Publications
2026
Ma H., Khushutdinova A.N., Chernikova T.N., Ferrer M., Yakunin A.F., Golyshina O.V. and Golyshin P.N. (2026) Cold-adapted carboxylesterases from Alcanivoracaceae active with a wide range of synthetic polyesters. Applied Microbiology and Biotechnology 110(1):59. DOI: 10.1007/s00253-026-13726-z.
Chernikova T.N., Khushutdinova A.N., Ma H., Ferrer M., Golyshina O.V., Yakunin A.F. and Golyshin P.N. (2026) Polyesterase activity and thermostability of carboxylesterases from Thermoleophilum album YS-3. The FEBS Journal DOI: 10.1111/febs.70478
Batyrova K.A., Khusnutdinova A.N., Yakunin A.F. (2026) Dithionite-supported biohydrogenation of muconic acid to adipic acid by lyophilized Escherichia coli cells expressing recombinant enoate reductase. Enzyme and Microbial Technology 194: 110797. doi: 10.1016/j.enzmictec.2025.110797
2025
El Houari A., Carpenter M., Chaplin D., Golyshin P. McDonald J.E (2025). Taxonomic description and genome sequence of Anaerorudis cellulosivorans gen. nov. sp. nov., a novel cellulose- and xylan-degrading bacterium of the Bacteroidota phylum isolated from a lab-scale methanogenic landfill bioreactor digesting municipal solid waste. Systematic and Applied Microbiology 48:126590. DOI: 10.1016/j.syapm.2025.126590
Ordonez A., Hussain U., Cambon M.C., Golyshin P.N., Downie J., McDonald J.E. (2025) Evaluating Agar-Plating and Dilution-to-Extinction Isolation Methods for Generating Oak-Associated Microbial Culture Collections. ISME Communications 5(1): ycaf019. DOI: 10.1093/ismeco/ycaf019
Zayulina K.S., Frolov E.N., Stracke C., Klyukina A.A., Khusnutdinova A.N., Stogios P., Skarina T., Yakunin A.F., Golyshin P.N., Siebers B., Shugaeva T.E., Kublanov I.V. (2025) Structural and functional insights into extreme thermal stability and activity of two GH12 domains of a multidomain glycosidase from a hyperthermophilic euryarchaeon. The FEBS Journal 292(14):3771-3794. doi: 10.1111/febs.70095
Gaines M.C., Isupov M.N. McLaren M., Ul Haque R., Recalde A., Bargiela R., Gold V.A.M., Albers S.-V., Golyshin P.N., Golyshina O.V. and Daum B. (2025) Unusual cell surfaces, pili and archaella of Thermoplasmatales archaea. The ISME Journal 19(1):wraf176. DOI: 10.1093/ismejo/wraf176.
Scott J., Golyshin P.N., Holland S.I., Pereira R., Ngo H.T.T., Kaiser M., Gutierrez T. (2025) Systematic critical review of studies and methods assessing microbial degradation of plastics in the marine environment: evidence base and recommendations. Science of the Total Environment 999:180277. doi: 10.1016/j.scitotenv.2025.180277.
Lea-Smith D.J., Hassard F., Coulon F., Partridge N., Horsfall L., Parker K.D.J., Smith R.D.J., McCarthy R.R., McKew B., Gutierrez T., Kumar V., Dotro G., Yang Z; EBIC partners (Thomas P Curtis, Peter Golyshin, Sonia Heaven, Bruce Jefferson, Paul Jeffrey, Davey L Jones, Kristell Le Corre Pidou, Yongqiang Liu, Tao Lyu, Cindy Smith, Alexander Yakunin, Yue Zhang) and Krasnogor N. (2025) Engineering biology applications for environmental solutions: potential and challenges. Nature Communications 16(1):3538. doi:10.1038/s41467-025-58492-0.
Graf M., Choiselat E., Reay M., Bargiela R., Dimitriou A., Liu Q. Elias R.N., Golyshin P.N., Griffiths R., Chadwick D.R., Jones D.L. (2025) Biodegradable mulch films exhibit slower-than-expected degradation with negligible effects on soil microbial communities Journal of Hazardous Materials 498:139871. DOI: 10.1016/j.jhazmat.2025.139871.
El Houari A., Carpenter M., Chaplin D., Golyshin P.N. and McDonald J.E (2025). Anaerozeibacter quisquiliarum, gen. nov ., sp. nov., a novel mesophilic bacterium isolated from a laboratory-scale methanogenic landfill bioreactor digesting maize, and proposal of Anaerozeibacteraceae fam. nov., representing a new family in the order Eubacteriales. International Journal of Systematic and Evolutionary Microbiology DOI: 10.1099/ijsem.0.006985
Thakur A., Khusnutdinova A.N, Navarro Márquez M., Kumar V., Ma H., Golyshin P.N., Lyu T., Yakunin A.F., Kumar G., Nithya K., Gutiérrez Soto G., Hafiz I., Gutierrez T., Coulon F., Parra Saldivar R. (2025) Comprehensive strategies for the remediation of per- and polyfluoroalkyl substances (PFAS): mechanisms, technologies, and future perspectives. Ecotoxicology and Environmental Safety DOI: 10.1016/j.ecoenv.2025.119374
Ma H., Khusnutdinova A.N. Lemak S., Chernikova T.N., Golyshina O.V., Almendral D., Ferrer M., Golyshin P.N. and Yakunin A.F. (2024) Polyesterase activity is widespread in the family IV carboxylesterases from bacteria. Journal of Hazardous Materials 481:136540. DOI: 10.1016/j.jhazmat.2024.136540
Makarova K.S., Shmakov S.A., Wolf Y.I., Mutz P., Altae-Tran H., Beisel C.L., Brouns S.J.J., Charpentier E., Cheng D., Doudna J., Haft D.H., Horvath P., Moineau S., Mojica F.J.M., Pausch P., Redondo R.P., Shah S.A., Siksnys V., Terns M.P., Tordoff J., Venclovas C., White M.F., Yakunin A.F., Zhang F., Garret R.A., Backofen R., van der Oost J., Barrangou R., and Koonin E.V. (2025) An updated evolutionary classification CRISPR-Cas systems including rare variants. Nature Microbiology 10: 3346-3361. doi: 10.1038/s41564-025-02180-8
Nishikawa S., Yu W.-C., Chiang Y.-R., Wu T.-Y., Tang I., Khusnutdinova A., Yakunin A., Fujishima K., Wang P.-H. (2025) Methanol-driven, one-pot chemoenzymatic S-adenosylmethionine regeneration for ambient cobalamin-dependent methyltransferase reactions. ACS Catalysis 15: 13689-13703. DOI: 10.1021/acscatal.5c03683.s001
Choolaei Z., Khusnutdinova A.N., Skarina T., Stogios P., Diep P., Lemak S., Edwards E.A., Savchenko A., Yakunin A.F. (2025) Structural and biochemical insights into lignin-oxidizing activity of bacterial peroxidases against soluble substrates and kraft lignin. ACS Chemical Biology 20: 830844. doi: 10.1021/acschembio.4c00788
2024
Khusnutdinova A.N., Batyrova K.A., Wang P.-H., Flick R., Edwards E.A., and Yakunin A.F. (2024) Enzyme cascades for in vitro and in vivo FMN prenylation and UbiD (de)carboxylase activation under aerobic conditions. Methods in Enzymology 708:151-173.doi: 10.1016/bs.mie.2024.10.015..
Golyshina O.V., Lunev E.A., Distaso M.A., Bargiela R, Gaines M.C., Daum B., Ferrer M., Bale N.J., Koenen M., Sinninghe Damsté J.S., Yakimov M.M. and Golyshin P.N. (2024) Oxyplasma meridianum gen. nov. sp. nov., an extremely acidophilic organotrophic member of the order Thermoplasmatales. International Journal of Systematic and Evolutionary Microbiology 74(8):006499. doi: 10.1099/ijsem.0.006499.
Srivastava P.L., Johns S.T., Voice A., Morley K., Escorcia A.M., Miller D.J., Allemann R.K. and van der Kamp M.W, (2024) Simulation-guided engineering enables a functional switch in selinadiene synthase towards hydroxylation. ACS Catalysis 14(14):11034-11043, DOI: 10.1021/acscatal.4c02032.
Nishikawa S., Yu W.-C., Jia T.Z., He M.-J., Khusnutdinova A., Yakunin A.F., Chiang Y.-R., Fujishima K., and Wang P.-H. (2024) Amino acid self-regenerating cell-free protein synthesis system that feeds on PLA plastics, CO2, ammonium, and a-ketoglutarate. ACS Catalysis 14:7696-7706.
Khusnutdinova A.N., Tran H., Devlekar S., Distaso M.A., Kublanov I.V., Stogios P., Savchenko A., Ferrer M., Golyshina O.V., Yakunin A.F. and Golyshin P.N. (2024) Moderately thermostable GH1 b-glucosidases from hyperacidophilic archaeon Cuniculiplasma divulgatum S5. FEMS Microbiology Ecology 100: fiae114. doi: 10.1093/femsec/fiae114
Lemak S., Brown G., Makarova K.S., Koonin E.V. and Yakunin A.F. (2024) Biochemical plasticity of the Escherichia coli CRISPR Cascade revealed by in vitro reconstitution of Cascade activities from purified Cas proteins. The FEBS Journal doi:10.1111/febs.17295
Urbanus M.L., Zheng T.M., Khusnutdinova A.N., Banh D., O'Connor Mount H., Gupta A., Stogios P.J., Savchenko A., Isberg R.R., Yakunin A.F., and Ensminger A.W. (2024) A random mutagenesis screen enriched for missense mutations in bacterial effector proteins. G3 (Bethesda) 14(9):jkae158. doi:10.1093/g3journal/jkae158
Graf M., Greenfield L.M., Reay M.K., Bargiela R., Golyshin P.N., Evershed R.P., Lloyd C.E.M., Williams G.B., Chadwick D.R., Jones D.L. (2024) Field-based assessment of the effect of conventional and biodegradable plastic mulch film on nitrogen partitioning, soil microbial diversity, and maize biomass. Applied Soil Ecology 202:105595. DOI: 10.1016/j.apsoil.2024.105595.
Requena V.G., Srivastava P.L., Miller D.J. and Allemann R.K. (2024) Single Point Mutation Abolishes Water Capture in Germacradien-4-ol Synthase, Chembiochem e202400290. DOI: 10.1002/cbic.202400290.
Srivastava P.L., Johns S.T., Miller D.J., Allemann R.K. (2024) Production of non-natural terpenoids through chemoenzymatic synthesis using substrate analogs, Methods in Enzymology 699:207-230. DOI: 10.1016/bs.mie.2024.03.015.
Reay M.K., Graf M., Greenfield L., Bargiela R., Onyije C., Lloyd C.E.M., Bull I.D., Evershed R. P., Golyshin P., Chadwick D., Jones D.L. (2024) Microbial degradation of bioplastic (PHBV) is limited by nutrient availability at high microplastic loadings. Environmental Sciences: Advances DOI: 10.1039/D4VA00311J
Hassard F., Curtis T.P., Dotro G.C., Golyshin P., Gutierrez T., Heaven S., Horsfall L., Jefferson B., Jones D.L., Krasnogor N., Kumar V., Lea-Smith D.J., Le Corre Pidou K., Liu Y., Lyu T., McCarthy R.R., McKew B., Smith C., Yakunin A., Yang Z., Zhang Y., Coulon F. (2024) Scaling-up Engineering Biology for Enhanced Environmental Solutions. ACS Synthetic Biology. 13(6):1586-1588. doi: 10.1021/acssynbio.4c00292.
Diep P., Stogios P.J., Evdokimova E., Savchenko A., Mahadevan R., Yakunin A.F. (2024) Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies. FEBS Journal. 291(13):2980-2993. doi: 10.1111/febs.17125.
Tulloch C.L., Bargiela R., Williams, G.B. Chernikova T.N., Cotterell B.M., Wellington E.M.H., Christie-Oleza J.A., Thomas D.N., Jones D.L., and Golyshin P.N. (2024) Temporal dynamics of microbial communities colonising plastics during transition from the wastewater treatment plant to marine waters. Environmental Microbiome. 19(1):27. doi:10.1186/s40793-024-00569-2.
Tulloch C.L., Cotterell B.M., Pântea I., Jones D.L. and Golyshin P.N. (2024) Selective microbial attachment to LDPE plastic beads during passage through the wastewater network. Chemosphere. 14:142618. DOI: 10.1016/j.chemosphere.2024.142618.
2023
Graf, M., Greenfield, L.M., Reay, M.K., Bargiela, R., Williams, G.B., Onyije, C., Lloyd, C.E.M., Bull, I.D., Evershed, R.P., Golyshin, P.N., Chadwick, D.R., and Jones D.L. (2023). Increasing concentration of pure micro- and macro-LDPE and PP plastic negatively affect crop biomass, nutrient cycling, and microbial biomass. Journal of Hazardous Materials, 458:131932.
La Cono, V., Messina, E., Reva, O., Smedile, F., La Spada, G., Crisafi, F., Marturano, L, Miguez, N., Ferrer, M., Selivanova, E.A., Golyshina, O.V., Golyshin, P.N., Rohde, M., Krupovic, M., Merkel, A.Y., Sorokin, D.Y., Hallsworth ,J.E., and Yakimov M.M. (2023). Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea. Microbial Biotechnology, 16(9):1803-1822.
Williams, G.B., Ma, H., Khusnutdinova, A.N., Yakunin, A.F. and Golyshin, P.N. (2023) Harnessing extremophilic carboxylesterases for applications in polyester depolymerisation and plastic waste recycling. Essays in Biochemistry, 67(4):715-729.
Bargiela, R., Korzhenkov, A.A., McIntosh, O.A., Toshchakov, S.V., Yakimov, M.M., Golyshin, P.N., and Golyshina, O.V. (2023). Evolutionary patterns of archaea predominant in acidic environment. Environmental Microbiome 18:61.
Lin, Y.-H., Nishikawa, S., Jia, T. Z., Yeh, F.-I., Khusnutdinova, A.N., Yakunin, A.F., Fujishima, K., and Wang, P.-H. One-pot chemo-enzymatic synthesis and one-step recovery of length-variable long-chain polyphosphates from microalgal biomass. RSC Green Chemistry, 25:9896, 2023
Khusnutdinova, A.N., Batyrova, K.A., Brown, G., Fedorchuk, T., Chai, Y.S., Skarina, T., Flick, R., Petit, A-P., Savchenko, A., Stogios, P., and Yakunin, A.F. (2023). Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases. FEBS Journal, 290:4966-4983,
Diep, P., Shen, S., Wiesner, J.A., Mykytczuk, N., Papangelakis, V., Yakunin, A.F., and Mahadevan, R. (2023) Engineering nickel bioaccumulation in Escherichia coli by NikABCDE transporter and metallothionein overexpression. Engineering in Life Sciences, e2200133,
Diep, P., Kell, B., Yakunin, A.F., Hilfinger, A., and Mahadevan, R. (2023). Quantifying metal-binding specificity of CcNikZ-II from Clostridium carboxidivorans in the presence of competing metal ions. Analytical Biochemistry, 676:115182
Karlikow, M., Amalfitano, E., Yang, X., Doucet, J., Chapman, A., Sadat-Moussavi, P., Homme, P., Sutyrina, P., Chan, W., Lemak, S., Yakunin, A.F., Dolezal, A.G., Kelley, S., Foster, L.J., Harpur, B., and Pardee, K. (2023) A PAM-free CRISPR induced DNA reorganization for multiplexed nucleic acid detection. Nature Communications, 14(1):1505.
Molina-Espeja, P., Sanz-Aparicio, S., Golyshin, P.N., et al., The FuturEnzyme Consortium (2023). Enzymes for consumer products to achieve climate neutrality. Oxford Open Climate Change, kgad003 doi: 10.1093/oxfclm/kgad003
Molina-Espeja, P., Fernandez-Lopez, L., Golyshin, P.N., and Ferrer, M. (2023). Assigning Functions of Unknown Enzymes by High-Throughput Enzyme Characterization. Methods in Molecular Biology 2555:181-194. doi: 10.1007/978-1-0716-2795-2_13.
El Houari, A., Carpenter, M., Chaplin, D., Golyshin, P.N., and McDonald, J.E. (2023) Lutispora saccharofermentans sp. nov., a mesophilic, non-spore-forming bacterium isolated from a lab-scale methanogenic landfill bioreactor digesting anaerobic sludge, and emendation of the genus Lutispora to include species which are non-spore-forming and mesophilic. International Journal of Systematic and Evolurionary Microbiology 73(1). doi: 10.1099/ijsem.0.005683.
Liu Y., Khusnutdinova A., Chen J., Crisante D., Batyrova K., Venkatesan K., Feigis M., Shirsadi E., Wang X., Dorakhan R., Wang X., Stogios P., Yakunin A.F., Sargent E., Mahadevan R. (2022) Systems engineering of Escherichia coli for net-zero emission butane production. Metabolic Engineering 74:98-107, doi: 10.1016/j.ymben.2022.10.001.
Jones, D. L., Grimsley, J.M., Kevill, J. L., Williams, R., Pellett, C., Lambert-Slosarska, K., Singer, A. C., Williams, G. B., Bargiela, R., Brown, R. W., Wade, M. J., & Farkas, K. (2022). Critical evaluation of different passive sampler materials and approaches for the recovery of SARS-COV-2, faecal-indicator viruses and bacteria from wastewater. Water, 14(21):3568.
Chakroborty, A., Pritchard, D., Bouillon, M.E., Cervi, A., Kraehenbuehl, R., Wild, C., Fenn, C., Holdsworth, P., Capner, C., Padalino, G., Forde-Thomas, JE., Payne, J., Smith, B.G., Fisher, M., Lahmann, M., Baird, M.S., and Hoffmann, K.F. (2023) Modified Hederagenin Derivatives Demonstrate Ex Vivo Anthelmintic Activity against Fasciola hepatica. Pharmaceutics. 15(7):1869.
Farkas, K., Pellett, C., Alex-Sanders, N., Bridgman, M. T., Corbishley, A., Grimsley, J. M., Kasprzyk-Hordern, B., Kevill, J. L., Pântea, I., Richardson-O’Neill, I. S., Lambert-Slosarska, K., Woodhall, N., & Jones, D. L. (2022). Comparative assessment of filtration- and precipitation-based methods for the concentration of SARS-COV-2 and other viruses from wastewater. Microbiology Spectrum 10(4):01102-22
Kevill, J. L., Lambert-Slosarska, K., Pellett, C., Woodhall, N., Richardson-O’Neill, I., Pântea, I., Alex-Sanders, N., Farkas, K., & Jones, D. L. (2022). Assessment of two types of passive sampler for the efficient recovery of SARS-COV-2 and other viruses from wastewater. Science of The Total Environment 838:156580.
Distaso, M., Cea-Rama, I., Coscolín, C., Chernikova T.N., Tran, H., Ferrer, M., Sanz-Aparicio, J., & Golyshin, P.N. (2023). The Mobility of the Cap Domain Is Essential for the Substrate Promiscuity of a Family IV Esterase from Sorghum Rhizosphere Microbiome. Applied and Environmental Microbiology, 89:e0180722. doi:10.1128/aem.01807-22
Distaso, M.A., Chernikova, T.N., Bargiela, R., Coscolin, C., Stogios, P., Gonzalez-Alfonso, J.L., Lemak, S., Khusnutdinova, A.N., Plou, F.J., Evdokimova, E., Savchenko, A., Lunev, E.A., Yakimov, M.M., Golyshina, O.V., Ferrer, M., Yakunin, A.F., & Golyshin, P.N. (2023) Thermophilic carboxylesterases from hydrothermal vents of the volcanic island of Ischia active on synthetic and biobased polymers and mycotoxins. Applied and Environmental Microbiology 89: e0170422. doi: 10.1128/aem.01704-22
Marasco, R., Fusi, M., Coscolín, C., Barozzi, A., Almendral, D., Bargiela, R., Gohlke neé Nutschel, C., Pfleger, C., Dittrich, J., Gohlke, H., Matesanz, R., Sanchez-Carrillo, S., Mapelli, F., Chernikova, T.N., Golyshin, P.N., Ferrer, M. and Daffonchio, D. (2023) Enzymes adaptation to habitat thermal legacy explains the plasticity of marine microbiomes Nature Communications 14(1):1045 doi: 10.1038/s41467-023-36610-0.
Dell'Anno, F., Joaquim van Zyl, L., Trindade, M., Buschi, E., Cannavacciuolo, A., Pepi, M., Sansone, C., Brunet, C., Ianora, A., de Pascale, D., Golyshin, P.N., Dell'Anno, A., and Rastelli, E. (2023) Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation. Environmental Pollution 317:120772. doi:10.1016/j.envpol.2022.120772.
2022
Vidal P., Martinez-Martinez M., Fernandez-Lopez L., Roda S., Mendez-Garcia C., Golyshina O.V., Guallar V., Pelaez A.I., Ferrer M. (2022) Metagenomic mining for esterases in the microbial community of Los Rueldos acid mine drainage formation. Frontiers in Microbiology 13:868839. doi: 10.3389/fmicb.2022.868839.
Greenfield L.M., Graf M., Rengaraj S., Bargiela R., Williams G., Golyshin P.N., Chadwick D.R. and Jones D.L. (2022) Field response of N2O emissions, microbial communities and soil biochemical processes to the addition of conventional and biodegradable microplastics”) Agriculture, Ecosystems & Environment 336: 108023. https://doi.org/10.1016/j.agee.2022.108023 .
Zadjelovic V., l Erni-Cassola G., Lester D., Eley Y., Gibson M.I., Dorador C., Golyshin P.N., Black S., Wellington E.M.H., and Christie-Oleza J.A. (2022) A mechanistic understanding of polyethylene biodegradation by the marine bacterium Alcanivorax, Journal of Hazardous Materials 436:129278. doi: 10.1016/j.jhazmat.2022.129278
Sorokin D.Y., Merkel A., Messina E., Tugui C., Pabst M., Golyshin P.N. and Yakimov M.M. (2022) Anaerobic carboxydotrophy in sulfur-respiring haloarchaea from hypersaline lake. The ISME Journal doi:10.1038/s41396-022-01206-x 2022
Leoni C., Manzari C., Tran H., Golyshin P.N., Pesole G., Volpicella M., Ceci L.R. (2022) Identification of an Amylomaltase from the Halophilic Archaeon Haloquadratum walsbyi by Functional Metagenomics: Structural and Functional Insights. Life 12(1): 85. https://doi.org/10.3390/life12010085
Lemak S., Serbanescu M.A., Khusnutdinova A., Ruszkowski M., Beloglazova N., Xu X., Brown G., Cui H., Tan K., Joachimiak A., Cvitkovitch D.G., Savchenko A., Yakunin A.F. (2022) Structural and biochemical insights into CRISPR RNA processing by the Cas5c ribonuclease SMU1763 from Streptococcus mutans. Journal of Biological Chemistry 297: 101251.
Chigor C.B., Ibangha I.I., Nweze N.O., Onuora V.C., Ozochi C.A., Titilawo Y., Enebe M.C., Chernikova T.N., Golyshin P.N., Chigor V.N. (2022) Prevalence of integrons in multidrug-resistant Escherichia coli isolates from waters and vegetables in Nsukka and Enugu, Southeast Nigeria. Environmental Science and Pollution Research doi:10.1007/s11356-022-20254-6
Yakimov M.M., Bargiela R, Golyshin P.N. (2022) Calm and Frenzy: marine obligate hydrocarbonoclastic bacteria sustain ocean wellness. Current Opinion in Biotechnology 73:337-345. doi: 10.1016/j.copbio.2021.09.015
Distaso M.A., Bargiela R., Johnson B., McIntosh O.A., Williams G.B., Jones D.L., Golyshin P.N., Golyshina O.V. (2022) Microbial Diversity of a Disused Copper Mine Site (Parys Mountain, UK), Dominated by Intensive Eukaryotic Filamentous Growth. Microorganisms 10(9):1694. doi: 10.3390/microorganisms10091694.
Haas D., Thamm A., Sun J., Huang L., Sun L., Beaudoin G., Wise K., Lerma-Ortiz C., Bruner S., Breuer M., Luthey-Schulten Z., Lin J., Wilson M., Brown G., Yakunin A., Kurilyak I., Folz J., Fiehn O., Glass J., Hanson A., Henry C., de Crecy-Lagard V. (2022) Metabolite damage and damage-control in a minimal genome. mBio 13: e0163022.
Diep P., Cadavid J.L., Yakunin A.F., McGuigan A.P., Mahadevan R. (2022) REVOLVER: A low-cost automated protein purifier based on parallel preparative gravity column workflows. HardwareX 11:e00291. doi:10.1016/j.ohx.2022.e00291.
Chan P.W.Y., Chakrabarti N., Ing C., Halgas O., To T.K.W., Wälti M., Petit A.P., Tran C., Savchenko A., Yakunin A.F., Edwards E.A., Pomès R., Pai E.F. (2022) Defluorination capability of L-2-Haloacid dehalogenases in the HAD-like hydrolase superfamily correlates with active site compactness. ChemBioChem, 23:e202100414. doi: 10.1002/cbic.202100414.
2021
Cea-Rama I., Coscolín C., Katsonis P., Bargiela R., Golyshin, P.N., Lichtarge O., Ferrer M., Julia -Aparicio J. (2021) Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase. Computational and Structural Biotechnology Journal 19:2307-2317 https://doi.org/10.1016/j.csbj.2021.04.041.
Eronen-Rasimus E., Hultman J., Hai T., Pessi I.S., Collins E., Wright S., Laine P., Viitamäki S., Lyra C., Thomas D.N., Golyshin P.N., Luhtanen A.M., Kuosa H., Kaartokallio H. (2021) Sea-Ice Bacteria Halomonas sp. Strain 363 and Paracoccus sp. Strain 392 Produce Multiple Types of Poly-3-Hydroxyalkaonoic Acid (PHA) Storage Polymers at Low Temperature. Applied and Environmental Microbiology 87(17):e0092921. doi: 10.1128/AEM.00929-21.
Brailsford F.L., Glanville H.C., Marshall M.R., Yates C.A., Owen A.T., Golyshin P.N., Johnes P.J., Jones D.L. (2021) Land cover and nutrient enrichment regulates low-molecular weight dissolved organic matter turnover in freshwater ecosystems. Limnology and Oceanography 66: 2979–2987. doi: 10.1002/lno.11852
Khasimov M.K., Petushkova E.P.., Khusnutdinova A.N, Zorin N.A,. Batyrova K.A., Yakunin A.F., Tsygankov A.A. (2021) The HydS C-terminal domain of the Thiocapsa bogorovii HydSL hydrogenase is involved in membrane anchoring and electron transfer. Biochimimica et Biophysica Acta Bioenergetics 1862(12):148492. doi:10.1016/j.bbabio.2021.148492.
Lemak S,. Serbanescu M.A., Khusnutdinova A.N., Ruszkowski M., Beloglazova N., Xu X., Brown G., Cui H., Tan K., Joachimiak A., Cvitkovitch D.G., Savchenko A., Yakunin A.F. (2021). Structural and biochemical insights into CRISPR RNA processing by the Cas5cribonuclease SMU1763 from Streptococcus mutans. Journal of Biological Chemistry 297(5):101251. doi: 10.1016/j.jbc.2021.101251.
Raj K., Venayak N., Diep P., Golla S.A., Yakunin A.F., Mahadevan R. (2021) Automation assisted anaerobic phenotyping for metabolic engineering. Microbial Cell Factories 20(1):184. doi: 10.1186/s12934-021-01675-3.
Choolaei Z., Flick R., Khusnutdinova A.N., Edwards E.A., Yakunin AF. (2021) Lignin-oxidizing activity of bacterial laccases characterized using soluble substrates and polymeric lignin. Journal of Biotechnology 325:128-137. Doi:10.1016/j.jbiotec.2020.11.007.
2020
Alonso Rubido S., Santiago G., Cea-Rama I., Fernandez-Lopez L., Coscolín C., Modregger J., Ressmann A., Martínez-Martínez 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. (2020) Genetically Engineered Proteins with Two Active Sites for Enhanced Biocatalysis and Synergistic Chemo- and Biocatalysis. Nature Catalysis 3:313-328. doi:10.1038/s41929-019-0394-4
Gregson B.H., Metodieva G., Metodiev M.V., Golyshin P.N., McKew B.A. (2020) Protein expression in the obligate hydrocarbon-degrading psychrophile Oleispira antarctica RB-8 during alkane degradation and cold tolerance. Environmental Microbiology 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. and Jones D.L. (2020). Rapid depletion of dissolved organic sulphur (DOS) in freshwaters. Biogeochemistry 149:105-113. https://doi.org/10.1007/s10533-020-00669-4
Bargiela R., Lanthaler K., Potter C.M., Ferrer M., Yakunin A.F., Paizs B., Golyshin P.N. and Golyshina O.V. (2020) Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum. Microorganisms 8: 759.
Dell’Anno F., Brunet C., van Zyl L.J., Trindade, M., Golyshin P.N., Dell’Anno A., Ianora A. and Sansone C. (2020) Degradation of Hydrocarbons and Heavy Metal Reduction by Marine Bacteria in Highly Contaminated Sediments. Microorganisms 8:1402.
La Cono V., Messina E., Arcadi E., Ciordia S., Crisafi F., Denaro R., Ferrer M., Giuliano L., Golyshin P.N., Golyshina O.V., Hallsworth J., La Spada G., Mena M., Rohde M., Goeva M., Smedile F., Sorokin D.Y., Toshchakov S.V., and Yakimov M.M. (2020) Symbiosis between nanohaloarchaeon and haloarchaeon is based on utilization of different polysaccharides Proceedings of the National Academy of Sciences of the U.S.A. 117 (33): 20223–20234. doi:10.1073/pnas.2007232117.
Chernyh N.A., Neukirchen S., Frolov E.N., Sousa F.L., Miroshnichenko M.L., Merkel A.Y., Pimenov N.V., Sorokin D.Y., Ciordia S., Mena M., Ferrer M., Golyshin P.N., Lebedinsky A.V., Cardoso Pereira I.A., Bonch-Osmolovskaya E.A. (2020) Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur metabolism. Nature Microbiology 5(11):1428-1438. DOI: 10.1038/s41564-020-0776-z
Ghuneim L.A.J., Distaso M.A., Chernikova T.N., Bargiela R., Lunev E.A., Korzhenkov A.A., Toshchakov S.V., Rojo D., Barbas C., Ferrer M., Golyshina O.V., Golyshin P.N., Jones D.L. (2020) Utilization of low molecular weight organic compounds by the filterable fraction of a lotic microbiome. FEMS Microbiology Ecology (7(2):fiaa244. doi: 10.1093/femsec/fiaa244.)
Chernikova T.N., Bargiela R., Toshchakov S.V., Lunev E.A., Shivaraman V., Yakimov M.M., Thomas D.N. and Golyshin P.N. (2020) Hydrocarbon-degrading bacteria Alcanivorax and Marinobacter associated with microalgae Pavlova lutheri and Nannochloropsis oculata. Frontiers in Microbiology 11:2650.
Distaso M.A., Bargiela R., Brailsford F., Williams G.B., Wright S.F., Lunev E.A., Toshchakov S.V. Yakimov M.M., Jones D.L., Golyshin P.N. and Golyshina O.V. (2020) High representation of archaea across all depths in oxic and low-pH sediment layers underlying an acidic stream. Frontiers in Microbiology 11: 2871. https://doi.org/10.3389/fmicb.2020.576520.
2018-2019
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.
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.
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 85(2): e02404-18. 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.