June 23, 2011 
Knowledge could improve microorganism as a renewable energy
source
RICHLAND, Wash. – A new computer model of
blue-green algae can predict which of the organism's genes are
central to capturing energy from sunlight and other critical
processes.
Described in a paper published in the journal Molecular
BioSystems, the model could advance efforts to produce biofuel
and other energy sources from blue-green algae, known as
cyanobacteria. Researchers from the Department of Energy's Pacific
Northwest National Laboratory, Washington University in St. Louis and
Purdue University developed the
model, which was made for the single-celled marine cyanobacterium
Cyanothece 51142.
"Our model is the first of its kind for cyanobacteria," said the
paper's lead author, PNNL computational biologist Jason
McDermott. "Previous models have only zoomed in on specific
aspects of cyanobacteria. Ours looks at the entire organism to find
out what makes Cyanothece tick."
The research was funded by EMSL, the Department of
Energy's Environmental Molecular Sciences Laboratory, a national
user facility at PNNL, as part of EMSL's Membrane
Biology Grand Challenge. The challenge encouraged scientists to
take a systems biology approach to understand the network of genes
and proteins that are responsible for photosynthesis and nitrogen
fixation in cyanobacteria.
Cyanobacteria are noteworthy because they share qualities with
both plants and microbes. They use the sun's energy to make
sugar via photosynthesis like plants. And, like microbes,
cyanobacteria also convert atmospheric nitrogen — an
important nutrient for many organisms — into accessible
forms, a process called nitrogen fixation.
Working day and night
Many cyanobacteria physically separate their photosynthetic and
nitrogen fixation activities in different cells. But
Cyanothece is unusual because the same cell switches
between these functions every 12 hours. It makes sugar when there's
daylight and then spends the night breaking down that sugar to fix
nitrogen and to produce other compounds.
"By understanding which genes trigger Cyanothece to
start and stop photosynthesis and other important energy production
functions, we may be able to better use cyanobacteria to make
renewable energy," McDermott said. Genes serve as the blueprint for
the creation of proteins, the cell's workers.
Mapping a gene's purpose
Researchers — many of whom also worked on the model
— sequenced
Cyanothece's genome in 2008. But knowing how many
genes an organism has doesn't necessarily explain what those genes
do. So scientists kept studying Cyanothece in the
lab. By making a simple linear graph of when different genes were
expressed over a 24-hour cycle, McDermott and his co-authors saw
that many genes were expressed at similar levels and at similar
times. The team hypothesized that such genes were involved in
similar processes, such as photosynthesis or nitrogen fixation.
But there isn't always a straight line between one gene being
turned on and a cellular process starting. Sometimes a series of
genes have to be turned on or off before a process can begin. To
better understand these complex relationships, McDermott crafted a
circular graph that illustrates how genes are expressed around the
clock. Each point on the graph represented a gene being expressed
at a particular time. Lines connecting the dots demonstrated how
some related genes are expressed one after another in a series.
Points of control
The wreath-like graph revealed a complicated, intertwined
network of Cyanothece genes. In some cases, different
series of related genes expressed one after another intersected at
the same place, at an individual gene or a handful of genes. It
appeared that the genes at these intersections serve as
bottlenecks, or control points, for the subsequent expression of
other genes down the road. The team predicted that if the
bottleneck genes were removed, expression of the downstream genes
would be affected. Amazingly, 11 of the 25 top bottlenecks
identified were genes or proteins whose specific role in
Cyanothece weren't previously known.
The next challenge was to figure out how each of these
bottlenecks affects Cyanothece's daily life. The team
could have done experiments in the lab, removing each of these
bottlenecks one at the time from the organism's genome to see what
happened. But such experiments can be time-consuming. Seeking a
simpler, more methodical solution, the authors built a computer
model that would predict the roles of individual genes in
Cyanothece.
Central players
They started with a previous whole-organism modeling approach
called the Inferelator, which was developed at the Institute for Systems
Biology in Seattle for a different microorganism. The team
adapted the Inferelator's code to compute the cyclic nature of the
connections between Cyanothece's genes. They also added
code to improve their ability to test the model's accuracy.
When looking at low-oxygen conditions similar to those
encountered by Cyanothece at night, the model predicted
gene expression levels correctly the equivalent of about 75 percent
of the time, in comparison to actual measurements.
The model predicted the roles that a number of bottleneck genes
play for Cyanothece. For example, the model predicted that
the patB gene is a bottleneck for the production of
nitrogenase, the enzyme needed to fix nitrogen. If patB
were removed from Cyanothece, the model predicted that
nitrogenase production could decrease by as much as 80 percent. The
model also identified an unnamed gene, currently labeled as gene
cce_0678, as being key to the cyanobacterium's production
of RuBisCO, a well-known enzyme that's important in photosynthesis.
Without cce_0678, the model predicted RuBisCO production
would decrease by about 60 percent.
Next, the research team will seek to further validate the model
with lab experiments. They'll remove or increase the expression of
specific genes predicted to be bottlenecks to test whether or not
they impact Cyanothece's energy production as the model
predicted. The researchers will also use the model to examine the
complex interactions between important processes in cyanobacteria,
such as photosynthesis and nitrogen fixation.
"This model can serve as a first step toward a complete
simulation of Cyanothece," McDermott said. "Knowing the
detailed inner workings of cyanobacteria could be used to design
efficient methods to make bioenergy and manage the carbon cycle,
including the greenhouse gas carbon dioxide."
REFERENCE: Jason E. McDermott, Christopher S. Oehmen, Lee Ann
McCue, Eric Hill, Daniel M. Choi, Jana Stöckel, Michelle
Liberton, Himadri B. Pakrasi and Louis A. Sherman, A model of
cyclic transcriptomic behavior in the cyanobacterium
Cyanothece sp. ATCC 51142, Molecular BioSystems, published
online June 23, 2011, DOI: 10.1039/C1MB05006K.
http://pubs.rsc.org/en/content/articlelanding/2011/mb/c1mb05006k
Tags: Energy, Fundamental
Science, Biology, Biomolecular
Science
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