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For: Chen L, Vitkup D. Distribution of orphan metabolic activities. Trends Biotechnol 2007;25:343-8. [PMID: 17580095 DOI: 10.1016/j.tibtech.2007.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 04/17/2007] [Accepted: 06/01/2007] [Indexed: 10/23/2022]
Number Cited by Other Article(s)
1
Zarin S, Shariq M, Rastogi N, Ahuja Y, Manjunath P, Alam A, Hasnain SE, Ehtesham NZ. Rv2231c, a unique histidinol phosphate aminotransferase from Mycobacterium tuberculosis, supports virulence by inhibiting host-directed defense. Cell Mol Life Sci 2024;81:203. [PMID: 38698289 PMCID: PMC11065945 DOI: 10.1007/s00018-024-05200-8] [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: 06/23/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 05/05/2024]
2
Rhee KY, Jansen RS, Grundner C. Activity-based annotation: the emergence of systems biochemistry. Trends Biochem Sci 2022;47:785-794. [PMID: 35430135 PMCID: PMC9378515 DOI: 10.1016/j.tibs.2022.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/10/2022] [Accepted: 03/22/2022] [Indexed: 01/21/2023]
3
Tounta V, Liu Y, Cheyne A, Larrouy-Maumus G. Metabolomics in infectious diseases and drug discovery. Mol Omics 2021;17:376-393. [PMID: 34125125 PMCID: PMC8202295 DOI: 10.1039/d1mo00017a] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
4
Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. Nat Commun 2020;11:1960. [PMID: 32327655 PMCID: PMC7181641 DOI: 10.1038/s41467-020-15876-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/31/2020] [Indexed: 01/01/2023]  Open
5
Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application. CRYSTALS 2019. [DOI: 10.3390/cryst9110597] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
6
Emerging Approaches to Tuberculosis Drug Development: At Home in the Metabolome. Trends Pharmacol Sci 2017;38:393-405. [PMID: 28169001 DOI: 10.1016/j.tips.2017.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 01/24/2023]
7
Sévin DC, Fuhrer T, Zamboni N, Sauer U. Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Nat Methods 2016;14:187-194. [DOI: 10.1038/nmeth.4103] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/19/2016] [Indexed: 12/14/2022]
8
Vianello A, Passamonti S. Biochemistry and physiology within the framework of the extended synthesis of evolutionary biology. Biol Direct 2016;11:7. [PMID: 26861860 PMCID: PMC4748562 DOI: 10.1186/s13062-016-0109-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/01/2016] [Indexed: 11/10/2022]  Open
9
Monk J, Nogales J, Palsson BO. Optimizing genome-scale network reconstructions. Nat Biotechnol 2015;32:447-52. [PMID: 24811519 DOI: 10.1038/nbt.2870] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
10
Hartman TE, Rhee KY. Microbial Metabolomics: Fifty Shades of Metabolism. ACS Infect Dis 2015;1:73-5. [PMID: 27620146 DOI: 10.1021/id500041w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
11
Jacobson MP, Kalyanaraman C, Zhao S, Tian B. Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. Trends Biochem Sci 2014;39:363-71. [PMID: 24998033 DOI: 10.1016/j.tibs.2014.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/26/2014] [Accepted: 05/29/2014] [Indexed: 02/06/2023]
12
Sorokina M, Stam M, Médigue C, Lespinet O, Vallenet D. Profiling the orphan enzymes. Biol Direct 2014;9:10. [PMID: 24906382 PMCID: PMC4084501 DOI: 10.1186/1745-6150-9-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/29/2014] [Indexed: 11/10/2022]  Open
13
Prosser GA, Larrouy-Maumus G, de Carvalho LPS. Metabolomic strategies for the identification of new enzyme functions and metabolic pathways. EMBO Rep 2014;15:657-69. [PMID: 24829223 PMCID: PMC4197876 DOI: 10.15252/embr.201338283] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
14
Shearer AG, Altman T, Rhee CD. Finding sequences for over 270 orphan enzymes. PLoS One 2014;9:e97250. [PMID: 24826896 PMCID: PMC4020792 DOI: 10.1371/journal.pone.0097250] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 04/16/2014] [Indexed: 01/04/2023]  Open
15
Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput Biol 2013;9:e1003126. [PMID: 23935467 PMCID: PMC3730674 DOI: 10.1371/journal.pcbi.1003126] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 05/20/2013] [Indexed: 11/18/2022]  Open
16
Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity. Biochem J 2013;449:427-35. [PMID: 23067238 DOI: 10.1042/bj20120980] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
17
Fragment and conquer: from structure to complexes to function. Structure 2013;20:1617-9. [PMID: 23063007 DOI: 10.1016/j.str.2012.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
18
The mitochondrial permeability transition pore (PTP) — An example of multiple molecular exaptation? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012;1817:2072-86. [DOI: 10.1016/j.bbabio.2012.06.620] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 06/19/2012] [Accepted: 06/21/2012] [Indexed: 11/21/2022]
19
Creek DJ, Chokkathukalam A, Jankevics A, Burgess KEV, Breitling R, Barrett MP. Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation. Anal Chem 2012;84:8442-7. [PMID: 22946681 PMCID: PMC3472505 DOI: 10.1021/ac3018795] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
20
The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PLoS Comput Biol 2012;8:e1002540. [PMID: 22693442 PMCID: PMC3364942 DOI: 10.1371/journal.pcbi.1002540] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 04/01/2012] [Indexed: 12/17/2022]  Open
21
Ehrt S, Rhee K. Mycobacterium tuberculosis metabolism and host interaction: mysteries and paradoxes. Curr Top Microbiol Immunol 2012;374:163-88. [PMID: 23242856 DOI: 10.1007/82_2012_299] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
22
Galeazzi L, Bocci P, Amici A, Brunetti L, Ruggieri S, Romine M, Reed S, Osterman AL, Rodionov DA, Sorci L, Raffaelli N. Identification of nicotinamide mononucleotide deamidase of the bacterial pyridine nucleotide cycle reveals a novel broadly conserved amidohydrolase family. J Biol Chem 2011;286:40365-75. [PMID: 21953451 PMCID: PMC3220592 DOI: 10.1074/jbc.m111.275818] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/29/2011] [Indexed: 11/06/2022]  Open
23
Rolfsson O, Palsson BØ, Thiele I. The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC SYSTEMS BIOLOGY 2011;5:155. [PMID: 21962087 PMCID: PMC3224382 DOI: 10.1186/1752-0509-5-155] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 10/01/2011] [Indexed: 11/29/2022]
24
Mu F, Unkefer CJ, Unkefer PJ, Hlavacek WS. Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds. Bioinformatics 2011;27:1537-45. [PMID: 21478194 PMCID: PMC3102224 DOI: 10.1093/bioinformatics/btr177] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 02/23/2011] [Accepted: 03/25/2011] [Indexed: 12/30/2022]  Open
25
Central carbon metabolism in Mycobacterium tuberculosis: an unexpected frontier. Trends Microbiol 2011;19:307-14. [PMID: 21561773 DOI: 10.1016/j.tim.2011.03.008] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 03/29/2011] [Accepted: 03/31/2011] [Indexed: 11/23/2022]
26
Pritchard L, Birch P. A systems biology perspective on plant-microbe interactions: biochemical and structural targets of pathogen effectors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011;180:584-603. [PMID: 21421407 DOI: 10.1016/j.plantsci.2010.12.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/13/2010] [Accepted: 12/15/2010] [Indexed: 05/22/2023]
27
Orth JD, Palsson BØ. Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng 2010;107:403-12. [PMID: 20589842 DOI: 10.1002/bit.22844] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
28
Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ. A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC SYSTEMS BIOLOGY 2010;4:140. [PMID: 20959003 PMCID: PMC2978158 DOI: 10.1186/1752-0509-4-140] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 10/19/2010] [Indexed: 12/16/2022]
29
de Carvalho LPS, Zhao H, Dickinson CE, Arango NM, Lima CD, Fischer SM, Ouerfelli O, Nathan C, Rhee KY. Activity-based metabolomic profiling of enzymatic function: identification of Rv1248c as a mycobacterial 2-hydroxy-3-oxoadipate synthase. ACTA ACUST UNITED AC 2010;17:323-32. [PMID: 20416504 DOI: 10.1016/j.chembiol.2010.03.009] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 03/01/2010] [Accepted: 03/11/2010] [Indexed: 12/24/2022]
30
Saito N, Ohashi Y, Soga T, Tomita M. Unveiling cellular biochemical reactions via metabolomics-driven approaches. Curr Opin Microbiol 2010;13:358-62. [DOI: 10.1016/j.mib.2010.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 04/07/2010] [Accepted: 04/08/2010] [Indexed: 12/18/2022]
31
'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it. Biochem J 2009;425:1-11. [PMID: 20001958 DOI: 10.1042/bj20091328] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
32
Zamboni N, Sauer U. Novel biological insights through metabolomics and 13C-flux analysis. Curr Opin Microbiol 2009;12:553-8. [PMID: 19744879 DOI: 10.1016/j.mib.2009.08.003] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 07/31/2009] [Accepted: 08/06/2009] [Indexed: 11/28/2022]
33
Saito N, Robert M, Kochi H, Matsuo G, Kakazu Y, Soga T, Tomita M. Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli. J Biol Chem 2009;284:16442-16451. [PMID: 19372223 DOI: 10.1074/jbc.m109.002089] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
34
Lacroix V, Cottret L, Thébault P, Sagot MF. An introduction to metabolic networks and their structural analysis. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2008;5:594-617. [PMID: 18989046 DOI: 10.1109/tcbb.2008.79] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
35
New surveyor tools for charting microbial metabolic maps. Nat Rev Microbiol 2008;6:156-61. [PMID: 18026122 DOI: 10.1038/nrmicro1797] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
36
Fuhrer T, Chen L, Sauer U, Vitkup D. Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli. J Bacteriol 2007;189:8073-8. [PMID: 17873044 PMCID: PMC2168661 DOI: 10.1128/jb.01027-07] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
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