The Scope, Functions, and Dynamics of Posttranslational Protein Modifications

Waves of regulated protein expression and phosphorylation rewire the proteome to drive gametogenesis in budding yeast

Sexually reproducing eukaryotes employ a developmentally regulated cell division program-meiosis-to generate haploid gametes from diploid germ cells. To understand how gametes arise, we generated a proteomic census encompassing the entire meiotic program of budding yeast. We found that concerted waves of protein expression and phosphorylation modify nearly all cellular pathways to support meiotic entry, meiotic progression, and gamete morphogenesis. Leveraging this comprehensive resource, we pinpointed dynamic changes in mitochondrial components and showed that phosphorylation of the FoF1-ATP synthase complex is required for efficient gametogenesis. Furthermore, using cryoET as an orthogonal approach to visualize mitochondria, we uncovered highly ordered filament arrays of Ald4ALDH2, a conserved aldehyde dehydrogenase that is highly expressed and phosphorylated during meiosis. Notably, phosphorylation-resistant mutants failed to accumulate filaments, suggesting that phosphorylation regulates context-specific Ald4ALDH2 polymerization. Overall, this proteomic census constitutes a broad resource to guide the exploration of the unique sequence of events underpinning gametogenesis.

Lysine acetylproteome analysis reveals the lysine acetylation in developing fruit and a key acetylated protein involved in sucrose accumulation in Rosa roxburghii Tratt

Lysine acetylation is a common post-translational modification of proteins in plants. Rosa roxburghii Tratt. is an economically important fruit tree known for its high nutritional value. However, the characteristics of acetylome-related proteins during fruit development in this crop remain unknown. This study aimed to explore the global acetylproteome of R. roxburghii fruit to identify key lysine-acetylated proteins associated with its quality traits. A total of 4280 acetylated proteins were identified, among them, 981 proteins exhibited differential acetylation (DA) while 19 proteins showed increased acetylation level consistently on individual sites. Functional classification revealed that these DA proteins were primarily associated with central metabolic pathways, carbohydrate metabolism, terpenoids and polyketides metabolism, lipid metabolism, and amino acid metabolism, highlighting the importance of lysine acetylation in fruit quality formation. Notably, the most significant up-regulated acetylation occurred in sucrose synthase (SuS1), a key enzyme in sucrose biosynthesis. Enzyme assays, RNA-seq and proteome analysis indicated that SuS activity, which was independent of its transcriptome and proteome level, may be enhanced by up-acetylation, ultimately increasing sucrose accumulation. Thus, these findings offer a better understanding of the global acetylproteome of R. roxburghii fruit, while also uncover a novel mechanism of acetylated SuS-mediated in sucrose metabolism in plant. SIGNIFICANCE: Rosa roxburghii Tratt. is an important horticultural crop whose commercial value is closely linked to its fruit quality. Acetylation modification is a post-translational mechanism observed in plants, which regulates the physiological functions and metabolic fluxes involved in various biological processes. The regulatory mechanism of lysine acetylation in the fruit quality formation in perennial woody plants has not been fully elucidated, while most of the research has primarily focused on annual crops. Therefore, this study, for the first time, uses Rosaceae fruits as the research material to elucidate the regulatory role of lysine-acetylated proteins in fruit development, identify key metabolic processes influencing fruit quality formation, and provide valuable insights for cultivation strategies.

Exploring Ubiquitin-specific proteases as therapeutic targets in Glioblastoma

Glioblastoma (GB) remains a formidable challenge and requires new treatment strategies. The vital part of the Ubiquitin-proteasome system (UPS) in cellular regulation has positioned it as a potentially crucial target in GB treatment, given its dysregulation oncolines. The Ubiquitin-specific proteases (USPs) in the UPS system were considered due to the garden role in the cellular processes associated with oncolines and their vital function in the apoptotic process, cell cycle regulation, and autophagy. The article provides a comprehensive summary of the evidence base for targeting USPs as potential factors for neoplasm treatment. The review considers the participation of the UPS system in the development, resulting in the importance of p53, Rb, and NF-κB, and evaluates specific goals for therapeutic administration using midnight proteasomal inhibitors and small molecule antagonists of E1 and E2 enzymes. Despite the slowed rate of drug creation, recent therapeutic discoveries based on USP system dynamics hold promise for specialized therapies. The review concludes with an analysis of future wanderers and the feasible effects of targeting USPs on personalized GB therapies, which can improve patient hydration in this current and unattractive therapeutic landscape. The manuscript emphasizes the possibility of USP oncogene therapy as a promising alternative treatment line for GB. It stresses the direct creation of research on the medical effectiveness of the approach.

Comprehensive Proteome and Acetylome Analysis of Needle Senescence in Larix gmelinii

Leaf senescence is essential for the growth and development of deciduous trees in the next season. Larix gmelinii, a deciduous coniferous tree, exhibits its most distinctive feature by turning yellow in the autumn and eventually shedding its leaves, resulting in significant changes in its appearance during the fall. Lysine acetylation plays an important role in diverse cellular processes; however, limited knowledge is available regarding acetylations in the needle senescence of L. gmelinii. In this study, the proteomics and acetylated modification omics of two phenotypic leaves, yellow and green (senescent and non-senescent) needles, were analyzed before autumn defoliation. In total, 5022 proteins and 4469 unique acetylation sites in 2414 lysine acylated proteins were identified, and this resulted in the discovery of 1335 differentially expressed proteins (DEPs) and 605 differentially expressed acetylated proteins (DAPs) in yellow versus green needles. There are significant differences between the proteome and acetylome; only 269 proteins were found to be DEP and DAP, of which 136 proteins were consistently expressed in both the DEP and DAP, 91 proteins were upregulated, and 45 proteins were down-regulated. The DEPs participate in the metabolism of starch and sucrose, while the DAPs are involved in glycolysis and the tricarboxylic acid cycle. Among them, DEPs underwent significant changes in glycolysis and citric acid cycling. Most of the enzymes involved in glycolysis and the citrate cycle were acetylated. DAPs were down-regulated in glycolysis and up-regulated in the citrate cycle. In all, the results of this study reveal the important role of lysine acetylation in the senescence of L. gmelinii needles and provide a new perspective for understanding the molecular mechanism of leaf senescence and tree seasonal growth.

What Can Be Learned from the Partitioning Behavior of Proteins in Aqueous Two-Phase Systems?

This review covers the analytical applications of protein partitioning in aqueous two-phase systems (ATPSs). We review the advancements in the analytical application of protein partitioning in ATPSs that have been achieved over the last two decades. Multiple examples of different applications, such as the quality control of recombinant proteins, analysis of protein misfolding, characterization of structural changes as small as a single-point mutation, conformational changes upon binding of different ligands, detection of protein-protein interactions, and analysis of structurally different isoforms of a protein are presented. The new approach to discovering new drugs for a known target (e.g., a receptor) is described when one or more previous drugs are already available with well-characterized biological efficacy profiles.

The mechanism of USP43 in the development of tumor: a literature review

Ubiquitination of the proteins is crucial for governing protein degradation and regulating fundamental cellular processes. Deubiquitinases (DUBs) have emerged as significant regulators of multiple pathways associated with cancer and other diseases, owing to their capacity to remove ubiquitin from target substrates and modulate signaling. Consequently, they represent potential therapeutic targets for cancer and other life-threatening conditions. USP43 belongs to the DUBs family involved in cancer development and progression. This review aims to provide a comprehensive overview of the existing scientific evidence implicating USP43 in cancer development. Additionally, it will investigate potential small-molecule inhibitors that target DUBs that may have the capability to function as anti-cancer medicines.

Ethylene insensitive 2 (EIN2) destiny shaper: The post-translational modification

PTMs (Post-Translational Modifications) of proteins facilitate rapid modulation of protein function in response to various environmental stimuli. The EIN2 (Ethylene Insensitive 2) protein is a core regulatory of the ethylene signaling pathway. Recent findings have demonstrated that PTMs, including protein phosphorylation, ubiquitination, and glycosylation, govern EIN2 trafficking, subcellular localization, stability, and physiological roles. The cognition of multiple PTMs in EIN2 underscores the stringent regulation of protein. Consequently, a thorough review of the regulatory role of PTMs in EIN2 functions will improve our profound comprehension of the regulation mechanism and various physiological processes of EIN2-mediated signaling pathways. This review discusses the evolution, functions, structure and characteristics of EIN2 protein in plants. Additionally, this review sheds light on the progress of protein ubiquitination, phosphorylation, O-Glycosylation in the regulation of EIN2 functions, and the unresolved questions and future perspectives.

An Escherichia coli-Based Phosphorylation System for Efficient Screening of Kinase Substrates

Posttranslational modifications (PTMs), particularly phosphorylation, play a pivotal role in expanding the complexity of the proteome and regulating diverse cellular processes. In this study, we present an efficient Escherichia coli phosphorylation system designed to streamline the evaluation of potential substrates for Arabidopsis thaliana plant kinases, although the technology is amenable to any. The methodology involves the use of IPTG-inducible vectors for co-expressing kinases and substrates, eliminating the need for radioactive isotopes and prior protein purification. We validated the system's efficacy by assessing the phosphorylation of well-established substrates of the plant kinase SnRK1, including the rat ACETYL-COA CARBOXYLASE 1 (ACC1) and FYVE1/FREE1 proteins. The results demonstrated the specificity and reliability of the system in studying kinase-substrate interactions. Furthermore, we applied the system to investigate the phosphorylation cascade involving the A. thaliana MKK3-MPK2 kinase module. The activation of MPK2 by MKK3 was demonstrated to phosphorylate the Myelin Basic Protein (MBP), confirming the system's ability to unravel sequential enzymatic steps in phosphorylation cascades. Overall, this E. coli phosphorylation system offers a rapid, cost-effective, and reliable approach for screening potential kinase substrates, presenting a valuable tool to complement the current portfolio of molecular techniques for advancing our understanding of kinase functions and their roles in cellular signaling pathways.

Structure-guided discovery of protein and glycan components in native mastigonemes

Mastigonemes, the hair-like lateral appendages lining cilia or flagella, participate in mechanosensation and cellular motion, but their constituents and structure have remained unclear. Here, we report the cryo-EM structure of native mastigonemes isolated from Chlamydomonas at 3.0 Å resolution. The long stem assembles as a super spiral, with each helical turn comprising four pairs of anti-parallel mastigoneme-like protein 1 (Mst1). A large array of arabinoglycans, which represents a common class of glycosylation in plants and algae, is resolved surrounding the type II poly-hydroxyproline (Hyp) helix in Mst1. The EM map unveils a mastigoneme axial protein (Mstax) that is rich in heavily glycosylated Hyp and contains a PKD2-like transmembrane domain (TMD). Mstax, with nearly 8,000 residues spanning from the intracellular region to the distal end of the mastigoneme, provides the framework for Mst1 assembly. Our study provides insights into the complexity of protein and glycan interactions in native bio-architectures.

Mesenteric artery smooth muscle cells from hypertensive rats have increased microtubule acetylation

The dynamic nature of the microtubule network is dependent in part by post-translational modifications (PTMs) - particularly through acetylation, which stabilizes the microtubule network. Whether PTMs of the microtubule network in vascular smooth muscle cells (VSMCs) contribute to the pathophysiology of hypertension is unknown. The aim of this study was to determine the acetylated state of the microtubule network in the mesenteric arteries of spontaneously hypertensive rats (SHR). Experiments were performed on male normotensive rats and SHR mesenteric arteries. Western blotting and mass spectrometry determined changes in tubulin acetylation. Wire myography was used to investigate the effect of tubacin on isoprenaline-mediated vasorelaxations. Isolated cells from normotensive rats were used for scanning ion conductance microscopy (SICM). Mass spectrometry and Western blotting showed that tubulin acetylation is increased in the mesenteric arteries of the SHR compared with normotensive rats. Tubacin enhanced the β-adrenoceptor-mediated vasodilatation by isoprenaline when the endothelium was intact, but attenuated relaxations when the endothelium was denuded or nitric oxide production was inhibited. By pre-treating vessels with colchicine to disrupt the microtubule network, we were able to confirm that the effects of tubacin were microtubule-dependent. Using SICM, we examined the cell surface Young's modulus of VSMCs, but found no difference in control, tubacin-treated, or taxol-treated cells. Acetylation of tubulin at Lys40 is elevated in mesenteric arteries from the SHR. Furthermore, this study shows that tubacin has an endothelial-dependent bimodal effect on isoprenaline-mediated vasorelaxation.

The role of N-terminal phosphorylation of DGK-θ

Diacylglycerol kinases (DGKs) are lipid kinases that mediate the phosphorylation of diacylglycerol (DAG) leading to the production of phosphatidic acid (PtdOH). To examine the role of phosphorylation on DGK-θ, we first identified the phosphorylated sites on endogenous DGK-θ from mouse brain and found four sites: S15, S17, which we refer to phosphomotif-1 sites, and S22 and S26 which we refer to as phosphomotif-2 sites. This study focused on the role of these phosphorylated sites on enzyme activity, membrane binding, thermal stability, and cellular half-life of DGK-θ. After generating a construct devoid of all non-catalytic phosphorylation sites (4A), we also generated other constructs to mimic phosphorylation of these residues by mutating them to glutamate (E). Our data demonstrate that an increase in membrane affinity requires the phosphorylation of all four endogenous sites as the phosphomimetic 4E but not other phosphomimietics. Furthermore, 4E also shows an increase in basal activity as well as an increase in the Syt1-induced activity compared to 4A. It is noteworthy that these phosphorylations had no effect on the thermal stability or cellular half-life of this enzyme. Interestingly, when only one phosphorylation domain (phosphomotif-1 or phosphomotif-2) contained phosphomimetics (S15E/S17E or S22E/S26E), the basal activity was also increased but membrane binding affinity was not increased. Furthermore, when only one residue in each domain mimicked an endogenous phosphorylated serine (S15E/S22E or S17E/S26E), the Syt1-induced activity as well as membrane binding affinity decreased relative to 4A. These results indicate that these endogenous phosphorylation sites contribute differentially to membrane binding and enzymatic activity.

Regulation of Disease-Resistance Genes against CWMV Infection by NbHAG1-Mediated H3K36ac

Post-translational modification of proteins plays a critical role in plant-pathogen interactions. Here, we demonstrate in Nicotiana benthamiana that knockout of NbHAG1 promotes Chinese wheat mosaic virus (CWMV) infection, whereas NbHAG1 overexpression inhibits infection. Transcriptome sequencing indicated that a series of disease resistance-related genes were up-regulated after overexpression of NbHAG1. In addition, cleavage under targets and tagmentation (Cut&Tag)-qPCR results demonstrated that NbHAG1 may activate the transcription of its downstream disease-resistance genes by facilitating the acetylation level of H3K36ac. Therefore, we suggest that NbHAG1 is an important positive regulator of resistance to CWMV infestation.

OsCSN2 orchestrates Oryza sativa L. growth and development through modulation of the GA and BR pathways

The COP9 signalosome (CSN) is a conserved protein complex found in higher eukaryotes, consisting of eight subunits, and it plays a crucial role in regulating various processes of plant growth and development. Among these subunits, CSN2 is one of the most conserved components within the COP9 signalosome complex. Despite its prior identification in other species, its specific function in Oryza sativa L. (Rice) has remained poorly understood. In this study, we investigated the role of CSN2 in rice using gene editing CRISPR/Cas9 technology and overexpression techniques. We created two types of mutants: the oscsn2 mutant and the OsCSN2-OE mutant, both in the background of rice, and also generated point mutants of OsCSN2 (OsCSN2K64E, OsCSN2K67E, OsCSN2K71E and OsCSN2K104E) to further explore the regulatory function of OsCSN2. Phenotypic observation and gene expression analysis were conducted on plants from the generated mutants, tracking their growth from the seedling to the heading stages. The results showed that the loss and modification of OsCSN2 had limited effects on plant growth and development during the early stages of both the wild-type and mutant plants. However, as the plants grew to 60 days, significant differences emerged. The OsCSN2 point mutants exhibited increased tillering compared to the OsCSN2-OE mutant plants, which were already at the tillering stage. On the other hand, the OsCSN2 point mutant had already progressed to the heading and flowering stages, with the shorter plants. These results, along with functional predictions of the OsCSN2 protein, indicated that changes in the 64th, 67th, 71st, and 104th amino acids of OsCSN2 affected its ubiquitination site, influencing the ubiquitination function of CSN and consequently impacting the degradation of the DELLA protein SLR1. Taken together, it can be speculated that OsCSN2 plays a key role in GA and BR pathways by influencing the functional regulation of the transcription factor SLR1 in CSN, thereby affecting the growth and development of rice and the number of tillers.

Protein methylation characterization using NMR without isotopic labeling

Protein methylation is crucial in epigenetics, and targeting the involved methyltransferases shows great potential for therapeutic intervention with several inhibitors in clinical trials for oncology indications. Therefore, characterization of protein methylation is essential for understanding the methyltransferase function and discovering chemical inhibitors and antagonists. While NMR has been used to measure methylation rates, isotopic labeling of protein or methyl donors can be costly and cannot characterize demethylation of proteins extracted from natural sources. Our method employs a four-quantum filter 1H-13C experiment that selectively detects methyl groups, providing a simple way to characterize methylation and demethylation features of methyltransferases and demethylases, respectively, without requiring isotopic labeling. In our experiments, we successfully observed the methylation of H3 under lysate from various cells and tissues of mice with cancerous growth. The results revealed that H3 undergoes both mono- and dimethylation in all the tested lysates, but at varying rates and degrees. Significantly lower H3 methylation rates and levels were observed in both cervical tumor and breast tumor lysates compared with the corresponding cancerous cells and healthy cells lysates. These findings highlight the variability of histone H3 methylation patterns among healthy cells, cancerous cells, tumor tissues, and different tumor types, and suggest that this method has great potential in facilitating the development of effective interventions against these diseases. By characterizing the methylation features of suspected tumors or areas of concern, it provides valuable insights into the underlying mechanisms of cancer development and aids in identifying potential targets for therapeutic interventions.

A unified approach to dissecting biphasic responses in cell signaling

Biphasic responses are encountered at all levels in biological systems. At the cellular level, biphasic dose-responses are widely encountered in cell signaling and post-translational modification systems and represent safeguards against overactivation or overexpression of species. In this paper, we provide a unified theoretical synthesis of biphasic responses in cell signaling systems, by assessing signaling systems ranging from basic biochemical building blocks to canonical network structures to well-characterized exemplars on one hand, and examining different types of doses on the other. By using analytical and computational approaches applied to a range of systems across levels (described by broadly employed models), we reveal (i) design principles enabling the presence of biphasic responses, including in almost all instances, an explicit characterization of the parameter space (ii) structural factors which preclude the possibility of biphasic responses (iii) different combinations of the presence or absence of enzyme-biphasic and substrate-biphasic responses, representing safeguards against overactivation and overexpression, respectively (iv) the possibility of broadly robust biphasic responses (v) the complete alteration of signaling behavior in a network due to biphasic interactions between species (biphasic regulation) (vi) the propensity of different co-existing biphasic responses in the Erk signaling network. These results both individually and in totality have a number of important consequences for systems and synthetic biology.

Large-scale phosphoproteome analysis in wheat seedling leaves provides evidence for extensive phosphorylation of regulatory proteins during CWMV infection

BACKGROUND

Chinese wheat mosaic virus (CWMV) often causes severe damage to wheat (Triticum aestivum L.) growth and yield. It is well known that a successful infection in plants depends on a complex interaction between the host plant and the pathogen. Post-translational modification (PTM) of proteins is considered to be one of the main processes that decides the outcome of the plant-pathogen arms race during this interaction. Although numerous studies have investigated PTM in various organisms, there has been no large-scale phosphoproteomic analysis of virus-infected wheat plants. We therefore aimed to investigate the CWMV infection-induced phosphoproteomics changes in wheat by high-resolution liquid chromatography-tandem mass spectroscopy (LC-MS/MS) using affinity-enriched peptides followed by comprehensive bioinformatics analysis.

RESULTS

Through this study, a total of 4095 phosphorylation sites have been identified in 1968 proteins, and 11.6% of the phosphorylated proteins exhibited significant changes (PSPCs) in their phosphorylation levels upon CWMV infection. The result of Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that most of the PSPCs were associated with photosynthesis, plant-pathogen interactions, and MAPK signaling pathways. The protein-protein interaction (PPI) network analysis result showed that these PSPCs were mainly participated in the regulation of biosynthesis and metabolism, protein kinase activities, and transcription factors. Furthermore, the phosphorylation levels of TaChi1 and TaP5CS, two plant immunity-related enzymes, were significantly changed upon CWMV infection, resulting in a significant decrease in CWMV accumulation in the infected plants.

CONCLUSIONS

Our results indicate that phosphorylation modification of protein plays a critical role in wheat resistance to CWMV infection. Upon CWMV infection, wheat plants will regulate the levels of extra- and intra-cellular signals and modifications of enzyme activities via protein phosphorylation. This novel information about the strategies used by wheat to resist CWMV infection will help researchers to breed new CWMV-resistant cultivars and to better understand the arms race between wheat and CWMV.

PLK1 maintains DNA methylation and cell viability by regulating phosphorylation-dependent UHRF1 protein stability

PLK1 is a key serine/threonine kinase as well as a master mitotic regulator, but it has never been reported that PLK1 regulates DNA methylation. In the present study, we for the first time found that PLK1 inhibition disrupted global DNA methylation and elevated the expression level of tumor suppressor genes. Mechanistically, we found that PLK1 interacts UHRF1 protein to induce its phosphorylation at serine 265. Phosphorylation is required for the maintenance of UHRF1 protein stability by recruiting a deubiquitinase USP7. Conversely, PLK1 inhibition decreases UHRF1 protein interaction with USP7 and activates the ubiquitin-proteasome pathway, thereby accelerating UHRF1 protein degradation. UHRF1 degradation decreases the recruitment of DNMT1 to chromatin, and decreases the level of genome-wide DNA methylation, thereby elevating the expression of tumor suppressor genes and decreasing cell viability. We here presented the first report on the novel role of PLK1 in DNA methylation maintenance through UHRF1-DNMT1 pathway, and revealed a novel anticancer mechanism of PLK1 inhibitors.

SUMOylation of yeast Pso2 enhances its translocation and accumulation in the mitochondria and suppresses methyl methanesulfonate-induced mitochondrial DNA damage

Saccharomyces cerevisiae Pso2/SNM1 is essential for DNA interstrand crosslink (ICL) repair; however, its mechanism of action remains incompletely understood. While recent work has revealed that Pso2/Snm1 is dual-localized in the nucleus and mitochondria, it remains unclear whether cell-intrinsic and -extrinsic factors regulate its subcellular localization and function. Herein, we show that Pso2 undergoes ubiquitination and phosphorylation, but not SUMOylation, in unstressed cells. Unexpectedly, we found that methyl methanesulfonate (MMS), rather than ICL-forming agents, induced robust SUMOylation of Pso2 on two conserved residues, K97 and K575, and that SUMOylation markedly increased its abundance in the mitochondria. Reciprocally, SUMOylation had no discernible impact on Pso2 translocation to the nucleus, despite the presence of steady-state levels of SUMOylated Pso2 across the cell cycle. Furthermore, substitution of the invariant residues K97 and K575 by arginine in the Pso2 SUMO consensus motifs severely impaired SUMOylation and abolished its translocation to the mitochondria of MMS-treated wild type cells, but not in unstressed cells. We demonstrate that whilst Siz1 and Siz2 SUMO E3 ligases catalyze Pso2 SUMOylation, the former plays a dominant role. Notably, we found that the phenotypic characteristics of the SUMOylation-defective mutant Pso2K97R/K575R closely mirrored those observed in the Pso2Δ petite mutant. Additionally, leveraging next-generation sequencing analysis, we demonstrate that Pso2 mitigates MMS-induced damage to mitochondrial DNA (mtDNA). Viewed together, our work offers previously unknown insights into the link between genotoxic stress-induced SUMOylation of Pso2 and its preferential targeting to the mitochondria, as well as its role in attenuating MMS-induced mtDNA damage.

Ubiquitylome analysis reveals the involvement of ubiquitination in the cold responses of banana seedling leaves

Low temperature is a crucial environmental factor limiting the productivity and distribution of banana. Ubiquitination (Kub) is one of the main posttranslational modifications (PTMs) involved in plant responses to abiotic stresses. However, little information is available on the effects of Kub on banana under cold stress. In this study, we used label-free quantification (LFQ) to identify changes in the protein expression and Kub levels in banana seedling leaves after chilling treatment. In total, 4156 proteins, 1089 ubiquitinated proteins and 2636 Kub sites were quantified. Western blot assays showed that Kub was abundant in leaves after low-temperature treatment. Our results show that the proteome and ubiquitylome were negatively correlated, indicating that Kub could be involved in the degradation of proteins in banana after chilling treatment. Based on bioinformatics analysis, low-temperature stress-related signals and metabolic pathways such as cold acclimation, glutathione metabolism, calcium signaling, and photosynthesis signaling were identified. In addition, we found that transcription factors and chromatin remodeling factors related to low-temperature stress were ubiquitinated. Overall, our work presents the first systematic analysis of the Kub proteome in banana under cold stress and provides support for future studies on the regulatory mechanisms of Kub during the cold stress response in plants. SIGNIFICANCE: Banana is a typical tropical fruit tree with poor low-temperature tolerance,however, the role of PTMs such as Kub in the cold response of banana remains unclear. This study highlights the fact that the effects of low-temperature on proteome and ubiquitylome in the banana seedling leaves, we discussed the correlation between transcriptome and proteome, ubiquitylome and proteome, and we analyzed the expression and the changes of ubiquitination levels of low-temperature related proteins and pathway after chilling treatment, and we found that transcription factors and chromatin remodeling factors related to low-temperature stress were ubiquitinated. This study provides new insights into the ubiquitination pathway of banana under cold stress.

Proteomics profiling and lysine malonylation analysis in primary Sjogren's syndrome

Primary Sjogren's Syndrome (pSS) is a chronic autoimmune disease, with unclear pathogenies. Lysine-malonylation (Kmal) as a novel post-translational modification (PTMs) was found associated with metabolic, immune, and inflammatory processes. For purpose of investigating the proteomic profile and functions of kmal in pSS, liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based analysis and bioinformatics analysis are performed based on twenty-eight pSS patients versus twenty-seven healthy controls (HCs). A total of 331 down-regulated proteins and 289 up-regulated proteins are observed in differentially expressed proteins (DEPs) of pSS. We discover the expression of transforming growth factor beta-1 (TGFB1) and CD40 ligand downregulate which enriches in the inflammatory associated pathway. Expression of signal transducer and activator of transcription 1-alpha/beta (STAT1) show upregulation and enrich in type I interferon signaling pathway and IL-27-mediated signaling pathway. In differentially malonylated proteins (DMPs) of pSS, we identify 3 proteins are down-regulated in 7 sites and 18 proteins are up-regulated in 19 sites. Expression of malonylated integrin-linked kinase (ILK) significantly enrich in the focal adhesion pathway. Together, our data provide evidence that downregulation of TGFB1 and CD40LG play a critical role in the inflammatory process of pSS, while upregulation of STAT1 may be associated with IL-27 immunity and pSS immune dysfunction. Moreover, kmal modification at the kinase domain of ILK may destabilize ILK that thus contributing to pSS pathogenies by regulating the focal adhesion pathway. SIGNIFICANCE: Our research offered the first characterization of Kmal, a newly identified form of lysine acylation in pSS, as well as proteomic data on individuals with pSS. In this study, we found that several key DMPs were associated with focal adhesion pathway, which contributes to the development of pSS. The present results provide an informative dataset for the future exploration of Kmal in pSS.

USP32 deubiquitinase: cellular functions, regulatory mechanisms, and potential as a cancer therapy target

An essential protein regulatory system in cells is the ubiquitin-proteasome pathway. The substrate is modified by the ubiquitin ligase system (E1-E2-E3) in this pathway, which is a dynamic protein bidirectional modification regulation system. Deubiquitinating enzymes (DUBs) are tasked with specifically hydrolyzing ubiquitin molecules from ubiquitin-linked proteins or precursor proteins and inversely regulating protein degradation, which in turn affects protein function. The ubiquitin-specific peptidase 32 (USP32) protein level is associated with cell cycle progression, proliferation, migration, invasion, and other cellular biological processes. It is an important member of the ubiquitin-specific protease family. It is thought that USP32, a unique enzyme that controls the ubiquitin process, is closely linked to the onset and progression of many cancers, including small cell lung cancer, gastric cancer, breast cancer, epithelial ovarian cancer, glioblastoma, gastrointestinal stromal tumor, acute myeloid leukemia, and pancreatic adenocarcinoma. In this review, we focus on the multiple mechanisms of USP32 in various tumor types and show that USP32 controls the stability of many distinct proteins. Therefore, USP32 is a key and promising therapeutic target for tumor therapy, which could provide important new insights and avenues for antitumor drug development. The therapeutic importance of USP32 in cancer treatment remains to be further proven. In conclusion, there are many options for the future direction of USP32 research.

Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet

The most extreme environments are the most vulnerable to transformation under a rapidly changing climate. These ecosystems harbor some of the most specialized species, which will likely suffer the highest extinction rates. We document the steepest temperature increase (2010-2021) on record at altitudes of above 4,000 m, triggering a decline of the relictual and highly adapted moss Takakia lepidozioides. Its de-novo-sequenced genome with 27,467 protein-coding genes includes distinct adaptations to abiotic stresses and comprises the largest number of fast-evolving genes under positive selection. The uplift of the study site in the last 65 million years has resulted in life-threatening UV-B radiation and drastically reduced temperatures, and we detected several of the molecular adaptations of Takakia to these environmental changes. Surprisingly, specific morphological features likely occurred earlier than 165 mya in much warmer environments. Following nearly 400 million years of evolution and resilience, this species is now facing extinction.

Histone deacetylase III interactions with BK polyomavirus large tumor antigen may affect protein stability

BACKGROUND

Human polyomavirus BK (BKPyV) causes associated nephropathy and contributes to urinary tract cancer development in renal transplant recipients. Large tumor antigen (LT) is an early protein essential in the polyomavirus life cycle. Protein acetylation plays a critical role in regulating protein stability, so this study investigated the acetylation of the BKPyV LT protein.

METHODS

The BKPyV LT nucleotide was synthesized, and the protein was expressed by transfection into permissive cells. The BKPyV LT protein was immunoprecipitated and subjected to LC-MS/MS analysis to determine the acetylation residues. The relative lysine was then mutated to arginine in the LT nucleotide and BKPyV genome to analyze the role of LT lysine acetylation in the BKPyV life cycle.

RESULTS

BKPyV LT acetylation sites were identified at Lys3 and Lys230 by mass spectrometry. HDAC3 and HDAC8 and their deacetylation activity are required for BKPyV LT expression. In addition, mutations of Lys3 and Lys230 to arginine increased LT expression, and the interaction of HDAC3 and LT was confirmed by coimmunoprecipitation.

CONCLUSIONS

HDAC3 is a newly identified protein that interacts with BKPyV LT, and LT acetylation plays a vital role in the BKPyV life cycle.

Acetyl-Proteomic Profiling of Sorghum bicolor Seedlings after Chitin Treatment Reveals the Involvement of Acetylated Chlorophyll a/b Binding Proteins in the Innate Immune Response

Plant pathogen-associated molecular pattern-triggered immunity (PTI) is affected by post-translational modifications, but the role of acetylation in the PTI responses of Sorghum bicolor remains unclear. In this study, a comprehensive acetyl-proteomic analysis was performed on sorghum seedlings treated with chitin based on label-free protein quantification. Chitin rapidly induced 15 PTI-related genes and 5 defense enzymes. Acetylation was upregulated in sorghum after the chitin treatment, and 579, 895, and 929 acetylated proteins, peptides, and sites, respectively, were identified using high-performance liquid chromatography-tandem mass spectrometry. Acetylation and expression of chlorophyll a/b binding proteins (Lhcs) were significantly upregulated, and they were localized in chloroplasts. Additionally, we found that the expression of Lhcs in vivo enhanced chitin-mediated acetylation. The findings of this study provide a comprehensive assessment of the lysine acetylome in sorghum and a foundation for future study into the regulatory mechanisms of acetylation during chlorophyll synthesis.

Discovery of benzofuran-2-carboxylic acid derivatives as lymphoid tyrosine phosphatase (LYP) inhibitors for cancer immunotherapy

Lymphoid-tyrosine phosphatase (LYP) is mainly expressed in the immune system and plays an important role in the T-cell receptor (TCR) signaling pathway and tumor immunity. Herein, we identify benzofuran-2-carboxylic acid as a potent pTyr mimic and design a new series of new LYP inhibitors. The most active compound, D34 and D14, reversibly inhibits LYP (K_i = 0.93 μM and 1.34 μM) and possess a certain degree of selectivity toward other phosphatases. Meanwhile, D34 and D14 regulate the TCR signaling by specifically inhibiting LYP. In particular, D34 and D14 significantly suppress tumor growth in an MC38 syngeneic mouse model by boosting antitumor immunity, including activation of T-cell and inhibition of M2 macrophage polarization. Moreover, treatment of D34 or D14 upregulate PD-1/PD-L1 expression, which can be leveraged with PD-1/PD-L1 inhibition to augment immunotherapy. In summary, our study demonstrates the feasibility of targeting LYP for cancer immunotherapy and provides new lead compounds for further drug development.

Deciphering the Atlas of Post-Translational Modification in Sugarcane

In plants, lysine acetylation (Kac), 2-hydroxyisobutyrylation (Khib), and lysine lactylation (Kla), the three new types of post-translational modification (PTM), play very important roles in growth, development, and resistance to adverse environmental stresses. Herein, we report the first global acetylome, 2-hydroxyisobutyrylome, and lactylome in sugarcane. A total of 8573 Kac, 4637 Khib, and 215 Kla sites across 3903, 1507, and 139 modified proteins were identified. Besides, homology analyses revealed the Kac, Khib, and Kla sites on histones were conserved between sugarcane and rice or poplar. Functional annotations demonstrated that the Kac, Khib, and Kla proteins were mainly involved in energy metabolism. In addition, a number of modified transcription factors and stress-related proteins, which were constitutively expressed in different tissues of sugarcane and induced by drought, cold or Sporisorium scitamineum stress, were identified. Finally, a proposed working mode on how PTM functions in sugarcane was depicted. We thus concluded that PTM should play a role in sugarcane growth, development, and response to biotic and abiotic stresses, but the mechanisms require further investigation. The present study provided the all-new comprehensive profile of proteins Kac, Khib, and Kla and a new perspective to understand the molecular mechanisms of protein PTMs in sugarcane.

Anthocyanins distribution, transcriptional regulation, epigenetic and post-translational modification in fruits

Anthocyanins have indispensable functions in plant resistance, human health, and fruit coloring, which arouse people's favorite. It has been reported that anthocyanins are widely found in fruits, and can be affected by numerous factors. In this review, we systematically summarize anthocyanin functions, classifications, distributions, biosynthesis, decoration, transportation, transcriptional regulation, DNA methylation, and post-translational regulation in fruits.

Targeting Peptides: The New Generation of Targeted Drug Delivery Systems

Peptides can act as targeting molecules, analogously to oligonucleotide aptamers and antibodies. They are particularly efficient in terms of production and stability in physiological environments; in recent years, they have been increasingly studied as targeting agents for several diseases, from tumors to central nervous system disorders, also thanks to the ability of some of them to cross the blood-brain barrier. In this review, we will describe the techniques employed for their experimental and in silico design, as well as their possible applications. We will also discuss advancements in their formulation and chemical modifications that make them even more stable and effective. Finally, we will discuss how their use could effectively help to overcome various physiological problems and improve existing treatments.

Inhibition of SIZ1-mediated SUMOylation of HOOKLESS1 promotes light-induced apical hook opening in Arabidopsis

The apical hook protects cotyledons and the shoot apical meristem from mechanical injuries during seedling emergence from the soil. HOOKLESS1 (HLS1) is a central regulator of apical hook development, as a terminal signal onto which several pathways converge. However, how plants regulate the rapid opening of the apical hook in response to light by modulating HLS1 function remains unclear. In this study, we demonstrate that the small ubiquitin-like modifier (SUMO) E3 ligase SAP AND MIZ1 DOMAIN-CONTAINING LIGASE1 (SIZ1) interacts with HLS1 and mediates its SUMOylation in Arabidopsis thaliana. Mutating SUMO attachment sites of HLS1 results in impaired function of HLS1, indicating that HLS1 SUMOylation is essential for its function. SUMOylated HLS1 was more likely to assemble into oligomers, which are the active form of HLS1. During the dark-to-light transition, light induces rapid apical hook opening, concomitantly with a drop in SIZ1 transcript levels, resulting in lower HLS1 SUMOylation. Furthermore, ELONGATED HYPOCOTYL5 (HY5) directly binds to the SIZ1 promoter and suppresses its transcription. HY5-initiated rapid apical hook opening partially depended on HY5 inhibition of SIZ1 expression. Taken together, our study identifies a function for SIZ1 in apical hook development, providing a dynamic regulatory mechanism linking the post-translational modification of HLS1 during apical hook formation and light-induced apical hook opening.

Polar localization of a rice silicon transporter requires isoleucine at both C- and N-termini as well as positively charged residues

Silicon (Si) is important for stable and high yields in rice (Oryza sativa), a typical Si hyperaccumulator. The high Si accumulation is achieved by the cooperation of 2 Si transporters, LOW SILICON 1 (OsLsi1) and OsLsi2, which are polarly localized in cells of the root exodermis and endodermis. However, the mechanism underlying their polar localization is unknown. Here, we identified amino acid residues critical for the polar localization of OsLsi1. Deletion of both N- and C-terminal regions resulted in the loss of its polar localization. Furthermore, the deletion of the C-terminus inhibited its trafficking from the endoplasmic reticulum to the plasma membrane. Detailed site-directed mutagenesis analysis showed that Ile18 at the N-terminal region and Ile285 at the C-terminal region were essential for the polar localization of OsLsi1. Moreover, a cluster of positively charged residues at the C-terminal region is also required for polar localization. Phosphorylation and Lys modifications of OsLsi1 are unlikely to be involved in its polar localization. Finally, we showed that the polar localization of OsLsi1 is required for the efficient uptake of Si. Our study not only identified critical residues required for the polar localization of OsLsi1, but also provided experimental evidence for the importance of transporter polarity for efficient nutrient uptake.

Comparative oxidation proteomics analyses suggest redox regulation of cytosolic translation in rice leaves upon Magnaporthe oryzae infection

Pathogen attack can increase plant levels of reactive oxygen species (ROS), which act as signaling molecules to activate plant defense mechanisms. Elucidating these processes is crucial for understanding redox signaling pathways in plant defense responses. Using an iodo-tandem mass tag (TMT)-based quantitative proteomics approach, we mapped 3362 oxidized cysteine sites in 2275 proteins in rice leaves. Oxidized proteins were involved in gene expression, peptide biosynthetic processes, stress responses, ROS metabolic processes, and translation pathways. Magnaporthe oryzae infection led to increased oxidative modification levels of 512 cysteine sites in 438 proteins, including many transcriptional regulators and ribosomal proteins. Ribosome profiling (Ribo-seq) analysis revealed that the oxidative modification of ribosomal proteins promoted the translational efficiency of many mRNAs involved in defense response pathways, thereby affecting rice immunity. Our results suggest that increased oxidative modification of ribosomal proteins in rice leaves promotes cytosolic translation, thus revealing a novel function of post-translational modifications. Furthermore, the oxidation-sensitive proteins identified here provide a valuable resource for research on protein redox regulation and can guide future mechanistic studies.

Technological development of multidimensional liquid chromatography-mass spectrometry in proteome research

Liquid chromatography-mass spectrometry (LC-MS) is the method of choice for high-throughput proteomic research. Limited by the peak capacity, the separation performance of conventional single-dimensional LC hampers the development of proteomics. Combining different separation modes orthogonally, multidimensional liquid chromatography (MDLC) with high peak capacity was developed to address this challenge. MDLC has evolved rapidly since its establishment, and the progress of proteomics has been greatly facilitated by the advent of novel MDLC-MS-based methods. In this paper, we will review the advances of MDLC-MS-based methodologies and technologies in proteomics studies, from different perspectives including novel application scenarios and proteomic targets, automation, miniaturization, and the improvement of the classic methods in recent years. In addition, attempts regarding new MDLC-MS models are also mentioned together with the outlook of MDLC-MS-based proteomics methods.

In silico analysis of the profilaggrin sequence indicates alterations in the stability, degradation route, and intracellular protein fate in filaggrin null mutation carriers

Background: Loss of function mutation in FLG is the major genetic risk factor for atopic dermatitis (AD) and other allergic manifestations. Presently, little is known about the cellular turnover and stability of profilaggrin, the protein encoded by FLG. Since ubiquitination directly regulates the cellular fate of numerous proteins, their degradation and trafficking, this process could influence the concentration of filaggrin in the skin. Objective: To determine the elements mediating the interaction of profilaggrin with the ubiquitin-proteasome system (i.e., degron motifs and ubiquitination sites), the features responsible for its stability, and the effect of nonsense and frameshift mutations on profilaggrin turnover. Methods: The effect of inhibition of proteasome and deubiquitinases on the level and modifications of profilaggrin and processed products was assessed by immunoblotting. Wild-type profilaggrin sequence and its mutated variants were analysed in silico using the DEGRONOPEDIA and Clustal Omega tool. Results: Inhibition of proteasome and deubiquitinases stabilizes profilaggrin and its high molecular weight of presumably ubiquitinated derivatives. In silico analysis of the sequence determined that profilaggrin contains 18 known degron motifs as well as multiple canonical and non-canonical ubiquitination-prone residues. FLG mutations generate products with increased stability scores, altered usage of the ubiquitination marks, and the frequent appearance of novel degrons, including those promoting C-terminus-mediated degradation routes. Conclusion: The proteasome is involved in the turnover of profilaggrin, which contains multiple degrons and ubiquitination-prone residues. FLG mutations alter those key elements, affecting the degradation routes and the mutated products' stability.

Identification and functional characterization of the SUMO system in sweet potato under salt and drought stress

Sumoylation is a crucial post-translation modification (PTM) that is the covalent attachment of SUMO molecules to the substrate catalyzed by enzyme cascade. Sumoylation is essential in almost every physiological process of plants, particularly in response to abiotic stress. However, little is known about sumoylation in sweet potato (Ipomoea batatas), the world's seventh most important food crop. In this study, 17 sweet potato SUMO system genes have been cloned and functionally characterized. Multiple sequence alignment and phylogenetic analysis showed sweet potato SUMO system proteins had conserved domains and activity sites. IbSUMOs, IbSAE1, and IbSCE1 were localized in the cytoplasm and nucleus. E3 SUMO ligases showed nuclear or punctate localization. In vitro sumoylation assay confirmed the catalytic activity of sweet potato SUMO system components. Heterologous expression of IbSIZ1 genes in Arabidopsis atsiz1 mutant rescued the defective germination and growth phenotype. IbSCE1a/b and IbSIZ1a/b/c were salt and drought responsive genes. Heterologous expression of IbSCE1a/b/c improved the drought tolerance of Arabidopsis thaliana, while IbSIZ1a/b/c significantly enhanced the salt and drought tolerance. Our findings define that the SUMO system in sweet potato shared with conserved function but also possessed specific characterization. The resources presented here would facilitate uncovering the significance of sumoylation in sweet potato.

Molecular determinants of protein half-life in chloroplasts with focus on the Clp protease system

Proteolysis is an essential process to maintain cellular homeostasis. One pathway that mediates selective protein degradation and which is in principle conserved throughout the kingdoms of life is the N-degron pathway, formerly called the ‘N-end rule’. In the cytosol of eukaryotes and prokaryotes, N-terminal residues can be major determinants of protein stability. While the eukaryotic N-degron pathway depends on the ubiquitin proteasome system, the prokaryotic counterpart is driven by the Clp protease system. Plant chloroplasts also contain such a protease network, which suggests that they might harbor an organelle specific N-degron pathway similar to the prokaryotic one. Recent discoveries indicate that the N-terminal region of proteins affects their stability in chloroplasts and provides support for a Clp-mediated entry point in an N-degron pathway in plastids. This review discusses structure, function and specificity of the chloroplast Clp system, outlines experimental approaches to test for an N-degron pathway in chloroplasts, relates these aspects into general plastid proteostasis and highlights the importance of an understanding of plastid protein turnover.

Understanding the Proteomes of Plant Development and Stress Responses in Brassica Crops

Brassica crops have great economic value due to their rich nutritional content and are therefore grown worldwide as oilseeds, vegetables, and condiments. Deciphering the molecular mechanisms associated with the advantageous phenotype is the major objective of various Brassica improvement programs. As large technological advancements have been achieved in the past decade, the methods to understand molecular mechanisms underlying the traits of interest have also taken a sharp upturn in plant breeding practices. Proteomics has emerged as one of the preferred choices nowadays along with genomics and other molecular approaches, as proteins are the ultimate effector molecules responsible for phenotypic changes in living systems, and allow plants to resist variable environmental stresses. In the last two decades, rapid progress has been made in the field of proteomics research in Brassica crops, but a comprehensive review that collates the different studies is lacking. This review provides an inclusive summary of different proteomic studies undertaken in Brassica crops for cytoplasmic male sterility, oil content, and proteomics of floral organs and seeds, under different biotic and abiotic stresses including post-translational modifications of proteins. This comprehensive review will help in understanding the role of different proteins in controlling plant phenotypes, and provides information for initiating future studies on Brassica breeding and improvement programs.

Charting plant gene functions in the multi-omics and single-cell era

Despite the increased access to high-quality plant genome sequences, the set of genes with a known function remains far from complete. With the advent of novel bulk and single-cell omics profiling methods, we are entering a new era where advanced and highly integrative functional annotation strategies are being developed to elucidate the functions of all plant genes. Here, we review different multi-omics approaches to improve functional and regulatory gene characterization and highlight the power of machine learning and network biology to fully exploit the complementary information embedded in different omics layers. Finally, we discuss the potential of emerging single-cell methods and algorithms to further increase the resolution, allowing generation of functional insights about plant biology.

Ubiquitin specific peptidases and prostate cancer

Protein ubiquitination is an important post-translational modification mechanism, which regulates protein stability and activity. The ubiquitination of proteins can be reversed by deubiquitinating enzymes (DUBs). Ubiquitin-specific proteases (USPs), the largest DUB subfamily, can regulate cellular functions by removing ubiquitin(s) from the target proteins. Prostate cancer (PCa) is the second leading type of cancer and the most common cause of cancer-related deaths in men worldwide. Numerous studies have demonstrated that the development of PCa is highly correlated with USPs. The expression of USPs is either high or low in PCa cells, thereby regulating the downstream signaling pathways and causing the development or suppression of PCa. This review summarized the functional roles of USPs in the development PCa and explored their potential applications as therapeutic targets for PCa.

Pseudophosphorylation of Arabidopsis jasmonate biosynthesis enzyme lipoxygenase 2 via mutation of Ser600 inhibits enzyme activity

Jasmonates are oxylipin phytohormones critical for plant resistance against necrotrophic pathogens and chewing herbivores. An early step in their biosynthesis is catalyzed by non-heme iron lipoxygenases (LOX; EC 1.13.11.12). In Arabidopsis thaliana, phosphorylation of Ser⁶⁰⁰ of AtLOX2 was previously reported, but whether phosphorylation regulates AtLOX2 activity is unclear. Here, we characterize the kinetic properties of recombinant WT AtLOX2 (AtLOX2^WT). AtLOX2^WT displays positive cooperativity with α-linolenic acid (α-LeA, jasmonate precursor), linoleic acid (LA), and arachidonic acid (AA) as substrates. Enzyme velocity with endogenous substrates α-LeA and LA increased with pH. For α-LeA, this increase was accompanied by a decrease in substrate affinity at alkaline pH; thus, the catalytic efficiency for α-LeA was not affected over the pH range tested. Analysis of Ser⁶⁰⁰ phosphovariants demonstrated that pseudophosphorylation inhibits enzyme activity. AtLOX2 activity was not detected in phosphomimics Atlox2^S600D and Atlox2^S600M when α-LeA or AA were used as substrates. In contrast, phosphonull mutant Atlox2^S600A exhibited strong activity with all three substrates, α-LeA, LA, and AA. Structural comparison between the AtLOX2 AlphaFold model and a complex between 8R-LOX and a 20C polyunsaturated fatty acid suggests a close proximity between AtLOX2 Ser⁶⁰⁰ and the carboxylic acid head group of the polyunsaturated fatty acid. This analysis indicates that Ser⁶⁰⁰ is located at a critical position within the AtLOX2 structure and highlights how Ser⁶⁰⁰ phosphorylation could affect AtLOX2 catalytic activity. Overall, we propose that AtLOX2 Ser⁶⁰⁰ phosphorylation represents a key mechanism for the regulation of AtLOX2 activity and, thus, the jasmonate biosynthesis pathway and plant resistance.

Analysis of higher plant N-degron pathway components and substrates via expression in S. cerevisiae

Heterologous expression of enzymes can generate a background-free environment that facilitates investigation of enzyme properties, for instance to focus on particular isoforms in case of gene families, or on individual splicing variants. If a proper host can be found, in vivo assays are often simpler than overexpression and purification, followed by in vitro measurements, would be. We expressed plant ubiquitin ligase PRT6 in the budding yeast Saccharomyces cerevisiae for studies on activity and substrate preferences. Expression of this large enzyme profits from the eukaryotic folding catalysis provided by budding yeast, and from the presence of endogenous ubiquitin activating enzyme. While yeast encodes a ubiquitin ligase, Ubr1, that is functionally related to PRT6, a strain with deletion of the UBR1 gene offers a background-free host. Two different substrates were analyzed. One was a model substate, and the other one a natural substrate fused to a reporter. Two different methods were compared for assessment of protein stability. A method based on internal standardization via tandem fluorescent timer measurement turned out to be complementary to standardization based on cell culture density.

Optimising expression and extraction of recombinant proteins in plants

Recombinant proteins are of paramount importance for research, industrial and medical use. Numerous expression chassis are available for recombinant protein production, and while bacterial and mammalian cell cultures are the most widely used, recent developments have positioned transgenic plant chassis as viable and often preferential options. Plant chassis are easily maintained at low cost, are hugely scalable, and capable of producing large quantities of protein bearing complex post-translational modification. Several protein targets, including antibodies and vaccines against human disease, have been successfully produced in plants, highlighting the significant potential of plant chassis. The aim of this review is to act as a guide to producing recombinant protein in plants, discussing recent progress in the field and summarising the factors that must be considered when utilising plants as recombinant protein expression systems, with a focus on optimising recombinant protein expression at the genetic level, and the subsequent extraction and purification of target proteins, which can lead to substantial improvements in protein stability, yield and purity.

Acetylome reprograming participates in the establishment of fruit metabolism during polyploidization in citrus

Polyploidization leads to novel phenotypes and is a major force in evolution. However, the relationship between the evolution of new traits and variations in the post-translational modifications (PTM) of proteins during polyploidization has not been studied. Acetylation of lysine residues is a common protein PTM that plays a critical regulatory role in central metabolism. To test whether changes in metabolism in citrus fruit is associated with the reprogramming of lysine acetylation (Kac) in non-histone proteins during allotetraploidization, we performed a global acetylome analysis of fruits from a synthetic allotetraploid citrus and its diploid parents. A total of 4,175 Kac sites were identified on 1,640 proteins involved in a wide range of fruit traits. In the allotetraploid, parental dominance (i.e. resemblance to one of the two parents) in specific fruit traits, such as fruit acidity and flavonol metabolism, was highly associated with parental Kac level dominance in pertinent enzymes. This association is due to Kac-mediated regulation of enzyme activity. Moreover, protein Kac probably contributes to the discordance between the transcriptomic and proteomic variations during allotetraploidization. The acetylome reprogramming can be partially explained by the expression pattern of several lysine deacetylases (KDACs). Overexpression of silent information regulator 2 (CgSRT2) and histone deacetylase 8 (CgHDA8) diverted metabolic flux from primary metabolism to secondary metabolism and partially restored a metabolic status to the allotetraploid, which expressed attenuated levels of CgSRT2 and CgHDA8. Additionally, KDAC inhibitor treatment greatly altered metabolism in citrus fruit. Collectively, these findings reveal the important role of acetylome reprogramming in trait evolution during polyploidization.

Thirty years of molecular dynamics simulations on posttranslational modifications of proteins

Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.

N-terminal modifications, the associated processing machinery, and their evolution in plastid-containing organisms

The N-terminus is a frequent site of protein modifications. Referring primarily to knowledge gained from land plants, here we review the modifications that change protein N-terminal residues and provide updated information about the associated machinery, including that in Archaeplastida. These N-terminal modifications include many proteolytic events as well as small group additions such as acylation or arginylation and oxidation. Compared with that of the mitochondrion, the plastid-dedicated N-terminal modification landscape is far more complex. In parallel, we extend this review to plastid-containing Chromalveolata including Stramenopiles, Apicomplexa, and Rhizaria. We report a well-conserved machinery, especially in the plastid. Consideration of the two most abundant proteins on Earth-Rubisco and actin-reveals the complexity of N-terminal modification processes. The progressive gene transfer from the plastid to the nuclear genome during evolution is exemplified by the N-terminus modification machinery, which appears to be one of the latest to have been transferred to the nuclear genome together with crucial major photosynthetic landmarks. This is evidenced by the greater number of plastid genes in Paulinellidae and red algae, the most recent and fossil recipients of primary endosymbiosis.

Deciphering combinatorial post-translational modifications by top-down mass spectrometry

Post-translational modifications (PTMs) create vast structural and functional diversity of proteins, ultimately modulating protein function and degradation, influencing cellular signaling, and regulating transcription. The combinatorial patterns of PTMs increase the heterogeneity of proteins and further mediates their interactions. Advances in mass spectrometry-based proteomics have resulted in identification of thousands of proteins and allowed characterization of numerous types and sites of PTMs. Examination of intact proteins, termed the top-down approach, offers the potential to map protein sequences and localize multiple PTMs on each protein, providing the most comprehensive cataloging of proteoforms. This review describes some of the dividends of using mass spectrometry to analyze intact proteins and showcases innovative strategies that have enhanced the promise of top-down proteomics for exploring the impact of combinatorial PTMs in unsurpassed detail.

Proteome-wide identification of S-sulfenylated cysteines reveals metabolic response to freezing stress after cold acclimation in Brassica napus

Redox regulation plays a wide role in plant growth, development, and adaptation to stresses. Sulfenylation is one of the reversible oxidative post-transcriptional modifications. Here we performed an iodoTMT-based proteomic analysis to identify the redox sensitive proteins in vivo under freezing stress after cold acclimation in Brassica napus. Totally, we obtained 1,372 sulfenylated sites in 714 proteins. The overall sulfenylation level displayed an increased trend under freezing stress after cold acclimation. We identified 171 differentially sulfenylated proteins (DSPs) under freezing stress, which were predicted to be mainly localized in chloroplast and cytoplasm. The up-regulated DSPs were mainly enriched in photosynthesis and glycolytic processes and function of catalytic activity. Enzymes involved in various pathways such as glycolysis and Calvin-Benson-Bassham (CBB) cycle were generally sulfenylated and the metabolite levels in these pathways was significantly reduced under freezing stress after cold acclimation. Furthermore, enzyme activity assay confirmed that the activity of cytosolic pyruvate kinase and malate dehydrogenase 2 was significantly reduced under H₂O₂ treatment. Our study provides a landscape of redox sensitive proteins in B. napus in response to freezing stress after cold acclimation, which proposes a basis for understanding the redox regulation in plant metabolic response to freezing stress after cold acclimation.

Ethylene augments root hypoxia tolerance via growth cessation and reactive oxygen species amelioration

Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pretreatment on hypoxia survival of Arabidopsis (Arabidopsis thaliana) primary root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells, and ethylene pretreatments reduced this damage. Ethylene pretreatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation, and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrated that ethylene limited excessive ROS formation during hypoxia and subsequent re-oxygenation and improved oxidative stress survival in a PHYTOGLOBIN1-dependent manner. In addition, we showed that root growth cessation via ethylene and auxin occurred rapidly and that this quiescence behavior contributed to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival.

Endoplasmic reticulum oxidoreductin provides resilience against reductive stress and hypoxic conditions by mediating luminal redox dynamics

Oxidative protein folding in the endoplasmic reticulum (ER) depends on the coordinated action of protein disulfide isomerases and ER oxidoreductins (EROs). Strict dependence of ERO activity on molecular oxygen as the final electron acceptor implies that oxidative protein folding and other ER processes are severely compromised under hypoxia. Here, we isolated viable Arabidopsis thaliana ero1 ero2 double mutants that are highly sensitive to reductive stress and hypoxia. To elucidate the specific redox dynamics in the ER in vivo, we expressed the glutathione redox potential (EGSH) sensor Grx1-roGFP2iL-HDEL with a midpoint potential of -240 mV in the ER of Arabidopsis plants. We found EGSH values of -241 mV in wild-type plants, which is less oxidizing than previously estimated. In the ero1 ero2 mutants, luminal EGSH was reduced further to -253 mV. Recovery to reductive ER stress induced by dithiothreitol was delayed in ero1 ero2. The characteristic signature of EGSH dynamics in the ER lumen triggered by hypoxia was affected in ero1 ero2 reflecting a disrupted balance of reductive and oxidizing inputs, including nascent polypeptides and glutathione entry. The ER redox dynamics can now be dissected in vivo, revealing a central role of EROs as major redox integrators to promote luminal redox homeostasis.

Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis

Since plants are sessile organisms, developmental plasticity in response to environmental stresses is essential for their survival. Upon exposure to drought, lateral root development is suppressed to induce drought tolerance. However, the molecular mechanism by which the development of lateral roots is inhibited by drought is largely unknown. In this study, the auxin signaling repressor IAA15 was identified as a novel substrate of mitogen-activated protein kinases (MPKs) and was shown to suppress lateral root development in response to drought through stabilization by phosphorylation. Both MPK3 and MPK6 directly phosphorylated IAA15 at the Ser-2 and Thr-28 residues. Transgenic plants overexpressing a phospho-mimicking mutant of IAA15 (IAA15^DD OX) showed reduced lateral root development due to a higher accumulation of IAA15. In addition, MPK-mediated phosphorylation strongly increased the stability of IAA15 through the inhibition of polyubiquitination. Furthermore, IAA15^DD OX plants showed the transcriptional downregulation of two key transcription factors LBD16 and LBD29, responsible for lateral root development. Overall, this study provides the molecular mechanism that explains the significance of the MPK-Aux/IAA module in suppressing lateral root development in response to drought.