RESUMEN
BACKGROUND: Mitochondria, essential for cellular energy production through oxidative phosphorylation (OXPHOS), integrate mt-DNA and nuclear-encoded genes. This cooperation extends to the mitochondrial translation machinery, involving crucial mtDNA-encoded RNAs: 22 tRNAs (mt-tRNAs) as adapters and two rRNAs (mt-rRNAs) for ribosomal assembly, enabling mitochondrial-encoded mRNA translation. Disruptions in mitochondrial gene expression can strongly impact energy generation and overall animal health. Our study investigates the tissue-specific expression patterns of mt-tRNAs and mt-rRNAs in buffalo. MATERIAL AND METHODS: To investigate the expression patterns of mt-tRNAs and mt-rRNAs in different tissues and gain a better understanding of tissue-specific variations, RNA-seq was performed on various tissues, such as the kidney, heart, brain, and ovary, from post-pubertal female buffaloes. Subsequently, we identified transcripts that were differentially expressed in various tissue comparisons. RESULTS: The findings reveal distinct expression patterns among specific mt-tRNA and mt-rRNA genes across various tissues, with some exhibiting significant upregulation and others demonstrating marked downregulation in specific tissue contexts. These identified variations reflect tissue-specific physiological roles, underscoring their significance in meeting the unique energy demands of each tissue. Notably, the brain exhibits the highest mtDNA copy numbers and an abundance of mitochondrial mRNAs of our earlier findings, potentially linked to the significant upregulation of mt-tRNAs in brain. This suggests a plausible association between mtDNA replication and the regulation of mtDNA gene expression. CONCLUSION: Overall, our study unveils the tissue-specific expression of mitochondrial-encoded non-coding RNAs in buffalo. As we proceed, our further investigations into tissue-specific mitochondrial proteomics and microRNA studies aim to elucidate the intricate mechanisms within mitochondria, contributing to tissue-specific mitochondrial attributes. This research holds promise to elucidate the critical role of mitochondria in animal health and disease.
Asunto(s)
Búfalos , Perfilación de la Expresión Génica , Genoma Mitocondrial , Mitocondrias , Especificidad de Órganos , ARN Ribosómico , ARN de Transferencia , Transcriptoma , Animales , Búfalos/genética , Búfalos/metabolismo , ARN de Transferencia/genética , Especificidad de Órganos/genética , Perfilación de la Expresión Génica/métodos , Genoma Mitocondrial/genética , Femenino , Transcriptoma/genética , Mitocondrias/genética , Mitocondrias/metabolismo , ARN Ribosómico/genética , ADN Mitocondrial/genética , ARN Mitocondrial/genética , ARN Mitocondrial/metabolismo , Fosforilación Oxidativa , Regulación de la Expresión Génica/genéticaRESUMEN
The mechanisms of RNA-binding proteins (RBPs)-mediated post-transcriptional regulation of pre-existing mRNAs, which is essential for spermatogenesis, remain poorly understood. In this study, we identify that a germline-specific mitochondrial RBP AMG-1(abnormal mitochondria in germline 1), a homolog of mammalian leucine-rich PPR motif-containing protein (LRPPRC), is required for spermatogenesis in Caenorhabditis elegans. The amg-1 mutation hinders germline development without affecting somatic development and leads to the aberrant mitochondrial morphology and structure associated with mitochondrial dysfunctions specifically in the germline. We demonstrate that AMG-1 is most frequently bound to mtDNA-encoded 12S and 16S ribosomal RNA, the essential components of mitochondrial ribosomes, and that 12S rRNA expression mediated by AMG-1 is crucial for germline mitochondrial protein homeostasis. Furthermore, steroid receptor RNA activator (SRA) stem loop interacting RNA binding protein (SLRP-1), a homolog of mammalian SRA stem loop interacting RNA binding protein (SLIRP) in C. elegans, interacts with AMG-1 genetically to regulate germline development and reproductive success in C. elegans. Overall, these findings reveal the novel function of mtRBP, specifically in regulating germline development.
Asunto(s)
Proteínas de Caenorhabditis elegans , Caenorhabditis elegans , Animales , Masculino , Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/genética , Células Germinativas/metabolismo , Espermatogénesis/genética , Mitocondrias/metabolismo , Proteínas de Unión al ARN/genética , Mamíferos/metabolismoRESUMEN
Background: Epigenetic regulations of the tumor microenvironment (TME) and immunotherapy have been investigated in recent years. Nevertheless, the potential value of mitochondrial ribosomal RNA (mt-rRNA) modification in regulation of the TME and immunotherapy remains unknown. Methods: We comprehensively investigated the mt-rRNA-modification patterns in glioma patients based on nine regulators of mt-rRNA. Subsequently, these modification patterns were correlated systematically with immunologic characteristics and immunotherapy. An "mt-rRNA predictor" was constructed and validated in multiple publicly available cohorts to provide guidance for prognosis prediction and immunotherapy of glioma patients. Results: Two distinct patterns of mt-rRNA modification were determined based on the evidence that nine regulators of mt-rRNA correlated significantly with most clinicopathologic characteristics, immunomodulators, TME, immune-checkpoint blockers (ICBs), and prognosis. Patients with mt-rRNA subtype II presented significantly poorer overall survival/progression-free survival (OS/PFS), but higher tumor mutational burden (TMB), more somatic mutations, and copy number variation (CNV). These two mt-rRNA subtypes had distinct TME patterns and responses to ICB therapy. An mt-rRNA predictor was constructed and validated in four glioma cohorts. The subtype with high mt-rRNA score, characterized by increased TMB, infiltration of immune cells, and activation of immunity, suggested an immune-activated phenotype, and was also linked to greater sensitivity to immunotherapy using anti-programmed cell death protein 1 (PD-1) but resistance to temozolomide. Conclusions: Regulators of mt-rRNA modification have indispensable roles in the complexity and diversity of the TME and prognosis. This novel classification based on patterns of mt-rRNA modification could provide an effective prognostic predictor and guide more appropriate immunotherapy/chemotherapy strategies for glioma patients.
Asunto(s)
Glioma/genética , Glioma/mortalidad , Mitocondrias/genética , Procesamiento Postranscripcional del ARN , ARN Ribosómico/genética , Biomarcadores de Tumor , Biología Computacional/métodos , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Glioma/inmunología , Glioma/terapia , Humanos , Inmunohistoquímica , Inmunoterapia , Linfocitos Infiltrantes de Tumor/inmunología , Linfocitos Infiltrantes de Tumor/metabolismo , Linfocitos Infiltrantes de Tumor/patología , Anotación de Secuencia Molecular , Pronóstico , Curva ROC , Resultado del Tratamiento , Microambiente Tumoral/inmunologíaRESUMEN
Mitochondrial DNA gene expression is coordinately regulated both pre- and post-transcriptionally, and its perturbation can lead to human pathologies. Mitochondrial rRNAs (mt-rRNAs) undergo a series of nucleotide modifications after release from polycistronic mitochondrial RNA precursors, which is essential for mitochondrial ribosomal biogenesis. Cytosine N4-methylation (m4C) at position 839 (m4C839) of the 12S small subunit mt-rRNA was identified decades ago; however, its biogenesis and function have not been elucidated in detail. Here, using several approaches, including immunofluorescence, RNA immunoprecipitation and methylation assays, and bisulfite mapping, we demonstrate that human methyltransferase-like 15 (METTL15), encoded by a nuclear gene, is responsible for 12S mt-rRNA methylation at m4C839 both in vivo and in vitro We tracked the evolutionary history of RNA m4C methyltransferases and identified a difference in substrate preference between METTL15 and its bacterial ortholog rsmH. Additionally, unlike the very modest impact of a loss of m4C methylation in bacterial small subunit rRNA on the ribosome, we found that METTL15 depletion results in impaired translation of mitochondrial protein-coding mRNAs and decreases mitochondrial respiration capacity. Our findings reveal that human METTL15 is required for mitochondrial function, delineate the evolution of methyltransferase substrate specificities and modification patterns in rRNA, and highlight a differential impact of m4C methylation on prokaryotic ribosomes and eukaryotic mitochondrial ribosomes.