Acetylproteomics analyses reveal critical features of lysine-ε-acetylation in Arabidopsis and a role of 14-3-3 protein acetylation in alkaline response

Lysine-ε-acetylation (Kac) is a post-translational modification (PTM) that is critical for metabolic regulation and cell signaling in mammals. However, its prevalence and importance in plants remain to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein lysine acetylation in five representative Arabidopsis organs with 2 ~ 3 biological replicates per organ. A total of 2887 Kac proteins and 5929 Kac sites were identified. This comprehensive catalog allows us to analyze proteome-wide features of lysine acetylation. We found that Kac proteins tend to be more uniformly expressed in different organs, and the acetylation status exhibits little correlation with the gene expression level, indicating that acetylation is unlikely caused by stochastic processes. Kac preferentially targets evolutionarily conserved proteins and lysine residues, but only a small percentage of Kac proteins are orthologous between rat and Arabidopsis. A large portion of Kac proteins overlap with proteins modified by other PTMs including ubiquitination, SUMOylation and phosphorylation. Although acetylation, ubiquitination and SUMOylation all modify lysine residues, our analyses show that they rarely target the same sites. In addition, we found that “reader” proteins for acetylation and phosphorylation, i.e., bromodomain-containing proteins and GRF (General Regulatory Factor)/14-3-3 proteins, are intensively modified by the two PTMs, suggesting that they are main crosstalk nodes between acetylation and phosphorylation signaling. Analyses of GRF6/14-3-3λ reveal that the Kac level of GRF6 is decreased under alkaline stress, suggesting that acetylation represses plant alkaline response. Indeed, K56ac of GRF6 inhibits its binding to and subsequent activation of the plasma membrane H+-ATPase AHA2, leading to hypersensitivity to alkaline stress. These results provide valuable resources for protein acetylation studies in plants and reveal that protein acetylation suppresses phosphorylation output by acetylating GRF/14-3-3 proteins.

Proteomics Readjustment of the Yarrowia lipolytica Yeast in Response to Increased Temperature and Alkaline Stress

Yeasts cope with a wide range of environmental challenges using different adaptive mechanisms. They can prosper at extreme ambient pH and high temperatures; however, their adaptation mechanisms have not been entirely investigated. Previously, we showed the pivotal role and flexibility of the sugar and lipid composition of Yarrowia lipolytica W 29 upon adaptation to unfavorable conditions. In this study, we showed that extreme pH provoked significant changes in the cell wall proteins expression, with an increase in both the chaperones of heat shock protein HSP60 and some other proteins with chaperone functions. The mitochondria activity changes inducing the VDAC and malate dehydrogenase played an essential role in the adaptation, as did the altered carbohydrate metabolism, promoting its shift towards the pyruvate formation rather than gluconeogenesis. The elevated temperature led to changes in the cell wall proteins and chaperones, the induced expression of the proteins involved in the cell structural organization, ribosomal proteins, and the enzymes of formaldehyde degradation. Moreover, the readjustment of the protein composition and amount under combined stress indicated the promotion of catabolic processes related to scavenging the damaged proteins and lipids. Under all of the stress conditions studied, the process of folding, stress resistance, redox adaptation, and oxidative phosphorylation were the dominant pathways. The combined chronic alkaline and heat stress (pH 9.0, 38 °C) led to cross-adaptation, which caused “switching” over the traditional metabolism to the adaptation to the most damaging stress factor, namely the increased temperature.

Validation of Analytical Methods for Tacrolimus Determination in Poly(ε-caprolactone) Nanocapsules and Identification of Drug Degradation Products

The aim of this paper was to use chromatographic tools for validating an analytical method for the tacrolimus (TAC) determination in polymeric nanocapsules and for identifying the drug degradation products after alkaline stress. A rapid Ultra-High-Performance Liquid Chromatography coupled with photo-diode array (UHPLC-PDA) method was successfully performed using the following chromatographic conditions: the Shimadzu Shim-pack XR-ODS III C18 column (100 mm×2.00 mm, 2.2 μm), the mobile phase consisting of methanol and acidified ultrapure water (89:11 v/v), the flow rate of 0.55 mL·min−1, and the ultraviolet (UV) detection at 235 nm. This method was validated as per International Council for Harmonisation (ICH) guidelines. In addition, a TAC forced degradation assay was carried out after alkaline stress and its degradation products were investigated using Liquid Chromatography coupled tandem mass spectroscopy (LC-MS/MS). The calibration curve was linear in the range of 100.0–300.0 μg·mL−1 (r >0.9999). Accuracy was confirmed by the TAC recovery of 96.55 to 98.19%. Precision (intraday and interday) were demonstrated by relative standard deviation lower than 0.89% and 3.25%, respectively. Selectivity and robustness were also proved. The method developed it was successfully applied to quantify TAC from polymeric nanocapsules, showing a high loading efficiency rate (>96.47%). The main drug degradation product observed in a multiple reaction monitoring (MRM) experiment was m/z 844, confirming the susceptibility of TAC under alkaline conditions; this finding was first time described.

Influence of Epichloë bromicola endophytic fungi on secondary metabolites following alkali tolerance improvement in host, Hordeum bogdanii

Purpose: The aim of this study was to investigate how endophytic fungi affect secondary metabolites of H. bogdanii under alkaline stress at different concentrations. It is currently unclear whether the mechanism via which endophytic fungi improve the alkali tolerance of Hordeum bogdanii affects secondary metabolites. Unveiling this knowledge is crucial for understanding the tolerance mechanism of H. bogdanii to alkaline stress. Methods: Endophyte-infected (E+) and endophyte-free (E-) individuals of H. bogdanii were used as materials in this study. Vermiculite was used for plant cultivation and was carried out in the laboratory. After mixed alkali stress treatment, the roots, stems, and leaves of the plants were collected to measure the indicators related to secondary metabolites. Results: The results showed that endophytic fungi significantly increased the contents of phosphorus, polyphenols, and alkaloids, and the activities of polyphenol oxidase and acid phosphatase, and significantly reduced flavonoid content. The content of polyphenols and alkaloids in stems, polyphenol oxidase activity in stems and leaves, and acid phosphatase activity in leaves were significantly affected. In general, endophytic fungi improved the alkali resistance of H. bogdanii by improving the related indicators of secondary metabolites. Conclusions: The findings of this study may aid in amplifying the alkali resistance mechanism of endophytic fungi to H. bogdanii as well as provide insights into improving the alkali resistance of other plants.

Substrate dependent homeostatic control of c-di-AMP synthase (MsDisA) and hydrolase (MsPDE) from Mycobacterium smegmatis

In bacteria, cyclic-di-nucleotide based second messengers regulate various physiological processes including the stress response. For the past few decades, cyclic diadenosine monophosphate (c-di-AMP) is emerging as a crucial second messenger in bacterial world. It being an essential molecule, is implicated in fatty acid metabolism, antibiotic resistance, biofilm formation, virulence and activates the cytosolic pathway of innate immunity in host cell. The level of c-di-AMP is maintained within the cell by the action of two opposing enzymes, namely diadenylate cyclases and phosphodiesterases. However, such kind of c-di-AMP modulation remains to be explored in Mycobacterium smegmatis. Here, we systematically investigate the c-di-AMP synthase (MsDisA) and a hydrolase (MsPDE) from M. smegmatis at different pHs and osmolytic conditions. Our biochemical assays showed that the MsDisA activity is enhanced during the alkaline stress and c-di-AMP is readily produced without any intermediates. At pH 9.4, the MsDisA promoter activity increases significantly, further strengthening this observation. However, under physiological conditions, the activity of MsDisA is moderate with the formation of intermediates. We also observe that the size of MsDisA is significantly increased upon incubation with substrate. To further get deep insights into the structural characteristics, we report a 3.8 Å cryo-EM structure of the MsDisA protein, distinct from the earlier reported structure of DisA from Thermotoga maritima. The domain mutant experiments prove that the N-terminal minimal region can form a functional octamer. Thus, our results reveal how mycobacterial c-di-AMP is biochemically and structurally regulated in response to different environments. Keywords: Mycobacteria, second messengers, stress response, Cyclic-di-AMP, MsDisA, MsPDE, Cryo-EM

Insight Between the Epigenetics and Transcription Responding of Cotton Hypocotyl Cellular Elongation Under Salt-Alkaline Stress

Gossypium barbadense is a cultivated cotton not only known for producing superior fiber but also for its salt and alkaline resistance. Here, we used Whole Genome Bisulfite Sequencing (WGBS) technology to map the cytosine methylation of the whole genome of the G. barbadense hypocotyl at single base resolution. The methylation sequencing results showed that the mapping rates of the three samples were 75.32, 77.54, and 77.94%, respectively. In addition, the Bisulfite Sequence (BS) conversion rate was 99.78%. Approximately 71.03, 53.87, and 6.26% of the cytosine were methylated at CG, CHG, and CHH sequence contexts, respectively. A comprehensive analysis of DNA methylation and transcriptome data showed that the methylation level of the promoter region was a positive correlation in the CHH context. Saline-alkaline stress was related to the methylation changes of many genes, transcription factors (TFs) and transposable elements (TEs), respectively. We explored the regulatory mechanism of DNA methylation in response to salt and alkaline stress during cotton hypocotyl elongation. Our data shed light into the relationship of methylation regulation at the germination stage of G. barbadense hypocotyl cell elongation and salt-alkali treatment. The results of this research help understand the early growth regulation mechanism of G. barbadense in response to abiotic stress.