- Open Access
ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome
© Ling et al; licensee BioMed Central Ltd. 2010
- Received: 23 April 2010
- Accepted: 19 October 2010
- Published: 19 October 2010
Maize (Zea mays ssp. mays L.) is an important model for plant basic and applied research. In 2009, the B73 maize genome sequencing made a great step forward, using clone by clone strategy; however, functional annotation and gene classification of the maize genome are still limited. Thus, a well-annotated datasets and informative database will be important for further research discoveries. Signal transduction is a fundamental biological process in living cells, and many protein families participate in this process in sensing, amplifying and responding to various extracellular or internal stimuli. Therefore, it is a good starting point to integrate information on the maize functional genes involved in signal transduction.
Here we introduce a comprehensive database 'ProFITS' (Protein Families Involved in the Transduction of Signalling), which endeavours to identify and classify protein kinases/phosphatases, transcription factors and ubiquitin-proteasome-system related genes in the B73 maize genome. Users can explore gene models, corresponding transcripts and FLcDNAs using the three abovementioned protein hierarchical categories, and visualize them using an AJAX-based genome browser (JBrowse) or Generic Genome Browser (GBrowse). Functional annotations such as GO annotation, protein signatures, protein best-hits in the Arabidopsis and rice genome are provided. In addition, pre-calculated transcription factor binding sites of each gene are generated and mutant information is incorporated into ProFITS. In short, ProFITS provides a user-friendly web interface for studies in signal transduction process in maize.
ProFITS, which utilizes both the B73 maize genome and full length cDNA (FLcDNA) datasets, provides users a comprehensive platform of maize annotation with specific focus on the categorization of families involved in the signal transduction process. ProFITS is designed as a user-friendly web interface and it is valuable for experimental researchers. It is freely available now to all users at http://bioinfo.cau.edu.cn/ProFITS.
- Maize Genome
- Signal Transduction Process
- Comprehensive Annotation
- Bind Site Consensus Sequence
- InterPro Accession
Maize (Zea mays ssp. mays L.) is an important economic crop, and has served as a model organism for plant genetic research for several decades. The B73 maize genome was sequenced in 2009 [1–3], providing unprecedented opportunities for genome-wide annotation, classification and comparative genomics research. However, the comprehensive maize genome sequence repositories, MaizeSequence http://www.maizesequence.org  and maizeGDB http://www.maizegdb.org/  provide limited information concerning gene families' categorization. The thriving of research discoveries may be hampered under these circumstances.
Signal transduction is a fundamental biological process in living cells for sensing, amplifying and responding to various extracellular or internal stimuli . Many gene products (proteins) are involved in this process. During the signal transduction process, the status of protein-protein interaction, protein three-dimensional architecture, and the localization of proteins could be altered by rapid changes in protein activities or stabilities. Protein phosphorylation and ubiquitination are two major donators of these changes through post-translation covalent modification. Furthermore, when they are associated with transcription factors (TFs) that can lead to the multitude transcription cascades, these proteins act as switches allowing the proper and timely response of signal information flow and avoiding overreaction. In the past two decades, identifying the components involved in signal transduction and determining specific signalling pathways have both been functional research hotspots. However, genome-wide classification of gene families involved in signal transduction of maize is still limited.
With the aim to facilitate studies on signal transduction in the maize genome, we developed the 'ProFITS' (Protein Families Involved in the Transduction of Signalling) of maize, a database which categorizes TFs, protein kinases/phosphatases (PKs/PPs) and ubiquitin-proteasome-system (UPS)-related genes in maize.
The B73 maize genome dataset (version 4a.53) which includes gene, transcript and protein sequences were downloaded from MaizeSequence http://www.maizesequence.org/index.html . Four maize full-length cDNA (FLcDNA) datasets [3, 6–8] were obtained from GenBank  by the searching key 'FLI-CDNA'. To the FLcDNA dataset generated by Alexandrov , only high quality sequences labelled as 'completed cds' were selected for further analysis. To those FLcDNAs whose corresponding protein sequences were not available in GenBank, the EMBOSS suite  was applied for protein translation and the longest one of each FLcDNA was selected for further analysis. In addition, consensus sequences of TF binding sites (TFBS) were retrieved from two publicly accessible comprehensive plant cis-element databases, PLACE  and AtcisDB . These two datasets were further merged into one by performing manual curation that low-quality or redundant TFBS consensus sequences were filtered or integrated. Furthermore, mutant information including mutant gene name, phenotype and location were obtained from MaizeGDB .
Comprehensive annotation to the maize genome and FLcDNA sequences
First of all, InterProScan was performed against the maize genome protein sequences and FLcDNA translations, and GO (gene ontology)  annotations were generated based on InterProScan results. In addition to InterProScan, Pfam search was implemented separately using the newest version of Pfam database (Version 24.0, as of July 2010), because Pfam accessions were key identifiers used for TF classification. The gathering cut-off (-cut_ga), which is the minimum score a sequence must attain when building a full alignment of a Pfam entry, is applied as threshold. After that, the FLcDNA sequences were localized to the maize genome using GMAP  and correlated with maize genome transcripts using BLAST search . Appearance of TFBS within 3 kb upstream sequences of each transcript was also computed by short sequence match with curated binding site consensus sequences using regular expression method. Then, putative homologs in Arabidopsis and rice genomes were identified using BLAST (E-value ≤ 1e-40 and Coverage ≥ 0.5).
We specifically classified three protein families involved in signal transduction: the TFs, the PKs/PPs and the UPS-related genes. Different strategies were designed and depicted as follow.
The identification approach of TFs is adopted from PlnTFDB , that TFs were predicted and classified based on protein domains identified by the Pfam search. For each TF family, there exists one or more required domains, while several families contain forbidden domains (See detailed rules in Additional File 1).
As for PKs/PPs, a modified PlantsP kinase Classification/PlantsP Phosphatase Classification (PPC)  is used for family classification. The H and No_PPC (not included in PPC yet) classes were added in this modified PPC system. The H class consists of two-component system related genes (e.g. histidine kinases), while No_PPC contains Hpt genes, casein kinase II and other kinases/phosphatases that cannot be classified in the original PPC classification. The sequences associated with required protein domains defined by InterPro accessions (which generated by InterProScan) were selected firstly. Then BLAST (E-value ≤ 1e-10 and Coverage ≥ 0.5) was done on candidate sequences against PPC classified Arabidopsis PKs/PPs sequences. The candidates were assigned to different PPC groups according to their best hit in the reference. The required InterPro accessions and a modified PPC criterion which intend to gather all the protein phosphorylation related genes in one category can be explored in Additional File 1.
Lastly, we identified UPS-related genes employing same method as in plantsUPS . A group of InterPro accessions (see Additional File 1) were used for classification of different UPS-related gene families. Since there is no consensus accessions for RBX (Ring-Box) and DDB which is a component of CDD (CUL4-RBX1-CDD complex) families, BLAST search (E-value ≤ 1e-10 and Coverage ≥ 0.5) against protein sequences of these family members in Arabidopsis were implemented for identification.
We constructed and configured ProFITS upon a typical LAMP (Linux + Apache + MySQL + PHP) platform. The dataset was stored in MySQL 5.0 http://www.mysql.com, and the web interface was built by PHP scripts http://www.php.net on Red Hat Linux, powered by an Apache server http://www.apache.org. Server-side scripts were developed using Python http://www.python.org.
Web interface overview
Feature tools and functionalities
ProFITS provides several analysis and exploration tools to facilitate users' research. An advanced search tool in ProFITS supports not only maize sequence IDs, but also IDs of Arabidopsis or rice, and Arabidopsis gene names. Additionally, we integrated an adopted GO enrichment analysis tool from agriGO , which facilitates users to uncover hidden biological meanings from a user-prepared list of gene IDs.
Genome browsers have been shown as one kind of useful tools in inspecting sequence structures and locations in a direct and visualized way - thus we set up and configured two different browsers, GBrowse  and JBrowse (Additional File 2) , catering to users' different requirements. Mutual links between the database and GBrowse/JBrowse are available so that users can easily switch aspects of the investigation to interesting targets.
Statistics of three identified categories in ProFITS
Total number of three identified categories in ProFITS
Full length cDNA
Although information concerning maize TFs and UPS-related genes can be found in PlnTFDB  and PlantsUPS , a complete profile of these two categories in the maize genome is still deficient. Based on gene annotation of the B73 maize genome (version 4a.53) and FLcDNA datasets, ProFITS provides a basic platform for maize functional genome research - the three key categories involved in signal transduction are particularly identified and classified. In addition, the predicted TFBS of genes together with TFs in ProFITS may provide clues to determine the possible effective TFs in a specific signal transduction pathway.
Jasmonate (JA) is a plant hormone (phytohormone) which participates in multiple developmental processes. The core of the JA-signalling module in Arabidopsis, SCFCOI1/JAZ/MYC2, has been defined . SCFCOI1 is an E3 ubiquitin ligase complex. After hormone perception by SCFCOI1, JAZ (JAsmonate ZIM domain) repressors are targeted for proteasome degradation, releasing MYC2 and de-repressing transcriptional activation . We checked the putative maize homologs of these genes using reciprocal BLAST (data not shown), and found that they were all in the corresponding categories of ProFITS.
We collected all 1,230 Arabidopsis genes classified in the signal transduction process (GO:0007165), and then explored their annotation of molecular function. Interestingly, among 1,169 genes annotated to have catalytic activities, > 60% have protein kinase activity (725) and about 10% have phosphatase activity (133). Only 0.8% of genes have protein ligase activity; however, this is threefold that of the 0.28% of all annotated with protein ligase activity genes in the Arabidopsis genome, which indicates their important roles in signal transduction processes. Other genes such as receptors, TFs, two-component response regulators and protein phosphatase type 2A regulators are under molecular transducer activity, transcription regulator activity and enzyme regulator activity terms, respectively (see Additional File 3). The GO distribution is consistent with our definition of ProFITS.
As ProFITS provides a platform of maize information, its expansibility will be useful when new data is available or a new gene family needs to be categorized.
ProFITS provides users with a comprehensive profile of genes involved in signal transduction. Sequences of the maize genome and four maize FLcDNA projects are available, making it valuable for experimental researchers. It is freely available now to all users at http://bioinfo.cau.edu.cn/ProFITS.
We thank Ms. Wenying Xu and Dr. Yifang Chen for discussions and critical suggestions. This work was supported by grants from the Ministry of Science and Technology of China (2006CB100105) and the Ministry of Agriculture of China for Transgenic Research (No. 2008ZX08009-002).
- Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA: The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science. 2009, 326 (5956): 1112-1115. 10.1126/science.1178534.PubMedView ArticleGoogle Scholar
- Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J: A First-Generation Haplotype Map of Maize. Science. 2009, 326 (5956): 1115-1117. 10.1126/science.1177837.PubMedView ArticleGoogle Scholar
- Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, Currie J, Angelova A, Collura K, Wissotski M, Ashley E: Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs. PLoS Genet. 2009, 5 (11): e1000740-10.1371/journal.pgen.1000740.PubMed CentralPubMedView ArticleGoogle Scholar
- Sen TZ, Andorf CM, Schaeffer ML, Harper LC, Sparks ME, Duvick J, Brendel VP, Cannon E, Campbell DA, Lawrence CJ: MaizeGDB becomes 'sequence-centric'. Database. 2010, 2009: bap020-10.1093/database/bap020.View ArticleGoogle Scholar
- The Gene Ontology Consortium: The Gene Ontology in 2010: extensions and refinements. Nucl Acids Res. 2010, 38 (suppl_1): D331-335.PubMed CentralView ArticleGoogle Scholar
- Jia J, Fu J, Zheng J, Zhou X, Huai J, Wang J, Wang M, Zhang Y, Chen X, Zhang J: Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings. Plant J. 2006, 48 (5): 710-727. 10.1111/j.1365-313X.2006.02905.x.PubMedView ArticleGoogle Scholar
- Lai J, Dey N, Kim CS, Bharti AK, Rudd S, Mayer KF, Larkins BA, Becraft P, Messing J: Characterization of the maize endosperm transcriptome and its comparison to the rice genome. Genome Res. 2004, 14 (10A): 1932-1937. 10.1101/gr.2780504.PubMed CentralPubMedView ArticleGoogle Scholar
- Alexandrov N, Brover V, Freidin S, Troukhan M, Tatarinova T, Zhang H, Swaller T, Lu YP, Bouck J, Flavell R: Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol. 2009, 69 (1): 179-194. 10.1007/s11103-008-9415-4.PubMed CentralPubMedView ArticleGoogle Scholar
- Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW: GenBank. Nucl Acids Res. 2010, D46-51. 10.1093/nar/gkp1024. 38 DatabaseGoogle Scholar
- Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000, 16 (6): 276-277. 10.1016/S0168-9525(00)02024-2.PubMedView ArticleGoogle Scholar
- Higo K, Ugawa Y, Iwamoto M, Korenaga T: Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucl Acids Res. 1999, 27 (1): 297-300. 10.1093/nar/27.1.297.PubMed CentralPubMedView ArticleGoogle Scholar
- Molina C, Grotewold E: Genome wide analysis of Arabidopsis core promoters. BMC Genomics. 2005, 6 (1): 25-10.1186/1471-2164-6-25.PubMed CentralPubMedView ArticleGoogle Scholar
- Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L: InterPro: the integrative protein signature database. Nucl Acids Res. 2009, 37 (suppl_1): D211-215. 10.1093/nar/gkn785.PubMed CentralPubMedView ArticleGoogle Scholar
- Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K: The Pfam protein families database. Nucl Acids Res. 2010, D211-222. 10.1093/nar/gkp985. 38 DatabaseGoogle Scholar
- Wu TD, Watanabe CK: GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005, 21 (9): 1859-1875. 10.1093/bioinformatics/bti310.PubMedView ArticleGoogle Scholar
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res. 1997, 25 (17): 3389-3402. 10.1093/nar/25.17.3389.PubMed CentralPubMedView ArticleGoogle Scholar
- Perez-Rodriguez P, Riano-Pachon DM, Correa LG, Rensing SA, Kersten B, Mueller-Roeber B: PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Research. 2010, D822-827. 10.1093/nar/gkp805. 38 DatabaseGoogle Scholar
- Gribskov M, Fana F, Harper J, Hope DA, Harmon AC, Smith DW, Tax FE, Zhang G: PlantsP: a functional genomics database for plant phosphorylation. Nucleic Acids Research. 2001, 29 (1): 111-113. 10.1093/nar/29.1.111.PubMed CentralPubMedView ArticleGoogle Scholar
- Du Z, Zhou X, Li L, Su Z: plantsUPS: a database of plants' Ubiquitin Proteasome System. BMC Genomics. 2009, 10: 227-10.1186/1471-2164-10-227.PubMed CentralPubMedView ArticleGoogle Scholar
- Du Z, Zhou X, Ling Y, Zhang Z, Su Z: agriGO: a GO analysis toolkit for the agricultural community. Nucl Acids Res. 2010, gkq310-Google Scholar
- Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ: The UCSC Genome Browser database: update 2010. Nucl Acids Res. 2010, 38 (suppl_1): D613-619. 10.1093/nar/gkp939.PubMed CentralPubMedView ArticleGoogle Scholar
- Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH: JBrowse: a next-generation genome browser. Genome Res. 2009, 19 (9): 1630-1638. 10.1101/gr.094607.109.PubMed CentralPubMedView ArticleGoogle Scholar
- Dardick C, Chen J, Richter T, Ouyang S, Ronald P: The Rice Kinase Database. A Phylogenomic Database for the Rice Kinome. Plant Physiol. 2007, 143 (2): 579-586. 10.1104/pp.106.087270.PubMed CentralPubMedView ArticleGoogle Scholar
- Hamel LP, Nicole MC, Sritubtim S, Morency MJ, Ellis M, Ehlting J, Beaudoin N, Barbazuk B, Klessig D, Lee J: Ancient signals: comparative genomics of plant MAPK and MAPKK gene families. Trends Plant Sci. 2006, 11 (4): 192-198. 10.1016/j.tplants.2006.02.007.PubMedView ArticleGoogle Scholar
- Gfeller A, Liechti R, Farmer EE: Arabidopsis jasmonate signaling pathway. Sci Signal: STKE. 2010, 3 (109): cm4-10.1126/scisignal.3109cm4.Google Scholar
- Fonseca S, Chico JM, Solano R: The jasmonate pathway: the ligand, the receptor and the core signalling module. Currt Opin Plant Biol. 2009, 12 (5): 539-547. 10.1016/j.pbi.2009.07.013.View ArticleGoogle Scholar
- Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res. 1994, 22 (22): 4673-4680. 10.1093/nar/22.22.4673.PubMed CentralPubMedView ArticleGoogle Scholar
- Kumar S, Nei M, Dudley J, Tamura K: MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008, bbn017-Google Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.