bims-tricox 2024-08-11 papers

Issue of 2024–08–11
five papers selected by
Yash Verma, University of Zurich

Genome Biol Evol. 2024 Aug 09. pii: evae173. [Epub ahead of print]

Reduction of ribosomal expansion segments in yeast species of the Magnusiomyces/Saprochaete clade.

Filip Brázdovič, Broňa Brejová, Barbara Siváková, Peter Baráth, Filip Kerák, Viktória Hodorová, Tomáš Vinař, Ľubomír Tomáška, Jozef Nosek.

Ribosomes are ribonucleoprotein complexes highly conserved across all domains of life. The size differences of ribosomal RNAs (rRNAs) can be mainly attributed to variable regions termed expansion segments (ESs) protruding out from the ribosomal surface. The ESs were found to be involved in a range of processes including ribosome biogenesis and maturation, translation, and co-translational protein modification. Here, we analyze the rRNAs of the yeasts from the Magnusiomyces/Saprochaete clade belonging to the basal lineages of the subphylum Saccharomycotina. We find that these yeasts are missing more than 400 nt from the 25S rRNA and 150 nt from the 18S rRNAs when compared to their canonical counterparts in Saccharomyces cerevisiae. The missing regions mostly map to ESs, thus representing a shift toward a minimal rRNA structure. Despite the structural changes in rRNAs, we did not identify dramatic alterations of the ribosomal protein inventories. We also show that the size-reduced rRNAs are not limited to the species of the Magnusiomyces/Saprochaete clade, indicating that the shortening of ESs happened independently in several other lineages of the subphylum Saccharomycotina.

Keywords: Magnusiomyces ; expansion segments; ribosomal RNA; ribosome; yeast

DOI: https://doi.org/10.1093/gbe/evae173

Methods Mol Biol. 2024 ;2845 1-14

Fluorescence Microscopy and Immunoblotting for Mitophagy in Budding Yeast.

Yuki Nakayama, Koji Okamoto.

Selective removal of excess or damaged mitochondria is an evolutionarily conserved process that contributes to mitochondrial quality and quantity control. This catabolic event relies on autophagy, a membrane trafficking system that sequesters cytoplasmic constituents into double membrane-bound autophagosomes and delivers them to lysosomes (vacuoles in yeast) for hydrolytic degradation and is thus termed mitophagy. Dysregulation of mitophagy is associated with various diseases, highlighting its physiological relevance. In budding yeast, the pro-mitophagic single-pass membrane protein Atg32 is upregulated under prolonged respiration or nutrient starvation, anchored on the surface of mitochondria, and activated to recruit the autophagy machinery for the formation of autophagosomes surrounding mitochondria. In this chapter, we provide protocols to assess Atg32-mediated mitophagy using fluorescence microscopy and immunoblotting.

Keywords: Atg32; Budding yeast; Fluorescence microscopy; Immunoblotting; Mitochondria

DOI: https://doi.org/10.1007/978-1-0716-4067-8_1

Biochem J. 2024 Aug 07. 481(15): 1015-1042

Evolution and maintenance of mtDNA gene content across eukaryotes.

Shibani Veeraragavan, Maria Johansen, Iain G Johnston.

Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.

Keywords: genome evolution; mitochondrial evolution; mtDNA

DOI: https://doi.org/10.1042/BCJ20230415

Science. 2024 Aug 09. 385(6709): 589

What's killing lab yeast around the world?

Molly Herring.

Multiple researchers are reporting toxic agar, but the ultimate culprit remains unclear.

DOI: https://doi.org/10.1126/science.ads2946

Genome Biol Evol. 2024 Aug 05. pii: evae160. [Epub ahead of print]16(8):

Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.

H B Rappaport, Angela M Oliverio.

From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.

Keywords: extreme environments; extremophiles; genomic adaptation; microbial eukaryotes; molecular adaptation

DOI: https://doi.org/10.1093/gbe/evae160