Metabolic Pathways Collection at SRI International the Largest in the World
Database allows researchers to glimpse the “big picture” of the biochemical networks inside a cell
MENLO PARK, Calif., April 24, 2013 /PRNewswire/ — Researchers at SRI International, in collaboration with the Boyce Thompson Institute and the Carnegie Institution, have reached a milestone in their development of MetaCyc, a database and web site (MetaCyc.org) that consolidates much known information about metabolism. MetaCyc now includes 2,000 pathways, each a collection of metabolic reactions and the enzymes that catalyze them, making the database the most comprehensive compilation of metabolic pathway information in the world.
MetaCyc catalogs the universe of metabolism–how organisms biochemically transform one compound to another through intricate networks of synthesis and degradation–by integrating many of the biochemical reactions that have been documented in different forms of life. It includes information about more than 10,900 reactions and more than 10,400 compounds from 35,000 cited publications. More than 2,300 organisms are currently represented, from bacteria, archaea and yeast to plants and animals, including humans.
“As researchers know, there are so many scientific articles available that it can be challenging to synthesize all this information,” said Peter Karp, Ph.D., director of the Bioinformatics Research Group at SRI International. “MetaCyc integrates the fragmented, sometimes inaccessible, data throughout the scientific literature. The synthesis of all these individual publications in MetaCyc provides the big picture.”
One example is the MetaCyc compound page for L-glutamate, which contains reactions and pathways from a wide variety of organisms that synthesize and degrade this important compound. MetaCyc can reconcile seemingly disparate pathways that involve the same compounds called by different names by different research teams.
Another contribution of MetaCyc to the scientific enterprise is to combine the published work of individual laboratories in individual publications into pathways that were not previously recognized by those researchers. For example, the pathway for 3-phosphoinositide degradation was assembled from studies by several different laboratories that characterized the individual reactions and enzymes within the pathway.
MetaCyc, one of the databases in SRI’s BioCyc database collection, is a free online reference source used by thousands of researchers in government, academia, and industry. Scientists use MetaCyc to predict biochemical pathways that are present in a newly sequenced organism and to better understand where in the metabolic network a particular gene or metabolite of interest is involved. This view inside of a cell can help in a range of applications, especially metabolic engineering, where cells are manipulated to produce a specific substance, such as antibiotics or biofuels. It is also helpful for understanding how to degrade particular compounds, such as pesticides or chemicals released after an oil spill.
SRI International research was funded by grant GM080746 from the NIH National Institute of General Medical Sciences and by grant DE-SC0004878 from the Department of Energy.
Contribution from Carnegie Institution was funded by grants IOS-1026003 and DBI-0640769 from the National Science Foundation.
About SRI International
Innovations from SRI International have created new industries, billions of dollars of marketplace value, and lasting benefits to society–touching our lives every day. SRI, a nonprofit research and development institute based in Silicon Valley, brings its innovations to the marketplace through technology licensing, new products, and spin-off ventures. Government and business clients come to SRI for pioneering R&D and solutions in computing and communications, chemistry and materials, education, energy, health and pharmaceuticals, national defense, robotics, sensing, and more.
About Carnegie Institution
Andrew Carnegie established a unique organization in 1902 dedicated to scientific discovery “to encourage, in the broadest and most liberal manner, investigation, research, and discovery and the application of knowledge to the improvement of mankind…” The philosophy was and is to devote the institution’s resources to “exceptional” individuals so that they can explore the most intriguing scientific questions in an atmosphere of complete independence. Carnegie and his trustees realized that flexibility and independence were essential to the institution’s success and that tradition is the foundation of the institution today as it supports research in the Earth, space, and life sciences.
About the Boyce Thompson Institute (BTI)
William Boyce Thompson founded BTI in 1924, believing that basic plant research could lead to real societal benefits. BTI’s mission is to advance and communicate scientific knowledge in plant biology to improve agriculture, protect the environment, and enhance human health. To this end, BTI hosts 17 faculty-run research laboratories performing basic plant research with potential applications to improve important food crops, to better understand plant and human immune systems; and to explore alternative sources of energy. Along with its rigorous research program, BTI’s work includes outreach to teachers, students, and community members.
SOURCE SRI International