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For: Bastard K, Smith AAT, Vergne-vaxelaire C, Perret A, Zaparucha A, De Melo-minardi R, Mariage A, Boutard M, Debard A, Lechaplais C, Pelle C, Pellouin V, Perchat N, Petit J, Kreimeyer A, Medigue C, Weissenbach J, Artiguenave F, De Berardinis V, Vallenet D, Salanoubat M. Revealing the hidden functional diversity of an enzyme family. Nat Chem Biol 2014;10:42-9. [DOI: 10.1038/nchembio.1387] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/02/2013] [Indexed: 11/08/2022]
Number Cited by Other Article(s)
1
Satanowski A, Marchal DG, Perret A, Petit JL, Bouzon M, Döring V, Dubois I, He H, Smith EN, Pellouin V, Petri HM, Rainaldi V, Nattermann M, Burgener S, Paczia N, Zarzycki J, Heinemann M, Bar-Even A, Erb TJ. Design and implementation of aerobic and ambient CO2-reduction as an entry-point for enhanced carbon fixation. Nat Commun 2025;16:3134. [PMID: 40169551 PMCID: PMC11961710 DOI: 10.1038/s41467-025-57549-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 02/25/2025] [Indexed: 04/03/2025]  Open
2
Burroughs AM, Nicastro GG, Aravind L. The Lipocone Superfamily: A Unifying Theme In Metabolism Of Lipids, Peptidoglycan And Exopolysaccharides, Inter-Organismal Conflicts And Immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.14.632903. [PMID: 40236132 PMCID: PMC11996534 DOI: 10.1101/2025.01.14.632903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
3
Qian W, Wang X, Huang Y, Kang Y, Pan P, Hsieh CY, Hou T. Deep Learning-Driven Insights into Enzyme-Substrate Interaction Discovery. J Chem Inf Model 2025;65:187-200. [PMID: 39721977 DOI: 10.1021/acs.jcim.4c01801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2024]
4
Wang J, Kong J, Zhang X. Riboflavin-induced photo-ATRP electrochemical strategy for detection of biomarker trypsin. Talanta 2024;277:126386. [PMID: 38876027 DOI: 10.1016/j.talanta.2024.126386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/28/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
5
Li Y, Xu T, Tu Y, Li T, Wei Y, Zhou Y. An aldolase-dependent phloroglucinol degradation pathway in Collinsella sp. zg1085. Appl Environ Microbiol 2024;90:e0104724. [PMID: 39028195 PMCID: PMC11337842 DOI: 10.1128/aem.01047-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]  Open
6
Han Y, Zhang H, Zeng Z, Liu Z, Lu D, Liu Z. Descriptor-augmented machine learning for enzyme-chemical interaction predictions. Synth Syst Biotechnol 2024;9:259-268. [PMID: 38450325 PMCID: PMC10915406 DOI: 10.1016/j.synbio.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024]  Open
7
Atallah C, James K, Ou Z, Skelton J, Markham D, Burridge MS, Finnigan J, Charnock S, Wipat A. A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem. Biosystems 2024;236:105105. [PMID: 38160995 DOI: 10.1016/j.biosystems.2023.105105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
8
Yuan B, Yang D, Qu G, Turner NJ, Sun Z. Biocatalytic reductive aminations with NAD(P)H-dependent enzymes: enzyme discovery, engineering and synthetic applications. Chem Soc Rev 2024;53:227-262. [PMID: 38059509 DOI: 10.1039/d3cs00391d] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
9
Pinotsis N, Krüger A, Tomas N, Chatziefthymiou SD, Litz C, Mortensen SA, Daffé M, Marrakchi H, Antranikian G, Wilmanns M. Discovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex. Nat Commun 2023;14:7649. [PMID: 38012138 PMCID: PMC10682391 DOI: 10.1038/s41467-023-43354-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/07/2023] [Indexed: 11/29/2023]  Open
10
Brunetti AE, Lyra ML, Bauermeister A, Bunk B, Boedeker C, Müsken M, Neto FC, Mendonça JN, Caraballo-Rodríguez AM, Melo WG, Pupo MT, Haddad CF, Cabrera GM, Overmann J, Lopes NP. Host macrocyclic acylcarnitines mediate symbiotic interactions between frogs and their skin microbiome. iScience 2023;26:108109. [PMID: 37867936 PMCID: PMC10587524 DOI: 10.1016/j.isci.2023.108109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/23/2023] [Accepted: 09/28/2023] [Indexed: 10/24/2023]  Open
11
Zhou Y, Wei Y, Jiang L, Jiao X, Zhang Y. Anaerobic phloroglucinol degradation by Clostridium scatologenes. mBio 2023;14:e0109923. [PMID: 37341492 PMCID: PMC10470551 DOI: 10.1128/mbio.01099-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 06/22/2023]  Open
12
Zhou Y, Wei Y, Jiang L, Zhang Y, Jiao X. A (S)-3-Hydroxybutyrate Dehydrogenase Belonging to the 3-Hydroxyacyl-CoA Dehydrogenase Family Facilitates Hydroxyacid Degradation in Anaerobic Bacteria. Appl Environ Microbiol 2023;89:e0036623. [PMID: 37255440 PMCID: PMC10305046 DOI: 10.1128/aem.00366-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/12/2023] [Indexed: 06/01/2023]  Open
13
Singh R, Sledzieski S, Bryson B, Cowen L, Berger B. Contrastive learning in protein language space predicts interactions between drugs and protein targets. Proc Natl Acad Sci U S A 2023;120:e2220778120. [PMID: 37289807 PMCID: PMC10268324 DOI: 10.1073/pnas.2220778120] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/10/2023] [Indexed: 06/10/2023]  Open
14
Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023;66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
15
Role of carnitine in adaptation of Chromohalobacter salexigens DSM 3043 and its mutants to osmotic and temperature stress in defined medium. Extremophiles 2022;26:28. [DOI: 10.1007/s00792-022-01276-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022]
16
Perchat N, Dubois C, Mor-Gautier R, Duquesne S, Lechaplais C, Roche D, Fouteau S, Darii E, Perret A. Characterization of a novel β-alanine biosynthetic pathway consisting of promiscuous metabolic enzymes. J Biol Chem 2022;298:102067. [PMID: 35623386 PMCID: PMC9213253 DOI: 10.1016/j.jbc.2022.102067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 10/28/2022]  Open
17
Caparco AA, Dautel DR, Champion JA. Protein Mediated Enzyme Immobilization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022;18:e2106425. [PMID: 35182030 DOI: 10.1002/smll.202106425] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/22/2021] [Indexed: 06/14/2023]
18
Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing. Appl Environ Microbiol 2022;88:e0243021. [PMID: 35285712 DOI: 10.1128/aem.02430-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
19
Lee JA, Stolyar S, Marx CJ. Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae. Front Microbiol 2022;13:849573. [PMID: 35359736 PMCID: PMC8963497 DOI: 10.3389/fmicb.2022.849573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/16/2022] [Indexed: 11/18/2022]  Open
20
Li S, Horsman GP. An inventory of early branch points in microbial phosphonate biosynthesis. Microb Genom 2022;8. [PMID: 35188456 PMCID: PMC8942020 DOI: 10.1099/mgen.0.000781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
21
Machine learning modeling of family wide enzyme-substrate specificity screens. PLoS Comput Biol 2022;18:e1009853. [PMID: 35143485 PMCID: PMC8865696 DOI: 10.1371/journal.pcbi.1009853] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/23/2022] [Accepted: 01/21/2022] [Indexed: 11/19/2022]  Open
22
Rembeza E, Boverio A, Fraaije MW, Engqvist MKM. Discovery of Two Novel Oxidases Using a High-Throughput Activity Screen. Chembiochem 2022;23:e202100510. [PMID: 34709726 PMCID: PMC9299179 DOI: 10.1002/cbic.202100510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/27/2021] [Indexed: 12/17/2022]
23
Rahman ASMZ, Timmerman L, Gallardo F, Cardona ST. Identification of putative essential protein domains from high-density transposon insertion sequencing. Sci Rep 2022;12:962. [PMID: 35046497 PMCID: PMC8770471 DOI: 10.1038/s41598-022-05028-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/29/2021] [Indexed: 12/24/2022]  Open
24
Klaus M, Zurek PJ, Kaminski TS, Pushpanath A, Neufeld K, Hollfelder F. Ultrahigh-Throughput Detection of Enzymatic Alcohol Dehydrogenase Activity in Microfluidic Droplets with a Direct Fluorogenic Assay. Chembiochem 2021;22:3292-3299. [PMID: 34643305 PMCID: PMC9291573 DOI: 10.1002/cbic.202100322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/13/2021] [Indexed: 12/02/2022]
25
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class. PLoS Comput Biol 2021;17:e1009446. [PMID: 34555022 PMCID: PMC8491902 DOI: 10.1371/journal.pcbi.1009446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 10/05/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022]  Open
26
Bessonnet T, Mariage A, Petit JL, Pellouin V, Debard A, Zaparucha A, Vergne-Vaxelaire C, de Berardinis V. Purification and Characterization of Nit phym , a Robust Thermostable Nitrilase From Paraburkholderia phymatum. Front Bioeng Biotechnol 2021;9:686362. [PMID: 34277586 PMCID: PMC8280356 DOI: 10.3389/fbioe.2021.686362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022]  Open
27
Key amino acid residues in homoserine-acetyltransferase from M. tuberculosis give insight into the evolution of MetX family of enzymes - HAT, SAT and HST. Biochimie 2021;189:13-25. [PMID: 34090964 DOI: 10.1016/j.biochi.2021.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/23/2021] [Accepted: 05/30/2021] [Indexed: 11/22/2022]
28
Reynolds KA, Rosa-Molinar E, Ward RE, Zhang H, Urbanowicz BR, Settles AM. Accelerating biological insight for understudied genes. Integr Comp Biol 2021;61:2233-2243. [PMID: 33970251 DOI: 10.1093/icb/icab029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
29
Mehla J, Liechti G, Morgenstein RM, Caufield JH, Hosseinnia A, Gagarinova A, Phanse S, Goodacre N, Brockett M, Sakhawalkar N, Babu M, Xiao R, Montelione GT, Vorobiev S, den Blaauwen T, Hunt JF, Uetz P. ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis. J Biol Chem 2021;296:100700. [PMID: 33895137 PMCID: PMC8163987 DOI: 10.1016/j.jbc.2021.100700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 01/26/2023]  Open
30
Caparco AA, Pelletier E, Petit JL, Jouenne A, Bommarius BR, Berardinis V, Zaparucha A, Champion JA, Bommarius AS, Vergne‐Vaxelaire C. Metagenomic Mining for Amine Dehydrogenase Discovery. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000094] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
31
Pascoal F, Magalhães C, Costa R. The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential. Front Microbiol 2020;11:231. [PMID: 32140148 PMCID: PMC7042395 DOI: 10.3389/fmicb.2020.00231] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 01/31/2020] [Indexed: 12/15/2022]  Open
32
Domergue J, Erdmann D, Fossey-Jouenne A, Petit JL, Debard A, de Berardinis V, Vergne-Vaxelaire C, Zaparucha A. XszenFHal, a novel tryptophan 5-halogenase from Xenorhabdus szentirmaii. AMB Express 2019;9:175. [PMID: 31673806 PMCID: PMC6823310 DOI: 10.1186/s13568-019-0898-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 10/17/2019] [Indexed: 11/27/2022]  Open
33
Enzymes from Marine Polar Regions and Their Biotechnological Applications. Mar Drugs 2019;17:md17100544. [PMID: 31547548 PMCID: PMC6835263 DOI: 10.3390/md17100544] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022]  Open
34
Discovery of novel enzyme genes involved in the conversion of an arylglycerol-β-aryl ether metabolite and their use in generating a metabolic pathway for lignin valorization. Metab Eng 2019;55:258-267. [DOI: 10.1016/j.ymben.2019.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/03/2019] [Indexed: 11/20/2022]
35
Weissenbach J. Exploring biochemical diversity in bacteria. AN ACAD BRAS CIENC 2019;91:e20190252. [PMID: 31365611 DOI: 10.1590/0001-3765201920190252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/18/2019] [Indexed: 11/21/2022]  Open
36
Belkhelfa S, Roche D, Dubois I, Berger A, Delmas VA, Cattolico L, Perret A, Labadie K, Perdereau AC, Darii E, Pateau E, de Berardinis V, Salanoubat M, Bouzon M, Döring V. Continuous Culture Adaptation of Methylobacterium extorquens AM1 and TK 0001 to Very High Methanol Concentrations. Front Microbiol 2019;10:1313. [PMID: 31281294 PMCID: PMC6595629 DOI: 10.3389/fmicb.2019.01313] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/27/2019] [Indexed: 11/13/2022]  Open
37
A family of native amine dehydrogenases for the asymmetric reductive amination of ketones. Nat Catal 2019. [DOI: 10.1038/s41929-019-0249-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
38
Characterization of l-Carnitine Metabolism in Sinorhizobium meliloti. J Bacteriol 2019;201:JB.00772-18. [PMID: 30670548 DOI: 10.1128/jb.00772-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 11/20/2022]  Open
39
Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. mSystems 2019;4:mSystems00297-18. [PMID: 30746495 PMCID: PMC6365646 DOI: 10.1128/msystems.00297-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/12/2019] [Indexed: 12/13/2022]  Open
40
Rico J, Duquesne K, Petit JL, Mariage A, Darii E, Peruch F, de Berardinis V, Iacazio G. Exploring natural biodiversity to expand access to microbial terpene synthesis. Microb Cell Fact 2019;18:23. [PMID: 30709396 PMCID: PMC6359773 DOI: 10.1186/s12934-019-1074-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/24/2019] [Indexed: 12/05/2022]  Open
41
Hill A, Chen L, Mariage A, Petit JL, de Berardinis V, Karboune S. Discovery of new levansucrase enzymes with interesting properties and improved catalytic activity to produce levan and fructooligosaccharides. Catal Sci Technol 2019. [DOI: 10.1039/c9cy00135b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
42
Bastard K, Isabet T, Stura EA, Legrand P, Zaparucha A. Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family. Sci Rep 2018;8:16587. [PMID: 30410048 PMCID: PMC6224419 DOI: 10.1038/s41598-018-34795-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/23/2018] [Indexed: 12/19/2022]  Open
43
Franco M, D'haeseleer PM, Branda SS, Liou MJ, Haider Y, Segelke BW, El-Etr SH. Proteomic Profiling of Burkholderia thailandensis During Host Infection Using Bio-Orthogonal Noncanonical Amino Acid Tagging (BONCAT). Front Cell Infect Microbiol 2018;8:370. [PMID: 30406044 PMCID: PMC6206043 DOI: 10.3389/fcimb.2018.00370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/03/2018] [Indexed: 01/01/2023]  Open
44
Copp JN, Akiva E, Babbitt PC, Tokuriki N. Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry 2018;57:4651-4662. [PMID: 30052428 DOI: 10.1021/acs.biochem.8b00473] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
45
Carter MS, Zhang X, Huang H, Bouvier JT, Francisco BS, Vetting MW, Al-Obaidi N, Bonanno JB, Ghosh A, Zallot RG, Andersen HM, Almo SC, Gerlt JA. Functional assignment of multiple catabolic pathways for D-apiose. Nat Chem Biol 2018;14:696-705. [PMID: 29867142 DOI: 10.1038/s41589-018-0067-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
46
Vergne-Vaxelaire C, Mariage A, Petit JL, Fossey-Jouenne A, Guérard-Hélaine C, Darii E, Debard A, Nepert S, Pellouin V, Lemaire M, Zaparucha A, Salanoubat M, de Berardinis V. Characterization of a thermotolerant ROK-type mannofructokinase from Streptococcus mitis: application to the synthesis of phosphorylated sugars. Appl Microbiol Biotechnol 2018;102:5569-5583. [DOI: 10.1007/s00253-018-9018-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/29/2018] [Accepted: 04/10/2018] [Indexed: 01/08/2023]
47
Vanacek P, Sebestova E, Babkova P, Bidmanova S, Daniel L, Dvorak P, Stepankova V, Chaloupkova R, Brezovsky J, Prokop Z, Damborsky J. Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03523] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Transcriptional Regulation of Carnitine Catabolism in Pseudomonas aeruginosa by CdhR. mSphere 2018;3:mSphere00480-17. [PMID: 29435492 PMCID: PMC5806209 DOI: 10.1128/msphere.00480-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/16/2018] [Indexed: 01/26/2023]  Open
49
Underground metabolism: network-level perspective and biotechnological potential. Curr Opin Biotechnol 2018;49:108-114. [DOI: 10.1016/j.copbio.2017.07.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/18/2022]
50
.Newton MS, Arcus VL, Gerth ML, Patrick WM. Enzyme evolution: innovation is easy, optimization is complicated. Curr Opin Struct Biol 2018;48:110-116. [DOI: 10.1016/j.sbi.2017.11.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
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