Extensive functional diversification of the Populus glutathione S-transferase supergene family

Genome-wide study of glutathione transferases and their regulation in flufenacet susceptible and resistant black-grass (Alopecurus myosuroides Huds.)

BACKGROUND

Glutathione transferases (GSTs) are enzymes with a wide range of functions, including herbicide detoxification. Up-regulation of GSTs and their detoxification activity enables the grass weed black-grass (Alopecurus myosuroides Huds.) to metabolize the very-long-chain fatty acid synthesis inhibitor flufenacet and other herbicides leading to multiple herbicide resistance. However, the genomic organization and regulation of GSTs genes is still poorly understood.

RESULTS

In this genome-wide study the location and expression of 115 GSTs were investigated using a recently published black-grass genome. Particularly, the most abundant GSTs of class tau and phi were typically clustered and often followed similar expression patterns but possessed divergent upstream regulatory regions. Similarities were found in the promoters of the most up-regulated GSTs, which are located next to each other in a cluster. The binding motif of the E2F/DP transcription factor complex in the promoter of an up-regulated GST was identical in susceptible and resistant plants, however, adjacent sequences differed. This led to a stronger binding of proteins to the motif of the susceptible plant, indicating repressor activity.

CONCLUSIONS

This study constitutes the first analysis dealing with the genomic investigation of GST genes found in black-grass and their transcriptional regulation. It highlights the complexity of the evolution of GSTs in black-grass, their duplication and divergence over time. The large number of GSTs allows weeds to detoxify a broad spectrum of herbicides. Ultimately, more research is needed to fully elucidate the regulatory mechanisms of GST expression. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Poplar glutathione S-transferase PtrGSTF8 contributes to reactive oxygen species scavenging and salt tolerance

Glutathione S-transferases (GSTs) constitute a protein superfamily encoded by a large gene family and play a crucial role in plant growth and development. However, their precise functions in wood plant responses to abiotic stress are not fully understood. In this study, we isolated a Phi class glutathione S-transferase-encoding gene, PtrGSTF8, from poplar (Populus alba × P. glandulosa), which is significantly up-regulated under salt stress. Moreover, compared with wild-type (WT) plants, transgenic tobacco plants exhibited significant salt stress tolerance. Under salt stress, PtrGSTF8-overexpressing tobacco plants showed a significant increase in plant height and root length, and less accumulation of reactive oxygen species. In addition, these transgenic tobacco plants exhibited higher superoxide dismutase, peroxidase, and catalase activities and reduced malondialdehyde content compared with WT plants. Quantitative real-time PCR experiments showed that the overexpression of PtrGSTF8 increased the expression of numerous genes related to salt stress. Furthermore, PtrMYB108, a MYB transcription factor involved in salt resistance in poplar, was found to directly activate the promoter of PtrGSTF8, as demonstrated by yeast one-hybrid assays and luciferase complementation assays. Taken together, these findings suggest that poplar PtrGSTF8 contributes to enhanced salt tolerance and confers multiple growth advantages when overexpressed in tobacco.

Flowering time regulator qFT13-3 involved in soybean adaptation to high latitudes

Soybean is a short-day plant that typically flowers earlier when exposed to short-day conditions. However, the identification of genes associated with earlier flowering time but without a yield penalty is rare. In this study, we conducted genome-wide association studies (GWAS) using two re-sequencing datasets that included 113 wild soybeans (G. soja) and 1192 cultivated soybeans (G. max), respectively, and simultaneously identified a candidate flowering gene, qFT13-3, which encodes a protein homologous to the pseudo-response regulator (PRR) transcription factor. We identified four major haplotypes of qFT13-3 in the natural population, with haplotype H4 (qFT13-3H4) being lost during domestication, while qFT13-3H1 underwent natural and artificial selection, increasing in proportion from 4.5% in G. soja to 43.8% in landrace and to 81.9% in improve cultivars. Notably, most cultivars harbouring qFT13-3H1 were located in high-latitude regions. Knockout of qFT13-3 accelerated flowering and maturity time under long-day conditions, indicating that qFT13-3 functions as a flowering inhibitor. Our results also showed that qFT13-3 directly downregulates the expression of GmELF3b-2 which is a component of the circadian clock evening complex. Field trials revealed that the qft13-3 mutants shorten the maturity period by 11 days without a concomitant penalty on yield. Collectively, qFT13-3 can be utilized for the breeding of high-yield cultivars with a short maturity time suitable for high latitudes.

G-site residue S67 is involved in the fungicide-degrading activity of a tau class glutathione S-transferase from Carica papaya

Thiram is a toxic fungicide extensively used for the management of pathogens in fruits. Although it is known that thiram degrades in plant tissues, the key enzymes involved in this process remain unexplored. In this study, we report that a tau class glutathione S-transferase (GST) from Carica papaya can degrade thiram. This enzyme was easily obtained by heterologous expression in Escherichia coli, showed low promiscuity toward other thiuram disulfides, and catalyzed thiram degradation under physiological reaction conditions. Site-directed mutagenesis indicated that G-site residue S67 shows a key influence for the enzymatic activity toward thiram, while mutation of residue S13, which reduced the GSH oxidase activity, did not significantly affect the thiram-degrading activity. The formation of dimethyl dithiocarbamate, which was subsequently converted into carbon disulfide, and dimethyl dithiocarbamoylsulfenic acid as the thiram degradation products suggested that thiram undergoes an alkaline hydrolysis that involves the rupture of the disulfide bond. Application of the GST selective inhibitor 4-chloro-7-nitro-2,1,3-benzoxadiazole reduced papaya peel thiram-degrading activity by 95%, indicating that this is the main degradation route of thiram in papaya. GST from Carica papaya also catalyzed the degradation of the fungicides chlorothalonil and thiabendazole, with residue S67 showing again a key influence for the enzymatic activity. These results fill an important knowledge gap in understanding the catalytic promiscuity of plant GSTs and reveal new insights into the fate and degradation products of thiram in fruits.

Regulation of the trade-off between cold stress and growth by glutathione S-transferase phi class 10 (BcGSTF10) in non-heading Chinese cabbage

Cold stress is a serious threat to global crop production and food security, but plant cold resistance is accompanied by reductions in growth and yield. In this study, we determined that the novel gene BcGSTF10 in non-heading Chinese cabbage [NHCC; Brassica campestris (syn. Brassica rapa) ssp. chinensis] is implicated in resistance to cold stress. Biochemical and genetic analyses demonstrated that BcGSTF10 interacts with BcICE1 to induce C-REPEAT BINDING FACTOR (CBF) genes that enhance freezing tolerance in NHCC and in Arabidopsis. However, BcCBF2 represses BcGSTF10 and the latter promotes growth in NHCC and Arabidopsis. This dual function of BcGSTF10 indicates its pivotal role in balancing cold stress and growth, and this important understanding has the potential to inform the future development of strategies to breed crops that are both climate-resilient and high-yielding.

PtoMYB031, the R2R3 MYB transcription factor involved in secondary cell wall biosynthesis in poplar

Introduction

The biosynthesis of the secondary cell wall (SCW) is orchestrated by an intricate hierarchical transcriptional regulatory network. This network is initiated by first-layer master switches, SCW-NAC transcription factors, which in turn activate the second-layer master switches MYBs. These switches play a crucial role in regulating xylem specification and differentiation during SCW formation. However, the roles of most MYBs in woody plants are yet to be fully understood.

Methods

In this study, we identified and isolated the R2R3-MYB transcription factor, PtoMYB031, from Populus tomentosa. We explored its expression, mainly in xylem tissues, and its role as a transcriptional repressor in the nucleus. We used overexpression and RNA interference techniques in poplar, along with Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, to analyze the regulatory effects of PtoMYB031.

Results

Overexpression of PtoMYB031 in poplar significantly reduced lignin, cellulose, and hemicellulose content, and inhibited vascular development in stems, resulting in decreased SCW thickness in xylem tissues. Gene expression analysis showed that structural genes involved in SCW biosynthesis were downregulated in PtoMYB031-OE lines. Conversely, RNA interference of PtoMYB031 increased these compounds. Additionally, PtoMYB031 was found to recruit the repressor PtoZAT11, forming a transcriptional inhibition complex.

Discussion

Our findings provide new insights into how PtoMYB031, through its interaction with PtoZAT11, forms a complex that can suppress the expression of key regulatory genes, PtoWND1A and PtoWND2B, in SCW biosynthesis. This study enhances our understanding of the transcriptional regulation involved in SCW formation in poplar, highlighting the significant role of PtoMYB031.

Genome-Wide Analysis of Family I84 Protease Inhibitor Genes in Three Bivalves Reveals Important Information About the Protein Family's Evolution

Family I84 serine protease inhibitors are believed to be mollusk specific proteins involved in host defense. The molecular evolution of the family, however, remains to be understood. In this study, the genes of Family I84 protease inhibitors in 3 bivalves, Crassostrea gigas, Crassostrea virginica and Tegillarca granosa, were analyzed at the genomic level. A total of 66 Family I84 genes (22 in C. gigas, 28 in C. virginica and 16 in T. granosa) were identified from the 3 species. They distributed unevenly in the genomes involving 4 chromosomes in C. gigas and 5 chromosomes in C. virginica and T. granosa and some genes were tandemly duplicated. Most genes had 3 exons with 12 genes having 4 exons and 1 gene having 2 exons. All genes but 1 from C. gigas and 1 from T. granosa encoded peptides with a signal sequence at the N-terminus, and the properties of the predicted mature molecules were similar. Four conserved motifs were identified in the 66 amino acid sequences. Collinear analysis revealed higher collinearity between the 2 oyster species in general genes and in Family I84 genes. Phylogenetic analysis of the 66 genes with those previously reported from 3 other bivalves and 1 gastropod showed that Family I84 protease inhibitor genes from the same species tended to be grouped together in terminal branches of the constructed Maximum likelihood tree, but most internal nodes were poorly supported by the bootstrap values. In addition, differences in expression patterns between the genes of a same species were observed in the developmental stages and tissues of C. gigas and T. granosa. Moreover, the co-expression of genes within Family I84 and Family I84 genes with non-Family I84 were also detected in C. gigas and T. granosa. These results suggested that Family I84 protease inhibitor genes evolved by active duplications and structural and functional diversifications after the speciation of related mollusks, and the diversified protease inhibitor family was likely multifunctional.

Genome-wide characterization of 2OGD superfamily for mining of susceptibility factors responding to various biotic stresses in Musa spp

Bananas are an important staple food and cash crop, but they are vulnerable to a variety of pests and diseases that substantially reduce yield and quality. Banana diseases are challenging to control and necessitate an integrated strategy, and development of resistant cultivars is one of the effective ways of managing diseases. Lasting disease resistance is the main goal in crop improvement and resistance mediated by a single resistant (R) gene mostly lack durability. However, long-term resistance can be obtained by inactivating susceptibility factors (S), which facilitate pathogen infection and proliferation. Identification and inactivation of susceptibility factors against the major pathogens like Fusarium oxysporum f. sp. cubense (Foc), Pseudocercospora eumusae and Pratylenchus coffeae in banana will be an effective way in developing banana varieties with more durable resistance. Downy mildew resistance 6 (DMR6) and DMR-like oxygenases (DLO1) are one such susceptibility factors and they belong to 2-oxoglutarate Fe(II) dependent oxygenases (2OGD) superfamily. 2OGDs are known to catalyze a plethora of reactions and also confer resistance to different pathogens in various crops, but not much is known about the 2OGD in Musa species. Through a comprehensive genome-wide analysis, 133 and 122 potential 2OGDs were systematically identified and categorized from the A and B genomes of banana, respectively. Real time expression of dmr6 and dlo1 genes showed positive correlation with transcriptome data upon Foc race1 and TR4 infection and examination of expression pattern of Macma4_04_g22670 (Ma04_g20880) and Macma4_02_g13590 (Ma02_g12040) genes revealed their involvement in Foc race1 and TR4 infections, respectively. Further the expression profile of 2OGDs, specifically Macma4_04_g25310 (Ma04_g23390), Macma4_08_g11980 (Ma08_g12090) and Macma4_04_g38910 (Ma04_g36640) shows that they may play a significant role as a susceptibility factor, particularly against P. eumusae and P. coffeae, implying that they can be exploited as a candidate gene for editing in developing resistant cultivars against these diseases. In summary, our findings contribute to a deeper comprehension of the evolutionary and functional aspects of 2OGDs in Musa spp. Furthermore, they highlight the substantial functions of these family constituents in the progression of diseases. These insights hold significance in the context of enhancing the genetic makeup of bananas to attain extended and more durable resistance against pathogens.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01380-y.

Species-specific dynamics of specialized metabolism in germinating sorghum grain revealed by temporal and tissue-resolved transcriptomics and metabolomics

Seed germination is crucial for plant productivity, and the biochemical changes during germination affect seedling survival, plant health and yield. While the general metabolism of germination is extensively studied, the role of specialized metabolism is less investigated. We therefore analyzed the metabolism of the defense compound dhurrin during sorghum (Sorghum bicolor) grain germination and early seedling development. Dhurrin is a cyanogenic glucoside, which is catabolized into different bioactive compounds at other stages of plant development, but its fate and role during germination is unknown. We dissected sorghum grain into three different tissues and investigated dhurrin biosynthesis and catabolism at the transcriptomic, metabolomic and biochemical level. We further analyzed transcriptional signature differences of cyanogenic glucoside metabolism between sorghum and barley (Hordeum vulgare), which produces similar specialized metabolites. We found that dhurrin is de novo biosynthesized and catabolized in the growing embryonic axis as well as the scutellum and aleurone layer, two tissues otherwise mainly acknowledged for their involvement in release and transport of general metabolites from the endosperm to the embryonic axis. In contrast, genes encoding cyanogenic glucoside biosynthesis in barley are exclusively expressed in the embryonic axis. Glutathione transferase enzymes (GSTs) are involved in dhurrin catabolism and the tissue-resolved analysis of GST expression identified new pathway candidate genes and conserved GSTs as potentially important in cereal germination. Our study demonstrates a highly dynamic tissue- and species-specific specialized metabolism during cereal grain germination, highlighting the importance of tissue-resolved analyses and identification of specific roles of specialized metabolites in fundamental plant processes.

Genome-wide identification, characterization, and evolutionary analysis of NBS genes and their association with disease resistance in Musa spp

Banana is an important food crop that is susceptible to a wide range of pests and diseases that can reduce yield and quality. The primary objective of banana breeding programs is to increase disease resistance, which requires the identification of resistance (R) genes. Despite the fact that resistant sources have been identified in bananas, the genes, particularly the nucleotide-binding site (NBS) family, which play an important role in protecting plants against pathogens, have received little attention. As a result, this study included a thorough examination of the NBS disease resistance gene family's classification, phylogenetic analysis, genome organization, evolution, cis-elements, differential expression, regulation by microRNAs, and protein-protein interaction. A total of 116 and 43 putative NBS genes from M. acuminata and M. balbisiana, respectively, were identified and characterized, and were classified into seven sub-families. Structural analysis of NBS genes revealed the presence of signal peptides, their sub-cellular localization, molecular weight and pI. Eight commonly conserved motifs were found, and NBS genes were unevenly distributed across multiple chromosomes, with the majority of NBS genes being located in chr3 and chr1 of the A and B genomes, respectively. Tandem duplication occurrences have helped bananas' NBS genes spread throughout evolution. Transcriptome analysis of NBS genes revealed significant differences in expression between resistant and susceptible cultivars of fusarium wilt, eumusae leaf spot, root lesion nematode, and drought, implying that they can be used as candidate resistant genes. Ninety miRNAs were discovered to have targets in 104 NBS genes from the A genome, providing important insights into NBS gene expression regulation. Overall, this study offers a valuable genomic resource and understanding of the function and evolution of NBS genes in relation to rapidly evolving pathogens, as well as providing breeders with selection targets for fast-tracking breeding of banana varieties with more durable resistance to pathogens.

The chromosome-scale genome of Phoebe bournei reveals contrasting fates of terpene synthase (TPS)-a and TPS-b subfamilies

Terpenoids, including aromatic volatile monoterpenoids and sesquiterpenoids, function in defense against pathogens and herbivores. Phoebe trees are remarkable for their scented wood and decay resistance. Unlike other Lauraceae species investigated to date, Phoebe species predominantly accumulate sesquiterpenoids instead of monoterpenoids. Limited genomic data restrict the elucidation of terpenoid variation and functions. Here, we present a chromosome-scale genome assembly of a Lauraceae tree, Phoebe bournei, and identify 72 full-length terpene synthase (TPS) genes. Genome-level comparison shows pervasive lineage-specific duplication and contraction of TPS subfamilies, which have contributed to the extreme terpenoid variation within Lauraceae species. Although the TPS-a and TPS-b subfamilies were both expanded via tandem duplication in P. bournei, more TPS-a copies were retained and constitutively expressed, whereas more TPS-b copies were lost. The TPS-a genes on chromosome 8 functionally diverged to synthesize eight highly accumulated sesquiterpenes in P. bournei. The essential oil of P. bournei and its main component, β-caryophyllene, exhibited antifungal activities against the three most widespread canker pathogens of trees. The TPS-a and TPS-b subfamilies have experienced contrasting fates over the evolution of P. bournei. The abundant sesquiterpenoids produced by TPS-a proteins contribute to the excellent pathogen resistance of P. bournei trees. Overall, this study sheds light on the evolution and adaptation of terpenoids in Lauraceae and provides valuable resources for boosting plant immunity against pathogens in various trees and crops.

The Glutathione S-Transferase PtGSTF1 Improves Biomass Production and Salt Tolerance through Regulating Xylem Cell Proliferation, Ion Homeostasis and Reactive Oxygen Species Scavenging in Poplar

Glutathione S-transferases (GSTs) play an essential role in plant cell detoxification and secondary metabolism. However, their accurate functions in the growth and response to abiotic stress in woody plants are still largely unknown. In this work, a Phi class Glutathione S-transferase encoding gene PtGSTF1 was isolated from poplar (P. trichocarpa), and its biological functions in the regulation of biomass production and salt tolerance were investigated in transgenic poplar. PtGSTF1 was ubiquitously expressed in various tissues and organs, with a predominant expression in leaves and inducible expression by salt stress. Transgenic poplar overexpressing PtGSTF1 showed improved shoot growth, wood formation and improved salt tolerance, consistent with the increased xylem cell number and size under normal condition, and the optimized Na⁺ and K⁺ homeostasis and strengthened reactive oxygen species scavenging during salt stress. Further transcriptome analyses demonstrated that the expressions of genes related to hydrolase, cell wall modification, ion homeostasis and ROS scavenging were up- or down-regulated in transgenic plants. Our findings imply that PtGSTF1 improves both biomass production and salt tolerance through regulating hydrolase activity, cell wall modification, ion homeostasis and ROS scavenging in transgenic poplar, and that it can be considered as a useful gene candidate for the genetic breeding of new tree varieties with improved growth under salt stress conditions.

Biochemical and Structural Insights on the Poplar Tau Glutathione Transferase GSTU19 and 20 Paralogs Binding Flavonoids

Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in xenobiotic detoxification and/or in specialized metabolism. Populus trichocarpa genome (V4.1 assembly, Phytozome 13) consists of 74 genes coding for full-length GSTs and ten likely pseudogenes. These GSTs are divided into 11 classes, in which the tau class (GSTU) is the most abundant with 54 isoforms. PtGSTU19 and 20, two paralogs sharing more than 91% sequence identity (95% of sequence similarity), would have diverged from a common ancestor of P. trichocarpa and P. yatungensis species. These enzymes display the distinctive glutathione (GSH)-conjugation and peroxidase activities against model substrates. The resolution of the crystal structures of these proteins revealed significant structural differences despite their high sequence identity. PtGSTU20 has a well-defined deep pocket in the active site whereas the bottom of this pocket is disordered in PtGSTU19. In a screen of potential ligands, we were able to identify an interaction with flavonoids. Some of them, previously identified in poplar (chrysin, galangin, and pinocembrin), inhibited GSH-conjugation activity of both enzymes with a more pronounced effect on PtGSTU20. The crystal structures of PtGSTU20 complexed with these molecules provide evidence for their potential involvement in flavonoid transport in P. trichocarpa.

Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow

BACKGROUND

Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated genes in poplar and willow, the role of conversion between duplicates generated from polyploidization remains poorly understood.

RESULTS

Here, through genomic synteny analyses, we identified duplicate genes generated by the Salicaceae common tetraploidization (SCT) in the poplar and willow genomes. We estimated that at least 0.58% and 0.25% of poplar and willow duplicates were affected by whole-gene conversion after the poplar-willow divergence, with more (5.73% and 2.66%) affected by partial-gene conversion. Moreover, we found that the converted duplicated genes were unevenly distributed on each chromosome in the two genomes, and the well-preserved homoeologous chromosome regions may facilitate the conversion of duplicates. Notably, we found that conversion maintained the similarity of duplicates, likely contributing to the conservation of certain sequences, but is essentially accelerated the rate of evolution and increased species divergence. In addition, we found that converted duplicates tended to have more similar expression patterns than nonconverted duplicates. We found that genes associated with multigene families were preferentially converted. We also found that the genes encoding conserved structural domains associated with specific traits exhibited a high frequency of conversion.

CONCLUSIONS

Extensive conversion between duplicate genes generated from the SCT contributes to the diversification of the family Salicaceae and has had long-lasting effects on those genes with important biological functions.

Genome-wide identification and characterization of glutathione S-transferase gene family in Musa acuminata L. AAA group and gaining an insight to their role in banana fruit development

Glutathione S-transferases are a multifunctional protein superfamily that is involved in diverse plant functions such as defense mechanisms, signaling, stress response, secondary metabolism, and plant growth and development. Although the banana whole-genome sequence is available, the distribution of GST genes on banana chromosomes, their subcellular localization, gene structure, their evolutionary relation with each other, conserved motifs, and their roles in banana are still unknown. A total of 62 full-length GST genes with the canonical thioredoxin fold have been identified belonging to nine GST classes, namely tau, phi, theta, zeta, lambda, DHAR, EF1G, GHR, and TCHQD. The 62 GST genes were distributed into 11 banana chromosomes. All the MaGSTs were majorly localized in the cytoplasm. Gene architecture showed the conservation of exon numbers in individual GST classes. Multiple Em for Motif Elicitation analyses revealed few class-specific motifs and many motifs were found in all the GST classes. Multiple sequence alignment of banana GST amino acid sequences with rice, Arabidopsis, and soybean sequences revealed the Ser and Cys as conserved catalytic residues. Gene duplication analyses showed the tandem duplication as a driving force for GST gene family expansion in banana. Cis-regulatory element analysis showed the dominance of light-responsive element followed by stress- and hormone-responsive elements. Expression profiling analyses were also done by RNA-seq data. It was observed that MaGSTs are involved in various stages of fruit development. MaGSTU1 was highly upregulated. The comprehensive and organized studies of MaGST gene family provide groundwork for further functional analysis of MaGST genes in banana at molecular level and further for plant breeding approaches.

Pieces of evidence of enhanced cellulose biosynthesis in the low-Cd cultivar and high expression level of transportation genes in the high-Cd cultivar of Lactuca sativa

To investigate the molecular mechanism of Cd-accumulating difference between Lactuca sativa cultivars, full-length transcriptome comparison, as well as biochemical validation, have been conducted between Cd pollution-safe cultivar (Cd-PSC, cv. LYDL) and high-Cd-accumulating cultivar (cv. HXDWQ). The full-length transcriptome of L. sativa cultivars was achieved for the first time. The results showed high Cd compartmentalization in the cell wall of cv. LYDL was ascribed to the enhanced cell wall biosynthesis under Cd stress, which was consistent with the high cellular debris Cd level (32.10-43.58%). The expression levels of transporter genes in cv. HXDWQ were about 1.19 to 1.21-fold higher than those in cv. LYDL, which was in accordance with the high ratio of easy migrative Cd chemical forms (68.59-81.98%), indicating the high Cd accumulation in the shoot of cv. HXDWQ was ascribed to the higher transportation capacity in cv. HXDWQ. Moreover, the Cd-induced endoplasmic reticulum (ER) stress was associated with the higher Cd detoxification and tolerance in cv. HXDWQ rather than in cv. LYDL. The study provides new insights into the Cd-induced transcriptomic difference between L. sativa cultivars and further contributes to the molecular breeding of L. sativa Cd-PSC.

Genome-wide analysis of pathogenesis-related protein 1 (PR-1) gene family from Musa spp. and its role in defense response during stresses

Pathogenesis related protein-1 (PR-1) is the most abundantly produced protein during defense response against many biotic and abiotic stresses. However, knowledge on PR-1 gene family and its evolutionary relationship in banana is very limited. In order to study the potential role of PR-1 genes in banana, genome wide identification, structure analysis and expressions were performed. A total of 15 and 11 PR-1 genes were identified from A and B genomes of banana and the proteins encoded by this gene family are of varying lengths and harbor conserved domains and motifs. PR-1 genes are unevenly dispersed on 11 chromosomes with segmental duplication in both A and B genome, suggesting an important contribution of duplication in expansion of PR-1 gene family in banana. qRT-PCR analysis of PR-1 gene showed positive correlation with the RNAseq data under various stresses and examination of expression pattern of selected MaPR-1 genes in banana revealed its role in biotic and abiotic stresses in general and fusarium wilt in particular. This study provides significant insight into the functions of PR-1 genes which can be further exploited as a promising candidate for developing multiple stress tolerant banana varieties.

Genome-wide identification, characterization of expansin gene family of banana and their expression pattern under various stresses

Expansin, a cell wall-modifying gene family, has been well characterized and its role in biotic and abiotic stress resistance has been proven in many monocots, but not yet studied in banana, a unique model crop. Banana is one of the staple food crops in developing countries and its production is highly influenced by various biotic and abiotic factors. Characterizing the expansin genes of the ancestor genome (M. acuminata and M. balbisiana) of present day cultivated banana will enlighten their role in growth and development, and stress responses. In the present study, 58 (MaEXPs) and 55 (MbaEXPs) putative expansin genes were identified in A and B genome, respectively, and were grouped in four subfamilies based on phylogenetic analysis. Gene structure and its duplications revealed that EXPA genes are highly conserved and are under negative selection whereas the presence of more number of introns in other subfamilies revealed that they are diversifying. Expression profiling of expansin genes showed a distinct expression pattern for biotic and abiotic stress conditions. This study revealed that among the expansin subfamilies, EXPAs contributed significantly towards stress-resistant mechanism. The differential expression of MaEXPA18 and MaEXPA26 under drought stress conditions in the contrasting cultivar suggested their role in drought-tolerant mechanism. Most of the MaEXPA genes are differentially expressed in the root lesion nematode contrasting cultivars which speculated that this expansin subfamily might be the susceptible factor. The downregulation of MaEXPLA6 in resistant cultivar during Sigatoka leaf spot infection suggested that by suppressing this gene, resistance may be enhanced in susceptible cultivar. Further, in-depth studies of these genes will lead to gain insight into their role in various stress conditions in banana.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-021-03106-x.

Divergence of active site motifs among different classes of Populus glutaredoxins results in substrate switches

Enzymes are essential components of all biological systems. The key characteristics of proteins functioning as enzymes are their substrate specificities and catalytic efficiencies. In plants, most genes encoding enzymes are members of large gene families. Within such families, the contributions of active site motifs to the functional divergence of duplicate genes have not been well elucidated. In this study, we identified 41 glutaredoxin (GRX) genes in the Populus trichocarpa genome. GRXs are ubiquitous enzymes in plants that play important roles in developmental and stress tolerance processes. In poplar, GRX genes were divided into four classes based on clear differences in gene structure and expression pattern, subcellular localization, enzymatic activity, and substrate specificity of the encoded proteins. Using site-directed mutagenesis, this study revealed that the divergence of the active site motif among different classes of GRX proteins resulted in substrate switches and thus provided new insights into the molecular evolution of these important plant enzymes.

Genome-wide analysis of the Glutathione S-Transferase family in wild Medicago ruthenica and drought-tolerant breeding application of MruGSTU39 gene in cultivated alfalfa

Transformation of MruGSTU39 in M. ruthenica and alfalfa enhanced growth and survival of transgenic plants by up-regulating GST and glutathione peroxidase activity to detoxify ROS under drought stress. Glutathione S-transferases (GSTs) are ubiquitous supergene family which play crucial roles in detoxification of reactive oxygen species (ROS). Despite studies on GSTs, few studies have focused on them in perennial, wild plant species with high tolerance to environmental stress. Here, we identified 66 MruGST genes from the genome of Medicago ruthenica, a perennial legume species native to temperate grasslands with high tolerance to environmental stress. These genes were divided into eight classes based on their conserved domains, phylogenetic tree and gene structure, with the tau class being the most numerous. Duplication analysis revealed that GST family in M. ruthenica was expanded by segmental and tandem duplication. Several drought-responsive MruGSTs were identified by transcriptomic analyses. Of them, expression of MruGSTU39 was up-regulated much more in a tolerant accession by drought stress. Transformation of MruGSTU39 in M. ruthenica and alfalfa (Medicago sativa) enhanced growth and survival of transgenic seedlings than their wild-type counterparts under drought. We demonstrated that MruGSTU39 can detoxify ROS to reduce its damage to membrane by up-regulating activities of GST and glutathione peroxidase. Our findings provide full-scale knowledge on GST family in the wild legume M. ruthenica with high tolerance to drought, and highlight improvement tolerance of legume forages to drought using genomic information of M. ruthenica.

Probing the functions of friedelane-type triterpene cyclases from four celastrol-producing plants

Triterpenes are among the most diverse plant natural products, and their diversity is closely related to various triterpene skeletons catalyzed by different 2,3-oxidosqualene cyclases (OSCs). Celastrol, a friedelane-type triterpene with significant bioactivities, is specifically distributed in higher plants, such as Celastraceae species. Friedelin is an important precursor for the biosynthesis of celastrol, and it is synthesized through the cyclization of 2,3-oxidosqualene, with the highest number of rearrangements being catalyzed by friedelane-type triterpene cyclases. However, the molecular mechanisms underlying the catalysis of friedelin production by friedelane-type triterpene cyclases have not yet been fully elucidated. In this study, transcriptome data of four celastrol-producing plants from Celastraceae were used to identify a total of 21 putative OSCs. Through functional characterization, the friedelane-type triterpene cyclases were separately verified in the four plants. Analysis of the selection pressure showed that purifying selection acted on these OSCs, and the friedelane-type triterpene cyclases may undergo weaker selective restriction during evolution. Molecular docking and site-directed mutagenesis revealed that changes in some amino acids that are unique to friedelane-type triterpene cyclases may lead to variations in catalytic specificity or efficiency, thereby affecting the synthesis of friedelin. Our research explored the functional diversity of triterpene synthases from a multispecies perspective. It also provides some references for further research on the relative mechanisms of friedelin biosynthesis.

Identification and Comprehensive Genome-Wide Analysis of Glutathione S-Transferase Gene Family in Sweet Cherry (Prunus avium) and Their Expression Profiling Reveals a Likely Role in Anthocyanin Accumulation

Glutathione S-transferases (GSTs) in plants are multipurpose enzymes that are involved in growth and development and anthocyanins transportation. However, members of the GST gene family were not identified in sweet cherry (Prunus avium). To identify the GST genes in sweet cherry, a genome-wide analysis was conducted. In this study, we identified 67 GST genes in P. avium genome and nomenclature according to chromosomal distribution. Phylogenetic tree analysis revealed that PavGST genes were classified into seven chief subfamily: TCHQD, Theta, Phi, Zeta, Lambda, DHAR, and Tau. The majority of the PavGST genes had a relatively well-maintained exon-intron and motif arrangement within the same group, according to gene structure and motif analyses. Gene structure (introns-exons) and conserved motif analysis revealed that the majority of the PavGST genes showed a relatively well-maintained motif and exons-introns configuration within the same group. The chromosomal localization, GO enrichment annotation, subcellular localization, syntenic relationship, Ka/Ks analysis, and molecular characteristics were accomplished using various bioinformatics tools. Mode of gene duplication showed that dispersed duplication might play a key role in the expansion of PavGST gene family. Promoter regions of PavGST genes contain numerous cis-regulatory components, which are involved in multiple stress responses, such as abiotic stress and phytohormones responsive factors. Furthermore, the expression profile of sweet cherry PavGSTs showed significant results under LED treatment. Our findings provide the groundwork for future research into induced LED anthocyanin and antioxidants deposition in sweet cherries.

Non-synonymous substitution of evolutionarily conserved residue in Tau class glutathione transferases alters structural and catalytic features

Plant-specific tau glutathione transferases (GSTs) are basically involved in catalysing γ-glutathione (GSH)-dependent conjugation reactions with pesticides and herbicides, which play an important role in the detoxification of pollutants. Given the lack of systematic biochemical and structural information on tau GSTs, the study of their mediated defence mechanisms against toxic compounds has been greatly hindered. Here, we reveal the importance of the Ile residue closely interacting with GSH for the structural stability and catalytic function of GST. Evolutionary conservation analysis indicated that the crucial G-site Ile55 in the SbGSTU6 was converted to Thr53 of SbGSTU7. The comparative biochemical data on SbGSTU6, SbGSTU7 and their mutants showed that the substitution of Ile by Thr caused significant decrease in the affinity and catalytic efficiency of the GSTs. The unfavourable structural flexibility and pKa distribution of the active cavity residues were also demonstrated. Crystallography studies and molecular dynamics simulations showed that the conversion resulted in the hydrogen bond recombination with GSH and conformational rearrangement of GST active cavity, in which the Ile residue was more conducive to the formation of enzyme substrate complexes. The extensive biochemical and structural data not only reveal the critical role of the conserved G-site Ile residue in catalysing GSH-conjugate reactions but also provide valuable resources for the development of GST engineering in analytical and agricultural biotechnology.

Genome-Wide Analysis of the Glutathione S-Transferase (GST) Genes and Functional Identification of MdGSTU12 Reveals the Involvement in the Regulation of Anthocyanin Accumulation in Apple

Anthocyanins have essential biological functions, affecting the development of horticultural production. They are synthesized in the cytoplasm through flavonoid metabolic pathways and finally transported into vacuoles for storage. Plant glutathione S-transferases (GSTs) are multifunctional enzymes involved in anthocyanin transportation. In this study, we identified 38 GSTs from the apple (Malus domestica) genome (HFTH1 Whole Genome v1.0) based on the sequence similarity with the GST family proteins of Arabidopsis. These MdGST genes could be grouped into nine chief subclasses: U, F, L, Z, T, GHR, EF1Bγ, TCHQD, and DHAR. The structures, motifs, three-dimensional models, and chromosomal distribution of MdGST genes were further analyzed. Elements which are responsive for some hormones and stress, and others that involve genes related to flavonoid biosynthesis were forecast in the promoter of MdGST. In addition, we identified 32 orthologous gene pairs between apple and Arabidopsis. These genes indicated that numerous apple and Arabidopsis counterparts appeared to be derived from a common ancestor. Amongst the 38 MdGST genes, MdGSTU12 was considerably correlated with anthocyanin variation in terms of extracting expression profiles from reported. Finally, further functional identification in apple transgenic calli and subcellular localization confirmed that MdGSTU12 was of great significance in anthocyanin accumulation in apple.

A Novel Glutathione S-Transferase Gtt2 Class (VpGSTT2) Is Found in the Genome of the AHPND/EMS Vibrio parahaemolyticus Shrimp Pathogen

Glutathione S-transferases are a family of detoxifying enzymes that catalyze the conjugation of reduced glutathione (GSH) with different xenobiotic compounds using either Ser, Tyr, or Cys as a primary catalytic residue. We identified a novel GST in the genome of the shrimp pathogen V. parahaemolyticus FIM- S1708⁺, a bacterial strain associated with Acute Hepatopancreatic Necrosis Disease (AHPND)/Early Mortality Syndrome (EMS) in cultured shrimp. This new GST class was named Gtt2. It has an atypical catalytic mechanism in which a water molecule instead of Ser, Tyr, or Cys activates the sulfhydryl group of GSH. The biochemical properties of Gtt2 from Vibrio parahaemolyticus (VpGSTT2) were characterized using kinetic and crystallographic methods. Recombinant VpGSTT2 was enzymatically active using GSH and CDNB as substrates, with a specific activity of 5.7 units/mg. Low affinity for substrates was demonstrated using both Michaelis–Menten kinetics and isothermal titration calorimetry. The crystal structure showed a canonical two-domain structure comprising a glutathione binding G-domain and a hydrophobic ligand H domain. A water molecule was hydrogen-bonded to residues Thr9 and Ser 11, as reported for the yeast Gtt2, suggesting a primary role in the reaction. Molecular docking showed that GSH could bind at the G-site in the vicinity of Ser11. G-site mutationsT9A and S11A were analyzed. S11A retained 30% activity, while T9A/S11A showed no detectable activity. VpGSTT2 was the first bacterial Gtt2 characterized, in which residues Ser11 and Thr9 coordinated a water molecule as part of a catalytic mechanism that was characteristic of yeast GTT2. The GTT2 family has been shown to provide protection against metal toxicity; in some cases, excess heavy metals appear in shrimp ponds presenting AHPND/EMS. Further studies may address whether GTT2 in V. parahaemolyticus pathogenic strains may provide a competitive advantage as a novel detoxification mechanism.

Elevated production of reactive oxygen species is related to host plant resistance to sugarcane aphid in sorghum

Sugarcane aphid (Melanaphis sacchari) is a phloem-feeding insect that severely affects the growth and productivity of sorghum and other related crops. While a growing body of knowledge is accumulating regarding plant, and insect interactions, the role of reactive oxygen species (ROS) against aphid infestation in sorghum has not been established yet. Here, the involvement of H2O2 and ROS detoxification enzymes in host plant resistance to sugarcane aphid in sorghum was demonstrated. The H2O2 accumulation and expression patterns of selected ROS scavenging enzymes including ascorbate peroxidase (APX), glutathione S transferase (GST), superoxide dismutase (SOD), and catalase (CAT) in response to sugarcane aphid infestation at 3, 6, 9, and 12 days post infestation (dpi) in resistant (Tx2783) and susceptible (Tx7000) sorghum genotypes were assessed, respectively. A significant increase in H2O2 accumulation was observed in resistant genotypes at all time points studied as compared to susceptible plants. Furthermore, gene expression analysis revealed that in responding to attack by sugarcane aphid, antioxidant genes were induced in both genotypes, but much stronger in the resistant line. Furthermore, aphid survival and fecundity were significantly inhibited in resistant plants compared to susceptible plants. Taken together, our results suggest that the elevated accumulation of H2O2 and the strong upregulation of the antioxidant genes in sorghum may have contributed to host plant resistance in Tx2783 against sugarcane aphid but the weak expression of those antioxidant genes in Tx7000 resulted in the failure of attempting defense against sugarcane aphid. This report also provides the experimental evidence for the role of ROS involvement in the early defensive response to an attack by sugarcane aphid in sorghum.

Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes

The reactive oxygen species (ROS) gene network, consisting of both ROS-generating and detoxifying enzymes, adjusts ROS levels in response to various stimuli. We performed a cross-kingdom comparison of ROS gene networks to investigate how they have evolved across all Eukaryotes, including protists, fungi, plants and animals. We included the genomes of 16 extremotolerant Eukaryotes to gain insight into ROS gene evolution in organisms that experience extreme stress conditions. Our analysis focused on ROS genes found in all Eukaryotes (such as catalases, superoxide dismutases, glutathione reductases, peroxidases and glutathione peroxidase/peroxiredoxins) as well as those specific to certain groups, such as ascorbate peroxidases, dehydroascorbate/monodehydroascorbate reductases in plants and other photosynthetic organisms. ROS-producing NADPH oxidases (NOX) were found in most multicellular organisms, although several NOX-like genes were identified in unicellular or filamentous species. However, despite the extreme conditions experienced by extremophile species, we found no evidence for expansion of ROS-related gene families in these species compared to other Eukaryotes. Tardigrades and rotifers do show ROS gene expansions that could be related to their extreme lifestyles, although a high rate of lineage-specific horizontal gene transfer events, coupled with recent tetraploidy in rotifers, could explain this observation. This suggests that the basal Eukaryotic ROS scavenging systems are sufficient to maintain ROS homeostasis even under the most extreme conditions.

Cloning, purification and biochemical characterization of two glutathione S-transferase isoforms from Rutilus frisii kutum

Glutathione S-transferases are an important multifunctional family of intracellular enzymes that their detoxification function has been reported in fishes since 1970, but no studies have been conducted on Rutilus frisii kutum GSTs yet. In the present study, RkGSTA and RkGSTM encoding genes were cloned and sequenced and their nucleotide sequences were submitted to NCBI GenBank. In order to reduce the expression challenges of recombinant proteins including low solubility, low yield and insufficient purity issues in E. coli, the pKJE7 chaperone plasmid was used to increase the recovery of expressed proteins in the soluble fractions. Best expression clone was selected for purification by Ni-NTA affinity chromatography. The three-dimensional structural models were constructed by I-TASSER. The optimum temperature of purified RkGSTA and RkGSTM was 35 and 30 °C, with optimum activity at pH 9.0 and 8.5, respectively. The thermostability and pH stability results indicated that RkGSTA is more heat-tolerant than RkGSTM though both of them retained more than 80% of their activities at pH 6.5 to 9.0. Overall, this study represents a comprehensive perspective on the structural and biochemical aspects of this enzyme that would be even used in further researches such as drug design studies in order to eliminate toxicant compounds from the body and environment of fishes to protect them against undesired harmful damages.

Genome-wide survey of soybean papain-like cysteine proteases and their expression analysis in root nodule symbiosis

BACKGROUND

Plant papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes and play important roles in root nodule symbiosis (RNS), while the whole-genome studies of PLCP family genes in legume are quite limited, and the roles of Glycine max PLCPs (GmPLCPs) in nodulation, nodule development and senescence are not fully understood.

RESULTS

In the present study, we identified 97 GmPLCPs and performed a genome-wide survey to explore the expansion of soybean PLCP family genes and their relationships to RNS. Nineteen paralogous pairs of genomic segments, consisting of 77 GmPLCPs, formed by whole-genome duplication (WGD) events were identified, showing a high degree of complexity in duplication. Phylogenetic analysis among different species showed that the lineage differentiation of GmPLCPs occurred after family expansion, and large tandem repeat segment were specifically in soybean. The expression patterns of GmPLCPs in symbiosis-related tissues and nodules identified RNS-related GmPLCPs and provided insights into their putative symbiotic functions in soybean. The symbiotic function analyses showed that a RNS-related GmPLCP gene (Glyma.04G190700) really participate in nodulation and nodule development.

CONCLUSIONS

Our findings improved our understanding of the functional diversity of legume PLCP family genes, and provided insights into the putative roles of the legume PLCPs in nodulation, nodule development and senescence.

Structure and expression analysis of seven salt-related ERF genes of Populus

Ethylene response factors (ERFs) are plant-specific transcription factors (TFs) that play important roles in plant growth and stress defense and have received a great amount of attention in recent years. In this study, seven ERF genes related to abiotic stress tolerance and response were identified in plants of the Populus genus. Systematic bioinformatics, including sequence phylogeny, genome organisation, gene structure, gene ontology (GO) annotation, etc. were detected. Expression-pattern of these seven ERF genes were analyzed using RT-qPCR and cross validated using RNA-Seq. Data from a phylogenetic tree and multiple alignment of protein sequences indicated that these seven ERF TFs belong to three subfamilies and contain AP2, YRG, and RAYD conserved domains, which may interact with downstream target genes to regulate the plant stress response. An analysis of the structure and promoter region of these seven ERF genes showed that they have multiple stress-related motifs and cis-elements, which may play roles in the plant stress-tolerance process through a transcriptional regulation mechanism; moreover, the cellular_component and molecular_function terms associated with these ERFs determined by GO annotation supported this hypothesis. In addition, the spatio-temporal expression pattern of these seven ERFs, as detected using RT-qPCR and RNA-seq, suggested that they play a critical role in mediating the salt response and tolerance in a dynamic and tissue-specific manner. The results of this study provide a solid basis to explore the functions of the stress-related ERF TFs in Populus abiotic stress tolerance and development process.

Physiological and Transcriptomic Response of Grey Poplar (Populus ×canescens Aiton Sm.) to Cadmium Stress

(1) Background: Populus ×canescens (Aiton) Sm. is a fast-growing woody plant belonging to the family Salicaceae. Two poplar genotypes characterized by unique phenotypic traits (TP11 and TP20) were chosen to be characterized and tested for a physiological and transcriptomic response to Cd stress. (2) Methods: A comparative analysis of the effects of exposure to high cadmium (Cd) concentrations (10 µM and 100 µM) of TP11 and TP20 was performed. (3) Results: Neither of the tested Cd concentration negatively affected plant growth; however, the chlorophyll content significantly decreased. The potassium (K) content was higher in the shoots than in the roots. The magnesium concentrations were only slightly affected by Cd treatment. The zinc content in the shoots of TP20 was lower than that in the shoots of TP11. Cd accumulation was higher in the roots than in the shoots. After 10 days of exposure, 10 µM Cd resulted in comparable amounts of Cd in the roots and shoots of TP20. The most significant change in transcript amount was observed in endochitinase 2, 12-oxophytodienoate reductase 1 and phi classglutathione S-transferase. (4) Conclusions: Our study provided new insights for effective assessing the ability of different poplar genotypes to tolerate Cd stress and underlying Cd tolerance.

Genome-wide identification, characterization, and expression analysis related to autotoxicity of the GST gene family in Cucumis melo L

Glutathione S-transferase (GST) plays an important role in plant resistance to biotic and abiotic stresses. In this paper, the characteristics of melon GST gene family members were analyzed from a genome-wide perspective. Forty-nine GSTs were identified in melon genome, belonging to eight classes. Through the phylogenetic analysis of GST proteins in melon and other plants, it was found that members from the same subfamily in different species clustered together, indicating that the subfamilies of GST have diversified before the divergence within these species. The results of chromosome mapping showed that GSTs were present in all chromosomes except for chromosome 5. Gene replication events played an important role in the expansion and evolution of melon GST gene family. Ten GSTs with significant differential expression were screened in the transcriptome database related to melon autotoxicity stress. The differential expression of these 10 GSTs was detected in roots and leaves of melon seedlings treated with cinnamic acid. The relative expression level of CmGSTU7, CmGSTU10, CmGSTU18, CmGSTF2 and CmGSTL1 in roots of melon seedlings was significantly higher than that in control group. It suggested that the five GSTs might play an important role in cinnamic acid mediated autotoxicity stress in melon. The results of this paper were helpful to reveal the evolution and functional succession of GST family and further understand the response of GST to autotoxicity stress in melon.

Molecular Evolutionary and Expression Pattern Analysis of AKR Genes Shed New Light on GalUR Functional Characteristics in Brassica rapa

The aldo-keto reductase (AKR) superfamily plays a major role in oxidation-reduction in plants. _D-galacturonic acid reductase (GalUR), an ascorbic acid (AsA) biosynthetic enzyme, belongs to this superfamily. However, the phylogenetic relationship and evolutionary history of the AKR gene family in plants has not yet been clarified. In this study, a total of 1268 AKR genes identified in 36 plant species were used to determine this phylogenetic relationship. The retention, structural characteristics, and expression patterns of AKR homologous genes in Brassica rapa and Arabidopsis thaliana were analyzed to further explore their evolutionary history. We found that the AKRs originated in algae and could be divided into A and B groups according to the bootstrap value; GalURs belonged to group A. Group A AKR genes expanded significantly before the origin of angiosperms. Two groups of AKR genes demonstrated functional divergence due to environmental adaptability, while group A genes were more conservative than those in group B. All 12 candidate GalUR genes were cloned, and their expression patterns under stress were analyzed, in Pak-choi. These genes showed an obvious expression divergence under multiple stresses, and BrcAKR22 exhibited a positive correlation between its expression trend and AsA content. Our findings provide new insights into the evolution of the AKR superfamily and help build a foundation for further investigations of GalUR’s functional characteristics.

Genome-wide identification and comparative analysis of GST gene family in apple (Malus domestica) and their expressions under ALA treatment

Anthocyanins, a subclass of flavonoids, are synthesized at the cytoplasmic surface of the endoplasmic reticulum (ER), which then accumulate in vacuoles. Plant glutathione S-transferase (GST) genes are involved in anthocyanin transportation. Here, a total of 52, 42, 50, and 29 GST genes were identified from apple, pear, peach, and strawberry, respectively, through a comprehensive genome-wide survey. Based on phylogenetic analyses, the GST proteins of the four crops could be divided into the classes Phi, Tau, DHAR, TCHQD, and Lambda. The structure and chromosomal distribution of apple GST genes were further analyzed. The GST gene family expansion in apple likely occurred through tandem duplications, and purifying selection played a pivotal role in the evolution of GST genes. Synteny analysis showed strong microsynteny between apple and Arabidopsis/strawberry, but no microsynteny was detected between apple/strawberry/Arabidopsis and rice. Aminolevulinic acid (ALA), a key precursor of tetrapyrrole compounds, can significantly improve anthocyanin accumulation in fruits, Using RNA-seq and qRT-PCR analysis, we found that ALA treatment led to the differential expression of GST genes in apples. MdGSTF12 was strongly induced by ALA, suggesting that MdGSTF12 may play a role in ALA-induced anthocyanin accumulation. These results provide a detailed overview of GST genes in four Rosaceae species and indicate that GSTs are involved in ALA-induced anthocyanin accumulation.

Glutathione S-transferase: a versatile protein family

Glutathione-S transferase (GST) is a most ancient protein superfamily of multipurpose roles and evolved principally from gene duplication of an ancestral GSH binding protein. They have implemented in diverse plant functions such as detoxification of xenobiotic, secondary metabolism, growth and development, and majorly against biotic and abiotic stresses. The vital structural features of GSTs like highly divergent functional topographies, conserved integrated architecture with separate binding pockets for substrates and ligand, the stringent structural fidelity with high Tm values (50º-60º), and stress-responsive cis-regulatory elements in the promoter region offer this protein as most flexible plant protein for plant breeding approaches, biotechnological applications, etc. This review article summarizes the recent information of GST evolution, and their distribution and structural features with emphasis on the assorted roles of Ser and Cys GSTs with the signature motifs in their active sites, alongside their recent biotechnological application in the area of agriculture, environment, and nanotechnology have been highlighted.

The pivotal function of dehydroascorbate reductase in glutathione homeostasis in plants

Under natural conditions, plants are exposed to various abiotic and biotic stresses that trigger rapid changes in the production and removal of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). The ascorbate-glutathione pathway has been recognized to be a key player in H2O2 metabolism, in which reduced glutathione (GSH) regenerates ascorbate by reducing dehydroascorbate (DHA), either chemically or via DHA reductase (DHAR), an enzyme belonging to the glutathione S-transferase (GST) superfamily. Thus, DHAR has been considered to be important in maintaining the ascorbate pool and its redox state. Although some GSTs and peroxiredoxins may contribute to GSH oxidation, analysis of Arabidopsis dhar mutants has identified the key role of DHAR in coupling H2O2 to GSH oxidation. The reaction of DHAR has been proposed to proceed by a ping-pong mechanism, in which binding of DHA to the free reduced form of the enzyme is followed by binding of GSH. Information from crystal structures has shed light on the formation of sulfenic acid at the catalytic cysteine of DHAR that occurs with the reduction of DHA. In this review, we discuss the molecular properties of DHAR and its importance in coupling the ascorbate and glutathione pools with H2O2 metabolism, together with its functions in plant defense, growth, and development.

Biochemical Functions of Glutathione S-Transferase Family of Salix babylonica

Glutathione S-transferases (GSTs) are ubiquitous enzymes that are encoded by a large gene family, and they contribute to the detoxification of endogenous or xenobiotic compounds and oxidative stress metabolism in plants. Although the GSTs gene family has been reported in many land plants, our knowledge of the evolution and function of the willow GSTs is still limited. In this study, 22 full-length GST genes were cloned from Salix babylonica and divided into three classes based on the conserved domain analysis, phylogenetic tree and gene structure: tau, phi and DHAR. The tissue-specific expression patterns were substantially different among the tau and phi GSTs. The Salix GST proteins showed functional divergences in the substrate specificities, substrate activities and kinetic characteristics. The site-directed mutagenesis studies revealed that a single amino acid mutation (Ile/Val53→Thr53) resulted in the lowest activity of SbGSTU7 among the Salix GSTs. These results suggest that non-synonymous substitution of an amino acid at the putative glutathione-binding site may play an important role in the divergence of enzymatic functions of Salix GST family.

Comparative structural and functional analysis of phi class glutathione transferases involved in multiple-herbicide resistance of grass weeds and crops

Multiple-herbicide resistant (MHR) weeds are a global problem and a looming threat to weed control in crops. MHR weeds express a specific phi class glutathione transferase (MHR-GSTF) which seems to contribute to herbicide resistance. The present work aims to investigate the structure and catalytic properties of the MHR-GSTFs from different grass weeds and crops (Alopecurus myosuroides, Lolium rigidum, Hordeum vulgare, Triticum aestivum). Recombinant MHR-GSTFs were expressed in E. coli and purified by affinity chromatography. Kinetic analysis of substrate specificity using a range of thiol substrates and xenobiotic compounds suggested that all enzymes display a broad range of specificity and are capable of detoxifying major stress-induced toxic products. Notably, all tested enzymes exhibited high activity towards organic hydroperoxides. The crystal structure of MHR-GSTF from Alopecurus myosuroides (AmGSTF) was determined by molecular replacement at 1.33 Å resolution. The enzyme was resolved with bound glutathione sulfenic acid (GSOH) at the G-site and succinic acid at the H-site. The enzyme shows conserved structural features compared to other Phi class GSTs. However, some differences were observed at the C-terminal helix H9 that may affect substrate specificity. The structural and functional features of AmGSTF were compared with those of the homologue crop enzymes (HvGSTF and TaGSTF) and discussed in light of their contribution to the MHR mechanism.

Compensation of Mutation in Arabidopsis glutathione transferase (AtGSTU) Genes under Control or Salt Stress Conditions

Glutathione transferases (GSTs) play a crucial role in detoxification processes due to the fact of their glutathione (GSH) conjugating activity, and through glutathione peroxidase or dehydroascorbate reductase (DHAR) activities, they influence the redox state of GSH and ascorbate (AsA). The plant-specific tau (GSTU) group is the largest class of Arabidopsis GSTs, and their members are involved in responses to different abiotic stresses. We investigated the effect of salt stress on two-week-old Arabidopsis thaliana wild-type (Col-0), Atgstu19 and Atgstu24 mutant plants after applying 150 mM NaCl for two days. The Atgstu19 seedlings had lower GST activity and vitality both under control conditions and after salt stress than the wild-type, but the level of total ROS was similar to the Col-0 plants. The GST activity of the knockout Atgstu24 mutant was even higher under control conditions compared to the Col-0 plants, while the ROS level and its vitality did not differ significantly from the wild-type. Analysis of the AtGSTU expression pattern revealed that the mutation in a single AtGSTU gene was accompanied by the up- and downregulation of several other AtGSTUs. Moreover, elevated AsA and GSH levels, an altered GSH redox potential and increased DHAR and glutathione reductase activities could help to compensate for the mutation of AtGSTU genes. The observed changes in the mutants suggest that the investigated isoenzymes influence the redox homeostasis under control conditions and after NaCl treatment in Arabidopsis seedlings. These data indicate for the first time the more general role of a temporary shift of redox status as part of GST mechanisms and regulation.

Expression of Heterologous OsDHAR Gene Improves Glutathione (GSH)-Dependent Antioxidant System and Maintenance of Cellular Redox Status in Synechococcus elongatus PCC 7942

An excess of reactive oxygen species (ROS) can cause severe oxidative damage to cellular components in photosynthetic cells. Antioxidant systems, such as the glutathione (GSH) pools, regulate redox status in cells to guard against such damage. Dehydroascorbate reductase (DHAR, EC 1.8.5.1) catalyzes the glutathione-dependent reduction of oxidized ascorbate (dehydroascorbate) and contains a redox active site and glutathione binding-site. The DHAR gene is important in biological and abiotic stress responses involving reduction of the oxidative damage caused by ROS. In this study, transgenic Synechococcus elongatus PCC 7942 (TA) was constructed by cloning the Oryza sativa L. japonica DHAR (OsDHAR) gene controlled by an isopropyl β-D-1-thiogalactopyranoside (IPTG)-inducible promoter (Ptrc) into the cyanobacterium to study the functional activities of OsDHAR under oxidative stress caused by hydrogen peroxide exposure. OsDHAR expression increased the growth of S. elongatus PCC 7942 under oxidative stress by reducing the levels of hydroperoxides and malondialdehyde (MDA) and mitigating the loss of chlorophyll. DHAR and glutathione S-transferase activity were higher than in the wild-type S. elongatus PCC 7942 (WT). Additionally, overexpression of OsDHAR in S. elongatus PCC 7942 greatly increased the glutathione (GSH)/glutathione disulfide (GSSG) ratio in the presence or absence of hydrogen peroxide. These results strongly suggest that DHAR attenuates deleterious oxidative effects via the glutathione (GSH)-dependent antioxidant system in cyanobacterial cells. The expression of heterologous OsDHAR in S. elongatus PCC 7942 protected cells from oxidative damage through a GSH-dependent antioxidant system via GSH-dependent reactions at the redox active site and GSH binding site residues during oxidative stress.

Genome-wide phylogenetic and structural analysis reveals the molecular evolution of the ABA receptor gene family

The plant hormone abscisic acid (ABA) plays a crucial role during the plant life cycle as well as in adaptive responses to environmental stresses. The core regulatory components of ABA signaling in plants are the pyrabactin resistance1/PYR1-like/regulatory component of ABA receptor family (PYLs), which comprise the largest plant hormone receptor family known. They act as negative regulators of members of the protein phosphatase type 2C family. Due to the biological importance of PYLs, many researchers have focused on their genetic redundancy and consequent functional divergence. However, little is understood of their evolution and its impact on the generation of regulatory diversity. In this study, we identify positive selection and functional divergence in PYLs through phylogenetic reconstruction, gene structure and expression pattern analysis, positive selection analysis, functional divergence analysis, and structure comparison. We found the correlation of desensitization of PYLs under specific modifications in the molecular recognition domain with functional diversification. Hence, an interesting antagonistic co-evolutionary mechanism is proposed for the functional diversification of ABA receptor family proteins. We believe a compensatory evolutionary pathway may have occurred.

MicroRNAs and their targeted genes associated with phase changes of stem explants during tissue culture of tea plant

Elucidation of the molecular mechanism related to the dedifferentiation and redifferentiation during tissue culture will be useful for optimizing regeneration system of tea plant. In this study, an integrated sRNAome and transcriptome analyses were carried out during phase changes of the stem explant culture. Among 198 miRNAs and 8001 predicted target genes, 178 differentially expressed miRNAs and 4264 potential targets were screened out from explants, primary calli, as well as regenerated roots and shoots. According to KEGG analysis of the potential targets, pathway of "aminoacyl-tRNA biosynthesis", "proteasome" and "glutathione metabolism" was of great significance during the dedifferentiation, and pathway of "porphyrin and chlorophyll metabolism", "mRNA surveillance pathway", "nucleotide excision repair" was indispensable for redifferentiation of the calli. Expression pattern of 12 miRNAs, including csn-micR390e, csn-miR156b-5p, csn-miR157d-5p, csn-miR156, csn-miR166a-3p, csn-miR166e, csn-miR167d, csn-miR393c-3p, csn-miR394, csn-miR396a-3p, csn-miR396 and csn-miR396e-3p, was validated by qRT-PCR among 57 differentially expressed phase-specific miRNAs. Validation also confirmed that regulatory module of csn-miR167d/ERF3, csn-miR156/SPB1, csn-miR166a-3p/ATHB15, csn-miR396/AIP15A, csn-miR157d-5p/GST and csn-miR393c-3p/ATG18b might play important roles in regulating the phase changes during tissue culture of stem explants.

Effects of Substrate-Binding Site Residues on the Biochemical Properties of a Tau Class Glutathione S-Transferase from Oryza sativa

Glutathione S-transferases (GSTs)—an especially plant-specific tau class of GSTs—are key enzymes involved in biotic and abiotic stress responses. To improve the stress resistance of crops via the genetic modification of GSTs, we predicted the amino acids present in the GSH binding site (G-site) and hydrophobic substrate-binding site (H-site) of OsGSTU17, a tau class GST in rice. We then examined the enzyme activity, substrate specificity, enzyme kinetics and thermodynamic stability of the mutant enzymes. Our results showed that the hydrogen bonds between Lys42, Val56, Glu68, and Ser69 of the G-site and glutathione were essential for enzyme activity and thermal stability. The hydrophobic side chains of amino acids of the H-site contributed to enzyme activity toward 4-nitrobenzyl chloride but had an inhibitory effect on enzyme activity toward 1-chloro-2,4-dinitrobenzene and cumene hydroperoxide. Different amino acids of the H-site had different effects on enzyme activity toward a different substrate, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole. Moreover, Leu112 and Phe162 were found to inhibit the catalytic efficiency of OsGSTU17 to 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole, while Pro16, Leu112, and Trp165 contributed to structural stability. The results of this research enhance the understanding of the relationship between the structure and function of tau class GSTs to improve the abiotic stress resistance of crops.

The zinc-regulated protein (ZIP) family genes and glutathione s-transferase (GST) family genes play roles in Cd resistance and accumulation of pak choi (Brassica campestris ssp. chinensis)

The molecular mechanisms of the differences among the Cd tolerance and accumulation of different pak choi cultivars are essential to further breed Cd-safe genotypes pak choi. In our research, via morphological comparison, qRT-PCR and yeast function complementary approaches, we explored the differences of Cd tolerance and capacity for Cd uptake in nine various pak choi varieties. Results showed that higher expressions of BcZIPs involved in Cd uptake in 'Kang Re605' may lead to its higher capacity for Cd accumulation. The lowest expressions of transporter gene in 'Wu Yueman' were consistent with its fewest ability to uptake Cd. Beyond that, the difference of resistance was very great among varieties. Meanwhile, the expressions of the BcGSTUs were differentially induced by Cd exposure in different pak choi varieties, and 'Kang Re605' performed the highest BcGSTUs expression overall. To verify the role of GSTUs played in Cd resistance of pak choi, four BcGSTUs, BcGSTU4, BcGSTU11, BcGSTU12 and BcGSTU22 in a high-Cd accumulation and tolerance variety 'Kang Re605' were cloned, quantitated and transferred to Cd-sensitive yeast mutant strain. And finally found that BcGSTU11 increased the Cd tolerance of yeast, which may associate with a high Cd resistance of 'Kang Re605'. Simultaneously, less BcGSTUs abundance in 'Shang Haiqing' may result in its weak tolerance to Cd. These findings will help us to comprehend the roles of BcZIPs and BcGSTUs in Cd absorption and detoxification as well as promote our understanding of the Cd-resistant and Cd-accumulated mechanisms in pak choi.

Genome-wide identification of the glutathione transferase superfamily in the model organism Brachypodium distachyon

The detoxification of harmful metabolites can determine the effectiveness of plant stress responses. Scavenging some of these toxic stress by-products through the reduced form of glutathione is catalysed by members of the glutathione transferase (GST) enzyme superfamily. The involvement of these enzymes was studied in the model organism Brachypodium distachyon (L.)P.Beauv. Bd21 and in its derivative Bd21-3, a more drought tolerant line. Osmotic stress treatment resulted in a decrease in the water potential of both Brachypodium genotypes, the difference between the control and treated plant's ψw decreased by the last sampling day in Bd21-3, suggesting some degree of adaptation to the applied osmotic stress. Increased GST activity revealed a severe defence reaction against the harmful imbalance of the redox environment. Screening for the gene sequences led to the identification of 91 full-length or partial GST sequences. Although purple false brome has a relatively small genome, the number of identified GST genes was almost as high as the number predicted in wheat. The estimation of GST expression showed stress-induced differences: higher expression levels or the fast induction of BdGSTF8, BdGSTU35 and BdGSTU42 gene products presumably indicate a strong detoxification under osmotic stress.

Three Camellia sinensis glutathione S-transferases are involved in the storage of anthocyanins, flavonols, and proanthocyanidins

Biochemical, transgenic, and genetic complementation data demonstrate that three glutathione S-transferases are involved in the storage of anthocyanins, flavonols, and proanthocyanins in plant cells. Flavonoids are compounds in tea (Camellia sinensis) that confer the characteristic astringent taste of tea beverages; these compounds have numerous benefits for human health. In plant cells, flavonoids are synthesized in different locations within the cytoplasm and are then transported and finally stored in vacuoles. To date, the mechanism involved in the intracellular transport of flavonoids in tea has not been well elucidated. In this study, we report the functional characterization of three cDNAs encoding glutathione S-transferases (CsGSTs) of C. sinensis, namely, CsGSTa, CsGSTb, and CsGSTc. The expression profiles of CsGSTa and CsGSTb were positively correlated with the accumulation of flavonols, anthocyanins and proanthocyanins in tea tissues and cultivars. These three recombinant CsGSTs showed a high affinity for flavonols (kaempferol-3-O-glucoside and quercetin-3-O-glucoside) and anthocyanin (cyanidin-3-O-glucoside) in vitro but had no or weak affinity for epicatechin. In vivo, CsGSTa, CsGSTb and CsGSTc fully or partially restored the storage of anthocyanins and proanthocyanidins in transgenic tt19 mutants. Metabolic profiling revealed that the contents of anthocyanins, flavonols, and proanthocyanidins were increased in the transgenic petals of Nicotiana tabacum. Taken together, all data showed that CsGSTa, CsGSTb, and CsGSTc are associated with the storage of anthocyanins, flavonols, and proanthocyanins in C. sinensis cells.