Grant No. IOS-1025398
Comparative Genomics-driven Discovery of Maize Metabolic Functions


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Project Personnel

Last Name First name Institution Role Email
Hanson Andrew U. Florida PI adha@ufl.edu
de Crécy-Lagard Valérie U. Florida Co-PI vcrecy@ufl.edu
McCarty Donald U. Florida Co-PI drm@ufl.edu
Gregory Jesse U. Florida Co-PI jfgy@ufl.edu
Frelin Océane U. Florida Postdoctoral ofrelin@ufl.edu
Hasnain Ghulam U. Florida Postdoctoral hasnaing@ufl.edu
El Yacoubi Basma U. Florida Postdoctoral basma@ufl.edu
Zallot Rémi U. Florida Postdoctoral remizallot@ufl.edu
Niehaus Thomas U. Florida Postdoctoral tomniehaus@ufl.edu
Huang Lili U. Florida Postdoctoral lilihuang@ufl.edu
Guan Jiahn Chou U. Florida Postdoctoral guanjc@ufl.edu
Gerdes Svetlana U. Florida Bioinformatics sveta@thefig.info
Lerma-Ortiz Claudia U. Florida Bioinformatics clerma@ufl.edu
Henry Christopher U. Chicago Co-PI chrisshenry@gmail.com
Seaver Sam U. Chicago Postdoctoral samseaver@gmail.com

 


Senior collaborators: Andrei Osterman (Burnham Institute for Medical Research)

Summary

The rapid progress in sequencing plant genomes and genes has exposed the lack of information regarding the function of >70% of the proteins encoded. In addition, these studies have shown that many such unknowns also occur in bacteria and archaea. Comparative genomics is a powerful approach to uncover gene function, as is advanced in silico reconstruction of an organism's metabolism. In this project, both approaches will be used to improve the accuracy of functions assigned to maize metabolic genes and to predict functions for unknown genes, with special emphasis on B vitamins (folate, niacin, thiamin, pyridoxine, riboflavin, pantothenate, and biotin). The ten most promising functional predictions will be experimentally validated by combining genetic and metabolic profiling approaches in bacteria with biochemical assays of recombinant proteins and with genetic tests in maize. The expected overall outcome of this project is the implementation of a comparative genomics prediction and validation pipeline for maize gene function discovery, using B vitamin metabolism as a paradigm. Gene functions (annotations) will be publicly available via MaizeCyc (http://pathway-dev.gramene.org/gramene/maizecyc.shtml) and the SEED (http://theseed.uchicago.edu/FIG/index.cgi) databases, with metabolic reconstructions available via the Model SEED website (www.theseed.org/models/).

The project will implement an interdisciplinary approach to gene function discovery that is extendable to any metabolic network. In the process, it will enrich the maize genome by imposing consistency on thousands of metabolic gene annotations, and by improving the annotations of hundreds of unknown genes. Both impacts will advance future function discovery. Furthermore, by developing genome-scale in silico metabolic reconstructions, the work will initiate a systems approach to understanding maize metabolism. Integrally, the work will provide cross-disciplinary training in comparative genomics, metabolic biochemistry, and microbial genetics to students, postdoctoral associates, and faculty. In addition the project will provide for an annual 3-day hands-on workshop at the University of Florida to train researchers at all levels to predict functions using the SEED and other comparative genomics databases, with special emphasis on training faculty from minority serving institutions. Finally the project will develop an undergraduate bioinformatics course in which the students participate in unknown gene identification and metabolic reconstructions using comparative genomics and a graduate course module in which students develop functional predictions for unknowns in the project.