Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Model helps pinpoint cyanobacterial genes that capture the sun’s energy

24.06.2011
Knowledge could improve microorganism as a renewable energy source

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

EMSL, the Environmental Molecular Sciences Laboratory, is a national scientific user facility sponsored by the Department of Energy's Office of Science that is located at Pacific Northwest National Laboratory. EMSL offers an open, collaborative environment for scientific discovery to researchers around the world. EMSL's technical experts and suite of custom and advanced instruments are unmatched. Its integrated computational and experimental capabilities enable researchers to realize fundamental scientific insights and create new technologies. Follow EMSL on Facebook.

Pacific Northwest National Laboratory is a Department of Energy Office of Science national laboratory where interdisciplinary teams advance science and technology and deliver solutions to America's most intractable problems in energy, the environment and national security. PNNL employs 4,900 staff, has an annual budget of nearly $1.1 billion, and has been managed by Ohio-based Battelle since the lab's inception in 1965. Follow PNNL on Facebook, LinkedIn and Twitter.

Franny White | EurekAlert!
Further information:
http://www.pnnl.gov

More articles from Life Sciences:

nachricht Cancer diagnosis: no more needles?
25.05.2018 | Christian-Albrechts-Universität zu Kiel

nachricht Less is more? Gene switch for healthy aging found
25.05.2018 | Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut e.V. (FLI)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Powerful IT security for the car of the future – research alliance develops new approaches

The more electronics steer, accelerate and brake cars, the more important it is to protect them against cyber-attacks. That is why 15 partners from industry and academia will work together over the next three years on new approaches to IT security in self-driving cars. The joint project goes by the name Security For Connected, Autonomous Cars (SecForCARs) and has funding of €7.2 million from the German Federal Ministry of Education and Research. Infineon is leading the project.

Vehicles already offer diverse communication interfaces and more and more automated functions, such as distance and lane-keeping assist systems. At the same...

Im Focus: Molecular switch will facilitate the development of pioneering electro-optical devices

A research team led by physicists at the Technical University of Munich (TUM) has developed molecular nanoswitches that can be toggled between two structurally different states using an applied voltage. They can serve as the basis for a pioneering class of devices that could replace silicon-based components with organic molecules.

The development of new electronic technologies drives the incessant reduction of functional component sizes. In the context of an international collaborative...

Im Focus: LZH showcases laser material processing of tomorrow at the LASYS 2018

At the LASYS 2018, from June 5th to 7th, the Laser Zentrum Hannover e.V. (LZH) will be showcasing processes for the laser material processing of tomorrow in hall 4 at stand 4E75. With blown bomb shells the LZH will present first results of a research project on civil security.

At this year's LASYS, the LZH will exhibit light-based processes such as cutting, welding, ablation and structuring as well as additive manufacturing for...

Im Focus: Self-illuminating pixels for a new display generation

There are videos on the internet that can make one marvel at technology. For example, a smartphone is casually bent around the arm or a thin-film display is rolled in all directions and with almost every diameter. From the user's point of view, this looks fantastic. From a professional point of view, however, the question arises: Is that already possible?

At Display Week 2018, scientists from the Fraunhofer Institute for Applied Polymer Research IAP will be demonstrating today’s technological possibilities and...

Im Focus: Explanation for puzzling quantum oscillations has been found

So-called quantum many-body scars allow quantum systems to stay out of equilibrium much longer, explaining experiment | Study published in Nature Physics

Recently, researchers from Harvard and MIT succeeded in trapping a record 53 atoms and individually controlling their quantum state, realizing what is called a...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

In focus: Climate adapted plants

25.05.2018 | Event News

Save the date: Forum European Neuroscience – 07-11 July 2018 in Berlin, Germany

02.05.2018 | Event News

Invitation to the upcoming "Current Topics in Bioinformatics: Big Data in Genomics and Medicine"

13.04.2018 | Event News

 
Latest News

In focus: Climate adapted plants

25.05.2018 | Event News

Flow probes from the 3D printer

25.05.2018 | Machine Engineering

Less is more? Gene switch for healthy aging found

25.05.2018 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>