To elucidate the structure and function of organelles, it is necessary to analyze them from various aspects including molecular biology and cell biology. Many studies on organelles were undertaken in the budding yeast Saccharomyces cerevisiae, known as a unicellular eukaryotic cell model. Once after discovery in yeast, it is possible to expand the studies on organelles in even higher animal and plant cells. From this point of view, we organized a symposium at the 81th convention of the Botanical Society of Japan (jointly organized with the Japanese Society of Plant Morphology and Integrated Imaging Research Support), aiming to introduce the recent progress in the structure and function of organelles in S. cerevisiae and to discuss the various related problems in plant cells.

Yeast, known as a model system of eukaryotic cells, has advantages not only in genetics and biochemistry but also in morphology. We have developed state-of-the-art super-resolution confocal live imaging microscopy, which overturns many paradigms of membrane traffic.

Sphingolipids are one of the major lipid species constituting eukaryotic membranes: ceramide, their hydrophobic backbone, is composed of a long-chain base (LCB) and a fatty acid. LCB degradation is an important process for sphingolipid homeostasis. Recently, we reported detailed metabolic pathways for LCBs, including the specific reactions and genes involved. Among them, the LCB phytosphingosine, which has a C4 hydroxyl group, was found to undergo fatty acid α-oxidation during its metabolism, and be converted to odd-numbered fatty acids. To date, fatty acid α-oxidation has been thought to occur in peroxisomes, but our finding was completely new in that the observed α-oxidation takes place in the endoplasmic reticulum. In this review, we introduce the structure of sphingolipids and the latest findings about LCB metabolism and fatty acid α-oxidation, including from our own analyses using yeast and mammalian cells. Furthermore, based on our findings, we discuss the metabolism of LCBs in plants.

Activity, morphology and size of an organelle are not constant, but vary dependent on extracellular and intracellular conditions. The endoplasmic reticulum (ER) is the location where secretory and transmembrane proteins are folded. Dysfunction or overwork of the ER, which is mostly accompanied by ER accumulation of unfolded client proteins, leads to transcriptional induction of proteins that work in and/or for the ER. This cellular event, known as the unfolded protein response (UPR), is observed in a wide variety of eukaryotic species, and its mechanism has been mainly uncovered through studies using yeast Saccharomyces cerevisiae as a simple model organism. The intracellular signaling pathway of the UPR contains various remarkable features, which include the involvement of regulatory splicing of transcription-factor mRNAs that is performed by the ER-located transmembrane endoribonuclease Ire1 in the cytoplasm. In this article, we describe our current understanding about Ire1 and the UPR in cells of S. cerevisiae and other eukaryotic species including plants.

Autophagy delivers not only cytoplasmic proteins and RNA but also various organelles, such as the endoplasmic reticulum, mitochondria, peroxisomes, and lipid droplets to lysosomes/vacuoles for degradation. Thus, a considerable amount of membrane lipids is also transported into lysosomes/vacuole via autophagy. However, little is known about degradation and recycling of lipids, and the mechanism and physiological significance of these processes, compared with those of proteins and RNA. In this review, we summarize our current knowledge on relationships between lipid metabolism and autophagy and discuss the involvement of autophagy in lipid homeostasis.

In eukaryotic cells, mitochondria serve as the central source of cellular energy. As a byproduct of energy production, mitochondria also generate reactive oxygen species. Because accumulation of oxidative damage causes diverse pathologies, cells must maintain a proper pool of functional mitochondria in response to energetic demands and various stimuli. Selective removal of mitochondria by autophagy, called mitophagy, is thought to contribute to elimination of excess or dysfunctional mitochondria to maintain mitochondrial homeostasis. Mitophagy is a catabolic process where a part of mitochondria is engulfed into double-membrane vesicles termed autophagosomes, which then fuse with lysosomes/vacuoles, resulting in cargo degradation by lysosomal/vacuolar proteases. Studies using the budding yeast Saccharomyces cerevisiae as a model organism have significantly contributed to the understating of the mechanism, regulation, and functional roles of mitophagy. In S. cerevisiae, Atg32, a mitochondrial surface protein, is a key molecule in mitophagy, serving as a mitophagy receptor that connects a part of mitochondria to the autophagy machinery through its direct interaction with autophagy proteins required for autophagosome formation. Mitophagy induction in yeast is tightly controlled through transcriptional and post-translational regulations of Atg32. Furthermore, physiological functions of mitophagy have been explored using cells deleted for Atg32 as mitophagy-deficient mutants since Atg32 is a mitophagy-specific protein. In this review, by focusing on yeast mitophagy, we overview recent advances in our understanding of the molecular mechanism and physiological functions of autophagic degradation of mitochondria.

tRNAs, a class of small RNAs essential for translation, were thought to be stable molecules partly because of their indispensable roles in gene expression. However, when looking at the early part of their life, one may notice that tRNAs receive various and extensive processing for their maturation despite of their rather short bodies with around 80 nucleotides. In this century, researchers have been piling up facts that the processing steps of tRNAs are carried out both in the nucleus and in the cytoplasm, and that even the steps carried out in the nucleus, which include transcription as the first step, are finely arranged in sub-nuclear compartments. In parallel, it has been demonstrated that tRNAs are actually mobile molecules in the cell during and even after their maturation. Recent reports also describe that the amount and repertoire of tRNAs are regulated to cope with changes of both intracellular and extracellular physiological conditions. These findings now change the image of tRNAs from house-keeping molecules to dynamic molecules in various aspects. In this review, I will mainly overview two dynamics of tRNAs among several dynamics attracting interest of researchers in these years; the dynamics of molecular shape during tRNA maturation and the intracellular dynamics of tRNAs, especially focusing on their dyamics in the nucleus, which is an important place for tRNA maturation. I will also provide fundamental knowledge to prospect for future development of tRNA research.

1,3-β-glucan is a polysaccharide commonly present in plants and fungi, and it is a major constituent of the cell wall in particular in the budding yeast. In this article, we reviewed two recent studies on 1,3-β-glucan synthesis, i.e., (1) the role of the1,3-β-glucan synthesis in cell wall integrity checkpoint and (2) new antifungal agent targeting 1,3-β-glucan synthesis. The cell wall integrity checkpoint is one of the cell cycle check point activated when the synthesis of 1,3-β-glucan is perturbed. The outline of the checkpoint mechanism has recently been clarified. When the sensor embedded in the cell wall senses perturbation of the cell wall synthesis, it results in repressed transcription of the M phase cyclin Clb2 via two MAP kinases and the transcription factor cascade, leading to cell cycle arrest at the G2 phase. It is interesting that higher plants also have a mechanism linking cell wall synthesis and cell proliferation. It is widely accepted that synthesis of 1,3-β-glucan is indispensable for cell proliferation and has long been a target of antifungal agents. Recently a new antifungal agent named poacic acid was investigated. Poacic acid is derived from the hydrolytic product from the lignocellulose of the plant Poaceae. Studies using yeast cells revealed that poacic acid binds to 1,3-β-glucan and inhibits the activity of its synthetic enzyme. Since it acts on a broad spectrum of fungi, it is expected as plant-derived next-generation agrichemicals.

Mitochondrial DNA (mtDNA) is associated with specific proteins to form mitochondrial nucleoids (mt-nucleoids). We investigated morphological changes in mt-nucleoids during life cycle of the yeast, Saccharomyces cerevisiae by DAPI-fluorescence microscopy. The mt-nucleoids showed a string-of-beads appearance in log-phase cells and a small spherical one in stationary-phase cells, respectively. During meiosis and sporulation, the mt-nucleoids formed a distinct network during meiotic prophase and were distributed into spores. During the course of anaerobic culture, the mt-nucleoids formed large aggregates in stationary-phase cells. These large mt-nucleoids elongated and were dynamically dispersed into small ones during the transition from anaerobic to aerobic culture. The morphology of mt-nucleoids in rho^- respiratory-deficient cells significantly varied depending on the unit length of their mtDNA sequence. We analyzed the protein components of the isolated mt-nucleoids. A DNA-binding protein Abf2p is a major component of the mt-nucleoids and plays roles in packaging mtDNA. A number of proteins other than Abf2p are also associated with mt-nucleoids. By comparison of Abf2p homologues in several yeast species, we revealed that Abf2p is a highly diverged protein among the mt-nucleoid proteins.

Chloroplasts possess ~100 copies of their own DNA (chloroplast DNA: cpDNA) that are packaged into chloroplast nucleoids, cpDNA-protein complexes. For the faithful segregation of gigantic genomic DNA molecules, Holliday junctions, four-stranded DNA structures formed during homologous recombination, are required to be disentangled prior to the division. Holliday junction is resolved with resolvases which have been identified in prokaryotes and eukaryotes but not in chloroplasts. We first identified Monokaryotic chloroplast 1 (MOC1) as a Holliday junction resolvase in chloroplasts by the analysis of a green alga Chlamydomonas reinhardtii mutant defective in chloroplast nucleoid segregation. MOC1s are crucial for the chloroplast nucleoid segregation and cpDNA maintenance across a wide range of green plants. Here we trace the history of Holliday junction study by focusing on the significance of our finding of the Holliday junction resolvases in chloroplasts.

Chloroplasts arose from a cyanobacterial endosymbiont. Most algae with a single or a few chloroplasts per cell synchronize chloroplast division with the host cell cycle. This synchronization is regulated via interactions between the cell and chloroplast. The onset of chloroplast division is regulated by S-phase-specific expression of the nuclear-encoded chloroplast division genes; however, in the unicellular alga Nannochloris bacillaris, one of the plastid division genes, FtsZ2, is expressed throughout the cell cycle. Plastid-dividing (PD) machinery usually forms a ring complex only during the division phase, although the number of the FtsZ rings, and not of PD rings, is increased in N. bacillaris cells under phosphate-enriched mixotrophic condition where the chloroplast DNA is excessively replicated. Therefore, among components of the PD machinery, only FtsZ ring formation is promoted by chloroplast DNA synthesis under certain conditions. During chloroplast division, the onset of chloroplast constriction allows the progression of cell cycle to metaphase. The blockage of PD machinery formation before its assembly arrests the cell cycle in prophase in the unicellular alga, Cyanidioschyzon merolae; however, once DRP5B is recruited to the chloroplast division site, the cell cycle progresses despite the failure of chloroplast fission. A similar phenomenon has been observed in the glaucophyte Cyanophora paradoxa suggesting that the mechanism of the chloroplast division checkpoint is established early in chloroplast acquisition.