Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors

AbstractThe electron-transport chains of Escherichia coli are composed of many different dehydrogenases and terminal reductases (or oxidases) which are linked by quinones (ubiquinone, menaquinone and demethylmenaquinone). Quinol:cytochrome c oxido-reductase (`bc1 complex') is not present. For various electron acceptors (O2, nitrate) and donors (formate, H2, NADH, glycerol-3-P) isoenzymes are present. The enzymes show great variability in membrane topology and energy conservation. Energy is conserved by conformational proton pumps, or by arrangement of substrate sites on opposite sides of the membrane resulting in charge separation. Depending on the enzymes and isoenzymes used, the H+/e− ratios are between 0 and 4 H+/e− for the overall chain. The expression of the terminal reductases is regulated by electron acceptors. O2 is the preferred electron acceptor and represses the terminal reductases of anaerobic respiration. In anaerobic respiration, nitrate represses other terminal reductases, such as fumarate or DMSO reductases. Energy conservation is maximal with O2 and lowest with fumarate. By this regulation pathways with high ATP or growth yields are favoured. The expression of the dehydrogenases is regulated by the electron acceptors, too. In aerobic growth, non-coupling dehydrogenases are expressed and used preferentially, whereas in fumarate or DMSO respiration coupling dehydrogenases are essential. Coupling and non-coupling isoenzymes are expressed correspondingly. Thus the rationale for expression of the dehydrogenases is not maximal energy yield, but could be maximal flux or growth rates. Nitrate regulation is effected by two-component signal transfer systems with membraneous nitrate/nitrite sensors (NarX, NarQ) and cytoplasmic response regulators (NarL, NarP) which communicate by protein phosphorylation. O2 regulates by a two-component regulatory system consisting of a membraneous sensor (ArcB) and a response regulator (ArcA). ArcA is the major regulator of aerobic metabolism and represses the genes of aerobic metabolism under anaerobic conditions. FNR is a cytoplasmic O2 responsive regulator with a sensory and a regulatory DNA-binding domain. FNR is the regulator of genes required for anaerobic respiration and related pathways. The binding sites of NarL, NarP, ArcA and FNR are characterized for various promoters. Most of the genes are regulated by more than one of the regulators, which can act in any combination and in a positive or negative mode. By this the hierarchical expression of the genes in response to the electron acceptors is achieved. FNR is located in the cytoplasm and contains a 4Fe4S cluster in the sensory domain. The regulatory concentrations of O2 are 1–5 mbar. Under these conditions O2 diffuses to the cytoplasm and is able to react directly with FNR without involvement of other specific enzymes or protein mediators. By oxidation of the FeS cluster, FNR is converted to the inactive state in a reversible process. Reductive activation could be achieved by cellular reductants in the absence of O2. In addition, O2 may cause destruction and loss of the FeS cluster. It is not known whether this process is required for regulation of FNR function

Identification of senescence and death in Emiliania huxleyi and Thalassiosira pseudonana: Cell staining, chlorophyll alterations, and dimethylsulfoniopropionate (DMSP) metabolism

We measured membrane permeability, hydrolytic enzyme, and caspase-like activities using fluorescent cell stains to document changes caused by nutrient exhaustion in the coccolithophore Emiliania huxleyi and the diatom Thalassiosira pseudonana, during batch-culture nutrient limitation. We related these changes to cell death, pigment alteration, and concentrations of dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) to assess the transformation of these compounds as cell physiological condition changes. E. huxleyi persisted for 1 month in stationary phase; in contrast, T. pseudonana cells rapidly declined within 10 d of nutrient depletion. T. pseudonana progressively lost membrane integrity and the ability to metabolize 5-chloromethylfluorescein diacetate (CMFDA; hydrolytic activity), whereas E. huxleyi developed two distinct CMFDA populations and retained membrane integrity (SYTOX Green). Caspase-like activity appeared higher in E. huxleyi than in T. pseudonana during the post-growth phase, despite a lack of apparent mortality and cell lysis. Photosynthetic pigment degradation and transformation occurred in both species after growth; chlorophyll a (Chl a) degradation was characterized by an increase in the ratio of methoxy Chl a : Chl a in T. pseudonana but not in E. huxleyi, and the increase in this ratio preceded loss of membrane integrity. Total DMSP declined in T. pseudonana during cell death and DMS increased. In contrast, and in the absence of cell death, total DMSP and DMS increased in E. huxleyi. Our data show a novel chlorophyll alteration product associated with T. pseudonana death, suggesting a promising approach to discriminate nonviable cells in nature

Tribology of particle suspensions in rolling-sliding soft contacts

We investigate the lubrication of microsphere suspensions between compliant substrates, and probe the influence of matrix viscosity, particle phase volume, surface roughness and wetting, and slide-to-roll ratio (SRR). In general, the suspensions behave as a continuum in the elastohydrodynamic regime provided the film thickness, which is predicted from the product of speed and viscosity, is greater than the particle diameter. Below this, the frictional response is characteristic of the mixed and boundary regimes. In the boundary regime, friction is independent of phase volume above 5% and it is governed by the rolling friction associated with particles being entrained into the contact that is independent of SRR, which is made possible by substrate deformation. This study provides a benchmark for soft-tribology and biotribology studies involving more complex particle suspensions and particle-containing soft materials

The impact of brief intensive trauma-focused treatment for PTSD on symptoms of borderline personality disorder

Objective: To investigate the effects of a brief, intensive, direct trauma-focused treatment programme for individuals with PTSD on BPD symptom severity. Methods: Individuals (n = 72) with severe PTSD (87.5% had one or more comorbidities; 52.8% fulfilled the criteria for the dissociative subtype of PTSD) due to multiple traumas (e.g. 90.3% sexual abuse) participated in an intensive eight-day trauma-focused treatment programme consisting of eye movement desensitization and reprocessing (EMDR) and prolonged exposure (PE) therapy, physical activity, and psychoeducation. Treatment did not include any form of stabilization (e.g. emotion regulation training) prior to trauma-focused therapy. Assessments took place at pre- and post-treatment (Borderline Symptom List, BSL-23; PTSD symptom severity, Clinician Administered PTSD Scale for DSM-5, CAPS-5), and across the eight treatment days (PTSD Checklist, PCL-5). Results: Treatment resulted in significant decreases of BPD symptoms (Cohen’s d = 0.70). Of the 35 patients with a positive screen for BPD at pre-treatment, 32.7% lost their positive screen at post-treatment. No adverse events nor dropouts occurred during the study time frame, and none of the patients experienced symptom deterioration in response to treatment. Conclusion: The results suggest that an intensive trauma-focused treatment is a feasible and safe treatment for PTSD patients with clinically elevated symptoms of BPD, and that BPD symptoms decrease along with the PTSD symptoms

Seroprevalence of HIV, hepatitis b, and hepatitis c among opioid drug users on methadone treatment in the netherlands

Background: Injecting drug users (IDU) remain an important population at risk for blood-borne infections such as human immunodeficiency virus (HIV), hepatitis B virus (HBV) and hepatitis C virus (HCV). In the Netherlands, a program is being implemented to offer annual voluntary screening for these infections to opioid drug users (ODUs) screened in methadone care. At two care sites where the program is now operating, our study aimed to estimate the seroprevalence among ODUs screened for HIV, HBV and HCV; to evaluate HBV vaccination coverage; and to assess the feasibility of monitoring seroprevalence trends by using routine annual screening data.Methods: Opioid drug users on methadone treatment are routinely offered voluntary screening for infectious diseases such as HIV, HBV and HCV. Data on uptake and outcome of anti-HIV, anti-HBc, and anti-HCV screening among ODUs receiving methadone were obtained from two regions: Amsterdam from 2004 to 2008 and Heerlen from 2003 to 2009.Findings: Annual screening uptake for HIV, HBV and HCV varied from 34 to 69%, depending on disease and screening site. Of users screened, 2.5% were HIV-positive in Amsterdam and 11% in Heerlen; 26% were HCV-positive in Amsterdam and 61% in Heerlen. Of those screened for HBV, evidence of current or previous infection (anti-HBc) was found among 33% in Amsterdam and 48% in Heerlen. In Amsterdam, 92% were fully vaccinated for HBV versus 45% in Heerlen.Conclusion: Annual screening for infectious diseases in all ODUs in methadone care is not fully implemented in the Netherlands. On average, more than half of the ODUs in methadone care in Heerlen and Amsterdam were screened for HIV, HBV and HCV. In addition, screening data indicate that HBV vaccination uptake was rather high. While the HIV prevalence among these ODUs was relatively low compared to other drug-using populations, the high HCV prevalence among this group underscores the need to expand annual screening and interventions to monitor HIV, HBV and HCV in the opioid drug-using population

Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.H.L. was supported by an Australian Research Council grant (DP150101875) awarded to M.A. R. and C.X.C. T.G.S. is supported by an Australian Government Research Training Program Scholarship. R.A.G.-P. is supported by an International Postgraduate Research Scholarship and a University of Queensland Centenary Scholarship. This project was supported by the computational resources of the Australian National Computational Infrastructure (NCI) National Facility systems through the NCI Merit Allocation Scheme (Project d85) awarded to M.A.R. and C.X.C. The data used in this project were funded by the Great Barrier Reef Foundation’s Resilient Coral Reefs Successfully Adapting to Climate Change research and development program in collaboration with the Australian Government, Bioplatforms Australia through the National Collaborative Research Infrastructure Strategy (NCRIS), Rio Tinto and a family foundation. The authors also acknowledge the work done by the Reef Future Genomics (ReFuGe) 2020 Consortium. Access to data generated by the consortium can be accessed via reefgenomics.org. In memory of S.F., our friend and colleague who is sorely missed

Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts

Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species’ responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure

Global Phylogenomic Assessment of \u3ci\u3eLeptoseris\u3c/i\u3e and \u3ci\u3eAgaricia\u3c/i\u3e Reveals Substantial Undescibed Diversity at Mesophotic Depths

Background: Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. Results: Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were consistently detected across different methods. Conclusions: The repeated observation of genetically divergent lineages associated with mesophotic depths highlights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted

Ensemble Modeling for Aromatic Production in Escherichia coli

Ensemble Modeling (EM) is a recently developed method for metabolic modeling, particularly for utilizing the effect of enzyme tuning data on the production of a specific compound to refine the model. This approach is used here to investigate the production of aromatic products in Escherichia coli. Instead of using dynamic metabolite data to fit a model, the EM approach uses phenotypic data (effects of enzyme overexpression or knockouts on the steady state production rate) to screen possible models. These data are routinely generated during strain design. An ensemble of models is constructed that all reach the same steady state and are based on the same mechanistic framework at the elementary reaction level. The behavior of the models spans the kinetics allowable by thermodynamics. Then by using existing data from the literature for the overexpression of genes coding for transketolase (Tkt), transaldolase (Tal), and phosphoenolpyruvate synthase (Pps) to screen the ensemble, we arrive at a set of models that properly describes the known enzyme overexpression phenotypes. This subset of models becomes more predictive as additional data are used to refine the models. The final ensemble of models demonstrates the characteristic of the cell that Tkt is the first rate controlling step, and correctly predicts that only after Tkt is overexpressed does an increase in Pps increase the production rate of aromatics. This work demonstrates that EM is able to capture the result of enzyme overexpression on aromatic producing bacteria by successfully utilizing routinely generated enzyme tuning data to guide model learning