A pathway for every product? Tools to discover and design plant metabolism
Abstract
The vast diversity of plant natural products is a powerful indication of the biosynthetic capacity of plant metabolism. Synthetic biology seeks to capitalize on this ability by understanding and reconfiguring the biosynthetic pathways that generate this diversity to produce novel products with improved efficiency. In this work, we review the algorithms and databases that presently support the design and manipulation of metabolic pathways in plants, starting from metabolic models of native biosynthetic pathways, progressing to novel combinations of known reactions, and finally proposing new reactions that may be carried out by existing enzymes. We show how these tools are useful for proposing new pathways as well as identifying side reactions that may affect engineering goals.
- Authors:
-
- Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
- OSTI Identifier:
- 1474405
- Grant/Contract Number:
- AC02-06CH11357; MCB 1611952; IOS 1444202
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Plant Science
- Additional Journal Information:
- Journal Volume: 273; Journal Issue: C; Journal ID: ISSN 0168-9452
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING
Citation Formats
Jeffryes, James G., Seaver, Samuel M. D., Faria, José P., and Henry, Christopher S. A pathway for every product? Tools to discover and design plant metabolism. United States: N. p., 2018.
Web. doi:10.1016/j.plantsci.2018.03.025.
Jeffryes, James G., Seaver, Samuel M. D., Faria, José P., & Henry, Christopher S. A pathway for every product? Tools to discover and design plant metabolism. United States. https://doi.org/10.1016/j.plantsci.2018.03.025
Jeffryes, James G., Seaver, Samuel M. D., Faria, José P., and Henry, Christopher S. Fri .
"A pathway for every product? Tools to discover and design plant metabolism". United States. https://doi.org/10.1016/j.plantsci.2018.03.025. https://www.osti.gov/servlets/purl/1474405.
@article{osti_1474405,
title = {A pathway for every product? Tools to discover and design plant metabolism},
author = {Jeffryes, James G. and Seaver, Samuel M. D. and Faria, José P. and Henry, Christopher S.},
abstractNote = {The vast diversity of plant natural products is a powerful indication of the biosynthetic capacity of plant metabolism. Synthetic biology seeks to capitalize on this ability by understanding and reconfiguring the biosynthetic pathways that generate this diversity to produce novel products with improved efficiency. In this work, we review the algorithms and databases that presently support the design and manipulation of metabolic pathways in plants, starting from metabolic models of native biosynthetic pathways, progressing to novel combinations of known reactions, and finally proposing new reactions that may be carried out by existing enzymes. We show how these tools are useful for proposing new pathways as well as identifying side reactions that may affect engineering goals.},
doi = {10.1016/j.plantsci.2018.03.025},
journal = {Plant Science},
number = C,
volume = 273,
place = {United States},
year = {Fri Mar 30 00:00:00 EDT 2018},
month = {Fri Mar 30 00:00:00 EDT 2018}
}
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Works referenced in this record:
AtIPD: A Curated Database of Arabidopsis Isoprenoid Pathway Models and Genes for Isoprenoid Network Analysis
journal, August 2011
- Vranová, Eva; Hirsch-Hoffmann, Matthias; Gruissem, Wilhelm
- Plant Physiology, Vol. 156, Issue 4
Golden Rice: Introducing the β-Carotene Biosynthesis Pathway into Rice Endosperm by Genetic Engineering to Defeat Vitamin A Deficiency
journal, March 2002
- Beyer, Peter; Al-Babili, Salim; Ye, Xudong
- The Journal of Nutrition, Vol. 132, Issue 3
A highly selective biosynthetic pathway to non-natural C50 carotenoids assembled from moderately selective enzymes
journal, July 2015
- Furubayashi, Maiko; Ikezumi, Mayu; Takaichi, Shinichi
- Nature Communications, Vol. 6, Issue 1
Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets
journal, June 2013
- Kotera, Masaaki; Tabei, Yasuo; Yamanishi, Yoshihiro
- Bioinformatics, Vol. 29, Issue 13
A genome-scale metabolic network reconstruction of tomato ( Solanum lycopersicum L.) and its application to photorespiratory metabolism
journal, January 2016
- Yuan, Huili; Cheung, C. Y. Maurice; Poolman, Mark G.
- The Plant Journal, Vol. 85, Issue 2
Optimization of a heterologous pathway for the production of flavonoids from glucose
journal, July 2011
- Santos, Christine Nicole S.; Koffas, Mattheos; Stephanopoulos, Gregory
- Metabolic Engineering, Vol. 13, Issue 4, p. 392-400
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics
journal, August 2015
- Jeffryes, James G.; Colastani, Ricardo L.; Elbadawi-Sidhu, Mona
- Journal of Cheminformatics, Vol. 7, Issue 1
Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity
journal, December 2011
- Mintz-Oron, S.; Meir, S.; Malitsky, S.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 1
Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways
journal, April 2013
- McClymont, Kent; Soyer, Orkun S.
- Nucleic Acids Research, Vol. 41, Issue 11
Medicine is not health care, food is health care: plant metabolic engineering, diet and human health
journal, August 2017
- Martin, Cathie; Li, Jie
- New Phytologist, Vol. 216, Issue 3
Data, information, knowledge and principle: back to metabolism in KEGG
journal, November 2013
- Kanehisa, Minoru; Goto, Susumu; Sato, Yoko
- Nucleic Acids Research, Vol. 42, Issue D1
In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner
journal, July 2014
- Sachdeva, Gairik; Garg, Abhishek; Godding, David
- Nucleic Acids Research, Vol. 42, Issue 14
Metabolite damage and repair in metabolic engineering design
journal, November 2017
- Sun, Jiayi; Jeffryes, James G.; Henry, Christopher S.
- Metabolic Engineering, Vol. 44
EcoSynther: A Customized Platform To Explore the Biosynthetic Potential in E. coli
journal, October 2017
- Ding, Shaozhen; Liao, Xiaoping; Tu, Weizhong
- ACS Chemical Biology, Vol. 12, Issue 11
Optimization based automated curation of metabolic reconstructions
journal, January 2007
- Satish Kumar, Vinay; Dasika, Madhukar S.; Maranas, Costas D.
- BMC Bioinformatics, Vol. 8, Issue 1
Path finding methods accounting for stoichiometry in metabolic networks
journal, January 2011
- Pey, Jon; Prada, Joaquín; Beasley, John E.
- Genome Biology, Vol. 12, Issue 5
Prediction of novel synthetic pathways for the production of desired chemicals
journal, January 2010
- Cho, Ayoun; Yun, Hongseok; Park, Jin
- BMC Systems Biology, Vol. 4, Issue 1
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind
journal, April 2016
- Kuwahara, Hiroyuki; Alazmi, Meshari; Cui, Xuefeng
- Nucleic Acids Research, Vol. 44, Issue W1
MetaCrop 2.0: managing and exploring information about crop plant metabolism
journal, November 2011
- Schreiber, F.; Colmsee, C.; Czauderna, T.
- Nucleic Acids Research, Vol. 40, Issue D1
New developments in engineering plant metabolic pathways
journal, December 2016
- Tatsis, Evangelos C.; O’Connor, Sarah E.
- Current Opinion in Biotechnology, Vol. 42
Predicting drug metabolism: experiment and/or computation?
journal, April 2015
- Kirchmair, Johannes; Göller, Andreas H.; Lang, Dieter
- Nature Reviews Drug Discovery, Vol. 14, Issue 6
Predicting novel substrates for enzymes with minimal experimental effort with active learning
journal, November 2017
- Pertusi, Dante A.; Moura, Matthew E.; Jeffryes, James G.
- Metabolic Engineering, Vol. 44
Epimetabolites: discovering metabolism beyond building and burning
journal, February 2017
- Showalter, Megan R.; Cajka, Tomas; Fiehn, Oliver
- Current Opinion in Chemical Biology, Vol. 36
Development of a commercial scale process for production of 1,4-butanediol from sugar
journal, December 2016
- Burgard, Anthony; Burk, Mark J.; Osterhout, Robin
- Current Opinion in Biotechnology, Vol. 42
BKM-react, an integrated biochemical reaction database
journal, January 2011
- Lang, Maren; Stelzer, Michael; Schomburg, Dietmar
- BMC Biochemistry, Vol. 12, Issue 1
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
journal, May 2011
- Yim, Harry; Haselbeck, Robert; Niu, Wei
- Nature Chemical Biology, Vol. 7, Issue 7
Progress in plant metabolic engineering
journal, April 2004
- Capell, Teresa; Christou, Paul
- Current Opinion in Biotechnology, Vol. 15, Issue 2
Computational tools for the synthetic design of biochemical pathways
journal, January 2012
- Medema, Marnix H.; van Raaphorst, Renske; Takano, Eriko
- Nature Reviews Microbiology, Vol. 10, Issue 3
MRSD: a web server for Metabolic Route Search and Design
journal, March 2011
- Xia, Deguo; Zheng, Haoran; Liu, Zhiqiang
- Bioinformatics, Vol. 27, Issue 11
MassBank: a public repository for sharing mass spectral data for life sciences
journal, July 2010
- Horai, Hisayuki; Arita, Masanori; Kanaya, Shigehiko
- Journal of Mass Spectrometry, Vol. 45, Issue 7
Using Genome-scale Models to Predict Biological Capabilities
journal, May 2015
- O’Brien, Edward J.; Monk, Jonathan M.; Palsson, Bernhard O.
- Cell, Vol. 161, Issue 5
‘Nothing of chemistry disappears in biology’: the Top 30 damage-prone endogenous metabolites
journal, June 2016
- Lerma-Ortiz, Claudia; Jeffryes, James G.; Cooper, Arthur J. L.
- Biochemical Society Transactions, Vol. 44, Issue 3
Key Applications of Plant Metabolic Engineering
journal, June 2014
- Lau, Warren; Fischbach, Michael A.; Osbourn, Anne
- PLoS Biology, Vol. 12, Issue 6
Rewriting yeast central carbon metabolism for industrial isoprenoid production
journal, September 2016
- Meadows, Adam L.; Hawkins, Kristy M.; Tsegaye, Yoseph
- Nature, Vol. 537, Issue 7622
The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters
journal, May 2011
- Bar-Even, Arren; Noor, Elad; Savir, Yonatan
- Biochemistry, Vol. 50, Issue 21
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm
journal, March 2015
- Seaver, Samuel M. D.; Bradbury, Louis M. T.; Frelin, Océane
- Frontiers in Plant Science, Vol. 6
Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model
journal, September 2014
- Simons, M.; Saha, R.; Amiour, N.
- PLANT PHYSIOLOGY, Vol. 166, Issue 3
Optimal metabolic route search based on atom mappings
journal, March 2014
- Latendresse, Mario; Krummenacker, Markus; Karp, Peter D.
- Bioinformatics, Vol. 30, Issue 14
Spatial organization of enzymes for metabolic engineering
journal, May 2012
- Lee, Hanson; DeLoache, William C.; Dueber, John E.
- Metabolic Engineering, Vol. 14, Issue 3
Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds
journal, April 2011
- Mu, Fangping; Unkefer, Clifford J.; Unkefer, Pat J.
- Bioinformatics, Vol. 27, Issue 11
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
journal, November 2004
- Rahman, S. A.; Advani, P.; Schunk, R.
- Bioinformatics, Vol. 21, Issue 7
PathPred: an enzyme-catalyzed metabolic pathway prediction server
journal, April 2010
- Moriya, Y.; Shigemizu, D.; Hattori, M.
- Nucleic Acids Research, Vol. 38, Issue Web Server
A synthetic pathway for the fixation of carbon dioxide in vitro
journal, November 2016
- Schwander, Thomas; Schada von Borzyskowski, Lennart; Burgener, Simon
- Science, Vol. 354, Issue 6314
PubChem Substance and Compound databases
journal, September 2015
- Kim, Sunghwan; Thiessen, Paul A.; Bolton, Evan E.
- Nucleic Acids Research, Vol. 44, Issue D1
Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production
journal, May 2014
- Arnold, Anne; Nikoloski, Zoran
- Plant Physiology, Vol. 165, Issue 3
Squalene hopene cyclases are protonases for stereoselective Brønsted acid catalysis
journal, December 2014
- Hammer, Stephan C.; Marjanovic, Antonija; Dominicus, Jörg M.
- Nature Chemical Biology, Vol. 11, Issue 2
Complete biosynthesis of opioids in yeast
journal, August 2015
- Galanie, S.; Thodey, K.; Trenchard, I. J.
- Science, Vol. 349, Issue 6252
Pfam: the protein families database
journal, November 2013
- Finn, Robert D.; Bateman, Alex; Clements, Jody
- Nucleic Acids Research, Vol. 42, Issue D1
Expression of the Platencin Biosynthetic Gene Cluster in Heterologous Hosts Yielding New Platencin Congeners
journal, November 2012
- Smanski, Michael J.; Casper, Jeffrey; Peterson, Ryan M.
- Journal of Natural Products, Vol. 75, Issue 12
Revealing strengths and weaknesses of methods for gene network inference
journal, March 2010
- Marbach, D.; Prill, R. J.; Schaffter, T.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 14
Metabolite Damage and Metabolite Damage Control in Plants
journal, April 2016
- Hanson, Andrew D.; Henry, Christopher S.; Fiehn, Oliver
- Annual Review of Plant Biology, Vol. 67, Issue 1
The Royal Society of Chemistry and the delivery of chemistry data repositories for the community
journal, August 2014
- Williams, Antony; Tkachenko, Valery
- Journal of Computer-Aided Molecular Design, Vol. 28, Issue 10
Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software
journal, October 2012
- Peach, Megan L.; Zakharov, Alexey V.; Liu, Ruifeng
- Future Medicinal Chemistry, Vol. 4, Issue 15
Evaluating enzymatic synthesis of small molecule drugs
journal, January 2016
- Moura, Matthew; Finkle, Justin; Stainbrook, Sarah
- Metabolic Engineering, Vol. 33
Frontiers in metabolic reconstruction and modeling of plant genomes
journal, January 2012
- Seaver, S. M. D.; Henry, C. S.; Hanson, A. D.
- Journal of Experimental Botany, Vol. 63, Issue 6
Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule
journal, July 2010
- Mishra, Nitish K.; Agarwal, Sandhya; Raghava, Gajendra PS
- BMC Pharmacology, Vol. 10, Issue 1
Inferring branching pathways in genome-scale metabolic networks
journal, October 2009
- Pitkänen, Esa; Jouhten, Paula; Rousu, Juho
- BMC Systems Biology, Vol. 3, Issue 1
Messy biology and the origins of evolutionary innovations
journal, September 2010
- Tawfik, Dan S.
- Nature Chemical Biology, Vol. 6, Issue 10
Synthetic metabolism: metabolic engineering meets enzyme design
journal, April 2017
- Erb, Tobias J.; Jones, Patrik R.; Bar-Even, Arren
- Current Opinion in Chemical Biology, Vol. 37
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
journal, November 2012
- Hastings, Janna; de Matos, Paula; Dekker, Adriano
- Nucleic Acids Research, Vol. 41, Issue D1
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
journal, January 2012
- Kumar, Akhil; Suthers, Patrick F.; Maranas, Costas D.
- BMC Bioinformatics, Vol. 13, Issue 1
UniProt: the universal protein knowledgebase
journal, November 2016
- :(unav),
- Nucleic Acids Research, Vol. 45, Issue D1, p. D158-D169
AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis
journal, December 2009
- de Oliveira Dal'Molin, Cristiana Gomes; Quek, Lake-Ee; Palfreyman, Robin William
- Plant Physiology, Vol. 152, Issue 2
Metabolic pathway balancing and its role in the production of biofuels and chemicals
journal, June 2015
- Jones, J. Andrew; Toparlak, Ö Duhan; Koffas, Mattheos AG
- Current Opinion in Biotechnology, Vol. 33
Using Accurate Mass Gas Chromatography–Mass Spectrometry with the MINE Database for Epimetabolite Annotation
journal, September 2017
- Lai, Zijuan; Kind, Tobias; Fiehn, Oliver
- Analytical Chemistry, Vol. 89, Issue 19
Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks
journal, August 2008
- Jankowski, Matthew D.; Henry, Christopher S.; Broadbelt, Linda J.
- Biophysical Journal, Vol. 95, Issue 3
ChEMBL: a large-scale bioactivity database for drug discovery
journal, September 2011
- Gaulton, A.; Bellis, L. J.; Bento, A. P.
- Nucleic Acids Research, Vol. 40, Issue D1
The PhytoClust tool for metabolic gene clusters discovery in plant genomes
journal, May 2017
- Töpfer, Nadine; Fuchs, Lisa-Maria; Aharoni, Asaph
- Nucleic Acids Research, Vol. 45, Issue 12
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
journal, November 2015
- Caspi, Ron; Billington, Richard; Ferrer, Luciana
- Nucleic Acids Research, Vol. 44, Issue D1
KNApSAcK Family Databases: Integrated Metabolite–Plant Species Databases for Multifaceted Plant Research
journal, November 2011
- Afendi, Farit Mochamad; Okada, Taketo; Yamazaki, Mami
- Plant and Cell Physiology, Vol. 53, Issue 2
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
journal, June 2014
- Seaver, Samuel M. D.; Gerdes, Svetlana; Frelin, Océane
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 26
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants
journal, February 2017
- Schläpfer, Pascal; Zhang, Peifen; Wang, Chuan
- Plant Physiology, Vol. 173, Issue 4
XTMS: pathway design in an eXTended metabolic space
journal, May 2014
- Carbonell, Pablo; Parutto, Pierre; Herisson, Joan
- Nucleic Acids Research, Vol. 42, Issue W1
Phytozome: a comparative platform for green plant genomics
journal, November 2011
- Goodstein, David M.; Shu, Shengqiang; Howson, Russell
- Nucleic Acids Research, Vol. 40, Issue D1
Network Context and Selection in the Evolution to Enzyme Specificity
journal, August 2012
- Nam, H.; Lewis, N. E.; Lerman, J. A.
- Science, Vol. 337, Issue 6098
Microbial Factories for the Production of Benzylisoquinoline Alkaloids
journal, March 2016
- Narcross, Lauren; Fossati, Elena; Bourgeois, Leanne
- Trends in Biotechnology, Vol. 34, Issue 3
The WEIZMASS spectral library for high-confidence metabolite identification
journal, August 2016
- Shahaf, Nir; Rogachev, Ilana; Heinig, Uwe
- Nature Communications, Vol. 7, Issue 1
Designing overall stoichiometric conversions and intervening metabolic reactions
journal, November 2015
- Chowdhury, Anupam; Maranas, Costas D.
- Scientific Reports, Vol. 5, Issue 1
An overview of data models for the analysis of biochemical pathways
journal, January 2003
- Deville, Y.
- Briefings in Bioinformatics, Vol. 4, Issue 3
AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development
journal, December 2009
- Matsuda, Fumio; Hirai, Masami Y.; Sasaki, Eriko
- Plant Physiology, Vol. 152, Issue 2
Formation of plant metabolic gene clusters within dynamic chromosomal regions
journal, August 2011
- Field, B.; Fiston-Lavier, A. -S.; Kemen, A.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 38
C4GEM, a Genome-Scale Metabolic Model to Study C 4 Plant Metabolism
journal, October 2010
- de Oliveira Dal’Molin, Cristiana Gomes; Quek, Lake-Ee; Palfreyman, Robin William
- Plant Physiology, Vol. 154, Issue 4
Regulatory network rewiring for secondary metabolism in Arabidopsis thaliana under various conditions
journal, January 2014
- Lv, Qi; Cheng, Rong; Shi, Tieliu
- BMC Plant Biology, Vol. 14, Issue 1
MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data
journal, October 2012
- Haug, Kenneth; Salek, Reza M.; Conesa, Pablo
- Nucleic Acids Research, Vol. 41, Issue D1
BRENDA in 2015: exciting developments in its 25th year of existence
journal, November 2014
- Chang, Antje; Schomburg, Ida; Placzek, Sandra
- Nucleic Acids Research, Vol. 43, Issue D1
Antioxidant properties, radical scavenging activity and biomolecule protection capacity of flavonoid naringenin and its glycoside naringin: a comparative study
journal, May 2010
- Cavia-Saiz, Monica; Busto, Maria D.; Pilar-Izquierdo, Maria Concepción
- Journal of the Science of Food and Agriculture, Vol. 90, Issue 7
FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants
journal, January 2016
- Ruprecht, Colin; Mendrinna, Amelie; Tohge, Takayuki
- Plant Physiology, Vol. 170, Issue 3
A Method for Finding Metabolic Pathways Using Atomic Group Tracking
journal, January 2017
- Huang, Yiran; Zhong, Cheng; Lin, Hai Xiang
- PLOS ONE, Vol. 12, Issue 1
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
journal, August 2016
- Wang, Mingxun; Carver, Jeremy J.; Phelan, Vanessa V.
- Nature Biotechnology, Vol. 34, Issue 8
plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
journal, April 2017
- Kautsar, Satria A.; Suarez Duran, Hernando G.; Blin, Kai
- Nucleic Acids Research, Vol. 45, Issue W1
Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology
journal, July 2008
- Tsesmetzis, Nicolas; Couchman, Matthew; Higgins, Janet
- The Plant Cell, Vol. 20, Issue 6
Characterizing and predicting carboxylic acid reductase activity for diversifying bioaldehyde production: Carboxylic Acid Reductases for Bioaldehydes
journal, November 2015
- Moura, Matthew; Pertusi, Dante; Lenzini, Stephen
- Biotechnology and Bioengineering, Vol. 113, Issue 5
Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone
journal, September 2015
- Lau, Warren; Sattely, Elizabeth S.
- Science, Vol. 349, Issue 6253
Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis
journal, January 2016
- Kotera, Masaaki; Goto, Susumu
- Biophysics and Physicobiology, Vol. 13, Issue 0
Production of the antimalarial drug precursor artemisinic acid in engineered yeast
journal, April 2006
- Ro, Dae-Kyun; Paradise, Eric M.; Ouellet, Mario
- Nature, Vol. 440, Issue 7086, p. 940-943
ReactPRED: a tool to predict and analyze biochemical reactions
journal, August 2016
- Sivakumar, Tadi Venkata; Giri, Varun; Park, Jin Hwan
- Bioinformatics, Vol. 32, Issue 22
MapMaker and PathTracer for tracking carbon in genome-scale metabolic models
journal, March 2016
- Tervo, Christopher J.; Reed, Jennifer L.
- Biotechnology Journal, Vol. 11, Issue 5
A k‐Nearest Neighbours Approach Using Metabolism‐related Fingerprints to Improve In Silico Metabolite Ranking
journal, October 2016
- Marchant, Carol A.; Rosser, Edward M.; Vessey, Jonathan D.
- Molecular Informatics, Vol. 36, Issue 3
Efficient searching and annotation of metabolic networks using chemical similarity
journal, December 2014
- Pertusi, Dante A.; Stine, Andrew E.; Broadbelt, Linda J.
- Bioinformatics, Vol. 31, Issue 7
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
journal, January 2013
- Ganter, M.; Bernard, T.; Moretti, S.
- Bioinformatics, Vol. 29, Issue 6
Metabolic engineering of strains: from industrial-scale to lab-scale chemical production
journal, November 2014
- Sun, Jie; Alper, Hal S.
- Journal of Industrial Microbiology & Biotechnology, Vol. 42, Issue 3
Network-level architecture and the evolutionary potential of underground metabolism
journal, July 2014
- Notebaart, R. A.; Szappanos, B.; Kintses, B.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 32
FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction
journal, October 2015
- Khosraviani, Mehrshad; Saheb Zamani, Morteza; Bidkhori, Gholamreza
- Bioinformatics, Vol. 32, Issue 3
Harnessing plant metabolic diversity
journal, October 2017
- Owen, Charlie; Patron, Nicola J.; Huang, Ancheng
- Current Opinion in Chemical Biology, Vol. 40
The Rise of Chemodiversity in Plants
journal, June 2012
- Weng, Jing-Ke; Philippe, Ryan N.; Noel, Joseph P.
- Science, Vol. 336, Issue 6089
What makes an enzyme promiscuous?
journal, April 2010
- Babtie, Ann; Tokuriki, Nobuhiko; Hollfelder, Florian
- Current Opinion in Chemical Biology, Vol. 14, Issue 2
The University of Minnesota Pathway Prediction System: multi-level prediction and visualization
journal, April 2011
- Gao, J.; Ellis, L. B. M.; Wackett, L. P.
- Nucleic Acids Research, Vol. 39, Issue suppl
What is flux balance analysis?
journal, March 2010
- Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø
- Nature Biotechnology, Vol. 28, Issue 3
Search in power-law networks
journal, September 2001
- Adamic, Lada A.; Lukose, Rajan M.; Puniyani, Amit R.
- Physical Review E, Vol. 64, Issue 4
Metabolite proofreading, a neglected aspect of intermediary metabolism
journal, January 2013
- Van Schaftingen, Emile; Rzem, Rim; Marbaix, Alexandre
- Journal of Inherited Metabolic Disease, Vol. 36, Issue 3
A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties
journal, September 2009
- Poolman, Mark G.; Miguet, Laurent; Sweetlove, Lee J.
- Plant Physiology, Vol. 151, Issue 3
New and continuing developments at PROSITE
journal, November 2012
- Sigrist, Christian J. A.; de Castro, Edouard; Cerutti, Lorenzo
- Nucleic Acids Research, Vol. 41, Issue D1
Targeting Tryptophan Decarboxylase to Selected Subcellular Compartments of Tobacco Plants Affects Enzyme Stability and in Vivo Function and Leads to a Lesion-Mimic Phenotype
journal, July 2002
- Di Fiore, Stefano; Li, Qiurong; Leech, Mark James
- Plant Physiology, Vol. 129, Issue 3
Biosynthesis of ethylene glycol in Escherichia coli
journal, December 2012
- Liu, Huaiwei; Ramos, Kristine Rose M.; Valdehuesa, Kris Niño G.
- Applied Microbiology and Biotechnology, Vol. 97, Issue 8
ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies
journal, June 2016
- Hadadi, Noushin; Hafner, Jasmin; Shajkofci, Adrian
- ACS Synthetic Biology, Vol. 5, Issue 10