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Characterization of metallothionein genes from Broussonetia papyrifera: metal binding and heavy metal tolerance mechanisms

BMC Genomics volume 25, Article number: 563 (2024) Cite this article

Abstract

Background

Broussonetia papyrifera is an economically significant tree with high utilization value, yet its cultivation is often constrained by soil contamination with heavy metals (HMs). Effective scientific cultivation management, which enhances the yield and quality of B. papyrifera, necessitates an understanding of its regulatory mechanisms in response to HM stress.

Results

Twelve Metallothionein (MT) genes were identified in B. papyrifera. Their open reading frames ranged from 186 to 372 bp, encoding proteins of 61 to 123 amino acids with molecular weights between 15,473.77 and 29,546.96 Da, and theoretical isoelectric points from 5.24 to 5.32. Phylogenetic analysis classified these BpMTs into three subclasses: MT1, MT2, and MT3, with MT2 containing seven members and MT3 only one. The expression of most BpMT genes was inducible by Cd, Mn, Cu, Zn, and abscisic acid (ABA) treatments, particularly BpMT2e, BpMT2d, BpMT2c, and BpMT1c, which showed significant responses and warrant further study. Yeast cells expressing these BpMT genes exhibited enhanced tolerance to Cd, Mn, Cu, and Zn stresses compared to control cells. Yeasts harboring BpMT1c, BpMT2e, and BpMT2d demonstrated higher accumulation of Cd, Cu, Mn, and Zn, suggesting a chelation and binding capacity of BpMTs towards HMs. Site-directed mutagenesis of cysteine (Cys) residues indicated that mutations in the C domain of type 1 BpMT led to increased sensitivity to HMs and reduced HM accumulation in yeast cells; While in type 2 BpMTs, the contribution of N and C domain to HMs’ chelation possibly corelated to the quantity of Cys residues.

Conclusion

The BpMT genes are crucial in responding to diverse HM stresses and are involved in ABA signaling. The Cys-rich domains of BpMTs are pivotal for HM tolerance and chelation. This study offers new insights into the structure-function relationships and metal-binding capabilities of type-1 and − 2 plant MTs, enhancing our understanding of their roles in plant adaptation to HM stresses.

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Background

Paper mulberry (Broussonetia papyrifera) is an economically significant tree species with diverse applications. It is used for high-quality pig feed, its phloem fibers are premium raw materials for papermaking, its roots and seeds have medicinal properties, and its sap can treat skin diseases [1, 2]. Additionally, it contains higher levels of phenolic substances, such as flavonoids, polyphenols, and fructose, compared to many other plants [1, 2], offering substantial potential for development and utilization. To realize the economic potential of B. papyrifera, significant cultivation is essential. Given the constraints of not competing with agricultural land, the expansion of B. papyrifera cultivation has focused on utilizing less favorable sites such as construction wastelands, riverbanks, and tailings areas. Over the past 10 to 20 years, the cultivation of paper mulberry on heavy metal (HM)-polluted sites has increased rapidly. However, the yields from these sites have generally been much lower than expected. The primary cause is often unscientific cultivation practices in suboptimal soil conditions, including HM pollution and salt retention, despite B. papyrifera’s role as a pioneer species in ecological restoration. To optimize cultivation, it is critical to understand the response mechanisms of paper mulberry to various stressors, particularly HMs.

Plants have developed sophisticated strategies to mitigate damage under adverse conditions, including releasing stress signals, adapting to stress stimuli, regulating gene expression, altering protein metabolism, and relying on hormone signaling [3]. Plant hormones, especially abscisic acid (ABA), play pivotal roles in stress responses. For example, in response to drought stress, ABA levels increase rapidly, binding to receptors in the PYR1/PYL/RCAR (PYLs) family of proteins [4, 5]. The ABA-PYL complex then inhibits downstream protein phosphatases in clade A of the PP2C family [6], leading to the activation of sucrose non-fermenting-1-related protein kinase-2s. These kinases phosphorylate downstream effectors to initiate protective responses [7]. Under HM stress, the application of exogenous ABA has been shown to enhance plant tolerance by influencing various physiological, biochemical, and molecular processes [8]. To improve resistance to HM stress, several genes related to ABA signaling have been identified, including HM ATPases, ABC transporters, Zn iron permeases, natural resistance-associated macrophage proteins, and metallothioneins (MTs) [9, 10].

MTs are a superfamily of small (< 10 kDa) cytosolic cysteine (Cys)-rich metal ion-coordinating proteins [9, 11]. Plant MTs are categorized into four types (MT1, MT2, MT3, and MT4), differentiated by the arrangement of their Cys residues. MT1 features six Cys residues clustered at both the amino (N)- and carboxyl-terminal (C) regions, forming Cys-X-Cys motifs (X represents any amino acid other than Cys). The N- and C-termini of MT2 contain eight and six Cys residues, respectively, while MT3 includes four Cys residues at the N-terminal and six at the C-terminal. MT4 is distinct in having three Cys-rich domains, each with five or six conserved Cys residues, separated by 10 to 15 amino acids [11, 12]. Research has increasingly shown that MTs participate in numerous vital biological processes, including protection, resistance to metal toxicity, stress response control, and physiological homeostasis regulation [12, 13]. MTs facilitate the storage, transport, and homeostasis of essential metal ions, such as ZnII and CuI, and play a critical role in the detoxification of toxic metal ions, such as CdII, HgII, and PbII [13,14,15,16]. Their exceptionally high Cys content and thiolate residues offer additional protection against reactive oxygen species (ROS), leading to the formation of disulfide bridges and subsequent metal ion release [13,14,15,16]. In cassava, 10 MT genes have been found to exhibit tissue-specific expression, acting as ROS scavengers [17]. In maize, nine MT genes display specific expression patterns across 23 tissues at various developmental stages and show varied transcriptional responses to HM stresses such as Cu, Cd, and Pb [16]. Furthermore, MTs are increasingly recognized for their roles in abiotic stress tolerance, including drought, salt, and abnormal temperature changes [13, 17, 18]. These findings underscore the need for further detailed studies to elucidate the critical roles of plant MTs.

Understanding the complexities of metal chelates in MTs is crucial for developing effective strategies to manage metal contamination. MTs chelate metals through the sulfhydryl groups of Cys residues, forming coordinate covalent bonds [13,14,15,16,17,18]. The chelating capacity of MTs is influenced by the number and arrangement of Cys residues within their domains [17, 18]. Despite this, the function of the highly heterogeneous Cys-rich domain in plant MTs remains largely unexplored [19], and current evidence does not indicate that the N- or C-terminal Cys residues in B. papyrifera MTs impact their HM tolerance. Therefore, further research is required to investigate the role of Cys distribution in B. papyrifera MT proteins under HM stress.

To enhance our understanding of B. papyrifera’s adaptation mechanisms to HM-polluted environments and to support its efficient cultivation and utilization, MT genes were identified from transcriptomes based on their basic sequence characteristics, conserved domains, protein motifs, and phylogenetic relationships. Given the potential link between MTs and ABA signaling, four HMs—Cd, Cu, Mn, and Zn—along with ABA treatments, were employed to examine the expression of selected MT genes. A yeast expression system was utilized to explore the capability and mechanism of HM chelation by MTs. This study provides new insights that will inform future research on the role of BpMTs in HM remediation.

Results

Sequence characteristics and phylogenesis of BpMTs

Fifteen putative BpMT genes were initially identified from the B. papyrifera transcriptome. Following a conserved domain analysis and a comparison of homologous proteins using BLASTP, three genes lacking MT domains were excluded. Consequently, 12 genes were confirmed as MT family members. The open reading frames (ORFs) of these 12 BpMT genes ranged from 186 to 372 bp; their deduced peptides comprised 61 to 123 amino acids, and their molecular weights (MWs) varied from 15,473.77 to 29,546.96 Da. The theoretical isoelectric points (pI) of these MTs ranged from 5.24 to 5.32, and they were predicted to be localized in the nucleus, cytoplasm, cell membrane, and chloroplasts (Table 1).

To elucidate the phylogenetic relationships of BpMT proteins among B. papyrifera and other plant species, an unrooted phylogenetic tree was constructed. This tree was based on the alignment of MT protein sequences from B. papyrifera, Glycine max, Oryza sativa, Zea mays, Arabidopsis thaliana, Vitis vinifera, and Malus pumila using the neighbor-joining method. The evolutionary tree’s topology grouped all MT proteins into four subclasses, with the 12 identified BpMTs distributed among three types, excluding MT4. The MT2 type was the most populated with BpMTs, including BpMT2a, BpMT2b, BpMT2c, BpMT2d, BpMT2e, BpMT2f, and BpMT2g, whereas the MT3 type contained only BpMT3a. The remaining four genes, BpMT1a, BpMT1b, BpMT1c, and BpMT1d, fell under the MT1 type (Fig. 1).

Table 1 Information of the MT gene family in B. papyrifera
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Fig. 1
figure 1

Phylogenetic relationship of BpMT proteins. Alignments of the MT proteins from B. papyrifera and other 6 species were performed with Clustal W. The phylogenetic tree was constructed using Neighbor-Joining method of MEGA7. Different colors mean different type members according to sequence similarity

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The motif composition analysis further validated the subclassification and revealed the conserved domain characteristics of these proteins. Using the MEME tool [24], 10 conserved motifs, each comprising 6–29 amino acids, were identified across the 12 BpMT proteins (Table 2). The most prevalent motifs included motif1, motif2, motif3, and motif4 (Fig. 2A). Motifs 2 and 3 were present in all BpMT proteins, motif1 was found in 11 of the BpMTs except for BpMT3a, and motif4 appeared in 10 of the proteins, excluding BpMT3a and BpMT2a. The amino acid sequences of motifs 1, 2, 3, and 4 were highly conserved, corresponding to the metallothio domain (Fig. 3). Among the BpMTs, BpMT2d possessed the most motifs (a total of eight). BpMT2a, BpMT2e, and BpMT2f each had five motifs, sharing motif1, motif2, and motif3. The unique motifs 10 and 4 in BpMT2f differentiated it from BpMT2a, which uniquely features motifs 8 and 9. Motif7 was exclusive to BpMT2e. BpMT3a had the fewest motifs, with only three—motif2, motif3, and motif9. The other six BpMTs shared four motifs: motif1, motif2, motif4, and motif3 (Fig. 2A). Additionally, PFAM analysis indicated that 11 of the BpMT proteins contained a unique metallothio_2 superfamily domain, while BpMT3a was characterized by a single metallothio superfamily domain (Fig. 2B). The metallothio_2 domain, richer in Cys residues than the metallothio domain, aligns closely with Class II MTs, suggesting a distinct specificity for BpMT3a compared to the other 11 BpMTs, warranting further confirmation and functional characterization of BpMT3a.

Table 2 Motif sequences of BpMT proteins identified by MEME tool
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Fig. 2
figure 2

The conserved motifs and domains of BpMT proteins. (A) The motifs distributed in the 12 BpMT proteins, the 10 conserved motifs are represented with different color boxes. The dark line shows the length of proteins. (B) Distribution of conserved domains within BpMT proteins. The relative positions of each domain are shown in color boxes, the names are indicated on the right

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Fig. 3
figure 3

Multiple sequence alignment of the motifs of 12 BpMT proteins (A) and the sequence logo of motif1, motif2, motif3 and motif4 (B)

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Expression patterns of BpMTs in response to HM stresses

To assess the potential function of BpMTs in HM stress responses, the expression patterns of 12 BpMTs were evaluated under stresses from CdCl2 (Cd), CuSO4 (Cu), MnCl2 (Mn), and ZnCl2 (Zn). Interestingly, all BpMTs showed high induction and reached peak expression levels in the roots, while generally exhibited the lowest and least induction in the leaves (Fig. 4).

Under Cd stress

The 12 BpMTs exhibited diverse expression profiles with tissue-specific responses, clustering into three groups. Group one, including BpMT2e, BpMT2a, BpMT2f, and BpMT1d, showed relatively lower expression levels compared to the other groups, peaking at 24 h in the roots. Another group comprised BpMT1b, BpMT3a, and BpMT1a, displaying intermediate transcription levels. The most significantly induced group included BpMT2c, BpMT1c, BpMT2d, BpMT2b, and BpMT2g. Notably, BpMT2c and BpMT1c were highly upregulated by Cd stress; in the roots, BpMT2c’s expression at 6 h ranged from 1.19- to 3.79-fold higher than the other BpMTs, and at 24 and 72 h, BpMT1c’s expression was 1.14- to 2.78- and 1.17- to 3.6-fold higher, respectively. In the leaves, BpMT2c’s expression increased 1.04- to 2.75-fold compared to other BpMTs (Fig. 4A). Furthermore, BpMT2g showed a high correlation with the other seven BpMTs under Cd stress (Fig. S1A).

Under Cu stress

The response levels of the 12 BpMTs to Cu stress were generally higher than under Cd stress, with expression values frequently exceeding 5.0 and 4.0. The BpMTs were grouped into two classes based on their transcription patterns. Class one included BpMT1c, BpMT1b, BpMT1a, BpMT2g, BpMT2d, and BpMT2b, whose transcription activities were slightly more pronounced than those of the second class comprising the remaining six BpMTs. In the roots, peak expressions for class one and BpMT2c occurred at 24 h, with BpMT1a, BpMT1c, and BpMT1b showing the highest expressions at 1.51-~3.09-fold, 1.50-~3.06-fold, and 1.29-~2.63-fold higher than the other nine BpMTs, respectively. In the stems, except for BpMT1c, BpMT1b, and BpMT2g peaking at 24 h with values of 5.17, 4.06, and 3.48, respectively, the other nine genes reached their maximum transcription at 72 h. In the leaves, eight BpMTs, excluding BpMT1c, BpMT2g, BpMT2d, and BpMT2b, were most expressed at 72 h, with BpMT1b recording the highest transcription at 3.85-fold greater than BpMT2b (Fig. 4B). Additionally, BpMT2d and BpMY3a showed significant correlations with the other four BpMTs (Fig. S1B), indicating that most BpMTs might be crucial genes collectively responding to Cu stress.

Under Mn stress

All 12 BpMT genes exhibited more pronounced induction than under Cd and Cu stresses and were divided into three groups based on their expression patterns. Group 1, displaying the most significant expression, included BpMT2e and BpMT2d. Group 2 consisted of BpMT1a, BpMT2g, BpMT1b, and BpMT1c. The remaining six genes (BpMT2b, BpMT2a, BpMT2c, BpMT1d, BpMT2f, and BpMT3a), forming Group 3, reached peak expression at 24 h, except for BpMT2b. In the roots, BpMT2d’s expression was 3.37 times that of BpMT1c. In the stems, BpMT2d showed the highest expression at 24 h, with transcription levels 1.22 to 2.64 times those of other BpMTs. In the leaves, half of the BpMTs had expression values exceeding 4.00 (Fig. 4C). Correlation analysis revealed that BpMT1d and BpMT2a were significantly associated with BpMT2b, BpMT2d, BpMT2e, and BpMT2f, suggesting a synergistic response to Mn stress (Fig. S1C).

Exposure to Zn stress

All BpMTs genes were upregulated and categorized into three groups. Group 1 consisted of BpMT2e, BpMT1c, BpMT2d, and BpMT2b. Group 2 included BpMT2f, BpMT1b, BpMT2c, and BpMT2g, while Group 3 comprised BpMT3a, BpMT2a, BpMT1d, and BpMT1a. In the roots, all BpMTs were significantly induced, showing maximum expression at 24 h, although BpMT1d’s expression was only 41% of BpMT2b’s. In the stems, BpMT2e and BpMT1b were notably upregulated at 6 h, while by 72 h, BpMT1a was the most highly transcribed, reaching levels 1.19 to 4.13 times those of other BpMTs. In the leaves, BpMT2b and BpMT2e were most prominent, with expression values 1.40 to 5.02 times and 1.28 to 4.60 times that of the other 10 BpMTs, respectively (Fig. 4D). Furthermore, all BpMTs exhibited significant co-expression with three other BpMTs (Fig. S1D), highlighting a broad co-expression network within the BpMT family in response to Zn stress, particularly involving BpMT2c and BpMT2d.

Fig. 4
figure 4

Expression patterns of BpMT genes under different HM stresses for 0, 6, 24, 72 h in the roots, stems and leaves. Heatmap of BpMT genes expression data was created by Tbtools with row clustering applied, and the blue/yellow/orange colors indicated the low/medium/high expression level. The expression was related to the internal reference gene and control conditions. (A) Cd stress. (B) Cu stress. (C) Mn stress. (D) Zn stress. The data followed by ‘ns’ means the difference between the time point and 0 h was not significant in the same tissue, while the data not marked were all significantly different to 0 h (P < 0.05)

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Transcription potential of BpMTs mediated by ABA signaling

To explore whether BpMTs participate in ABA signaling, the transcriptional responses of 12 BpMTs to ABA treatment were examined. The results demonstrated significant upregulation of all BpMT genes by ABA across roots, stems, and leaves during differentiation (Fig. 5A). In the roots, half of the 12 BpMTs (BpMT1a, BpMT2f, BpMT2a, BpMT1d, BpMT1c, and BpMT2g) reached their maximum expression levels at 6 h, all exceeding a value of 3.5. The remaining six BpMTs peaked at 24 h with expression values ranging from 3.60 to 6.88; notably, BpMT2f and BpMT3a were the most prominent, with values of 6.88 and 6.38, respectively. In the stems, the highest expression values at 6, 24, and 72 h involved different subsets of five, four, and three BpMTs, respectively. BpMT2d (6.09) exhibited the most significant induction at all measured time points, ranging from 1.16 to 3.78 times that of other genes. In the leaves, while BpMT2d, BpMT2b, and BpMT1a experienced a trough in expression at 24 h, BpMT2f increased to its peak at 24 h. The remaining eight BpMT genes reached maximum transcription at 24 h (Fig. 5A), suggesting a complex relationship between BpMTs and ABA signaling.

To determine if there was a functional relationship mediated by ABA signaling among these genes, correlation analysis was performed on the expression levels post-ABA treatment. In the roots, except for BpMT1d, all other BpMTs showed significant correlations with at least two other BpMTs. In stems, every BpMT gene exhibited significant correlations with another BpMT. Conversely, in the leaves, BpMT1a and BpMT2c did not correlate with any other BpMTs (Fig. 5B). These findings suggest that BpMTs response widely and deeply to ABA compared to HM stress (Fig. 6), indicating a potential reliance of BpMTs on the ABA signaling pathway.

Fig. 5
figure 5

Expression profiles and relativities of BpMT genes under ABA treatment for 0, 6, 24, 72 h in the roots, stems and leaves. The expression is relative to the internal reference gene and at control conditions. The heatmap of expression data was created by Tbtools same as Fig. 4. All the differences of each gene between different time points and 0 h were significant in the same tissue (P < 0.05). (A), the expression files. (B), the relativities

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Fig. 6
figure 6

Redundancy analysis (RDA) was employed using Canoco 5.0 for gene expression and experiment treatments, including heavy metal and ABA treatments at different time points (0, 6, 24, 72 h)

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Heterologous expression of BpMTs conferring HM tolerance in yeast

To investigate the role of BpMT genes in response to HM stimuli, all 12 BpMTs were individually expressed in yeast for HM stress resistance analysis. The yeast strain INVSCI harboring pYES2-BpMTs or control vector pYES2 was exposed to Cd, Cu, Mn, and Zn stress. Yeast clones were diluted 100-, 101-, 102-, 103-, and 104-fold, respectively, and spotted onto Sc-Ura plates. Under normal conditions, the growth and viability of INVSCI (pYES2) and INVSCI (pYES2-BpMTs) cells were comparable. However, under HM stress, INVSCI (pYES2) exhibited reduced or weaker growth compared to INVSCI (pYES2-BpMTs), particularly under Cu stress and at the highest dilution of 104 (Fig. 7A). Optical density (OD600) values of INVSCI (pYES2) and INVSCI (pYES2-BpMTs) were recorded under Cd, Cu, Mn, and Zn stress. While there were no significant differences under normal conditions, notable discrepancies were observed after exposure to HM stress. INVSCI (pYES2-BpMTs) consistently demonstrated higher OD600 values than INVSCI (pYES2), particularly under the HM conditions. Apart from INVSCI (pYES2-BpMT2f), INVSCI (pYES2-BpMT1d), and INVSCI (pYES2-BpMT1b) under Cd stress, and INVSCI (pYES2-BpMT2c) under Cu stress, all other yeast strains subjected to the four HM stresses exhibited significantly greater growth activities than the control INVSCI (pYES2) (Fig. 7B). These findings suggest a beneficial role of BpMTs in mediating HM stress responses.

Fig. 7
figure 7

Analysis of the heavy metal stress response function of BpMT genes in yeast. (A) The growth performance of the control and BpMTs transformed yeasts under HM stresses. The decreasing trend triangle above represents the dilution ratio of 00, 10− 1, 10− 2, 10− 3, 10− 4. (B) The yeast cell densities (OD600) of INVSCI (pYES2) and INVSCI (pYES2-BpMTs) under four HM treatments. Control was cultivated in a normal media without HM stress. The lowercase letters in the figure indicated the significant differences (P < 0.05) among different yeast lines

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BpMT-transformed yeast cells displayed higher HM accumulations

To assess the link between HM stress tolerance and metal accumulation, ICP-MS analysis was conducted to measure the concentrations of Cd, Cu, Mn, and Zn in yeasts transformed with BpMT1c, BpMT2d, and BpMT2e. Results depicted in Fig. 8 show that, compared to the control yeast, yeast cells expressing BpMT1c, BpMT2d, and BpMT2e accumulated significantly higher levels of Cd (2.94-, 3.45-, and 3.16-fold increase), Cu (2.14-, 2.49-, and 2.38-fold increase), Mn (3.29-, 3.07-, and 2.93-fold increase), and Zn (3.09-, 2.89-, and 3.00-fold increase) respectively, when supplemented with 20 µM Cd, 50 µM Cu, 20 µM Mn, and 10 µM Zn. However, between the control yeast and yeast strains transformed with BpMT1c, BpMT2d, and BpMT2e, no significant differences in growth were observed under non-stressed conditions (Fig. 8A). This indicates that overexpression of BpMTs enhances yeast resistance to HMs through increased metal accumulation.

Type 1 and 2 BpMTs depend differently on N- and C-terminal Cys-rich domains in HM toxicity resistance

To elucidate the mechanisms of BpMTs’ tolerance and chelation capabilities toward HMs, N- and C-terminal Cys residues were independently mutated and cloned into pYES2, generating mutated yeast expression recombinants of BpMT1c, BpMT2d, and BpMT2e. INVSC1 yeast strains harboring pYES2, pYES2-BpMT1c, pYES2-BpMT1c-mΔN, pYES2-BpMT1c-mΔC, pYES2-BpMT2d, pYES2-BpMT2d-mΔN, pYES2-BpMT2d-mΔC, pYES2-BpMT2e, pYES2-BpMT2e-mΔN, and pYES2-BpMT2e-mΔC were subjected to spot and growth assays under various HM stresses. The spot assay results indicated that all mutants exhibited reduced growth compared to their non-mutant counterparts (pYES2-BpMT1c, pYES2-BpMT2d, and pYES2-BpMT2e). Specifically, INVSC1(pYES2-BpMT1c-mΔC) displayed more growth inhibition than INVSC1(pYES2-BpMT1c-mΔN). Conversely, INVSC1(pYES2-BpMT2d-mΔC) and INVSC1(pYES2-BpMT2e-mΔC) did not show obvious inhibition compared to INVSC1(pYES2-BpMT2d-mΔN) and INVSC1(pYES2-BpMT2e-mΔN) respectively under Cd, Mn, and Zn stresses (Fig. 8A). No significant growth differences were observed under control conditions (Fig. 8A). ICP-MS analysis to quantify HM accumulation revealed that INVSC1(pYES2-BpMT1c-mΔC) accumulated only 31.57%, 40.12%, 28.21%, and 29.12% of the Cd, Cu, Mn, and Zn levels, respectively, seen in INVSC1(pYES2-BpMT1c). INVSC1(pYES2-BpMT2d-mΔC) and INVSC1(pYES2-BpMT2e-mΔC) chelated slightly more HMs than INVSC1(pYES2-BpMT2d-mΔN) and INVSC1(pYES2-BpMT2e-mΔN); however, most differences were not statistically significant excluding under Cu stress (Fig. 8B). The HM accumulation in INVSC1(pYES2-BpMT2d-mΔN) and INVSC1(pYES2-BpMT2e-mΔN) was 67.51% and 79.18% (Cd), 87.15% and 80.38% (Cu), 43.52% and 41.27% (Mn), 39.49% and 46.11% (Zn) of INVSC1(pYES2-BpMT2d) and INVSC1(pYES2-BpMT2e), respectively (Fig. 8B). These findings demonstrate the significant roles of BpMT1c, BpMT2d, and BpMT2e in HM detoxification, which is mediated through Cys residues located in their C-terminal or N-terminal domains.

Fig. 8
figure 8

HMs tolerance and accumulation study of yeast BpMTs’ mutants (N- and C-domain named as mΔN and mΔC, respectively) generated by site-directed mutagenesis in yeast. (A), Serially diluted transformed yeast INVSC1containing pYES2, pYES2-BpMT1c, pYES2-BpMT1c-mΔC, pYES2-BpMT1c-mΔN, pYES2-BpMT2d, pYES2-BpMT2d-mΔN, pYES2-BpMT2d-mΔC, pYES2-BpMT2e, pYES2-BpMT2e-mΔN, pYES2-BpMT2e-mΔC spotted on Sc-U selective media with and without metal (Control), Cd, Cu, Mn, Zn. (B), HMs accumulation in yeast cells according to (A). All data are mean ± SD (n = 3). Different letters above bars indicate significant differences among different yeast strains under the same HM stress (P < 0.05)

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Discussions

Plant MT genes are crucial components that respond to various environmental stimuli [12,13,14,15,16,17,18]. To inform scientific strategies for the cultivation and management of paper mulberry, understanding the molecular mechanisms of adaptation to adverse conditions is imperative. In this context, the transcriptomes of paper mulberry plants under different HM stresses were sequenced to establish a foundational database for identifying key genes that adapt or respond to environmental stresses. Owing to their significant transcription, abundant presence, and crucial roles in plant metal homeostasis and detoxification [9, 11], 12 BpMT genes were identified from the aforementioned transcriptome data. Based on their evolutionary relationships, these 12 BpMTs are classified into three types of MTs (MT1–3), excluding type MT4 (Fig. 1), which also influenced the nomenclature of BpMTs. Plant MTs are generally categorized into four types (MT1 ~ 4) [14, 19, 20]. However, in this study, the identified 12 BpMT genes did not include type MT4, likely because the BpMT family genes examined are shared genes screened from the root, stem, and leaf transcriptomes under various stresses, primarily representing transcriptionally expressed genes responsive to HM stress. This screening does not ensure that all members are induced under HM stress, nor does it allow for the identification of other tissue-specific genes. Type 4 MTs are typically confined to developing and mature seeds and diminish post-germination [12, 21]; hence, the 12 BpMTs identified from the root and leaf transcriptomes did not encompass any type 4 BpMTs. Nonetheless, the screening of these genes was predicated on their transcriptional expression under stress, which may relate to the regulation of HM stress.

To understand the biological functions of BpMTs, their evolutionary relationships were analyzed initially, revealing that the 12 BpMT proteins shared high similarity with MTs from other species such as A. thaliana, O. sativa, and V. vinifera (Fig. 1). Based on conserved domain analysis, 11 BpMTs were classified within the ‘metallothio_2 superfamily’ domain, whereas BpMT3a was associated with the ‘metallothio superfamily’ (Fig. 2B). Additionally, the 12 BpMTs exhibited various motif compositions, with the main motifs presumed to be markers of the metallothio superfamily [9, 22]. This foundational information confirmed the classification of the 12 BpMTs within the MT protein family.

To determine the involvement of these BpMTs in the HM stress response, the expression activities of the 12 BpMTs were analyzed under treatments with Cd, Cu, Mn, and Zn in roots, stems, and leaves. It was observed that all 12 BpMTs were inducible by these HMs, displaying tissue-specific expression patterns, particularly BpMT2c and BpMT1c in response to Cd, BpMT1a and BpMT1c to Cu, BpMT2d to Mn, and BpMT2e and BpMT2b to Zn (Fig. 4). The transcriptional activity of genes in response to stress can effectively predict their potential functions. For instance, nine MT genes in maize were induced with diverse expression patterns in response to Cu, Cd, and Pb stress, suggesting their role in maize’s resistance to HMs [16]. SaMT3 from Sedum alfredii, upregulated by Cd stress, was further confirmed to promote plant Cd tolerance by scavenging [22]. The chickpea MT1 gene displayed inconsistent upregulation against major toxic HMs, such as As [As(III) and As(V)], Cr(VI), and Cd toxicity; further assays confirmed that MT1 overexpression in transgenic lines could reduce As(V) and Cr(VI) accumulation, while enhance Cd accumulation; Arabidopsis transformed with the MT1 gene showed mitigated HM stress [23]. Canavalia rosea MTs exhibit habitat- and environmental stress-regulated patterns, which likely contributed to thermotolerance [15]. These reports, along with the inducible expression of BpMTs, suggest that BpMT genes play roles in HM stress responses. From the expression levels and relationships observed, the responses to Cd and Cu, Zn and Mn were more correlated than to Zn and Mn, Cd and Cu, accordingly; BpMT1c was particularly notable in the response to Cd and Cu, while BpMT2e and BpMT2d were significant in the response to Mn and Zn stress (Figs. 4 and 6, S1).

To further confirm the function of BpMTs in response to HM stress, 12 BpMTs were individually inserted into pYES2 vectors and transformed into INVSCI yeast cells for expression assays. The results demonstrated that transgenic yeasts expressing BpMTs exhibited improved growth compared to control yeast under HM conditions (Cd, Cu, Mn, and Zn) (Fig. 7), underscoring the beneficial role of BpMTs in mitigating HM stress. The yeast expression system is commonly employed as a rapid and straightforward method for investigating the functions of target genes, as evidenced by studies involving Caragana korshinskii CkMT4 [21], Silene vulgaris SvMT3 [24], and Leymus chinensis LcMT3 [25]. These findings further validate the effectiveness of BpMTs in the yeast expression system and their potential roles in regulating plant responses to HM stress.

The presence of Cys-rich domains is crucial for the chelation of metal ions [13,14,15,16]. Tolerance to HM stress or chelation is directly linked to the N- or C-terminal Cys-rich domains, although the specific roles of these domains can vary by species [17,18,19,20,21]. In this study, we observed that tolerance to Cd, Cu, Mn, and Zn stresses is not uniformly influenced by these domains across different types of BpMTs. The C-terminal domain exhibited a more pronounced response in type 1 MT genes than the N-terminal domain, whereas both C- and N-terminals played similar roles in type 2 MT genes in B. papyrifera (Fig. 8). This observation aligns with the function OsMT-I-Id, a type 1 MT from rice, which responds to Cd, Cu, and As stress [19], and underscores the characteristic features of type I MTs potentially conferred by the six C-X-C motifs distributed evenly across the N- and C-terminal domains [13,14,15,16,17]. In contrast, type 2 MTs are typically linked to HM detoxification [26]. Research by Singh et al. (2019) showed that both N- and C-terminal domains of CjMT2 bind Cd2+ ions [27]. Additionally, Li et al. (2023) reported that mutations in the C-terminal Cys residues of NtMT2F significantly impaired its HM chelation capacity [28]. Our findings revealed that mutations in the N- and C-terminal Cys residues of BpMT2d and BpMT2e notably reduced HM chelation, with no significant differences observed between N- and C-terminal mutations (Fig. 8). This suggests that the N- and C-terminals of type 2 MTs may function similarly in HM tolerance and chelation, with the N-terminal Cys domain’s slightly superior performance potentially due to a higher count of Cys residues compared to the C-terminus. This hypothesis merits further investigation to pinpoint the specific Cys residues involved.

Additionally, the ABA-dependent signaling pathway is well-known for its central role in abiotic stress responses and involves numerous genes. Further investigation is required to determine whether the chelation of MT with HMs depends on ABA signaling. To examine whether the response of BpMTs to HM stress is associated with ABA, B. papyrifera was treated with ABA concurrently with HM treatments (0, 6, 24, and 72 h), and the transcription levels of each BpMT were analyzed. All 12 BpMTs were significantly induced by ABA to varying extents (Fig. 5A). Additionally, the expression profiles of some BpMTs in each tissue under ABA treatment mirrored those under HM stress (Figs. 4 and 5A), indicating that BpMT transcription is sensitive to ABA, similar to other reported ABA-related genes. For example, cucumber MT family genes (CsMT2, CsMT3, and CsMT4) can be induced by NaCl, PEG, and ABA and are thought to depend on ABA signaling [29]. mRNA levels of CkMT4 are upregulated by ABA, and further studies have shown that CkMT4 facilitates the re-establishment of desiccation tolerance in C. korshinskii seeds through ABA signaling [21]. Comparative expression analysis of MT genes from rice and Arabidopsis also supports the broad stress response of MTs to ABA [30]. Notably, the responses of all BpMTs to Cd, Cu, Mn, and Zn were significantly correlated with ABA, especially those of BpMT1d, BpMT2b, BpMT1b, and BpMT3a (Figs. 5B and 6). Therefore, based on the behavior of BpMTs under both HM stress and ABA treatment in this study, alongside previous findings, it is suggested that the response of B. papyrifera MT family members to HM stress is linked to ABA signaling.

Moreover, plants grow in soil, and their roots are the first to come into contact with HMs. An effective response from the root system is a crucial pathway through which plants adapt to and transport HMs. It is common for members within the same family to co-express or interact with each other to fulfill their functions; for example, in Betula platyphylla, BplMYB46 can form homodimers and heterodimers with BplMYB6, BplMYB8, BplMYB11, BplMYB12, and BplMYB13 [31]. In walnuts, JrWRKY2 and JrWRKY7 can form homodimers and interact with each other in response to abiotic stress [32]. In peaches, pERF98-1/2 forms homodimers/heterodimers and interacts with two PpERF1 proteins to amplify the jasmonate/ethylene signaling pathway [33]. However, reports on co-expression among MT family members are scarce. To elucidate the functional relationships within the MT family, we analyzed the expression correlation of the 12 BpMTs in the roots under various HM stresses and found significant correlations among most BpMTs (Fig. S1, 6). We hypothesize that the potential mechanisms of BpMTs in responding to HM stress relate to root growth and regulation, involving co-expression and interaction within the family. Future research on B. papyrifera’s response to HM stress will explore these potential pathways, including root control and ABA signaling.

Materials and methods

Plant materials and treatments

B. papyrifera seeds were collected from a mine tailing area in Xiangtan, Hunan Province (112°45′E, 27°53′N) and identified by Prof. Zhao Yunlin, with permission (Grant No. 2016TP2007). The seeds were germinated in a greenhouse (relative humidity 70 ± 5%, temperature 22 ± 2 °C, light/dark cycle 14/10 h) [34]. Seedlings were selected based on comprehensive evaluations of growth and resistance to HMs. Specimens from selected plants were preserved at the Plant Factory of the Forestry College of Northwest A&F University. Plant stem segments were used to establish a tissue culture system. Uniform tissue culture seedlings from the same subculture line (approximately 4 cm in height) were transplanted to pots after seven days of seedling acclimatization and maintained in a greenhouse. The potting mix consisted of soil, vermiculite, and perlite in a 5:3:2 ratio. After 10 months of growth with regular tap water irrigation, the seedlings were subjected to HM stress and ABA treatment. Each treatment solution (0.2 mmol/L CdCl2, 0.5 mmol/L MnCl2, 0.6 mmol/L CuSO4, 0.2 mmol/L ZnCl2, and 30 µmol/L ABA) was applied in 1 L volumes in trays to ensure the plants remained stressed until the end of the sampling period. Roots, stems, and leaves were harvested at 0 (control), 6, 24, and 72 h and stored at − 80 °C for RNA isolation. Each treatment had three replicates, with each replicate containing five seedlings. Control seedlings were water irrigated synchronously in equal amounts.

Identification of MT genes in B. papyrifera

The root and leaf transcriptomes of B. papyrifera, subjected to treatments with 0.2 mmol/L CdCl2, 0.5 mmol/L MnCl2, 0.6 mmol/L CuSO4, 0.2 mmol/L ZnCl2, and 30 µmol/L ABA for 72 h, were sequenced to obtain a preliminary sequence set. The transcriptomes were assembled using Trinity. Gene functions were annotated against databases such as Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and GO [34]. Gene expression levels were estimated with RNA-seq by expectation maximization. Differential expression analyses under these conditions were conducted using the DESeq R package (version 1.10.1). Genes identified as differentially expressed by DESeq, with an adjusted P-value < 0.05, were considered for further analysis. The differentially expressed genes were screened for potential MT family candidates using a keyword search. Candidates were further validated through Basic Local Alignment Search Tool (nih.gov). The ORFs of potential MT genes were analyzed using ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/). Conserved domains were predicted using the online Conserved Domain Search Service (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi). The MT domain of all potential BpMTs was confirmed using the Hidden Markov Model by searching PFAM (http://pfam.sanger.ac.uk/search) and HMMER (https://www.ebi.ac.uk/tools/hmmer/search/phmmer) [35]. The conserved motifs were analyzed using the MEME online tool (http://alternate.meme-suite.org/) and Tbtools [36] with parameters set to a maximum of 10 motifs, allowing any number of repetitions, and a motif width range of 6–29. Following these analyses, the members of the BpMT family were confirmed. Cloning primers for the ORFs were designed based on cDNA and subsequently verified by sequencing. The MW, pI, and amino acid composition of the confirmed BpMTs were analyzed using the ExPASy server (https://web.expasy.org/protparam/).

Analysis of evolutionary relationship of BpMTs

To elucidate the evolutionary relationships of the B. papyrifera MT genes, MT protein sequences from G. max, O. sativa, Z. mays, (A) thaliana, V. vinifera, and M. pumila were downloaded from the database Phytozome v13 (https://phytozome-next.jgi.doe.gov/). The MT protein sequences from (B) papyrifera and these species were aligned using the Clustal W2 program. A phylogenetic tree was constructed using MEGA7 via the neighbor-joining method [37]. The evolutionary tree was visualized using the online software ITOL (https://itol.embl.de/) [38]. The BpMTs were classified into subclasses based on the topology of the phylogenetic tree.

Expression analysis of BpMTs under HM stress and ABA

Total RNA was extracted from each sample using the cetyltrimethylammonium bromide method [34]. The quality of the RNA was verified by 1% agarose gel electrophoresis, and its concentration was determined before reverse transcription, following digestion with DNase I (Takara, Dalian, China). Reverse transcription of RNA to cDNA was performed using the PrimeScript™ RT reagent Kit (CWBIO, Beijing, China). The resulting cDNA was diluted 10 times and used as a template for quantitative real-time PCR (qRT-PCR) analysis. qRT-PCR was carried out using SYBR Green Real-Time PCR Master Mix (CWBIO) on the StepOne™ Real-Time PCR system (Applied Biosystems). The reaction protocol included an initial denaturation at 94 °C for 30 s; 45 cycles of denaturation at 94 °C for 12 s, annealing at 60 °C for 45 s, and extension at 72 °C for 45 s; followed by a final melt curve step at 81 °C for 1 s. To ensure reproducibility, each qRT-PCR was performed in triplicate for each sample. Two B. papyrifera genes, actin [39] and GAPDH [40], served as internal reference genes. The quantitative results were analyzed using the 2–ΔΔCT method [41], and the relative expression levels were normalized to the average value of the two internal reference genes. All primers used for qRT-PCR are listed in Table S1.

HM stress response potential analysis in yeast

The ORFs of the BpMTs were amplified by PCR using primers containing specific restriction endonuclease cleavage sites (Table S2). The PCR-amplified products were digested with the corresponding enzymes and cloned into the yeast expression vector pYES2 to construct recombinant vectors pYES2-BpMTs. Both pYES2-BpMT and empty pYES2 were independently transformed into Saccharomyces cerevisiae INVSC1 (His, Leu, Trp, and Ura) using the lithium acetate method [42]. INVSC1 yeast colonies harboring empty pYES2 (control) and pYES2-BpMTs were designated as INVSC1(pYES2) and INVSC1(pYES2-BpMT1a) to INVSC1(pYES2-BpMT3a), respectively. These were cultivated in Sc-Ura medium containing 2% glucose at 30 °C to an OD600 of 0.6. Subsequently, the yeast was diluted in Sc-Ura medium including 2% galactose and maintained at 30 °C for approximately 20 h before re-collecting and adjusting the OD600 of the yeast to 1.8 for stress analysis.

For HM stress testing, the collected INVSC1(pYES2) and INVSC1(pYES2-BpMTs) were individually treated with 0.6 mmol/L CdCl2, 0.5 mmol/L MnCl2, 0.6 mmol/L CuSO4, and 0.2 mmol/L ZnCl2 for 6 h, followed by serial dilutions spotted onto Sc-Ura agar plates and incubated at 30 °C for about 48 h. To quantitatively compare survival rates under these stresses, OD600 values were tested and compared under both normal and stress conditions. Specifically, 5 mL yeast cultures starting at an OD600 of 1.8 were incubated with the listed HMs for 6 h. A 1 mL sample from these 5 mL cultures was then added to 30 mL of fresh lipid medium and incubated at 30 °C for 24 h with shaking at 185 rpm, after which cell densities (OD600) were measured. Each stress test was conducted in triplicate.

Mutation of Cys residues and HM tolerance analysis in yeast

The Cys (TGT and TGC) residues at the N-termini and C-termini of BpMT1c, BpMT2d, and BpMT2e, numbering 6, 8, and 8 at the N-termini and 6, 6, and 6 at the C-termini respectively, were mutated to Ser (AGC). The mutated N-terminal sequences were labeled as BpMT1c-mΔN, BpMT2d-mΔN, and BpMT2e-mΔN, and the C-terminal mutated genes as BpMT1c-mΔC, BpMT2d-mΔC, and BpMT2e-mΔC. These mutations were all PCR cloned using specific mutated primers (Table S2) based on the plasmid of pYESE-BpMT1c, pYESE-BpMT2d, and pYESE-BpMT2e, respectively, following a protocol of 37 °C for 20 min; 94 °C for 3 min; 35 cycles at 94 °C for 30 s, 65 °C for 30 s, 72 °C for 30 s; and a final extension at 72 °C for 7 min. The mutated sequences were then independently inserted into pYES2 to generate mutated yeast expression recombinants pYES2-BpMT1c-mΔN, pYES2-BpMT2d-mΔN, pYES2-BpMT2e-mΔN, pYES2-BpMT1c-mΔC, pYES2-BpMT2d-mΔC, and pYES2-BpMT2e-mΔC. Each recombinant protein was transfected into INVSC1 cells using the aforementioned method. The Cd, Cu, Mn, and Zn tolerance assays were conducted similarly to those for INVSC1(pYES2-BpMT1a) to INVSC1(pYES2-BpMT3a).

Quantification of HM accumulation by ICP-MS

To quantify the accumulation of HMs (Cd, Cu, Mn, and Zn), yeast strains harboring pYES2, pYES2-BpMT1c, pYES2-BpMT1c-mΔN, pYES2-BpMT1c-mΔC, pYES2-BpMT2d, pYES2-BpMT2d-mΔN, pYES2-BpMT2d-mΔC, pYES2-BpMT2e, pYES2-BpMT2e-mΔN, and pYES2-BpMT2e-mΔC were washed three times with sterilized ddH2O. The washed yeasts were then dried in a hot air oven at 40 °C. The dried yeast was dissolved in 6 mL of HNO3 and 2 mL of H2O2 within a microwave digester. The final volumes of the digested samples were adjusted to 10 mL, filtered to remove any impurities, and analyzed for Cd, Cu, Mn, and Zn using ICP-MS [43].

Statistical analysis

The data were processed using the SPSS package (SPSS, Chicago, Illinois, USA). Standard deviation means the sample variability. Expression differences between different time points and 0 d were evaluated by T test (P < 0.05). The differences among different yeast strains were confirmed using ANOVA analysis (P < 0.05). Some results were visualized in Tbtools software and Origin 2017 and showed as heat maps[46].

Conclusions

In this study, the MT family genes were analyzed within the B. papyrifera transcriptome, resulting in the identification of 12 BpMT genes. These genes are highly conserved and categorized into three types: MT1, MT2, and MT3. Each member of this family shares similar structures and conserved motifs. All BpMT genes were induced by Cd, Cu, Mn, and Zn stress, displaying various expression levels and demonstrating a positive role in the HM stress response via the ABA-dependent signaling pathway. There were significant correlations among BpMT family members in response to Cd, Cu, Mn, and Zn stress, suggesting that BpMT family genes may respond to HM stress through co-expression or interactions within the family. Furthermore, Cys residue mutation assays revealed that type 1 BpMT1c primarily achieved HM tolerance due to its C-terminal conserved domain, while type 2 BpMT2d and BpMT2e exhibited similar functions in both the N- and C-terminal domains. These findings provide novel insights into the MT family genes related to paper mulberry’s HM tolerance and chelation capabilities.

Data availability

All the data were presented in the main manuscript and additional supporting files. The Arabidopsis related datasets generated and/or analysed during the current study are available in the TAIR database (https://www.arabidopsis.org/). The MT protein sequences of G. max, O. sativa, Zea mays, A. thaliana, V. vinifera and M. pumila were downloaded from the database phytozome13v (https://phytozome-next.jgi.doe.gov/).

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Acknowledgements

Not applicable.

Funding

This work was supported by China Postdoctoral Science Foundation [2020M683592]; National Natural Science Foundation of China [42277121]; Natural Science Foundation of Shaanxi Province [2022JQ-202]. The funding agency was not involved in the design of the study, collection, analysis, interpretation of data and writing the manuscript.

Author information

Authors and Affiliations

  1. College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China

    Zhenggang Xu, Shen Yang, Chenhao Li, Muhong Xie, Yi He, Sisi Chen, Yan Tang, Dapei Li, Tianyu Wang & Guiyan Yang

  2. Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China

    Guiyan Yang

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  1. Zhenggang Xu
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  8. Dapei Li
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  9. Tianyu Wang
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  10. Guiyan Yang
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Contributions

XZG and YGY designed and wrote the paper; YS, LCH, XMH, HY, and CSS did all the experiments; TY, LDP, and WTY conducted data analysis, XZG and YGY checked the data analysis and revised the paper. All authors have read and approved the manuscript.

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Correspondence to Guiyan Yang.

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Xu, Z., Yang, S., Li, C. et al. Characterization of metallothionein genes from Broussonetia papyrifera: metal binding and heavy metal tolerance mechanisms. BMC Genomics 25, 563 (2024). https://doi.org/10.1186/s12864-024-10477-x

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  • DOI: https://doi.org/10.1186/s12864-024-10477-x

Keywords

BMC Genomics

ISSN: 1471-2164

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