Improved prediction of metabolic fluxes through genomic context analysis across organisms and stoichiometric analysis of carbon fluxes

2009 ◽  
Vol 108 ◽  
pp. S173
Author(s):  
Jong Myoung Park ◽  
Tae Yong Kim ◽  
Sang Yup Lee
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Trishnamoni Gautom ◽  
Dharmendra Dheeman ◽  
Colin Levy ◽  
Thomas Butterfield ◽  
Guadalupe Alvarez Gonzalez ◽  
...  

AbstractBiological degradation of Polyethylene terephthalate (PET) plastic and assimilation of the corresponding monomers ethylene glycol and terephthalate (TPA) into central metabolism offers an attractive route for bio-based molecular recycling and bioremediation applications. A key step is the cellular uptake of the non-permeable TPA into bacterial cells which has been shown to be dependent upon the presence of the key tphC gene. However, little is known from a biochemical and structural perspective about the encoded solute binding protein, TphC. Here, we report the biochemical and structural characterisation of TphC in both open and TPA-bound closed conformations. This analysis demonstrates the narrow ligand specificity of TphC towards aromatic para-substituted dicarboxylates, such as TPA and closely related analogues. Further phylogenetic and genomic context analysis of the tph genes reveals homologous operons as a genetic resource for future biotechnological and metabolic engineering efforts towards circular plastic bio-economy solutions.


2011 ◽  
Vol 12 (S1) ◽  
Author(s):  
Marinalva Martins-Pinheiro ◽  
Wanessa Cristina Lima ◽  
Cláudio A Oller ◽  
Carlos FM Menck

2018 ◽  
Vol 8 (4) ◽  
pp. 1115-1118 ◽  
Author(s):  
Mohammed Uddin ◽  
Marc Woodbury-Smith ◽  
Ada J. S. Chan ◽  
Ammar Albanna ◽  
Berge Minassian ◽  
...  

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Sara Calhoun ◽  
Magdalena Korczynska ◽  
Daniel J Wichelecki ◽  
Brian San Francisco ◽  
Suwen Zhao ◽  
...  

The functions of most proteins are yet to be determined. The function of an enzyme is often defined by its interacting partners, including its substrate and product, and its role in larger metabolic networks. Here, we describe a computational method that predicts the functions of orphan enzymes by organizing them into a linear metabolic pathway. Given candidate enzyme and metabolite pathway members, this aim is achieved by finding those pathways that satisfy structural and network restraints implied by varied input information, including that from virtual screening, chemoinformatics, genomic context analysis, and ligand -binding experiments. We demonstrate this integrative pathway mapping method by predicting the L-gulonate catabolic pathway in Haemophilus influenzae Rd KW20. The prediction was subsequently validated experimentally by enzymology, crystallography, and metabolomics. Integrative pathway mapping by satisfaction of structural and network restraints is extensible to molecular networks in general and thus formally bridges the gap between structural biology and systems biology.


2004 ◽  
Vol 32 (21) ◽  
pp. 6321-6326 ◽  
Author(s):  
Tobias Doerks ◽  
Christian von Mering ◽  
Peer Bork

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 1142 ◽  
Author(s):  
Ricardo Martí-Arbona ◽  
Fangping Mu ◽  
Kristy L Nowak-Lovato ◽  
Melinda S Wren ◽  
Clifford J Unkefer ◽  
...  

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0150772 ◽  
Author(s):  
Marinalva Martins-Pinheiro ◽  
Wanessa C. Lima ◽  
Huma Asif ◽  
Cláudio A. Oller ◽  
Carlos F. M. Menck

Sign in / Sign up

Export Citation Format

Share Document