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BioCycЧGenome and Metabolism.

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BioCyc—Genome and Metabolism
BioCyc is the logical extension of a successful concept initiated in 1992:
EcoCyc. As the gap continues to widen
rapidly between sequence data confirmed by the functional and biochemical characterization of proteins and primary data acquired by modern highthroughput sequencing and annotated
by bioinformatics approaches, the question about the reliability of genomic
information is becoming increasingly
important. It is therefore an outstanding
trait of BioCyc that, in the tradition of
EcoCyc, it is a database derived primarily from the biomedical literature, and
thus from experimental results. At first
glance it may be disappointing if a keyword search does not yield any results.
However, great importance is attached
to quality and depth of information,
rather than quantity. After all, BioCyc
represents the next level of EcoCyc,
Figure 1. Home page of BioCyc.
1908
aimed at the implementation of additional genomes. As most genomic data
collected so far are derived from bioinformatic approaches, some time may
be needed before all features of the
site become available.
The tidy and well-organized BioCyc
home page (Figure 1) offers a virtual
guided tour through the system, download options for specific software tools,
a variety of query functions, and a few
links, most of which are associated with
EcoCyc. Search options include a typical
BLAST search with various selectable
search algorithms and a keyword or
string search that can be refined based
on useful options, such as compound
names, EC numbers, and reactions. A
help function is only available for the
“Query page” and “ExpressionViewer”,
but as most options are self-explanatory,
BioCyc can be used immediately even
without the guided tour.
BioCyc has a very good hierarchical
structure, which allows a step-by-step
approach to familiarizing oneself with
the details of the site. For example, the
organization of metabolic pathways
into less- or more-detailed display
levels enables the user to choose the
required depth of information. However, the graphical design of the site
could be improved; most of the information is difficult to read. For example, it
would be desirable if gene names in
the genome maps were to be displayed
in a small pop-up window when the
cursor is moved over
the map and not as
an almost invisible
line at the bottom of
the window.
According to the
authors of the database project, BioCyc
will be updated four
times a year and will
include all information from the literature
about
the
genome, metabolic
pathways, and regulatory mechanisms
in E. coli.[1] BioCyc
also includes published data about
operons, promoters,
and terminators, as
well as transcription
2004 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
DOI: 10.1002/anie.200483067
factors and their binding sites. Moreover, the search options of BioCyc
make information about the interactions
between transcription factors and their
corresponding ligands accessible. This
tool allows the reconstruction of intracellular interactions and regulation
mechanisms and creates links between
genome, proteome, and transcriptome
data. A useful tool for this purpose is
the “ExpressionViewer”, a configurable
display of expression data from microarray experiments, which allows comparisons between different organisms and
the time- or nutrient-dependent analysis
of expression patterns.
The EcoCyc/BioCyc concept is
based on Pathway Tools software supported by Sun Microsystems. This software can be downloaded and installed
locally, thus allowing through its open
software architecture user-specific database optimization and extension with
additional genome data.
In summary, BioCyc is a versatile
tool for gaining insight into the organization and regulation of intracellular
processes. It is also a valuable database
for the evaluation of novel metabolic
pathways and their regulatory mechanisms. The search function for specific
small molecules and the corresponding
enzymes might become an important
tool for biosynthetic-pathway engineering and combinatorial biosynthesis. As
yet these tools are only fully functional
for the E. coli genome. Hopefully the
next updates will integrate the available
literature on additional genomes.
Ralf Petri, Claudia Schmidt-Dannert
University of Minnesota
St. Paul (USA)
[1] P. D. Karp, M. Arnaud, J. Collado-Vides,
J. Ingraham, I. T. Paulsen, M. H. Saier,
Jr. ASM News 2004, 70, 25.
For more information visit
http://www.biocyc.org/
or contact
biocyc-support@ai.sri.com
Angew. Chem. Int. Ed. 2004, 43, 1908
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