The Cardamine enshiensis genome reveals whole genome duplication and insight into selenium hyperaccumulation and tolerance

Selenium-Mediated (-)-Epigallocatechin-3-Gallate Dynamics via Flavanone-3-Hydroxylase Regulation of Flavonoid Biosynthesis in Fu Tea (Camellia sinensis (L.) O. Kuntze)

Tea (Camellia sinensis (L.) O. Kuntze) is a highly selenium enrichment capacity plant; high selenium concentration contributes to the occurrence of oxidative stress and protein misfolding in tea plants, whereas flavonoids can chelate heavy metals to protect plants from oxidative stress caused by metal exposure. Nevertheless, the role of catechins in flavonoid synthesis and nutrient metabolism under selenium stress remains unidentified. Combining Word2vec and HNSW utilizing UHPLC-Q-Orbitrap HRMS-MS/MS to implement rapid matching annotation of the structural information on metabolites in Fu tea, we found that selenium-mediated changes in catechins in Fu tea were mainly associated with flavonoid biosynthesis pathways. The results demonstrated that selenium treatment increased benign selenol analogues (glutathioselenol) in tea and identified the novel selenopeptide PRSeMW (m/z 636.22571, Pro-Arg-SeMet-Trp) in selenium-enriched Fu tea samples to enhance the health benefits of tea. The selenium levels were negatively correlated with N5-ethyl-l-glutamine (11.63 to 4.26 mg kg-1) and (-)-epigallocatechin (13.26 to 11.19 mg kg-1), increasing the accumulation of tea polyphenols ((-)-catechin gallate, (-)-epigallocatechin 3-gallate, and (+)-gallocatechin), and decreasing the level of caffeine. These discoveries provide new insights into the mechanism of tea polyphenol-mediated transformation of selenium in Fu tea and theoretical support for the quality assessment of selenium-enriched tea.

Gene identification, expression analysis, and molecular docking of SAT and OASTL in the metabolic pathway of selenium in Cardamine hupingshanensis

KEY MESSAGE

Identification of selenium stress-responsive expression and molecular docking of serine acetyltransferase (SAT) and O-acetyl serine (thiol) lyase (OASTL) in Cardamine hupingshanensis. A complex coupled with serine acetyltransferase (SAT) and O-acetyl serine (thiol) lyase (OASTL) is the key enzyme that catalyzes selenocysteine (Sec) synthesis in plants. The functions of SAT and OASTL genes were identified in some plants, but it is still unclear whether SAT and OASTL are involved in the selenium metabolic pathway in Cardamine hupingshanensis. In this study, genome-wide identification and comparative analysis of ChSATs and ChOASTLs were performed. The eight ChSAT genes were divided into three branches, and the thirteen ChOASTL genes were divided into four branches by phylogenetic analysis and sequence alignment, indicating the evolutionary conservation of the gene structure and its association with other plant species. qRT-PCR analysis showed that the ChSAT and ChOASTL genes were differentially expressed in different tissues under various selenium levels, suggesting their important roles in Sec synthesis. The ChSAT1;2 and ChOASTLA1;2 were silenced by the VIGS system to investigate their involvement in selenium metabolites in C. hupingshanensis. The findings contribute to understanding the gene functions of ChSATs and ChOASTLs in the selenium stress and provide a reference for further exploration of the selenium metabolic pathway in plants.

Whole genome identification, molecular docking and expression analysis of enzymes involved in the selenomethionine cycle in Cardamine hupingshanensis

BACKGROUND

The selenomethionine cycle (SeMTC) is a crucial pathway for the metabolism of selenium. The basic bioinformatics and functions of four enzymes involved in the cycle including S-adenosyl-methionine synthase (MAT), SAM-dependent methyltransferase (MTase), S-adenosyl-homocysteine hydrolase (SAHH) and methionine synthase (MTR), have been extensively reported in many eukaryotes. The identification and functional analyses of SeMTC genes/proteins in Cardamine hupingshanensis and their response to selenium stress have not yet been reported.

RESULTS

In this study, 45 genes involved in SeMTC were identified in the C. hupingshanensis genome. Phylogenetic analysis showed that seven genes from ChMAT were clustered into four branches, twenty-seven genes from ChCOMT were clustered into two branches, four genes from ChSAHH were clustered into two branches, and seven genes from ChMTR were clustered into three branches. These genes were resided on 16 chromosomes. Gene structure and homologous protein modeling analysis illustrated that proteins in the same family are relatively conserved and have similar functions. Molecular docking showed that the affinity of SeMTC enzymes for selenium metabolites was higher than that for sulfur metabolites. The key active site residues identified for ChMAT were Ala269 and Lys273, while Leu221/231 and Gly207/249 were determined as the crucial residues for ChCOMT. For ChSAHH, the essential active site residues were found to be Asn87, Asp139 and Thr206/207/208/325. Ile204, Ser111/329/377, Asp70/206/254, and His329/332/380 were identified as the critical active site residues for ChMTR. In addition, the results of the expression levels of four enzymes under selenium stress revealed that ChMAT3-1 genes were upregulated approximately 18-fold, ChCOMT9-1 was upregulated approximately 38.7-fold, ChSAHH1-2 was upregulated approximately 11.6-fold, and ChMTR3-2 genes were upregulated approximately 28-fold. These verified that SeMTC enzymes were involved in response to selenium stress to varying degrees.

CONCLUSIONS

The results of this research are instrumental for further functional investigation of SeMTC in C. hupingshanensis. This also lays a solid foundation for deeper investigations into the physiological and biochemical mechanisms underlying selenium metabolism in plants.

Transcriptome analysis reveals the molecular mechanism of different forms of selenium in reducing cadmium uptake and accumulation in wheat seedlings

Selenium (Se) can counteract cadmium (Cd) toxicity in wheat, but the molecular mechanism of different Se forms reducing Cd uptake and accumulation in wheat seedlings remain unclear. Here, a hydroponic experiment was conducted to investigate the effects of three Se forms (selenite (Se(IV)), selenate (Se(VI)) and seleno-L-methionine (SeMet)) on Cd2+ influx, Cd subcellular distribution, and Cd accumulation in wheat seedlings, and the underlying molecular mechanisms were investigated through transcriptome analysis. Consequently, Se(IV) and Se(VI) addition significantly reduced root Cd concentration by 74.3% and 80.8%, respectively, and all Se treatments significantly decreased shoot Cd concentration by approximately 34.2%-74.9%, with Se(IV) addition having the most pronounced reducing effect. Transcriptome analysis showed the reduction of Cd accumulation after Se(IV) addition was mainly due to the downregulation of Cd uptake genes. The inhibition of Cd accumulation after Se(VI) addition was not only associated with the downregulation of Cd uptake genes, but also related to the sequestration of Cd in vacuole. For SeMet addition, the reduction of Cd accumulation was mainly related to the sequestration of Cd in vacuole as GSH-Cd. The above findings provide novel insights to understand the effects of different forms of Se on Cd uptake and accumulation and tolerance in wheat.

Evolutionary Dynamics of FLC-like MADS-Box Genes in Brassicaceae

MADS-box genes encode transcription factors that play important roles in the development and evolution of plants. There are more than a dozen clades of MADS-box genes in angiosperms, of which those with functions in the specification of floral organ identity are especially well-known. From what has been elucidated in the model plant Arabidopsis thaliana, the clade of FLC-like MADS-box genes, comprising FLC-like genes sensu strictu and MAF-like genes, are somewhat special among the MADS-box genes of plants since FLC-like genes, especially MAF-like genes, show unusual evolutionary dynamics, in that they generate clusters of tandemly duplicated genes. Here, we make use of the latest genomic data of Brassicaceae to study this remarkable feature of the FLC-like genes in a phylogenetic context. We have identified all FLC-like genes in the genomes of 29 species of Brassicaceae and reconstructed the phylogeny of these genes employing a Maximum Likelihood method. In addition, we conducted selection analyses using PAML. Our results reveal that there are three major clades of FLC-like genes in Brassicaceae that all evolve under purifying selection but with remarkably different strengths. We confirm that the tandem arrangement of MAF-like genes in the genomes of Brassicaceae resulted in a high rate of duplications and losses. Interestingly, MAF-like genes also seem to be prone to transposition. Considering the role of FLC-like genes sensu lato (s.l.) in the timing of floral transition, we hypothesize that this rapid evolution of the MAF-like genes was a main contributor to the successful adaptation of Brassicaceae to different environments.

Selenium hyperaccumulator plant Cardamine enshiensis: from discovery to application

Selenium (Se) is an essential trace element for animals and humans. Se biofortification and Se functional agriculture are emerging strategies to satisfy the needs of people who are deficient in Se. With 200 km2 of Se-excess area, Enshi is known as the "world capital of Se." Cardamine enshiensis (C. enshiensis) is a Se hyperaccumulation plant discovered in the Se mine drainage area of Enshi. It is edible and has been approved by National Health Commission of the People's Republic of China as a new source of food, and the annual output value of the Se-rich industry in Enshi City exceeds 60 billion RMB. This review will mainly focus on the discovery and mechanism underlying Se tolerance and Se hyperaccumulation in C. enshiensis and highlight its potential utilization in Se biofortification agriculture, graziery, and human health.

Ferroptosis and tumor immunotherapy: A promising combination therapy for tumors

Low response rate and treatment resistance are frequent problems in the immunotherapy of tumors, resulting in the unsatisfactory therapeutic effects. Ferroptosis is a form of cell death characterized by the accumulation of lipid peroxides. In recent years, it has been found that ferroptosis may be related to the treatment of cancer. Various immune cells (including macrophages and CD8⁺ T cells) can induce ferroptosis of tumor cells, and synergistically enhance the anti-tumor immune effects. However, the mechanisms are different for each cell types. DAMP released in vitro by cancer cells undergoing ferroptosis lead to the maturation of dendritic cells, cross-induction of CD8⁺ T cells, IFN-γ production and M1 macrophage production. Thus, it activates the adaptability of the tumor microenvironment and forms positive feedback of the immune response. It suggests that induction of ferroptosis may contribute to reducing resistance of cancer immunotherapy and has great potential in cancer therapy. Further research into the link between ferroptosis and tumor immunotherapy may offer hope for those cancers that are difficult to treat. In this review, we focus on the role of ferroptosis in tumor immunotherapy, explore the role of ferroptosis in various immune cells, and discuss potential applications of ferroptosis in tumor immunotherapy.

Micro-analytical and molecular approaches for understanding the distribution, biochemistry, and molecular biology of selenium in (hyperaccumulator) plants

Micro-analytical techniques to untangle Se distribution and chemical speciation in plants coupled with molecular biology analysis enable the deciphering of metabolic pathways responsible for Se tolerance and accumulation. Selenium (Se) is not essential for plants and is toxic at high concentrations. However, Se hyperaccumulator plants have evolved strategies to both tolerate and accumulate > 1000 µg Se g^-1 DW in their living above-ground tissues. Given the complexity of the biochemistry of Se, various approaches have been adopted to study Se metabolism in plants. These include X-ray-based techniques for assessing distribution and chemical speciation of Se, and molecular biology techniques to identify genes implicated in Se uptake, transport, and assimilation. This review presents these techniques, synthesises the current state of knowledge on Se metabolism in plants, and highlights future directions for research into Se (hyper)accumulation and tolerance. We conclude that powerful insights may be gained from coupling information on the distribution and chemical speciation of Se to genome-scale studies to identify gene functions and molecular mechanisms that underpin Se tolerance and accumulation in these ecologically and biotechnologically important plants species. The study of Se metabolism is challenging and is a useful testbed for developing novel analytical approaches that are potentially more widely applicable to the study of the regulation of a wide range of metal(loid)s in hyperaccumulator plants.

Gene Identification, expression analysis and molecular docking of ATP sulfurylase in the selenization pathway of Cardamine hupingshanensis

BACKGROUND

ATP sulfurylase (ATPS) is a crucial enzyme for the selenate assimilation pathway in plants.

RESULTS

In this study, genome-wide and comparative analyses of ATPS in Cardamine hupingshanensis, including sequence and structural analyses, were performed. The expression of ChATPS gene family members in C. hupingshanensis under selenium (Se) stress was also investigated, and our results suggest that ChATPS1-2 play key roles in the response to Se stress. Nine ATPS genes were found from C. hupingshanensis, which share highly conserved sequences with ATPS from Arabidopsis thaliana. In addition, we performed molecular docking of ATP sulfurylase in complex with compounds ATP, selenate, selenite, sulfate, and sulfite. ChAPS3-1 was found to have stronger binding energies with all compounds tested. Among these complexes, amino acid residues Arg, Gly, Ser, Glu, and Asn were commonly present.

CONCLUSION

Our study reveals the molecular mechanism of C. hupingshanensis ATP sulfurylase interacting with selenate, which is essential for understanding selenium assimilation. This information will guide further studies on the function of the ChATPS gene family in the selenium stress response and lay the foundation for the selenium metabolic pathway in higher plants.

Investigation of Brassica and its relative genomes in the post-genomics era

The Brassicaceae family includes many economically important crop species, as well as cosmopolitan agricultural weed species. In addition, Arabidopsis thaliana, a member of this family, is used as a molecular model plant species. The genus Brassica is mesopolyploid, and the genus comprises comparatively recently originated tetrapolyploid species. With these characteristics, Brassicas have achieved the commonly accepted status of model organisms for genomic studies. This paper reviews the rapid research progress in the Brassicaceae family from diverse omics studies, including genomics, transcriptomics, epigenomics, and three-dimensional (3D) genomics, with a focus on cultivated crops. The morphological plasticity of Brassicaceae crops is largely due to their highly variable genomes. The origin of several important Brassicaceae crops has been established. Genes or loci domesticated or contributing to important traits are summarized. Epigenetic alterations and 3D structures have been found to play roles in subgenome dominance, either in tetraploid Brassica species or their diploid ancestors. Based on this progress, we propose future directions and prospects for the genomic investigation of Brassicaceae crops.

Complete chloroplast genome of Cardamine hupingshanensis K.M.Liu, L.B.Chen, H.F.Bai & L.H.Liu (Brassicaceae) in Enshi, Hubei

Cardamine hupingshanensis K.M.Liu, L.B.Chen, H.F.Bai & L.H.Liu 2008, also called Cardamine enshiensis, belongs to the genus Cardamine, Brassicaceae. As a plant with selenium enrichment ability, it has high development value. Here, we analyzed the chloroplast genome of C. hupingshanensis. The complete chloroplast genome had a total size of 154,832 bp with a typical quadripartite structure, including a large single-copy region (LSC, 83,908 bp) and a small single-copy region (SSC, 17,938 bp), separated by a pair of inverted repeat regions (IRs, 26,493 bp). Genome annotation showed the chloroplast genome contained 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. A total of 143 SSRs were found in the chloroplast genome. Phylogenetic analysis showed that C. hupingshanensis was closer to the C. circaeoides and C. lyrata. This chloroplast genome resource will be useful for study of the phylogeny and evolution of Cardamine in the future.

The amino acids, bacterial communities, and their correlations in Wuliangye-flavour liquor production

With the enhancement of people’s awareness of drinking health, the health factors in Wuliangye-flavour liquor is worth our attention. Bacterial communities in 4 layers of Zaopei from the same fermentation pit and amino acids as major health factors in 4 liquors directly related Zaopeis were investigated by Illumina MiSeq sequencing and liquid chromatography mass spectrometry, respectively. Results indicated that 18 amino acids were detected and 8 dominant bacteria (genus level) were observed. Meanwhile, total amino acids, 11 amino acids (Glu, Asp, Val, etc), bacterial diversity, and the percentages of Lactobacillus and Pseudomonas increased with the increase of Zaopei’s depth; 5 amino acids (Pro, Ser, Phe, etc) and the percentages of Pediococcus and Bacteroides first increased and then decreased with the increase of Zaopei’s depth. Moreover, 11 amino acids were significantly (P < 0.01) and strongly (|ρ| > 0.8) positively correlated with Lactobacillus and Pseudomonas numbers.