Comparative genomics study of industrial fungus seeks to better harness potential for biofuels applications
|Aspergillus niger, shown here with its DNA lit up in green, is a fungus that can be used on an industrial scale to produce enzymes or chemicals such as citric acid. Source: PNNL. Click to enlarge.|
An international team led by Scott Baker of the Pacific Northwest National Laboratory has compared the genome sequences of two strains of the fungus Aspergillus niger to, among other things, better harness its industrial potential in biofuels applications.
A. niger is an industrial workhorse, with different strains efficient in producing polysaccharide-degrading enzymes (particularly amylases, pectinases, and xylanases) or organic acids (mainly citric acid) in high amounts. (As of 2007, the global market for citric acid was estimated to be approximately $1.2 billion with more than 500,000 tons produced annually by fermentation.) The production process involving A. niger is thus a well understood fungal fermentation process. The PNNL-led study compares the genomes of an enzyme-producing strain and a citric-acid-producing strain.
Learning more about the genetic bases of the behaviors and abilities of these two industrially relevant fungal strains, wrote senior author Baker and his colleagues in a paper published in the journal Genome Research, will allow researchers to exploit their genomes towards the more efficient production of organic acids and other compounds, including biofuels.
Aspergillus niger is an industrial workhorse for enzymes and small molecules such as organic acids. We know that this single organism is used for production of organic acids and for enzymes, and it can degrade plant cell wall matter for sugar production. For biofuels it’s a highly relevant organism since it’s already been scaled up, shown to be safe, and used for enzyme production. That’s why it was such an important organism to further characterize through DNA sequencing.—Scott Baker
The US Department of Energy (DOE) Joint Genome Institute (JGI) generated the 35-million base genome of A. niger ATCC 1015, the wild-type strain that was used in research that led to the first patented citric acid process. The other A. niger strain used in the study (A. niger CBS 513.88, an industrial strain derived from A. niger NRRL 3122, a strain developed for enzyme production by classical mutagenesis and screening methods) was sequenced by DSM in the Netherlands and reported in the journal Nature Biotechnology in January 2007.
The PNNL-led study determined the genetic diversity of these two A. niger strains by applying systems biology tools as well as new bioinformatics methods to examine multi-level differences that distinguish the wild-type citric-acid-producing strain from the mutagenized enzyme–producing strain.
By analyzing the genomes on several levels—DNA, chromosome, gene and protein—Baker and his colleagues found several hundred unique genes in each strain that are key to their predominant characteristics. For example, A. niger ATCC 1015 had a higher expression of traits involved in high citric acid yields. On the other hand, the induced mutant strain had more elements related to efficient enzyme production. The team also noted that the genes involved in boosting enzyme production in the induced mutant strain of A. niger may have come from another Aspergillus strain via horizontal gene transfer, which allows one organism to acquire and use genes from other organisms.
In this study, we provide and compare the genomes of two strains of A. niger. These two strains have different phenotypes: one, the predecessor to efficient enzyme-producing strains having undergone some level of mutagenesis and selection, and the other a wild-type parent strain of high citric-acid-producing strains. This makes the comparison interesting both in terms of genomic research and industrial applications. We have supported the conclusions of our comparison with further experiments, allowing us to propose new hypotheses and conclusions within three main areas: (1) genetic diversity of the A. niger group, (2) horizontal gene transfer in fungi, and (3) fungal biotechnology.—Andersen et al.
Nearly a dozen additional Aspergillus strains that are used in industry are either being sequenced or in the queue to be at the DOE JGI, said study co-author Igor Grigoriev, head of the DOE JGI Fungal Genomics Program. Grigoriev noted that a better understanding of genomic content and organization and how rearrangements and mutations lead to desired traits should facilitate further optimization of these strains for different bio-products.
Having the genetic blueprint for a citric acid-producing fungus will increase our understanding of the organism’s metabolic pathways that can be fine-tuned to enhance productivity or alter its metabolism to generate other green chemicals and fuels from renewable and sustainable plant-derived sugars.—Randy Berka, Director, Novozymes, Inc., and co-author
The US Department of Energy Joint Genome Institute, supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup.
Mikael R Andersen et al. (2011) Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res. doi: 10.1101/gr.112169.110
Herman J Pel et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology 25, 221 – 231 doi: 10.1038/nbt1282