Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters

Abstract

Background: Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by forming a complex system of pumps and channels. Although studies have effectively characterized individual M. truncatula transporters in several databases, until now there has been no available systematic database that includes all transporters in M. truncatula.

Description: The M. truncatula transporter database (MTDB) contains comprehensive information on the transporters in M. truncatula. Based on the TransportTP method, we have presented a novel prediction pipeline. A total of 3,665 putative transporters have been annotated based on International Medicago Genome Annotated Group (IMGAG) V3.5 V3 and the M. truncatula Gene Index (MTGI) V10.0 releases and assigned to 162 families according to the transporter classification system. These families were further classified into seven types according to their transport mode and energy coupling mechanism. Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST) mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation. A chromosome distribution map and text-based Basic Local Alignment Search Tools were also created. In addition, we have provided a way to explore the expression of putative M. truncatula transporter genes under stress treatments.

Conclusions: In summary, the MTDB enables the exploration and comparative analysis of putative transporters in M. truncatula. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at http://bioinformatics.cau.edu.cn/MtTransporter/.

Figure 1

Computational prediction to identify Medicago truncatula transporters. We used Basic Local Alignment Search Tool (BLAST) and HMMER searches in computational predictions to identify M. truncatula transporters. First, we used the transport protein sequences of Arabidopsis thaliana and the Transporter Classification Database (TCDB) to conduct a BLAST search with M. truncatula protein sequences, provided by the International Medicago Genome Annotated Group (IMGAG). The preprocess data were then analyzed for the presence of a potential transmembrane domain (TMD) using two algorithms: TMHMM and HMMTOP 2.0. Afterward, we used the annotated sequences to conduct a HMMER search with the Pfam annotations from the Pfam database, version 24.0. In addition, all original transporters were compared with proteins of the M. truncatula transporter annotation at the Noble Foundation. We used Perl scripts to analyze the results.

Figure 2

Phylogenetic tree analysis of the Amt family. This figure shows the result of phylogenetic tree analysis of Amt, an example of the 162 families in the Medicago truncatula transporter database. Individual members of the Amt family were further clustered and color-coded based on the result of phylogenetic analysis and TC numbering system. M. truncatula Amts can be classified into two groups: Amt1 and Amt2. Green markers refer to Arabidopsis thaliana sequences. Red markers refer to M. truncatula sequences. Each group contains links to individual protein pages.

Figure 3

Individual protein page. Here we use a protein called "Medtr7g069640.1" from the Amt family as an example. This figure shows separate web pages where users can find detailed information such as transporter function annotation, transmembrane segment prediction by TMHMM, genomic locus information, expressed sequence tag mapping results, domain annotation prediction by Pfam, three-dimensional structure prediction, expression annotation, and protein/cDNA/spliced/transcript sequences.

Figure 4

Three-dimensional templates of Medicago truncatula transporters. Here we use a protein called "Medtr7g069640.1" from the Amt family as an example. We obtained the reference sequences from the protein data bank (PDB). There are 10 members in Amt family, all of which pick up four consensus templates named 2NMR (structure of the E. coli Amt), 2NS1 (structure of the E. coli Amt), 2B2F (structure of the A. fulgidus Amt) and 2NUU (structure of the E. coli Amt). Links to PDB and the M. truncatula transporter database are also provided. The result is graphic.