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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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Costs of Clock-Environment Misalignment in Individual Cyanobacterial Cells

Circadian rhythms are endogenously generated daily oscillations in physiology found in all kingdoms of life. Experimental studies have shown that the fitness of Synechococcus elongatus, a photosynthetic microorganism, is severely affected in non-24h environments. However, it has been difficult to study the effects of clock-environment mismatch on cellular physiology because such measurements require the precise determination of both clock state and growth rates in the same cell. Here, we designed a microscopy platform that allows us to expose cyanobacterial cells to pulses of light and dark while quantitatively measuring their growth, division rate, and circadian clock state over many days. Our measurements reveal that decreased fitness can result from a catastrophic growth arrest caused by unexpected darkness in a small subset of cells with incorrect clock times corresponding to the subjective morning. We find that the clock generates rhythms in the instantaneous growth rate of the cell, and that time of darkness vulnerability coincides with the time of most rapid growth. Thus, the clock mediates a fundamental trade-off between growth and starvation tolerance in cycling environments. By measuring the response of the circadian rhythm to dark pulses of varying lengths, we constrain a mathematical model of a populations fitness under arbitrary light/dark schedules. This model predicts that the circadian clock is only advantageous in highly regular cycling environments with frequencies sufficiently close to the natural frequency of the clock.

Cell Biology

Deep mutational scanning reveals tail anchor characteristics important for mitochondrial targeting

Proteins localized to mitochondria by a carboxyl-terminal tail anchor (TA) play roles in apoptosis, mitochondrial dynamics, and mitochondrial protein import. To reveal characteristics of TAs that may be important for mitochondrial targeting, we focused our attention upon the TA of the Saccharomyces cerevisiae Fis1 protein. Specifically, we generated a library of Fis1p TA variants fused to the Gal4 transcription factor, then, using next-generation sequencing, revealed which Fis1p TA mutations inhibited membrane insertion and allowed Gal4p activity in the nucleus. Prompted by our global analysis, we subsequently analyzed the ability of individual Fis1p TA mutants to localize to mitochondria. Our findings suggest that the membrane-associated domain of Fis1p TA may be bipartite in nature, and we encountered evidence that the positively charged patch at the carboxyl-terminus of Fis1p is required for both membrane insertion and organelle specificity. Furthermore, lengthening or shortening the Fis1 TA by up to three amino acids did not inhibit mitochondrial targeting, arguing against a model in which TA length directs insertion of TAs at specific organelles. Most importantly, positively charged residues were more acceptable at several positions within the membrane-associated domain of the Fis1p TA than negatively charged residues. These findings, emerging from the first high-resolution analysis of an organelle targeting sequence by deep mutational scanning, provide strong, in vivo evidence that lysine and arginine can \"snorkel,\" or become stably incorporated within a lipid bilayer by placing terminal charges of their side chains at the membrane interface.\n\nAbbreviations

Cell Biology

GDP to GTP exchange on the microtubule end can contribute to the frequency of catastrophe

Microtubules are dynamic polymers of {beta}-tubulin that have essential roles in chromosome segregation and organizing the cytoplasm. Catastrophe - the switch from growing to shrinking - occurs when a microtubule loses its stabilizing GTP cap. Recent evidence indicates that the nucleotide on the microtubule end controls how tightly an incoming subunit will be bound (trans-acting GTP), but most current models do not incorporate this information. We implemented transacting GTP into a computational model for microtubule dynamics. In simulations, growing microtubules often exposed terminal GDP-bound subunits without undergoing catastrophe. Transient GDP exposure on the growing plus end slowed elongation by reducing the number of favorable binding sites on the microtubule end. Slower elongation led to erosion of the GTP cap and an increase in the frequency of catastrophe. Allowing GDP to GTP exchange on terminal subunits in simulations mitigated these effects. Using mutant {beta}-tubulin or modified GTP, we showed experimentally that a more readily exchangeable nucleotide led to less frequent catastrophe. Current models for microtubule dynamics do not account for GDP to GTP exchange on the growing microtubule end, so our findings provide a new way of thinking about the molecular events that initiate catastrophe.

Cell Biology

Distinct Responses to Reduplicated Chromosomes Require Distinct Mad2 Responses

Duplicating chromosomes once each cell cycle produces sister chromatid pairs, which separate accurately at anaphase. In contrast, reduplicating chromosomes without separation frequently produces polytene chromosomes, a barrier to accurate mitosis. Chromosome reduplication occurs in many contexts, including: polytene tissue development, polytene tumors, and following treatment with mitosis-blocking chemotherapeutics. However, mechanisms responding to or resolving polyteny during mitosis are poorly understood. Here, using Drosophila, we uncover two distinct reduplicated chromosome responses. First, when reduplicated polytene chromosomes persist into metaphase, an anaphase delay prevents tissue malformation and apoptosis. Second, reduplicated polytene chromosomes can also separate prior to metaphase through a spindlePindependent mechanism termed Separation-Into-Recent-Sisters (SIRS). Both reduplication responses require the spindle assembly checkpoint protein Mad2. While Mad2 delays anaphase separation of metaphase polytene chromosomes, Mad2s control of overall mitotic timing ensures efficient SIRS. Our results pinpoint mechanisms enabling continued proliferation after genome reduplication, a finding with implications for cancer progression and prevention.

Cell Biology

The EARP Complex and its Interactor EIPR-1 are Required for Cargo Sorting to Dense-Core Vesicles

The dense-core vesicle is a secretory organelle that mediates the regulated release of peptide hormones, growth factors, and biogenic amines. Dense-core vesicles originate from the trans-Golgi of neurons and neuroendocrine cells, but it is unclear how this specialized organelle is formed and acquires its specific cargos. To identify proteins that act in dense-core vesicle biogenesis, we performed a forward genetic screen in Caenorhabditis elegans for mutants defective in dense-core vesicle function. We previously reported the identification of two conserved proteins that interact with the small GTPase RAB-2 to control normal dense-core vesicle cargo-sorting. Here we identify several additional conserved factors important for dense-core vesicle cargo sorting: the WD40 domain protein EIPR-1 and the endosome-associated recycling protein (EARP) complex. By assaying behavior and the trafficking of dense-core vesicle cargos, we show that mutants that lack EIPR-1 or EARP have defects in dense-core vesicle cargo-sorting similar to those of mutants in the RAB-2 pathway. Genetic epistasis data indicate that RAB-2, EIPR-1 and EARP function in a common pathway. In addition, using a proteomic approach in rat insulinoma cells, we show that EIPR-1 physically interacts with the EARP complex. Our data suggest that EIPR-1 is a new component of the EARP complex and that dense-core vesicle cargo sorting depends on the EARP-dependent retrieval of cargo from an endosomal sorting compartment.\n\nAuthor SummaryAnimal cells package and store many important signaling molecules in specialized compartments called dense-core vesicles. Molecules stored in dense-core vesicles include peptide hormones like insulin and small molecule neurotransmitters like dopamine. Defects in the release of these compounds can lead to a wide range of metabolic and mental disorders in humans, including diabetes, depression, and drug addiction. However, it is not well understood how dense-core vesicles are formed in cells and package the appropriate molecules. Here we use a genetic screen in the microscopic worm C. elegans to identify proteins that are important for early steps in the generation of dense-core vesicles, such as packaging the correct molecular cargos in the vesicles. We identify several factors that are conserved between worms and humans and point to a new role for a protein complex that had previously been shown to be important for controlling trafficking in other cellular compartments. The identification of this complex suggests new cellular trafficking events that may be important for the generation of dense-core vesicles.

Cell Biology

Syndecan functions to regulate Wnt-dependent axon guidance in C. elegans

Cell adhesion molecules are key to axon guidance during development, for example specific cues can instruct axons to terminate in a specific area, or to continue growth. Syndecans are conserved cell-surface receptors that function in multiple developmental contexts. Caenorhabditis elegans with mutations in the single syndecan gene, sdn-1, exhibited errors in anterior-posterior guidance, with axons that stopped short of, or grew past their stereotypical termination point. Syndecan function was cell non-autonomous for GABAergic axon outgrowth during early development, but was likely cell autonomous to inhibit growth later in development. sdn-1 appeared to regulate the inhibitory activity of the egl-20/Wnt ligand. Removing egl-20 from sdn-1 mutants resulted in fewer animals with prematurely terminating axons. The proteoglycan modifying enzymes hse-5 and hst-2, but not hst-6, had similar effects, suggesting specific heparan sulfate modifications regulated EGL-20 axon-terminating activity. sdn-1 functioned with lin-17/Frizzled, bar-1/{beta}-catenin and the egl-5 Hox-like transcription factor in EGL-20-depedent axon outgrowth. bar-1 was required for egl-5 expression in the most posterior GABAergic neurons. sdn-1 mutations did not eliminate egl-5 expression, but over-expression of egl-5 rescued sdn-1 phenotypes. Our results suggest syndecan is a component of Wnt-signaling events that are necessary for axons to recognize appropriate termination points.

Cell Biology

Bone marrow mesenchymal stem cells from osteoporotic patients do not show altered mitochondrial energetics or ultrastructure

As a consequence of the ongoing demographic change, osteoporosis is considered as one of the mayor challenges for the health care system of the 21st century. However, the exact etiology of osteoporosis is far from being understood. Some evidence suggests that changes in stem cell metabolism might contribute to development of the disease. Therefore we evaluated whether differences of the morphology and/or the energy metabolism of mitochondria can be observed between human bone marrow derived mesenchymal stem cells obtained from osteoporotic patients as compared to non-osteoporotic controls.\n\nMesenchymal stem cells were isolated from the bone marrow of senile osteoporotic and non osteoporotic patients, osteoporosis being assessed by dual energy X-ray absorptiometry. We then confirmed the stemness of the cells by FACS analysis of the expression of surface markers and by conducting multi-lineage differentiation experiments. And we finally investigated mitochondrial morphology and function with electron microscopy of cryo-fixed samples and by high-resolution respirometry, respectively. In addition we compared the energy metabolism of the stem cells to those of the osteosarcoma cell line MG-63.\n\nThe data show, for the first time, the applicability on stem cells of the methods used here. Furthermore, our results indicated that there are no obvious differences detectable in mitochondrial morphology between cells from osteoporotic and non osteoporotic donors and that these cells also seem to be energetically indistinguishable with unchanged rates of routine respiration and respiratory capacity as well as unaltered oxygen consumption rates linked to different respiratory complexes. In summary, we could not detect any evidence indicating major changes of mitochondrial features in cells from osteoporotic patients.

Cell Biology

Nanoscopic compartmentalization of membrane protein motion at the axon initial segment

The axon initial segment (AIS) is enriched in specific adaptor, cytoskeletal and transmembrane molecules. During AIS establishment, a membrane diffusion barrier is formed between the axon and the somatodendritic domain. Recently, an axonal periodic pattern of actin, spectrin and ankyrin forming 190 nm distanced, ring-like structures has been discovered. However, whether this structure is related to the diffusion barrier function is unclear.\n\nHere, we performed single particle tracking timecourse experiments on hippocampal neurons during AIS development. We analyzed the mobility of lipid-anchored molecules by high-speed single particle tracking and correlated positions of membrane molecules with the nanoscopic organization of the AIS cytoskeleton.\n\nWe observe a strong reduction in mobility early in AIS development. Membrane protein motion in the AIS plasma membrane is confined to a repetitive pattern of ~190 nm spaced segments along the AIS axis as early as DIV4 and this pattern alternates with actin rings. Our data provide a new model for the mechanism of the AIS diffusion barrier.

Cell Biology

Timing appearance and integration of actin-organizing palladin protein in dynamic myofibril assembly

The involvement of actin-associated protein palladin in myogenesis has been elucidated, however, palladin distribution in a functional myotube remains to be identified. Since actin is required for myofibrillogenesis, it is of great interest to enhance our understanding of the spatial arrangements of palladin during sarcomeric assembly. Surprisingly, palladin was found to be discretely organized in different stages of myofibrillogenesis. Palladin revealed stress-fiber-like structures at undifferentiated stages, subsequently displayed chaotic expression and strongly co-distributed with actin, -actinin, and myosin heavy chain of premyofibrils. At late stages, aggregates of palladin were spaced in a regular dot-like structure. On the other hand, palladin presents at I-Z-I bands of adult muscle. These observations suggest that palladin engages with sarcomeric proteins during the process of myoblast differentiation and that these interactions might occur in a temporally regulated fashion. In addition, transient overexpression of 140-kDa-palladin resulted in nonfilamentous actin arresting mature myotube formation. 200-kDa-palladin overexpression led to the early formation of Z-lines. Collectively, these findings suggest that palladin might serve a role in myofibrillogenesis by guiding and positioning sarcomeric proteins at the appropriate time and place. Our results highlight the involvement of palladin protein and the discrete functions of palladin isoforms in sarcomeric development in vitro.

Cell Biology

Nucleosome dynamics and maintenance of epigenetic states of CpG islands

Methylation in mammalian DNA occurs primarily at CpG sequences. The CpG sites are distributed in high density clusters (or islands) separated by extended regions of low density. Cluster methylation tends to be bimodal, being dominantly unmethylated or mostly methylated. For CpG clusters near promoters, low methylation is associated with transcriptional activity, while high methylation is associated with gene silencing. Alternative CpG methylation states are thought to be stable and heritable, conferring localized epigenetic memory that allows transient signals to create long-lived gene expression states. Positive feedback where methylated CpG sites recruit enzymes that methylate nearby CpGs, does not easily explain that as clusters increase in size or density they change from being primarily methylated to primarily unmethylated. Here, we show that an interaction between the methylation state of a cluster and its occupancy by nucleosomes provides a mechanism to reproduce epigenetic potential and the genome wide systematics of CpG islands.

Cell Biology

Expression of progerin does not result in an increased mutation rate.

In the premature ageing disease Hutchinson-Gilford progeria syndrome (HGPS) the underlying genetic defect in the lamin A gene leads to accumulation at the nuclear lamina of progerin - a mutant form of lamin A that cannot be correctly processed. This has been reported to result in defects in the DNA damage response and in DNA repair, leading to the hypothesis that, as in normal ageing and in other progeroid syndromes caused by mutation of genes of the DNA repair and DNA damage response pathways, increased DNA damage may be responsible for the premature ageing phenotypes in HGPS patients. However, this hypothesis is based upon the study of markers of the DNA damage response, rather than measurement of DNA damage per se or the consequences of unrepaired DNA damage -mutation. Here, using a mutation reporter cell line, we directly compared the inherent and induced mutation rates in cells expressing wild-type lamin A or progerin. We find no evidence for an elevated mutation rate in progerin-expressing cells. We conclude that the cellular defect in HGPS cells does not lie in the repair of DNA damage per se.

Cell Biology

Chm7 and Heh1 form a nuclear envelope subdomain for nuclear pore complex quality control

Mechanisms that ensure the integrity of the nuclear envelope rely on membrane remodeling proteins like the ESCRTs and the AAA ATPase Vps4, which help seal the nuclear envelope at the end of mitosis and prevent the formation of defective nuclear pore complexes (NPCs). Here, we show that the integral inner nuclear membrane proteins Heh1 and Heh2 directly bind the ESCRT-III, Snf7, and the ESCRT-II/III chimera, Chm7, in their open forms. Moreover, Heh1 is required for Chm7-recruitment to the nuclear envelope. As Chm7 accumulates on the nuclear envelope upon blocks to NPC assembly, but not to nuclear transport, interactions between ESCRTs and the Heh proteins might form a biochemically distinct nuclear envelope subdomain that delimits regions of assembling NPCs. Interestingly, deletion of CHM7 suppresses the formation of the storage of improperly assembled NPC compartment prevalent in vps4{Delta} strains. Thus, our data support that the Heh1-dependent recruitment of Chm7 is a key component of a quality control pathway whose local regulation by Vps4 and the transmembrane nup, Pom152, prevents loss of nuclear compartmentalization by defective NPCs.

Cell Biology

Membrane binding by CHMP7 coordinates ESCRT-III dependent nuclear envelope reformation

Amongst other cellular functions, the Endosomal Sorting Complex Required for Transport-III (ESCRT-III) machinery controls nuclear envelope (NE) reformation during mitotic exit by sealing holes in the reforming NE. ESCRT-III also acts to repair this organelle upon migration-induced rupture. The ESCRT-III component CHMP7 is responsible for recruitment of ESCRT-III to the NE. Here, we show that the N-terminus of CHMP7, comprising tandem Winged Helix (WH)-domains, is a membrane-binding module. This activity allows CHMP7 to bind to the Endoplasmic Reticulum (ER), an organelle continuous with the NE, and provides a platform to direct NE-recruitment of ESCRT-III during mitotic exit. Point mutations that disrupt membrane-binding prevent CHMP7 localising to the ER and its subsequent enrichment at the reforming NE. These mutations prevent both assembly of downstream ESCRT-III components at the reforming NE and proper establishment of post-mitotic nucleo-cytoplasmic compartmentalisation. These data identify a novel membrane-binding activity within an ESCRT-III subunit that is essential for post-mitotic nuclear regeneration.\n\nOne Sentence SummaryCHMP7s atypical N-terminus is a membrane-binding module that allows assembly and function of ESCRT-III at the nuclear envelope during mitotic exit.

Cell Biology

LEM2 and CHMP7 function in ESCRT-dependent nuclear envelope closure in yeast and human cells

ESCRT-III proteins have been implicated in sealing the nuclear envelope in mammals, spindle pole body dynamics in fission yeast, and surveillance of defective nuclear pore complexes in budding yeast. Here, we report that Lem2p (LEM2), a member of the LEM (Lap2-Emerin-Man1) family of inner nuclear membrane proteins, and the ESCRT-II/ESCRT-III hybrid protein Cmp7p (CHMP7), work together to recruit additional ESCRT-III proteins to holes in the nuclear membrane. In S. pombe, deletion of the ATPase vps4 leads to severe defects in nuclear morphology and integrity. These phenotypes are suppressed by loss-of-function mutations that arise spontaneously in lem2 or cmp7, implying that these proteins may function upstream in the same pathway. Building on these genetic interactions, we explored the role of LEM2 during nuclear envelope reformation in human cells. We found that CHMP7 and LEM2 enrich at the same region of the chromatin disc periphery during this window of cell division, and that CHMP7 can bind directly to the C-terminal domain of LEM2 in vitro. We further found that, during nuclear envelope formation, recruitment of the ESCRT factors CHMP7, CHMP2A and IST1/CHMP8 all depend on LEM2 in human cells. We conclude that Lem2p/LEM2 is a conserved nuclear site-specific adaptor that recruits Cmp7p/CHMP7 and downstream ESCRT factors to the nuclear envelope.

Cell Biology

CD44 Controls Endothelial Proliferation and Functions as Endogenous Inhibitor of Angiogenesis

CD44 transmembrane glycoprotein is involved in angiogenesis, but it is not clear whether CD44 functions as a pro- or antiangiogenic molecule. Here, we assess the role of CD44 in angiogenesis and endothelial proliferation by using Cd44-null mice and CD44 silencing in human endothelial cells. We demonstrate that angiogenesis is increased in Cd44-null mice compared to either wild-type or heterozygous animals. Silencing of CD44 expression in cultured endothelial cells results in their augmented proliferation and viability. The growth-suppressive effect of CD44 is mediated by its extracellular domain and is independent of its hyaluronan binding function. CD44-mediated effect on cell proliferation is independent of specific angiogenic growth factor stimulation. These results show that CD44 expression on endothelial cells constrains endothelial cell proliferation and angiogenesis. Thus, endothelial CD44 might serve as a therapeutic target both in the treatment of cardiovascular diseases, where endothelial protection is desired, as well as in cancer treatment, due to its antiangiogenic properties.

Cell Biology

Ayurvedic Amalaki Rasayana promotes improved stress tolerance and thus has anti-aging effects in Drosophila melanogaster

Ethnopharmacological relevanceAmalaki Rasayana (AR) is a common Ayurvedic herbal formulation of Phyllanthus emblica fruits and other ingredients and is used for general good health and healthy aging. We earlier reported it to improve life history traits and to suppress neurodegeneration as well as induced apoptosis in Drosophila.\n\nAim of the studyTo examine effects of dietary AR supplement on cell stress responses in Drosophila melanogaster.\n\nMaterials and methodsLarvae/flies, reared on normal food or on that supplemented with 0.5% (w/v) AR, were exposed to crowding, thermal or oxidative stress and examined for survival, stress tolerance and levels of lipid peroxides, SOD and HSPs.\n\nResultsWild type larvae/flies reared on AR supplemented food survived the various cell stresses much better than those reared on normal food. AR-fed mutant park13 or DJ-1{beta}Delta93 (Parkinsons disease model) larvae, however, showed only partial or no protection, respectively, against paraquat-induced oxidative stress, indicating essentiality of DJ-1{beta} for AR mediated oxidative stress tolerance. AR feeding reduced the accumulation of reactive oxygen species (ROS) and lipid peroxidation even in aged (35 day old) wild type flies while enhancing superoxide dismutase (SOD) activity. We show for the first time that while Hsp70 or Hsp83 expression under normal or stress conditions was not differentially affected by AR feeding, Hsp27 levels were elevated in AR fed wild type control as well as heat shocked larvae. Therefore, besides the known anti-oxidant activity of Phyllanthus emblica fruits, dietary AR also enhances cellular levels of Hsp27.\n\nConclusionIn the context of the reported \"anti-aging\" and \"healthy-aging\" effects of AR, the present in vivo study on a model organisms shows that AR feeding significantly improves tolerance to a variety of cell stresses through reduced ROS and lipid peroxidation and enhanced SOD activity and Hsp27. Such improved cellular defences following dietary AR provide better homeostasis and thereby improve the life-span and quality of organisms life.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC=\"FIGDIR/small/050476_figu1.gif\" ALT=\"Figure 1\">\nView larger version (36K):\norg.highwire.dtl.DTLVardef@4452a8org.highwire.dtl.DTLVardef@18eb595org.highwire.dtl.DTLVardef@33533aorg.highwire.dtl.DTLVardef@19d4590_HPS_FORMAT_FIGEXP M_FIG C_FIG

Cell Biology

Amyloid β-peptides interfere with mitochondrial preprotein import competence by a co-aggregation process

A{beta} peptides play a central role in the etiology of Alzheimer disease (AD) by exerting cellular toxicity correlated with aggregate formation. Experimental evidences showed an intraneuronal accumulation of A{beta} peptides and an interference with mitochondrial functions. Nevertheless, the relevance of intracellular A{beta} peptides in the pathophysiology of AD remained controversial. Here, we found that the two major species of A{beta} peptides, in particular A{beta}42, exhibited a strong inhibitory effect on the preprotein import reactions essential for mitochondrial biogenesis. However, A{beta} peptides interacted only weakly with mitochondria and did not affect the inner membrane potential or the structure of the preprotein translocase complexes. A{beta} peptides significantly decreased the import competence of mitochondrial precursor proteins through a extra-mitochondrial co-aggregation mechanism. Co-aggregation and import inhibition were significantly stronger in case of the longer peptide A{beta}42, correlating with its importance in AD pathology. Our results demonstrate that a direct interference of aggregation-prone A{beta} peptides with mitochondrial protein biogenesis represents a crucial aspect of the pathobiochemical mechanisms contributing to cellular damage in AD.

Cell Biology

Reconstitution of three-phase microtubule polymerisation dynamics

Cytoplasmic microtubules (MTs) undergo growth, shrinkage, and pausing. However, how MT polymerisation cycles are produced and spatiotemporally regulated at a molecular level is unclear, as the entire cycle has not been recapitulated in vitro with defined components. In this study, we reconstituted dynamic MT plus end behaviour involving all three phases, by mixing tubulin with five Drosophila proteins, EB1, XMAP215Msps, Sentin, kinesin-13Klp10A, and CLASPMast/Orbit. When singly mixed with tubulin, CLASPMast/Orbit strongly inhibited MT catastrophe and reduced the growth rate. However, in the presence of the other four factors, CLASPMast/Orbit acted as an inducer of pausing. The mitotic kinase Plk1Polo modulated the activity of CLASPMast/Orbit and kinesin-13Klp10A, and increased the dynamic instability of MTs, reminiscent of mitotic cells. These results suggest that five conserved proteins constitute the core factors for creating dynamic MTs in cells, and that Plk1-dependent phosphorylation is a crucial event for switching from the interphase to mitotic mode.

Cell Biology