The new program falls within the field of bioinformatics and it utilizes genome technology to shift through microbial genomes. The program will identify clusters of genes that point to an organism’s having the potential to synthesize various therapeutically promising molecules.
Biosynthesis describes an enzyme-catalyzed process that converts substrates into more complex products within living organisms. The process allows simple compounds to be transformed into more complex macromolecules. Examples include the production of lipid membrane components and nucleotides, such as proteins.
The bioinformatics tool has been developed by Professor of Chemistry Douglas Mitchell, from the University of Illinois at Urbana-Champaign. Bioinformatics is concerned with developing methods to understand biological data. This is the result of combining computer science, statistics, mathematics, and engineering to analyze and interpret biological data.
In a research note, Professor Mitchell explains the importance: “With genome sequencing going at the pace it has . . . there’s a dearth of functional information about what these genes are doing. It becomes increasingly important to make sense of and interpret metabolic pathways, especially biosynthetic gene clusters encoded by microbes.”
This research concern led to a new bioinformatics software tool which has been named RODEO (Rapid Open reading frame Description and Evaluation Online). Using RODEO, Professor Mitchell’s research team are focusing on molecules called RiPPs, (ribosomally synthesized and post-translationally modified peptides). These protein-like materials undergo chemical modification after they are made. One example is nisin, which is used as an antimicrobial additive in dairy products, meats, and beverages. The reason why RiPPs are of interest is because they have great potential for genetic re-engineering.
Discovering new RiPPs is difficult and this is the reason behind the new computer software. By scanning microbes using the new bioinformatics tool it should become faster to discover new drugs. Those of particular interest are a class of RiPPs called lasso peptides (these have a looping structure). These types of peptides are very robust and are not affected by many environmental factors (so they would, for instance, survive being ingested by a patient).
To date, the RODEO software has identified 1300 novel lasso peptides. Several of these are potential therapeutics. The research is published in the journal Nature Chemical Biology under the title “A new genome-mining tool redefines the lasso peptide biosynthetic landscape.”
