|Chang, Perng Kuang|
Submitted to: Journal of Genetics and Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/1/2014
Publication Date: 10/5/2014
Citation: Chang, P-K., Scharfenstein, L.L. 2014. Aspergillus flavus Blast2GO gene ontology database: elevated growth temperature alters amino acid metabolism. Journal of Genetics and Genome Research. 1:005.
Interpretive Summary: Aspergillus flavus, a saprophytic fungus in the soil, infects crops such as corn, cotton, peanuts, and nut trees and such infection often leads to contamination with aflatoxin B1, a toxic and potent carcinogenic compound. The genome of A. flavus is 37 Mb and contains more than 13,000 genes. With the advent of genomics genome-wide investigation has expanded enormously. However, the unavailability of an A. flavus-specific gene ontology (GO) database has hampered the progress of A. flavus functional genomics. In this work, we used a web-based tool and constructed a GO database. The database was evaluated by published dataset and proven useful. Researchers now can use this database to determine how biotic and abiotic factors influence expression of A. flavus genes belong to different functional categories.
Technical Abstract: The availability of a representative gene ontology (GO) database is a prerequisite for a successful functional genomics study. Using online Blast2GO resources we constructed a GO database of Aspergillus flavus. Of the predicted total 13,485 A. flavus genes 8,987 were annotated with GO terms. The mean GO level was 5.64. Using a low stringency setting of a sequence cut-off number of 10 and a node score of 20, we obtained 1,177 GO terms associated with biological process, 388 GO terms associated with molecular function and 200 GO terms associated with cellular component. Of the 8,987 annotated genes 4,232 were mapped to 129 reference pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The utility of the GO database was evaluated with published transcriptomic data by assessing physiological states in relation to the metabolic capacity of A. flavus growing at 30°C and 37°C. Results showed that growth at 30°C favored degradation of amino acids with nonpolar side chains, such as valine, leucine, isoleucine, phenylalanine and tryptophan. In contrast, growth at 37°C favored the degradation of arginine and histidine (basic), aspartate and glutamate (acidic), and serine and threonine (uncharged but polar) and biosynthesis of the aforementioned nonpolar-side-chain amino acids. KEGG pathways of amino acid degradation contributing to acetyl-CoA production, (saturated) fatty acid biosynthesis and degradation as well as biosynthesis of unsaturated fatty acids were active at 30°C, which suggests a requirement that A. flavus maintain a high content of unsaturated fatty acids at the optimal growth temperature. The proposition was supported by the finding that the GO cellular component involved at 30°C growth was mainly a fatty acid synthase complex. The constructed A. flavus GO database was proven to be useful in our functional genomics study.