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Authors: Pallavi Subhraveti Ron Caspi Quang Ong Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_900114035Cyc: Amycolatopsis sacchari DSM 44468 Cellular Overview Connections between pathways are omitted for legibility.

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METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase
Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0.
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Structure-Based Virtual Screening of Hypothetical Inhibitors of the Enzyme Longiborneol Synthase—A Potential Target to Reduce Fusarium Head Blight Disease
J Mol Model (2016) 22: 163 DOI 10.1007/s00894-016-3021-1 ORIGINAL PAPER Structure-based virtual screening of hypothetical inhibitors of the enzyme longiborneol synthase—a potential target to reduce Fusarium head blight disease E. Bresso1 & V. L ero ux 2 & M. Urban3 & K. E. Hammond-Kosack3 & B. Maigret2 & N. F. Martins1 Received: 17 December 2015 /Accepted: 27 May 2016 /Published online: 21 June 2016 # Springer-Verlag Berlin Heidelberg 2016 Abstract Fusarium head blight (FHB) is one of the most compounds from a library of 15,000 drug-like compounds. destructive diseases of wheat and other cereals worldwide. These putative inhibitors of longiborneol synthase provide a During infection, the Fusarium fungi produce mycotoxins that sound starting point for further studies involving molecular represent a high risk to human and animal health. Developing modeling coupled to biochemical experiments. This process small-molecule inhibitors to specifically reduce mycotoxin could eventually lead to the development of novel approaches levels would be highly beneficial since current treatments to reduce mycotoxin contamination in harvested grain. unspecifically target the Fusarium pathogen. Culmorin pos- sesses a well-known important synergistically virulence role Keywords Fusarium mycotoxins . Culmorin . Inhibitors . among mycotoxins, and longiborneol synthase appears to be a Homology modeling . Molecular dynamics . Ensemble key enzyme for its synthesis, thus making longiborneol syn- docking thase a particularly interesting target. This study aims to dis- cover potent and less toxic agrochemicals against FHB. These compounds would hamper culmorin synthesis by inhibiting Introduction longiborneol synthase. In order to select starting molecules for further investigation, we have conducted a structure- Fusarium head blight (FHB), caused by Fusarium based virtual screening investigation.
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A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium Smegmatis Is Involved in De Novo Cysteine Biosynthesis
University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2020 A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis Saroj Kumar Mahato University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Cell Biology Commons, Molecular Biology Commons, and the Pathogenic Microbiology Commons Citation Mahato, S. K. (2020). A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis. Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/3639 This Thesis is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Cell and Molecular Biology by Saroj Kumar Mahato Purbanchal University Bachelor of Science in Biotechnology, 2016 May 2020 University of Arkansas This thesis is approved for recommendation to the Graduate Council. ___________________________________ Young Min Kwon, Ph.D. Thesis Director ___________________________________ ___________________________________ Suresh Thallapuranam, Ph.D. Inés Pinto, Ph.D. Committee Member Committee Member ABSTRACT Mycobacteria include serious pathogens of humans and animals. Mycolicibacterium smegmatis is a non-pathogenic model that is widely used to study core mycobacterial metabolism. This thesis explores mycobacterial pathways of cysteine biosynthesis by generating and study of genetic mutants of M. smegmatis. Published in vitro biochemical studies had revealed three independent routes to cysteine synthesis in mycobacteria involving separate homologs of cysteine synthase, namely CysK1, CysK2, and CysM.
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Peroxidase Activity As an Indicator of the Iron Deficiency in Banana
IndianJ Plant Physiol., Vol. 5, No.4, (N.S.) pp. 389-391 (Oct.-Dec., 2000) SHORT COMMUNICATION PEROXIDASE ACTIVITY AS AN INDICATOR OF THE IRON DEFICIENCY IN BANANA K. BALAKRISHNAN Department ofCrop Physiology, Horticultural College and Research Institute, Periyakulam - 625 604 Received on 30 Sept., 1998, Revised on 30 Nov., 2000 Effect oflime induced iron chlorosis on enzyme activities was studied in Banana cv. Rasthali. Iron content decreased progressively as the intensity of chlorosis increased. Iron content had positive correlation with catalase, peroxidase, acid phosphatase, polyphenol oxidase and nitrate reductase. Among the enzymes, the activityofperoxidasehad highest positivesignificant(r=997**) associationwith Fecontent. Hence, peroxidase activity could serve as a diagnostic tool to indentify the Fe deficiency/Fe status in Banana. Key words: Banana, chlorosis, iron, peroxidase Among the micrountrients, Fe deficiency is the most ofgreenness in sixmonths old crop. This leafwas used for widespread in ourcountry(Takkar, 1996). Iron deficiency all the physiological analysis viz chlorophyll (Yoshida et is very common in calcareous soils and hence termed as al., 1976) chlorophyllase (Almela et al., 1990), catalase, lime induced iron chlorosis. In a normal green plant 60% peroxidase and polyphenol oxidase (Kar and Mishra, ofall leafiron is present in the chlorophyIl and hence any 1976), acid phosphatase (Parida and Mishra, 1980) and reduction in Fe contentcauses chlorosis (Chen and Barak, nitrate reductase (Klepperetal., 1973). The Fe content of 1982). Iron deficiency in plant not only causes chlorosis the plant sample was estimated using atomic absorption because of its involvement in chlorophyll synthesis, but spectrophotometry. Data were subjected to simple also reduces the activity ofcertain enzymes viz., catalase correlation co-efficient.
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Supplementary Information
doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig.
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The Classification of Esterases: an Important Gene Family Involved in Insecticide Resistance - a Review
Mem Inst Oswaldo Cruz, Rio de Janeiro, Vol. 107(4): 437-449, June 2012 437 The classification of esterases: an important gene family involved in insecticide resistance - A Review Isabela Reis Montella1,2, Renata Schama1,2,3/+, Denise Valle1,2,3 1Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brasil 2Instituto de Biologia do Exército, Rio de Janeiro, RJ, Brasil 3Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brasil The use of chemical insecticides continues to play a major role in the control of disease vector populations, which is leading to the global dissemination of insecticide resistance. A greater capacity to detoxify insecticides, due to an increase in the expression or activity of three major enzyme families, also known as metabolic resistance, is one major resistance mechanisms. The esterase family of enzymes hydrolyse ester bonds, which are present in a wide range of insecticides; therefore, these enzymes may be involved in resistance to the main chemicals employed in control programs. Historically, insecticide resistance has driven research on insect esterases and schemes for their classification. Currently, several different nomenclatures are used to describe the esterases of distinct species and a universal standard classification does not exist. The esterase gene family appears to be rapidly evolving and each insect species has a unique complement of detoxification genes with only a few orthologues across species. The examples listed in this review cover different aspects of their biochemical nature. However, they do not appear to contribute to reliably distinguish among the different resistance mechanisms.
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Generated by SRI International Pathway Tools Version 25.0, Authors S
An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility.
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United States Patent (19) 11 Patent Number: 5,981,835 Austin-Phillips Et Al
USOO598.1835A United States Patent (19) 11 Patent Number: 5,981,835 Austin-Phillips et al. (45) Date of Patent: Nov. 9, 1999 54) TRANSGENIC PLANTS AS AN Brown and Atanassov (1985), Role of genetic background in ALTERNATIVE SOURCE OF Somatic embryogenesis in Medicago. Plant Cell Tissue LIGNOCELLULOSC-DEGRADING Organ Culture 4:107-114. ENZYMES Carrer et al. (1993), Kanamycin resistance as a Selectable marker for plastid transformation in tobacco. Mol. Gen. 75 Inventors: Sandra Austin-Phillips; Richard R. Genet. 241:49-56. Burgess, both of Madison; Thomas L. Castillo et al. (1994), Rapid production of fertile transgenic German, Hollandale; Thomas plants of Rye. Bio/Technology 12:1366–1371. Ziegelhoffer, Madison, all of Wis. Comai et al. (1990), Novel and useful properties of a chimeric plant promoter combining CaMV 35S and MAS 73 Assignee: Wisconsin Alumni Research elements. Plant Mol. Biol. 15:373-381. Foundation, Madison, Wis. Coughlan, M.P. (1988), Staining Techniques for the Detec tion of the Individual Components of Cellulolytic Enzyme 21 Appl. No.: 08/883,495 Systems. Methods in Enzymology 160:135-144. de Castro Silva Filho et al. (1996), Mitochondrial and 22 Filed: Jun. 26, 1997 chloroplast targeting Sequences in tandem modify protein import specificity in plant organelles. Plant Mol. Biol. Related U.S. Application Data 30:769-78O. 60 Provisional application No. 60/028,718, Oct. 17, 1996. Divne et al. (1994), The three-dimensional crystal structure 51 Int. Cl. ............................. C12N 15/82; C12N 5/04; of the catalytic core of cellobiohydrolase I from Tricho AO1H 5/00 derma reesei. Science 265:524-528.
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Supporting Information
Supporting Information Figure S1. The functionality of the tagged Arp6 and Swr1 was confirmed by monitoring cell growth and sensitivity to hydeoxyurea (HU). Five-fold serial dilutions of each strain were plated on YPD with or without 50 mM HU and incubated at 30°C or 37°C for 3 days. Figure S2. Localization of Arp6 and Swr1 on chromosome 3. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 3L, Tel 3R, CEN3, and the RP gene are shown under the panels. Figure S3. Localization of Arp6 and Swr1 on chromosome 4. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) in the whole chromosome region are compared. The position of Tel 4L, Tel 4R, CEN4, SWR1, and RP genes are shown under the panels. Figure S4. Localization of Arp6 and Swr1 on the region including the SWR1 gene of chromosome 4. The binding of Arp6- FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position and orientation of the SWR1 gene is shown. Figure S5. Localization of Arp6 and Swr1 on chromosome 5. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 5L, Tel 5R, CEN5, and the RP genes are shown under the panels. Figure S6. Preferential localization of Arp6 and Swr1 in the 5′ end of genes. Vertical bars represent the binding ratio of proteins in each locus.
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Characterization of a Cytochrome P450 Monooxygenase Gene Involved in the Biosynthesis of Geosmin in Penicillium Expansum
Open Archive TOULOUSE Archive Ouverte (OATAO) OATAO is an open access repository that collects the work of Toulouse researchers and makes it freely available over the web where possible. This is an author-deposited version published in : http://oatao.univ-toulouse.fr/ Eprints ID : 10812 To link to this article : DOI : 10.5897/AJMR11.1361 URL : http://academicjournals.org/journal/AJMR/article- abstract/841ECBA21771 To cite this version : Siddique, Muhammad Hussnain and Liboz, Thierry and Bacha, Nafees and Puel, Olivier and Mathieu, Florence and Lebrihi, Ahmed Characterization of a cytochrome P450 monooxygenase gene involved in the biosynthesis of geosmin in Penicillium expansum. (2012) African Journal of Microbiology Research, vol. 6 (n° 19). pp. 4122-4127. ISSN 1996-0808 Any correspondance concerning this service should be sent to the repository administrator: [email protected] Characterization of a cytochrome P450 monooxygenase gene involved in the biosynthesis of geosmin in Penicillium expansum Muhammad Hussnain Siddique1,2, Thierry Liboz1,2, Nafees Bacha3, Olivier Puel4, Florence Mathieu1,2 and Ahmed Lebrihi1,2,5* 1Université de Toulouse, INPT-UPS, Laboratoire de Génie Chimique, avenue de l’Agrobiopole, 31326 Castanet-Tolosan Cedex, France. 2Le Centre national de la recherche scientifique (CNRS), Laboratoire de Génie Chimique, 31030 Toulouse, France. 3Centre of Biotechnology and Microbiology, University of Peshawar, Pakistan. 4Institut National de la Recherche Agronomique (INRA), Laboratoire de Pharmacologie Toxicologie, 31931 Toulouse, France. 5Université Moulay Ismail, Marjane 2, BP 298, Meknes, Morocco. Geosmin is a terpenoid, an earthy-smelling substance associated with off-flavors in water and wine. The biosynthesis of geosmin is well characterized in bacteria, but little is known about its production in eukaryotes, especially in filamentous fungi.
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Cysteine Dioxygenase 1 Is a Metabolic Liability for Non-Small Cell Lung Cancer Authors: Yun Pyo Kang1, Laura Torrente1, Min Liu2, John M
bioRxiv preprint doi: https://doi.org/10.1101/459602; this version posted November 1, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Cysteine dioxygenase 1 is a metabolic liability for non-small cell lung cancer Authors: Yun Pyo Kang1, Laura Torrente1, Min Liu2, John M. Asara3,4, Christian C. Dibble5,6 and Gina M. DeNicola1,* Affiliations: 1 Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA 2 Proteomics and Metabolomics Core Facility, Moffitt Cancer Center and Research Institute, Tampa, FL, USA 3 Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA, USA 4 Department of Medicine, Harvard Medical School, Boston, MA, USA 5 Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA, USA 6 Department of Pathology, Harvard Medical School, Boston, MA, USA *Correspondence to: [email protected]. Keywords: KEAP1, NRF2, cysteine, CDO1, sulfite Summary NRF2 is emerging as a major regulator of cellular metabolism. However, most studies have been performed in cancer cells, where co-occurring mutations and tumor selective pressures complicate the influence of NRF2 on metabolism. Here we use genetically engineered, non-transformed primary cells to isolate the most immediate effects of NRF2 on cellular metabolism. We find that NRF2 promotes the accumulation of intracellular cysteine and engages the cysteine homeostatic control mechanism mediated by cysteine dioxygenase 1 (CDO1), which catalyzes the irreversible metabolism of cysteine to cysteine sulfinic acid (CSA). Notably, CDO1 is preferentially silenced by promoter methylation in non-small cell lung cancers (NSCLC) harboring mutations in KEAP1, the negative regulator of NRF2.
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Development of a Phage Display Library for Discovery of Antigenic Brucella Peptides Jeffrey Williams Iowa State University
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2018 Development of a phage display library for discovery of antigenic Brucella peptides Jeffrey Williams Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Microbiology Commons Recommended Citation Williams, Jeffrey, "Development of a phage display library for discovery of antigenic Brucella peptides" (2018). Graduate Theses and Dissertations. 16896. https://lib.dr.iastate.edu/etd/16896 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Development of a phage display library for discovery of antigenic Brucella peptides by Jeffrey Williams A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Microbiology Program of Study Committee: Bryan H. Bellaire, Major Professor Steven Olsen Steven Carlson The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this thesis. The Graduate College will ensure this thesis is globally accessible and will not permit alterations after a degree is conferred. Iowa State University
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