The single-celled marine cyanobacterium Cyanothece 51142, captured by a light microscope. Image: Washington Univ. in St. Louis.
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 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 Univ., in St. Louis, and Purdue
Univ. 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 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
Researchers developed this wreath-like graph to visualize all the genes being expressed by the cyanobacterium Cyanothece over a 24-hour period. The graphic revealed the complex genetic network that enables Cyanothece to switch its cell between photosynthesis and nitrogen fixation as the day turns to night. Image: Pacific Northwest National Laboratory
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
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.
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% 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%. 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%.
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.”