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Folic Acid Antagonists: Antimicrobial and Immunomodulating Mechanisms and Applications
International Journal of Molecular Sciences Review Folic Acid Antagonists: Antimicrobial and Immunomodulating Mechanisms and Applications Daniel Fernández-Villa 1, Maria Rosa Aguilar 1,2 and Luis Rojo 1,2,* 1 Instituto de Ciencia y Tecnología de Polímeros, Consejo Superior de Investigaciones Científicas, CSIC, 28006 Madrid, Spain; [email protected] (D.F.-V.); [email protected] (M.R.A.) 2 Consorcio Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, 28029 Madrid, Spain * Correspondence: [email protected]; Tel.: +34-915-622-900 Received: 18 September 2019; Accepted: 7 October 2019; Published: 9 October 2019 Abstract: Bacterial, protozoan and other microbial infections share an accelerated metabolic rate. In order to ensure a proper functioning of cell replication and proteins and nucleic acids synthesis processes, folate metabolism rate is also increased in these cases. For this reason, folic acid antagonists have been used since their discovery to treat different kinds of microbial infections, taking advantage of this metabolic difference when compared with human cells. However, resistances to these compounds have emerged since then and only combined therapies are currently used in clinic. In addition, some of these compounds have been found to have an immunomodulatory behavior that allows clinicians using them as anti-inflammatory or immunosuppressive drugs. Therefore, the aim of this review is to provide an updated state-of-the-art on the use of antifolates as antibacterial and immunomodulating agents in the clinical setting, as well as to present their action mechanisms and currently investigated biomedical applications. Keywords: folic acid antagonists; antifolates; antibiotics; antibacterials; immunomodulation; sulfonamides; antimalarial 1. -
The Rnase H-Like Superfamily: New Members, Comparative Structural Analysis and Evolutionary Classification Karolina A
4160–4179 Nucleic Acids Research, 2014, Vol. 42, No. 7 Published online 23 January 2014 doi:10.1093/nar/gkt1414 The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification Karolina A. Majorek1,2,3,y, Stanislaw Dunin-Horkawicz1,y, Kamil Steczkiewicz4, Anna Muszewska4,5, Marcin Nowotny6, Krzysztof Ginalski4 and Janusz M. Bujnicki1,3,* 1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, 2Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA-22908, USA, 3Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, 4Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL-02-089 Warsaw, Poland, 5Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL-02-106 Warsaw, Poland and 6Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland Received September 23, 2013; Revised December 12, 2013; Accepted December 26, 2013 ABSTRACT revealed a correlation between the orientation of Ribonuclease H-like (RNHL) superfamily, also called the C-terminal helix with the exonuclease/endo- the retroviral integrase superfamily, groups together nuclease function and the architecture of the numerous enzymes involved in nucleic acid metab- active site. Our analysis provides a comprehensive olism and implicated in many biological processes, picture of sequence-structure-function relation- including replication, homologous recombination, ships in the RNHL superfamily that may guide func- DNA repair, transposition and RNA interference. -
Bioluminescent Properties of Semi-Synthetic Obelin and Aequorin Activated by Coelenterazine Analogues with Modifications of C-2, C-6, and C-8 Substituents
International Journal of Molecular Sciences Article Bioluminescent Properties of Semi-Synthetic Obelin and Aequorin Activated by Coelenterazine Analogues with Modifications of C-2, C-6, and C-8 Substituents 1, 2,3, 1 2, Elena V. Eremeeva y , Tianyu Jiang y , Natalia P. Malikova , Minyong Li * and Eugene S. Vysotski 1,* 1 Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia; [email protected] (E.V.E.); [email protected] (N.P.M.) 2 Key Laboratory of Chemical Biology (MOE), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China; [email protected] 3 State Key Laboratory of Microbial Technology, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Qingdao 266237, China * Correspondence: [email protected] (M.L.); [email protected] (E.S.V.); Tel.: +86-531-8838-2076 (M.L.); +7-(391)-249-44-30 (E.S.V.); Fax: +86-531-8838-2076 (M.L.); +7-(391)-290-54-90 (E.S.V.) These authors contributed equally to this work. y Received: 23 June 2020; Accepted: 27 July 2020; Published: 30 July 2020 Abstract: Ca2+-regulated photoproteins responsible for bioluminescence of a variety of marine organisms are single-chain globular proteins within the inner cavity of which the oxygenated coelenterazine, 2-hydroperoxycoelenterazine, is tightly bound. Alongside with native coelenterazine, photoproteins can also use its synthetic analogues as substrates to produce flash-type bioluminescence. However, information on the effect of modifications of various groups of coelenterazine and amino acid environment of the protein active site on the bioluminescent properties of the corresponding semi-synthetic photoproteins is fragmentary and often controversial. -
The Impact of Genetic Diversity on Gene Essentiality Within the E. Coli Species
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.25.114553; this version posted May 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The impact of genetic diversity on gene essentiality within the E. coli species François Rousset1,2, José Cabezas Caballero1, Florence Piastra-Facon1, Jesús Fernández-Rodríguez3, Olivier Clermont4, Erick Denamur4,5, Eduardo P.C. Rocha6 & David Bikard1,* 1- Synthetic Biology, Department of Microbiology, Institut Pasteur, Paris, France 2- Sorbonne Université, Collège Doctoral, F-75005Paris, France 3- Eligo Bioscience, Paris, France 4- Université de Paris, IAME, INSERM UMR1137, Paris, France 5- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France 6- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France. *To whom correspondence should be addressed: [email protected] Abstract Bacteria from the same species can differ widely in their gene content. In E. coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. While recent advances in bacterial genomics have enabled to unravel genes required for fitness in various experimental conditions at the genome scale, most studies have focused on model strains. As a result, the impact of this genetic diversity on core processes of the bacterial cell largely remains to be investigated. Here, we developed a new CRISPR interference platform for high- throughput gene repression that is compatible with most E. -
Discovery and Protein Engineering of Baeyer-Villiger Monooxygenases
Discovery and Protein Engineering of Baeyer-Villiger monooxygenases Inauguraldissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Ernst-Moritz-Arndt-Universität Greifswald vorgelegt von Andy Beier geboren am 11.10.1988 in Parchim Greifswald, den 02.08.2017 I Dekan: Prof. Dr. Werner Weitschies 1. Gutachter: Prof. Dr. Uwe T. Bornscheuer 2. Gutachter: Prof. Dr. Marko Mihovilovic Tag der Promotion: 24.10.2017 II We need to learn to want what we have, not to have what we want, in order to get stable and steady happiness. - The Dalai Lama - III List of abbreviations % Percent MPS Methyl phenyl sulfide % (v/v) % volume per volume MPSO Methyl phenyl sulfoxide % (w/v) % weight per volume MPSO2 Methyl phenyl sulfone °C Degrees Celsius MTS Methyl p-tolyl sulfide µM µmol/L MTSO Methyl p-tolyl sulfoxide aa Amino acids MTSO2 Methyl p-tolyl sulfone + AGE Agarose gel electrophoresis NAD Nicotinamide adenine dinucleotide, oxidized aq. dest. Distilled water NADH Nicotinamide adenine dinucleotide, reduced + BLAST Basic Local Alignment Search NADP Nicotinamide adenine dinucleotide Tool phosphate, oxidized bp Base pair(s) NADPH Nicotinamide adenine dinucleotide phosphate, reduced BVMO Baeyer-Villiger monooxyge- OD600 Optical density at 600 nm nase CHMO Cyclohexanone monooxyge- PAGE Polyacrylamide gel electrophoresis nase Da Dalton PAMO Phenylacetone monooxygenase DMF Dimethyl formamide PCR Polymerase chain reaction DMSO Dimethyl sulfoxide PDB Protein Data Bank DMSO2 Dimethyl sulfone rpm Revolutions per minute DNA Desoxyribonucleic acid rv Reverse dNTP Desoxynucleoside triphosphate SDS Sodium dodecyl sulfate E. coli Escherichia coli SOC Super Optimal broth with Catabolite repression ee Enantiomeric excess TAE TRIS-Acetate-EDTA FAD Flavin adenine dinucleotide TB Terrific broth Fig. -
Cloning of Firefly Luciferase Cdna and the Expression of Active
Proc. Natl. Acad. Sci. USA Vol. 82, pp. 7870-7873, December 1985 Biochemistry Cloning of firefly luciferase cDNA and the expression of active luciferase in Escherichia coli (bioluminescence/Photinus pyralis/antibody screening/expression vector/recombinant DNA) JEFFREY R. DE WET*, KEITH V. WOODt, DONALD R. HELINSKI*, AND MARLENE DELUCAt Departments of *Biology and tChemistry, University of California, San Diego, La Jolla, CA 92093 Communicated by W. D. McElroy, July 26, 1985 ABSTRACT A cDNA library was constructed from firefly library was screened with anti-P. pyralis luciferase antibody, (Photinuspyralis) lantern poly(A)I RNA, using the Escherichia using a chromogenic detection technique (8), and several coli expression vector Xgtll. The library was screened with cDNA clones were isolated and characterized. These clones anti-P. pyralis luciferase (Photinus luciferin:oxygen 4-oxidore- were found to be homologous to the mRNA that encodes ductase, EC 1.13.12.7) antibody, and several cDNA clones luciferase. The largest luciferase cDNA clone that was expressing luciferase antigens were isolated. One clone, ALucl, isolated was able to direct the synthesis of active luciferase contained 1.5 kilobase pairs of cDNA that hybridized to a 1.9- in E. coli. to 2.0-kilobase band on a nitrocellulose blot of electrophoreti- cally fractionated lantern RNA. Hybridization of the cloned MATERIALS AND METHODS cDNA to lantern poly(A)I RNA selected an RNA that directed the in vitro synthesis of a single polypeptide. This polypeptide Enzymes and Strains. Restriction endonucleases and E. coli comigrated with luciferase on NaDodSO4/PAGE and produced DNA polymerase I were purchased from New England bioluminescence upon the addition of luciferin and ATP. -
Bioluminescence Is Produced by a Firefly-Like Luciferase but an Entirely
www.nature.com/scientificreports OPEN New Zealand glowworm (Arachnocampa luminosa) bioluminescence is produced by a Received: 8 November 2017 Accepted: 1 February 2018 frefy-like luciferase but an entirely Published: xx xx xxxx new luciferin Oliver C. Watkins1,2, Miriam L. Sharpe 1, Nigel B. Perry 2 & Kurt L. Krause 1 The New Zealand glowworm, Arachnocampa luminosa, is well-known for displays of blue-green bioluminescence, but details of its bioluminescent chemistry have been elusive. The glowworm is evolutionarily distant from other bioluminescent creatures studied in detail, including the frefy. We have isolated and characterised the molecular components of the glowworm luciferase-luciferin system using chromatography, mass spectrometry and 1H NMR spectroscopy. The purifed luciferase enzyme is in the same protein family as frefy luciferase (31% sequence identity). However, the luciferin substrate of this enzyme is produced from xanthurenic acid and tyrosine, and is entirely diferent to that of the frefy and known luciferins of other glowing creatures. A candidate luciferin structure is proposed, which needs to be confrmed by chemical synthesis and bioluminescence assays. These fndings show that luciferases can evolve independently from the same family of enzymes to produce light using structurally diferent luciferins. Glowworms are found in New Zealand and Australia, and are a major tourist attraction at sites located across both countries. In contrast to luminescent beetles such as the frefy (Coleoptera), whose bioluminescence has been well characterised (reviewed by ref.1), the molecular details of glowworm bioluminescence have remained elusive. Tese glowworms are the larvae of fungus gnats of the genus Arachnocampa, with eight species endemic to Australia and a single species found only in New Zealand2. -
1 SUPPLEMENTARY DATA Table S1
Electronic Supplementary Material (ESI) for Food & Function. This journal is © The Royal Society of Chemistry 2020 SUPPLEMENTARY DATA Table S1: Effects of catalase, protease, papain and pH treatments on the antimicrobial activity (%) of the CFS of S. thermophilus strain against G. vaginalis ATCC 14018. The antimicrobial activity of the strain was highest under acidic pH conditions. Remaining antimicrobial activity (%) Strains 5 mg mL-1 1 mg mL-1 1 mg mL-1 pH treatments catalase proteinase K papain 3.5 4.0 5.0 6.0 6.5 7.0 S. thermophilus KLDS 3.1003 90.49±0.62 100±0 100±0 100±0 100±0 67.02±0.08 6.35±0.03 0±0 0±0 All values were determined in triplicate Values were expressed as mean ± SD 1 Table S2: Weekly weights of study animals before and after S. aureus ATCC25923 infection. Significant variations (at P > 0.05) were observed in the weight of study animals during the study. Period C C C C Week 0 22.00b 23.57b 19.34e 23.24a 20.90d 22.84c 20.19d 22.60b 23.92a 23.70b 20.56c 23.78a 20.89d 23.10c 20.00d 23.51a Average 22.43 23.30 20.02 23.28 SD 1.29 0.40 0.51 0.51 C TST TSA TSTSA 24.92a 24.15a 21.19c 20.98c Week 1 23.34a 23.13c 20.26d 22.68b 21.98b 22.96d 20.85c 22.86b 22.60b 22.36d 24.28a 22.33b Average 23.21 23.15 21.65 22.21 SD 1.27 0.74 1.80 0.86 23.25a 24.28a 19.94d 20.39d Week 2 21.32c 22.09e 18.46f 20.35d 20.29d 21.82e 19.40e 16.68e 21.27c 22.89d 22.74b 20.09d Average 21.53 22.77 20.14 19.38 SD 1.24 1.10 1.84 1.80 Values with the same alphabet along the same column are not significantly different (P > 0.05) Composition of control and trial diets are given in Table 1. -
Muscle Regeneration Controlled by a Designated DNA Dioxygenase
Wang et al. Cell Death and Disease (2021) 12:535 https://doi.org/10.1038/s41419-021-03817-2 Cell Death & Disease ARTICLE Open Access Muscle regeneration controlled by a designated DNA dioxygenase Hongye Wang1, Yile Huang2,MingYu3,YangYu1, Sheng Li4, Huating Wang2,5,HaoSun2,5,BingLi 3, Guoliang Xu6,7 andPingHu4,8,9 Abstract Tet dioxygenases are responsible for the active DNA demethylation. The functions of Tet proteins in muscle regeneration have not been well characterized. Here we find that Tet2, but not Tet1 and Tet3, is specifically required for muscle regeneration in vivo. Loss of Tet2 leads to severe muscle regeneration defects. Further analysis indicates that Tet2 regulates myoblast differentiation and fusion. Tet2 activates transcription of the key differentiation modulator Myogenin (MyoG) by actively demethylating its enhancer region. Re-expressing of MyoG in Tet2 KO myoblasts rescues the differentiation and fusion defects. Further mechanistic analysis reveals that Tet2 enhances MyoD binding by demethylating the flanking CpG sites of E boxes to facilitate the recruitment of active histone modifications and increase chromatin accessibility and activate its transcription. These findings shed new lights on DNA methylation and pioneer transcription factor activity regulation. Introduction Ten-Eleven Translocation (Tet) family of DNA dioxy- 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Skeletal muscles can regenerate due to the existence of genases catalyze the active DNA demethylation and play muscle stem cells (MuSCs)1,2. The normally quiescent critical roles in embryonic development, neural regen- MuSCs are activated after muscle injury and further dif- eration, oncogenesis, aging, and many other important – ferentiate to support muscle regeneration3,4. -
Generate Metabolic Map Poster
Authors: Pallavi Subhraveti Anamika Kothari Quang Ong Ron Caspi 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 Peter D Karp Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Csac1394711Cyc: Candidatus Saccharibacteria bacterium RAAC3_TM7_1 Cellular Overview Connections between pathways are omitted for legibility. Tim Holland TM7C00001G0420 TM7C00001G0109 TM7C00001G0953 TM7C00001G0666 TM7C00001G0203 TM7C00001G0886 TM7C00001G0113 TM7C00001G0247 TM7C00001G0735 TM7C00001G0001 TM7C00001G0509 TM7C00001G0264 TM7C00001G0176 TM7C00001G0342 TM7C00001G0055 TM7C00001G0120 TM7C00001G0642 TM7C00001G0837 TM7C00001G0101 TM7C00001G0559 TM7C00001G0810 TM7C00001G0656 TM7C00001G0180 TM7C00001G0742 TM7C00001G0128 TM7C00001G0831 TM7C00001G0517 TM7C00001G0238 TM7C00001G0079 TM7C00001G0111 TM7C00001G0961 TM7C00001G0743 TM7C00001G0893 TM7C00001G0630 TM7C00001G0360 TM7C00001G0616 TM7C00001G0162 TM7C00001G0006 TM7C00001G0365 TM7C00001G0596 TM7C00001G0141 TM7C00001G0689 TM7C00001G0273 TM7C00001G0126 TM7C00001G0717 TM7C00001G0110 TM7C00001G0278 TM7C00001G0734 TM7C00001G0444 TM7C00001G0019 TM7C00001G0381 TM7C00001G0874 TM7C00001G0318 TM7C00001G0451 TM7C00001G0306 TM7C00001G0928 TM7C00001G0622 TM7C00001G0150 TM7C00001G0439 TM7C00001G0233 TM7C00001G0462 TM7C00001G0421 TM7C00001G0220 TM7C00001G0276 TM7C00001G0054 TM7C00001G0419 TM7C00001G0252 TM7C00001G0592 TM7C00001G0628 TM7C00001G0200 TM7C00001G0709 TM7C00001G0025 TM7C00001G0846 TM7C00001G0163 TM7C00001G0142 TM7C00001G0895 TM7C00001G0930 Detoxification Carbohydrate Biosynthesis DNA combined with a 2'- di-trans,octa-cis a 2'- Amino Acid Degradation an L-methionyl- TM7C00001G0190 superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. -
Roles of Vitamin Metabolizing Genes in Multidrug-Resistant Plasmids of Superbugs
bioRxiv preprint doi: https://doi.org/10.1101/285403; this version posted March 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Roles of Vitamin Metabolizing Genes in Multidrug-Resistant Plasmids of Superbugs Asit Kumar Chakraborty, Genetic Engineering Laboratory, Department of Biotechnology & Biochemistry, Oriental Institute of Science & Technology, Vidyasagar University, Midnapore 721102, West Bengal, India. Abstract Superbug crisis has rocked this world with million deaths due to failure of potent antibiotics. Thousands mdr genes with hundreds of mutant isomers are generated. Small integrons and R-plasmids have combined with F'-plasmids creating a space for >10-20 of mdr genes that inactivate antibiotics in different mechanisms. Mdr genes are created to save bacteria from antibiotics because gut microbiota synthesize >20 vitamins and complex bio-molecules needed for >30000 biochemical reactions of human metabolosome. In other words, mdr gene creation is protected from both sides, intestinal luminal cells and gut bacteria in a tight symbiotic signalling system. We have proposed, to avert the crisis all vitamin metabolizing genes will be acquired in MDR- plasmids if we continue oral antibiotics therapy. Therefore, we have checked the plasmid databases and have detected thiamine, riboflavin, folate, cobalamine and biotin metabolizing enzymes in MDR plasmids. Thus vit genes may mobilise recently into MDR-plasmids and are likely essential for gut microbiota protection. Analysis found that cob and thi genes are abundant and likely very essential than other vit genes. -
Letters to Nature
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