD mice and MPP⁺ iodide-induced PC12 cells. MPTP-induced mice were subjected to behavioral testing to assess PD-like behaviors. Various molecular biological techniques including ELISA, Western blot, TUNEL assay, flow cytometry, and the important instruments Seahorse XF24 Extracellular and high performance liquid chromatography (HPLC), were used to identify the underlying molecular events of mitochondria. Treatment with the AMPK activator GSK621 dramatically ameliorated PD by increasing the levels of dopamine and rescuing the loss of dopaminergic neurons, which is dependent on the mitochondrial pathway. Moreover, regulation of AMPK/GSK-3β/PP2A pathway-related proteins by GSK621 was partially inhibited the development of PD, suggesting a negative feedback loop exists between AMPK action and mitochondrial dysfunction-mediated apoptosis. Our data preliminarily indicated that mitochondrial dysfunction and apoptosis in the pathogenesis of PD might be mediated by AMPK/GSK-3β/PP2A pathway action, which might be a promising new option for future therapy of PD.

Regulation of Age-Related Protein Toxicity

Proteome damage plays a major role in aging and age-related neurodegenerative diseases. Under healthy conditions, molecular quality control mechanisms prevent toxic protein misfolding and aggregation. These mechanisms include molecular chaperones for protein folding, spatial compartmentalization for sequestration, and degradation pathways for the removal of harmful proteins. These mechanisms decline with age, resulting in the accumulation of aggregation-prone proteins that are harmful to cells. In the past decades, a variety of fast- and slow-aging model organisms have been used to investigate the biological mechanisms that accelerate or prevent such protein toxicity. In this review, we describe the most important mechanisms that are required for maintaining a healthy proteome. We describe how these mechanisms decline during aging and lead to toxic protein misassembly, aggregation, and amyloid formation. In addition, we discuss how optimized protein homeostasis mechanisms in long-living animals contribute to prolonging their lifespan. This knowledge might help us to develop interventions in the protein homeostasis network that delay aging and age-related pathologies.

Sudden unexpected death in asymptomatic infants due to PPA2 variants

Background

Sudden death in children is a tragic event that often remains unexplained after comprehensive investigation. We report two asymptomatic siblings who died unexpectedly at approximately 1 year of age found to have biallelic (compound heterozygous) variants in PPA2.

Methods

The index case, parents, and sister were enrolled in the Sudden Unexplained Death in Childhood Registry and Research Collaborative, which included next‐generation genetic screening. Prior published cases of PPA2 variants, along with the known biology of PPA2, were also summarized.

Results

Whole exome sequencing in both siblings revealed biallelic rare missense variants in PPA2: c.182C > T (p.Ser61Phe) and c.380G > T (p.Arg127Leu). PPA2 encodes a mitochondrially located inorganic pyrophosphatase implicated in progressive and lethal cardiomyopathies. As a regulator and supplier of inorganic phosphate, PPA2 is central to phosphate metabolism. Biological roles include the following: mtDNA maintenance; oxidative phosphorylation and generation of ATP; reactive oxygen species homeostasis; mitochondrial membrane potential regulation; and possibly, retrograde signaling between mitochondria and nucleus.

Conclusions

Two healthy and asymptomatic sisters died unexpectedly at ages 12 and 10 months, and were diagnosed by molecular autopsy to carry biallelic variants in PPA2. Our cases add additional details to those reported thus far, and broaden the spectrum of clinical and molecular features of PPA2 variants.