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Dong G, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model 2014; 54:1687-99. [PMID: 24802635 PMCID: PMC4068255 DOI: 10.1021/ci5001554] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Indexed: 01/07/2023]
Abstract
Enzymes in the glutathione transferase (GST) superfamily catalyze the conjugation of glutathione (GSH) to electrophilic substrates. As a consequence they are involved in a number of key biological processes, including protection of cells against chemical damage, steroid and prostaglandin biosynthesis, tyrosine catabolism, and cell apoptosis. Although virtual screening has been used widely to discover substrates by docking potential noncovalent ligands into active site clefts of enzymes, docking has been rarely constrained by a covalent bond between the enzyme and ligand. In this study, we investigate the accuracy of docking poses and substrate discovery in the GST superfamily, by docking 6738 potential ligands from the KEGG and MetaCyc compound libraries into 14 representative GST enzymes with known structures and substrates using the PLOP program [ Jacobson Proteins 2004 , 55 , 351 ]. For X-ray structures as receptors, one of the top 3 ranked models is within 3 Å all-atom root mean square deviation (RMSD) of the native complex in 11 of the 14 cases; the enrichment LogAUC value is better than random in all cases, and better than 25 in 7 of 11 cases. For comparative models as receptors, near-native ligand-enzyme configurations are often sampled but difficult to rank highly. For models based on templates with the highest sequence identity, the enrichment LogAUC is better than 25 in 5 of 11 cases, not significantly different from the crystal structures. In conclusion, we show that covalent docking can be a useful tool for substrate discovery and point out specific challenges for future method improvement.
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Affiliation(s)
- Guang
Qiang Dong
- Department
of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical
Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco, California 94158, United States
| | - Sara Calhoun
- Department
of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical
Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco, California 94158, United States
| | - Hao Fan
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore SG 1386715
| | - Chakrapani Kalyanaraman
- Department
Pharmaceutical Chemistry, California Institute for Quantitative Biosciences
(QB3), University of California at San Francisco, San Francisco, California 94158, United States
| | - Megan C. Branch
- Departments
of Biochemistry and Chemistry, Center in Molecular Toxicology, and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232-0146, United States
| | - Susan T. Mashiyama
- Department
of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical
Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco, California 94158, United States
| | - Nir London
- Department
Pharmaceutical Chemistry, California Institute for Quantitative Biosciences
(QB3), University of California at San Francisco, San Francisco, California 94158, United States
| | - Matthew P. Jacobson
- Department
Pharmaceutical Chemistry, California Institute for Quantitative Biosciences
(QB3), University of California at San Francisco, San Francisco, California 94158, United States
| | - Patricia C. Babbitt
- Department
of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical
Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco, California 94158, United States
| | - Brian K. Shoichet
- Faculty
of Pharmacy, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1
| | - Richard N. Armstrong
- Departments
of Biochemistry and Chemistry, Center in Molecular Toxicology, and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232-0146, United States
| | - Andrej Sali
- Department
of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical
Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco, California 94158, United States
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Mashiyama ST, Malabanan MM, Akiva E, Bhosle R, Branch MC, Hillerich B, Jagessar K, Kim J, Patskovsky Y, Seidel RD, Stead M, Toro R, Vetting MW, Almo SC, Armstrong RN, Babbitt PC. Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PLoS Biol 2014; 12:e1001843. [PMID: 24756107 PMCID: PMC3995644 DOI: 10.1371/journal.pbio.1001843] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/14/2014] [Indexed: 12/11/2022] Open
Abstract
Global networks of the cytosolic glutathione S-transferases illuminate sequence-structure-function relationships across more than 13,000 members of this superfamily, including experimental confirmation of enzymatic activity for 82 members and new crystal structures for 27. The cytosolic glutathione transferase (cytGST) superfamily comprises more than 13,000 nonredundant sequences found throughout the biosphere. Their key roles in metabolism and defense against oxidative damage have led to thousands of studies over several decades. Despite this attention, little is known about the physiological reactions they catalyze and most of the substrates used to assay cytGSTs are synthetic compounds. A deeper understanding of relationships across the superfamily could provide new clues about their functions. To establish a foundation for expanded classification of cytGSTs, we generated similarity-based subgroupings for the entire superfamily. Using the resulting sequence similarity networks, we chose targets that broadly covered unknown functions and report here experimental results confirming GST-like activity for 82 of them, along with 37 new 3D structures determined for 27 targets. These new data, along with experimentally known GST reactions and structures reported in the literature, were painted onto the networks to generate a global view of their sequence-structure-function relationships. The results show how proteins of both known and unknown function relate to each other across the entire superfamily and reveal that the great majority of cytGSTs have not been experimentally characterized or annotated by canonical class. A mapping of taxonomic classes across the superfamily indicates that many taxa are represented in each subgroup and highlights challenges for classification of superfamily sequences into functionally relevant classes. Experimental determination of disulfide bond reductase activity in many diverse subgroups illustrate a theme common for many reaction types. Finally, sequence comparison between an enzyme that catalyzes a reductive dechlorination reaction relevant to bioremediation efforts with some of its closest homologs reveals differences among them likely to be associated with evolution of this unusual reaction. Interactive versions of the networks, associated with functional and other types of information, can be downloaded from the Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu). Cytosolic glutathione transferases (cytGSTs) are a large and diverse superfamily of enzymes that have important roles in metabolism and defense against oxidative damage. They have been studied for several decades but because of the synthetic nature of the chemicals used to test these proteins to determine if they have cytGST activity, little is known about the physiological reactions and roles of cytGSTs. In this large, collaborative study, we constructed networks where more than 13,000 cytGST sequences were grouped by sequence similarity and then used these networks to prioritize new targets for experimental characterization in relatively unexplored regions of the superfamily. We report here experimental results confirming GST-like activity for 82 of them, along with 37 new three-dimensional molecular structures determined for 27 targets. These new data, along with experimental data previously reported in the literature, were painted onto the networks to generate a global view of their sequence-structure-function relationships. The results show how proteins of both known and unknown function relate to each other across the entire superfamily and illuminate the complex ways in which their variations in sequence and structure affect our ability to predict unknown functional properties.
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Affiliation(s)
- Susan T. Mashiyama
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - M. Merced Malabanan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Rahul Bhosle
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Megan C. Branch
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Brandan Hillerich
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Kevin Jagessar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jungwook Kim
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yury Patskovsky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Ronald D. Seidel
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Mark Stead
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Rafael Toro
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Matthew W. Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (SCA); (RNA); (PCB)
| | - Richard N. Armstrong
- Departments of Biochemistry and Chemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail: (SCA); (RNA); (PCB)
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (SCA); (RNA); (PCB)
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Ndao M, Nath-Chowdhury M, Sajid M, Marcus V, Mashiyama ST, Sakanari J, Chow E, Mackey Z, Land KM, Jacobson MP, Kalyanaraman C, McKerrow JH, Arrowood MJ, Caffrey CR. A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection. Antimicrob Agents Chemother 2013; 57:6063-73. [PMID: 24060869 PMCID: PMC3837922 DOI: 10.1128/aac.00734-13] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 09/16/2013] [Indexed: 02/06/2023] Open
Abstract
Cryptosporidiosis, caused by the protozoan parasite Cryptosporidium parvum, can stunt infant growth and can be lethal in immunocompromised individuals. The most widely used drugs for treating cryptosporidiosis are nitazoxanide and paromomycin, although both exhibit limited efficacy. To investigate an alternative approach to therapy, we demonstrate that the clan CA cysteine protease inhibitor N-methyl piperazine-Phe-homoPhe-vinylsulfone phenyl (K11777) inhibits C. parvum growth in mammalian cell lines in a concentration-dependent manner. Further, using the C57BL/6 gamma interferon receptor knockout (IFN-γR-KO) mouse model, which is highly susceptible to C. parvum, oral or intraperitoneal treatment with K11777 for 10 days rescued mice from otherwise lethal infections. Histologic examination of untreated mice showed intestinal inflammation, villous blunting, and abundant intracellular parasite stages. In contrast, K11777-treated mice (210 mg/kg of body weight/day) showed only minimal inflammation and no epithelial changes. Three putative protease targets (termed cryptopains 1 to 3, or CpaCATL-1, -2, and -3) were identified in the C. parvum genome, but only two are transcribed in infected mammals. A homology model predicted that K11777 would bind to cryptopain 1. Recombinant enzymatically active cryptopain 1 was successfully targeted by K11777 in a competition assay with a labeled active-site-directed probe. K11777 exhibited no toxicity in vitro and in vivo, and surviving animals remained free of parasites 3 weeks after treatment. The discovery that a cysteine protease inhibitor provides potent anticryptosporidial activity in an animal model of infection encourages the investigation and development of this biocide class as a new, and urgently needed, chemotherapy for cryptosporidiosis.
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Affiliation(s)
- Momar Ndao
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Milli Nath-Chowdhury
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Mohammed Sajid
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
- Leiden University Medical Center, Leiden, Netherlands
| | - Victoria Marcus
- Department of Pathology, McGill University Health Centre, Montreal General Hospital, Montreal, Canada
| | - Susan T. Mashiyama
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Judy Sakanari
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
| | - Eric Chow
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
| | - Zachary Mackey
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
| | - Kirkwood M. Land
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
- Department of Biological Sciences, University of the Pacific, Stockton, California, USA
| | - Matthew P. Jacobson
- Departments of Pharmaceutical Sciences
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Chakrapani Kalyanaraman
- Departments of Pharmaceutical Sciences
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - James H. McKerrow
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
| | - Michael J. Arrowood
- Division of Parasitic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
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Akiva E, Brown S, Almonacid DE, Barber AE, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC. The Structure-Function Linkage Database. Nucleic Acids Res 2013; 42:D521-30. [PMID: 24271399 PMCID: PMC3965090 DOI: 10.1093/nar/gkt1130] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Structure–Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies ‘look alike’, making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity.
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Affiliation(s)
- Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Santiago 8370146, Chile, Nodality, Inc., South San Francisco, CA 94080, USA, Department of Electrical and Computer Engineering, College of Engineering, Boston University, Boston, MA 02215, USA, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA, Center for Bioinformatics (ZBH), University of Hamburg, Hamburg 20146, Germany, Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA, UC Berkeley - UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94158 and Berkeley, CA 94720, USA and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
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Mashiyama ST, Koupparis K, Caffrey CR, McKerrow JH, Babbitt PC. A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets. PLoS Negl Trop Dis 2012; 6:e1942. [PMID: 23236535 PMCID: PMC3516576 DOI: 10.1371/journal.pntd.0001942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/23/2012] [Indexed: 01/26/2023] Open
Abstract
We performed a genome-level computational study of sequence and structure similarity, the latter using crystal structures and models, of the proteases of Homo sapiens and the human parasite Trypanosoma brucei. Using sequence and structure similarity networks to summarize the results, we constructed global views that show visually the relative abundance and variety of proteases in the degradome landscapes of these two species, and provide insights into evolutionary relationships between proteases. The results also indicate how broadly these sequence sets are covered by three-dimensional structures. These views facilitate cross-species comparisons and offer clues for drug design from knowledge about the sequences and structures of potential drug targets and their homologs. Two protease groups (“M32” and “C51”) that are very different in sequence from human proteases are examined in structural detail, illustrating the application of this global approach in mining new pathogen genomes for potential drug targets. Based on our analyses, a human ACE2 inhibitor was selected for experimental testing on one of these parasite proteases, TbM32, and was shown to inhibit it. These sequence and structure data, along with interactive versions of the protein similarity networks generated in this study, are available at http://babbittlab.ucsf.edu/resources.html. Human African trypanosomiasis (HAT) is caused by the protozoan parasite Trypanosoma brucei. HAT is fatal unless treated, yet the current treatment itself can cause death. New treatments are urgently needed. Our study focuses on proteases, which are enzymes that break down proteins. Because of their roles in many centrally important biological processes, proteases are targets for drugs to treat a variety of diseases including parasite infection. The recent explosion of protein sequence and structure information in public databases has made surveys of proteins on a genomic scale possible. However, collecting specific data of interest from diverse databases and synthesizing them in a way that is easy to interpret can be difficult. We used T. brucei and human protease sequences, crystal structures, and models to create network views that show how proteases cluster by similarity. Such views are valuable not only for understanding the evolution of the protein repertoire in each species, but also can give important clues for drug design. Two T. brucei protease groups (“M32” and “C51”) that are very different in sequence from human proteases were examined in structural detail. Based on our analyses, a human ACE2 inhibitor was selected for experimental testing on one of these parasite proteases, TbM32, and was shown to inhibit it.
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Affiliation(s)
- Susan T. Mashiyama
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biomedical Research (QB3), University of California San Francisco, San Francisco, California, United States of America
- Center for Discovery and Innovation in Parasitic Diseases, and Department of Pathology, QB3, University of California San Francisco, San Francisco, California, United States of America
| | - Kyriacos Koupparis
- Center for Discovery and Innovation in Parasitic Diseases, and Department of Pathology, QB3, University of California San Francisco, San Francisco, California, United States of America
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, and Department of Pathology, QB3, University of California San Francisco, San Francisco, California, United States of America
| | - James H. McKerrow
- Center for Discovery and Innovation in Parasitic Diseases, and Department of Pathology, QB3, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (JHM); (PCB)
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biomedical Research (QB3), University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (JHM); (PCB)
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Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, Coulson R, Day TA, Delcher A, DeMarco R, Djikeng A, Eyre T, Gamble JA, Ghedin E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D, Macedo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ, Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR, White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell BG, El-Sayed NM. The genome of the blood fluke Schistosoma mansoni. Nature 2009; 460:352-8. [PMID: 19606141 PMCID: PMC2756445 DOI: 10.1038/nature08160] [Citation(s) in RCA: 801] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2009] [Accepted: 05/22/2009] [Indexed: 11/24/2022]
Abstract
Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. We report here analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and novel families of micro-exon genes that undergo frequent alternate splicing. As the first sequenced flatworm, and a representative of the lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, while the identification of membrane receptors, ion channels and more than 300 proteases, provide new insights into the biology of the life cycle and novel targets. Bioinformatics approaches have identified metabolic chokepoints while a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.
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Dvorák J, Mashiyama ST, Sajid M, Braschi S, Delcroix M, Schneider EL, McKerrow WH, Bahgat M, Hansell E, Babbitt PC, Craik CS, McKerrow JH, Caffrey CR. SmCL3, a gastrodermal cysteine protease of the human blood fluke Schistosoma mansoni. PLoS Negl Trop Dis 2009; 3:e449. [PMID: 19488406 PMCID: PMC2685030 DOI: 10.1371/journal.pntd.0000449] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Accepted: 05/01/2009] [Indexed: 12/23/2022] Open
Abstract
Background Blood flukes of the genus Schistosoma are platyhelminth parasites that infect 200 million people worldwide. Digestion of nutrients from the host bloodstream is essential for parasite development and reproduction. A network of proteolytic enzymes (proteases) facilitates hydrolysis of host hemoglobin and serum proteins. Methodology/Principal Findings We identified a new cathepsin L termed SmCL3 using PCR strategies based on S. mansoni EST sequence data. An ortholog is present in Schistosoma japonicum. SmCL3 was heterologously expressed as an active enzyme in the yeast, Pichia pastoris. Recombinant SmCL3 has a broad pH activity range against peptidyl substrates and is inhibited by Clan CA protease inhibitors. Consistent with a function in degrading host proteins, SmCL3 hydrolyzes serum albumin and hemoglobin, is localized to the adult gastrodermis, and is expressed mainly in those life stages infecting the mammalian host. The predominant form of SmCL3 in the parasite exists as a zymogen, which is unusual for proteases. This zymogen includes an unusually long prodomain with alpha helical secondary structure motifs. The striking specificity of SmCL3 for amino acids with large aromatic side chains (Trp and Tyr) at the P2 substrate position, as determined with positional scanning-synthetic combinatorial library, is consistent with a molecular model that shows a large and deep S2 pocket. A sequence similarity network (SSN) view clusters SmCL3 and other cathepsins L in accordance with previous large-scale phylogenetic analyses that identify six super kingdoms. Conclusions/Significance SmCL3 is a gut-associated cathepsin L that may contribute to the network of proteases involved in degrading host blood proteins as nutrients. Furthermore, this enzyme exhibits some unusual sequence and biophysical features that may result in additional functions. The visualization of network inter-relationships among cathepsins L suggests that these enzymes are suitable ‘marker sequences’ for inclusion in future phylogenetic analyses. Parasitic infection caused by blood flukes of the genus Schistosoma is a major global health problem. More than 200 million people are infected. Identifying and characterizing the constituent enzymes of the parasite's biochemical pathways should reveal opportunities for developing new therapies (i.e., vaccines, drugs). Schistosomes feed on host blood, and a number of proteolytic enzymes (proteases) contribute to this process. We have identified and characterized a new protease, SmCL3 (for Schistosoma mansoni cathepsin L3), that is found within the gut tissue of the parasite. We have employed various biochemical and molecular biological methods and sequence similarity analyses to characterize SmCL3 and obtain insights into its possible functions in the parasite, as well as its evolutionary position among cathepsin L proteases in general. SmCL3 hydrolyzes major host blood proteins (serum albumin and hemoglobin) and is expressed in parasite life stages infecting the mammalian host. Enzyme substrate specificity detected by positional scanning-synthetic combinatorial library was confirmed by molecular modeling. A sequence analysis placed SmCL3 to the cluster of other cathepsins L in accordance with previous phylogenetic analyses.
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Affiliation(s)
- Jan Dvorák
- Sandler Center for Basic Research in Parasitic Diseases, California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America.
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Dvořák J, Mashiyama ST, Braschi S, Sajid M, Knudsen GM, Hansell E, Lim KC, Hsieh I, Bahgat M, Mackenzie B, Medzihradszky KF, Babbitt PC, Caffrey CR, McKerrow JH. Differential use of protease families for invasion by schistosome cercariae. Biochimie 2008; 90:345-58. [DOI: 10.1016/j.biochi.2007.08.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2007] [Accepted: 08/30/2007] [Indexed: 10/22/2022]
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Mashiyama ST, Hansen CM, Roitman E, Sarmiento S, Leklem JE, Shultz TD, Ames BN. An assay for uracil in human DNA at baseline: effect of marginal vitamin B6 deficiency. Anal Biochem 2008; 372:21-31. [PMID: 17963712 PMCID: PMC2175266 DOI: 10.1016/j.ab.2007.08.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Revised: 08/25/2007] [Accepted: 08/27/2007] [Indexed: 11/21/2022]
Abstract
Improvements are made to our gas-chromatography-mass-spectrometry-based assay for quantifying low levels of DNA-uracil. Folate deficiency leads to increased deoxyuridine monophosphate/thymidylate (dUMP/dTMP) ratios and uracil misincorporation into DNA, which may increase cancer risk. Vitamin B6 (B6) deficiency might also result in increased DNA-uracil because B6 is a cofactor for serine hydroxymethyltransferase, which catalyzes the methylation of tetrahydrofolate (THF) to methylene-THF, the folate form that is required to convert dUMP to dTMP. However, the low baseline levels of DNA-uracil in healthy human lymphocytes are difficult to measure accurately. This version of the assay (Uracil assay V3) has an approximately 10-fold increase in signal strength over the previous method and a 10-fold lower detection limit (0.2 pg uracil). Five micrograms of DNA, the amount in about 1 ml of human blood, is a suitable amount for this assay. Using this improved assay, DNA-uracil was measured in lymphocytes from 12 healthy smoking or nonsmoking young men and women who consumed a B6-restricted diet (0.7 mg B6/day, or approximately half the recommended dietary allowance) for 28 days. DNA-uracil concentration was not significantly related to B6 status or smoking. More severe and/or prolonged B6 deficiency may be necessary to detect significant changes in DNA-uracil in humans. The average concentration of DNA-uracil in these subjects was found to be approximately 3,000 uracils per diploid lymphocyte, which is comparable to steady state levels of one of the oxidative adducts of DNA, 8-oxoguanine.
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Affiliation(s)
- Susan T Mashiyama
- Department of Cell and Molecular Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720, U.S.A
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Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 2007; 5:e16. [PMID: 17355171 PMCID: PMC1821046 DOI: 10.1371/journal.pbio.0050016] [Citation(s) in RCA: 667] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Accepted: 08/15/2006] [Indexed: 02/04/2023] Open
Abstract
Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed light on their evolution. These observations are illustrated using several protein families, including phosphatases, proteases, ultraviolet-irradiation DNA damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity added by GOS data has implications for choosing targets for experimental structure characterization as part of structural genomics efforts. Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature. The rapidly emerging field of metagenomics seeks to examine the genomic content of communities of organisms to understand their roles and interactions in an ecosystem. Given the wide-ranging roles microbes play in many ecosystems, metagenomics studies of microbial communities will reveal insights into protein families and their evolution. Because most microbes will not grow in the laboratory using current cultivation techniques, scientists have turned to cultivation-independent techniques to study microbial diversity. One such technique—shotgun sequencing—allows random sampling of DNA sequences to examine the genomic material present in a microbial community. We used shotgun sequencing to examine microbial communities in water samples collected by the Sorcerer II Global Ocean Sampling (GOS) expedition. Our analysis predicted more than six million proteins in the GOS data—nearly twice the number of proteins present in current databases. These predictions add tremendous diversity to known protein families and cover nearly all known prokaryotic protein families. Some of the predicted proteins had no similarity to any currently known proteins and therefore represent new families. A higher than expected fraction of these novel families is predicted to be of viral origin. We also found that several protein domains that were previously thought to be kingdom specific have GOS examples in other kingdoms. Our analysis opens the door for a multitude of follow-up protein family analyses and indicates that we are a long way from sampling all the protein families that exist in nature. The GOS data identified 6.12 million predicted proteins covering nearly all known prokaryotic protein families, and several new families. This almost doubles the number of known proteins and shows that we are far from identifying all the proteins in nature.
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Affiliation(s)
- Shibu Yooseph
- J. Craig Venter Institute, Rockville, Maryland, United States of America.
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11
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Hansen CM, Mashiyama ST, Roitman E, Sarmiento S, Leklem JE, Shultz TD, Ames BN. Marginal vitamin B‐6 deficiency does not increase uracil concentration in lymphocyte DNA. FASEB J 2007. [DOI: 10.1096/fasebj.21.5.a346-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Susan T. Mashiyama
- Cell & Molec. Biol.Univ. of CA, BerkeleyDiv. of Biochem. and Molec. Biol.BerkeleyCA94720
- Children's Hosp. Oakland Res. Inst.5700 Martin Luther King Jr. WayOaklandCA94609
| | - Esther Roitman
- Cell & Molec. Biol.Univ. of CA, BerkeleyDiv. of Biochem. and Molec. Biol.BerkeleyCA94720
- Children's Hosp. Oakland Res. Inst.5700 Martin Luther King Jr. WayOaklandCA94609
| | - Stella Sarmiento
- Cell & Molec. Biol.Univ. of CA, BerkeleyDiv. of Biochem. and Molec. Biol.BerkeleyCA94720
- Children's Hosp. Oakland Res. Inst.5700 Martin Luther King Jr. WayOaklandCA94609
| | - James E. Leklem
- Nutr. & Food Mgmt.Oregon St. Univ.Milam HallCorvallisOR97331
| | | | - Bruce N. Ames
- Cell & Molec. Biol.Univ. of CA, BerkeleyDiv. of Biochem. and Molec. Biol.BerkeleyCA94720
- Children's Hosp. Oakland Res. Inst.5700 Martin Luther King Jr. WayOaklandCA94609
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Courtemanche C, Elson-Schwab I, Mashiyama ST, Kerry N, Ames BN. Folate deficiency inhibits the proliferation of primary human CD8+ T lymphocytes in vitro. J Immunol 2004; 173:3186-92. [PMID: 15322179 DOI: 10.4049/jimmunol.173.5.3186] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Folate is required for one-carbon transfer reactions and the formation of purines and pyrimidines for DNA and RNA synthesis. Deficiency of folate can lead to many clinical abnormalities, including macrocytic anemia, cardiovascular diseases, birth defects, and carcinogenesis. The nucleotide imbalance due to folate deficiency causes cell cycle arrest in the S phase and uracil misincorporation into DNA, which may result in DNA double-strand breaks during repair. The role of folate in the immune system has not been fully characterized. We cultured PHA-activated human T lymphocytes in varying concentrations of folate, and measured proliferation, cell cycle, apoptosis, uracil misincorporation, and proportions of Th cells (CD4(+)) and cytotoxic T (CD8(+)) cells. Folate deficiency reduced proliferation of T lymphocytes, induced cell cycle arrest in the S phase, induced apoptosis, and increased the level of uracil in DNA. Folate deficiency also increased the CD4(+) to CD8(+) ratio due to a marked reduction of CD8(+) cell proliferation. Folate or nucleoside repletion of folate-deficient cells rapidly restored T lymphocyte proliferation and normal cell cycle, reduced the DNA uracil content, and lowered the CD4(+) to CD8(+) ratio. These data suggest that folate status may affect the immune system by reducing the capacity of CD8(+) cells to proliferate in response to activation.
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Affiliation(s)
- Chantal Courtemanche
- University of California, Berkeley, and Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
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Mashiyama ST, Courtemanche C, Elson-Schwab I, Crott J, Lee BL, Ong CN, Fenech M, Ames BN. Uracil in DNA, determined by an improved assay, is increased when deoxynucleosides are added to folate-deficient cultured human lymphocytes. Anal Biochem 2004; 330:58-69. [PMID: 15183762 DOI: 10.1016/j.ab.2004.03.065] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2003] [Indexed: 10/26/2022]
Abstract
Folate deficiency leads to increased dUMP/dTMP ratios and uracil misincorporation into DNA, which may increase cancer risk. We improved a previously described gas chromatography-mass spectrometry (GC-MS) assay for uracil in DNA and validated the assay by analyzing the DNA-uracil content of normal, primary human lymphocytes that were cultured in 0-3000 nM folic acid. In addition, the effects of nucleoside mixtures T or TdCA (T, thymidine; A, adenosine; dC, deoxycytidine) were investigated. Over 4 consecutive days, the inter- and intraassay coefficients of variation (CVs) were 2.3-3.9 and 0.6-2.2%. Mean recovery was 99.4%. Oligonucleotides containing 100 pg of uracil yielded a mean uracil measurement of 110.1 pg (CV=2.7%). Cells grown in different concentrations of folate showed a bimodal response, with maximum DNA-uracil at 12 nM, and minima at 0 and 3000 nM folate. Extremely folate-deficient cells may incorporate less uracil because DNA synthesis is reduced. A wide response to folate deficiency was seen in cells from different donors, suggesting that genetic background plays a critical role in individual susceptibility to DNA damage and cancer risk. Unexpectedly, TdCA supplementation caused increased DNA-uracil (vs 3000 nM folate for 10 days, P > 0.05), probably due to the conversion of deoxycytidine to deoxyuridine by cytidine deaminase, leading to elevated dUMP/dTMP ratios. This improved uracil assay could serve as a useful tool in the study of the mechanism of uracil misincorporation into DNA. The assay requires 3 microg of DNA per folate-deficient sample, but more may be required for baseline DNA-uracil detection in healthy humans.
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Affiliation(s)
- Susan T Mashiyama
- Department of Cell and Molecular Biology, University of California, Berkley, CA 94720, USA
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Crott JW, Mashiyama ST, Ames BN, Fenech M. The effect of folic acid deficiency and MTHFR C677T polymorphism on chromosome damage in human lymphocytes in vitro. Cancer Epidemiol Biomarkers Prev 2001; 10:1089-96. [PMID: 11588136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
We performed a comprehensive study on the genotoxic and cytotoxic effects of in vitro folic acid deficiency on primary human lymphocytes. Lymphocytes were cultured in medium containing 12-120 nM folic acid for 9 days in a novel cytokinesis-block micronucleus (CBMN) assay system (n = 20). Besides identifying optimal folic acid concentrations for in vitro genomic stability, we tested the hypothesis that lymphocytes from individuals homozygous for the C677T methylenetetrahydrofolate reductase (MTHFR) polymorphism (TTs, n = 10) are protected against chromosome damage relative to controls (CCs, n = 10) under conditions of folic acid deficiency. This hypothesis is based on the assumption that reduced MTHFR activity in TT lymphocytes causes a diversion of 5,10-methylene tetrahydrofolate toward thymidine synthesis, which minimizes uracil-induced double-stranded DNA breakage. Cells were scored for micronuclei, apoptosis, necrosis, nucleoplasmic bridges, and nuclear budding. The latter two endpoints are indicative of chromosome rearrangements and gene amplification, respectively, and to the best of our knowledge, this is the first report of their association with folic acid concentration. Folic acid concentration correlated significantly (P < 0.0001) and negatively (r, -0.63 to -0.74) with all markers of chromosome damage, which were minimized at 60-120 nM folic acid, much greater than concentrations assumed "normal," but not necessarily optimal in plasma. Two-way ANOVA revealed no effect of the MTHFR genotype on any of the endpoints. Results show that the C677T polymorphism does not affect the ability of a cell to resist chromosome damage induced by folic acid deficiency in this in vitro system.
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Affiliation(s)
- J W Crott
- Department of Physiology, Adelaide University, Adelaide, South Australia 5005, Australia
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Crott JW, Mashiyama ST, Ames BN, Fenech MF. Methylenetetrahydrofolate reductase C677T polymorphism does not alter folic acid deficiency-induced uracil incorporation into primary human lymphocyte DNA in vitro. Carcinogenesis 2001; 22:1019-25. [PMID: 11408344 DOI: 10.1093/carcin/22.7.1019] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) is an enzyme which converts 5,10-methylene tetrahydrofolate (5,10-MnTHF) to 5-methyl tetrahydrofolate. A common C to T transition (C677T) in the MTHFR gene is reported to reduce the risk for colorectal cancer and acute lymphocytic leukemia in homozygotes (TTs). It is hypothesized that because TTs have reduced MTHFR activity, more 5,10-MnTHF is available to provide methyl groups for the conversion of uracil to thymidine. Folic acid deficiency causes the intracellular accumulation of dUMP and the subsequent incorporation of uracil into DNA. The removal of uracil from DNA may result in double-stranded DNA breaks, the accumulation of which is a putative risk factor for cancer. We tested whether human lymphocytes taken from TTs (n = 10) were more able to resist uracil incorporation into DNA than controls (n = 14 CCs and 6 CTs) when cultured in medium containing 12-120 nM folic acid for 9 days. DNA uracil content of these lymphocytes was measured by CG-MS. TTs and controls showed a dose-dependent increase in DNA uracil content during folic acid deficiency (P < 0.0001, R2 = 0.23 for TTs and P < 0.0001, R2 = 0.19 for controls). DNA uracil content was not different between the two groups at any of the folic acid concentrations (two-way ANOVA: media [folic acid], P < 0.0001; genotype, P = 0.4). The results show that, in this in vitro system, the MTHFR C677T polymorphism does not affect the cell's ability to resist uracil incorporation into DNA. Chromosome breakage, as measured by micronuclei, was also shown to correlate with folic acid concentration in a preliminary experiment (P < 0.0001). Although the results appear not to support the hypothesis that a reduced risk for certain cancers in TTs is due to diversion of folic acid to thymidine synthesis, differences between the in vivo and in vitro situation make this conclusion not definitive.
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Affiliation(s)
- J W Crott
- Department of Physiology, Adelaide University, SA 5005, Australia
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16
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Abstract
The oxidized DNA base 8-oxoguanine has been commonly measured by enzymatic digestion of DNA to nucleosides followed by high-performance liquid chromatography (HPLC) separation of the adduct 8-oxodeoxyguanosine. There has recently been an enormous debate surrounding the validity of this approach, from which it has become clear that artifactual oxidation of the native base to 8-oxoguanine can occur at numerous stages in sample preparation. Hence, we have designed an alternative protocol to traditional enzymatic digestion of DNA which (i) limits the potential for artifactual oxidation, (ii) speeds up the assay markedly, (iii) increases the assay's sensitivity moderately, and (iv) addresses criticisms that have been raised concerning the efficiency of DNA digestion by nucleases. In short, we use the Escherichia coli repair enzyme formamidopyrimidine (Fapy) glycosylase to release the base 8-oxoguanine from full-length DNA, then separate 8-oxoguanine from high molecular weight molecules by ultrafiltration (10,000 Da exclusion) and analyze the base adduct by reverse-phase HPLC. Benefits of this approach include (i) rapid removal of the roughly million-fold molar excess of unaltered bases from the sample, (ii) reduction in the length of enzymatic incubations and the number of steps, (iii) elimination of high temperature incubation, (iv) a very clean chromatographic separation, and (v) rapid elution of the analyte and correspondingly greater throughput. Using this improved method, we have followed the induction of 8-oxoguanine in the DNA of peroxide-treated HeLa cells, an experiment that had proved cumbersome with traditional methods.
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Affiliation(s)
- K B Beckman
- Children's Hospital Oakland Research Institute, CA 94609, USA.
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el-Askari G, Freestone J, Irizarry C, Kraut KL, Mashiyama ST, Morgan MA, Walton S. The Healthy Neighborhoods Project: a local health department's role in catalyzing community development. Health Educ Behav 1998; 25:146-59. [PMID: 9548057 DOI: 10.1177/109019819802500204] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Studies show that community development approaches to health education may lead not only to improved social, economic, and health status but also to increased individual participation in health education and preventive health care activities. However, because of categorical funding restraints and philosophical issues, local health departments have rarely given control of defining project outcomes to the community. One such project was in a low-income urban neighborhood in the San Francisco Bay Area. In this Healthy Neighborhoods Project, the health department catalyzed community development and organization in a multiethnic public housing complex. As a result, an empowered community successfully advocated to improve public safety by installing street speed humps and increased street lighting. After project completion, residents initiated several additional health actions, including the removal of a neighborhood tobacco billboard. This article describes the project, which may serve as a model for other urban public health programs to explore their role in community empowerment.
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Affiliation(s)
- G el-Askari
- Community Wellness & Prevention Program, Contra Costa County Health Services Department, California, USA.
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