Synchronized assembly of the oxidative phosphorylation system controls mitochondrial respiration in yeast

The two yeast cytochrome c isoforms differentially regulate supercomplex assembly and mitochondrial electron flow

Mitochondria play a crucial role in cellular energy production, signaling and homeostasis. Respiratory supercomplexes represent evolutionary well-conserved, stable associations between membrane complexes and molecules, including proteins and lipids, within the inner mitochondrial membrane. They dynamically respond to metabolic demands and enhance the electron transfer rate, thereby reducing the production of ROS. Recent research has unveiled cytochrome c, a mobile electron carrier between complexes III and IV, as a potential key player in orchestrating the formation of these supra-associations. This study centers on elucidating the role of cytochrome c in modulating the assembly of supercomplexes, using the Saccharomyces cerevisiae yeast as a model system for mitochondrial metabolism. BN-PAGE and mass spectrometry-based proteomic analysis were employed to examine supercomplex organization in yeast strains expressing different cytochrome c isoforms, grown under fermentative and respiratory conditions. Our results demonstrate that both isoforms of cytochrome c contribute to supercomplex assembly, with isoform-2 significantly improving electron transfer and lowering ROS levels. We propose a model in which cytochrome c acts as a scaffold for the recruitment of assembly factors, facilitating the formation of higher order supercomplexes such as III2IV2. This model highlights cytochrome c's role beyond electron transfer, as it regulates supercomplex assembly and mitochondrial homeostasis.

Elucidating the mechanisms of echinocandin B biosynthesis under fatty acid feeding in Aspergillus nidulans based on genome and transcriptome sequencing

Echinocandin B (ECB), a non-ribosomal lipopeptide synthesized by ascomycete fungi, serves as a first-line therapeutic agent for invasive fungal infections. While the biosynthetic gene clusters of ECB have been identified in several Aspergillus species, the regulatory mechanisms governing its intracellular biosynthesis remain poorly understood, hindering the development of efficient ECB-producing cell factories. To address this issue, we elucidated the mechanisms underlying echinocandin B (ECB) biosynthesis in Aspergillus nidulans ZJB16068 under fatty acid feeding conditions through genome and transcriptome sequencing. The genome of ZJB16068 was sequenced using Oxford Nanopore Technology, yielding a 32.67 Mbp assembly with 11 scaffolds and a GC content of 50.23%. A total of 10,505 protein-coding genes were annotated, revealing 66 secondary metabolite gene clusters. Comparative transcriptomics between ZJB16068 and the reference strain ZJB0817 identified 2,342 differentially expressed genes (DEGs) under fatty acid supplementation. The KEGG analysis of the top 20 DEGs highlighted predominant metabolic pathways, including translation, energy metabolism, cofactor supply and lipid metabolism. We found that the up-regulation of genes related to the fatty acid metabolic pathway, pantothenic acid and CoA synthesis pathway accelerated the synthesis of acetyl-CoA, and the down-regulation of TCA pathway contributed to the throttling of acetyl-CoA. In addition, the genes involved in oxidative phosphorylation are fully upregulated, providing sufficient ATP for ECB synthesis. These pathways synergistically enhance the synthesis of ECB. These findings highlight the critical role of acetyl-CoA synthesis and energy supply in ECB synthesis and provide potential direction for future metabolic engineering aiming at increasing ECB production.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04331-4.

Biochar mediated differential regulation of oxidative stress and energy supply in Bacillus subtilis and Rhizoctonia solani

Biochar (BC) significantly influences microbial metabolism, but its contrasting effects on different microorganisms remain unclear. This research explores the distinct regulatory mechanisms of BC on B. subtilis and R. solani. BC, consisting of micro-BC and nano-BC, generates reactive oxygen species (ROS), causing oxidative stress. Nano-BC can penetrate cells, leading to damage. In B. subtilis, BC initially inhibits growth, triggering endospore formation to expel nano-BC. B. subtilis secreted extracellular polymeric substances (EPS), which aggregated nano-BC, enhanced cell adhesion, and reduced intracellular ROS (from 2.0 to 1.5-fold), promoting growth later with BC's nutrient support. Conversely, R. solani cannot block nano-BC entry, activating mitophagy and suppressing genes like ATP1,2 involved in oxidative phosphorylation and tricarboxylic acid cycle. This results in ATP deficiency, collapses antioxidant system, raises ROS (from 3.9 to 4.5-fold), decreases cell survival, and leads to cell death. These findings highlight BC's selective microbial regulation and its potential for safe agricultural and environmental use.

Coupling genome-wide continuous perturbation with biosensor screening reveals the potential targets in yeast isopentanol synthesis network

The increasing consumption of fossil fuels is contributing to global resource depletion and environmental pollution. Branched-chain higher alcohols, such as isopentanol and isobutanol, have attracted significant attention as next-generation biofuels. Biofuel production through microbial fermentation offers a green, sustainable, and renewable alternative to chemical synthesis. While enhanced production of isopentanol has been achieved in a variety of chassis, the fermentation yield has not yet reached levels suitable for industrial-scale production. In this study, we employed a continuous perturbation tool to construct a genome-scale perturbation library, combined with an isopentanol biosensor to screen for high-yielding mutants. We identified five high-yielding mutants, each exhibiting an increased glucose conversion rate and isopentanol titer. The F2 strain, in particular, achieved an isopentanol titer of 1.57 ± 0.014 g/L and a yield of 14.04 ± 0.251 mg/g glucose (10% glucose), surpassing the highest values reported to date in engineered Saccharomyces cerevisiae. Systematic transcriptome analysis of the isopentanol synthesis, glycolysis, glycerol metabolism, and ethanol synthesis pathways revealed that MPC, OAC1, BAT2, GUT2, PDC6, and ALD4 are linked to efficient isopentanol production. Further analysis of differentially expressed genes (DEGs) identified 17 and 12 co-expressed DEGs (co-DEGs) in all mutants and the two second-round mutants, respectively. In addition, we validated the knockout or overexpression of key co-DEGs. Our results confirmed the critical roles of HOM3 and DIP5 in isopentanol production, along with genes associated with the aerobic respiratory chain (SDH3, CYT1, COX7, ROX1, and ATG41) and cofactor balance (BNA2 and NDE1). Additionally, functional analysis of the co-DEGs revealed that MAL33 is associated with the synthesis of branched-chain higher alcohols, expanding the intracellular metabolic network and offering new possibilities for green, cost-effective biofuel production.

The Importance of Mitochondrial Processes in the Maturation and Acquisition of Competences of Oocytes and Embryo Culture

Mitochondria, as multifunctional and partially independent structures, play a crucial role in determining essential life processes. Recently, their significance in reproductive biology has gained increasing attention. This review aims to comprehensively analyse the role of mitochondrial processes in oocyte maturation and embryo culture. A comprehensive literature review was conducted to highlight the importance of mitochondrial activity in the early stages of life formation. Proper mitochondrial function provides energy, maintains genomic stability, and ensures optimal conditions for fertilisation and embryo progression. Understanding these processes is essential to optimise culture conditions and identify new mitochondrial biomarkers that improve reproductive success and improve assisted reproductive technologies (ARTs). Enhancing mitochondrial function in female reproductive cells is the key to improving oocyte and embryo quality, which can lead to better in vitro fertilisation and embryo transfer. Furthermore, advances in diagnostic techniques, such as mitochondrial genome sequencing, offer a more precise understanding of the relationship between mitochondrial health and oocyte quality. However, fully understanding mitochondrial functions is only part of the challenge. Expanding knowledge of the interactions between mitochondria and other cellular structures is crucial for future advancements in reproductive medicine. Understanding these complex relationships will provide deeper insight into improving reproductive outcomes and embryo development.

Mitochondrial mRNA and the small subunit rRNA in budding yeasts undergo 3'-end processing at conserved species-specific elements

Respiration in eukaryotes depends on mitochondrial protein synthesis, which is performed by organelle-specific ribosomes translating organelle-encoded mRNAs. Although RNA maturation and stability are central events controlling mitochondrial gene expression, many of the molecular details in this pathway remain elusive. These include cis- and trans-regulatory factors that generate and protect the 3' ends. Here, we mapped the 3' ends of mitochondrial mRNAs of yeasts classified into multiple families of the subphylum Saccharomycotina. We found that the processing of mitochondrial 15S rRNA and mRNAs involves species-specific sequence elements, which we term 3'-end RNA processing elements (3'-RPEs). In Saccharomyces cerevisiae, the 3'-RPE has long been recognized as a conserved dodecamer sequence, which recent studies have shown specifically interacts with the nuclear genome-encoded pentatricopeptide repeat protein Rmd9. We also demonstrate that, analogous to Rmd9 in S. cerevisiae, two Rmd9 orthologs from the Debaryomycetaceae family interact with their respective 3'-RPEs found in mRNAs and 15S rRNA. Thus, Rmd9-dependent processing of mitochondrial RNA precursors may be a common mechanism among the families of the Saccharomycotina subphylum. Surprisingly, we observed that 3'-RPEs often occur upstream of stop codons in complex I subunit mRNAs from yeasts of the CUG-Ser1 clade. We examined two of these mature mRNAs and found that their stop codons are indeed removed. Thus, translation of these stop-codon-less transcripts would require a noncanonical termination mechanism. Our findings highlight Rmd9 as a key evolutionarily conserved factor in both mitochondrial mRNA metabolism and mitoribosome biogenesis in a variety of yeasts.