Search bioRxiv⌕ Search

Biology subjects

Goshima, G.

Publications and source records attributed to Goshima, G..

At least 19 recordsLinked to original sources

RNAi reveals a unique kinesin mediating chloroplast motility in the giant cytoplasm of Bryopsis, a coenocytic green alga

RNA interference (RNAi) is a powerful tool for protein knockdown and is widely used in model animals and plants. Here, we applied this technique to Bryopsis, the green feather alga that develops a >10 cm coenocytic body in the wild and in laboratory culture. We mixed in vitro-transcribed double-stranded RNA (dsRNA) with extruded cytoplasm in the presence of polyethylene glycol or injected it directly into the cytoplasm, followed by thallus regeneration. After several days, we observed a reduction in the target gene transcript as well as expected phenotypes, indicating the effectiveness of RNAi. We prepared dsRNAs for the sole myosin and all 34 kinesin genes of the model Bryopsis strain, and performed RNAi and time-lapse microscopy to trace chloroplast movement. In addition to KCBP-type kinesins known to drive retrograde chloroplast transport in land plants, RNAi of a Bryopsidales-specific kinesin-14 (Kin14VIc) almost completely suppressed chloroplast motility. Cytoplasmic microtubules remained broadly aligned parallel to the main axis of the thallus following Kin14VIc RNAi. Purified Kin14VIc motor protein showed microtubule-gliding activity and, when artificially tetramerised, processive motility in vitro ([~]250 nm/s), similar to plant KCBP. Thus, this study introduces a powerful gene loss-of-function tool in a coenocytic organism and identifies a uniquely evolved kinesin as a critical driver of chloroplast motility in the giant cytoplasm.

cell biology↗

Live-cell imaging under centrifugation characterized the cellular force for nuclear centration in the Caenorhabditis elegans embryo

Organelles in cells are appropriately positioned, despite crowding in the cytoplasm. However, our understanding of the force required to move large organelles, such as the nucleus, inside the cytoplasm is limited, in part owing to a lack of accurate methods for measurement. We devised a novel method to apply forces to the nucleus of living, wild-type Caenorhabditis elegans embryos to measure the force generated inside the cell. We utilized a centrifuge polarizing microscope (CPM) to apply centrifugal force and orientation-independent differential interference contrast (OI-DIC) microscopy to characterize the mass density of the nucleus and cytoplasm. The cellular forces moving the nucleus toward the cell center increased linearly at [~]14 pN/m depending on the distance from the center. The frictional coefficient was [~]1,100 pN s/m. The measured values were smaller than previously reported estimates for sea urchin embryos. The forces were consistent with the centrosome-organelle mutual pulling model for nuclear centration. Frictional coefficient was reduced when microtubules were shorter or detached from nuclei in mutant embryos, demonstrating the contribution of astral microtubules. Finally, the frictional coefficient was higher than a theoretical estimate, indicating the contribution of uncharacterized properties of the cytoplasm.

biophysics↗

Genome sequence and cell biological toolbox of the highly regenerative, coenocytic green feather alga Bryopsis

Green feather algae (Bryopsidales) undergo a unique life cycle in which a single cell repeatedly executes nuclear division without cytokinesis, resulting in the development of a thallus (> 100 mm) with characteristic morphology called coenocyte. Bryopsis is a representative coenocytic alga that has exceptionally high regeneration ability: extruded cytoplasm aggregates rapidly in seawater, leading to the formation of protoplasts. However, the genetic basis of the unique cell biology of Bryopsis remains poorly understood. Here, we present a high-quality assembly and annotation of the nuclear genome of Bryopsis sp. (90.7 Mbp, 27 contigs, N50 = 6.7 Mbp, 14,034 protein-coding genes). Comparative genomic analyses indicate that the genes encoding BPL-1/Bryohealin, the aggregation-promoting lectin, are heavily duplicated in Bryopsis, whereas homologous genes are absent in other Ulvophycean algae, suggesting the basis of regeneration capability of Bryopsis. Bryopsis sp. possesses >30 kinesins but only a single myosin, which differs from other green algae that have multiple types of myosin genes. Consistent with this biased motor toolkit, we observed that the bidirectional motility of chloroplasts in the cytoplasm was dependent on microtubules but not actin in Bryopsis sp. Unexpectedly, most genes required for cytokinesis in plants are present in Bryopsis, including those in the SNARE or kinesin superfamily. Nevertheless, a kinesin crucial for cytokinesis initiation in plants (NACK/Kinesin-7II) is hardly expressed in the coenocytic part of the thallus, possibly underlying the lack of cytokinesis in this portion. The present genome sequence lays the foundation for experimental biology in coenocytic macroalgae. Significance statementThe exceptionally coenocytic body and remarkable regeneration ability of Bryopsis have attracted biologists for years. However, molecular biological tools remain underdeveloped, partly due to the lack of genome information. Here, we report high-quality assembly and annotation of the genome, providing a crucial resource for experimental biology and genomics studies of Bryopsis. Furthermore, comparative genomic analysis reveals a unique gene repertoire that possibly underlies the highly regenerative coenocytic body.

plant biology↗

Physcomitrella SUN2 mediates MTOC association to the nuclear envelope and facilitates chromosome alignment during spindle assembly

Plant cells lack centrosomes and instead utilise acentrosomal microtubule organising centres (MTOCs) to rapidly increase the number of microtubules at the onset of spindle assembly. Although several proteins required for MTOC formation have been identified, how the MTOC is positioned at the right place is not known. Here, we show that the inner nuclear membrane protein SUN2 is required for MTOC association with the nuclear envelope (NE) during mitotic prophase in the moss Physcomitrium patens. In actively dividing protonemal cells, microtubules accumulate around the NE during prophase. In particular, regional MTOC is formed at the apical surface of the nucleus. However, microtubule accumulation around the NE was impaired and apical MTOCs were mislocalised in sun2 knockout (KO) cells. In addition, chromosome distribution in the nucleus was skewed, suggesting that SUN2 mediates the linking of microtubules with chromosomes. Upon nuclear envelope breakdown (NEBD), the mitotic spindle was assembled with mislocalised MTOC, which were a source of microtubules in sun2 KO plants. However, completion of chromosome alignment in the spindle was delayed; in severe cases, the chromosome was transiently detached from the spindle body. SUN2 tended to localise to the apical surface of the nucleus during prophase in a microtubule-dependent manner. Based on these results, we propose that SUN2 facilitates the attachment of microtubules to chromosomes during spindle assembly by linking them prior to NEBD. Furthermore, this study suggests that trans-NE microtubule-chromosome linking, a well-known function of SUN in animals and yeast, is conserved in plants.

plant biology↗

Armadillo repeat-containing kinesin represents the versatile plus-end-directed transporter in plants

Kinesin-1, also known as conventional kinesin, is widely utilised for microtubule plus-end-directed ("anterograde") transport of various cargos in animal cells. However, a motor functionally equivalent to the conventional kinesin has not been identified in plants, which lack the kinesin-1 genes. Here, we show that plant-specific armadillo repeat-containing kinesin (ARK) is the long sought-after versatile anterograde transporter in plants. In ARK mutants of the moss Physcomitrium patens, the anterograde motility of nuclei, chloroplasts, mitochondria, and secretory vesicles was suppressed. Ectopic expression of non-motile or tail-deleted ARK did not restore organelle distribution. Another prominent macroscopic phenotype of ARK mutants was the suppression of cell tip growth. We showed that this defect was attributed to the mislocalisation of actin regulators, including RopGEFs; expression and forced apical localisation of RopGEF3 suppressed the growth phenotype of the ARK mutant. The mutant phenotypes were partially rescued by ARK homologues in Arabidopsis thaliana, suggesting the conservation of ARK functions in plants.

cell biology↗

Mitotic spindle formation in the absence of Polo kinase

Mitosis is a fundamental process in every eukaryote, in which chromosomes are segregated into two daughter cells by the action of the microtubule (MT)-based spindle. Despite this common principle, genes essential for mitosis are variable among organisms. This indicates that the loss of essential genes or bypass-of-essentiality (BOE) occurred multiple times during evolution. While many BOE relationships have been recently revealed experimentally, the BOE of mitosis regulators (BOE-M) has been scarcely reported and how this occurs remains largely unknown. Here, by mutagenesis and subsequent evolutionary repair experiments, we isolated viable fission yeast strains that lacked the entire coding region of Polo-like kinase (Plk), a versatile essential mitotic kinase. The BOE of Plk was enabled by specific mutations in the downstream machinery, including the MT-nucleating {gamma}-tubulin complex, and more surprisingly, through downregulation of glucose uptake, which is not readily connected to mitosis. The latter bypass was dependent on casein kinase I (CK1), which has not been considered as a major mitotic regulator. Our genetic and phenotypic data suggest that CK1 constitutes an alternative mechanism of MT nucleation, which is normally dominated by Plk. A similar relationship was observed in a human colon cancer cell line. Thus, our study shows that BOE-M can be achieved by simple genetic or environmental changes, consistent with the occurrence of BOE-M during evolution. Furthermore, the identification of BOE-M constitutes a powerful means to uncover a hitherto under-studied mechanism driving mitosis and also hints at the limitations and solutions for selecting chemotherapeutic compounds targeting mitosis.

cell biology↗

Cell tip growth underlies injury response of marine macroalgae

Regeneration is a widely observed phenomenon by which the integrity of an organism is recovered after damage. So far, studies on the molecular and cellular mechanisms of regeneration have been limited to a handful of model multicellular organisms. Here, we systematically surveyed the regeneration ability of marine macroalgae (Rhodophyta, Phaeophyceae, Chlorophyta) after thallus severing and applied live cell microscopy on them to uncover the cellular response to the damage. We observed three types of responses - budding, rhizoid formation and/or sporulation - in 25 species among 66 examined, demonstrating the high potential of regeneration of macroalgae. In contrast, callus formation, which often accompanies plant regeneration, was never observed. We monitored the cellular and nuclear dynamics during cell repair or rhizoid formation of four phylogenetically diverged Rhodophyta and Chlorophyta species (Colaconema sp., Dasya sessilis, Cladophora albida, Codium fragile). We observed tip growth of the cells near the damaged site as a common response, despite the difference in the number of nuclei and cells across species. Nuclear translocation follows tip growth, enabling overall uniform distribution of multinuclei (Dasya sessilis, Cladophora albida, Codium fragile) or central positioning of the mononucleus (Colaconema sp.). In contrast, the control of cell cycle events, such as nuclear division and septation, varied in these species. In Dasya sessilis, the division of multinuclei was synchronised, whereas it was not the case in Cladophora albida. Septation was tightly coupled with nuclear division in Colaconema and Dasya but not in others. These observations show that marine macroalgae utilise a variety of regeneration pathways, with some common features. This study also provides a novel methodology of live cell biology in macroalgae, offering a foundation for the future of this under-studied taxon.

cell biology↗

Microtubule-associated proteins promote microtubule generation in the absence of γ-tubulin in human colon cancer cells

{gamma}-Tubulin complex acts as the predominant microtubule (MT) nucleator that initiates MT formation and is therefore an essential factor for cell proliferation. Nonetheless, cellular MTs are formed after experimental depletion of the {gamma}-tubulin complex, suggesting that cells possess other factors that drive MT nucleation. Here, by combining gene knockout, auxin-inducible degron, RNA interference, MT depolymerisation/regrowth assay, and live microscopy, we identified four microtubule-associated proteins (MAPs), ch-TOG, CLASP1, CAMSAPs, and TPX2, which are involved in {gamma}-tubulin-independent MT generation in human colon cancer cells. In the mitotic MT regrowth assay, nucleated MTs organised non-centriolar MT organising centres (ncMTOCs) in the absence of {gamma}-tubulin. Depletion of CLASP1 or TPX2 substantially delayed ncMTOC formation, suggesting that they promote MT nucleation in the absence of {gamma}-tubulin. In contrast, depletion of CAMSAPs or ch-TOG did not affect the timing of ncMTOC appearance. CLASP1 also accelerates {gamma}-tubulin-independent MT regrowth during interphase. Thus, MT generation can be promoted by MAPs without the {gamma}-tubulin template.

cell biology↗

Growth and division mode plasticity by cell density in marine-derived black yeasts

The diversity and ecological contribution of the fungus kingdom in the marine environment remain under-studied. A recent survey in the Atlantic (Woods Hole, MA, USA) brought to light the diversity and unique biological features of marine fungi. The study revealed that black yeast species undergo an unconventional cell division cycle, which has not been documented in conventional model yeast species such as Saccharomyces cerevisiae (budding yeast) and Schizosaccharomyces pombe (fission yeast). The prevalence of this unusual property is unknown. Here, I collected and identified 65 marine fungi species across 40 genera from the surface ocean water, sediment, and the surface of macroalgae (seaweeds) in the Pacific (Sugashima, Toba, Japan). The Sugashima collection largely did not overlap with the Woods Hole collection and included several unidentifiable species, further illustrating the diversity of marine fungi. Three black yeast species were isolated, two of which were commonly found in Woods Hole (Aureobasidium pullulans, Hortaea werneckii). Surprisingly, their cell division mode was dependent on cell density, and the previously reported unconventional division mode was reproduced only at a certain cell density. For all three black yeast species, cells underwent filamentous growth with septations at low cell density and immediately formed buds at high cell density. At intermediate cell density, two black yeasts (H. werneckii and an unidentifiable species) showed rod cells undergoing septation at the cell equator. In contrast, all eight budding yeast species showed a consistent division pattern regardless of cell density. This study suggests the plastic nature of the growth/division mode of marine-derived black yeast.

cell biology↗

The 3D architecture and molecular foundations of de novo centriole assembly via bicentrioles

Abstract/SummaryCentrioles are structurally conserved organelles, composing both centrosomes and cilia. In animal cycling cells, centrioles often form through a highly characterized process termed canonical duplication. However, a large diversity of eukaryotes form centrioles de novo through uncharacterized pathways. This unexplored diversity is key to understanding centriole assembly mechanisms and how they evolved to assist specific cellular functions. Here, combining electron microscopy and tomography, we show that during spermatogenesis of the moss Physcomitrium patens, centrioles are born as a co-axially oriented centriole pair united by a cartwheel. We observe that microtubules emanate from those bicentrioles, which localize to the spindle poles during cell division. Thereafter, each bicentriole breaks apart, and the two resulting sister centrioles mature asymmetrically, elongating specific microtubule triplets and a naked cartwheel. Subsequently, two cilia are assembled which are capable of beating asynchronously. We further show that conserved cartwheel and centriole wall components, SAS6, BLD10 and POC1 are expressed during spermatogenesis and are required for this de novo biogenesis pathway. Our work supports a scenario where centriole biogenesis is more diverse than previously thought and that conserved molecular modules underlie diversification of this essential pathway.

cell biology↗

Cytoplasm Biophysical Properties Madolute Microtubule Dynamics

The cytoplasm is a crowded, visco-elastic environment whose physical properties change according to physiological or developmental states. How the physical properties of the cytoplasm impact cellular functions in vivo remain poorly understood. Here, we probed the effects of cytoplasmic concentration on microtubules by applying osmotic shifts to fission yeast, moss, and mammalian cells. We show that both the rates of microtubule polymerization and depolymerization scale linearly and inversely with cytoplasmic concentration; an increase in cytoplasmic concentration decreases the rates of microtubule polymerization and depolymerization proportionally, while a decrease in cytoplasmic concentration leads to the opposite. Numerous lines of evidence indicate that these effects are due to changes in cytoplasmic viscosity rather than cellular stress responses or macromolecular crowding per se. We reconstituted these effects on microtubules in vitro by tuning viscosity. Our findings indicate that, even in normal conditions, the viscosity of cytoplasm modulates the reactions underlying microtubule dynamic behaviors.

cell biology↗

Spindle position dictates division site during asymmetric cell division in moss

Asymmetric cell division (ACD) underlies the development of multicellular organisms. It is considered that the division site in land plants is predetermined prior to mitosis and that the localization of the mitotic spindle does not govern the division plane. This contrasts with animal ACD, in which the division site is defined by active spindle-positioning mechanisms. Here, we isolated a hypomorphic mutant of the conserved microtubule-associated protein TPX2 in the moss Physcomitrium patens and observed abnormal spindle motility during cell division. This defect compromised the position of the division site and produced inverted daughter cell sizes in the first ACD of gametophore (leafy shoot) development. The phenotype was rescued by restoring endogenous TPX2 function and, unexpectedly, by depolymerizing actin filaments. Thus, we have identified an active spindle-positioning mechanism that, reminiscent of acentrosomal ACD in animals, involves microtubules and actin filaments and sets the division site in plants.

plant biology↗

Novel roles of Kinesin-13 and Kinesin-8 during cell growth and division in the moss Physcomitrella patens

Kinesin-13 and -8 are well-known microtubule (MT) depolymerases that regulate MT length and chromosome movement in animal mitosis. While much is unknown about plant Kinesin-8, Arabidopsis and rice Kinesin-13 have been shown to depolymerise MTs in vitro. However, mitotic function of both kinesins has yet to be understood in plants. Here, we generated the complete null mutants in plants of Kinesin-13 and -8 in the moss Physcomitrella patens. Both kinesins were found to be non-essential for viability, but the Kinesin-13 knockout (KO) line had increased mitotic duration and reduced spindle length, whereas the Kinesin-8 KO line did not display obvious mitotic defects. Surprisingly, spindle MT poleward flux, for which Kinesin-13 is responsible for in animals, was retained in the absence of Kinesin-13. Concurrently, MT depolymerase activity of either moss kinesins could not be observed, with MT catastrophe inducing (Kinesin-13) or MT gliding (Kinesin-8) activity observed in vitro. Interestingly, both KO lines showed waviness in their protonema filaments, which correlated with positional instability of the MT foci in their tip cells. Taken together, the results suggest that plant Kinesin-13 and -8 have diverged in both mitotic function and molecular activity, acquiring new roles in regulating MT foci positioning for directed tip-growth.\n\nOne sentence summaryThis study uncovered the roles of Kinesin-13 and Kinesin-8 in regulating microtubule dynamics for mitotic spindle formation and straight tip cell growth in the moss Physcomitrella patens

cell biology↗

Identification of 15 new bypassable essential genes of fission yeast

Every organism has a different set of genes essential for its viability. This indicates that an organism can become tolerant to the loss of an essential gene under certain circumstances during evolution, via the manifestation of masked alternative mechanisms. In our quest to systematically uncover masked mechanisms in eukaryotic cells, we developed an extragenic suppressor screening method using haploid spores deleted of an essential gene in the fission yeast Schizosaccharomyces pombe. We screened for the bypass suppressors of lethality of 92 randomly selected genes that are essential for viability in standard laboratory culture conditions. Remarkably, extragenic mutations bypassed the essentiality of as many as 20 genes (22%), 15 of which have not been previously reported. Half of the bypass-suppressible genes were involved in mitochondria function; we also identified multiple genes regulating RNA processing. 18 suppressible genes were conserved in the budding yeast Saccharomyces cerevisiae, but 13 of them were non-essential in that species. These trends are consistent with a recent independent bypass-of-essentiality (BOE) screening of 142 fission yeast genes conducted with more elaborate methodology (Li et al., 2019). Thus, our study reinforces the emerging view that BOE is not a rare event and that each organism may be endowed with secondary or backup mechanisms that can substitute for primary mechanisms in various biological processes. Furthermore, the robustness of our simple spore-based methodology paves the way for genome-scale BOE screening.

genetics↗

A versatile microfluidic device for highly inclined thin illumination microscopy in the moss Physcomitrella patens

High-resolution microscopy is a valuable tool to study cellular processes, such as signalling, membrane trafficking, or cytoskeleton remodelling. Several techniques of inclined illumination microscopy allow imaging at near single molecular level; however, the application of these methods to plant cells is limited, due to thick cell walls and necessity to excise a part of the tissue for sample preparation. In this study, we developed simple, easy-to-use microfluidic device for highly inclined and laminated optical sheet (HILO) microscopy using a model plant Physcomitrella patens. We demonstrated that microfluidic device can be used to culture living cells and enables high-resolution HILO imaging of microtubules without perturbing their dynamics. In addition, our microdevice enables the supply and robust washout of compounds during HILO microscopy imaging, for example to perform microtubule regrowth assay. Furthermore, we tested long-term (48 h) HILO imaging using a microdevice and visualised the developmental changes in the microtubule dynamics during tissue regeneration. The microfluidic device designed in this study provides a novel tool to conduct long-term HILO microscopy and washout assays using plant cells.

plant biology↗

Fast, Efficient, and Precise Gene Editing in the Moss Physcomitrella patens

Recent years, the bryophyte moss Physcomitrella patens has become an emerging model organism for studying conserved signaling pathways and developmental processes during plant evolution. Its short life cycle, ease of cultivation, and high rate of homologous recombination have made it an ideal system for genetic analysis. However, the presence of highly redundant genes and the difficulty of isolating hypomorphic mutants have limited its broader use. Here we developed a simple, fast, and efficient method to generate customized mutants in P. patens. We show that transient cotransformation of CRISPR/Cas9 and oligonucleotide templates enables microindel knock-in with high efficiency and accuracy. Using this method, we generated strains carrying various types of mutations, including amino acid substitution, out-of-frame deletion/insertion, splice site alteration, and small tag integration. We also demonstrate that multiplex gene editing can be efficiently achieved to generate putative null and hypomorphic mutants of redundant genes in one step. Thus our method will not only simplify multiple-gene knockout, but also allows the generation of hypomorphic mutants of genes of interest, especially those that are essential for viability.

plant biology↗

Critical domains of moss KCBP kinesin for cargo transport

KCBP is a microtubule (MT) minus-end-directed kinesin widely conserved in plants. It was shown in Arabidopsis that KCBP controls trichome cell shape by orchestrating MT and actin cytoskeletons using its tail and motor domains. In contrast, the KCBP knockout (KO) line in the moss Physcomitrella patens showed a defect in nuclear and organelle positioning in apical stem cells. Moss KCBP is postulated to transport the nucleus and chloroplast via direct binding to their membranes, since it binds to and transports liposomes composed of phospholipids in vitro. However, domains required for cargo transport in vivo have not been mapped. Here, we performed a structure-function analysis of moss KCBP. We found that the FERM domain in the tail region, which is known to bind to lipids as well as other proteins, is essential for both nuclear and chloroplast positioning, whereas the proximal MyTH4 domain plays a supporting role in chloroplast transport. After anaphase but prior to nuclear envelope re-formation, KCBP accumulates on the chromosomes, in particular at the centromeric region in a FERM-dependent manner. In the KCBP knockout line, poleward chromosome motility in anaphase was reduced and lagging chromosomes occasionally appeared. These results suggest that KCBP binds to non-membranous naked chromosomes via an unidentified protein(s) for their transport. Finally, the liverwort orthologue of KCBP rescued the chromosome/chloroplast mis-positioning of the moss KCBP KO line, suggesting that the cargo transport function is conserved at least in bryophytes.

plant biology↗

Importin-β targets HURP to kinetochore-fibers in coordination with Ran-GTP in human mitotic cells

During mitosis, a bipolar spindle is assembled around chromosomes to efficiently capture chromosomes. Previous work proposed that a chromosome-derived Ran-GTP gradient promotes spindle assembly around chromosomes by liberating spindle assembly factors (SAFs) from inhibitory importins. However, Rans dual functions in interphase nucleocytoplasmic transport and mitotic spindle assembly have made it difficult to assess its mitotic roles in somatic cells. Here, using auxin-inducible degron technology in human cells, we developed acute mitotic degradation assays to dissect Rans mitotic roles systematically and separately from its interphase function. In contrast to the prevailing model, we found that the Ran pathway is not essential for spindle assembly activities that occur at sites spatially separated from chromosomes, including activating NuMA for spindle pole focusing or for targeting TPX2. In contrast, Ran-GTP is required to localize HURP and HSET specifically at chromosome-proximal regions. We demonstrated that Ran-GTP and importin-{beta} coordinately promote HURPs dynamic microtubule binding-dissociation cycle near chromosomes, which results in stable kinetochore-fiber formation. Intriguingly, this pathway acts to establish proper spindle length preferentially during prometaphase, rather than metaphase. Together, we propose that the Ran pathway is required to activate SAFs specifically near chromosomes, but not generally during human mitotic spindle assembly. Ran-dependent spindle assembly is likely coupled with parallel pathways to activate SAFs, including NuMA, for spindle pole focusing away from chromosomes. HighlightsO_LIUsing auxin-inducible degron technology, we developed mitotic degradation assays for the Ran pathway in human cells. C_LIO_LIThe Ran pathway is non-essential to activate NuMA for spindle pole focusing. C_LIO_LIThe Ran pathway dynamically polarizes HURP and defines mitotic spindle length preferentially during prometaphase. C_LIO_LIRan-GTP is required to activate SAFs specifically near chromosomes, but not generally, in human mitotic cells. C_LI

cell biology↗