Genomic inventory and transcriptional analysis of Medicago truncatula transporters

Abstract

Transporters move hydrophilic substrates across hydrophobic biological membranes and play key roles in plant nutrition, metabolism, and signaling and, consequently, in plant growth, development, and responses to the environment. To initiate and support systematic characterization of transporters in the model legume Medicago truncatula, we identified 3,830 transporters and classified 2,673 of these into 113 families and 146 subfamilies. Analysis of gene expression data for 2,611 of these transporters identified 129 that are expressed in an organ-specific manner, including 50 that are nodule specific and 36 specific to mycorrhizal roots. Further analysis uncovered 196 transporters that are induced at least 5-fold during nodule development and 44 in roots during arbuscular mycorrhizal symbiosis. Among the nodule- and mycorrhiza-induced transporter genes are many candidates for known transport activities in these beneficial symbioses. The data presented here are a unique resource for the selection and functional characterization of legume transporters.

Figure 1.

Genomic analysis of M. truncatula membrane transporters. A, Number of genome-predicted genes (IMGAG version 2) and transcripts (MTGI) and overlap between databases. B, Number of IMGAG-predicted proteins with at least two TMD (2+ TMD) according to different algorithms. C, Overlap between the 2,039 IMGAG-predicted proteins with significant similarity (e-value < e-3) to TCDB members and the 4,161 proteins with at least two TMD predicted by at least two topology algorithms. D, Number of identified membrane transporters derived from IMGAG version 2.0 or MTGI version 8. *, Note that the total number of MTGI sequences is higher than shown in Table I due to gene redundancy or multiple probe set mapping.

Figure 2.

Nodule-enhanced and nodule-specific membrane transporters in M. truncatula. Gene expression represents signal strength of Affymetrix Medicago GeneChip identifiers from the Medicago Gene Expression Atlas (Benedito et al., 2008) and Gomez et al. (2009). Samples for the mature organ series were taken from noninoculated 28-d-old plants (except nodules) growing at optimal conditions (Benedito et al., 2008). For nodule samples (Nod), numbers indicate days postinoculation with rhizobia. Myc indicate root samples with (+) or without (−) mycorrhizal association. Error bars indicate se of three biological replicates. Affymetrix probe sets and their respective TC (Saier et al., 2006) numbers and family acronyms are shown for each transcript. A, Member of the H⁺-dependent Oligopeptide Transporter family (POT/PTR). B and C, Members of the Major Intrinsic Protein family (MIP; aquaporins). D and E, Members of the Sulfate Permease family (SulP/SULTR). F and G, Members of the Nitrate/Nitrite Porter family (NNP), which belong to the Major Facilitator Superfamily (MFS). H, Member of the Drug/Metabolite Transporter superfamily (DMT). I, A member of the K⁺ Uptake Permease (KUP) family, homolog to LjKUP1 from L. japonicus.