Publications

2020

  • Alonso Rubido S., Santiago G., Cea-Rama I., Fernandez-Lopez L., Coscolin C., Modregger J., Ressmann A., Martinez-Martinez M., Marrero H., Bargiela R., Pita M., Gonzalez-Alfonso J., Briand M., Rojo D., Barbas C., Plou F., Golyshin P.N., Shahgaldian P., Sanz-Aparicio J., Guallar V. and Ferrer M. Genetically Engineered Proteins with Two Active Sites for Enhanced Biocatalysis and Synergistic Chemo- and Biocatalysis. Nature Catalysis, 2020; 3: 319–328. doi:10.1038/s41929-019-0394-4.
  • Gregson B.H., Metodieva G., Metodiev M.V., Golyshin P.N., McKew B.A. Protein expression in the obligate hydrocarbon-degrading psychrophile Oleispira antarctica RB-8 during alkane degradation and cold tolerance. Environmental Microbiology, 2020 May; 22(5):1870-1883. doi: 10.1111/1462-2920.14956.
  • Brailsford, F.L., Glanville, H.C., Wang, D., Golyshin, P.N., Johnes, P. J., Yates, C. A., Jones, D.L. Rapid depletion of dissolved organic sulphur (DOS) in freshwaters. Biogeochemistry, 2020 https://doi.org/10.1007/s10533-020-00669-4.
  • Boeckemeier L., Kraehenbuehl R., Keszthelyi A., Gasasira M. U., Vernon E. G., Beardmore R., Vågbø C. B., Chaplin D., Gollins S., Krokan H. E., Lambert S. A. E., Paizs B., Hartsuiker E. Mre11 exonuclease activity removes the chain-terminating nucleoside analog gemcitabine from the nascent strand during DNA replication. Science Advances, 2020 May 29; 6(22): eaaz4126. doi: 10.1126/sciadv.aaz4126. PMID: 32523988.
  • Liu Y., Chen J., Khusnutdinova A.N., Correia K., Diep P., Batyrova K.A., Nemr K., Flick R., Stogios P., Yakunin A.F., Mahadevan R. A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution. Biotechnol. Biofuels, 2020 13:114. doi: 10.1186/s13068-020-01753-5.
  • Batyrova K.A., Khusnutdinova A.N., Wang P.H., Di Leo R., Flick R., Edwards E.A., Savchenko A., Yakunin A.F. Biocatalytic in Vitro and in Vivo FMN Prenylation and (De)carboxylase Activation. ACS Chem. Biol., 2020 doi: 10.1021/acschembio.0c00136.
  • Bargiela R., Lanthaler K., Potter C.M., Ferrer M., Yakunin A.F., Paizs B., Golyshin P.N., Golyshina O.V. Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum. Microorganisms, 2020 May 19;8(5):759. doi: 10.3390/microorganisms8050759.
  • Diep P., Mahadevan R., Yakunin A.F. A microplate screen to estimate metal-binding affinities of metalloproteins. Anal. Biochem., 2020 Aug 1:113836. doi: 10.1016/j.ab.2020.113836. Online ahead of print.
  • La Cono V., Messina E., Rohde M., Arcadi E., Ciordia S., Crisafi F., Denaro R., Ferrer M., Giuliano L., Golyshin P.N., Golyshina O.V., Hallsworth J.E., La Spada G., Mena M.C., Merkel A.Y., Shevchenko M.A., Smedile F., Sorokin D.Y., Toshchakov S.V., and Yakimov M.M. Symbiosis between nanohaloarchaeon and haloarchaeon is based on utilization of different polysaccharides. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 2020 Aug 5, https://doi.org/10.1073/pnas.2007232117
  • Fedorchuk T.P., Khusnutdinova A.N., Evdokimova E., Flick R., Di Leo R., Stogios P., Savchenko A., Yakunin A.F. 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., 142: 1038-1048, 2020 (Epub 2020 Jan 7).
  • Makarova K.S., 17 co-authors, Yakunin A.F., 7 co-authors. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nature Rev. Microbiol., 18: 67-83, 2020 (Epub 2019 Dec 19).
  • Wang P.H., Fujishima K., Berhanu S., Kuruma Y., Jia T.Z., Khusnutdinova A.N., Yakunin A.F., McGlynn S.E. A bifunctional polyphosphate kinase driving the regeneration of nucleoside triphosphate and reconstituted cell-free protein synthesis. ACS Synth. Biol., 9: 36-42, 2020 (Epub 2019 Dec 19).
  • Kim T., Stogios P.J., Khusnutdinova A.N., Nemr K., Skarina T., Flick R., Joo J.C., Mahadevan R., Savchenko A., Yakunin A.F. Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol. J. Biol. Chem., 295: 597-609, 2020 (Epub 2019 Dec 5).
  • Dell'Anno F., Brunet C., van Zyl L.J., Trindade M., Golyshin P.N., Dell'Anno A., Ianora A., Sansone C. Degradation of Hydrocarbons and Heavy Metal Reduction by Marine Bacteria in Highly Contaminated Sediments. Microorganisms, 2020 8(9):1402. doi: 10.3390/microorganisms8091402.
  • Chernyh N.A., Neukirchen S., Frolov E.N., Sousa F.L., Miroshnichenko M.L., Merkel A.Y., Pimenov NV, Sorokin DY, Ciordia S, Mena MC, Ferrer M, Golyshin PN, Lebedinsky AV, Cardoso Pereira IA, Bonch-Osmolovskaya EA. Dissimilatory sulfate reduction in the archaeon 'Candidatus Vulcanisaeta moutnovskia' sheds light on the evolution of sulfur metabolism. Nature  Microbiology, 2020. 5(11):1428-1438. doi:10.1038/s41564-020-0776-z.
  • Chernikova T.N., Bargiela R., Toshchakov S.V., Shivaraman V., Lunev E.A., Yakimov M.M.,Thomas D.N., Golyshin P.N. Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter Associated With Microalgae Pavlova lutheri and Nannochloropsis oculata. Frontiers in Microbiology, 2020. 11:572931. doi:10.3389/fmicb.2020.572931.

  • Distaso M.A., Bargiela R., Brailsford F., Williams G.B., Wright S., Lunev E.A., Toshchakov S.V., Yakimov M.M., Jones D.L., Golyshin P.N. and Golyshina O.V. High representation of archaea across all depths in oxic and low-pH sediment layers underlying an acidic stream. Frontiers in Microbiology, 2020. 11: 2871. https://doi.org/10.3389/fmicb.2020.576520

  • Potter C.M., Jones D.L. Polyphenolic profiling of forestry waste by UPLC-HDMSE Processes (MDPI), 2020. 8:1411.

2019

  • Golyshina O.V., Bargiela R., Golyshin P.N. (2019). Cuniculiplasmataceae, their ecogenomic and metabolic patterns, and interactions with 'ARMAN'. Extremophiles,  23(1):1-7 doi: 10.1007/s00792-018-1071-2.
  • Ferrer M., Méndez-García C., Bargiela R., Chow J., Alonso S., García-Moyano A., Bjerga G.E.K., Steen I.H., Schwabe T, Blom C, Vester J, Weckbecker A, Shahgaldian P., de Carvalho CCCR, Meskys R, Zanaroli G, Glöckner FO, Fernández-Guerra A, Thambisetty S., de la Calle F., Golyshina O.V., Yakimov M.M., Jaeger K.E., Yakunin A.F., Streit W.R., McMeel O., Calewaert J.B., Tonné N., Golyshin P.N.; INMARE Consortium. (2019) Decoding the ocean's microbiological secrets for marine enzyme biodiscovery. FEMS Microbiology Letters, 366(1) doi: 10.1093/femsle/fny285.
  • Khusnutdinova A.N., Xiao J., Wang P.H., Batyrova K.A., Flick R., Edwards E.A. and Yakunin A.F. (2019) Prenylated FMN: Biosynthesis, purification, and Fdc1 activation. Methods in Enzymology, 620:469-488. doi: 10.1016/bs.mie.2019.03.021.
  • Yates C.A., Johnes P.J., Owen A.T., Brailsford F.L., Glanville H.C., Evans C.D., Marshall, M.R., Jones D.L., Lloyd C.E.M., Jickells T., Evershed R.P. (2019) Variation in dissolved organic matter (DOM) stoichiometry in U.K. freshwaters: Assessing the influence of land cover and soil C:N ratio on DOM composition. Limnology and Oceanography,  https://doi.org/10.1002/lno.11186.
  • Brailsford F.L., Glanville H.C., Golyshin P.N., Johnes P.J., Yates C.A., Jones D.L. (2019)  Microbial uptake kinetics of dissolved organic carbon (DOC) compound groups from river water and sediments. Scientific Reports, 9(1):11229. doi: 10.1038/s41598-019-47749-6.
  • Fedorchuk T.P., Khusnutdinova A.N., Flick R., Yakunin A.F. Site-directed mutagenesis and stability of the carboxylic acid reductase MAB4714 from Mycobacterium abscessus. J. Biotechnol., 303: 72-79, 2019 (Epub 2019 Aug 2).
  • Brailsford F.L., Glanville H.C., Golyshin P.N., Marshall M.R., Lloyd C.E., Johnes P.J., Jones D.L.. Nutrient enrichment induces a shift in dissolved organic carbon (DOC) metabolism in oligotrophic freshwater sediments. Sci. Total Environ., 2019 Nov 10; 690:1131-1139. doi: 10.1016/j.scitotenv.2019.07.054.
  • Gavrilov S.N., Korzhenkov A.A., Kublanov I.V., Bargiela R., Zamana L.V., Popova A.A., Toshchakov S.V., Golyshin P.N., Golyshina O.V. (2019). Microbial Communities of Polymetallic Deposits' Acidic Ecosystems of Continental Climatic Zone With High Temperature Contrasts. Frontiers in Microbiology, 10:1573. doi: 10.3389/fmicb.2019.01573
  • Golyshina O.V., Bargiela R., Toshchakov S.V., Chernyh N.A., Ramayah S., Korzhenkov A.A., Kublanov I.V., Golyshin P.N. (2019). Diversity of "Ca. Micrarchaeota" in Two Distinct Types of Acidic Environments and Their Associations with Thermoplasmatales. Genes (Basel), 10(6). pii: E461. doi: 10.3390/genes10060461.

2018

  • Korzhenkov A. A., Teplyuk A. V., Lebedinsky A. V., Khvashchevskaya A. A., Kopylova Yu. G., Arakcha K. D., Golyshin P. N., Lunev E. A., Golyshina O. V., Kublanov I. V., Toshchakov S. V. and Gavrilov S. N. (2018) Members of the Uncultured Taxon OP1 (“Acetothermia”) Predominate in the Microbial Community of an Alkaline Hot Spring at East-Tuvinian Upland. Microbiology, 87(6):783–795.
  • Gregson B.H., Metodieva G., Metodiev M.V., Golyshin P.N., McKew B.A. (2018). Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1. Frontiers in Microbiology, 9:3130. doi: 10.3389/fmicb.2018.03130.
  • Matallana-Surget S., Werner J., Wattiez R., Lebaron K., Intertaglia L, Regan C, Morris J., Teeling H., Ferrer M., Golyshin P.N., Gerogiorgis D., Reilly S.I., and Lebaron P. (2018). Proteogenomic Analysis of Epibacterium mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean. Frontiers in Microbiology, 9:3125. doi: 10.3389/fmicb.2018.03125.
  • Hajighasemi M., Tchigvintsev A., Nocek B.P., Flick R., Popovic A., Hai T., Khusnutdinova A.N., Brown G., Xu X., Cui H., Anstett J., Chernikova T.N., Bruls T., Le Paslier D., Yakimov M.M., Joachimiak A., Golyshina O.V., Savchenko A., Golyshin P.N., Edwards E.A. and Yakunin A.F. (2018). Screening and characterization of novel polyesterases from environmental metagenomes with high hydrolytic activity against synthetic polyesters. Environmental Science and Technology, 13(1):225-234. doi: 10.1021/acs.est.8b04252.
  • Santiago G., Martínez-Martínez M., Alonso S., Bargiela R., Coscolín C., Golyshin P.N., Guallar V. and Ferrer M. (2018) Rational Engineering of Multiple Active Sites in an Ester Hydrolase. Biochemistry, 57(15):2245-2255. doi: 10.1021/acs.biochem.8b00274.
  • Coscolín C., Katzke N., García-Moyano A., Navarro-Fernández J., Almendral D., Martínez-Martínez M., Bollinger A., Bargiela R., Gertler C., Chernikova T.N., Rojo D., Barbas C., Hai T., Golyshina O.V., Koch R., Yakimov M.M., Bjerga G.E.K., Golyshin P.N., Jaeger K.-E. and Ferrer M; INMARE Consortium (2018). Bioprospecting reveals class III ω-transaminases converting bulky ketones and environmentally relevant polyamines. Applied and Environmental Microbiology, doi: 10.1128/AEM.02404-18.
  • Martinez-Martinez M., Coscolín C., Santiago G., Chow J., Stogios P., Bargiela R., Gertler C., Navarro-Fernández J., Bollinger A., Thies S., Méndez-García C., Popovic A., Brown G., Chernikova T.N., García-Moyano A., Bjerga G., Pérez-García P., Tran H., Del Pozo M., Stokke R., Steen I., Cui H., Xu X., Nocek B., Alcaide M., Distaso M., Mesa V., Peláez A., Sanchez J., Buchholz P., Pleiss J., Fernández-Guerra A., Glöckner F.O., Golyshina O.V., Yakimov M.M., Jaeger K.E., Savchenko A., Yakunin A.F., Streit W.R., Golyshin P.N., Guallar V. and Ferrer M. INMARE Consortium  (2018) Determinants and distribution of substrate promiscuity patterns in microbial ester-hydrolases. ACS Chemical Biology, 13(1):225-234. doi: 10.1021/acschembio.7b00996.
  • Coscolín C., Martínez-Martínez, M., Chow, J., Bargiela, R., García-Moyano, A., Bjerga, G.E.K., Bollinger, A., Stokke, R., Steen, I.H., Golyshina, O.V., Yakimov, M.M., Jaeger, K.-E., Yakunin, A.F., Streit, W.R., Golyshin, P.N., Ferrer, M. (2018) Relationships between Substrate Promiscuity and Chiral Selectivity of Esterases from Phylogenetically and Environmentally Diverse Microorganisms. Catalysts, 8(1):10. doi:10.3390/catal8010010
  • Ghuneim L-A.J., Jones D.L., Golyshin P.N. and Golyshina O.V. (2018) Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function. Frontiers in Microbiology, 9:1971. DOI:10.3389/fmicb.2018.
  • Sorokin D.Y., Messina E., La Cono V, Ferrer M., Ciordia S., Mena C.M., Toshchakov S.V., Golyshin P.N. and Yakimov M.M. (2018) Sulfur respiration in a group of facultatively anaerobic natronoarchaea ubiquitous in hypersaline soda lakes.  Frontiers in Microbiology, doi:10.3389/fmicb.2018.02359.