Joshua Heazlewood talks with
ScienceWatch.com and answers a few questions about
this month's Fast Moving Front in the field of Plant &
Animal Science.
Article: SUBA: The
Arabidopsis subcellular
database
Authors: Heazlewood,
JL;Verboom, RE;Tonti-Filippini, J;Small, I;Millar,
AH
Journal: NUCL ACID RES, 35: D213-D218 Sp. Iss. SI JAN
2007
Univ Western Australia, ARC Ctr Excellence Plant Energy
Biol, 35 Stirling Highway,CMS Bldg,M316, Crawley, WA 6009,
Australia.
Univ Western Australia, ARC Ctr Excellence Plant Energy
Biol, Crawley, WA 6009, Australia.
Why do you think your paper is highly
cited?
The Arabidopsis thaliana genome was sequenced nearly 10 years ago
and, in the time since, a significant worldwide investment has been made to
determine the function of the ~30,000 proteins encoded by this model plant.
Knowing the subcellular location of a protein provides a researcher with
clues that assist in the discovery of function, interaction partners, and
biochemical pathways for a protein of interest. SUBA has thus served as a
starting point for many researchers seeking to discover biological
mechanisms from within a collection of unknown proteins.
Does it describe a new discovery, methodology, or
synthesis of knowledge?
"...we plan to expand SUBA, which
currently only houses data from the model
dicot Arabidopsis, to the model monocot,
rice."
The SUBA database brings together thousands of individual pieces of
information from a collection of both experimental and predicted
subcellular protein localizations in Arabidopsis thaliana. The
database provides a web-based, dynamic query construction tool that allows
researchers to query subcellular information in a powerful way.
Would you summarize the significance of your paper
in layman's terms?
Plants (and animals) are built from billions of individual cells and each
one of these cells has its own internal structure complete with organelles
that are responsible for doing specific jobs at a subcellular level. For
example, within the cells of a plant's leaves are plastids, organelles that
act as tiny solar cells, converting solar energy into chemical energy for
the cell (and the entire plant) to survive.
Being able to reverse engineer and describe how these tiny biological
machines work is of great scientific interest and sometimes leads to useful
technological applications. Within a cell, proteins are assembled together
to build more complex biological machines (or may function entirely on
their own).
SUBA provides information about where proteins are located within a single
cell and therefore gives researchers important information about which
proteins may be working together to perform specific biological roles.
How did you become involved in this research and
were any particular problems encountered along the way?
Our initial research involved using mass spectrometry to discover proteins
found within plant mitochondria. While describing the proteome of this
organelle, it was important to assess potential contamination from other
components within the cell.
We subsequently commenced curation of our findings and that of others to
build an Excel spreadsheet that later evolved into SUBA. In the process, we
added fluorescent protein localization data, subcellular prediction data,
and subcellular annotation information.
Where do you see your research leading in the
future?
The SUBA database is an extremely useful resource for the community and is
continually updated as new research is undertaken and published. There is
currently a considerable effort by the Arabidopsis community to
produce a protein-protein interaction network and it is likely that the
information in SUBA will provide useful validation as interacting proteins
would presumably localize to the same subcellular location.
Finally, we plan to expand SUBA, which currently only houses data from the
model dicot Arabidopsis, to the model monocot, rice.
Joshua Heazlewood, Ph.D.
Director of Systems Biology
The Joint BioEnergy Institute
Lawrence Berkeley National Labs
Berkeley, CA, USA Web |
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