Download Ecological Genomics: Construction of Molecular Pathways

Ecological Genomics: Construction of Molecular Pathways Responsible for Gene
Regulation and Adaptation to Heavy Metal Stress in Arabidopsis thaliana and
Raphanus sativus.
By: Lynda Villagomez, Dr. Tatiana Tatarinova and Dr. Gary Kuleck
Understanding the many factors involved in gene regulation in plants adapted to
environmental stress in harsh, polluted environments remains a major challenge. Utilizing
advanced bioinformatics tools and comprehensive Arabidopsis thaliana databases, this
challenge can be addressed. First, Ariadne Genomics Pathway Studio was used to explore
molecular responses in Arabidopsis to identify genes associated with heavy metal stress
responsiveness. This computational tool constructs complex pathways by extracting
molecular relationships from scientific journal articles and published microarray datasets.
These pathways can be verified in controlled laboratory conditions by analyzing A.
thaliana plants grown under heavy metal stress. Secondly, R. sativus ESTs are used to
determine the similarities between these two species. The R. sativus genome has not been
sequenced, consequently the DNA sequence similarity to A. thaliana’s sequence is
unknown. In order to accurately analyze the data, the level of sequence similarity
between Arabidopsis and R. sativus was estimated. Using BLASTN, the results of
alignment of R. sativus EST sequences to Arabidopsis genes indicated that ~50% of
Arabidopsis genes (15,974) match to R. sativus. Using a conservative threshold of 95%
sequence similarity, 8,059 pairs of putative orthologs between R. sativus and Arabidopsis
were identified. From 50 heavy metal-responsive genes in Arabidopsis identified in the
first phase, candidate genes in R. sativus likely to play a role in heavy metal response
were selected. Pathway Studio was used to build a prototype heavy metal response
network in R. sativus and to select candidates for RT-PCR validation of computational
predictions.