GRASSIUS: A first step in establishing regulatory networks in maize and other grasses

Palaniswamy, S¹; Gray, J²; Davuluri, R¹; Grotewold, E³

¹Dept. Mol Virology, Immunology, & Medical Genetics, ³Dept of Plant Cellular & Molecular Biology, The Ohio State University, Columbus, OH 43210 and ²Dept. of Biology, University of Toledo, Toledo OH 43606

 

The increasing amount of genome sequence information in maize and other grasses makes it possible to start building genome-wide regulatory networks. Towards this goal, we have initiated the development of GRASSIUS, the Grass Regulatory Information Server (http://grassius.org/). The ultimate goal of GRASSIUS is the integration of information on transcription factors and cis-regulatory elements into regulatory motifs, the building blocks of regulatory networks, across the grasses. Thus, GRASSIUS contains growing databases on maize, rice, sorghum and sugarcane transcription factors (GRASSTFDB) and promoter elements (GRASSPROMDB). As a first step towards the generation of GRASSIUS, a uniform nomenclature system for proteins corresponding to transcription factor was adopted, in which an organismal identifier (e.g., Zm) is followed by a letter code corresponding to the transcription factor family member (e.g., MYB) followed by a number. In this way, for example, a synonym for the C1-encoded protein would be ZmMYB1. Transcription factors from these grasses are currently being grouped into 43 families (Fig. 1), representing the major classes of regulatory proteins identified in other plants (e.g., Arabidopsis, see http://arabidopsis.med.ohio-state.edu/). GRASSIUS is expected to significantly benefit from community input, for example through voluntary curation contributions. The Grass Annotation Tool (GAT) is under implementation, which would facilitate easy submission, curation and validation of new and existing experimental data. Experimental data will include plasmid clone descriptions/maps and validated sequences from full length cDNAs for each transcription family member. Distribution information for clones generated will be made available, translating into time and cost savings for community users. Web services provide a standard way of accessing, publishing applications and data sources over the internet, enabling mass acquisition and dissemination of knowledge. We would be making use of existing web services (WSDbfetch, CitationExplorer) to semi-automate the process of acquiring new data for GRASSIUS from literature and from other existing resources and we would be also making GRASSIUS data available as web services (Bio Moby) in a phased manner when a specific plant module in our database is completed. The Web interface for GRASSIUS was developed using the Java J2EE platform, and the databases were developed using MySql. The GRASSIUS database will be constantly updated, thus stay tuned.

 

 

 

Fig. 1: Initial classification of regulatory proteins into 43 families