Role of Rubisco in
Photosynthesis
Anu Murphy
Dept. of Molecular and Integrative Physiology,
University of Illinois at Urbana-Champaign
Introduction
• We will use the Biology Workbench (BW)
to study rubisco, a protein used in
photosynthesis.
• Outline of presentation:
– What is rubisco?
– Using BW to obtain rubisco sequences from
different plants/trees
– Manipulate obtained sequences using BW tools
Photosynthesis
• Process by which green plants use CO2 and
H2O to form glucose in the presence of
sunlight:
• 6 CO2+ 6 H2O + light energy  C6H12O6 + 6 O2
• Process involves light reactions and dark
reactions, enzymes, chlorophyll
What is rubisco?
• Rubisco, ribulose bisphosphate carboxylase,
is a protein molecule present in plant cells.
It takes part in photosynthesis and converts
inorganic CO2 into organic forms containing
C-C bonds and H atoms. These are used to
sustain plants in the form of sucrose (table
sugar) or stored as starch.
Using the Biology Workbench
• BW is available at:
http://peptide.ncsa.uiuc.edu/
– click on “Student Interface to the Biology
Workbench”
– Click on “Register” to obtain accounts; type in
full name, e-mail address (ex.,
murphya@oakland.edu), user ID, and password
Using BW Contd. ...
• In the BW menu, click on “Create a NEW
Session”, name it “Rubisco Analysis”
• Click on “Protein Tools” at the top of the page
• In the search box near top of page, type “rubisco
wheat”, click on “GenBank Plant Sequences” in
the “Select one or more Databases” box, then click
on “Ndjinn” button on the right
• Select 1 or 2 sequences with highest scores that
mention “ribulose bisphosphate carboxylase”
Using BW Contd. …
• Click on the “Import Sequences” button: selected protein
sequences will appear on bottom of Rubisco Analysis
session page
• Repeat process with a few other plants (I.e., type in
“rubisco lily”, “rubisco oat”, etc. for other plants of
interest, then import top few sequences into your Rubisco
Analysis session
• To view sequences, select them and click on “View” near
bottom of Rubisco Analysis page
• Click on “View Records” for more information on how
and from where the sequence was obtained
Using BW Contd..
• After obtaining and viewing rubisco sequences, return to
Rubisco Analysis page and select relevant ones (I.e., try to
omit sequence fragments)
• Click on “CLUSTALW” next to the “Align multiple
protein sequences with each other” box
• The alignment can be viewed in the CLUSTALW page:
note how certain segments of the rubisco sequence are
very similar between the different species of plants. These
parts of the sequence might have common evolutionary
origin and play functionally similar roles in photosynthesis
Using BW Contd..
• Click on “Import Alignment”: this will take you to the
Alignment Tools page
• Select the alignment (at bottom of page) and try out the
different alignment tools listed: you can color code the
sequence alignment, draw phylogenetic trees to examine
evolutionary relationships between your plants, etc.