Rock geochemistry induces stress and starvation responses in the bacterial proteome

Interactions between microorganisms and rocks play an important role in Earth system processes. However, little is known about the molecular capabilities microorganisms require to live in rocky environments. Using a quantitative label‐free proteomics approach, we show that a model bacterium (Cupriavidus metallidurans CH34) can use volcanic rock to satisfy some elemental requirements, resulting in increased rates of cell division in both magnesium‐ and iron‐limited media. However, the rocks also introduced multiple new stresses via chemical changes associated with pH, elemental leaching and surface adsorption of nutrients that were reflected in the proteome. For example, the loss of bioavailable phosphorus was observed and resulted in the upregulation of diverse phosphate limitation proteins, which facilitate increase phosphate uptake and scavenging within the cell. Our results revealed that despite the provision of essential elements, rock chemistry drives complex metabolic reorganization within rock‐dwelling organisms, requiring tight regulation of cellular processes at the protein level. This study advances our ability to identify key microbial responses that enable life to persist in rock environments.     

Molecular mechanisms regulating formation,trafficking and processing of annular gap junctions

Internalization of gap junction plaques results in the formation of annular gap junction vesicles. The factors that regulate the coordinated internalization of the gap junction plaques to form annular gap junction vesicles, and the subsequent events involved in annular gap junction processing have only relatively recently been investigated in detail. However it is becoming clear that while annular gap junction vesicles have been demonstrated to be degraded by autophagosomal and endo-lysosomal pathways, they undergo a number of additional processing events. Here, we characterize the morphology of the annular gap junction vesicle and review the current knowledge of the processes involved in their formation, fission, fusion, and degradation. In addition, we address the possibility for connexin protein recycling back to the plasma membrane to contribute to gap junction formation and intercellular communication. Information on gap junction plaque removal from the plasma membrane and the subsequent processing of annular gap junction vesicles is critical to our understanding of cell-cell communication as it relates to events regulating development, cell homeostasis, unstable proliferation of cancer cells, wound healing, changes in the ischemic heart, and many other physiological and pathological cellular phenomena.     

A nuclear lamina‐chromatin‐Ran GTPase axis modulates nuclear import and DNA damage signaling

The Ran GTPase regulates nuclear import and export by controlling the assembly state of transport complexes. This involves the direct action of RanGTP, which is generated in the nucleus by the chromatin‐associated nucleotide exchange factor, RCC1. Ran interactions with RCC1 contribute to formation of a nuclear:cytoplasmic (N:C) Ran protein gradient in interphase cells. In previous work, we showed that the Ran protein gradient is disrupted in fibroblasts from Hutchinson–Gilford progeria syndrome (HGPS) patients. The Ran gradient disruption in these cells is caused by nuclear membrane association of a mutant form of Lamin A, which induces a global reduction in heterochromatin marked with Histone H3K9me3 and Histone H3K27me3. Here, we have tested the hypothesis that heterochromatin controls the Ran gradient. Chemical inhibition and depletion of the histone methyltransferases (HMTs) G9a and GLP in normal human fibroblasts reduced heterochromatin levels and caused disruption of the Ran gradient, comparable to that observed previously in HGPS fibroblasts. HMT inhibition caused a defect in nuclear localization of TPR, a high molecular weight protein that, owing to its large size, displays a Ran‐dependent import defect in HGPS. We reasoned that pathways dependent on nuclear import of large proteins might be compromised in HGPS. We found that nuclear import of ATM requires the Ran gradient, and disruption of the Ran gradient in HGPS causes a defect in generating nuclear γ‐H2AX in response to ionizing radiation. Our data suggest a lamina–chromatin–Ran axis is important for nuclear transport regulation and contributes to the DNA damage response.     

Divergent responses of Atlantic cod to ocean acidification and food limitation

In order to understand the effect of global change on marine fishes, it is imperative to quantify the effects on fundamental parameters such as survival and growth. Larval survival and recruitment of the Atlantic cod (Gadus morhua) were found to be heavily impaired by end‐of‐century levels of ocean acidification. Here, we analysed larval growth among 35–36 days old surviving larvae, along with organ development and ossification of the skeleton. We combined CO₂ treatments (ambient: 503 µatm, elevated: 1,179 µatm) with food availability in order to evaluate the effect of energy limitation in addition to the ocean acidification stressor. As expected, larval size (as a proxy for growth) and skeletogenesis were positively affected by high food availability. We found significant interactions between acidification and food availability. Larvae fed ad libitum showed little difference in growth and skeletogenesis due to the CO₂ treatment. Larvae under energy limitation were significantly larger and had further developed skeletal structures in the elevated CO₂ treatment compared to the ambient CO₂ treatment. However, the elevated CO₂ group revealed impairments in critically important organs, such as the liver, and had comparatively smaller functional gills indicating a mismatch between size and function. It is therefore likely that individual larvae that had survived acidification treatments will suffer from impairments later during ontogeny. Our study highlights important allocation trade‐off between growth and organ development, which is critically important to interpret acidification effects on early life stages of fish.     

Landscape and organismal factors affecting sagebrush‐seedling transplant survival after megafire restoration

Larger and more frequent disturbances are motivating efforts to accelerate recovery of foundational perennial species by focusing efforts into establishing island patches to sustain keystone species and facilitate recovery of the surrounding plant community. Evaluating the variability in abiotic and biotic factors that contribute to differences in survival and establishment can provide useful insight into the relative importance of these factors. In the western United States, severe degradation of the sagebrush steppe has motivated substantial efforts to restore native perennial cover, but success has been mixed. In this study, we evaluated survival of more than 3,000 sagebrush seedlings transplanted on 12 patches totaling 650 ha within a 113,000 ha burn area, and related the survival to organismal and subtaxonomic traits, and to landscape variables. Big sagebrush has high intraspecific diversity attributed to subspecies and cytotypes identifiable through ultraviolet (UV)‐induced fluorescence, length:width of leaves, or genome size (ploidy). Of these organismal traits, survival was related only to UV fluorescence, and then only so when landscape variables were excluded from analyses. The most significant landscape variable affecting survival was soil taxonomic subgroup, with much lower survival where buried restrictive layers reduce deep water infiltration. Survival also decreased with greater slope steepness, exotic annual grass cover, and burn severity. Survival was optimal where perennial bunchgrasses comprised 8–14% of total cover. These soil, topographic, and community condition factors revealed through monitoring of landscape‐level treatments can be used to explain the success of plantings and to strategically plan future restoration projects.     

Remodelling of the zero-stress state and residual strains in apoE-deficient mouse aorta

Atherosclerosis is the most frequent cause of death and severe chronic disability in North America and Europe. The atherosclerosis-prone apolipoprotein E (apoE)-deficient mice contain the entire spectrum of lesions observed during atherogenesis. Significant remodelling of the artery occurs in atherosclerosis. The aim was to study the remodelling of the zero-stress state of the aorta in apoE-deficient mice up to 56 weeks of age. Normal wild-type mice served as control groups. The mice were euthanised at ages 10, 28 and 56 weeks and tissue rings where excised from several locations along the aorta. The rings where photographed in the no-load state (without any external forces applied), then cut radially to obtain the zero-stress state and photographed again. The cross-sectional wall area and wall thickness increased over time in apoE-deficient mice compared to controls (P<0.001). The residual strains at the inner and outer surface varied as function of aortic location both in controls and apoE-deficient mice (P<0.001). From age 28 to age 56 weeks a gradual increase in positive strain at the outer surface and negative strain at the inner surface was found in the apoE-deficient mice when compared to age-matched control mice (P<0.001). Furthermore, the inner residual strain in the plaque location was significantly smaller than in the non-plaque location in the rings with atherosclerotic plaques (P<0.001). The change over time of the opening angle was especially pronounced in the aortic arch. The opening angle increased to app. 200 degrees in the aortic arch in apoE-deficient mice at 56 weeks of age whereas it in age-matched controls was app. 125 degrees. Correspondingly, atherosclerotic plaques were prominent in the apoE-deficient mice, especially at week 56 in the ascending aorta and the aortic arch. In conclusion, a pronounced remodelling of the biomechanical properties in aorta was found in apoE-deficient mice. The stress gradient across the vessel wall in the plaque region is likely larger in vivo due to the smaller residual strain in the plaque area.     

A molecular link between malaria and Epstein-Barr virus reactivation

Although malaria and Epstein-Barr (EBV) infection are recognized cofactors in the genesis of endemic Burkitt lymphoma (BL), their relative contribution is not understood. BL, the most common paediatric cancer in equatorial Africa, is a high-grade B cell lymphoma characterized by c-myc translocation. EBV is a ubiquitous B lymphotropic virus that persists in a latent state after primary infection, and in Africa, most children have sero-converted by 3 y of age. Malaria infection profoundly affects the B cell compartment, inducing polyclonal activation and hyper-gammaglobulinemia. We recently identified the cystein-rich inter-domain region 1alpha (CIDR1alpha) of the Plasmodium falciparum membrane protein 1 as a polyclonal B cell activator that preferentially activates the memory compartment, where EBV is known to persist. Here, we have addressed the mechanisms of interaction between CIDR1alpha and EBV in the context of B cells. We show that CIDR1alpha binds to the EBV-positive B cell line Akata and increases the number of cells switching to the viral lytic cycle as measured by green fluorescent protein (GFP) expression driven by a lytic promoter. The virus production in CIDR1alpha-exposed cultures was directly proportional to the number of GFP-positive Akata cells (lytic EBV) and to the increased expression of the EBV lytic promoter BZLF1. Furthermore, CIDR1alpha stimulated the production of EBV in peripheral blood mononuclear cells derived from healthy donors and children with BL. Our results suggest that P. falciparum antigens such as CIDR1alpha can directly induce EBV reactivation during malaria infection that may increase the risk of BL development for children living in malaria-endemic areas. To our knowledge, this is the first report to show that a microbial protein can drive a latently infected B cell into EBV replication.     

Experimental Test of Connector Rotation during DNA Packaging into Bacteriophage ϕ29 Capsids

The bacteriophage ϕ29 generates large forces to compact its double-stranded DNA genome into a protein capsid by means of a portal motor complex. Several mechanical models for the generation of these high forces by the motor complex predict coupling of DNA translocation to rotation of the head-tail connector dodecamer. Putative connector rotation is investigated here by combining the methods of single-molecule force spectroscopy with polarization-sensitive single-molecule fluorescence. In our experiment, we observe motor function in several packaging complexes in parallel using video microscopy of bead position in a magnetic trap. At the same time, we follow the orientation of single fluorophores attached to the portal motor connector. From our data, we can exclude connector rotation with greater than 99% probability and therefore answer a long-standing mechanistic question.