Pedobacter heparinus Genome Project


David A. Essig, PhD
Department of Biology

Rodney Austin, PhD
Department of Chemistry

Geneva College
3200 College Avenue
Beaver Falls, PA 15010

Description of GEBA Organism (Learn more...)

Geneva College Biology and Chemistry Departments were selected by the JGI to help annotate the recently sequenced genome of the soil bacterium Pedobacter heparinus (P. heparinus).  Its genome has been subjected to pipeline annotation.  This is a GEBA bacterium and is a founding member of the genus Pedobacter.  P. heparinus is a aerobic gram negative rod which grows optimally at 25 degrees.  The bacterium exhibits colongy spreading on low nutrient and low percent agar plates presumably through a gliding mechanism.  A unique feature is that P. heparinus is capable of degrading heteromucopolysaccharhides such as heparin.  Enzymes purified from this species were helpful in mapping the structure of various types of heparins.   Interestingly, P. heparinus has been found in close proximity to the roots of several plant species including rice and certain dune grasses and may have a symbiotic or pathogenic relationship with these plants.  

Summary of Project Goals (Learn more...)

Facilitate student learning
  • Reinforce basic concepts in genetics, molecular biology, biochemistry and genomics
  • Discovery based research experience
  • Responsibility and satisfaction of contributing to a larger project
Produce a high quality annotation of all genes in the genome
  • verfiy start codons
  • predict cellular localization
  • catalog genome wide operons
  • compare to genes studied experimentally in related organisms
  • improve the characterization of hypothetical genes by prediction of 
    • cellular localization
    • conservation within genus
    • operon context
  • connect each in the genome to a pathway
  • initiate functional genomics on selected genes
Establish the ecological niche as rhizospheric and connect to gene annotation findings
  • Verify plant bacterial relationship in microcosm and field studies
  • Emphasize the study of ecologically relevant pathways
    • virulence operons
    • root cell wall degradation enzymes
    • exopolysaccharide synthesis enzymes
    • plant hormone biosynthesis
    • chemotaxis and motility
    • quorum sensing
    • secondary metabolites
    • antibiotics

Annotation Tally
  • Number of open reading frames (ORFs) annotated in this organism: 210
  • The number of ORFs confirmed by functional analysis: 0
  • Number of biochemical pathways annotated in this organism: 0
  • Number of partial biochemical pathways annotated in this organism: 3

Are you interested in joining the Interpret a Genome program?  More information and the opportunity to receive training can be found at the DOE/JGI Interpret a Genome Program and the Microbial Genome Annotation Network (MGAN) websites (See navigation bar). 

This program is a collaboration with the Department of Energy (DOE) Joint Genome Institute (JGI) as part of the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project using the Integrated Microbial Genomes Annotation Collaboration Tool (IMG-ACT).

 The Design of this website template was funded by NSF (RCN-UBE-DBI 0954829)