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CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli.

Autor: Rodionova IA; Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA. rodionovairina.ucsd@gmail.com., Lim HG; Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA.; Department of Biological Sciences and Bioengineering, Inha University, Incheon, Korea., Gao Y; Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA.; The Second Hospital of Shandong University, Jinan, Shandong, PR China., Rodionov DA; Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, CA, USA., Hutchison Y; Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA., Szubin R; Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA., Dalldorf C; Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA., Monk J; Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA., Palsson BO; Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA. palsson@ucsd.edu.; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. palsson@ucsd.edu.; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark. palsson@ucsd.edu.

Publikováno v: Communications biology [Commun Biol] 2024 Sep 17; Vol. 7 (1), pp. 1160. Date of Electronic Publication: 2024 Sep 17.

E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding.

Autor: Rodionova IA; Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA. irodionova@ucsd.edu.; Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA, 92093-0116, USA. irodionova@ucsd.edu., Hosseinnia A; Department of Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada., Kim S; Department of Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada., Goodacre N; Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA., Zhang L; Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA.; College of Food Science and Engineering, Ocean University of China, Yushan Road, Shinan District, Qingdao, 266003, China., Zhang Z; Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA., Palsson B; Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA, 92093-0116, USA.; Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark., Uetz P; Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA., Babu M; Department of Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada., Saier MH Jr; Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA. msaier@ucsd.edu.

Publikováno v: Scientific reports [Sci Rep] 2023 May 05; Vol. 13 (1), pp. 7345. Date of Electronic Publication: 2023 May 05.

A roadmap for the functional annotation of protein families: a community perspective.

Autor: de Crécy-Lagard V; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA., Amorin de Hegedus R; Genetics Institute, University of Florida, Gainesville, FL 32611, USA., Arighi C; Department of Computer and Information Sciences, University of Delaware, Newark, DE 19713, USA., Babor J; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA., Bateman A; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK., Blaby I; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Blaby-Haas C; Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA., Bridge AJ; Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva 4 CH-1211, Switzerland., Burley SK; RCSB Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA., Cleveland S; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA., Colwell LJ; Departmenf of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK., Conesa A; Spanish National Research Council, Institute for Integrative Systems Biology, Paterna, Valencia 46980, Spain., Dallago C; TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology, i12, Boltzmannstr. 3, Garching/Munich 85748, Germany., Danchin A; School of Biomedical Sciences, Li KaShing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, SAR Hong Kong 999077, China., de Waard A; Research Collaboration Unit, Elsevier, Jericho, VT 05465, USA., Deutschbauer A; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Dias R; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA., Ding Y; Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, USA., Fang G; NYU-Shanghai, Shanghai 200120, China., Friedberg I; Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA., Gerlt J; Institute for Genomic Biology and Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA., Goldford J; Physics of Living Systems, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Gorelik M; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA., Gyori BM; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA., Henry C; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA., Hutinet G; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA., Jaroch M; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA., Karp PD; Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA., Kondratova L; Genetics Institute, University of Florida, Gainesville, FL 32611, USA., Lu Z; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA., Marchler-Bauer A; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA., Martin MJ; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK., McWhite C; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA., Moghe GD; Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA., Monaghan P; Department of Agricultural Education and Communication, University of Florida, Gainesville, FL 32611, USA., Morgat A; Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva 4 CH-1211, Switzerland., Mungall CJ; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Natale DA; Georgetown University Medical Center, Washington, DC 20007, USA., Nelson WC; Biological Sciences Division, Pacific Northwest National Laboratories, Richland, WA 99354, USA., O'Donoghue S; School of Biotechnology and Biomolecular Sciences, University of NSW, Sydney, NSW 2052, Australia., Orengo C; Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK., O'Toole KH; New England Biolabs, Ipswich, MA 01938, USA., Radivojac P; Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA., Reed C; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA., Roberts RJ; New England Biolabs, Ipswich, MA 01938, USA., Rodionov D; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA., Rodionova IA; Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA 92093-0412, USA., Rudolf JD; Department of Chemistry, University of Florida, Gainesville, FL 32611, USA., Saleh L; New England Biolabs, Ipswich, MA 01938, USA., Sheynkman G; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA., Thibaud-Nissen F; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA., Thomas PD; Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA., Uetz P; Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284, USA., Vallenet D; LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Évry, Université Paris-Saclay, CNRS, Evry 91057, France., Carter EW; Department of Plant Pathology, University of Florida Citrus Research and Education Center, 700 Experiment Station Rd., Lake Alfred, FL 33850, USA., Weigele PR; New England Biolabs, Ipswich, MA 01938, USA., Wood V; Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK., Wood-Charlson EM; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Xu J; Department of Plant Pathology, University of Florida Citrus Research and Education Center, 700 Experiment Station Rd., Lake Alfred, FL 33850, USA.

Publikováno v: Database : the journal of biological databases and curation [Database (Oxford)] 2022 Aug 12; Vol. 2022.

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli.

Autor: Rodionova IA; Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA. irodionova@ucsd.edu.; Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA. irodionova@ucsd.edu., Gao Y; Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA.; Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA., Sastry A; Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA., Hefner Y; Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA., Lim HG; Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA., Rodionov DA; Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA.; A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia., Saier MH Jr; Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA. msaier@ucsd.edu., Palsson BO; Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA. palsson@ucsd.edu.; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark. palsson@ucsd.edu.

Publikováno v: Communications biology [Commun Biol] 2021 Aug 19; Vol. 4 (1), pp. 991. Date of Electronic Publication: 2021 Aug 19.