Single-molecule in vivo imaging of bacterial respiratory complexes indicates delocalized oxidative phosphorylation

Chemiosmotic energy coupling through oxidative phosphorylation (OXPHOS) is crucial to life, requiring coordinated enzymes whose membrane organization and dynamics are poorly understood. We quantitatively explore localization, stoichiometry, and dynamics of key OXPHOS complexes, functionally fluorescent protein-tagged, in Escherichia coli using low-angle fluorescence and superresolution microscopy, applying single-molecule analysis and novel nanoscale co-localization measurements. Mobile 100–200 nm membrane domains containing tens to hundreds of complexes are indicated. Central to our results is that domains of different functional OXPHOS complexes do not co-localize, but ubiquinone diffusion in the membrane is rapid and long-range, consistent with a mobile carrier shuttling electrons between islands of different complexes. Our results categorically demonstrate that electron transport and proton circuitry in this model bacterium are spatially delocalized over the cell membrane, in stark contrast to mitochondrial bioenergetic supercomplexes. Different organisms use radically different strategies for OXPHOS membrane organization, likely depending on the stability of their environment.     

Chromatin regulation of virus infection

Cellular chromatin forms a dynamic structure that maintains the stability and accessibility of the host DNA genome. Viruses that enter and persist in the nucleus must, therefore, contend with the forces that drive chromatin formation and regulate chromatin structure. In some cases, cellular chromatin inhibits viral gene expression and replication by suppressing DNA accessibility. In other cases, cellular chromatin provides essential structure and organization to the viral genome and is necessary for successful completion of the viral life cycle. Consequently, viruses have acquired numerous mechanisms to manipulate cellular chromatin to ensure viral genome survival and propagation.     

The Nature of Evolutionary Radiations: A Case Study Involving Devonian Trilobites

Evolutionary radiations, times of profound diversification of species against a broader background of more muted evolutionary change, have long been considered one of the fundamental patterns in the fossil record. Further, given the important role geological, environmental, and climatic processes play in causing speciation, analyzing the biogeographic context of radiations can yield important insight into their evolutionary mechanisms. In this study we examine biogeographic patterns and quantify rates of speciation in a diverse group of Devonian trilobites, the calmoniids, that has been hailed as a classic paleontological example of an evolutionary radiation. In particular, a phylogenetic biogeographic analysis—modified Brooks Parsimony Analysis—was used to examine the processes and geographic setting of speciation within the group. Results indicate that the Malvinokaffric Realm was a geographically complex area, and this geographic complexity created various opportunities for speciation via geodispersal and vicariance that created the fuel that fed the speciation in these taxa. Part of the geographic complexity was created not only by the inherent geologic backdrop of the region, but the overlying changes of sea level rise and fall. Rates of speciation were highest when sea level was lowest. Low sea level encouraged isolation of faunas in different tectonic basins. By contrast, sea level rise facilitated range expansion and geodispersal to other distinct tectonic basins, and speciation rates concomitantly fell; however, the taxa with the expanded ranges were later fodder for diversification when sea level fell again. Here we present a view of evolutionary radiations driven fundamentally by external abiotic factors—geology and climate—that cause range expansion and opportunities for geographic isolation with resultant rapid speciation.     

THE COEVOLUTION OF HUMAN HANDS AND FEET

Human hands and feet have longer, more robust first digits, and shorter lateral digits compared to African apes. These similarities are often assumed to be independently evolved adaptations for manipulative activities and bipedalism, respectively. However, hands and feet are serially homologous structures that share virtually identical developmental blueprints, raising the possibility that digital proportions coevolved in human hands and feet because of underlying developmental linkages that increase phenotypic covariation between them. Here we show that phenotypic covariation between serially homologous fingers and toes in Homo and Pan is not only higher than expected, it also causes these digits to evolve along highly parallel trajectories under episodes of simulated directional selection, even when selection pressures push their means in divergent directions. Further, our estimates of the selection pressures required to produce human‐like fingers and toes from an African ape‐like ancestor indicate that selection on the toes was substantially stronger, and likely led to parallel phenotypic changes in the hands. Our data support the hypothesis that human hands and feet coevolved, and suggest that the evolution of long robust big toes and short lateral toes for bipedalism led to changes in hominin fingers that may have facilitated the emergence of stone tool technology.     

Molecular basis for antagonism between PDGF and the TGFβ family of signalling pathways by control of miR‐24 expression

Modulation of the vascular smooth‐muscle‐cell (vSMC) phenotype from a quiescent ‘contractile’ phenotype to a proliferative ‘synthetic’ phenotype has been implicated in vascular injury repair, as well as pathogenesis of vascular proliferative diseases. Both bone morphogenetic protein (BMP) and transforming growth factor‐β (TGFβ)‐signalling pathways promote a contractile phenotype, while the platelet‐derived growth factor‐BB (PDGF‐BB)‐signalling pathway promotes a switch to the synthetic phenotype. Here we show that PDGF‐BB induces microRNA‐24 (miR‐24), which in turn leads to downregulation of Tribbles‐like protein‐3 (Trb3). Repression of Trb3 coincides with reduced expression of Smad proteins and decrease in BMP and TGFβ signalling, promoting a synthetic phenotype in vSMCs. Inhibition of miR‐24 by antisense oligonuclotides abrogates the downregulation of Trb3 as well as pro‐synthetic activity of the PDGF‐signalling pathway. Thus, this study provides a molecular basis for the antagonism between the PDGF and TGFβ pathways, and its effect on the control of the vSMC phenotype.     

A novel peptide tag for detection and purification of recombinant expressed proteins

Peptide tags have proven useful for the detection and purification of recombinant proteins. However cross reactions of antibodies raised to the tag are frequently observed due to the presence of host proteins containing all or parts of the tag. In this report we have identified a unique viral peptide sequence, R-tag, that by blast searches is absent from the commonly expression hosts Arabidopsis thaliana, Escherichia coli, Pichia pastoris and mouse myeloma cell NSO. We have prepared monoclonal antibodies to this peptide and confirmed the absence of this peptide sequence from the above genomes by Western blotting. We have also modified protein expression vectors to incorporate this sequence as a fusion tag in expressed proteins and shown its use to successfully purify recombinant proteins by immunoaffinity procedures.     

Bmi-1 extends the life span of normal human oral keratinocytes by inhibiting the TGF-β signaling

We previously demonstrated that Bmi-1 extended the in vitro life span of normal human oral keratinocytes (NHOK). We now report that the prolonged life span of NHOK by Bmi-1 is, in part, due to inhibition of the TGF-β signaling pathway. Serial subculture of NHOK resulted in replicative senescence and terminal differentiation and activation of TGF-β signaling pathway. This was accompanied with enhanced intracellular and secreted TGF-β1 levels, phosphorylation of Smad2/3, and increased expression of p15^INK4B and p57^KIP2. An ectopic expression of Bmi-1 in NHOK (HOK/Bmi-1) decreased the level of intracellular and secreted TGF-β1 induced dephosphorylation of Smad2/3, and diminished the level of p15^INK4B and p57^KIP2. Moreover, Bmi-1 expression led to the inhibition of TGF-β-responsive promoter activity in a dose-specific manner. Knockdown of Bmi-1 in rapidly proliferating HOK/Bmi-1 and cancer cells increased the level of phosphorylated Smad2/3, p15^INK4B, and p57^KIP2. In addition, an exposure of senescent NHOK to TGF-β receptor I kinase inhibitor or anti-TGF-β antibody resulted in enhanced replicative potential of cells. Taken together, these data suggest that Bmi-1 suppresses senescence of cells by inhibiting the TGF-β signaling pathway in NHOK.     

Growth-stimulatory action of plasma membrane-associated growth factor. A synergistic effect with platelet-poor plasma

Growth factor activity was partially purified from mouse liver plasma membranes and its growth-stimulatory action on cultured mouse fibroblasts was studied. The plasma membrane-associated growth factor (PMGF) was unable to support the proliferation of mouse fibroblasts in monolayer when added as the sole source of growth factor. However, it stimulated the growth of fibroblasts in the presence of CM-Sephadex-treated human platelet-poor plasma (h-CMP) which by itself is not growth-stimulatory. The stimulation of DNA synthesis in quiescent fibroblasts was also observed upon the addition of PMGF and h-CMP. Under the same conditions, both platelet-derived growth factor (PDGF) and fibroblast growth factor (FGF) showed the same effect as did PMGF. The synergistic action of h-CMP with PMGF on quiescent cells was partially reproduced by insulin at microgram quantities or by insulin-like growth factor I(IGF-I) at nanogram quantities. Thus, the data presented here indicates that the action of PMGF is similar to that of the family of growth factors termed 'competence factor', and distinct from that of plasma growth factors termed 'progression factor'.