Identification of the TgAMTs family members and analysis of their fundamental characteristics
This study identified ten members of the AMT gene family from the Torreya grandis genome, which were numbered TgAMT1–TgAMT10 (Table 1). TgAMTs were found to be located on chromosomes 1, 2, 5, 6, 7, and 8, with two tandem repeating genes, namely TgAMT4 and TgAMT5 (Fig. 1). The length of the CDSs ranged from 975–1629 bp (Table 1).
Table 1
Physicochemical properties of the AMT genes family in Torreya grandis.
Gene | Gene ID | Chromosome location | CDS Length | Protein size | Molecular mass | pI | GRAVY | Trans- membrane | Subcellular location |
TgAMT1 | PTG007578L.5 | Chr01 | 1431 | 476 | 51628.55 | 8.16 | 0.526 | 11 | plas vacu E.R. |
TgAMT2 | PTG006090L.35 | Chr01 | 1518 | 505 | 54464.56 | 6.39 | 0.410 | 11 | plas E.R nucl |
TgAMT3 | PTG006814L.93 | Chr02 | 1521 | 506 | 54574.42 | 6.29 | 0.376 | 11 | plas chlo nucl vacu E.R. |
TgAMT4 | PTG002221L.98 | Chr05 | 1413 | 470 | 50896.98 | 6.36 | 0.624 | 11 | plas vacu |
TgAMT5 | PTG002221L.99 | Chr05 | 1431 | 476 | 51681.85 | 6.79 | 0.567 | 11 | plas vacu |
TgAMT6 | PTG006706L.7 | Chr05 | 975 | 324 | 35056.80 | 9.80 | 0.714 | 11 | plas vacu E.R. |
TgAMT7 | PTG015048L.1 | Chr06 | 1629 | 542 | 59003.83 | 6.96 | 0.261 | 11 | plas |
TgAMT8 | PTG013339L.7 | Chr06 | 1470 | 489 | 52987.02 | 8.16 | 0.482 | 9 | plas |
TgAMT9 | PTG004123L.21 | Chr07 | 1443 | 480 | 53067.92 | 6.10 | 0.490 | 10 | plas vacu E.R. |
TgAMT10 | PTG027016L.5 | Chr08 | 1467 | 488 | 52682.75 | 6.41 | 0.545 | 11 | plas |
The physical and chemical properties of the encoded proteins were also analyzed. The number of encoded amino acids ranged from 324–542, and the isoelectric point range of the protein was 6.10–9.80. The hydrophilic coefficients of all were positive. The number of transmembrane domains encoded by TgAMT8 was nine, that by TgAMT9 was ten, and that by the others was 11. In addition, the prediction of subcellular localization revealed that TgAMTs was mainly confined to membrane structures and was also distributed in the vacuole, endoplasmic reticulum, and nuclear membranes. They may be related to cellular ammonium transport. The protein sequences are compared in Fig. S1. They are dominated by α coils, followed by random coils, and a relatively small proportion of extension chains and β-angles (Table 2).
Table 2
Secondary structure prediction of AMT gene in Torreya grandis.
Gene | Alpha helix/% | Beta turn/% | Random coil/% | Extended strand/% |
TgAMT1 | 44.54 | 5.46 | 31.51 | 18.49 |
TgAMT2 | 44.75 | 3.76 | 31.68 | 19.8 |
TgAMT3 | 42.69 | 5.14 | 27.87 | 24.31 |
TgAMT4 | 42.55 | 6.17 | 33.40 | 17.87 |
TgAMT5 | 41.60 | 5.04 | 33.40 | 19.96 |
TgAMT6 | 45.37 | 5.25 | 26.85 | 22.53 |
TgAMT7 | 39.67 | 6.64 | 34.32 | 19.37 |
TgAMT8 | 43.15 | 7.16 | 31.08 | 18.61 |
TgAMT9 | 42.71 | 5.00 | 32.50 | 19.79 |
TgAMT10 | 43.85 | 5.74 | 33.61 | 16.80 |
Phylogenetic evolutionary tree of the TgAMTs
A phylogenetic tree was constructed based on the protein sequences encoded by the AMTs and the TgAMTs families from Arabidopsis, Oryza sativa, Ginkgo biloba, Populus trichocarpa, and L. esculentum (Fig. 2). Based on the results, the TgAMTs family was divided into three evolutionary branches: TgAMT1, TgAMT2a, and TgAMT2b. Among the ten TgAMTs, only TgAMT2 and TgAMT3 belonged to the TgAMT1 subfamily, while four each belonged to the TgAMT2a and TgAMT2b subfamilies. TgAMTs were most closely related to poplar. Within the AMT2a subfamily, TgAMT7 was most highly correlated to the other three AMT families. TgAMT6, TgAMT8, and TgAMT10 clustered with OsAMT3.1, PtrAMT3.1, and PbAMT3, respectively.
Analyses of the TgAMTs gene family structure, conserved motifs, and cis-acting promoter elements
The structure and conserved motifs of the TgAMTs family were analyzed to understand the sequence characteristics (Fig. 3A). The results revealed structural variations among the different TgAMTs. The TgAMT family genes were within the same cluster, with insignificant structural differences between them. Conserved motif analysis of TgAMTs was performed to understand the protein sequence structure (Fig. 3B). The results showed that Motif 1, Motif 3, and Motif 4 were conserved, while Motif 10 was unique to TgAMT6, TgAMT8, and TgAMT10. TgAMTs were highly conserved structurally; Motif 4 was present at the 5' terminals of TgAMT2, TgAMT3, and TgAMT6, while Motif 7 was at the 5' terminals of the other TgAMTs. Thus, it can be inferred that the TgAMTs family plays a vital role in the stable transport of ammonium salts.
The upstream promoter sequences of TgAMTs were analyzed (Fig. 3C) and found to contain multiple functional elements. In addition to GAAT- and TATA-boxes, methyl jasmonate-induced, light-responsive, and multiple MYB binding elements were present, which play an essential role in the tolerance to adversity and abiotic stresses. In addition, the binding site of W-box element was also identified on the 2000bp promoter upstream of TgAMT5, which is closely related to biological processes such as plant growth, development and signal transduction
Tissue-specific expression patterns of TgAMTs
RT-qPCR experiments were conducted to ascertain the expression patterns of TgAMTs in different tissues (Fig. 4). The expression levels of TgAMTs were relatively high in leaves and low in fruits. The expression of TgAMT5 was elevated in stems, leaves, and roots than in fruits. In addition, the levels of TgAMT4, TgAMT7, and TgAMT9 were enhanced in specific tissues. For example, that of TgAMT4 was comparatively more in leaves and roots but lower in stems and roots.
Response of TgAMTs to Nitrogen stress
An analysis of the cis-acting promoter elements of this gene family indicated the presence of abiotic stress-related elements. RNA was extracted from the roots of plants grown at different nitrogen levels for 7 and 14 days to clarify the expression patterns of TgAMTs under nitrogen stress (Fig. 5A). The results showed that the relative expression levels of TgAMT1, TgAMT4, TgAMT5, and TgAMT7 in T. grandis roots were elevated after 7 and 14 days of nitrate nitrogen treatment; those of TgAMT10 were higher after 7 and 14 days of ammonium nitrogen treatment; and those of TgAMT3 were higher after seven days of nitrogen deficiency treatment. However, those of TgAMT2 and TgAMT8 declined post-treatment with varying nitrogen concentrations. The expression level of TgAMT6 did not alter. As shown in Fig. 5B, under different nitrogen conditions, the expression of TgAMTs in Torreya grandis leaves and roots was similar but was relatively enhanced in leaves. Thus, different nitrogen level stresses had varying effects on the expression patterns of TgAMTs. Most TgAMTs were up-regulated, most remarkably under nitrate nitrogen stress.
Allogeneic expression of TgAMT5
The expression of TgAMT5 in T. grandis was high and relatively stable under different nitrogen stress conditions. Therefore, it may have a high affinity for the absorption and transport of ammonium. First, the secondary and tertiary structures of TgAMT5 were predicted (Fig.S2). Arabidopsis plants were allogeneously transformed with TgAMT5 to investigate its function. As shown in Fig. 6A, semi-quantitative PCR assays showed that TgAMT5 was independently expressed in three different Arabidopsis lines, while no TgAMT5-related transcripts were detected in the wild-type (WT). As shown in Fig. 6B, without NH4 addition, the growth trends of the wild-type and overexpression lines were roughly identical. However, under the exogenous addition of 1 mM NH4, the root lengths of the WT and overexpression lines were markedly elevated compared to those without NH4. However, there were no remarkable differences between the root lengths of the WT and overexpression lines. Under the exogenous addition of 10 mM NH4, the root lengths of the WT and overexpression lines varied conspicuously; those of the latter were significantly longer, which may be due to the robust NH4 absorption capacity of TgAMT5, which promoted plant growth. The root length and fresh weight reflected more directly the differences between the wild type and overexpression plants, with those of the latter being higher (Fig. 6C).
Identification of candidate TFs regulating TgAMT5
Analysis of the cis-acting elements of the TgAMTs gene family showed that the promoters could interact with MYB, W-box, and other transcription factors to enhance gene expression. Therefore, the WRKY and MYB family genes were selected for the dual-luciferase assay. The 2000 bp promoter of TgAMT5 was cloned and fused to the DNA fragment encoding the N-terminal of the firefly luciferase protein (FLUC), which also contains the renilla luciferase (REN). As shown in Fig. 7B, only TgWRKY2 enhanced the activity of the TgAMT5 promoter, while other transcription factors had no remarkable regulatory effects on the promoters of the candidate genes. Similarly, the fluorescence image of the tobacco experimental group plants was indeed brighter than that of the control group plants (Fig. 7C). Next, the yeast single hybridization technique was used to detect whether TgWRKY2 could interact with the TgAMT5 promoter. It was found that TgWRKY2 directly interacted with A1 (Fig. 7D). The growth of the transformants in SD/-Trp/-Ura solid medium is shown in Fig. S3.