Friday, June 1, 2012

DOE JGI Science Highlights: Comparative genomics method to tag novel nitrogen-fixation genes

Nitrogen is crucial for plant growth but plants cannot harness it directly from the atmosphere. In the United States, legume crops such as soybeans and peas rely on nitrogen fertilizers to boost yields; in 2007, 13 million tons of industrially-produced fertilizers were applied.

Sinorhizobium nodules in alfalfa roots.  
(Image from A. Becker & E.G. Biondi, University of Florence)
Soil bacteria such as Sinorhizobium meliloti have a symbiotic relationship with plant hosts such as alfalfa, providing them with the needed nitrogen. One of the DOE JGI’s 2009 Community Sequencing Program projects focused on sequencing this microbe’s genome in order to learn more about the nitrogen fixation process and how symbiotic relationships are formed.

In a study published May 15, 2012 in BMC Microbiology, researchers from Florida State University conducted a comparative genomic study using the DOE JGI’s Integrated Microbial Genomes (IMG) portal to look for open reading frames (ORFs) -- the part of a gene that codes for a protein -- in S. meliloti that are involved in nitrogen fixation. 

The team conducted their search by comparing ORFs from nitrogen-fixing bacteria with those from closely-related but non-nitrogen-fixing bacteria such as plant or mammalian pathogens. They reported that their comparative genomics method “rediscovered” 19 ORFs that had previously been shown to be important for nodulation and/or nitrogen fixation. They were also able to identify nine S. meliloti ORFs that may play a role in forming a symbiotic relationship between bacterium and plant host. “The comparative genomics method described above might be very effective for identifying factors… that have not yet been studied by classical transposon mutagenesis screens,” they wrote.

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