Biology Professor and Students Publish Research Article

April 12, 2016

Dr. Michael LaGier, in collaboration with Biology majors Brittany Bowman, Mark McDaniel, Michael Foggia, Kelsey Brend, and Katherine Hobbs, have published a research article, “Improved Functional Prediction of Hypothetical Proteins from Listeria monocytogenes 08-5578.” The article will appear in an upcoming issue of The Journal of the Iowa Academy of Science.  A summary of the project is included below.

Listeria monocytogenes is a foodborne human pathogen responsible for listerosis.  The genomes of several L. monocytogenes strains have been recently sequenced.  The genome of L. monocytogenes 08-5578, which was in part responsible for a significant listerosis outbreak in 2008, contains an unexpectedly high percentage of protein-encoding genes (1,927 out of 3,161; 60.96%) autonomously annotated as hypothetical proteins.  The aim of this study was to test whether a manual annotation strategy could be used to assign more meaningful functional names to the hypothetical proteins of 08-5578.  A holistic, manual gene annotation strategy that utilized sequence homology, cellular localization predictions, structure-based evidence, phylogeny, and protein-protein interaction data was used to assign potential cellular roles to 79 out of 100 hypothetical proteins randomly selected from the genome of 08-5578.  Of significance, 5 of the 79 hypothetical proteins assigned a more meaningful name may contribute to the virulence of L. monocytogenes 08-5578; by contributing to chemotaxis, cell surface protein sorting, cell wall biosynthesis, and cold adaptation.  The findings here support the notion that manual annotations, using a combination of diverse bioinformatics tools, can improve the quality of genomic information provided by automated genome annotation methods alone.