Dynamic regulation of mitochondrial transcription as a mechanism of cellular adaptation

Epigenetic inheritance of diet-induced and sperm-borne mitochondrial RNAs

Spermatozoa harbour a complex and environment-sensitive pool of small non-coding RNAs (sncRNAs)1, which influences offspring development and adult phenotypes1-7. Whether spermatozoa in the epididymis are directly susceptible to environmental cues is not fully understood8. Here we used two distinct paradigms of preconception acute high-fat diet to dissect epididymal versus testicular contributions to the sperm sncRNA pool and offspring health. We show that epididymal spermatozoa, but not developing germ cells, are sensitive to the environment and identify mitochondrial tRNAs (mt-tRNAs) and their fragments (mt-tsRNAs) as sperm-borne factors. In humans, mt-tsRNAs in spermatozoa correlate with body mass index, and paternal overweight at conception doubles offspring obesity risk and compromises metabolic health. Sperm sncRNA sequencing of mice mutant for genes involved in mitochondrial function, and metabolic phenotyping of their wild-type offspring, suggest that the upregulation of mt-tsRNAs is downstream of mitochondrial dysfunction. Single-embryo transcriptomics of genetically hybrid two-cell embryos demonstrated sperm-to-oocyte transfer of mt-tRNAs at fertilization and suggested their involvement in the control of early-embryo transcription. Our study supports the importance of paternal health at conception for offspring metabolism, shows that mt-tRNAs are diet-induced and sperm-borne and demonstrates, in a physiological setting, father-to-offspring transfer of sperm mitochondrial RNAs at fertilization.

Comprehensive analysis of the mitochondrial genome of Rehmannia glutinosa: insights into repeat-mediated recombinations and RNA editing-induced stop codon acquisition

Rehmannia glutinosa is an economically significant medicinal plant. Yet, the structure and sequence of its mitochondrial genome has not been published, which plays a crucial role in evolutionary analysis and regulating respiratory-related macromolecule synthesis. In this study, the R. glutinosa mitogenome was sequenced employing a combination of Illumina short reads and Nanopore long reads, with subsequent assembly using a hybrid strategy. We found that the predominant configuration of the R. glutinosa mitogenome comprises two circular chromosomes. The primary structure of the mitogenome encompasses two mitochondrial chromosomes corresponding to the two major configurations, Mac1-1 and Mac1-2. The R. glutinosa mitogenome encoded an angiosperm-typical set of 24 core genes, nine variable genes, three rRNA genes, and 15 tRNA genes. A phylogenetic analysis using the 16 shared protein-coding genes (PCG) yielded a tree consistent with the phylogeny of Lamiales species and two outgroup taxa. Mapping RNA-seq data to the coding sequences (CDS) of the PCGs revealed 507 C-to-U RNA editing sites across 31 PCGs of the R. glutinosa mitogenome. Furthermore, one start codon (nad4L) and two stop codons (rpl10 and atp6) were identified as products of RNA editing events in the R. glutinosa mitogenome.

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.

Molecular Profile of Mitochondrial Dysfunction in Kidney Transplant Biopsies Is Associated With Poor Allograft Outcome

BACKGROUND

In kidney transplantation (KT), progression of chronic histological damage with subclinical inflammation is associated with poor long-term allograft survival. The role of nonimmunological pathways in chronic allograft injury has not been fully assessed.

METHODS

We analyzed a public microarray dataset that used 1-year protocol kidney transplant biopsy specimens to investigate whether nonimmunological genes and pathways might influence long-term allograft outcome. The selected microarray dataset included 3 patient/sample groups based on their histological findings: normal histology (n = 25), interstitial fibrosis alone (IF alone, n = 24), and interstitial fibrosis with inflammation (IF+i, n = 16). The IF+i group had lower death-censored graft survival and renal function in patients with a mean follow-up of 4 years. We performed statistical analysis comparing gene expression patterns in the 3 group samples.

RESULTS

Gene cluster enrichment and group-specific expression patterns demonstrated a divergent pattern between mitochondrial and immune response genes, with downregulation of mitochondrial genes in the IF+i group. Gene ontological analysis of the downregulated mitochondrial genes identified generation of precursor metabolite and energy, and response to oxidative stress as the most significant biological processes. The transcription regulation pathway analysis of downregulated gene cluster demonstrated transcription factors involved in mitochondrial biogenesis.

CONCLUSIONS

The molecular signature of mitochondrial dysfunction reflects mitochondrial energetic insufficiency, and inadequate antioxidant response involved in mitochondria biogenesis pathways is associated with IF+i and worse long-term allograft survival. Thus, mitochondria function impairment appears to be an important nonimmune factor involved in chronic allograft injury.

Delaunay algorithm and principal component analysis for 3D visualization of mitochondrial DNA nucleoids by Biplane FPALM/dSTORM

Data segmentation and object rendering is required for localization super-resolution microscopy, fluorescent photoactivation localization microscopy (FPALM), and direct stochastic optical reconstruction microscopy (dSTORM). We developed and validated methods for segmenting objects based on Delaunay triangulation in 3D space, followed by facet culling. We applied them to visualize mitochondrial nucleoids, which confine DNA in complexes with mitochondrial (mt) transcription factor A (TFAM) and gene expression machinery proteins, such as mt single-stranded-DNA-binding protein (mtSSB). Eos2-conjugated TFAM visualized nucleoids in HepG2 cells, which was compared with dSTORM 3D-immunocytochemistry of TFAM, mtSSB, or DNA. The localized fluorophores of FPALM/dSTORM data were segmented using Delaunay triangulation into polyhedron models and by principal component analysis (PCA) into general PCA ellipsoids. The PCA ellipsoids were normalized to the smoothed volume of polyhedrons or by the net unsmoothed Delaunay volume and remodeled into rotational ellipsoids to obtain models, termed DVRE. The most frequent size of ellipsoid nucleoid model imaged via TFAM was 35 × 45 × 95 nm; or 35 × 45 × 75 nm for mtDNA cores; and 25 × 45 × 100 nm for nucleoids imaged via mtSSB. Nucleoids encompassed different point density and wide size ranges, speculatively due to different activity stemming from different TFAM/mtDNA stoichiometry/density. Considering twofold lower axial vs. lateral resolution, only bulky DVRE models with an aspect ratio >3 and tilted toward the xy-plane were considered as two proximal nucleoids, suspicious occurring after division following mtDNA replication. The existence of proximal nucleoids in mtDNA-dSTORM 3D images of mtDNA "doubling"-supported possible direct observations of mt nucleoid division after mtDNA replication.

Augmented Wnt signaling as a therapeutic tool to prevent ischemia/reperfusion injury in liver: Preclinical studies in a mouse model

The Wnt signaling pathway has established biological roles in liver development, regeneration, and carcinogenesis. Given the common need for cellular energy utilization in each of these processes, we hypothesized that Wnt signaling would directly regulate hepatocyte mitochondrial function. Mice were engineered to overexpress Wnt1 in hepatocytes under the control of a tetracycline analogue. Wnt1 and wild-type mice underwent ischemia/reperfusion injury (IRI) to induce oxidative mitochondrial injury. Alpha mouse liver 12 (AML12) hepatocytes were exposed to Wnt agonists for in vitro hypoxia/reoxygenation (H-R) experiments. We observed stabilized mitochondrial membrane potential and reduced levels of hepatocyte apoptosis involving the mitochondrial pathway in Wnt1 mice compared to controls following IRI. Wnt1 mice also demonstrated increased mitochondrial DNA copy number, as well as an increased tricarboxylic acid cycle activity and adenosine triphosphate levels indicating that mitochondrial function is preserved by Wnt1 overexpression following IRI. AML12 cells treated by Wnt3a or the glycogen synthase kinase 3β inhibitor LiCl exposed to H-R demonstrated decreased reactive oxygen species and reduced apoptosis compared to controls. Increased nucleus-localized PGC-1α and phosphorylated SIRT1 was observed in both Wnt1+ mice as well as AML12 cells treated with Wnt3a or LiCl. Activated Wnt signaling protects hepatocytes against oxidative injury and apoptosis through mitochondrial stabilization and preserved oxidative phosphorylation function. Mechanistically, these effects are accompanied by an increase in phosphorylated SIRT1 and nucleus-localized PGC-1α. These findings expand the understanding of Wnt signaling biology in hepatocytes and suggest the potential for the therapeutic application of Wnt pathway manipulation in a variety of clinical applications including organ transplantation.

Mitochondrial divergence between slow- and fast-aging garter snakes

Mitochondrial function has long been hypothesized to be intimately involved in aging processes--either directly through declining efficiency of mitochondrial respiration and ATP production with advancing age, or indirectly, e.g., through increased mitochondrial production of damaging free radicals with age. Yet we lack a comprehensive understanding of the evolution of mitochondrial genotypes and phenotypes across diverse animal models, particularly in species that have extremely labile physiology. Here, we measure mitochondrial genome-types and transcription in ecotypes of garter snakes (Thamnophis elegans) that are adapted to disparate habitats and have diverged in aging rates and lifespans despite residing in close proximity. Using two RNA-seq datasets, we (1) reconstruct the garter snake mitochondrial genome sequence and bioinformatically identify regulatory elements, (2) test for divergence of mitochondrial gene expression between the ecotypes and in response to heat stress, and (3) test for sequence divergence in mitochondrial protein-coding regions in these slow-aging (SA) and fast-aging (FA) naturally occurring ecotypes. At the nucleotide sequence level, we confirmed two (duplicated) mitochondrial control regions one of which contains a glucocorticoid response element (GRE). Gene expression of protein-coding genes was higher in FA snakes relative to SA snakes for most genes, but was neither affected by heat stress nor an interaction between heat stress and ecotype. SA and FA ecotypes had unique mitochondrial haplotypes with amino acid substitutions in both CYTB and ND5. The CYTB amino acid change (Isoleucine → Threonine) was highly segregated between ecotypes. This divergence of mitochondrial haplotypes between SA and FA snakes contrasts with nuclear gene-flow estimates, but correlates with previously reported divergence in mitochondrial function (mitochondrial oxygen consumption, ATP production, and reactive oxygen species consequences).

Coupled aggregation of mitochondrial single-strand DNA-binding protein tagged with Eos fluorescent protein visualizes synchronized activity of mitochondrial nucleoids

Oligomer aggregation of green-to-red photoconvertible fluorescent protein Eos (EosFP) is a natural feature of the wild‑type variant. The aim of the present study was to follow up mitochondrial nucleoid behavior under natural conditions of living cells transfected with mitochondrial single‑strand DNA‑binding protein (mtSSB) conjugated with EosFP. HEPG2 and SH‑SY5Y cells were subjected to lentiviral transfection and subsequently immunostained with anti‑DNA, anti‑transcription factor A, mitochondrial (TFAM) or anti‑translocase of the inner membrane 23 antibodies. Fluorescent microscopy, conventional confocal microscopy, superresolution biplane fluorescence photo-activation localization microscopy and direct stochastic optical reconstruction microscopy were used for imaging. In the two cell types, apparent couples of equally‑sized mtSSB‑EosFP‑visualized dots were observed. During the time course of the ongoing transfection procedure, however, a small limited number of large aggregates of mtSSB‑EosFP‑tagged protein started to form in the cells, which exhibited a great co‑localization with the noted coupled positions. Antibody staining and 3D immunocytochemistry confirmed that nucleoid components such as TFAM and DNA were co‑localized with these aggregates. Furthermore, the observed reduction of the mtDNA copy number in mtSSB‑EosFP‑transfected cells suggested a possible impairment of nucleoid function. In conclusion, the present study demonstrated that coupled nucleoids are synchronized by mtSSB‑EosFP overexpression and visualized through their equal binding capacity to mtSSB‑EosFP‑tagged protein. This observation suggested parallel replication and transcription activity of nucleoid couples native from a parental one. Preserved coupling in late stages of artificial EosFP‑mediated aggregation of tagged proteins suggested a rational manner of mitochondrial branching that may be cell-type specifically dependent on hierarchical nucleoid replication.

Yeast DEAD box protein Mss116p is a transcription elongation factor that modulates the activity of mitochondrial RNA polymerase

DEAD box proteins have been widely implicated in regulation of gene expression. Here, we show that the yeast Saccharomyces cerevisiae DEAD box protein Mss116p, previously known as a mitochondrial splicing factor, also acts as a transcription factor that modulates the activity of the single-subunit mitochondrial RNA polymerase encoded by RPO41. Binding of Mss116p stabilizes paused mitochondrial RNA polymerase elongation complexes in vitro and favors the posttranslocated state of the enzyme, resulting in a lower concentration of nucleotide substrate required to escape the pause; this mechanism of action is similar to that of elongation factors that enhance the processivity of multisubunit RNA polymerases. In a yeast strain in which the RNA splicing-related functions of Mss116p are dispensable, overexpression of RPO41 or MSS116 increases cell survival from colonies that were exposed to low temperature, suggesting a role for Mss116p in enhancing the efficiency of mitochondrial transcription under stress conditions.

MicroRNAs as regulators of mitochondrial function: role in cancer suppression

BACKGROUND

Mitochondria, essential to the cell homeostasis maintenance, are central to the intrinsic apoptotic pathway and their dysfunction is associated with multiple diseases. Recent research documents that microRNAs (miRNAs) regulate important signalling pathways in mitochondria, and many of these miRNAs are deregulated in various diseases including cancers.

SCOPE OF REVIEW

In this review, we summarise the role of miRNAs in the regulation of the mitochondrial bioenergetics/function, and discuss the role of miRNAs modulating the various metabolic pathways resulting in tumour suppression and their possible therapeutic applications.

MAJOR CONCLUSIONS

MiRNAs have recently emerged as key regulators of metabolism and can affect mitochondria by modulating mitochondrial proteins coded by nuclear genes. They were also found in mitochondria. Reprogramming of the energy metabolism has been postulated as a major feature of cancer. Modulation of miRNAs levels may provide a new therapeutic approach for the treatment of mitochondria-related pathologies, including neoplastic diseases.

GENERAL SIGNIFICANCE

The elucidation of the role of miRNAs in the regulation of mitochondrial activity/bioenergetics will deepen our understanding of the molecular aspects of various aspects of cell biology associated with the genesis and progression of neoplastic diseases. Eventually, this knowledge may promote the development of innovative pharmacological interventions. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.