Extending Biochemical Databases by Metabolomic Surveys

被引：61

作者：

Fiehn, Oliver ^{[1
]}

Barupal, Dinesh K. ^{[1
]}

Kind, Tobias ^{[1
]}

机构：

[1] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA

来源：

JOURNAL OF BIOLOGICAL CHEMISTRY | 2011年 / 286卷 / 27期

关键词：

ESCHERICHIA-COLI; BIOLOGICAL PATHWAYS; MASS-SPECTROMETRY; PROTEIN SUPERFAMILIES; ENZYME PROMISCUITY; PLANT METABOLOMICS; INFORMATION-SYSTEM; STRUCTURAL BASIS; KEGG ATLAS; GC-MS;

D O I：

10.1074/jbc.R110.173617

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Metabolomics can map the large metabolic diversity in species, organs, or cell types. In addition to gains in enzyme specificity, many enzymes have retained substrate and reaction promiscuity. Enzyme promiscuity and the large number of enzymes with unknown enzyme function may explain the presence of a plethora of unidentified compounds in metabolomic studies. Cataloguing the identity and differential abundance of all detectable metabolites in metabolomic repositories may detail which compounds and pathways contribute to vital biological functions. The current status in metabolic databases is reviewed concomitant with tools to map and visualize the metabolome.

引用

收藏

页码：23637 / 23643

页数：7

相关论文

共 79 条

[1] The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase [J].

Afriat, Livnat ;

Roodveldt, Cintia ;

Manco, Giuseppe ;

Tawfik, Dan S. .

BIOCHEMISTRY, 2006, 45 (46) :13677-13686

[2] The 'evolvability' of promiscuous protein functions [J].

Aharoni, A ;

Gaidukov, L ;

Khersonsky, O ;

Gould, SM ;

Roodveldt, C ;

Tawfik, DS .

NATURE GENETICS, 2005, 37 (01) :73-76

[3]

[Anonymous], 2007, ANGEW CHEM INT EDIT

[4] TICL - a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics [J].

Antonov, Alexey V. ;

Dietmann, Sabine ;

Wong, Philip ;

Mewes, Hans W. .

FEBS JOURNAL, 2009, 276 (07) :2084-2094

[5] The metabolic world of Escherichia coli is not small [J].

Arita, M .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (06) :1543-1547

[6] Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database [J].

Arita, Masanori ;

Suwa, Kazuhiro .

BIODATA MINING, 2008, 1 (1)

[7] Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies [J].

Atkinson, Holly J. ;

Morris, John H. ;

Ferrin, Thomas E. ;

Babbitt, Patricia C. .

PLOS ONE, 2009, 4 (02)

[8] Pathguide: a Pathway Resource List [J].

Bader, Gary D. ;

Cary, Michael P. ;

Sander, Chris .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D504-D506

[9] PlantMetabolomics.org: A Web Portal for Plant Metabolomics Experiments [J].

Bais, Preeti ;

Moon, Stephanie M. ;

He, Kun ;

Leitao, Ricardo ;

Dreher, Kate ;

Walk, Tom ;

Sucaet, Yves ;

Barkan, Lenore ;

Wohlgemuth, Gert ;

Roth, Mary R. ;

Wurtele, Eve Syrkin ;

Dixon, Philip ;

Fiehn, Oliver ;

Lange, B. Markus ;

Shulaev, Vladimir ;

Sumner, Lloyd W. ;

Welti, Ruth ;

Nikolau, Basil J. ;

Rhee, Seung Y. ;

Dickerson, Julie A. .

PLANT PHYSIOLOGY, 2010, 152 (04) :1807-1816

[10] Pathway databases and tools for their exploitation: benefits, current limitations and challenges [J].

Bauer-Mehren, Anna ;

Furlong, Laura I. ;

Sanz, Ferran .

MOLECULAR SYSTEMS BIOLOGY, 2009, 5

← 1 2 3 4 5 6 7 8 →