• A roadmap for global synthesis of the plant tree of life

      Eiserhardt, Wolf L.; Antonelli, Alexandre; Bennett, Dominic J.; Botigue, Laura R.; Burleigh, J. Gordon; Dodsworth, Steven; Enquist, Brian J.; Forest, Felix; Kim, Jan T.; Kozlov, Alexey M.; et al. (Wiley, 2018-03-31)
      Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.
    • Role of endogenous annexin-A1 in the regulation of thymocyte positive and negative selection

      Paschalidis, Nikolaos; Huggins, A.; Rowbotham, Nicola J.; Furmanski, Anna L.; Crompton, Tessa; Flower, R.J.; Perretti, M.; D'Acquisto, Fulvio; Queen Mary University of London (Taylor & Francis, 2010-02-15)
      We have recently shown that endogenous Annexin-A1 (AnxA1) plays a homeostatic regulatory role in mature T cells by modulating the strength of TCR signaling. In this study we investigated the role of endogenous AnxA1 in thymocyte maturation. Analysis of AnxA1(-/-) thymocyte populations at the immature CD4(-)CD8(-) double negative (DN) stage showed a proportional decrease in the DN1 and an increase in the DN3 subsets compared to control littermates. There were no significant differences in thymocyte numbers or proportions of CD4(+) and CD8(+) single positive (SP) populations between Anx1(-/-) and AnxA1(+/+) mice. However, when we crossed AnxA1(-/-) mice onto HY-TCR transgenic mice, we observed an increase in CD4(+)CD8(+) double positive (DP) and CD4 SP cells in male AnxA1(-/-)/HY-TCR compared to AnxA1(+/+)/HY-TCR. Conversely, female AnxA1(-/-)/HY-TCR mice showed an increase in DP and a decrease in CD8 (SP) cells compared to female AnxA1(+/+)/HY-TCR. Biochemical analysis of the signaling pathways responsible for these effects showed a decrease in anti-CD3-induced Erk phosphorylation and NFkappaB activation in AnxA1(-/-) thymocytes compared to control littermates. Together these findings demonstrate a role for endogenous AnxA1 in regulating both positive and negative selection of the TCR repertoire. These results suggest that targeting AnxA1 expression or function in T cells could represent a useful approach for the development of novel therapies for the treatment of autoimmune diseases.
    • Role of Hedgehog signalling at the transition from double-positive to single-positive thymocyte

      Furmanski, Anna L.; Saldana, Jose Ignacio; Rowbotham, Nicola J.; Ross, Susan; Crompton, Tessa (Wiley, 2011-11-21)
      In the thymus, developing T cells receive signals that determine lineage choice, specificity, MHC restriction and tolerance to self‐antigen. One way in which thymocytes receive instruction is by secretion of Sonic hedgehog (Shh) from thymic epithelial cells. We have previously shown that Hedgehog (Hh) signalling in the thymus decreases the CD4:CD8 single‐positive (SP) thymocyte ratio. Here, we present data indicating that double‐positive (DP) thymocytes are Hh‐responsive and that thymocyte‐intrinsic Hh signalling plays a role in modulating the production of CD4+ (SP4), CD8+ (SP8) and unconventional T‐cell subsets. Repression of physiological Hh signalling in thymocytes altered the proportions of DP and SP4 cells. Thymocyte‐intrinsic Hh‐dependent transcription also attenuated both the production of mature SP4 and SP8 cells, and the establishment of peripheral T‐cell compartments in TCR‐transgenic mice. Additionally, stimulation or withdrawal of Hh signals in the WT foetal thymus impaired or enhanced upregulation of the CD4 lineage‐specific transcription factor Gata3 respectively. These data together suggest that Hh signalling may play a role in influencing the later stages of thymocyte development.
    • The role of histone protein modifications and mutations in histone modifiers in pediatric b-cell progenitor acute lymphoblastic leukemia

      Janczar, Szymon; Janczar, Karolina; Pastorczak, Agata; Harb, Hani; Paige, Adam J.W.; Zalewska-Szewczyk, Beata; Danilewicz, Marian; Mlynarski, Wojciech; Medical University of Lodz; Philipps University Marburg; et al. (MDPI, 2017-01-03)
      While cancer has been long recognized as a disease of the genome, the importance of epigenetic mechanisms in neoplasia was acknowledged more recently. The most active epigenetic marks are DNA methylation and histone protein modifications and they are involved in basic biological phenomena in every cell. Their role in tumorigenesis is stressed by recent unbiased large-scale studies providing evidence that several epigenetic modifiers are recurrently mutated or frequently dysregulated in multiple cancers. The interest in epigenetic marks is especially due to the fact that they are potentially reversible and thus druggable. In B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) there is a relative paucity of reports on the role of histone protein modifications (acetylation, methylation, phosphorylation) as compared to acute myeloid leukemia, T-cell ALL, or other hematologic cancers, and in this setting chromatin modifications are relatively less well studied and reviewed than DNA methylation. In this paper, we discuss the biomarker associations and evidence for a driver role of dysregulated global and loci-specific histone marks, as well as mutations in epigenetic modifiers in BCP-ALL. Examples of chromatin modifiers recurrently mutated/disrupted in BCP-ALL and associated with disease outcomes include MLL1, CREBBP, NSD2, and SETD2. Altered histone marks and histone modifiers and readers may play a particular role in disease chemoresistance and relapse. We also suggest that epigenetic regulation of B-cell differentiation may have parallel roles in leukemogenesis.
    • The role of zinc in renal pathological changes in diabetic status

      Fernando, Julie; Zhou, Shaobo; University of Bedfordshire (OMICS International, 2015-06-13)
      Diabetes mellitus (DM) was the 8th leading cause of death in 2011, resulting in 1.4 million deaths worldwide. One of the complications of DM is chronic kidney disease, which accounts for nearly 44% of all new cases of kidney failure in the US in 2011. Zinc (Zn), an essential trace element, plays an important role in regulating carbohydrate metabolism. Several studies have shown the beneficial effects of Zn on renal pathological changes in Type 1 and Type 2 diabetic subjects, by reducing levels of oxidative stress, glomerular damage, and urinary albumin excretion after Zn supplementation. In contrast, other studies have shown little effects of Zn supplementation on renal damage. This paper reviewed recent research developments and found promising results of Zn in reducing, and in some cases, completely preventing renal damage. Nevertheless, the use of Zn as a potential treatment and especially its long-term impact against renal pathological symptoms in DM patients needs to be further studied.
    • Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization

      Lee, Yung-I; Yap, Jing Wei; Izan, Shairul; Leitch, Ilia J.; Fay, Michael F.; Lee, Yi-Ching; Hidalgo, Oriane; Dodsworth, Steven; Smulders, Marinus J.M.; Gravendeel, Barbara; et al. (BioMed Central Ltd., 2017-11-24)
      Background: Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA. Results: SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26–28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific. Conclusions: We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.
    • Separation and purification of the bovine milk fat globule membrane protein and its effect on improvement of C2C12 mouse skeletal muscle cell proliferation

      Li, He; Xu, Weili; Ma, Ying; Zhou, Shaobo; Harbin Institute of Technology; University of Bedfordshire (Royal Society of Chemistry, 2017-06-07)
      A novel method to improve the proliferation activity of C2C12 cells by the bovine milk fat globule membrane (MFGM) protein was established in this study. The MFGM protein was extracted and isolated into 4 fractions using an electric cream separator, and purified by a cellulose DEAE-52 column. Fraction 2 accounted for 57.8% of the total MFGM protein, and was used in the following study. The MTT assay showed that it induced cell proliferation activity, increased the cell survival rate and the cell number using flow cytometry and fluorescence microscopy analysis. There were only subtle changes in the morphology as observed using confocal scanning laser microscopy, but the number of mitochondria was significantly increased as observed using transmission electron microscopy analysis. Furthermore, the mRNA expression of MyoD, cyclin D1, p70S6K and mTOR was up-regulated as determined utilizing the quantitative real-time PCR assay, and the activation of Akt and mTOR phosphorylation was up regulated as determined using the Western blot assay. The main protein in fraction 2, assayed by 1-D gel electrophoresis and MALDI TOF-TOF, was identified as milk fat globule-EGF factor 8, the content was 65.6% of the total protein in fraction 2. The results elucidate a new molecular mechanism of the MFGM protein fraction 2: the activation of the Akt signal pathway in promoting cell proliferation.
    • Sequence-divergent units of the ABA-1 polyprotein array of the nematode Ascaris suum have similar fatty-acid- and retinol-binding properties but different binding-site environments

      Moore, Joyce; McDermott, Lindsay C.; Price, Nicholas C.; Kelly, Sharon M.; Cooper, Alan; Kennedy, Malcolm W. (Portland Press, 1999-05-15)
      Polyproteins comprise long polypeptides that are post-translationally cleaved into proteins of different function, or tandemly repetitive polypeptides which are processed into multiple versions of proteins which are presumed to have the same function. In the latter case the individual units of the polyprotein can differ substantially in sequence. Identity of function between the different units therefore cannot be assumed. Here we have examined the ABA-1 polyprotein allergen of the parasitic nematode Ascaris suum and found it to contain units which show a 50% difference in amino acid sequence. The parasite therefore produces at least two radically different forms of the allergen encoded within the polyprotein array. In fluorescence-based ligand-binding assays, recombinant polypeptides representing the two forms (designated ABA-1A1 and ABA-1B1) showed similar binding affinities for a range of fluorescent active-site probes [retinol, dansylundecanoic acid, dansyl-DL-alpha-amino-octanoic acid, cis-parinaric acid (cPnA)] and for the non-specific hydrophobic surface probe 8-anilinonaphthalene-1-sulphonic acid. However, the molecular environments in the active sites are markedly different, as indicated by disparate fluorescence emission peaks and intensities of bound probes. CD showed that the proteins have similar secondary structures but differ in susceptibility to chemical denaturation/unfolding by guanidinium chloride. Both retain a single conserved tryptophan residue in a characteristic non-polar environment, as revealed by extreme fluorescence blue shift. Thus the gross differences in sequence of the two proteins are not reflected in their ligand-binding specificities but in their binding-site environments.
    • Setting evolutionary-based conservation priorities for a phylogenetically data-poor taxonomic group (Scleractinia)

      Curnick, D.J.; Head, C.; Huang, D.; Crabbe, M. James C.; Gollock, M.; Hoeksema, B.; Johnson, K.G.; Jones, R.; Koldeway, H.J.; Obura, D.O.; et al. (Wiley, 2015-01-22)
      Given the current extinction crisis coupled with the shortfall in funding, there is a pressing need to establish species conservation priorities. The prioritization of phylogenetic diversity and evolutionary distinctiveness is one approach; however, taking such an approach requires more phylogenetic data than are currently available for most taxa. Here, we investigate the effects of increased phylogenetic knowledge on the accuracy of evolutionary distinctiveness (ED) scores over time using scleractinian corals as a case study. ED scores were calculated from four molecular-based phylogenies from 2008 to 2013, each one representing a chronological step of increased phylogenetic knowledge for scleractinian corals, finally resulting in a full species-level phylogeny which is used here as the reference dataset. As expected, the most complete and up-to-date phylogenies performed well at predicting scores taken from a recent, full-coverage species-level phylogeny of scleractinian corals. Surprisingly, however, older phylogenies and scores derived from expert opinion also performed well. More unexpectedly, the expert opinion-led scores, when used as a basis for imputing scores for missing species, achieved a close second in terms of prediction accuracy compared with the most recent and largest tree, which had nearly 10 times more taxonomic coverage. We recommend, once tested further, that ED score imputation be considered for assessing the conservation priorities for other poorly studied groups.
    • The solution structure of the complement deregulator FHR5 reveals a compact dimer and provides new insights into CFHR5 nephropathy

      Kadkhodayi-Kholghi, Nilufar; Gor, Jayesh; McDermott, Lindsay C.; Gale, Daniel P.; Perkins, Stephen J.; Bhatt, Jayesh S. (American Society for Biochemistry and Molecular Biology (United States), 2020-09-14)
      The human complement Factor H-related 5 protein (FHR5) antagonizes the main circulating complement regulator Factor H, resulting in the deregulation of complement activation. FHR5 normally contains nine short complement regulator (SCR) domains, but a FHR5 mutant has been identified with a duplicated N-terminal SCR-1/2 domain pair that causes CFHR5 nephropathy. To understand how this duplication causes disease, we characterized the solution structure of native FHR5 by analytical ultracentrifugation and small-angle X-ray scattering. Sedimentation velocity and Xray scattering indicated that FHR5 was dimeric, with a radius of gyration RG of 5.5 ± 0.2 nm and a maximum protein length of 20 nm for its 18 domains. This result indicated that FHR5 was even more compact than the main regulator Factor H which showed an overall length of 26-29 nm for its 20 SCR domains. Atomistic modelling for FHR5 generated a library of 250,000 physically-realistic trial arrangements of SCR domains for scattering curve fits. Only compact domain structures in this library fit well to the scattering data, and these structures readily accommodated the extra SCR-1/2 domain pair present in CFHR5 nephropathy. This model indicated that mutant FHR5 can form oligomers that possess additional binding sites for C3b in FHR5. We conclude that the deregulation of complement regulation by the FHR5 mutant can be rationalized by the enhanced binding of FHR5 oligomers to C3b deposited on host cell surfaces. Our FHR5 structures thus explained key features of the mechanism and pathology of CFHR5 nephropathy.
    • The solution structure of the human complement regulator CFHR5 reveals a compact dimeric structure by X-ray scattering and analytical ultracentrifugation

      Kadkhodayi-Kholghi, Nilufar; Gor, Jayesh; Ferlin, Anna; McDermott, Lindsay C.; Gale, Daniel P.; Perkins, Stephen J.; University College London; University of Bedfordshire (Elsevier, 2016-10-31)
    • Sonic hedgehog negatively regulates pre-TCR-induced differentiation by a Gli2-dependent mechanism

      Rowbotham, Nicola J.; Hager-Theodorides, Ariadne L.; Furmanski, Anna L.; Ross, Susan; Outram, Susan V.; Dessens, Johannes T.; Crompton, Tessa (American Society of Hematology, 2009-05-21)
      Hedgehog signaling regulates differentiation, survival, and proliferation of the earliest double-negative (DN) thymocytes, but its importance at later stages of T-cell development is controversial. Here we use loss- and gain-of-function mouse models to show that Shh, by signaling directly to the developing thymocyte, is a negative regulator of pre-TCR–induced differentiation from DN to double-positive (DP) cell. When hedgehog signaling was reduced, in the Shh−/− and Gli2−/− thymus, or by T lineage–specific transgenic expression of a transcriptional-repressor form of Gli2 (Gli2ΔC2), differentiation to DP cell after pre-TCR signal transduction was increased. In contrast, when Hh signaling was constitutively activated in thymocytes, by transgenic expression of a constitutive transcriptional-activator form of Gli2 (Gli2ΔN2), the production of DP cells was decreased. Gene expression profiling showed that physiologic Hh signaling in thymocytes maintains expression of the transcription factor FoxA2 on pre-TCR signal transduction.
    • Spatial genetic and epigenetic structure of Thlaspi arvense (field pennycress) in China

      Guan, Yabin; Qu, Peng; Lu, Shugang; Crabbe, M. James C.; Zhang, Ti-Cao; Geng, Yu-peng; Yunnan University; Oxford University; Shanxi University; University of Bedfordshire; et al. (Genetics Society of Japan, 2020-11-11)
      (Received 13 May 2020, accepted 15 July 2020; J-STAGE Advance published date: 11 November 2020) Thlaspi arvense (field pennycress) is widespread in temperate regions of the northern hemisphere. We estimated the genetic and epigenetic structure of eight T. arvense populations (131 individuals) in China using amplified fragment length polymorphism and methylation-sensitive amplified polymorphism molecularmarker techniques. We detected low diversity at both genetic (mean = 0.03; total = 0.07) and epigenetic (mean = 0.04; total = 0.07) levels, while significant genetic (FST = 0.42, P < 0.001) and epigenetic (FST = 0.32, P < 0.001) divergence was found across the distribution range. Using Mantel testing, we found spatial genetic and epigenetic differentiation, consistent with isolation-by-distance models. We also identified a strong correlation between genetic and epigenetic differentiation (r = 0.7438, P < 0.001), suggesting genetic control of the epigenetic variation. Our results indicate that mating system, natural selection and gene flow events jointly structure spatial patterns of genetic and epigenetic variation. Moreover, epigenetic variation may serve as a basis of natural selection and ecological evolution to enable species to adapt to heterogeneous habitats. Our study provides novel clues for the adaptation of T. arvense.
    • Spleen tyrosine kinase inhibition attenuates autoantibody production and reverses experimental autoimmune GN

      McAdoo, Stephen P.; Reynolds, John; Bhangal, Gurjeet; Smith, Jennifer; McDaid, John P.; Tanna, Anisha; Jackson, William D.; Masuda, Esteban S.; Cook, H. Terence; Pusey, Charles D.; et al. (American Society of Nephrology, 2014-10-31)
      Spleen tyrosine kinase (SYK) has an important role in immunoreceptor signaling, and SYK inhibition has accordingly attenuated immune-mediated injury in several in vivo models. However, the effect of SYK inhibition on autoantibody production remains unclear, and SYK inhibition has not been studied in an autoimmune model of renal disease. We, therefore, studied the effect of SYK inhibition in experimental autoimmune GN, a rodent model of antiglomerular basement membrane disease. We show glomerular SYK expression and activation by immunohistochemistry in both experimental and clinical disease, and we show that treatment with fostamatinib, a small molecule kinase inhibitor selective for SYK, completely prevents the induction of experimental autoimmune GN. In established experimental disease, introduction of fostamatinib treatment led to cessation of autoantibody production, reversal of renal injury, preservation of biochemical renal function, and complete protection from lung hemorrhage. B cell ELISpot and flow cytometric analysis suggest that short-term fostamatinib treatment inhibits the generation and activity of antigen-specific B cells without affecting overall B-cell survival. Additionally, fostamatinib inhibited proinflammatory cytokine production by nephritic glomeruli ex vivo and cultured bone marrow-derived macrophages in vitro, suggesting additional therapeutic effects independent of effects on autoantibody production that are likely related to inhibited Fc receptor signaling within macrophages in diseased glomeruli. Given these encouraging results in an in vivo model that is highly applicable to human disease, we believe clinical studies targeting SYK in GN are now warranted.
    • Stimulation of GLP-1 secretion downstream of the ligand-gated ion channel TRPA1

      Emery, Edward C.; Diakogiannaki, Eleftheria; Gentry, Clive; Psichas, Arianna; Habib, Abdella M.; Bevan, Stuart; Fischer, Michael J.M.; Reimann, Frank; Gribble, Fiona M.; ; et al. (American Diabetes Association Inc., 2014-10-16)
      Stimulus-coupled incretin secretion from enteroendocrine cells plays a fundamental role in glucose homeostasis and could be targeted for the treatment of type 2 diabetes. Here, we investigated the expression and function of transient receptor potential (TRP) ion channels in enteroendocrine L cells producing GLP-1. By microarray and quantitative PCR analysis, we identified trpa1 as an L cell-enriched transcript in the small intestine. Calcium imaging of primary L cells and the model cell line GLUTag revealed responses triggered by the TRPA1 agonists allyl-isothiocyanate (mustard oil), carvacrol, and polyunsaturated fatty acids, which were blocked by TRPA1 antagonists. Electrophysiology in GLUTag cells showed that carvacrol induced a current with characteristics typical of TRPA1 and triggered the firing of action potentials. TRPA1 activation caused an increase in GLP-1 secretion from primary murine intestinal cultures and GLUTag cells, an effect that was abolished in cultures from trpa1-/- mice or by pharmacological TRPA1 inhibition. These findings present TRPA1 as a novel sensory mechanism in enteroendocrine L cells, coupled to the facilitation of GLP-1 release, which may be exploitable as a target for treating diabetes.
    • Strong and weak zinc binding sites in human zinc-α2-glycoprotein

      Kumar, Aditya Arun; Hati, Debolina; Thaker, Thana'a Mohajer; Miah, Layeque; Cunningham, Phil; Domene, Carmen; Bui, Tam T. T.; Drake, Alex F.; McDermott, Lindsay C.; King's College London (Wiley, 2013-11-01)
      Zinc-α2-glycoprotein (ZAG) is an adipokine with an MHC class I-like protein fold. Even though zinc causes ZAG to precipitate from plasma during protein purification, no zinc binding has been identified to date. Using mass spectrometry, we demonstrated that ZAG contains one strongly bound zinc ion, predicted to lie close to the α1 and α2 helical groove. UV, CD and fluorescence spectroscopies detected weak zinc binding to holo-ZAG, which can bind up to 15 zinc ions. Zinc binding to 11-(dansylamino) undecanoic acid was enhanced by holo-ZAG. Zinc binding may be important for ZAG binding to fatty acids and the β-adrenergic receptor.
    • Structural and functional analysis of fatty acid-binding proteins

      Storch, Judith; McDermott, Lindsay C.; Rutgers University; King's College London (American Society for Biochemistry and Molecular Biology, 2009-04-30)
      The mammalian FA-binding proteins (FABPs) bind long-chain FA with high affinity. The large number of FABP types is suggestive of distinct functions in specific tissues. Multiple experimental approaches have shown that individual FABPs possess both unique and overlapping functions, some of which are based on specific elements in the protein structure. Although FA binding affinities for all FABPs tend to correlate directly with FA hydrophobicity, structure-function studies indicate that subtle three-dimensional changes that occur upon ligand binding may promote specific protein-protein or protein-membrane interactions that ultimately determine the function of each FABP. The conformational changes are focused in the FABP helical/portal domain, a region that was identified by in vitro studies to be vital for the FA transport properties of the FABPs. Thus, the FABPs modulate intracellular lipid homeostasis by regulating FA transport in the nuclear and extra-nuclear compartments of the cell; in so doing, they also impact systemic energy homeostasis.
    • Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations

      Glasser, Nathaniel R.; Oyala, Paul H.; Osborne, Thomas H.; Santini, Joanne M.; Newman, Dianne K. (National Academy of Sciences, 2018-08-13)
      Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we report the structure of an Arr complex (solved by X-ray crystallography to 1.6-Å resolution), which was enabled by an improved Arr expression method in the genetically tractable arsenate respirer Shewanella sp. ANA-3. We also obtained structures bound with the substrate arsenate (1.8 Å), the product arsenite (1.8 Å), and the natural inhibitor phosphate (1.7 Å). The structures reveal a conserved active-site motif that distinguishes Arr [(R/K)GRY] from the closely related arsenite respiratory oxidase (Arx) complex (XGRGWG). Arr activity assays using methyl viologen as the electron donor and arsenate as the electron acceptor display two-site ping-pong kinetics. A Mo(V) species was detected with EPR spectroscopy, which is typical for proteins with a pyranopterin guanine dinucleotide cofactor. Arr is an extraordinarily fast enzyme that approaches the diffusion limit (Km = 44.6 ± 1.6 μM, kcat = 9,810 ± 220 seconds-1), and phosphate is a competitive inhibitor of arsenate reduction (Ki = 325 ± 12 μM). These observations, combined with knowledge of typical sedimentary arsenate and phosphate concentrations and known rates of arsenate desorption from minerals in the presence of phosphate, suggest that (i) arsenate desorption limits microbiologically induced arsenate reductive mobilization and (ii) phosphate enhances arsenic mobility by stimulating arsenate desorption rather than by inhibiting it at the enzymatic level.
    • A surface-associated retinol- and fatty acid-binding protein (Gp-FAR-1) from the potato cyst nematode Globodera pallida: lipid binding activities, structural analysis and expression pattern

      Prior, Alison; Jones, John T.; Blok, Vivian C.; Beauchamp, Jeremy; McDermott, Lindsay C.; Cooper, Alan; Kennedy, Malcolm W.; Scottish Crop Research Institute; University of Glasgow (Portland Press, 2001-06-01)
      Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Here we describe a protein (Gp-FAR-1) from the plant-parasitic nematode Globodera pallida, which is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localizes to the surface of this species, placing it in a strategic position for interaction with the host. Recombinant Gp-FAR-1 was found to bind retinol, cis-parinaric acid and the fluorophore-tagged lipids 11-(dansylamino)undecanoic acid and dansyl-D,L-alpha-amino-octanoic acid. The fluorescence emission characteristics of the dansylated analogues indicated that the entire ligand enters the binding cavity. Fluorescence competition experiments showed that Gp-FAR-1 binds fatty acids in the range C(11) to C(24), with optimal binding at C(15). Intrinsic fluorescence analysis of a mutant protein into which a tryptophan residue had been inserted supported computer-based predictions of the position of this residue at the protein's interior and possibly also at the binding site. Of direct relevance to plant defence systems was the observation that Gp-FAR-1 binds two lipids (linolenic and linoleic acids) that are precursors of plant defence compounds and the jasmonic acid signalling pathway. Moreover, Gp-FAR-1 was found to inhibit the lipoxygenase-mediated modification of these substrates in vitro. Thus not only does Gp-FAR-1 function as a broad-spectrum retinol- and fatty-acid-binding protein, the results are consistent with the idea that Gp-FAR-1 is involved in the evasion of primary host plant defence systems.