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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

Cyclin B3 promotes APC/C activation and anaphase I onset in oocyte meiosis

As obligate kinase partners, cyclins control the switch-like cell cycle transitions that orchestrate orderly duplication and segregation of genomes. Meiosis, the cell division that generates gametes for sexual reproduction, poses unique challenges because two rounds of chromosome segregation must be executed without intervening DNA replication. Mammalian cells express numerous, temporally regulated cyclins, but how these proteins collaborate to control meiosis remains poorly understood. Here, we delineate an essential function for mouse cyclin B3 in the first meiotic division of oocytes. Females genetically ablated for cyclin B3 are viable, indicating the protein is dispensable for mitotic divisions, but are sterile. Mutant oocytes appear normal until metaphase I but then display a highly penetrant failure to transition to anaphase I. They arrest with hallmarks of defective APC/C activation, including no separase activity and high MPF, cyclin B1, and securin levels. Partial APC/C activation occurs, however, as exogenously expressed APC/C substrates can be degraded and arrest can be suppressed by inhibiting MPF kinase. Cyclin B3 is itself targeted for degradation by the APC/C. Cyclin B3 forms active kinase complexes with CDK1, and meiotic progression requires cyclin B3-associated kinase activity. Collectively, our findings indicate that cyclin B3 is essential for oocyte meiosis because it fine-tunes APC/C activity as a kinase-activating CDK partner. Cyclin B3 homologs from frog, zebrafish, and fruitfly rescue meiotic progression in cyclin B3-deficient mouse oocytes, indicating conservation of the biochemical properties and possibly cellular functions of this germline-critical cyclin.

cell biology↗

bioRxiv2018

Nutritional and meiotic induction of heritable stress resistance states in budding yeast

Transient exposures to environmental stresses induce altered physiological states in exposed cells that persist after the stresses have been removed. These states, referred to as cellular memory, can even be passed on to daughter cells and may thus be thought of as embodying a form of epigenetic inheritance. We find that meiotically produced spores in the budding yeast S. cerevisiae possess a state of heightened stress resistance that, following their germination, persists for numerous mitotic generations. As yeast meiotic development is essentially a starvation response that a/alpha diploid cells engage, we sought to model this phenomenon by subjecting haploid cells to starvation conditions. We find also that haploid cells exposed to glucose withdrawal acquire a state of elevated stress resistance that persists after the reintroduction of these cells to glucose-replete media. Following release from lengthy durations of glucose starvation, we confirm that this physiological state of enhanced stress resistance is propagated in descendants of the exposed cells through two mitotic divisions before fading from the population. In both haploid starved cells and diploid produced meiotic spores we show that their cellular memories are not attributable to trehalose, a widely regarded stress protectant that accumulates in these cell types. Moreover, the heritable stress resistant state induced by glucose starvation in haploid cells is independent of the Msn2/4 transcription factors, which are known to program cellular memory induced by exposure of cells to NaCl. Our findings identify new developmentally and nutritionally induced states of cellular memory that exhibit striking degrees of perdurance and mitotic heritability.

cell biology↗

bioRxiv2018

Cyclin B3 is specifically required for metaphase to anaphase transition in mouse oocyte meiosis I

Meiosis, a cell division to generate gametes for sexual reproduction in eukaryotes, executes a single round of DNA replication and two successive rounds of chromosome segregation [1]. The extraordinary reliability of the meiotic cycle requires the activities of cyclin-dependent kinases (Cdks) associated with specific cyclins [2-4]. Cyclins are the regulatory subunits of protein kinases, which are the main regulators of maturation promoting factor or mitosis promoting factor (MPF) [5, 6] and anaphase-promoting complex/cyclosome (APC/C) [7, 8] in eukaryotic cell division. But how cyclins collaborate to control meiosis is still largely unknown. Cyclin B3 (Ccnb3) shares homology with A- and B-type cyclins [9], and is conserved during higher eukaryote evolution [10-17]. Previous studies have shown that Ccnb3-deleted females are sterile with oocytes unable to complete meiosis I in Drosophila [18], implying that Ccnb3 may have a special role in meiosis. To clarify the function of Ccnb3 in meiosis in mammalian species, we generated Ccnb3 mutant mice by CRISPR/Cas9, and found that Ccnb3 mutation caused female infertility with the failure of metaphase-anaphase transition in meiosis I. Ccnb3 was necessary for APC/C activation to initiate anaphase I, but not required for oocytes maturation, meiosis II progression, or early embryonic development. Our study reveals the differential cell cycle regulation between meiosis I and meiosis II, as well as meiosis between males and females, which shed light on the cell cycle control of meiosis.\n\nHighlightsO_LIIdentification of a female meiosis-specific cyclin in mouse\nC_LIO_LICyclin B3 is required for metaphase-anaphase transition in oocyte meiosis I\nC_LIO_LICyclin B3 is not essential for oocyte maturation and sister chromosome segregation\nC_LIO_LICyclin B3 is necessary for APC/C activation and MPF kinase activity through Cdk1\nC_LI

cell biology↗

bioRxiv2018

Fine Tuning of Histone Demethylase KDM6A/B Improves the Development of Nuclear Transfer Embryo

Despite the success of the production of animals by somatic cell nuclear transfer (SCNT) in many species, the method is limited by a low efficiency. After zygotic genome activation (ZGA), a large number of endogenous retroviruses (ERVs) are expressed, including the murine endogenous retrovirus-L (MuERVL/MERVL). In this study, we generated a series of MERVL-reporter mouse strains to detect the ZGA event in embryos. We found that the majority of SCNT embryos exhibited ZGA failure, and histone H3 lysine 27 trimethylation (H3K27me3) prevented SCNT reprogramming. Overexpression of the H3K27me3-specific demethylase KDM6A, but not KDM6B, improved the efficiency of SCNT. Conversely, knockdown KDM6B not only facilitate ZGA, but also impede ectopic Xist expression in SCNT reprogramming. Furthermore, the knockdown of KDM6B increased the rate of SCNT-derived Duchenne muscular dystrophy embryonic stem cell establishment, indicate that these results not only provide insight into the mechanisms underlying failures of SCNT, but also may extend the applications of SCNT.

cell biology↗

bioRxiv2018

Cell-cell signaling elicits local Ca2+ transients in melanocyte dendrites and dendritic spine-like structures

Compartmentalized cytoplasmic fluctuations of Ca2+ within dendrites and dendritic spines regulate a variety of neuronal functions. Like some neurons and glia, melanocytes are neural crest derived and possess dendrites (Adameyko et al., 2009; Erickson et al., 1992; Fitzpatrick and Szabo, 1959). Here, we show that primary human melanocytes, when observed in situ have extensive dendritic branches with dendritic spines similar to neurons. When co-cultured with primary human keratinocytes, they have local Ca2+ transients within these spines and within the dendrites. These are elicited by secreted factors from adjacent keratinocytes. Thus other cell types with dendrites are capable of compartmentalized Ca2+ fluctuations in response to cell-cell communication. Furthermore, our observations within intact human skin suggest a more complex communication network between adjacent melanocytes and keratinocytes, and thus a more complex physiology to skin than previous appreciated.

cell biology↗

bioRxiv2018

Conserved phosphorylation hotspots in eukaryotic protein domain families

Protein phosphorylation is the best characterized post-translational modification that regulates almost all cellular processes through diverse mechanisms such as changing protein conformations, interactions, and localization. While the inventory for phosphorylation sites across different species has rapidly expanded, their functional role remains poorly investigated. Here, we have combined 537,321 phosphosites from 40 eukaryotic species to identify highly conserved phosphorylation \"hotspot\" regions within domain families. Mapping these regions onto structural data revealed that they are often found at interfaces, near catalytic residues and tend to harbor functionally important phosphosites. Notably, functional studies of a phospho-deficient mutant in the C-terminal hotspot region within the Ribosomal S11 domain in the yeast ribosomal protein uS11 showed cold-sensitive phenotype and impaired 20S pre-rRNA processing. Altogether, our study identified phosphorylation hotspots for 162 protein domains suggestive of an ancient role for the control of diverse eukaryotic domain families.

cell biology↗

bioRxiv2018

The sterol-responsive RNF145 E3 ubiquitin ligase mediates the degradation of HMG-CoA reductase together with gp78 and Hrd1

HMG-CoA reductase (HMGCR), the rate-limiting enzyme of the cholesterol biosynthetic pathway and the therapeutic target of statins, is post-transcriptionally regulated by sterol-accelerated degradation. Under cholesterol-replete conditions, HMGCR is ubiquitinated and degraded, but the identity of the E3 ubiquitin ligase(s) responsible for mammalian HMGCR turnover remains controversial. Using systematic, unbiased CRISPR/Cas9 genome-wide screens with a sterol-sensitive endogenous HMGCR reporter, we comprehensively map the E3 ligase landscape required for sterol-accelerated HMGCR degradation. We find that RNF145 and gp78, independently co-ordinate HMGCR ubiquitination and degradation. RNF145, a sterol-responsive ER-resident E3 ligase, is unstable but accumulates following sterol depletion. Sterol addition triggers RNF145 recruitment to HMGCR and Insig-1, promoting HMGCR ubiquitination and proteasome-mediated degradation. In the absence of both RNF145 and gp78, Hrd1, a third UBE2G2-dependent ligase partially regulates HMGCR activity. Our findings reveal a critical role for the sterol-responsive RNF145 in HMGCR regulation and elucidate the complexity of sterol-accelerated HMGCR degradation.

cell biology↗

bioRxiv2018

Intracellular mechanisms of fungal space searching in microenvironments

The underlying intracellular mechanisms involved in the fungal growth received considerable attention, but the experimental and theoretical work did not take into account the modulation of these processes by constraining microenvironments similar to many natural fungal habitats. To fill this gap in the scientific knowledge, we used time-lapse live-cell imaging of Neurospora crassa growth in custom-built confining microfluidics environments. We show that the position and dynamics of the Spitzenkorper-microtubules system in constraining environments differs markedly from that associated with unconstrained growth. First, when hyphae encounter an obstacle at shallow angles, the Spitzenkorper moves from its central position in the apical dome off-axis towards a contact with the obstacle, thus functioning as a compass preserving the directional memory of the initial growth. The trajectory of Spitzenkorper is also followed by microtubules, resulting in a cutting corners pattern of the cytoskeleton in constrained geometries. Second, when an obstacle blocks a hypha at nearnormal incidence, the Spitzenkorper-microtubule system temporarily disintegrates, followed by the formation of two equivalent systems in the proto-hyphae - the basis of obstacle-induced branching. Third, a hypha, passing a lateral opening along a wall, continues to grow largely unperturbed while a lateral proto-hypha gradually branches into the opening, which starts forming its own Spitzenkorper-microtubule system. These observations suggest that the Spitzenkorper-microtubules system conserves the directional memory of the hyphae when they navigate around obstacles, but in the absence of the Spitzenkorper-microtubule system during constrainment-induced apical splitting and lateral branching, the probable driving force of obstacle-induced branching is the isotropic turgor pressure.

cell biology↗

bioRxiv2018

A Chemical Toolbox for the Study of Bromodomains and Epigenetic Signaling

Bromodomains (BRDs) are evolutionary conserved epigenetic protein interaction modules which recognize (\"read\") acetyl-lysine, however their role(s) in regulating cellular states and their potential as targets for the development of targeted treatment strategies is poorly understood. Here we present a set of 25 chemical probes, selective tool small molecule inhibitors, covering 29 human bromodomain targets. We comprehensively evaluate the selectivity of this probe-set using BROMOscan(R) and demonstrate the utility of the set using studies of muscle cell differentiation and triple negative breast cancer (TNBC). We identified cross talk between histone acetylation and the glycolytic pathway resulting in a vulnerability of TNBC cell lines to inhibition of BRPF2/3 BRDs under conditions of glucose deprivation or GLUT1 inhibition. This chemical probe set will serve as a resource for future applications in the discovery of new physiological roles of bromodomain proteins in normal and disease states, and as a toolset for bromodomain target validation.

cell biology↗

bioRxiv2018

The N-end Rule Pathway and Ubr1 mediate clearance of mis-translocated proteins from the cytosol via P2-encoded cellular location signals

The Arg/N-end rule pathway, a mechanism of protein degradation conserved from yeast to humans, is involved in cellular protein quality control, but its role has only been vaguely understood. Through systematic examination of single residue mutants of model misfolded substrates, and global analyses of yeast proteins, we discovered that Ubr1, an E3 ligase of the Arg/N-end rule, degrades organellar proteins that fail to reach their intended subcellular compartments. We determined that recognition by Ubr1 is dependent on location signals that are naturally embedded into the 2nd amino acid residue of the majority of proteins. The N-end rule pathway is thus likely to have been critical to the evolution of endosymbiotic relationships which paved the way for advanced eukaryotic cellular life. Significance StatementThis work elucidates a novel role for the N-end Rule Pathway, a protein degradation pathway highly conserved from yeast to humans. We demonstrate that the N-end rule pathway enforces the cellular compartmentalization of ER and mitochondrial proteins by degrading them when they fail to successfully translocate into their intended destinations and thus become mislocalized to the cytosol. This mechanism prevents the accumulation of toxic foreign proteins within the cytosol. Recognition of the displaced proteins is dependent on cellular location signals programmed into the 2nd residue of the target proteins, as well as the tendency for the proteins to misfold in a foreign environment. These findings have significant relevance to research on the mechanisms causing human diseases involving protein misfolding.

cell biology↗

bioRxiv2018

Protein Kinase A activity is regulated by actomyosin contractility during cell migration and is required for durotaxis

Dynamic subcellular regulation of Protein kinase A (PKA) activity is important for the motile behavior of many cell types, yet the mechanisms governing PKA activity during cell migration remain largely unknown. The motility of SKOV-3 epithelial ovarian cancer (EOC) cells has been shown to be dependent on both localized PKA activity and, more recently, on mechanical reciprocity between cellular tension and extracellular matrix (ECM) rigidity. Here, we investigated the possibility that PKA is regulated by mechanical signaling during migration. We find that localized PKA activity in migrating cells rapidly decreases upon inhibition of actomyosin contractility (specifically, of myosin ATPase, ROCK (Rho kinase), or MLCK (myosin light chain kinase) activity). Moreover, PKA activity is spatially and temporally correlated with cellular traction forces in migrating cells. Additionally, PKA is rapidly and locally activated by mechanical stretch in an actomyosin contractility-dependent manner. Finally, inhibition of PKA activity inhibits mechanically-guided migration, also known as durotaxis. These observations establish PKA as a locally-regulated effector of cellular mechanotransduction and as a regulator of mechanically-guided cell migration.

cell biology↗

bioRxiv2018

Lsm12 mediates Polη deubiquitination to help Saccharomyces cerevisiae resist oxidative stress

In Saccharomyces cerevisiae, the Y-family DNA polymerase {eta} (Pol{eta}) regulates genome stability in response to different forms of environmental stress by translesion DNA synthesis. To elucidate the role of Pol{eta} in oxidative stress-induced DNA damage, we deleted or overexpressed the corresponding gene RAD30, and used transcriptome analysis to screen the potential genes associated with RAD30 to respond to DNA damage. Under 2 mM H2O2, deletion of RAD30 resulted in a 2.2-fold decrease in survival and a 2.8-fold increase in DNA damage, whereas overexpression of RAD30 increased survival and decreased DNA damage by 1.2- and 1.4-fold, respectively, compared with that of the wild-type strain. Transcriptome and phenotypic analysis identified Lsm12 as a main factor involved in oxidative stress-induced DNA damage. Deleting LSM12 caused growth defects while its overexpression enhanced cell growth under 2 mM H2O2. This effect was due to the physical interaction of Lsm12 with the UBZ domain of Pol{eta} to enhance Pol{eta} deubiquitination through Ubp3, and consequently promote Pol{eta} recruitment. Overall, these findings demonstrate that Lsm12 is a novel regulator mediating Pol{eta} deubiquitination to promote its recruitment under oxidative stress. Furthermore, this study provides a potential strategy to maintain the genome stability of industrial strains during fermentation.\n\nIMPORTANCEPol{eta} was shown to be critical for cell growth in the yeast Saccharomyces cerevisiae, and deletion of its corresponding gene RAD30 caused a severe growth defect under exposure to oxidative stress with 2 mM H2O2. Furthermore, we found that Lsm12 physically interacts with Pol{eta} and promotes Pol{eta} deubiquitination and recruitment. Overall, these findings indicate Lsm12 as a novel regulator mediating Pol{eta} deubiquitination that regulates its recruitment in response to DNA damage induced by oxidative stress.

cell biology↗

bioRxiv2018

Genetic control of cellular morphogenesis in Müller glia

Of all the cells in the body, those with the greatest variety of shapes reside in the central nervous system yet they all start their postmitotic lives as simple elongated cells of the neuroepithelium1.The molecular processes by which these, or indeed any, cells gain their particular cell-specific anatomies remain largely unexplored.We, therefore, developed a strategy to identify the genes involved in cellular morphogenesis using Muller glial (MG) cells in the vertebrate retina as a model system.These radially oriented cells, discovered by Heinrich Muller in 1851 and named in his honour2, are astonishingly complex yet, as the great neurohistologist Ramon y Cajal first noted, they share a conserved set of key anatomical features3.Using genomic and CRISPR based strategies in zebrafish, combined with a temporal dissection of the process, we found more than 40 genes involved in MG cell morphogenesis.Strikingly, the sequential steps of anatomical feature addition are regulated by successive expression of cohorts of interrelated genes, revealing unprecedented insights into the developmental genetics of cellular morphogenesis.

cell biology↗

bioRxiv2018

MicroRNA regulation of CTP synthase and cytoophidium in Drosophila melanogaster

CTPsyn is a crucial metabolic enzyme which synthesizes CTP molecules through the de novo or salvage pathway. It has the extraordinary ability to compartmentalize into filaments termed cytoophidia. Although this property is retained amongst orthologues, and cytoophidia are therefore found across kingdoms, the mechanisms behind their formation remain unknown. Micro-RNAs (miRNAs) are single-stranded RNA with length of 20 - 22 nucleotides, capable of exerting mRNA silencing and degradation as a form of regulation. D. melanogaster itself has a high total gene count to miRNA gene number ratio, alluding to the possibility that CTPsyn may too come under the regulatory effects of these small RNAs. A thorough miRNA overexpression involving 123 UAS-miRNA lines, followed by staining of ovarian cytoophidia dme-egg chambers, revealed a small group of candidates which confer either a lengthening or truncating effect on the structure. Prime candidates are identified on the basis of consistency. MiR-975 and miR-1014 are both cytoophidia-elongating, whereas miR-190 and miR-932 are cytoophidia-shortening. Though target prediction shows that miR-975 and miR-932 do indeed have binding sites on CTPsyn mRNA, in vitro assays instead revealed that none of the four candidates may actually do so. This suggests that the effects asserted by overexpressed miRNAs indirectly reach CTPsyn and its cytoophidia through the actions of middling elements. In silico target prediction and qPCR quantification indicated that, at least for miR-932 and miR-1014, these undetermined elements may be players in fat metabolism. This is the first study to thoroughly investigate miRNAs in connection to CTPsyn expression and activity in any species. The findings presented could serve as a basis for further queries into not only the fundamental aspects of the enzymes regulation, but may uncover new facets of closely related pathways as well.

cell biology↗

bioRxiv2018

Bradycardic mice undergo effective heart rate improvement after specific homing to the sino-atrial node and differentiation of adult muscle derived stem cells.

Current treatments for heart automaticity disorders still lack a safe and efficient source of stem cells to restore normal biological pacemaking. Since adult Muscle-Derived Stem Cells (MDSC) show multi-lineage differentiation in vitro including into spontaneously beating cardiomyocytes, we questioned whether they could effectively differentiate into cardiac pacemakers, a specific population of cardiomyocytes producing electrical impulses in the sino-atrial node (SAN) of adult heart. We show here that beating cardiomyocytes, differentiated from MDSC in vitro, exhibit typical characteristics of cardiac pacemakers: expression of markers of the SAN lineage Hcn4, Tbx3 and Islet1, as well as spontaneous calcium transients and hyperpolarization-activated "funny" current and L-type Cav1.3 channels. Pacemaker-like myocytes differentiated in vitro from Cav1.3-deficient mouse stem cells produced slower rate of spontaneous Ca2+ transients, consistent with the reduced activity of native pacemakers in mutant mice. In vivo, undifferentiated wild type MDSC migrated and homed with increased engraftment to the SAN of bradycardic mutant Cav1.3-/- within 2-3 days after systemic I.P. injection. The increased homing of MDSCs corresponded to increased levels of the chemokine SDF1 and its receptor CXCR4 in mutant SAN tissue and was ensued by differentiation of MDSCs into Cav1.3-expressing pacemaker-like myocytes within 10 days and a significant improvement of the heart rate maintained for up to 40 days. Optical mapping and immunofluorescence analyses performed after 40 days on SAN tissue from transplanted wild type and mutant mice showed MDSCs integrated as pacemaking cells both electrically and functionally within recipient mouse SAN. These findings identify MDSCs as directly transplantable stem cells that efficiently home, differentiate and improve heart rhythm in mouse models of congenital bradycardia.

cell biology↗

bioRxiv2018

Adhesion to nanofibers drives cell membrane remodeling through 1D wetting

The shape of cellular membranes is highly regulated by a set of conserved mechanisms. These mechanisms can be manipulated by bacterial pathogens to infect cells. Human endothelial cell plasma membrane remodeling by the bacterium Neisseria meningitidis is thought to be essential during the blood phase of meningococcal infection, but the underlying mechanisms are unknown. Here we show that plasma membrane remodeling occurs independently of F-actin, along meningococcal type IV pili fibers, by a novel physical mechanism we term \" onedimensional\" membrane wetting. We provide a theoretical model that gives the physical basis of 1D wetting and show that this mechanism occurs in model membranes interacting with model nanofibers, and in human cells interacting with model extracellular matrices. It is thus a new general principle driving the interaction of cells with their environment at the nanoscale that is diverted by meningococcus during infection.

cell biology↗

bioRxiv2018

Balancing dynamic tradeoffs to drive cellular reprogramming

Although cellular reprogramming continues to generate new cell types, reprogramming remains a rare cellular event. The molecular mechanisms that limit reprogramming, particularly to somatic lineages, remain unclear. By examining fibroblast-to-motor neuron conversion, we identify a previously unappreciated dynamic between transcription and replication that determines reprogramming competency. Transcription factor overexpression forces most cells into states that are refractory to reprogramming and are characterized by either hypertranscription with little cell division, or hyperproliferation with low transcription. We identify genetic and chemical factors that dramatically increase the number of cells capable of both hypertranscription and hyperproliferation. Hypertranscribing, hyperproliferating cells reprogram at 100-fold higher, near-deterministic rates. We demonstrate that elevated topoisomerase expression endows cells with privileged reprogramming capacity, suggesting that biophysical constraints limit cellular reprogramming to rare events.

cell biology↗

bioRxiv2018

Mesenchymal stem cells protect retinal ganglion cells from degeneration via mitochondrial donation

Retinal ganglion cell (RGC) degeneration is extremely hard to repair or regenerate and is often coupled with mitochondrial dysfunction. Mesenchymal stem cells (MSCs)-based treatment has been demonstrated beneficial for RGC against degeneration. However, underlying mechanisms of MSC-provided RGC protection are largely unknown other than neuropectective paracrine actions. In this study, we sought to investigate whether mitochondrial donation can preserve RGC functions, in a mitochondrial Ndufs4 deficient mouse model of RGC degeneration. The results revealed intravitreal transplanted by induced pluripotent stem cell derived-MSCs (iPSC-MSC) could donate their mitochondria through crossing inner limited membrane to host RGCs. Furthermore, the donated mitochondria effectively protected against RGC death and largely preserved retinal function in Ndufs4-KO mice. Importantly, the protective effects of mitochondrial donation from MSCs were associated with management of pro-inflammatory cytokines. Our data identified a novel role of MSCs-mitochondrial donation in protection of RGC from degeneration, and highlight a viable therapeutic strategy by manipulating stem cell mitochondrial donation for the treatment of retina degeneration in future.

cell biology↗