Diverse nucleotide substitutions in rice base editing mediated by novel TadA variants.

CRISPR-mediated base editors have been widely used to correct defective alleles and create novel alleles by artificial evolution for the rapid genetic improvement of crops. The editing capabilities of base editors strictly rely on the performance of various nucleotide modification enzymes. Compared with the well-developed adenine base editors (ABEs), cytosine base editors (CBEs) and dual base editors suffer from unstable editing efficiency and patterns at different genomic loci in rice, significantly limiting their application. Here, we comprehensively examined the base editing activities of multiple evolved TadA8e variants in rice. We found that both TadA-CDd and TadA-E27R/N46L achieved more robust C-to-T editing than previously reported hyperactive hAID∗Δ, and TadA-CDd outperformed TadA-E27R/N46L. A C-to-G base editor (CGBE) engineered with TadA-CDd and OsUNG performed highly efficient C-to-G editing in rice compared with that of TadA-N46P. In addition, a dual base editor constructed with a single protein, TadDE, enabled simultaneous, highly efficient C-to-T and A-to-G editing in rice. Collectively, our results demonstrate that TadA8e derivatives improve both CBEs and dual base editors in rice, providing a powerful way to induce diverse nucleotide substitutions for plant genome editing.

The effects of hyaluronan and proteoglycan link protein 1 (HAPLN1) in ameliorating spinal cord injury mediated by Nrf2.

Excessive inflammatory response and oxidative stress (OS) play an important role in the pathogenesis of spinal cord injury (SCI). Balance of inflammation and prevention of OS have been considered an effective strategy for the treatment of SCI. Hyaluronan and proteoglycan link protein 1 (HAPLN1), also known as cartilage link protein, has displayed a wide range of biological and physiological functions in different types of tissues and cells. However, whether HAPLN1 regulates inflammation and OS during SCI is unknown. Therefore, we aimed to examine whether HAPLN1 can have a protective effect on SCI. In this study, both in vitro and in vivo SCI models were established. Nissl staining and terminal deoxynucleotidyl transferase dUTP nick end labeling staining assays were used. Western blotting and enzyme-linked immunosorbent assay were employed to assess the expression of proteins. Our results demonstrate that the administration of HAPLN1 promoted the recovery of motor neurons after SCI by increasing the Basso mouse scale score, increasing the numbers of motor neurons, and preventing apoptosis of spinal cord cells. Additionally, HAPLN1 mitigated OS in spinal cord tissue after SCI by increasing the content of superoxide dismutase SOD and the activity of glutathione peroxidase but reducing the levels of malondialdehyde. Importantly, we found that HAPLN1 stimulated the activation of the nuclear factor erythroid 2-related factor 2 (Nrf2)/antioxidant response element (ARE) pathway and stimulated the expression of heme oxygenase-1 and nicotinamide adenine dinucleotide phosphate quinone oxidoreductase-1, which mediated the attenuation of HAPLN1 in activation of the NOD-like receptor protein 3 (NLRP3) inflammasome by reducing the levels of NLRP3, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), caspase-1, and interleukin-1ß. Correspondingly, in vitro experiments show that the presence of HAPLN1 suppressed the NLRP3 inflammasome and prevented cell injury against H2O2 in PC12 cells. These effects were mediated by the Nrf2/ARE pathway, and inhibition of Nrf2 with ML385 abolished the beneficial effects of HAPLN1. Based on these findings, we conclude that HAPLN1 inhibits the NLRP3 inflammasome through the stimulation of the Nrf2/ARE pathway, thereby suppressing neuroinflammation, enhancing motor neuronal survival, and improving the recovery of nerve function after SCI.

Efficacy and Safety Analysis of Joint Replacement in the Treatment of Senile Knee Degenerative Osteoarthritis.

Objective: To study the effectiveness and safety of joint replacement in the clinical treatment of elderly patients with knee degenerative osteoarthritis. To compare the results of arthroplasty with arthroscopic debridement and to investigate the overall effect of arthroplasty on various parameters. Methods: We included patients whose diagnostic criteria for mid-knee osteoarthritis involved relevant content, and excluded patients with other diseases such as the immune system. The medical records of 90 patients (senile degenerative knee osteoarthritis, 2021.1-2022.12) were selected for retrospective analysis, and patients were grouped according to the surgical treatment plan, and those treated with arthroscopic debridement surgery were included in the control group (a total of 45 cases), those treated with joint replacement were included in the observation group (45 cases in total). The changes in the levels of kinematic parameters, osteoarthritis indicators, quadriceps strength, inflammation indicators, and knee joint function indicators were compared between the groups, and the daily living abilities of the two groups were compared. Results: The active flexion angle of the observation group was greater than that of the control group, and the varus inclination was smaller than that of the control group, with P < .05; the joint function scores, pain scores, and stiffness scores of the observation group were all lower than those of the control group, with P < .05; the muscle strength of the voluntary movement of the bilateral quadriceps muscle and the maximum muscle strength under isometric contraction was higher than those of the control group, with P < .05; the measured values of interleukin-6, C-reactive protein, and white blood cell count (IL-6, CRP, WBC) in the observation group were lower than those of the control group, with P < .05; the scores of knee joint function and daily living ability in the observation group were higher than those in the control group, with P < .05. Conclusion: The curative effects of joint replacement in the treatment of senile knee degenerative osteoarthritis are significant, which can promote the improvement of early postoperative kinematic parameters and the recovery of joint function and reduce the inflammatory response. It also promotes the recovery of knee joint function, improves knee joint function, improves patient prognosis, and also improves the daily living abilities of elderly patients with knee joint degenerative osteoarthritis.

In-silico prediction, characterization, molecular docking and dynamic simulation studies for screening potential fungicides against leaf rust of Triticum aestivum.

Triticum aestivum is an important crop worldwide, which is a large source of food grain. T.aestivum demands on developed countries will grow every year, this increase in the demand is profoundly serious especially in the light climate change which would lead to a 29% reduction in final productivity. Rust fungus attacks the T.aestivum, specifically newly planted T.aestivum plants, which block the vascular system, stun, and finally damage grain and tillers. In present study we predict the 3D structure then find the binding pocket and conserved domains for MAPkinase-1 of Puccinia triticina. After that, screen the FungiPAD, PubChem, NPAtlas databases by physicochemical properties, docking, clustering, ADME (Absorption, distribution, metabolism, and excretion) and PAINS (pan assay interference compounds) filter analysis. Through this screening process screen the nine compounds, which are benzovindiflupyr, furametpyr, isopyrazam, fenaminstrobin, and flumorph from Fungicide database: zoxamide, vinclozolin, pentachloronitrobenzene, and dithianon from PubChem database, based on the binding energy, clustering, ADME and PAINS analysis. All these nine compounds bind in the same pocket and show the same pattern of interaction. Among these nine compounds, select the two compounds (PubChem:122087 (-6.96 kcal/mol) and FDBD02904 (-8.62 kcal/mol)) based on binding energy for 100 ns MD simulation and free energy calculation. MD simulation shows stability throughout the simulation, and it shows the sable interaction when compounds bind to the MAPKinase 1 protein which may help to protein kinase pathways in plant defense response. This result helps to design alternative fungicide against the wheat rust disease.Communicated by Ramaswamy H. Sarma.

High-Throughput Base Editing-Mediated Artificial Evolution Streamlines Trait Gene Identification in Rice.

Base Editing-Mediated Gene Evolution (BEMGE) method develops novel rice germplasms with mutations in any endogenous gene through employing both Cas9n-based cytosine and adenine base editors combined with an sgRNA library tiling the full-length coding region, for obtaining unknown functional SNPs. Here we describe the process of artificial evolution of OsALS1 in rice cells using BEMGE through Agrobacterium-mediated transformation. BEMGE method has the potential to generate numerous nucleotide changes to screen pivotal amino acids (AAs) and to accelerate crop improvement.

CRISPR/FnCas12a-mediated efficient multiplex and iterative genome editing in bacterial plant pathogens without donor DNA templates.

CRISPR-based genome editing technology is revolutionizing prokaryotic research, but it has been rarely studied in bacterial plant pathogens. Here, we have developed a targeted genome editing method with no requirement of donor templates for convenient and efficient gene knockout in Xanthomonas oryzae pv. oryzae (Xoo), one of the most important bacterial pathogens on rice, by employing the heterologous CRISPR/Cas12a from Francisella novicida and NHEJ proteins from Mycobacterium tuberculosis. FnCas12a nuclease generated both small and large DNA deletions at the target sites as well as it enabled multiplex genome editing, gene cluster deletion, and plasmid curing in the Xoo PXO99A strain. Accordingly, a non-TAL effector-free polymutant strain PXO99AD25E, which lacks all 25 xop genes involved in Xoo pathogenesis, has been engineered through iterative genome editing. Whole-genome sequencing analysis indicated that FnCas12a did not have a noticeable off-target effect. In addition, we revealed that these strategies are also suitable for targeted genome editing in another bacterial plant pathogen Pseudomonas syringae pv. tomato (Pst). We believe that our bacterial genome editing method will greatly expand the CRISPR study on microorganisms and advance our understanding of the physiology and pathogenesis of Xoo.

Co-evolved plant and blast fungus ascorbate oxidases orchestrate the redox state of host apoplast to modulate rice immunity.

Apoplastic ascorbate oxidases (AOs) play a critical role in reactive oxygen species (ROS)-mediated innate host immunity by regulating the apoplast redox state. To date, little is known about how apoplastic effectors of the rice blast fungus Magnaporthe oryzae modulate the apoplast redox state of rice to subvert plant immunity. In this study, we demonstrated that M. oryzae MoAo1 is an AO that plays a role in virulence by modulating the apoplast redox status of rice cells. We showed that MoAo1 inhibits the activity of rice OsAO3 and OsAO4, which also regulate the apoplast redox status and plant immunity. In addition, we found that MoAo1, OsAO3, and OsAO4 all exhibit polymorphic variations whose varied interactions orchestrate pathogen virulence and rice immunity. Taken together, our results reveal a critical role for extracellular redox enzymes during rice blast infection and shed light on the importance of the apoplast redox state and its regulation in plant-pathogen interactions.

T-LOC: A comprehensive tool to localize and characterize T-DNA integration sites.

Scientists have developed many approaches based on PCR or next-generation sequencing to localize and characterize integrated T-DNAs in transgenic plants generated by Agrobacterium tumefaciens-mediated T-DNA transfer. However, none of these methods has the robust ability to handle all transgenic plants with diversified T-DNA patterns. Utilizing the valuable information in the whole-genome sequencing data of transgenic plants, we have developed a comprehensive approach (T-LOC) to localize and characterize T-DNA integration sites (TISs). We evaluated the performance of T-LOC on genome sequencing data from 48 transgenic rice (Oryza sativa) plants that provide real and unbiased resources of T-DNA integration patterns. T-LOC discovered 75 full TISs and reported a diversified pattern of T-DNA integration: the ideal single-copy T-DNA between two borders, multiple-copy of T-DNAs in tandem or inverted repeats, truncated partial T-DNAs with or without the selection hygromycin gene, the inclusion of T-DNA backbone, the integration at the genome repeat region, and the concatenation of multiple ideal or partial T-DNAs. In addition, we reported that DNA fragments from the two A. tumefaciens plasmids can be fused with T-DNA and integrated into the plant genome. Besides, T-LOC characterizes the genomic changes at TISs, including deletion, duplication, accurate repair, and chromosomal rearrangement. Moreover, we validated the robustness of T-LOC using PCR, Sanger sequencing, and Nanopore sequencing. In summary, T-LOC is a robust approach to studying the TISs independent of the integration pattern and can recover all types of TISs in transgenic plants.

A large-scale genome and transcriptome sequencing analysis reveals the mutation landscapes induced by high-activity adenine base editors in plants.

BACKGROUND: The high-activity adenine base editors (ABEs), engineered with the recently-developed tRNA adenosine deaminases (TadA8e and TadA9), show robust base editing activity but raise concerns about off-target effects. RESULTS: In this study, we perform a comprehensive evaluation of ABE8e- and ABE9-induced DNA and RNA mutations in Oryza sativa. Whole-genome sequencing analysis of plants transformed with four ABEs, including SpCas9n-TadA8e, SpCas9n-TadA9, SpCas9n-NG-TadA8e, and SpCas9n-NG-TadA9, reveal that ABEs harboring TadA9 lead to a higher number of off-target A-to-G (A>G) single-nucleotide variants (SNVs), and that those harboring CRISPR/SpCas9n-NG lead to a higher total number of off-target SNVs in the rice genome. An analysis of the T-DNAs carrying the ABEs indicates that the on-target mutations could be introduced before and/or after T-DNA integration into plant genomes, with more off-target A>G SNVs forming after the ABEs had integrated into the genome. Furthermore, we detect off-target A>G RNA mutations in plants with high expression of ABEs but not in plants with low expression of ABEs. The off-target A>G RNA mutations tend to cluster, while off-target A>G DNA mutations rarely clustered. CONCLUSION: Our findings that Cas proteins, TadA variants, temporal expression of ABEs, and expression levels of ABEs contribute to ABE specificity in rice provide insight into the specificity of ABEs and suggest alternative ways to increase ABE specificity besides engineering TadA variants.

Discovery of antimicrobial agent targeting tryptophan synthase.

Antibiotic resistance is a continually growing challenge in the treatment of various bacterial infections worldwide. New drugs and new drug targets are necessary to curb the threat of infectious diseases caused by multidrug-resistant pathogens. The tryptophan biosynthesis pathway is essential for bacterial growth but is absent in higher animals and humans. Drugs that can inhibit the bacterial biosynthesis of tryptophan offer a new class of antibiotics. In this work, we combined a structure-based strategy using in silico docking screening and molecular dynamics (MD) simulations to identify compounds targeting the α subunit of tryptophan synthase with experimental methods involving the whole-cell minimum inhibitory concentration (MIC) test, solution state NMR, and crystallography to confirm the inhibition of L-tryptophan biosynthesis. Screening 1,800 compounds from the National Cancer Institute Diversity Set I against α subunit revealed 28 compounds for experimental validation; four of the 28 hit compounds showed promising activity in MIC testing. We performed solution state NMR experiments to demonstrate that a one successful inhibitor, 3-amino-3-imino-2-phenyldiazenylpropanamide (Compound 1) binds to the α subunit. We also report a crystal structure of Salmonella enterica serotype Typhimurium tryptophan synthase in complex with Compound 1 which revealed a binding site at the αß interface of the dimeric enzyme. MD simulations were carried out to examine two binding sites for the compound. Our results show that this small molecule inhibitor could be a promising lead for future drug development.

Protocol for targeted modification of the rice genome using base editing.

Base editing is a precision genome-editing approach that is widely utilized to generate single-nucleotide variants (SNVs) in genomes. Here, we present a protocol to perform targeted adenine (A)-to-guanine (G) substitution in rice using adenine base editor (ABE). We detail the design of sgRNA, CRISPR plasmid construction, rapid genetic transformation of rice, and genotyping of editing events. This protocol can be applied to cytosine base editing in rice as well. For complete details on the use and execution of this protocol, please refer to Yan et al. (2021).1.

CRISPR/Sc++ -mediated genome editing in rice.

Streptococcus canis Cas9 (ScCas9) is an RNA-guided endonuclease with NNG protospacer adjacent motif (PAM) specificity whose genome-editing activity in rice is locus-dependent. Here we investigated the performance of a ScCas9 variant named Sc++ at different NNG PAM sites in the rice genome; Sc++ harbors a T1227K mutation and the substitution of a positively charged loop (residues 367-376). Sc++ nuclease achieved broader genome editing compared to the original ScCas9, and its nickase improved targeted base editing in transgenic rice plants. Using the high-efficiency adenine base editor rBE73b, we generated many new OsGS1 alleles suitable for screening of rice germplasm for potential herbicide resistance in the future. The CRISPR/Sc++ system expands the genome-editing toolkit for rice.

Poaceae-specific cell wall-derived oligosaccharides activate plant immunity via OsCERK1 during Magnaporthe oryzae infection in rice.

Many phytopathogens secrete cell wall degradation enzymes (CWDEs) to damage host cells and facilitate colonization. As the major components of the plant cell wall, cellulose and hemicellulose are the targets of CWDEs. Damaged plant cells often release damage-associated molecular patterns (DAMPs) to trigger plant immune responses. Here, we establish that the fungal pathogen Magnaporthe oryzae secretes the endoglucanases MoCel12A and MoCel12B during infection of rice (Oryza sativa). These endoglucanases target hemicellulose of the rice cell wall and release two specific oligosaccharides, namely the trisaccharide 31-ß-D-Cellobiosyl-glucose and the tetrasaccharide 31-ß-D-Cellotriosyl-glucose. 31-ß-D-Cellobiosyl-glucose and 31-ß-D-Cellotriosyl-glucose bind the immune receptor OsCERK1 but not the chitin binding protein OsCEBiP. However, they induce the dimerization of OsCERK1 and OsCEBiP. In addition, these Poaceae cell wall-specific oligosaccharides trigger a burst of reactive oxygen species (ROS) that is largely compromised in oscerk1 and oscebip mutants. We conclude that 31-ß-D-Cellobiosyl-glucose and 31-ß-D-Cellotriosyl-glucose are specific DAMPs released from the hemicellulose of rice cell wall, which are perceived by an OsCERK1 and OsCEBiP immune complex during M. oryzae infection in rice.