Ammonium triggered the response mechanism of lysine crotonylome in tea plants

AdNAC20 Regulates Lignin and Coumarin Biosynthesis in the Roots of Angelica dahurica var. Formosana

Angelica dahurica var. formosana (ADF), which belongs to the Umbelliferae family, is one of the original plants of herbal raw material Angelicae Dahuricae Radix. ADF roots represent an enormous biomass resource convertible for disease treatment and bioproducts. But, early bolting of ADF resulted in lignification and a decrease in the coumarin content in the root, and roots lignification restricts its coumarin for commercial utility. Although there have been attempts to regulate the synthesis ratio of lignin and coumarin through biotechnology to increase the coumarin content in ADF and further enhance its commercial value, optimizing the biosynthesis of lignin and coumarin remains challenging. Based on gene expression analysis and phylogenetic tree profiling, AdNAC20 as the target for genetic engineering of lignin and coumarin biosynthesis in ADF was selected in this study. Early-bolting ADF had significantly greater degrees of root lignification and lower coumarin contents than that of the normal plants. In this study, overexpression of AdNAC20 gene plants were created using transgenic technology, while independent homozygous transgenic lines with precise site mutation of AdNAC20 were created using CRISPR/Cas9 technology. The overexpressing transgenic ADF plants showed a 9.28% decrease in total coumarin content and a significant 12.28% increase in lignin content, while knockout mutant plants showed a 16.3% increase in total coumarin content and a 33.48% decrease in lignin content. Furthermore, 29,671 differentially expressed genes (DEGs) were obtained by comparative transcriptomics of OE-NAC20, KO-NAC20, and WT of ADF. A schematic diagram of the gene network interacting with AdNAC20 during the early-bolting process of ADF was constructed by DEG analysis. AdNAC20 was predicted to directly regulate the transcription of several genes with SNBE-like motifs in their promoter, such as MYB46, C3H, and CCoAOMT. In this study, AdNAC20 was shown to play a dual pathway function that positively enhanced lignin formation but negatively controlled coumarin formation. And the heterologous expression of the AdNAC20 gene at Arabidopsis thaliana proved that the AdNAC20 gene also plays an important role in the process of bolting and flowering.

Protein crotonylation: Basic research and clinical diseases

Crotonylation is an importantly conserved post-translational modification, which is completely different from acetylation. In recent years, it has been confirmed that crotonylation occurs on histone and non-histone. Crotonylated Histone primarily affects gene expression through transcriptional regulation, while non-histone Crotonylation mainly regulates protein functions including protein activity, localization, and stability, as well as protein-protein interactions. The change in protein expression and function will affect the physiological process of cells and even cause disease. Reviewing previous studies, this article summarizes the mechanisms of histone and non-histone crotonylation in regulating diseases and cellular physiological processes to explore the possibility of precise regulation of crotonylation sites as potential targets for disease treatment.

The crotonylated and succinylated proteins of jujube involved in phytoplasma-stress responses

BACKGROUND

Protein posttranslational modifications (PTMs) are fast and early responses to environmental changes, including pathogen infection. Jujube witches' broom (JWB) is a phytoplasma disease causing great economic loss in jujube production. After phytoplasma infection, the transcriptional, translational, and metabolic levels in jujube were activated, enabling it to survive during phytoplasma invasion. However, no study has yet reported on PTMs in jujube. Lysine crotonylation (Kcr) and lysine succinylation (Ksu) have been popular studies in recent years and their function in plant phytoplasma-stress responses remains unclear.

RESULTS

Here, 1656 crotonylated and 282 succinylated jujube proteins were first identified under phytoplasma-stress, of which 198 were simultaneously crotonylated and succinylated. Comparative analysis revealed that 656 proteins, 137 crotonylated and 43 succinylated proteins in jujube were regulated by phytoplasma infection, suggesting that Kcr was more universal than Ksu. Kcr differentially expressed proteins (DEPs) were related to ribosomes, photosynthetic and carbon metabolism, while Ksu DEPs were mainly involved in carbon metabolism, the TCA cycle and secondary metabolite biosynthesis. The crosstalk network among proteome, crotonylome and succinylome showed that DEPs related to ribosomal, peroxidases and glutathione redox were enriched. Among them, ZjPOD51 and ZjPHGPX2 significantly increased at the protein and Kcr level under phytoplasma-stress. Notably, 7 Kcr sites were identified in ZjPHGPX2, a unique antioxidant enzyme. After inhibitor nicotinamide (NAM) treatment, GPX enzyme activity in jujube seedlings was reduced. Further, site-directed mutagenesis of key Kcr modification sites K130 and/or K135 in ZjPHGPX2 significantly reduced its activity.

CONCLUSIONS

This study firstly provided large-scale datasets of Kcr and Ksu in phytoplasma-infected jujube and revealed that Kcr modification in ZjPHGPX2 positively regulates its activity.

Proteomics and phosphoproteomics reveal the different drought-responsive mechanisms of priming with (Z)-3-hexenyl acetate in two tea cultivars

Drought is an important abiotic stress that constrains the quality and quantity of tea plants. The green leaf volatiles Z-3-hexenyl acetate (Z-3-HAC) have been reported to play an essential role in stress responses. However, the underlying mechanisms of drought tolerance in tea plants remain elusive. This study investigated the physiological, proteomic, and phosphoproteomic profiling of two tea plant varieties of Longjingchangye (LJCY) and Zhongcha 108 (ZC108) with contrasting drought tolerance characteristics under drought stress. Physiological data showed that spraying Z-3-HAC exhibited higher activities of superoxide dismutase (SOD) and catalase (CAT) in both LJCY and ZC108 but lower content of malondialdehyde (MDA) in LJCY under drought stress. The proteomic and phosphoproteomic analysis suggested that the drought tolerance mechanism of Z-3-HAC in LJCY and ZC108 was different. Proteomic analyses revealed that Z-3-HAC enhanced the drought tolerance of LJCY by fructose metabolism while enhancing the drought tolerance of ZC108 by promoting glucan biosynthesis and galactose metabolism. Furthermore, the differential abundance phosphoproteins (DAPPs) related to intracellular protein transmembrane transport and protein transmembrane transport were enriched in LJCY, and the regulation of response to osmotic stress and regulation of mRNA processing were enriched in ZC108. In addition, protein-phosphoprotein interactions (PPI) analyses suggested that energy metabolism and starch and sucrose metabolic processes might play critical roles in LJCY and ZC108, respectively. These results will help to understand the mechanisms by which Z-3-HAC enhances the drought resistance of tea plants at the protein level. SIGNIFICANT: Green leaf volatiles (GLVs) are important volatile organic compounds that play essential roles in plant defense against biotic and abiotic stresses. To understand the mechanisms of Z-3-HAC in improving the drought tolerance of tea plants, two contrasting drought tolerance varieties (LJCY and ZC108) were comparatively evaluated by proteomics and phosphoproteomics. This analysis evidenced changes in the abundance of proteins involved in energy metabolism and starch and sucrose metabolic processes in LJCY and ZC108, respectively. These proteins may elucidate new molecular aspects of the drought resistance mechanism of Z-3-HAC, providing a theoretical basis for drought resistance breeding of tea plants.

Nitrogen transport and assimilation in tea plant (Camellia sinensis): a review

Nitrogen is one of the most important nutrients for tea plants, as it contributes significantly to tea yield and serves as the component of amino acids, which in turn affects the quality of tea produced. To achieve higher yields, excessive amounts of N fertilizers mainly in the form of urea have been applied in tea plantations where N fertilizer is prone to convert to nitrate and be lost by leaching in the acid soils. This usually results in elevated costs and environmental pollution. A comprehensive understanding of N metabolism in tea plants and the underlying mechanisms is necessary to identify the key regulators, characterize the functional phenotypes, and finally improve nitrogen use efficiency (NUE). Tea plants absorb and utilize ammonium as the preferred N source, thus a large amount of nitrate remains activated in soils. The improvement of nitrate utilization by tea plants is going to be an alternative aspect for NUE with great potentiality. In the process of N assimilation, nitrate is reduced to ammonium and subsequently derived to the GS-GOGAT pathway, involving the participation of nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH). Additionally, theanine, a unique amino acid responsible for umami taste, is biosynthesized by the catalysis of theanine synthetase (TS). In this review, we summarize what is known about the regulation and functioning of the enzymes and transporters implicated in N acquisition and metabolism in tea plants and the current methods for assessing NUE in this species. The challenges and prospects to expand our knowledge on N metabolism and related molecular mechanisms in tea plants which could be a model for woody perennial plant used for vegetative harvest are also discussed to provide the theoretical basis for future research to assess NUE traits more precisely among the vast germplasm resources, thus achieving NUE improvement.

Large-scale analysis of protein crotonylation reveals its diverse functions in Pinellia ternata

BACKGROUND

Pinellia ternata is an important traditional medicine in China, and its growth is regulated by the transcriptome or proteome. Lysine crotonylation, a newly identified and important type of posttranslational modification, plays a key role in many aspects of cell metabolism. However, little is known about its functions in Pinellia ternata.

RESULTS

In this study, we generated a global crotonylome analysis of Pinellia ternata and examined its overlap with lysine succinylation. A total of 2106 crotonylated sites matched on 1006 proteins overlapping in three independent tests were identified, and we found three specific amino acids surrounding crotonylation sites in Pinellia ternata: K^crF, K***Y**K^cr and K^cr****R. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that two crucial alkaloid biosynthesis-related enzymes and many stress-related proteins were also highly crotonylated. Furthermore, several enzymes participating in carbohydrate metabolism pathways were found to exhibit both lysine crotonylation and succinylation modifications.

CONCLUSIONS

These results indicate that lysine crotonylation performs important functions in many biological processes in Pinellia ternata, especially in the biosynthesis of alkaloids, and some metabolic pathways are simultaneously regulated by lysine crotonylation and succinylation.

Crotonylation versus acetylation in petunia corollas with reduced acetyl-CoA due to PaACL silencing

Protein acetylation and crotonylation are important posttranslational modifications of lysine. In animal cells, the correlation of acetylation and crotonylation has been well characterized and the lysines of some proteins are acetylated or crotonylated depending on the relative concentrations of acetyl-CoA and crotonyl-CoA. However, in plants, the correlation of acetylation and crotonylation and the effects of the relative intracellular concentrations of crotonyl-CoA and acetyl-CoA on protein crotonylation and acetylation are not well known. In our previous study, PaACL silencing changed the content of acetyl-CoA in petunia (Petunia hybrida) corollas, and the effect of PaACL silencing on the global acetylation proteome in petunia was analyzed. In the present study, we found that PaACL silencing did not significantly alter the content of crotonyl-CoA. We performed a global crotonylation proteome analysis of the corollas of PaACL-silenced and control petunia plants; we found that protein crotonylation was closely related to protein acetylation and that proteins with more crotonylation sites often had more acetylation sites. Crotonylated proteins and acetylated proteins were enriched in many common Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. However, PaACL silencing resulted in different KEGG pathway enrichments of proteins with different levels of crotonylation sites and acetylation sites. PaACLB1-B2 silencing did not led to changes in the opposite direction in crotonylation and acetylation levels at the same lysine site in cytoplasmic proteins, which indicated that cytoplasmic lysine acetylation and crotonylation might not depend on the relative concentrations of acetyl-CoA and crotonyl-CoA. Moreover, the global crotonylome and acetylome were weakly positively correlated in the corollas of PaACL-silenced and control plants.

Lysine decrotonylation of glutathione peroxidase at lysine 220 site increases glutathione peroxidase activity to resist cold stress in chrysanthemum

Lysine crotonylation is a protein post-translational modification that has been newly discovered in recent years. There are few studies on the lysine crotonylation of proteins in plants, and their functions in response to cold stress are still unclear. In this study, the chrysanthemum (Chrysanthemum morifolium Ramat.) glutathione peroxidase (GPX) gene was selected and named DgGPX1, and was found to be responsive to low temperature. Overexpression of DgGPX1 improved the cold resistance of transgenic chrysanthemum by increasing GPX activity to reduce the accumulation of reactive oxygen species (ROS) under low-temperature conditions. Furthermore, the level of DgGPX1 lysine crotonylation at lysine (K) 220 decreased under low temperature in chrysanthemum. Lysine decrotonylation of DgGPX1 at K220 further increased GPX activity to reduce ROS accumulation under cold stress, and thereby enhanced the cold resistance of chrysanthemum. The above results show that lysine decrotonylation of DgGPX1 at K220 increases GPX activity to resist cold stress in chrysanthemum.

Qualitative Proteome-Wide Analysis Reveals the Diverse Functions of Lysine Crotonylation in Dendrobium huoshanense

The lysine crotonylation of histone proteins is a newly identified posttranslational modification with diversified cellular functions. However, there are few reports on lysine crotonylation of non-histone proteins in medicinal plant cells. By using high-resolution liquid chromatography-mass spectrometry (LC-MS) coupled with highly sensitive-specific immune-affinity antibody analysis, a whole crotonylation proteome analysis of Dendrobium huoshanense was performed. In total, 1,591 proteins with 4,726 lysine crotonylation sites were identified; among them, 11 conserved motifs were identified. Bioinformatic analyses linked crotonylated proteins to the drought stress response and multiple metabolic pathways, including secondary metabolite biosynthesis, transport and catabolism, energy production and conversion, carbohydrate transport and metabolism, translation, and ribosomal structure and biogenesis. This study contributes toward understanding the regulatory mechanism of polysaccharide biosynthesis at the crotonylation level even under abiotic stress.

Comprehensive Profiling of Paper Mulberry (Broussonetia papyrifera) Crotonylome Reveals the Significance of Lysine Crotonylation in Young Leaves

Lysine crotonylation is a newly discovered and reversible posttranslational modification involved in various biological processes, especially metabolism regulation. A total of 5159 lysine crotonylation sites in 2272 protein groups were identified. Twenty-seven motifs were found to be the preferred amino acid sequences for crotonylation sites. Functional annotation analyses revealed that most crotonylated proteins play important roles in metabolic processes and photosynthesis. Bioinformatics analysis suggested that lysine crotonylation preferentially targets a variety of important biological processes, including ribosome, glyoxylate and dicarboxylate metabolism, carbon fixation in photosynthetic organisms, proteasome and the TCA cycle, indicating lysine crotonylation is involved in the common mechanism of metabolic regulation. A protein interaction network analysis revealed that diverse interactions are modulated by protein crotonylation. These results suggest that lysine crotonylation is involved in a variety of biological processes. HSP70 is a crucial protein involved in protecting plant cells and tissues from thermal or abiotic stress responses, and HSP70 protein was found to be crotonylated in paper mulberry. This systematic analysis provides the first comprehensive analysis of lysine crotonylation in paper mulberry and provides important resources for further study on the regulatory mechanism and function of the lysine crotonylated proteome.

The decrotonylase FoSir5 facilitates mitochondrial metabolic state switching in conidial germination of Fusarium oxysporum

Fusarium oxysporum is one of the most important pathogenic fungi with a broad range of plant and animal hosts. The first key step of its infection cycle is conidial germination, but there is limited information available on the molecular events supporting this process. We show here that germination is accompanied by a sharp decrease in expression of FoSir5, an ortholog of the human lysine deacetylase SIRT5. We observe that FoSir5 decrotonylates a subunit of the fungal pyruvate dehydrogenase complex (FoDLAT) at K148, resulting in inhibition of the activity of the complex in mitochondria. Moreover, FoSir5 decrotonylates histone H3K18, leading to a downregulation of transcripts encoding enzymes of aerobic respiration pathways. Thus, the activity of FoSir5 coordinates regulation in different organelles to steer metabolic flux through respiration. As ATP content is positively related to fungal germination, we propose that FoSir5 negatively modulates conidial germination in F. oxysporum through its metabolic impact. These findings provide insights into the multifaceted roles of decrotonylation, catalyzed by FoSir5, that support conidial germination in F. oxysporum.

Qualitative lysine crotonylome analysis in the ovarian tissue of Harmonia axyridis (Pallas)

Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM), which has been studied at the proteomics level in a few species, with the study of Kcr in female fertility and in insect species is still lacking. Harmonia axyridis (Pallas) is a well-known beneficial insect used as a natural biological control agent against aphids in agriculture. Here, global Kcr identification in ovarian tissue of H. axyridis at diapause stage was performed to reveal potential roles for Kcr in H. axyridis ovarian cellular processes, female fertility and diapause regulation. In total, 3084 Kcr sites in 920 proteins were identified. Bioinformatic analyses revealed the distribution of these proteins in multiple subcellular localization categories and their involvement in diverse biological processes and metabolism pathways. Carbohydrate and energy metabolism related cellular processes including citric acid cycle, glycolysis and oxidative phosphorylation appeared be affected by Kcr modification. In addition, regulation of translation and protein biosynthesis may reflect Kcr involvement in diapause in H. axyridis, with Kcr affecting ribosome activities and amino acid metabolism. Moreover, Kcr modulation H. axyridis ovary development regulation may share some common mechanism with Kcr participation in some disease progression. These processes and pathways were uncovered under diapause stage, but possibly not enriched/specific for diapause stage due to limitations of qualitative proteomics experimental design. Our results informs on the potential for Kcr modifications to regulate female fertility and insect physiology.

Protein Crotonylation Expert Review: A New Lens to Take Post-Translational Modifications and Cell Biology to New Heights

Genome regulation, temporal and spatial variations in cell function, continues to puzzle and interest life scientists who aim to unravel the molecular basis of human health and disease, not to mention plant biology and ecosystem diversity. Despite important advances in epigenomics and protein post-translational modifications over the past decade, there is a need for new conceptual lenses to understand biological mechanisms that can help unravel the fundamental regulatory questions in genomes and the cell. To these ends, lys crotonylation (Kcr) is a reversible protein modification catalyzed by protein crotonyl transferases and decrotonylases. First identified on histones, Kcr regulates cellular processes at the chromatin level. Research thus far has revealed that Kcr marks promoter sites of active genes and potential enhancers. Eventually, Kcr on a number of nonhistone proteins was reported. The abundance of Kcr on ribosomal and myofilament proteins indicates its functional roles in protein synthesis and muscle contraction. Kcr has also been associated with pluripotency, spermiogenesis, and DNA repair. In plants, large-scale mass spectrometry-based experiments validated the roles of Kcr in photosynthesis. In this expert review, we present the latest thinking and findings on lys crotonylation with an eye to regulation of cell biology. We discuss the enrichment techniques, putative biological functions, and challenges associated with studying this protein modification with vast biological implications. Finally, we reflect on the future outlook about the broader relevance of Kcr in animals, microbes, and plant species.

Protein lysine crotonylation: past, present, perspective

Lysine crotonylation has been discovered in histone and non-histone proteins and found to be involved in diverse diseases and biological processes, such as neuropsychiatric disease, carcinogenesis, spermatogenesis, tissue injury, and inflammation. The unique carbon–carbon π-bond structure indicates that lysine crotonylation may use distinct regulatory mechanisms from the widely studied other types of lysine acylation. In this review, we discussed the regulation of lysine crotonylation by enzymatic and non-enzymatic mechanisms, the recognition of substrate proteins, the physiological functions of lysine crotonylation and its cross-talk with other types of modification. The tools and methods for prediction and detection of lysine crotonylation were also described.

Lysine crotonylation of DgTIL1 at K72 modulates cold tolerance by enhancing DgnsLTP stability in chrysanthemum

Lysine crotonylation of proteins is a recently identified post-translational modification (PTM) in plants. However, the function of lysine-crotonylated proteins in response to abiotic stress in plants has not been reported. In this study, we identified a temperature-induced lipocalin-1-like gene (DgTIL1) from chrysanthemum and showed that it was notably induced in response to cold stress. Overexpression of DgTIL1 enhanced cold tolerance in transgenic chrysanthemum. Ubiquitin membrane yeast two-hybrid (MYTH) system and bimolecular fluorescence complementation (BIFC) assays showed that DgTIL1 interacts with a nonspecific lipid transfer protein (DgnsLTP), which can promote peroxidase (POD) gene expression and POD activity to reduce the accumulation of reactive oxygen species (ROS) and improve resistance to cold stress in DgnsLTP transgenic chrysanthemum. In addition, we found that DgTIL1 was lysine crotonylated at K72 in response to low temperature in chrysanthemum. Moreover, lysine crotonylation of DgTIL1 prevented DgnsLTP protein degradation in tobacco and chrysanthemum. Inhibition of DgnsLTP degradation by lysine crotonylation of DgTIL1 further enhanced POD expression and POD activity, reduced the accumulation of ROS under cold stress in DgTIL1 transgenic chrysanthemum, thus promoting the cold resistance of chrysanthemum.

Emerging roles of non-histone protein crotonylation in biomedicine

Crotonylation of proteins is a newly found type of post-translational modifications (PTMs) which occurs leadingly on the lysine residue, namely, lysine crotonylation (Kcr). Kcr is conserved and is regulated by a series of enzymes and co-enzymes including lysine crotonyltransferase (writer), lysine decrotonylase (eraser), certain YEATS proteins (reader), and crotonyl-coenzyme A (donor). Histone Kcr has been substantially studied since 2011, but the Kcr of non-histone proteins is just an emerging field since its finding in 2017. Recent advances in the identification and quantification of non-histone protein Kcr by mass spectrometry have increased our understanding of Kcr. In this review, we summarized the main proteomic characteristics of non-histone protein Kcr and discussed its biological functions, including gene transcription, DNA damage response, enzymes regulation, metabolic pathways, cell cycle, and localization of heterochromatin in cells. We further proposed the performance of non-histone protein Kcr in diseases and the prospect of Kcr manipulators as potential therapeutic candidates in the diseases.

A comprehensive examination of the lysine acetylation targets in paper mulberry based on proteomics analyses

Rocky desertification is a bottleneck that reduces ecological and environmental security in karst areas. Paper mulberry, a unique deciduous tree, shows good performance in rocky desertification areas. Its resistance mechanisms are therefore of high interest. In this study, a lysine acetylation proteomics analysis of paper mulberry seedling leaves was conducted in combination with the purification of acetylated protein by high-precision nano LC-MS/MS. We identified a total of 7130 acetylation sites in 3179 proteins. Analysis of the modified sites showed a predominance of nine motifs. Six positively charged residues: lysine (K), arginine (R), and histidine (H), serine (S), threonine (T), and tyrosine (Y) occurred most frequently at the +1 position, phenylalanine (F) was both detected both upstream and downstream of the acetylated lysines; and the sequence logos showed a strong preference for lysine and arginine around acetylated lysines. Functional annotation revealed that the identified enzymes were mainly involved in translation, transcription, ribosomal structure and biological processes, showing that lysine acetylation can regulate various aspects of primary carbon and nitrogen metabolism and secondary metabolism. Acetylated proteins were enriched in the chloroplast, cytoplasm, and nucleus, and many stress response-related proteins were also discovered to be acetylated, including PAL, HSP70, and ERF. HSP70, an important protein involved in plant abiotic and disease stress responses, was identified in paper mulberry, although it is rarely found in woody plants. This may be further examined in research in other plants and could explain the good adaptation of paper mulberry to the karst environment. However, these hypotheses require further verification. Our data can provide a new starting point for the further analysis of the acetylation function in paper mulberry and other plants.

Lysine crotonylation is widespread on proteins of diverse functions and localizations in Toxoplasma gondii

Lysine crotonylation (Kcr) is an evolutionally conserved post-translational modification (PTM) on histone proteins. However, information about Kcr and its involvement in the biology and metabolism of Toxoplasma gondii is limited. In the present study, a global Kcr proteome analysis using LC-MS/MS in combination with immune-affinity method was performed. A total of 12,152 Kcr sites distributed over 2719 crotonylated proteins were identified. Consistent with lysine acetylation and succinylation in Apicomplexa, Kcr was associated with various metabolic pathways, including carbon metabolism, pyrimidine metabolism, glycolysis, gluconeogenesis, and proteasome. Markedly, many stage-specific proteins, histones, and histone-modifying enzymes related to the stage transition were found to have Kcr sites, suggesting a potential involvement of Kcr in the parasite stage transformation. Most components of the apical secretory organelles were identified as crotonylated proteins which were associated with the attachment, invasion, and replication of T. gondii. These results expanded our understanding of Kcr proteome and proposed new hypotheses for further research of the Kcr roles in the pathobiology of T. gondii infection.

First comprehensive proteomics analysis of lysine crotonylation in leaves of peanut (Arachis hypogaea L.)

Lysine crotonylation is an important post-translational modification process. Most research in this area has been carried out on mammals and yeast, but there has been little research on it in plants. In the current study, large-scale lysine crotonylome analysis was performed by a combination of affinity enrichment and high-resolution LC-MS/MS analysis. Altogether, 6051 lysine crotonylation sites were identified in 2508 protein groups. Bioinformatics analysis showed that lysine-crotonylated proteins were involved in many biological processes, such as carbon fixation in photosynthetic organisms, biosynthesis of amino acids, ribosomes structure and function. In particular, subcellular localization analysis showed that 43% of the crotonylated proteins were located in the chloroplast. Twenty-nine crotonylation proteins were associated with photosynthesis and functional enrichment that these proteins were associated with the reaction center, photosynthetic electron transport, and ATP synthesis. Based on these results, further studies to expand on the lysine crotonylome analysis were suggested.

Proteome-wide and lysine crotonylation profiling reveals the importance of crotonylation in chrysanthemum (Dendranthema grandiforum) under low-temperature

BACKGROUND

Low-temperature severely affects the growth and development of chrysanthemum which is one kind of ornamental plant well-known and widely used in the world. Lysine crotonylation is a recently identified post-translational modification (PTM) with multiple cellular functions. However, lysine crotonylation under low-temperature stress has not been studied.

RESULTS

Proteome-wide and lysine crotonylation of chrysanthemum at low-temperature was analyzed using TMT (Tandem Mass Tag) labeling, sensitive immuno-precipitation, and high-resolution LC-MS/MS. The results showed that 2017 crotonylation sites were identified in 1199 proteins. Treatment at 4 °C for 24 h and - 4 °C for 4 h resulted in 393 upregulated proteins and 500 downregulated proteins (1.2-fold threshold and P < 0.05). Analysis of biological information showed that lysine crotonylation was involved in photosynthesis, ribosomes, and antioxidant systems. The crotonylated proteins and motifs in chrysanthemum were compared with other plants to obtain orthologous proteins and conserved motifs. To further understand how lysine crotonylation at K136 affected APX (ascorbate peroxidase), we performed a site-directed mutation at K136 in APX. Site-directed crotonylation showed that lysine decrotonylation at K136 reduced APX activity, and lysine complete crotonylation at K136 increased APX activity.

CONCLUSION

In summary, our study comparatively analyzed proteome-wide and crotonylation in chrysanthemum under low-temperature stress and provided insights into the mechanisms of crotonylation in positively regulated APX activity to reduce the oxidative damage caused by low-temperature stress. These data provided an important basis for studying crotonylation to regulate antioxidant enzyme activity in response to low-temperature stress and a new research ideas for chilling-tolerance and freezing-tolerance chrysanthemum molecular breeding.

Global Proteomic Analysis of Lysine Crotonylation in the Plant Pathogen Botrytis cinerea

Lysine crotonylation (Kcr), a recently discovered post-translational modification, plays a key role in the regulation of diverse cellular processes. Botrytis cinerea is a destructive necrotrophic fungal pathogen distributed worldwide with broad ranging hosts. However, the functions of Kcr are unknown in B. cinerea or any other plant fungal pathogens. Here, we comprehensively evaluated the crotonylation proteome of B. cinerea and identified 3967 Kcr sites in 1041 proteins, which contained 9 types of modification motifs. Our results show that although the crotonylation was largely conserved, different organisms contained distinct crotonylated proteins with unique functions. Bioinformatics analysis demonstrated that the majority of crotonylated proteins were distributed in cytoplasm (35%), mitochondria (26%), and nucleus (22%). The identified proteins were found to be involved in various metabolic and cellular processes, such as cytoplasmic translation and structural constituent of ribosome. Particularly, 26 crotonylated proteins participated in the pathogenicity of B. cinerea, suggesting a significant role for Kcr in this process. Protein interaction network analysis demonstrated that many protein interactions are regulated by crotonylation. Furthermore, our results show that different nutritional conditions had a significant influence on the Kcr levels of B. cinerea. These data represent the first report of the crotonylome of B. cinerea and provide a good foundation for further explorations of the role of Kcr in plant fungal pathogens.

Drought stress triggers proteomic changes involving lignin, flavonoids and fatty acids in tea plants

Drought stress triggers a series of physiological and biochemical changes in tea plants. It is well known that flavonoids, lignin and long-chain fatty acids play important roles in drought resistance. However, changes in proteins related to these three metabolic pathways in tea plants under drought stress have not been reported. We analysed the proteomic profiles of tea plants by tandem mass tag and liquid chromatography-tandem mass spectrometry. A total of 4789 proteins were identified, of which 11 and 100 showed up- and downregulation, respectively. The proteins related to the biosynthesis of lignin, flavonoids and long-chain fatty acids, including phenylalanine ammonia lyase, cinnamoyl-CoA reductase, peroxidase, chalcone synthase, flavanone 3-hydroxylase, flavonol synthase, acetyl-CoA carboxylase 1,3-ketoacyl-CoA synthase 6 and 3-ketoacyl-CoA reductase 1, were downregulated. However, the contents of soluble proteins, malondialdehyde, total phenols, lignin and flavonoids in the tea plants increased. These results showed that tea plants might improve drought resistance by inhibiting the accumulation of synthases related to lignin, flavonoids and long-chain fatty acids. The proteomic spectrum of tea plants provides a scientific basis for studying the pathways related to lignin, flavonoid and long-chain fatty acid metabolism in response to drought stress.

Exogenous abscisic acid induces the lipid and flavonoid metabolism of tea plants under drought stress

Abscisic acid (ABA) is an important phytohormone responsible for activating drought resistance, but the regulation mechanism of exogenous ABA on tea plants under drought stress was rarely reported. Here, we analyzed the effects of exogenous ABA on genes and metabolites of tea leaves under drought stress using transcriptomic and metabolomic analysis. The results showed that the exogenous ABA significantly induced the metabolic pathways of tea leaves under drought stress, including energy metabolism, amino acid metabolism, lipid metabolism and flavonoids biosynthesis. In which, the exogenous ABA could clearly affect the expression of genes involved in lipid metabolism and flavonoid biosynthesis. Meanwhile, it also increased the contents of flavone, anthocyanins, flavonol, isoflavone of tea leaves under drought stress, including, kaempferitrin, sakuranetin, kaempferol, and decreased the contents of glycerophospholipids, glycerolipids and fatty acids of tea leaves under drought stress. The results suggested that the exogenous ABA could alleviate the damages of tea leaves under drought stress through inducing the expression of the genes and altering the contents of metabolites in response to drought stress. This study will be helpful to understand the mechanism of resilience to abiotic stress in tea plant and provide novel insights into enhancing drought tolerance in the future.

First nitrosoproteomic profiling deciphers the cysteine S-nitrosylation involved in multiple metabolic pathways of tea leaves

Cysteine S-nitrosylation is a reversible protein post-translational modification and critically regulates the activity, localization and stability of proteins. Tea (Camellia sinensis (L.) O. Kuntze) is one of the most thoroughly studied evergreen crop due to its broad non-alcoholic beverage and huge economic impact in the world. However, little is known about the S-nitrosylome in this plant. Here, we performed a global analysis of cysteine S-nitrosylation in tea leaves. In total, 228 cysteine S-nitrosylation sites were identified in 191 proteins, representing the first extensive data on the S-nitrosylome in tea plants. These S-nitrosylated proteins were located in various subcellular compartments, especially in the chloroplast and cytoplasm. Furthermore, the analysis of functional enrichment and PPI network revealed that the S-nitrosylated proteins were mainly involved in multiple metabolic pathways, including glycolysis, pyruvate metabolism, Calvin cycle and TCA cycle. Overall, this study not only systematically identified the proteins of S-nitrosylation in cysteines of tea leaves, but also laid the solid foundation for further verifying the roles of S-nitrosylation in cysteines of tea plants.

Global Lysine Crotonylation and 2-Hydroxyisobutyrylation in Phenotypically Different Toxoplasma gondii Parasites

Toxoplasma gondii is a unicellular protozoan parasite of the phylum Apicomplexa. The parasite repeatedly goes through a cycle of invasion, division and induction of host cell rupture, which is an obligatory process for proliferation inside warm-blooded animals. It is known that the biology of the parasite is controlled by a variety of mechanisms ranging from genomic to epigenetic to transcriptional regulation. In this study, we investigated the global protein posttranslational lysine crotonylation and 2-hydroxyisobutyrylation of two T. gondii strains, RH and ME49, which represent distinct phenotypes for proliferation and pathogenicity in the host. Proteins with differential expression and modification patterns associated with parasite phenotypes were identified. Many proteins in T. gondii were crotonylated and 2-hydroxyisobutyrylated, and they were localized in diverse subcellular compartments involved in a wide variety of cellular functions such as motility, host invasion, metabolism and epigenetic gene regulation. These findings suggest that lysine crotonylation and 2-hydroxyisobutyrylation are ubiquitous throughout the T. gondii proteome, regulating critical functions of the modified proteins. These data provide a basis for identifying important proteins associated with parasite development and pathogenicity.