SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence [preprint]

It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH-sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in S. cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. We found that a glutamine-rich low complexity sequence (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, were required for efficient transcriptional reprogramming during carbon starvation. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to a model promoter in vitro. Simulations showed that protonation of histidines within the SNF5 QLC lead to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that that pH changes are a second messenger for transcriptional reprogramming during carbon starvation, and that the SNF5 QLC acts as a pH-sensor

Provision of supplementary food for wild birds may increase the risk of local nest predation

In countries such as the UK, USA and Australia, approximately half of households provide supplementary food for wild birds, making this the public’s most common form of active engagement with nature. Year round supplementary feeding is currently encouraged by major conservation charities in the UK as it is thought to be of benefit to bird conservation. However, little is understood of how the provision of supplementary food affects the behaviour and ecology of target and non-target species. Given the scale of supplementary feeding, any negative effects may have important implications for conservation. Potential nest predators are abundant in urban areas and some species frequently visit supplementary feeding stations. We asked if providing supplementary food affected the likelihood of nest predation in the vicinity of the feeder, by acting as a point attractant for potential nest predators. We provided feeding stations (empty, peanut feeder, peanut feeder with guard to exclude potential nest predators) in an area of suburban parkland in the UK and monitored the predation rate experienced by eggs placed in artificial nests located at distances which replicate the size of typical suburban gardens. Nest predators (Magpies Pica pica, Grey Squirrels Sciurus carolinensis) were frequent visitors to filled feeders, and predation caused by Magpies, European Jays Garrulus glandarius and Grey Squirrels was significantly higher when nests were adjacent to filled feeders. The presence of a feeder guard did not significantly reduce nest predation. As supplementary feeding is becoming increasingly common during the breeding season in suburban habitats, we suggest that providing point attractants to nest predators at this time may have previously unconsidered consequences for the breeding success of urban birds

Leishmania-Induced Inactivation of the Macrophage Transcription Factor AP-1 Is Mediated by the Parasite Metalloprotease GP63

Leishmania parasites have evolved sophisticated mechanisms to subvert macrophage immune responses by altering the host cell signal transduction machinery, including inhibition of JAK/STAT signalling and other transcription factors such as AP-1, CREB and NF-κB. AP-1 regulates pro-inflammatory cytokines, chemokines and nitric oxide production. Herein we show that upon Leishmania infection, AP-1 activity within host cells is abolished and correlates with lower expression of 5 of the 7 AP-1 subunits. Of interest, c-Jun, the central component of AP-1, is cleaved by Leishmania. Furthermore, the cleavage of c-Jun is dependent on the expression and activity of the major Leishmania surface protease GP63. Immunoprecipitation of c-Jun from nuclear extracts showed that GP63 interacts, and cleaves c-Jun at the perinuclear area shortly after infection. Phagocytosis inhibition by cytochalasin D did not block c-Jun down-regulation, suggesting that internalization of the parasite might not be necessary to deliver GP63 molecules inside the host cell. This observation was corroborated by the maintenance of c-Jun cleavage upon incubation with L. mexicana culture supernatant, suggesting that secreted, soluble GP63 could use a phagocytosis-independent mechanism to enter the host cell. In support of this, disruption of macrophage lipid raft microdomains by Methyl β-Cyclodextrin (MβCD) partially inhibits the degradation of full length c-Jun. Together our results indicate a novel role of the surface protease GP63 in the Leishmania-mediated subversion of host AP-1 activity

Long interspersed nuclear element-1 expression and retrotransposition in prostate cancer cells

Abstract Background Long Interspersed Nuclear Element-1 (LINE-1) is an autonomous retrotransposon that generates new genomic insertions through the retrotransposition of a RNA intermediate. Expression of LINE-1 is tightly repressed in most somatic tissues to prevent DNA damage and ensure genomic integrity. However, the reactivation of LINE-1 has been documented in cancer and the role of LINE-1 protein expression and retrotransposition has become of interest in the development, progression, and adaptation of many epithelial neoplasms, including prostate cancer. Results Here, we examined endogenous LINE-1 protein expression and localization in a panel of prostate cancer cells and observed a diverse range of LINE-1 expression patterns between cell lines. Subcellular localization of LINE-1 proteins, ORF1p and ORF2p, revealed distinct expression patterns. ORF1p, a nucleic acid chaperone that binds LINE-1 mRNA, was predominantly expressed in the cytoplasm, with minor localization in the nucleus. ORF2p, containing endonuclease and reverse transcriptase domains, exhibited punctate foci in the nucleus and also displayed co-localization with PCNA and γH2AX. Using a retrotransposition reporter assay, we found variations in LINE-1 retrotransposition between cell lines. Conclusions Overall, our findings reveal new insight into the expression and retrotransposition of LINE-1 in prostate cancer. The prostate cancer cells we investigated provide a unique model for investigating endogenous LINE-1 activity and provide a functional model for studying LINE-1 mechanisms in prostate cancer

Additional file 3: Figure S2. of Long interspersed nuclear element-1 expression and retrotransposition in prostate cancer cells

High and low molecular weight regions surrounding ORF1 and ORF2 western blots. (.pdf) Entire length of western blots presented in Fig. 1b, showing ORF2 and ORF1 expression in cellular fractions. (PDF 329 kb

Additional file 2: Table S1. of Long interspersed nuclear element-1 expression and retrotransposition in prostate cancer cells

Molecular characteristics and origins of prostate cancer cell lines. (DOCX 43 kb

Additional file 1: Figure S1. of Long interspersed nuclear element-1 expression and retrotransposition in prostate cancer cells

Androgen receptor expression and full length of blots shown in Fig. 1a (.pdf) A) Western blot analysis of the androgen receptor (AR) in prostate cancer cell lines. Antibody against the AR recognized both full length (FL) and the V7 spliced variant. Tubulin was used as a loading control. B) High and low molecular weight regions surrounding ORF2 and ORF1. Overexposed images are from the same blot as shown in Fig. 1a. (PDF 2780 kb

nucGEMs probe the biophysical properties of the nucleoplasm

Abstract The cell interior is highly crowded and far from thermodynamic equilibrium. This environment can dramatically impact molecular motion and assembly, and therefore influence subcellular organization and biochemical reaction rates. These effects depend strongly on length-scale, with the least information available at the important mesoscale (10-100 nanometers), which corresponds to the size of crucial regulatory molecules such as RNA polymerase II. It has been challenging to study the mesoscale physical properties of the nucleoplasm because previous methods were labor-intensive and perturbative. Here, we report nuclear Genetically Encoded Multimeric nanoparticles (nucGEMs). Introduction of a single gene leads to continuous production and assembly of protein-based bright fluorescent nanoparticles of 40 nm diameter. We implemented nucGEMs in budding and fission yeast and in mammalian cell lines. We found differences in particle motility between the nucleus and the cytosol at the mesoscale, that mitotic chromosome condensation ejects nucGEMs from the nucleus, and that nucGEMs are excluded from heterochromatin and the nucleolus. nucGEMs enable hundreds of nuclear rheology experiments per hour, and allow evolutionary comparison of the physical properties of the cytosol and nucleoplasm

Excessive Cell Growth Causes Cytoplasm Dilution And Contributes to Senescence

Cell size varies greatly between cell types, yet within a specific cell type and growth condition, cell size is narrowly distributed. Why maintenance of a cell-type specific cell size is important remains poorly understood. Here we show that growing budding yeast and primary mammalian cells beyond a certain size impairs gene induction, cell-cycle progression, and cell signaling. These defects are due to the inability of large cells to scale nucleic acid and protein biosynthesis in accordance with cell volume increase, which effectively leads to cytoplasm dilution. We further show that loss of scaling beyond a certain critical size is due to DNA becoming limiting. Based on the observation that senescent cells are large and exhibit many of the phenotypes of large cells, we propose that the range of DNA:cytoplasm ratio that supports optimal cell function is limited and that ratios outside these bounds contribute to aging. Optimal cell function requires maintenance of a narrow range of DNA:cytoplasm ratios and when cell size exceeds this ratio cytoplasmic dilution contributes to senescenceNational Institutes of Health (Grant HD085866)National Institutes of Health (Grant 1U54CA217377