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•SPINDLY (SPY) is a unique nucleocytoplasmic-localized protein O-fucosyltransferase (POFUT).•The sequence and predicted 3D structure of SPY are similar to the TPR domain-containing ...OGTs, but are distinct from ER-localized POFUTs.•O-fucosylation by SPY can regulate nuclear transcription factors/regulators by affecting protein stability or protein-protein interactions.•SPY regulates many developmental processes and responses to biotic and abiotic stresses in plants.•SPY-like genes are conserved in diverse organisms, except in fungi and metazoans.
In metazoans, protein O-fucosylation of Ser/Thr residues was only found in secreted or cell surface proteins, and this post-translational modification is catalyzed by ER-localized protein O-fucosyltransferases (POFUTs) in the GT65 family. Recently, a novel nucleocytoplasmic POFUT, SPINDLY (SPY), was identified in the reference plant Arabidopsis thaliana to modify nuclear transcription regulators DELLAs, revealing a new regulatory mechanism for gene expression. The paralog of AtSPY, SECRET AGENT (SEC), is an O-link-N-acetylglucosamine (GlcNAc) transferase (OGT), which O-GlcNAcylates Ser/Thr residues of target proteins. Both AtSPY and AtSEC are tetratricopeptide repeat-domain-containing glycosyltransferases in the GT41 family. The discovery that AtSPY is a POFUT clarified decades of miss-classification of AtSPY as an OGT. SPY and SEC play pleiotropic roles in plant development, and the interactions between SPY and SEC are complex. SPY-like genes are conserved in diverse organisms, except in fungi and metazoans, suggesting that O-fucosylation is a common mechanism in modulating intracellular protein functions.
Gibberellins control a range of growth and developmental processes in higher plants and have been widely used in the agricultural industry. By binding to a nuclear receptor, GIBBERELLIN INSENSITIVE ...DWARF1 (GID1), gibberellins regulate gene expression by promoting degradation of the transcriptional regulator DELLA proteins, including GIBBERELLIN INSENSITIVE (GAI). The precise manner in which GID1 discriminates and becomes activated by bioactive gibberellins for specific binding to DELLA proteins remains unclear. Here we present the crystal structure of a ternary complex of Arabidopsis thaliana GID1A, a bioactive gibberellin and the amino-terminal DELLA domain of GAI. In this complex, GID1A occludes gibberellin in a deep binding pocket covered by its N-terminal helical switch region, which in turn interacts with the DELLA domain containing DELLA, VHYNP and LExLE motifs. Our results establish a structural model of a plant hormone receptor that is distinct from the mechanism of the hormone perception and effector recognition of the known auxin receptors.
The incidence and prevalence of nonalcoholic fatty liver disease (NAFLD) are increasing and identification of people at risk of disease progression is extremely important. The current gold standard ...for diagnosing NAFLD/nonalcoholic steatohepatitis (NASH) is by liver biopsy, but it has several limitations. Noninvasive tests via biomarkers and transient elastography to assess NAFLD/NASH are being used in clinical practice. The most validated diagnostic panels include the NAFLD fibrosis score, FIB-4 (Fibrosis-4), and FibroMeter. Transient elastography is very useful in evaluating advanced fibrosis and cirrhosis.
Serratia marcescens is utilized as a significant enterobacteria in the production of various high‐value secondary metabolites. Acetoin serves as a crucial foundational compound of development and ...finds application in a broad range of fields. Furthermore, S. marcescens HBQA‐7 is capable of utilizing xylose as its exclusive carbon source for acetoin production. The objective of this study was to utilize a constitutive promoter screening strategy to enhance both xylose utilization and acetoin production in S. marcescens HBQA‐7. By utilizing RNA‐seq, we identified the endogenous constitutive promoter P6 that is the most robust, which facilitated the overexpression of the sugar transporter protein GlfL445I, α‐acetyl lactate synthase, and α‐acetyl lactate decarboxylase, respectively. The resultant recombinant strains exhibited enhanced xylose utilization rates and acetoin yields. Subsequently, a recombinant plasmid, denoted as pBBR1MCS‐P6‐glfL445IalsSalsD, was constructed, simultaneously expressing the aforementioned three genes. The resulting recombinant strain, designated as S3, demonstrated a 1.89‐fold boost in xylose consumption rate compared with the original strain during shake flask fermentation. resulting in the accumulation of 7.14 g/L acetoin in the final fermentation medium. Subsequently, in a 5 L fermenter setup, the acetoin yield reached 48.75 g/L, corresponding to a xylose‐to‐acetoin conversion yield of 0.375 g/g.
Clostridium aceticum DSM1496 is an acid‐resistant strain in which ornithine decarboxylase (ODC) plays a crucial role in acid resistance. In this study, we expressed ODC derived from C. aceticum ...DSM1496 in Escherichia coli BL21 (DE3) and thoroughly examined its enzymatic properties. The enzyme has a molecular weight of 55.27 kDa and uses pyridoxal‐5′‐phosphate (PLP) as a coenzyme with a Km = 0.31 mM. ODC exhibits optimal activity at pH 7.5, and it maintains high stability even at pH 4.5. The peak reaction temperature for ODC is 30°C. Besides, it can be influenced by certain metal ions such as Mn2+. Although l‐ornithine serves as the preferred substrate for ODC, the enzyme also decarboxylates l‐arginine and l‐lysine simultaneously. The results indicate that ODC derived from C. aceticum DSM1496 exhibits the ability to produce putrescine, cadaverine, and agmatine through decarboxylation. These polyamines have the potential to neutralize acid in an acidic environment, facilitating the growth of microorganisms. These significant findings provide a strong basis for further investigation into the acid‐resistant mechanisms contributed by ODC.
It has been almost a century since biologically active gibberellin (GA) was isolated. Here, we give a historical overview of the early efforts in establishing the GA biosynthesis and catabolism ...pathway, characterizing the enzymes for GA metabolism, and elucidating their corresponding genes. We then highlight more recent studies that have identified the GA receptors and early GA signaling components (DELLA repressors and F-box activators), determined the molecular mechanism of DELLA-mediated transcription reprograming, and revealed how DELLAs integrate multiple signaling pathways to regulate plant vegetative and reproductive development in response to internal and external cues. Finally, we discuss the GA transporters and their roles in GA-mediated plant development.
Peptides derived from dietary proteins, have been reported to display significant antioxidant activity, which may exert notably beneficial effects in promoting human health and in food processing. ...Recently, much research has focused on the generation, separation, purification and identification of novel peptides from various protein sources. Some researchers have tried to discover the structural characteristics of antioxidant peptides in order to lessen or avoid the tedious and aimless work involving the ongoing generated peptide preparation schemes. This review aims to summarize the current knowledge on the relationship between the structural features of peptides and their antioxidant activities. The relationship between the structure of the precursor proteins and their abilities to release antioxidant fragments will also be summarized and inferred. The preparation methods and antioxidant capacity evaluation assays of peptides and a prediction scheme of quantitative structure-activity relationship (QSAR) will also be pointed out and discussed.
Abstract
Variational quantum algorithms (VQAs) are widely applied in the noisy intermediate-scale quantum era and are expected to demonstrate quantum advantage. However, training VQAs faces ...difficulties, one of which is the so-called barren plateaus (BPs) phenomenon, where gradients of cost functions vanish exponentially with the number of qubits. In this paper, inspired by transfer learning, where knowledge of pre-solved tasks could be further used in a different but related work with training efficiency improved, we report a parameter initialization method to mitigate BP. In the method, a small-sized task is solved with a VQA. Then the ansatz and its optimum parameters are transferred to tasks with larger sizes. Numerical simulations show that this method could mitigate BP and improve training efficiency. A brief discussion on how this method can work well is also provided. This work provides a reference for mitigating BP, and therefore, VQAs could be applied to more practical problems.
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