PlnTFDB: an integrative plant transcription factor database

Abstract

Background: Transcription factors (TFs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or de-activation of upstream signaling cascades. TFs thus constitute master control elements of dynamic transcriptional networks. TFs have fundamental roles in almost all biological processes (development, growth and response to environmental factors) and it is assumed that they play immensely important functions in the evolution of species. In plants, TFs have been employed to manipulate various types of metabolic, developmental and stress response pathways. Cross-species comparison and identification of regulatory modules and hence TFs is thought to become increasingly important for the rational design of new plant biomass. Up to now, however, no computational repository is available that provides access to the largely complete sets of transcription factors of sequenced plant genomes.

Description: PlnTFDB is an integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. It also provides an access point to its daughter databases of a species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags (ESTs), domain architecture and scientific literature is provided for each family.

Conclusion: We have created lists of putatively complete sets of transcription factors and other transcriptional regulators for five plant genomes. They are publicly available through http://plntfdb.bio.uni-potsdam.de. Further data will be included in the future when the sequences of other plant genomes become available.

Figure 1

Pipeline for the identification and classification of TFs. The pipeline starts with the complete collection of predicted proteins for a given species. Then an HMM search is conducted over this collection keeping all significant hits and discarding all proteins containing a transposase-related domain. Finally the Classifier produces a list of putative TFs grouped into families.

Figure 2

Rules for the classification of TF families. Rules for the classification of TFs and other transcriptional regulators depicted as a bipartite graph. Blue squares represent families, TFs are indicated in solid color, other transcription regulators are indicated by shaded squares. Yellow circles represent protein domains from the PFAM database, orange circles represent domains generated in-house. Continuous edges appear when a domain must be present in members of the family. Discontinuous edges indicate that the domain must not appear in members of the family. The profile-HMMs representing the domains Alfin-like and NOZZLE were created based on outputs derived from PSI-BLAST searches at the NCBI protein database; profile-HMMs for the domains CCAAT-Dr1, DNC, G2-like, GRF, HRT, LUFS, NF-YB, NF-YC, STER_AP, trihelix, ULT and VOZ were created from published multiple sequence alignments. All remaining domains were represented by profile-HMMs downloaded from the PFAM database. This figure is accessible via the Plant Transcription Factor Database , and links are provided to the respective TF families and domains.

Figure 3

Database schemes. Panel A shows the scheme of the species-specific databases. Panel B shows the scheme followed by PlantTFDB. Nine tables structure the information stored in the species-centered databases. A: The tables sequences, present domains, orthologs and ESTs are connected to each other and to the table TFs by means of the cds_id field. The table domain_algn stores the alignments at the domain level for the members of a given family. All five tables contain information about the TFs. The tables families, relevant domains and papers are connected to each other and to the table TFs by means of the field family_id. They store the information concerning the TF families. B: A single table structures the information for Plant TFDB. Table names appear in blue background, and main keys in green background.

Figure 4

Web interface. Panel A shows the starting page for PlantTFDB. The tree menu in the center of the page allows browsing by species or by TF families. Panel B shows part of a typical page for a TF family; a short description and the domains that are important for the definition of the family are shown. Panel C shows part of the page for gene details, which is typical for each member of the DB. Alternative gene names are listed. Links to the genome databases and to the sister TFDBs where orthologs were found are provided.