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Lipiński O, Sonani RR, Dubin G. Crystal structure of glycerol kinase from Trypanosoma cruzi, a potential molecular target in Chagas disease. Acta Crystallogr D Struct Biol 2024; 80:629-638. [PMID: 39052317 DOI: 10.1107/s2059798324006594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. It bears a significant global health burden with limited treatment options, thus calling for the development of new and effective drugs. Certain trypanosomal metabolic enzymes have been suggested to be druggable and valid for subsequent inhibition. In this study, the crystal structure of glycerol kinase from T. cruzi, a key enzyme in glycerol metabolism in this parasite, is presented. Structural analysis allowed a detailed description of the glycerol binding pocket, while comparative assessment pinpointed a potential regulatory site which may serve as a target for selective inhibition. These findings advance the understanding of glycerol metabolism in eukaryotes and provide a solid basis for the future treatment of Chagas disease.
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Affiliation(s)
- Oskar Lipiński
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ravi R Sonani
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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2
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Ashraf MZ, Mogilicherla K, Sellamuthu G, Siino V, Levander F, Roy A. Comparative gut proteomics study revealing adaptive physiology of Eurasian spruce bark beetle, Ips typographus (Coleoptera: Scolytinae). FRONTIERS IN PLANT SCIENCE 2023; 14:1157455. [PMID: 38078109 PMCID: PMC10703158 DOI: 10.3389/fpls.2023.1157455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/01/2023] [Indexed: 01/23/2024]
Abstract
The bark beetle, Ips typographus (L.), is a major pest of Norway spruce, Picea abies (L.), causing enormous economic losses globally. The adult stage of the I. typographus has a complex life cycle (callow and sclerotized); the callow beetles feed ferociously, whereas sclerotized male beetles are more aggressive and pioneers in establishing new colonies. We conducted a comparative proteomics study to understand male and female digestion and detoxification processes in callow and sclerotized beetles. Proteome profiling was performed using high-throughput liquid chromatography-mass spectrometry. A total of >3000 proteins were identified from the bark beetle gut, and among them, 539 were differentially abundant (fold change ±2, FDR <0.05) between callow and sclerotized beetles. The differentially abundant proteins (DAPs) mainly engage with binding, catalytic activity, anatomical activity, hydrolase activity, metabolic process, and carbohydrate metabolism, and hence may be crucial for growth, digestion, detoxification, and signalling. We validated selected DAPs with RT-qPCR. Gut enzymes such as NADPH-cytochrome P450 reductase (CYC), glutathione S-transferase (GST), and esterase (EST) play a crucial role in the I. typographus for detoxification and digesting of host allelochemicals. We conducted enzyme activity assays with them and observed a positive correlation of CYC and GST activities with the proteomic results, whereas EST activity was not fully correlated. Furthermore, our investigation revealed that callow beetles had an upregulation of proteins associated with juvenile hormone (JH) biosynthesis and chitin metabolism, whereas sclerotized beetles exhibited an upregulation of proteins linked to fatty acid metabolism and the TCA cycle. These distinctive patterns of protein regulation in metabolic and functional processes are specific to each developmental stage, underscoring the adaptive responses of I. typographicus in overcoming conifer defences and facilitating their survival. Taken together, it is the first gut proteomic study comparing males and females of callow and sclerotized I. typographus, shedding light on the adaptive ecology at the molecular level. Furthermore, the information about bark beetle handling of nutritionally limiting and defence-rich spruce phloem diet can be utilized to formulate RNAi-mediated beetle management.
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Affiliation(s)
- Muhammad Zubair Ashraf
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Kanakachari Mogilicherla
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Gothandapani Sellamuthu
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Valentina Siino
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, Lund, Sweden
| | - Amit Roy
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
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3
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Ren Z, Zhang H, Yu H, Zhu X, Lin J. Roles of four targets in the pathogenesis of graves' orbitopathy. Heliyon 2023; 9:e19250. [PMID: 37810014 PMCID: PMC10558314 DOI: 10.1016/j.heliyon.2023.e19250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/29/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023] Open
Abstract
Graves' orbitopathy (GO) is an autoimmune disease that involves complex immune systems. The mainstays of clinical management for this disease are surgery, targeted drugs therapy, and no-targeted drugs drug therapy. targeted drugs can improve therapeutic efficacy and enhance the quality of life for GO patients. However, as a second-line treatment for GO, targeted drugs such as tocilizumab and rituximab have very limited therapeutic effects and may be accompanied by side effects. The introduction of Teprotumumab, which targets IGF-IR, has made significant progress in the clinical management of GO. The pathophysiology of GO still remains uncertain as it involves a variety of immune cells and fibroblast interactions as well as immune responses to relevant disease targets of action. Therfore, learning more about immune response feedback pathways and potential targets of action will assist in the treatment of GO. In this discussion, we explore the pathogenesis of GO and relevant work, and highlight four potential targets for GO: Interleukin-23 receptor (IL-23 R), Leptin receptor (LepR), Orbital fibroblast activating factors, and Plasminogen activator inhibitor-1 (PAI-1). A deeper understanding of the pathogenesis of GO and the role of potential target signaling pathways is crucial for effective treatment of this disease.
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Affiliation(s)
- Ziqiang Ren
- College of Life Sciences, Yantai University, Shandong, China
- Fengjin Biomedical Co., Ltd, Shandong, China
| | - Hailing Zhang
- College of Life Sciences, Yantai University, Shandong, China
| | - Haiwen Yu
- College of Life Sciences, Yantai University, Shandong, China
| | - Xiqiang Zhu
- Fengjin Biomedical Co., Ltd, Shandong, China
| | - Jian Lin
- College of Life Sciences, Yantai University, Shandong, China
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4
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Haglund S, Söderman J, Almer S. Differences in Whole-Blood Transcriptional Profiles in Inflammatory Bowel Disease Patients Responding to Vedolizumab Compared with Non-Responders. Int J Mol Sci 2023; 24:ijms24065820. [PMID: 36982892 PMCID: PMC10052064 DOI: 10.3390/ijms24065820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Vedolizumab is efficacious in the treatment of Crohn's disease (CD) and ulcerative colitis (UC). However, a significant proportion of patients present with a non-response. To investigate whether differences in the clinical response to vedolizumab is reflected in changes in gene expression levels in whole blood, samples were collected at baseline before treatment, and at follow-up after 10-12 weeks. Whole genome transcriptional profiles were established by RNA sequencing. Before treatment, no differentially expressed genes were noted between responders (n = 9, UC 4, CD 5) and non-responders (n = 11, UC 3, CD 8). At follow-up, compared with baseline, responders displayed 201 differentially expressed genes, and 51 upregulated (e.g., translation initiation, mitochondrial translation, and peroxisomal membrane protein import) and 221 downregulated (e.g., Toll-like receptor activating cascades, and phagocytosis related) pathways. Twenty-two of the upregulated pathways in responders were instead downregulated in non-responders. The results correspond with a dampening of inflammatory activity in responders. Although considered a gut-specific drug, our study shows a considerable gene regulation in the blood of patients responding to vedolizumab. It also suggests that whole blood is not optimal for identifying predictive pre-treatment biomarkers based on individual genes. However, treatment outcomes may depend on several interacting genes, and our results indicate a possible potential of pathway analysis in predicting response to treatment, which merits further investigation.
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Affiliation(s)
- Sofie Haglund
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Laboratory Medicine, Region Jönköping County, 551 85 Jönköping, Sweden
| | - Jan Söderman
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Laboratory Medicine, Region Jönköping County, 551 85 Jönköping, Sweden
| | - Sven Almer
- IBD-Unit, Division of Gastroenterology, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Department of Medicine, Karolinska Institutet-Solna, 171 76 Stockholm, Sweden
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5
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Loscalzo G, Scheel J, Ibañez-Cabellos JS, García-Lopez E, Gupta S, García-Gimenez JL, Mena-Mollá S, Perales-Marín A, Morales-Roselló J. Overexpression of microRNAs miR-25-3p, miR-185-5p and miR-132-3p in Late Onset Fetal Growth Restriction, Validation of Results and Study of the Biochemical Pathways Involved. Int J Mol Sci 2021; 23:ijms23010293. [PMID: 35008715 PMCID: PMC8745308 DOI: 10.3390/ijms23010293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 11/27/2022] Open
Abstract
In a prospective study, 48 fetuses were evaluated with Doppler ultrasound after 34 weeks and classified, according to the cerebroplacental ratio (CPR) and estimated fetal weight (EFW), into fetuses with normal growth and fetuses with late-onset fetal growth restriction (LO-FGR). Overexpression of miRNAs from neonatal cord blood belonging to LO-FGR fetuses, was validated by real-time PCR. In addition, functional characterization of overexpressed miRNAs was performed by analyzing overrepresented pathways, gene ontologies, and prioritization of synergistically working miRNAs. Three miRNAs: miR-25-3p, miR-185-5p and miR-132-3p, were significantly overexpressed in cord blood of LO-FGR fetuses. Pathway and gene ontology analysis revealed over-representation of certain molecular pathways associated with cardiac development and neuron death. In addition, prioritization of synergistically working miRNAs highlighted the importance of miR-185-5p and miR-25-3p in cholesterol efflux and starvation responses associated with LO-FGR phenotypes. Evaluation of miR-25-3p; miR-132-3p and miR-185-5p might serve as molecular biomarkers for the diagnosis and management of LO-FGR; improving the understanding of its influence on adult disease.
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Affiliation(s)
- Gabriela Loscalzo
- Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.P.-M.); (J.M.-R.)
- Department of Obstetrics and Gynecology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Correspondence: (G.L.); (J.S.)
| | - Julia Scheel
- Department of Systems Biology and Bioinformatics, University Rostock, 18055 Rostock, Germany;
- Correspondence: (G.L.); (J.S.)
| | - José Santiago Ibañez-Cabellos
- EpiDisease S.L, Parc Científic, University of Valencia, 46980 Paterna, Spain; (J.S.I.-C.); (E.G.-L.); (J.L.G.-G.); (S.M.-M.)
- Consortium Center for Biomedical Network Research on Rare Diseases (CIBERER), Carrer d’Alvaro de Bazan, 10, 46010 Valencia, Spain
| | - Eva García-Lopez
- EpiDisease S.L, Parc Científic, University of Valencia, 46980 Paterna, Spain; (J.S.I.-C.); (E.G.-L.); (J.L.G.-G.); (S.M.-M.)
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University Rostock, 18055 Rostock, Germany;
| | - José Luis García-Gimenez
- EpiDisease S.L, Parc Científic, University of Valencia, 46980 Paterna, Spain; (J.S.I.-C.); (E.G.-L.); (J.L.G.-G.); (S.M.-M.)
- Consortium Center for Biomedical Network Research on Rare Diseases (CIBERER), Carrer d’Alvaro de Bazan, 10, 46010 Valencia, Spain
- Institute of Health Carlos III, Biomedical Research Institute INCLIVA, 46010 Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| | - Salvador Mena-Mollá
- EpiDisease S.L, Parc Científic, University of Valencia, 46980 Paterna, Spain; (J.S.I.-C.); (E.G.-L.); (J.L.G.-G.); (S.M.-M.)
- Institute of Health Carlos III, Biomedical Research Institute INCLIVA, 46010 Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| | - Alfredo Perales-Marín
- Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.P.-M.); (J.M.-R.)
- Department of Obstetrics and Gynecology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| | - José Morales-Roselló
- Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.P.-M.); (J.M.-R.)
- Department of Obstetrics and Gynecology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
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6
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Nahalka J. Theoretical Analysis of S, M and N Structural Proteins by the Protein-RNA Recognition Code Leads to Genes/proteins that Are Relevant to the SARS-CoV-2 Life Cycle and Pathogenesis. Front Genet 2021; 12:763995. [PMID: 34659373 PMCID: PMC8511677 DOI: 10.3389/fgene.2021.763995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022] Open
Abstract
In this conceptual review, based on the protein-RNA recognition code, some theoretical sequences were detected in the spike (S), membrane (M) and capsid (N) proteins that may post-transcriptionally regulate the host genes/proteins in immune homeostasis, pulmonary epithelial tissue homeostasis, and lipid homeostasis. According to the review of literature, the spectrum of identified genes/proteins shows that the virus promotes IL1α/β-IL1R1 signaling (type 1 immunity) and immunity defense against helminths and venoms (type 2 immunity). In the alteration of homeostasis in the pulmonary epithelial tissue, the virus blocks the function of cilia and the molecular programs that are involved in wound healing (EMT and MET). Additionally, the protein-RNA recognition method described here identifies compatible sequences in the S1A-domain for the post-transcriptional promotion of PIKFYVE, which is one of the critical factors for SARS-CoV-2 entry to the host cell, and for the post-transcriptional repression of xylulokinase XYLB. A decrease in XYLB product (Xu5P) in plasma was proposed as one of the potential metabolomics biomarkers of COVID-19. In summary, the protein-RNA recognition code leads to protein genes relevant to the SARS-CoV-2 life cycle and pathogenesis.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
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7
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Medarametla P, Kronenberger T, Laitinen T, Poso A. Structural Characterization of LsrK as a Quorum Sensing Target and a Comparison between X-ray and Homology Models. J Chem Inf Model 2021; 61:1346-1353. [PMID: 33683884 PMCID: PMC8028047 DOI: 10.1021/acs.jcim.0c01233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Quorum sensing is
being investigated as an alternative therapeutic
strategy in antibacterial drug discovery programs aimed at combatting
bacterial resistance. LsrK is an autoinducer-2 kinase (belongs to
the sugar kinase family), playing a key role in the phosphorylation
of the autoinducer-2 (AI-2) signaling molecules involved in quorum
sensing. Inhibiting LsrK could result in reduced pathogenicity by
interfering with quorum sensing signaling. Previously, we have generated
homology models to employ in structure-based virtual screening and
successfully identified the first class of LsrK inhibitors. While
conducting these studies, the crystal structure of LsrK was released,
providing us with an opportunity to evaluate the reliability and quality
of our models. A comparative structural analysis of the crystal structure
and homology models revealed consistencies among them in the overall
structural fold and binding site. Furthermore, the binding characteristics
and conformational changes of LsrK have been investigated using molecular
dynamics to inspect whether LsrK undergoes similar conformational
changes as that of sugar kinases. These studies revealed the flexibility
of the LsrK C-terminal domain (Domain II) attributing to the conformational
changes in LsrK resulting in open and closed states during the phosphorylation.
Further, simulations provided us with insights into the flexibility
of a loop in Domain I that can influence the ligand accessibility
to the LsrK binding site.
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Affiliation(s)
- Prasanthi Medarametla
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Thales Kronenberger
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.,Department of Oncology and Pneumonology, Internal Medicine, University Hospital Tübingen, Otfried-Müller-Straße 10, DE 72076 Tübingen, Germany
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.,Department of Oncology and Pneumonology, Internal Medicine, University Hospital Tübingen, Otfried-Müller-Straße 10, DE 72076 Tübingen, Germany
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Patterns of Lignocellulosic Sugar Assimilation and Lipid Production by Newly Isolated Yeast Strains From Chilean Valdivian Forest. Appl Biochem Biotechnol 2020; 192:1124-1146. [PMID: 32700200 DOI: 10.1007/s12010-020-03398-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/16/2020] [Indexed: 12/19/2022]
Abstract
Three yeast strains were isolated from decaying wood of Chilean Valdivian forest and identified as Meyerozyma guilliermondii, Scheffersomyces coipomensis, and Sugiyamaella paludigena. These strains were able to efficiently grow on the major monomers contained in Pinus spp. and Eucalyptus spp. wood that includes glucose (Glc), xylose (Xyl), and mannose (Man), showing at 28 °C higher uptake rates for Man, and in some cases for Glc, than for Xyl, used as single carbon sources. Nevertheless, in cultures performed on sugar mixtures, the strains displayed a notable preference for Glc. Additionally, in sugar mixtures, the absence of regulatory mechanisms in sugar assimilation (e.g., catabolic repression) was observed and documented when the activities of several enzymes involved in sugar assimilation (i.e., phosphoglucose isomerase, phosphomannose isomerase, and xylulokinase) were determined. The activity of the key enzymes involved in the onset of lipid accumulation (i.e., NAD+-ICDH) and in fatty acid (FA) biosynthesis (i.e., ATP:CL) indicated a significant accumulation of storage lipids (i.e., up to 24%, w/w) containing oleic and palmitic acids as the major components. The present paper is the first report on the potential of M. guilliermondii, S. coipomensis, and S. paludigena as oleaginous yeasts. We conclude that the new isolates, being able to simultaneously assimilate the major lignocellulosic sugars and efficiently convert them into oily biomass, present a biotechnological potential which deserve further investigation.
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Richmond PA, van der Kloet F, Vaz FM, Lin D, Uzozie A, Graham E, Kobor M, Mostafavi S, Moerland PD, Lange PF, van Kampen AHC, Wasserman WW, Engelen M, Kemp S, van Karnebeek CDM. Multi-Omic Approach to Identify Phenotypic Modifiers Underlying Cerebral Demyelination in X-Linked Adrenoleukodystrophy. Front Cell Dev Biol 2020; 8:520. [PMID: 32671069 PMCID: PMC7330173 DOI: 10.3389/fcell.2020.00520] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
X-linked adrenoleukodystrophy (ALD) is a peroxisomal metabolic disorder with a highly complex clinical presentation. ALD is caused by mutations in the ABCD1 gene, and is characterized by the accumulation of very long-chain fatty acids in plasma and tissues. Disease-causing mutations are 'loss of function' mutations, with no prognostic value with respect to the clinical outcome of an individual. All male patients with ALD develop spinal cord disease and a peripheral neuropathy in adulthood, although age of onset is highly variable. However, the lifetime prevalence to develop progressive white matter lesions, termed cerebral ALD (CALD), is only about 60%. Early identification of transition to CALD is critical since it can be halted by allogeneic hematopoietic stem cell therapy only in an early stage. The primary goal of this study is to identify molecular markers which may be prognostic of cerebral demyelination from a simple blood sample, with the hope that blood-based assays can replace the current protocols for diagnosis. We collected six well-characterized brother pairs affected by ALD and discordant for the presence of CALD and performed multi-omic profiling of blood samples including genome, epigenome, transcriptome, metabolome/lipidome, and proteome profiling. In our analysis we identify discordant genomic alleles present across all families as well as differentially abundant molecular features across the omics technologies. The analysis was focused on univariate modeling to discriminate the two phenotypic groups, but was unable to identify statistically significant candidate molecular markers. Our study highlights the issues caused by a large amount of inter-individual variation, and supports the emerging hypothesis that cerebral demyelination is a complex mix of environmental factors and/or heterogeneous genomic alleles. We confirm previous observations about the role of immune response, specifically auto-immunity and the potential role of PFN1 protein overabundance in CALD in a subset of the families. We envision our methodology as well as dataset has utility to the field for reproducing previous or enabling future modifier investigations.
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Affiliation(s)
- Phillip A. Richmond
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Frans van der Kloet
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Pediatrics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Frederic M. Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Clinical Chemistry, Amsterdam Gastroenterology & Metabolism, Amsterdam, Netherlands
| | - David Lin
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Anuli Uzozie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital, Vancouver, BC, Canada
| | - Emma Graham
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael Kobor
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Sara Mostafavi
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Philipp F. Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital, Vancouver, BC, Canada
| | - Antoine H. C. van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Wyeth W. Wasserman
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Marc Engelen
- Department of Pediatric Neurology, Amsterdam Neuroscience, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Neurology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Stephan Kemp
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Clinical Chemistry, Amsterdam Gastroenterology & Metabolism, Amsterdam, Netherlands
- Department of Pediatric Neurology, Amsterdam Neuroscience, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Clara D. M. van Karnebeek
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Pediatrics, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, Netherlands
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10
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Hardt N, Kind S, Schoenenberger B, Eggert T, Obkircher M, Wohlgemuth R. Facile synthesis of D-xylulose-5-phosphate and L-xylulose-5-phosphate by xylulokinase-catalyzed phosphorylation. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1630385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | | | | | | | | | - Roland Wohlgemuth
- Sigma-Aldrich/Merck KGaA, Buchs, Switzerland
- Institute of Technical Biochemistry, Technical University Lodz, Lodz, Poland
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11
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l-Arabinose induces d-galactose catabolism via the Leloir pathway in Aspergillus nidulans. Fungal Genet Biol 2018; 123:53-59. [PMID: 30496805 DOI: 10.1016/j.fgb.2018.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/03/2018] [Accepted: 11/25/2018] [Indexed: 11/22/2022]
Abstract
l-Arabinose and d-galactose are the principal constituents of l-arabinogalactan, and also co-occur in other hemicelluloses and pectins. In this work we hypothesized that similar to the induction of relevant glycoside hydrolases by monomers liberated from these plant heteropolymers, their respective catabolisms in saprophytic and phytopathogenic fungi may respond to the presence of the other sugar to promote synergistic use of the complex growth substrate. We showed that these two sugars are indeed consumed simultaneously by Aspergillus nidulans, while l-arabinose is utilised faster in the presence than in the absence of d-galactose. Furthermore, the first two genes of the Leloir pathway for d-galactose catabolism - encoding d-galactose 1-epimerase and galactokinase - are induced more rapidly by l-arabinose than by d-galactose eventhough deletion mutants thereof grow as well as a wild type strain on the pentose. d-Galactose 1-epimerase is hyperinduced by l-arabinose, d-xylose and l-arabitol but not by xylitol. The results suggest that in A. nidulans, l-arabinose and d-xylose - both requiring NADPH for their catabolisation - actively promote the enzyme infrastructure necessary to convert β-d-galactopyranose via the Leloir pathway with its α-anomer specific enzymes, into β-d-glucose-6-phosphate (the starting substrate of the oxidative part of the pentose phosphate pathway) even in the absence of d-galactose.
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12
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Abstract
It is important to understand if, and to what extent, the pig can utilize xylose as an energy source if xylanase releases free xylose in the small intestine. The experimental objectives were to determine the effects of industry-relevant dietary xylose concentrations and adaptation time on xylose retention efficiency and metabolism, diet digestibility and energy value, nitrogen balance, and hindgut fermentation. Forty-eight pigs were housed in metabolism crates and randomly assigned to one of four treatments with increasing D-xylose levels (n = 12/treatment) in 2 replications of a 22-d experiment with 3 collection periods. The control diet was xylose-free (0%), to which either 2, 4, or 8% D-xylose was added. Adaptation effects were assessed during three fecal and urine collection periods: d 5-7, 12-14, and 19-21. On d 22, pigs from the 0 and 8% treatments were euthanized; cecal and colon digesta were collected. Dietary xylose did not affect the total tract digestibility of dry matter, gross energy, or crude protein (P>0.10). Digesta short chain fatty acids concentrations and molar proportions and cecal pH were not different (P>0.10). This experiment utilized a targeted metabolomics approach to characterize and quantify urine xylose and metabolite excretion. Xylose retention decreased from 60% to 47% to 41% when pigs were fed diets containing 2, 4, or 8% xylose, respectively. In the 4 and 8% treatments, xylose retention was greater in the 2nd and 3rd collection periods compared to the 1st. A comprehensive pathway for xylose metabolism was proposed and D-threitol was confirmed as the major urinary metabolite of xylose. In conclusion, pigs can metabolize xylose, but with considerably lower efficiency than glucose, and may be able to adapt with time to utilize xylose more efficiently.
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Affiliation(s)
- Nichole F. Huntley
- Department of Animal Science, Iowa State University, Ames, IA, United States of America
| | - John F. Patience
- Department of Animal Science, Iowa State University, Ames, IA, United States of America
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Ha JH, Hauk P, Cho K, Eo Y, Ma X, Stephens K, Cha S, Jeong M, Suh JY, Sintim HO, Bentley WE, Ryu KS. Evidence of link between quorum sensing and sugar metabolism in Escherichia coli revealed via cocrystal structures of LsrK and HPr. SCIENCE ADVANCES 2018; 4:eaar7063. [PMID: 29868643 PMCID: PMC5983913 DOI: 10.1126/sciadv.aar7063] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/18/2018] [Indexed: 05/30/2023]
Abstract
Quorum sensing (QS), a bacterial process that regulates population-scale behavior, is mediated by small signaling molecules, called autoinducers (AIs), that are secreted and perceived, modulating a "collective" phenotype. Because the autoinducer AI-2 is secreted by a wide variety of bacterial species, its "perception" cues bacterial behavior. This response is mediated by the lsr (LuxS-regulated) operon that includes the AI-2 transporter LsrACDB and the kinase LsrK. We report that HPr, a phosphocarrier protein central to the sugar phosphotransferase system of Escherichia coli, copurifies with LsrK. Cocrystal structures of an LsrK/HPr complex were determined, and the effects of HPr and phosphorylated HPr on LsrK activity were assessed. LsrK activity is inhibited when bound to HPr, revealing new linkages between QS activity and sugar metabolism. These findings help shed new light on the abilities of bacteria to rapidly respond to changing nutrient levels at the population scale. They also suggest new means of manipulating QS activity among bacteria and within various niches.
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Affiliation(s)
- Jung-Hye Ha
- Protein Structure Research Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungcheongbuk-do 28119, South Korea
- Department of Bio-Analytical Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, South Korea
- New Drug Development Center, 80 Cheombok-ro, Dong-gu, Daegu-si 41061, South Korea
| | - Pricila Hauk
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Kun Cho
- Biomedical Omics Group, Korea Basic Science Institute, Chungcheongbuk-do 28119, South Korea
| | - Yumi Eo
- Protein Structure Research Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungcheongbuk-do 28119, South Korea
| | - Xiaochu Ma
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Kristina Stephens
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Soyoung Cha
- Protein Structure Research Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungcheongbuk-do 28119, South Korea
| | - Migyeong Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Herman O. Sintim
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Kyoung-Seok Ryu
- Protein Structure Research Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungcheongbuk-do 28119, South Korea
- Department of Bio-Analytical Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, South Korea
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Xie Y, Li M, Chang W. Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana. PLoS One 2016; 11:e0156067. [PMID: 27223615 PMCID: PMC4880283 DOI: 10.1371/journal.pone.0156067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/09/2016] [Indexed: 11/20/2022] Open
Abstract
The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. Sequence alignment suggests that both kinases belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. However, their exact physiological function and real substrates remain unknown. Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. The two kinases exhibit nearly identical overall architecture, with both kinases possessing ATP hydrolysis activity in the absence of substrates. In addition, our enzymatic assays suggested that SePSK has the capability to phosphorylate D-ribulose. In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. Using mutation and activity analysis, we further verified the key residues important for its catalytic activity. Moreover, our structural comparison with other family members suggests that there are major conformational changes in SePSK upon substrate binding, facilitating the catalytic process. Together, these results provide important information for a more detailed understanding of the cofactor and substrate binding mode as well as the catalytic mechanism of SePSK, and possible similarities with its plant homologue AtXK-1.
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Affiliation(s)
- Yuan Xie
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (WC); (ML)
| | - Wenrui Chang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (WC); (ML)
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Guimarães MC, Silla JM, da Cunha EFF, Ramalho TC, Freitas MP. Is the bioconformation of 5-deoxy-5-fluoro-d-xylulose affected by intramolecular hydrogen bonds? RSC Adv 2016. [DOI: 10.1039/c6ra23423b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
5-Deoxy-5-fluoro-d-xylulose (DFX) binds to the xylulokinase enzyme and, as a free ligand, it has preferential conformations governed by intramolecular interactions, such as hydrogen bonds and hyperconjugative interactions.
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Affiliation(s)
| | - Josué M. Silla
- Department of Chemistry
- Federal University of Lavras
- Lavras
- Brazil
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16
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Matheis N, Lantz M, Grus FH, Ponto KA, Wolters D, Brorson H, Planck T, Shahida B, Pitz S, Pfeiffer N, Kahaly GJ. Proteomics of Orbital Tissue in Thyroid-Associated Orbitopathy. J Clin Endocrinol Metab 2015; 100:E1523-30. [PMID: 26451909 DOI: 10.1210/jc.2015-2976] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
CONTEXT A potentially altered protein expression profile in orbital tissue from patients with thyroid-associated orbitopathy (TAO) is suspected. OBJECTIVE To detect for the first time changes in proteomic patterns of orbital connective tissue in TAO and compare these with control tissue using mass spectrometry. DESIGN Proteomics cross-sectional, comparative study. SETTING Two academic endocrine institutions. SAMPLES A total of 64 orbital and peripheral adipose tissue samples were collected from 39 patients with TAO and 25 control subjects. METHODS Samples were analyzed and identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technology. MAIN OUTCOME MEASURES Mean intensity values of all identified peptides per protein. RESULTS Thirty-one proteins were identified, of which 16 differentiated between controls and patients with TAO. Different protein patterns between orbital and peripheral adipose tissue were observed. Compared to controls, 10 proteins were markedly up-regulated (≥ 2-fold) in the orbital tissue of untreated patients: beta IV spectrin (6.2-fold), GTP binding G protein 2 (5.6-fold), POTE ankyrin domain family member F (5.4-fold), xylulokinase (4.1-fold), kinesin family member 1A and lipocalin 1 (both 3.6-fold), semicarbazide-sensitive metalloproteinase amine oxidase 3 and polymerase I transcript release factor (both 3.4-fold), cell-cycle protein elongin A binding protein 1 (3.3-fold), annexin A2 and cavin (both 3-fold), protein pointing to cell proliferation histone H4 (2.8-fold), and ADAM metallopeptidase with thrombospondin type 1 motif 14 (2.7-fold). The highest protein up-regulations were noted in the orbital tissue of medically untreated patients. Steroid therapy markedly reduced up-regulation of these proteins, foremost in nonsmokers. CONCLUSIONS Proteins involved in tissue inflammation, adipose tissue differentiation, lipid metabolism, and tissue remodeling were up-regulated in orbital tissue of untreated patients with TAO. Steroids decreased the expression of these proteins, whereas smoking attenuated such effect.
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Affiliation(s)
- N Matheis
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
| | - M Lantz
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
| | - F H Grus
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
| | - K A Ponto
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
| | - D Wolters
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
| | - H Brorson
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
| | - T Planck
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
| | - B Shahida
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
| | - S Pitz
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
| | - N Pfeiffer
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
| | - G J Kahaly
- Molecular Thyroid Research Laboratory (N.M., G.J.K.), Department of Medicine I, Experimental Ophthalmology (N.M., F.H.G., D.W.), and Department of Ophthalmology (F.H.G., K.A.P., S.P., N.P.), Johannes Gutenberg University Medical Center (J.G.U.), Mainz 55101, Germany; Departments of Endocrinology (M.L., T.P., B.S.) and Plastic Surgery (H.B.), Lund University, 221 00 Lund, Sweden; and Skåne University Hospital, 214 28 Malmö, Sweden
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Genome-Wide Association Study with Targeted and Non-targeted NMR Metabolomics Identifies 15 Novel Loci of Urinary Human Metabolic Individuality. PLoS Genet 2015; 11:e1005487. [PMID: 26352407 PMCID: PMC4564198 DOI: 10.1371/journal.pgen.1005487] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/06/2015] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies with metabolic traits (mGWAS) uncovered many genetic variants that influence human metabolism. These genetically influenced metabotypes (GIMs) contribute to our metabolic individuality, our capacity to respond to environmental challenges, and our susceptibility to specific diseases. While metabolic homeostasis in blood is a well investigated topic in large mGWAS with over 150 known loci, metabolic detoxification through urinary excretion has only been addressed by few small mGWAS with only 11 associated loci so far. Here we report the largest mGWAS to date, combining targeted and non-targeted 1H NMR analysis of urine samples from 3,861 participants of the SHIP-0 cohort and 1,691 subjects of the KORA F4 cohort. We identified and replicated 22 loci with significant associations with urinary traits, 15 of which are new (HIBCH, CPS1, AGXT, XYLB, TKT, ETNPPL, SLC6A19, DMGDH, SLC36A2, GLDC, SLC6A13, ACSM3, SLC5A11, PNMT, SLC13A3). Two-thirds of the urinary loci also have a metabolite association in blood. For all but one of the 6 loci where significant associations target the same metabolite in blood and urine, the genetic effects have the same direction in both fluids. In contrast, for the SLC5A11 locus, we found increased levels of myo-inositol in urine whereas mGWAS in blood reported decreased levels for the same genetic variant. This might indicate less effective re-absorption of myo-inositol in the kidneys of carriers. In summary, our study more than doubles the number of known loci that influence urinary phenotypes. It thus allows novel insights into the relationship between blood homeostasis and its regulation through excretion. The newly discovered loci also include variants previously linked to chronic kidney disease (CPS1, SLC6A13), pulmonary hypertension (CPS1), and ischemic stroke (XYLB). By establishing connections from gene to disease via metabolic traits our results provide novel hypotheses about molecular mechanisms involved in the etiology of diseases. Human metabolism is influenced by genetic and environmental factors defining a person’s metabolic individuality. This individuality is linked to personal differences in the ability to react on metabolic challenges and in the susceptibility to specific diseases. By investigating how common variants in genetic regions (loci) affect individual blood metabolite levels, the substantial contribution of genetic inheritance to metabolic individuality has been demonstrated previously. Meanwhile, more than 150 loci influencing metabolic homeostasis in blood are known. Here we shift the focus to genetic variants that modulate urinary metabolite excretion, for which only 11 loci were reported so far. In the largest genetic study on urinary metabolites to date, we identified 15 additional loci. Most of the 26 loci also affect blood metabolite levels. This shows that the metabolic individuality seen in blood is also reflected in urine, which is expected when urine is regarded as “diluted blood”. Nonetheless, we also found loci that appear to primarily influence metabolite excretion. For instance, we identified genetic variants near a gene of a transporter that change the capability for renal re-absorption of the transporter’s substrate. Thus, our findings could help to elucidate molecular mechanisms influencing kidney function and the body’s detoxification capabilities.
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18
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Karplus PA, Diederichs K. Assessing and maximizing data quality in macromolecular crystallography. Curr Opin Struct Biol 2015. [PMID: 26209821 DOI: 10.1016/j.sbi.2015.07.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The quality of macromolecular crystal structures depends, in part, on the quality and quantity of the data used to produce them. Here, we review recent shifts in our understanding of how to use data quality indicators to select a high resolution cutoff that leads to the best model, and of the potential to greatly increase data quality through the merging of multiple measurements from multiple passes of single crystals or from multiple crystals. Key factors supporting this shift are the introduction of more robust correlation coefficient based indicators of the precision of merged data sets as well as the recognition of the substantial useful information present in extensive amounts of data once considered too weak to be of value.
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Affiliation(s)
- P Andrew Karplus
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA.
| | - Kay Diederichs
- University of Konstanz, Faculty of Biology, Box 647, D-78457 Konstanz, Germany.
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19
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Komeda H, Yamasaki-Yashiki S, Hoshino K, Asano Y. Identification and characterization of D-xylulokinase from the D-xylose-fermenting fungus, Mucor circinelloides. FEMS Microbiol Lett 2014; 360:51-61. [PMID: 25163569 DOI: 10.1111/1574-6968.12589] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 11/29/2022] Open
Abstract
D-Xylulokinase catalyzes the phosphorylation of D-xylulose in the final step of the pentose catabolic pathway to form d-xylulose-5-phosphate. The D-xylulokinase activity was found to be induced by both D-xylose and L-arabinose, as well as some of the other enzymes involved in the pentose catabolism, in the D-xylose-fermenting zygomycetous fungus, Mucor circinelloides NBRC 4572. The putative gene, xyl3, which may encode D-xylulokinase, was detected in the genome sequence of this strain. The amino acid sequence deduced from the gene was more similar to D-xylulokinases from an animal origin than from other fungi. The recombinant enzyme was purified from the E. coli transformant expressing xyl3 and then characterized. The ATP-dependent phosphorylative activity of the enzyme was the highest toward D-xylulose. Its kinetic parameters were determined as Km (D-xylulose) = 0.29 mM and Km (ATP) = 0.51 mM, indicating that the xyl3 gene encoded D-xylulokinase (McXK). Western blot analysis revealed that McXK was induced by L-arabinose as well as D-xylose and the induction was repressed in the presence of D-glucose, suggesting that the enzyme may be involved in the catabolism of D-xylose and L-arabinose and is subject to carbon catabolite repression in this fungus. This is the first study on D-xylulokinase from zygomycetous fungi.
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Affiliation(s)
- Hidenobu Komeda
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan
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Wang J, Wing RA. Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data. ACTA ACUST UNITED AC 2014; 70:1491-7. [PMID: 24816117 DOI: 10.1107/s1399004714005318] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 03/07/2014] [Indexed: 11/11/2022]
Abstract
Overwhelming evidence exists to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps improve the refinement of atomic models by imposing strong constraints on individual and overall temperature B factors and thus the quality of crystal structures. Some researchers consider these data to be of little value and opt to discard them during data processing, particularly at medium and low resolution, at which individual B factors of atomic models cannot be refined. Here, new evidence is provided to show that the inclusion of these data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry (NCS) averaging. Using electron-density correlation coefficients as criteria, the resolution of data has successfully been extended from 3.1 to 2.5 Å resolution with redundancy-independent merging R factors from below 100% to about 310%. It is further demonstrated that phase information can be fully extracted from observed amplitudes through de novo NCS averaging. Averaging starts with uniform density inside double-shelled spherical masks and NCS matrices that are derived from bound heavy-atom clusters at the vertices of cuboctahedrally symmetric protein particles.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Richard A Wing
- Laboratory of Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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