Cell Structure and Function

The central apparatus of motile cilia, consisting of central microtubules and various protein projections, is essential for dictating the ciliary movement. Although three proteins (FAP65, FAP147, and FAP70) have been localized to the C2a projection in Chlamydomonas reinhardtii, the full protein composition and functional roles of the vertebrate C2a remain inadequately defined. Here, we use three knockout mouse models corresponding to their respective homologs (Ccdc108, Mycbpap, and Cfap70) to systematically investigate their functions in vertebrates. Notably, all three knockout strains exhibit distinct phenotypes related to primary ciliary dyskinesia (PCD), including hydrocephalus and sinusitis. The ciliary incorporation of CCDC108, MYCBPAP, and CFAP70 is essential for one anothers stability, with the loss of any single component triggering C2a collapse, which destabilizes the central pair microtubules and ultimately alters the ciliary movement pattern. Furthermore, we significantly expand the vertebrate C2a proteome by identifying ARMC3 and MYCBP as additional C2a components. Collectively, our findings illuminate the proteomic composition and strict physiological requirements of the vertebrate C2a projection, providing new insights into the molecular pathogenesis of PCD.

Though whole-genome duplication (WGD) contributes to cancer progression, the mechanism of post-WGD cell proliferation remains unclear. Here, using 6-day live-imaging, we analyzed the proliferation dynamics of more than 150 post-WGD HCT116 cell lineages. A quantitative comparison of mitotic patterns and cell fates between proliferative and non-proliferative lineages revealed that multipolar chromosome segregation in early mitosis is a key factor limiting the proliferative capacity of post-WGD progenies. Multipolar chromosome segregation suppressed post-WGD cell viability, particularly when accompanied by drastic chromosome loss or when it repeatedly occurred. Tracing proliferative lineages elucidated that they proliferated mainly by imposing the risk of multipolar chromosome segregation on one of two sub-lineages that formed after the first bipolar division. Meanwhile, a considerable proportion of proliferative lineages consisted entirely of progeny of early multipolar chromosome segregation events. Our results highlight key cellular events that determine the proliferation dynamics and diversity of post-WGD progenies, providing a fundamental reference for understanding WGD-associated bioprocesses. Summary statementLive image tracing of >150 cell lineages reveals the cross-generation dynamics of multipolar chromosome segregation that determine the fates of post-whole-genome duplication progeny cells.

Tumor heterogeneity highlights the necessity of precision cancer medicine, making the evaluation and screening of anticancer drugs a core challenge in cancer therapy. However, current cell-based efficacy assessment methods struggle to quantify the holistic impact of drugs on cellular behavior through specific target engagement. Here, we proposed a novel approach (DL-TCP-FRET) that integrates phenotypic and target-related evaluations: the logistic fitting analysis is performed on time- and concentration-dependent cellular phenotypic characteristics to construct a phenotypic score (P), while a target score (T) is established based on the FRET efficiency between target proteins. These two scores were then further combined to generate a unified drug efficacy score (PT). Validation in A549 cells demonstrated that our method can reliably distinguish EGFR-TKIs from non-targeted drugs. DL-TCP-FRET simplifies the experimental workflow of drug efficacy evaluation and improves the accuracy of targeted drug identification, providing a novel strategy for advancing precision cancer therapy.

Centrosomal and microtubule-associated proteins such as CEP170 and WDR62 are essential in regulating mitotic spindle formation and pole orientation during cell division. MAPKBP1, a paralog of WDR62, is also a centrosomal protein, but its function is currently unclear. We have shown here that MAPKBP1 is localised to the subdistal appendages of the mother centriole, the pericentriolar material (PCM) of the centrosomes and the mitotic spindles during metaphase. Furthermore, MAPKBP1, WDR62 and CEP170 exists as a complex, where MAPKBP1 is recruited to the centrosomes by WDR62 and CEP170, and CEP170-MAPKBP1 interaction is mediated by WDR62. In addition, MAPKBP1 depletion leads to mitotic spindle defects and delayed mitosis that were further exacerbated with WDR62 knockout, indicating a possible redundancy between MAPKBP1 and WDR62. MAPKBP1 loss also leads to PCM fragmentation, which supports its role as a subdistal appendages protein vital in maintaining centrosome structure and PCM cohesion for proper anchoring of mitotic spindles. This study provides insight into how subdistal appendages and centrosome and microtubule associated proteins co-operate to tightly regulate mitotic spindle formation and stability.

G protein-coupled receptors (GPCRs) perceive spatially and temporally diverse stimuli and activate G protein heterotrimers comprising , {beta}, and {gamma} subunits, which broadcast signals through a broad range of effectors at various subcellular compartments. Therefore, understanding endogenous G protein activity dynamics at the subcellular level, thereby recapitulating in vivo signaling paradigms, will facilitate the identification of pathological signaling pathways. However, the lack of sensors for endogenous G proteins has been an obstacle. Here, we demonstrate the engineering of sensors to probe endogenous GiGTP and GqGTP. Compared to examining overexpressed and fluorescently tagged G, our sensors capture the magnitude and kinetics of endogenous GGTP dynamics, including their generation, equilibrium signaling, and hydrolysis, with native fidelity. Using the translocation-based GiGTP sensor, we show that heterotrimer dissociation upon Gi-GPCR activation is G{gamma}-subtype dependent. Confirming our previous findings, the GqGTP sensor showed that Gq expression is low and tightly regulated in most cells. Using optogenetic tools, we demonstrate that our sensors detect GGTP generation and hydrolysis during asymmetric GPCR-G protein activation, a capability that will be particularly useful in morphologically diverse cells such as neurons. Therefore, our engineered novel GGTP sensors can be highly beneficial in decoding subcellularly resolved endogenous G protein signaling dynamics.

Mitophagy is generally considered to promote cell survival by removing damaged mitochondria in response to mitochondrial stress, whereas apoptosis occurs during prolonged stress. However, the mechanisms that determine cell survival and cell death under these stress conditions remain poorly understood. Here, we showed that cytoplasmic mRNA granules, designated as mitophagy-induced mRNA granules (mitoRGs), were formed transiently and played an important role in cell fate decisions during PINK1/Parkin-dependent mitophagy. Although some components, such as G3BP1, were shared with stress granules (SGs), mitoRGs were distinct from SGs because mitoRG assembly required the mitochondrial protein phosphatase PGAM5. In response to mitochondrial stress, PGAM5 was released into the cytosol from mitochondria and incorporated into mitoRGs, but was then released back into the cytosol during mitoRG disassembly following prolonged mitochondrial stress, corresponding with the induction of apoptosis. Impairment of mitoRG assembly through G3BP1 depletion sensitized cells to apoptosis during mitophagy in a PGAM5-dependent manner. These results suggest that mitoRGs regulate cell fate decisions by spatiotemporally controlling PGAM5 and its pro-apoptotic activity during PINK1/Parkin mitophagy.

Acquiring nutrients is a fundamental biological process of all organisms, playing crucial roles in ecological sustainability. Diplonemids are highly abundant heterotrophic unicellular flagellates that are widespread in the worlds ocean. They have a highly complex microtubule-based feeding apparatus (cytostome-cytopharynx complex) located adjacent to the deep flagellar pocket from which two flagella emerge from parallel basal bodies. The apical papilla is a tongue-shaped structure unique to diplonemids that connects the cytopharynx and the flagellar pocket, the latter of which is formed by reinforcing microtubules (MTR) and two flagellar roots called intermediate and dorsal roots. Here we report identification of 17 proteins that localize at the feeding apparatus or flagellar apparatus in Diplonema papillatum. Using ultrastructure expansion microscopy, we show that Mad2 and its interaction partner MBP65 localize at the MTR, intermediate root, and dorsal root. Homologs of proteins that associate with the flagellar apparatus in Trypanosoma brucei (PFR2, KMP11, BILBO1) localize at the feeding apparatus in D. papillatum. We also identify proteins that localize at the apical papilla, MTR, parallel microtubule loop, or cytopharynx. By discovering components of the feeding apparatus for the first time in diplonemids, this work forms the foundation to understand molecular mechanisms of the feeding apparatus in these highly abundant marine plankton.

The cell cycle comprises different phases and is a tightly regulated process at the molecular level. During the cell cycle, two key events occurred: DNA duplication during the S phase and chromosome segregation during mitosis. Accurate cell cycle progression, achieved through faithful chromosome segregation, is essential for maintaining cell fidelity. Long noncoding RNAs are a subclass of noncoding RNA that are longer than 200 bp and form RNA protein complexes (RNPs) to regulate various biological processes. Herein, we demonstrate that lncRNA NORM is involved in regulating the cell cycle by maintaining proper chromosome segregation. NORM exhibited G2 phase-specific expression, and the depletion of NORM resulted in a significant G2/M arrest. NORM-depleted cells failed to progress in mitosis and showed defects in chromosome segregation. We further demonstrated that NORM binds to proteins such as Plk1 and Nsun2. Depletion of NORM hindered the interaction between Plk1 and Bub1, resulting in reduced kinetochore localization of Plk1 during prometaphase. Our results also show that the depletion of NORM affects the binding of Nsun2 protein to CDK1 mRNA and, consequently, the stabilization of CDK1 at the protein level. Altogether, our results demonstrate that NORM regulates chromosome segregation by mediating the interaction between Plk1 and Bub1.

Membrane trafficking is essential to maintain cellular homeostasis, enabling cells and organelles to exchange molecular components via vesicle transport. Therefore, it is tightly regulated, including by RAB GTPases. Among these, RAB21, which is primarily associated with early endosomes, plays a central role in coordinating endocytosis, sorting, and degradation. Like other RABs, it cycles between GTP- and GDP-bound forms. Although three specific guanine exchange factors (GEFs) for RAB21 have been identified, surprisingly, no GTPase-activating proteins (GAPs) have been found to directly modulate RAB21. Here, we describe a genetic modifier screen in Drosophila that identified Tre/Bub2/Cdc16 (TBC) domain family member 25 (TBC1D25) as a potential negative regulator of RAB21. We confirmed the RAB21-TBC1D25 interaction using co-immunoprecipitation and proximity ligation assays and further demonstrated that their association depends on the catalytic activity of TBC1D25. Genetic interaction studies revealed a functional link between TBC1D25 and RAB21 in autophagy and cargo sorting. Collectively, our results indicate that TBC1D25 negatively regulates RAB21, potentially by serving as a RAB21-specific GAP.

Cell contractility plays numerous essential roles in a healthy organism, while its malfunctioning can lead to disease. The ubiquitous actin-dependent motors of the nonmuscle myosin 2 (NM2) family, which includes NM2A and NM2B, are chiefly responsible for cell contractility because of their ability to polymerize into bipolar filaments. Polymerization/depolymerization of NM2 filaments allows cells to quickly reorganize their contractile system according to constantly changing shapes and positions of nonmuscle cells. Bipolar filament depolymerization is known to depend on the C-terminal features of the NM2A heavy chain. Here, we show that the motor activity of NM2A is another key component of NM2As depolymerization mechanism, which cooperates with tail-dependent mechanisms to facilitate NM2A turnover in cells and, through copolymerization with NM2B, to reorganize and dynamize NM2B in trans, thus generating a proper intracellular NM2A/NM2B distribution needed for efficient cell migration. Together, we show that NM2A motor activity is a key component of the bipolar filament depolymerization mechanism.

The secretion of glucagon from the pancreatic alpha () cell within the islets of Langerhans is physiologically regulated by nutrients (glucose, amino acids, fatty acids), neurotransmitters, and paracrine hormones. Insulin and somatostatin form an intra-islet paracrine network to control glucagon secretion through direct inhibitory effects on cell secretory granule exocytosis. In a potential new cellular pathway for the regulation of glucagon secretion, we have previously identified the neuronal trafficking protein Stathmin-2 (Stmn2) as a negative regulator of glucagon trafficking and secretion by directing glucagon to degradative lysosomes. In this study, we examined if insulin and somatostatin direct glucagon to lysosomes in a Stmn2-dependent manner as part of their paracrine mechanisms. Using the TC1-6 glucagon-secreting cell line and confocal microscopy of both fixed and live cells, we show that insulin and somatostatin direct glucagon, glucagon+LAMP1+ vesicles, and LAMP1-RFP to the intracellular region, away from sites of exocytosis. As visualized in live cells, insulin treatment resulted in the rapid retrograde transport of lysosomes from the cell periphery, and this effect was lost under siRNA-mediated silencing of Stmn2. Somatostatin appeared to enhance the intracellular retention of lysosomes, also in a Stmn2-dependent manner. We determined a possible mechanism for Stmn2 in the regulation of lysosome transport in TC1-6 cells through the Arf-like small GTPase Arl8, indicating that Stmn2 may function in lysosomal positioning along microtubules. We propose that Stmn2-mediated lysosomal transport may be a potential new pathway, in addition to inhibition of secretory granule exocytosis, through which insulin and somatostatin regulate glucagon secretion.

Coordination of metabolism, cell growth and cell division is essential to life. Recent single-cell measurements in S. cerevisiae have shown that metabolic processes and the cellular redox state are dynamic along the cell cycle. However, it is unknown whether similar metabolic oscillations also occur in other organisms. Until now, the dynamics of metabolism in other eukaryotes have predominantly been studied in cell cycle synchronised populations. Since cell cycle synchronisation methods can perturb metabolism, they may also introduce artefacts in the recorded dynamics. Here, we performed time-lapse microscopy analyses of exponentially growing single cells of the budding yeast S. cerevisiae, the fission yeast S. pombe and murine leukaemia L1210 cells. Measuring the NAD(P)H autofluorescence and the cell surface area growth rate in unsynchronised cells, we discovered oscillations along the cell cycle of the cellular redox state and lipid metabolism, respectively. Thus, our work shows that metabolism is dynamic along the cell cycle of these three evolutionarily distant eukaryotic organisms. This finding suggests that such metabolic oscillations could be a conserved characteristic among eukaryotes.

Autophagy contributes to normal cells physiology and is essential for progression of malignant tumors. While autophagy is mostly considered as a self-degradative and self-renewal process, it has non-degradative functions whose contribution to tumor progression is poorly explored. Here we use the autophagy dependent Drosophila RasV12, Scrib-/- carcinoma model to examine whether perturbation of distinct steps of autophagy differentially influences tumor progression. We found that inhibition of autophagosome formation, by mutating Atg13 or Atg6 either in the tumor or in the whole animal significantly decreased tumor growth. In contrast, blocking the later autophagosome-lysosome fusion (by loss of Vps39 or Syx17) and thereby autolysosomal degradation, does not reduce tumor size. We observed that an early (Atg13), but not a late (Vps39 or Syx17) block in autophagy showed reduced activity of JAK/STAT signaling, known to be critical for the progression of this tumor type. Importantly, we demonstrated that both Atg13 and Vps39 deficient tumors accumulated Stat92E inhibitor Su(var)2-10/dPIAS, a recently identified autophagic cargo, however in Vps39 mutants Su(var)2-10 is sequestered into autophagosomes. Finally, we found that reduction of Su(var)2-10 partially restores JAK/STAT signaling and rescues the growth of Atg13-deficient tumors, indicating its sequestration is a crucial mechanism to promote tumor progression.

Long noncoding RNAs (LncRNAs) have emerged as a class of important regulatory ncRNAs and are known to fine-tune numerous cellular processes including proliferation, differentiation and development; however, their role in quiescence still remains largely unexplored. A miRNA host gene lncRNA, MIR503HG, has been reported to play important role in cancer development. Here, we demonstrate the role of MIR503HG lncRNA in regulating cellular quiescence. MIR503HG displays elevated levels in human diploid fibroblasts induced to undergo quiescence. Depletion of MIR503HG in HDFs affects the entry of cells into quiescence but has no effect on cell cycle progression, suggesting its role in quiescence attainment and/or maintenance. Additionally, MIR503HG depletion led to a drastic decrease in the levels of miR508 target, PTEN with a concomitant increase in pAkt levels, indicating its role in negative regulation of miR508. Further, we demonstrate that the lncRNA MIR503HG regulates PTEN levels by acting as a ceRNA for miR508 to maintain cellular quiescence. Our studies illustrate that MIR503HG can function synergistically with miR503 to maintain cells under quiescence and both the miRNA-HG and the miRNA encoded by its gene locus synergistically control the same biological process in different ways by regulating different downstream genes.

Gap junction communication is reduced during mitosis as the junction protein connexin-43 (Cx43) is redistributed from gap junction plaques on the plasma membrane to cytoplasmic annular vesicles and actin-based mitotic nanotubes that transiently connect mitotic cells to neighboring cells. However, the dynamic details of Cx43 redistribution during cell entry into and exit from mitosis, and the roles of mitotic nanotubes and associated Cx43 in intercellular communication, remain poorly understood. Here, using confocal live-cell imaging, we show that as cells enter mitosis, plaque-derived Cx43 structures are transferred to mitotic nanotubes. Over time, these structures fragment and migrate along the length of the nanotubes, either being transferred to the cytoplasm of adjacent cells or being positioned at the nanotube ends where they could potentially enable communication. Functionally, mitotic nanotubes indeed facilitate gap junction-dependent intercellular communication, though at reduced rates compared interphase cells. Interestingly, knockdown of Cx43 resulted in impaired nanotube formation and intercellular communication while inhibition of Rho kinase (ROCK) with Y-27632 prevented mitotic cell rounding and nanotube elongation, and increased cell-cell communication during mitosis, suggesting that nanotube function is influenced by Cx43 expression and trafficking as well as actin remodeling via ROCK. Overall, these findings provide valuable insights into the mechanisms that regulate Cx43 and mitotic nanotube dynamics and reveal a novel role for mitotic nanotubes in facilitating cell-cell communication during cell division.

Hyperthermophiles, organisms that thrive at temperatures above 60 {degrees}C, have played important roles in biotechnology and promise to reveal new biology. However, how these cells live remains poorly understood in part due to the lack of bright, thermostable fluorescent proteins that can be used to study protein localisation and dynamics at high temperatures. To overcome this challenge, here we describe the development of "Matcha", a green fluorescent protein that we have engineered from Thermal Green Protein by directed evolution in the thermophilic archaeon Sulfolobus acidocaldarius. The screen identified 7 mutations that when combined led to an [~]50-fold increase in the brightness of Matcha in vivo at physiological temperatures. Since this is sufficient for live cell imaging, we were then able to use Matcha-fusion proteins to study the division ring dynamics in Sulfolobus. Remarkably, this analysis reveals that, while ESCRT-III rings are disassembled as cells complete division, CdvA forms a stable polymeric ring that persists, and is asymmetrically inherited by one of the two daughter cells following cytokinesis. This study highlights the power of Matcha as a tool to shed light on our understanding of the cell biology of hyperthermophiles.

Intraflagellar transport (IFT) is a conserved trafficking system in eukaryotes that moves proteins along microtubules. It is best known for its essential role in building and maintaining cilia and flagella. Intriguingly, several IFT components are still found in organisms that no longer possess flagella, raising important questions about their original functions and how they may have been repurposed during evolution. The filamentous alga Klebsormidium nitens, positioned at the base of the streptophyte lineage, offers a valuable model for exploring this transition. Here, we investigate the IFT machinery in K. nitens and its relationship with the blue-light photoreceptor phototropin. Comparative genomic analyses show that key IFT-A and IFT-B components are retained, despite the complete loss of flagella in vegetative state. Cellular detection and immunofluorescence studies revealed the presence and localisation of IFT components, interestingly, their co-localization with phototropin. Notably, IFT-139 and IFT-20 strongly co-localize with phototropin at plasma membrane-associated regions. Phototropin overlapping localization (plasma membrane associated) with conserved phospho-adaptor protein 14-3-3, pointing to a phosphorylation-dependent signaling network. Unlike in Chlamydomonas reinhardtii, where these proteins localize to flagella, their interaction in K. nitens occurs independently of cilia presence. Together, these results evidenced that IFT components were retained and repurposed early in streptophyte evolution and might support phototropin localization and signalling, revealing an ancestral, non-ciliary role for the IFT system.

Chromosome spatial organization plays critical roles in transcriptional regulation and DNA protection. In cyanobacteria--oxygenic photosynthetic bacteria that experience dramatic fluctuations in light intensity--chromosome reorganization may facilitate rapid transcriptional reprogramming and protect DNA from photodamage. However, direct observation of chromosome organization in these polyploid organisms has remained technically challenging, leaving light-dependent chromosomal responses unexplored. Here we show that local chromosome organization in Synechocystis sp. PCC 6803 is reorganized in response to high-light stress. We established fluorescence in situ hybridization (FISH) methods for this model cyanobacterium carrying multi-copy genomes, together with a computational pipeline for optimal same-genome-copy probe pairing. Under standard conditions, spatial distance between paired signals increased with genomic distance (slope {beta} = 0.972 nm/kbp, R{superscript 2} = 0.12), demonstrating that linear genome organization is reflected in three-dimensional chromosome structure at the 25-124 kbp scale. This genomic-spatial distance relationship substantially weakened under high-light conditions ({beta} = 0.450 nm/kbp, R{superscript 2} = 0.02), indicating that local chromosome organization is disrupted by elevated light intensity. Same-color nearest-neighbor distances further revealed that the spatial distribution of genome copies differed between conditions, independently supporting condition-dependent chromosome reorganization. Hi-C analysis corroborated these findings, revealing reduced short-range interactions within the 10-100 kbp genomic range under high-light conditions. Our integrative single-cell and population-level approach provides a framework for investigating how environmental signals modulate higher-order chromosome structure in polyploid bacteria.

Effective insulin secretion and blood glucose homeostasis depend on the multistep maturation of insulin secretory granules (ISGs), a process that includes lumen acidification, enzymatic insulin processing, and biophysical remodeling of the granule. An under studied aspect of ISG maturation is the role of inter-organelle contacts in organelle remodeling. While a correlation between ISG-mitochondria contacts and ISG maturation has been observed, many questions remain on how this interaction may impact maturation (1-5). We sought to address this gap in knowledge by using multi-scale imaging approaches (fluorescent microscopy, soft X-ray tomography, and cryo-electron tomography) to examine how the biophysical properties and spatial organization of ISGs change around the mitochondrial network. Our data suggests that ISGs in proximity to mitochondria exhibit lower pH, higher biomolecular density, and smaller vesicle diameter. Time-resolved imaging using a SNAP tag labelling system also shows that as ISGs age, their proximity to the mitochondria network is increased between 3-6 hours after biosynthesis, suggesting that ISG-mitochondria association is dynamically spatiotemporally regulated in pancreatic {beta}-cells. These data suggest that mitochondrial proximity contributes to the maturation and remodeling of ISGs in pancreatic beta cells.

Sphingomyelin is a critical sphingolipid found in plasma membranes of metazoa that provides structural and communicative functions. Sphingomyelin synthases are key enzymes that generate sphingomyelin but their precise functions in animal development and function are not fully understood. The Caenorhabditis elegans model encodes five sphingomyelin synthases (sms-1-5). Previously, egg-laying and locomotion phenotypes were observed in an sms-1(ok2399) deletion mutant. In this study, we attempted to replicate these findings to enable mechanistic dissection of sphingomyelin function. We indeed found that the sms-1(ok2399) mutant exhibited egg-laying and locomotion defects, however, we were unable to rescue this phenotype. Further, we generated two additional sms-1 deletion mutants (rp398 and rp399) and found that their egg-laying and locomotion behavior is not different to wild-type animals. We suggest that the sms-1(ok2399) contains a background mutation that causes behavioral deficits, and that SMS-1 loss does not overtly affect C. elegans egg-laying or locomotion.