Cyanobacteria In Nitrogen Fixation

Directional RNA deep sequencing sheds new light on the transcriptional ...

Cyanobacteria are potential sources of renewable chemicals and biofuels and serve as model organisms for bacterial photosynthesis, nitrogen fixation, and responses to environmental changes. Anabaena (Nostoc) sp.

strain PCC 7120 (hereafter Anabaena) is a multicellular filamentous cyanobacterium that can "fix"atmospheric nitrogen into ammonia when grown in the absence of a source of combined nitrogen. Because the nitrogenase enzyme is oxygen sensitive, Anabaena forms specialized cells called heterocysts that create a microoxic environment for nitrogen fixation.

We have employed directional RNA-seq to map the Anabaena transcriptome during vegetative cell growth and in response to combined-nitrogen deprivation, which induces filaments to undergo heterocyst development. Our data provide an unprecedented view of transcriptional changes in Anabaena filaments during the induction of heterocyst development and transition to diazotrophic growth.

Results: Using the Illumina short read platform and a directional RNA-seq protocol, we obtained deep sequencing data for RNA extracted from filaments at 0, 6, 12, and 21 hours after the removal of combined nitrogen.

The RNA-seq data provided information on transcript abundance and boundaries for the entire transcriptome. From these data, we detected novel antisense transcripts within the UTRs (untranslated regions) and coding regions of key genes involved in heterocyst development, suggesting that antisense RNAs may be important regulators of the nitrogen response.

In addition, many 5'UTRs were longer than anticipated, sometimes extending into upstream open reading frames (ORFs), and operons often showed complex structure and regulation. Finally, many genes that had not been previously identified as being involved in heterocyst development showed regulation, providing new candidates for future studies in this model organism.

Conclusions: Directional RNA-seq data were obtained that provide comprehensive mapping of transcript boundaries and abundance for all transcribed RNAs in Anabaena filaments during the response to nitrogen deprivation.

We have identified genes and noncoding RNAs that are transcriptionally regulated during heterocyst development. These data provide detailed information on the Anabaena transcriptome as filaments undergo heterocyst development and begin nitrogen fixation.

Model Helps Pinpoint Cyanobacterial Genes that Capture the Sun's ...

Richland, WA (Scicasts) – 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.

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