Mass Spec Facility Papers

Georgina C. Kalogerakis, Hardiljeet K. Boparai, Brent E. Sleep. “The Journey of Toluene to Complete Mineralization Via Heat-activated Peroxydisulfate in Water: Intermediates Analyses, CO2 Monitoring, and Carbon Mass Balance”. J Hazard Mater. 2022 Oct 15;440:129739.

Picott KJ, Flick R, Edwards EA. “Heterologous Expression of Active Dehalobacter Respiratory Reductive Dehalogenases in Escherichia coli”. Appl Environ Microbiol. 2022 Feb 8;88(3):e0199321.

Lam KY, Yu ZH, Flick R, Noble AJ, Passeport E. “Triclosan uptake and transformation by the green algae Euglena gracilis strain Z”. Sci Total Environ. 2022 Aug 10;833:155232.

Yuan J, Mortazavian S, Crowe G, Flick R, Passeport E, Hofmann R. “Evaluating the relative adsorption and biodegradation of 2-methylisoborneol and geosmin across granular activated carbon filter-adsorbers”. Water Res. 2022 May 15;215:118239.

Gu X, Rodgers TFM, Spraakman S, Van Seters T, Flick R, Diamond ML, Drake J, Passeport E. “Trace Organic Contaminant Transfer and Transformation in Bioretention Cells: A Field Tracer Test with Benzotriazole”. Environ Sci Technol. 2021 Sep 21;55(18):12281-12290.

Wu L, Suchana S, Flick R, Kümmel S, Richnow H, Passeport E. “Carbon, hydrogen and nitrogen stable isotope fractionation allow characterizing the reaction mechanisms of 1H-benzotriazole aqueous phototransformation. Water Res. 2021 Sep 15;203:117519.

Sudan S, Flick R, Nong L, Li J. “Potential Probiotic Bacillus subtilis Isolated from a Novel Niche Exhibits Broad Range Antibacterial Activity and Causes Virulence and Metabolic Dysregulation in Enterotoxic E. coli“. Microorganisms. 2021 Jul 12;9(7):1483.

Choolaei Z, Flick R, Khusnutdinova AN, Edwards EA, Yakunin AF. “Lignin-oxidizing activity of bacterial laccases characterized using soluble substrates and polymeric lignin. J Biotechnol. 2021 Jan 10;325:128-137.

Batyrova KA, Khusnutdinova AN, Wang PH, Di Leo R, Flick R, Edwards EA, Savchenko A, Yakunin AF. “Biocatalytic in Vitro and in Vivo FMN Prenylation and (De)carboxylase Activation”. ACS Chem Biol. 2020 Jul 17;15(7):1874-1882.

Kim T, Stogios PJ, Khusnutdinova AN, Nemr K, Skarina T, Flick R, Joo JC, Mahadevan R, Savchenko A, Yakunin AF. “Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol. J Biol Chem. 2020 Jan 10;295(2):597-609.

Liu Y, Chen J, Khusnutdinova AN, Correia K, Diep P, Khorcheska BA, Nemr K, Flick R, Stogios P, Yakunin AF, Mahadevan R. "A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution". Biotechnology for Biofuels. 2020;13:114.

Lomheim L, Laquitaine L, Rambinaising S, Flick R, Starostine A, Jean-Marius C, Edwards EA and Gaspard S. "Evidence for extensive anaerobic dechlorination and transformation of the pesticide chlordecone (C10Cl10O) by indigenous microbes in microcosms from Guadeloupe soil". PLOS ONE. 2020;15(4).

Fedorchuk TP, Khusnutdinova AN, Evdokimova E, Flick R, Di Leo R, Stogios P, Savchenko A and Yakunin A. "One-Pot Biocatalytic Transformation of Adipic Acid to 6-Aminocaproic Acid and 1,6-Hexamethylenediamine Using Carboxylic Acid Reductases and Transaminases" J Am Chem Soc. 2020;142(2):1038–1048.

Brudzynski K, Flick R. "Accumulation of soluble menaquinones MK-7 in honey coincides with death of Bacillus spp. present in honey" Food Chemistry: X. 2019;1:1-8.

Larsen C, Yu ZH, Flick R, Passeport E. "Mechanisms of pharmaceutical and personal care product removal in algae-based wastewater treatment systems" Sci Total Environ. 2019;695.

Khusnutdinova AN, Xiao J, Wang PH, Batyrova KA, Flick R, Edwards EA, Yakunin AF. "Prenylated FMN: Biosynthesis, purification, and Fdc1 activation" Methods in Enzymology. 2019;620:469-488.

Molinaro R, Mukherjee T, Flick R, Philpott DJ, Girardin SE. "Trace levels of peptidoglycan in serum underlie the NOD-dependent cytokine response to endoplasmic reticulum stress" J Biol Chem. 2019;294(22):9007–9015.

Cox MA, Duncan GS, Lin GHY, Steinberg BE, Yu LX, Brenner D, Buckler LN, Elia AJ, Wakeham AC, Nieman B, Dominguez-Brauer C, Elford AR, Gill KT, Kubli SP, Haight J, Berger T, Ohashi PS, Tracey KJ, Olofsson PS, Mak TW. "Choline acetyltransferase-expressing T cells are required to control chronic viral infection" Science. 2019;363(6427):639-644.

Wang PH, Correia K, Ho HC, Venayak N, Nemr K, Flick R, Mahadevan R, Edwards EA. "An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community" ISME J. 13(4):1042-1055.

Hajighasemi M, Tchigvintsev A, Nocek B, Flick R, Popovic A, Hai T, Khusnutdinova A, Brown G, Xu X, Cui H, Anstett J, Chernikova T, Brüls T, Le Paslier D, Yakimov M, Joachimiak A, Golyshina O, Savchenko A, Golyshin P, Edwards E, Yakunin A. "Screening and Characterization of Novel Polyesterases from Environmental Metagenomes with High Hydrolytic Activity against Synthetic Polyesters"
Environmental Science & Technology 52 (21), 12388-12401. 2018.

Wang PH, Khusnutdinova AN, Luo F, Xiao J, Nemr K, Flick R, Brown G, Mahadevan R, Edwards EA, Yakunin AF. "Biosynthesis and Activity of Prenylated FMN Cofactors"
Cell Chem Biol. 25(5):560-570. 2018.

B. Maccormick, T. V. Vuong, and E. R. Master, “Chemo-enzymatic synthesis of clickable xylo-oligosaccharide monomers from hardwood 4-o-methylglucuronoxylan” Biomacromolecules, vol. 19, iss. 2, pp. 521-530, 2018.

K. Raj, S. Partow, K. Correia, A. N. Khusnutdinova, A. F. Yakunin, and R. Mahadevan, “Biocatalytic production of adipic acid from glucose using engineered saccharomyces cerevisiae,” Metabolic engineering communications, vol. 6, pp. 28-32, 2018.

Yan J, Bi M, Bourdon AK, Farmer AT, Wang PH, Molenda O, Quaile AT, Jiang N, Yang Y, Yin Y, Şimşir B, Campagna SR, Edwards EA, Löffler FE. Purinyl-cobamide is a native prosthetic group of reductive dehalogenases. Nat Chem Biol. 2018;14(1):8-14.

Kim L, Brudzynski K. Identification of menaquinones (vitamin K2 homologues) as novel constituents of honey. Food Chemistry. 2018;249:184-192.

Khusnutdinova AN, Flick R, Popovic A, Brown G, Tchigvintsev A, Nocek B, Correia K, Joo JC, Mahadevan R, Yakunin AF. Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids. Biotechnol J. 2017;12(11).

Xu Z, Stogios PJ, Quaile AT, Forsberg KJ, Patel S, Skarina T, Houliston S, Arrowsmith C, Dantas G, Savchenko A. Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes. ACS Infect Dis. 2017;3(9):653-665.

Kim T, Flick R, Brunzelle J, Singer A, Evdokimova E, Brown G, Joo JC, Minasov GA, Anderson WF, Mahadevan R, Savchenko A, Yakunin AF. Novel Aldo-Keto Reductases for the Biocatalytic Conversion of 3-Hydroxybutanal to 1,3-Butanediol: Structural and Biochemical Studies. Appl Environ Microbiol. 2017;83(7). pii: e03172-16.

Joo JC, Khusnutdinova AN, Flick R, Kim T, Bornscheuer UT, Yakunin AF, Mahadevan R. Alkene hydrogenation activity of enoate reductases for an environmentally benign biosynthesis of adipic acid. Chem Sci. 2017;8(2):1406-1413.

Wang PH, Tang S, Nemr K, Flick R, Yan J, Mahadevan R, Yakunin AF, Löffler FE, Edwards EA. Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. ISME J. 2017;11(3):626-640.

Urbanus ML, Quaile AT, Stogios PJ, Morar M, Rao C, Di Leo R, Evdokimova E, Lam M, Oatway C, Cuff ME, Osipiuk J, Michalska K, Nocek BP, Taipale M, Savchenko A, Ensminger AW. Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila. Mol Syst Biol. 2016;12(12):893.

L. Huang, A. Khusnutdinova, B. Nocek, G. Brown, X. Xu, H. Cui, P. Petit, R. Flick, R. Zallot, K. Balmant, M. J. Ziemak, J. Shanklin, V. De Crécy-Lagard, O. Fiehn, J. F. Gregory, A. Joachimiak, A. Savchenko, A. F. Yakunin, and A. D. Hanson, “A family of metal-dependent phosphatases implicated in metabolite damage-control,” Nature chemical biology, vol. 12, iss. 8, pp. 621-627, 2016.

Hajighasemi M, Nocek BP, Tchigvintsev A, Brown G, Flick R, Xu X, Cui H, Hai T, Joachimiak A, Golyshin PN, Savchenko A, Edwards EA, Yakunin AF. Biochemical and structural insights into enzymatic depolymerization of polylactic acid and other polyesters by microbial carboxylesterases. Biomacromolecules. 2016;17(6):2027-2039.

Molenda O, Quaile AT, Edwards EA. Dehalogenimonas sp. Strain WBC-2 Genome and Identification of Its trans-Dichloroethene Reductive Dehalogenase, TdrA. Applied Environmental Microbiology. 2015;82(1):40-50.

Zarate-Muñoz S, Troncoso AB, Acosta E. The Cloud Point of Alkyl Ethoxylates and Its Prediction with the Hydrophilic-Lipophilic Difference (HLD) Framework. Langmuir. 2015;31(44):12000-12008.

Quaile A, Urbanus M, Stogios P, et al. Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila. Structure. 2015;23(8):1459-69.

Beloglazova N, Kuznedelov K, Flick R, et al. CRISPR RNA binding and DNA target recognition by purified Cascade complexes from Escherichia coli.Nucleic Acids Research. 2015;43(1):530-543.

Lemak S, Nocek B, Beloglazova N, et al. The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity. Nucleic Acids Research. 2014;42(17):11144-11155.

Lemak S, Beloglazova N, Nocek B, et al. Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S]-cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus. Journal of the American Chemical Society. 2013;135(46):17476-17487.

Tchigvintsev A, Tchigvintsev D, Flick R, et al. Biochemical and Structural Studies of Conserved Maf Proteins Revealed Nucleotide Pyrophosphatases with a Preference for Modified Nucleotides. Chemistry & Biology. 2013;20(11):1386-1398.

Additional Papers of Interest:

Rabinowitz D, and Kimball E. Acidic Acetonitrile for Cellular Metabolome Extraction from Escherichia coli. Analytical Chemistry. 2007:79(16):6167-6173.

Shevchenko A, Tomas H, Havlis J, et al. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protocols. 2006:1(6):2856-2860.

Kell D, Brown M, Davey H, et al. Metabolic footprinting and systems biology: the medium is the message. Nat Rev Microbiol. 2005:3(7):557-565.

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