Pedobacter heparinus is a non-pathogenic, free living, gram-negative rod shaped soil bacterium first isolated by Payza and Korn (1956). This bacterium was unusual since it could grow on heparin or sulfated acidic mucoheteropolysaccharides from various animal tissues as the sole source of carbon, nitrogen and energy. Five glycosaminoglycan-degrading enzymes have been purified from P. heparinus. These include heparinases I, II and III (see figure below) and chondroitinases AC and B (Yang et al. 1985). Eventually the genes for these enzymes were cloned to produce large quantities of the pure enzymes for commercial and research applications. For example, the heparinase enzymes were used to study structure of heparin, a drug widely used as an anticoagulant.
In spite of the discovery of these unique polysaccharide degrading enzymes, very little is known about the P. heparinus as a free living environmental bacterium. There are now 50 species in the Pedobacter genus and heparinus is the type species for the genus. However, as of 2015, there have only been about 20 published papers on this type species and mostly focused on enzyme purification.
In 2009, Han and associates at the DOE Joint Genome Institute (JGI) published the complete genome sequence of P. heparinus. The organism was selected for sequencing as a type species organism for the genus Pedobacter and was part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The circular genome is 5,167,383 bp long. Using a program called Prodigal, the DNA sequence was predicted to contain 4,341 genes, of which 4,287 were protein coding and 54 RNA coding.
In 2010, Geneva College was selected to participate in the Interpret a Genome in Education sponsored by the JGI. A major goal of this program was to “annotate” the genomes of newly sequenced genomes type species from a genus not well studied. Annotation is a type of manual curation in which of the gene in the genome is further studied to confirm the predictions by Prodigal. The gene curation was to be done by “massively parallel undergraduates” thus creating a research experience for many students and allowing for high throughput. Biology professor Dr. David Essig and Chemistry professor, Dr. Rodney Austin attended the January 2010 Bioinformatics workshop held at the JGI in Walnut Creek, CA. Shortly thereafter, workshop participants were encouraged to “adopt” the genome of an organism. Drs. Essig and Austin chose P. heparinus given that it was a relatively uncharacterized type of species (as described above), but also because it could be easily cultured at room temperature (a mesophile) in the presence of oxygen.
Since 2010, Geneva College Biology and Chemistry majors in several courses and independent studies have improved the annotation of over 300 genes and carried out experiments to test hypotheses from bioinformatic data. Some findings of interest include
Han, C. and 33 other authors. (2009) Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T). Standards in Genomic Science 1: 54-62.
Payza, A.N. and Korn, E.D. (1956) Bacterial degradation of heparin. Nature 177: 88-89.
Yang V.C., Linhardt., R. J., Bernstein, H., Cooney, C. L. and Langer. R. (1985). Purification and characterization of heparinase from Flavobacterium heparinium. J Biol Chem 260: 1849 – 1857.