CRISPR/Cas genome editing in plants: mechanisms, applications, and overcoming bottlenecks

The CRISPR/Cas systems have emerged as transformative tools for precisely manipulating plant genomes and enhancement. It has provided unparalleled applications from modifying the plant genomes to resistant enhancement. This review manuscript summarises the mechanism, application, and current challenges in the CRISPR/Cas genome editing technology. It addresses the molecular mechanisms of different Cas genes, elucidating their applications in various plants through crop improvement, disease resistance, and trait improvement. The advent of the CRISPR/Cas systems has enabled researchers to precisely modify plant genomes through gene knockouts, knock-ins, and gene expression modulation. Despite these successes, the CRISPR/Cas technology faces challenges, including off-target effects, Cas toxicity, and efficiency. In this manuscript, we also discuss these challenges and outline ongoing strategies employed to overcome these challenges, including the development of novel CRISPR/Cas variants with improved specificity and specific delivery methods for different plant species. The manuscript will conclude by addressing the future perspectives of the CRISPR/Cas technology in plants. Although this review manuscript is not conclusive, it aims to provide immense insights into the current state and future potential of CRISPR/Cas in sustainable and secure plant production.

Systematic Characterization of GATA Transcription Factors in Liriodendron chinense and Functional Validation in Abiotic Stresses

The Liriodendron chinense in the Magnoliaceae family is an endangered tree species useful for its socio-economic and ecological benefits. Abiotic stresses (cold, heat, and drought stress), among other factors, affect its growth, development, and distribution. However, GATA transcription factors (TFs) respond to various abiotic stresses and play a significant role in plant acclimatization to abiotic stresses. To determine the function of GATA TFs in L. chinense, we investigated the GATA genes in the genome of L. chinense. In this study, a total of 18 GATA genes were identified, which were randomly distributed on 12 of the total 17 chromosomes. These GATA genes clustered together in four separate groups based on their phylogenetic relationships, gene structures, and domain conservation arrangements. Detailed interspecies phylogenetic analyses of the GATA gene family demonstrated a conservation of the GATAs and a probable diversification that prompted gene diversification in plant species. In addition, the LcGATA gene family was shown to be evolutionarily closer to that of O. sativa, giving an insight into the possible LcGATA gene functions. Investigations of LcGATA gene duplication showed four gene duplicate pairs by the segmental duplication event, and these genes were a result of strong purified selection. Analysis of the cis-regulatory elements demonstrated a significant representation of the abiotic stress elements in the promoter regions of the LcGATA genes. Additional gene expressions through transcriptome and qPCR analyses revealed a significant upregulation of LcGATA17, and LcGATA18 in various stresses, including heat, cold, and drought stress in all time points analyzed. We concluded that the LcGATA genes play a pivotal role in regulating abiotic stress in L. chinense. In summary, our results provide new insights into understanding of the LcGATA gene family and their regulatory functions during abiotic stresses.

Oxidative Stress Response and Metal Transport in Roots of Macleaya cordata Exposed to Lead and Zinc

Heavy metal pollution possesses potential hazards to plant, animal and human health, which has become the focus of recent attention. Hence, phytoremediation has been regarded as one of the most important remediation technologies for heavy-metal-contaminated soils. In this research, a dominant mine tailing plant, Macleaya cordata, was used as the experimental material to compare the metal transport and oxidative stress response in its roots under lead (Pb) and zinc (Zn) treatments. The result showed that Pb was mainly accumulated in the roots of M. cordata under the Pb treatment; less than 1% Pb was transported to the parts above. An analysis of the Zn content demonstrated a 39% accumulation in the shoots. The production of reactive oxygen species was detected using the in situ histological staining of roots, which showed that hydrogen peroxide in the root tips was observed to increase with the increase in both Pb and Zn concentrations. No significant superoxide anion changes were noted in the root tips under the Pb treatment. An analysis of the root enzyme activity showed that increase in NADPH oxidase activity can be responsible for the production of superoxide anions, subsequent the inhibition of root growth and decrease in antioxidant enzyme activities in the roots of M. cordata exposed to excess Zn. In total, this research provides evidence that the root of M. cordata has a high antioxidant capacity for Pb stress, so it can accumulate more Pb without oxidative damage. On the other hand, the Zn accumulated in the roots of M. cordata causes oxidative damage to the root tips, which can stimulate more Zn transport to the shoots to reduce the damage to the roots. This result will provide a basis for the application of M. cordata in the phytoremediation of soil polluted by Pb-Zn compounds.

Genomic Survey of Heat Shock Proteins in Liriodendron chinense Provides Insight into Evolution, Characterization, and Functional Diversities

Heat shock proteins (HSPs) are conserved molecular chaperones whose main role is to facilitate the regulation of plant growth and stress responses. The HSP gene family has been characterized in most plants and elucidated as generally stress-induced, essential for their cytoprotective roles in cells. However, the HSP gene family has not yet been analyzed in the Liriodendron chinense genome. In current study, 60 HSP genes were identified in the L. chinense genome, including 7 LchiHSP90s, 23 LchiHSP70s, and 30 LchiHSP20s. We investigated the phylogenetic relationships, gene structure and arrangement, gene duplication events, cis-acting elements, 3D-protein structures, protein-protein interaction networks, and temperature stress responses in the identified L. chinense HSP genes. The results of the comparative phylogenetic analysis of HSP families in 32 plant species showed that LchiHSPs are closely related to the Cinnamomum kanehirae HSP gene family. Duplication events analysis showed seven segmental and six tandem duplication events that occurred in the LchiHSP gene family, which we speculated to have played an important role in the LchiHSP gene expansion and evolution. Furthermore, the Ka/Ks analysis indicated that these genes underwent a purifying selection. Analysis in the promoter region evidenced that the promoter region LchiHSPs carry many stress-responsive and hormone-related cis-elements. Investigations in the gene expression patterns of the LchiHSPs using transcriptome data and the qRT-PCR technique indicated that most LchiHSPs were responsive to cold and heat stress. In total, our results provide new insights into understanding the LchiHSP gene family function and their regulatory mechanisms in response to abiotic stresses.

Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology

The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown their presence in early land plants. In this paper, we performed a comparative discussion on the current knowledge of the TCP Transcription Factors in lower and higher plants: their evolutionary history based on the phylogenetics of 849 TCP proteins from 37 plant species, duplication events, and biochemical roles in some of the plants species. Phylogenetics investigations confirmed the classification of TCP TFs into Class I (the PCF1/2), and Class II (the C- clade) factors; the Class II factors were further divided into the CIN- and CYC/TB1- subclade. A trace in the evolution of the TCP Factors revealed an absence of the CYC/TB1subclade in lower plants, and an independent evolution of the CYC/TB1subclade in both eudicot and monocot species. 54% of the total duplication events analyzed were biased towards the dispersed duplication, and we concluded that dispersed duplication events contributed to the expansion of the TCP gene family. Analysis in the TCP factors functional roles confirmed their involvement in various biochemical processes which mainly included promoting cell proliferation in leaves in Class I TCPs, and cell division during plant development in Class II TCP Factors. Apart from growth and development, the TCP Factors were also shown to regulate hormonal and stress response pathways. Although this paper does not exhaust the present knowledge of the TCP Transcription Factors, it provides a base for further exploration of the gene family.

Proteomic Analysis Reveals Salicylic Acid as a Pivotal Signal Molecule in Rice Response to Blast Disease Infection

Rice blast disease caused by a fungus, Magnaporthe grisea, is one of the most destructive diseases in rice production worldwide, and salicylic acid (SA) can efficiently decrease the damage of M. grisea. Here, we combined the 2-Dimensional-Liquid Chromatography and the Matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (2D-LC-MALDI-TOF-TOF MS) techniques to compare and identify differentially expressed labelled proteins by the isobaric tags for relative and absolute quantitation (iTRAQ) between the blast-resistant cultivar Minghui and the susceptible rice cultivar Nipponbare in response to blast fungus infection. The group samples were treated with salicylic acid and compared to control samples. A total of 139 DEPs from the two cultivars showed either more than a two-fold change or alternating regulation patterns. Protein functionality analysis also exhibited that these proteins are involved in a wide range of molecular functions including: energy-related activity (30%), signal transduction (11%), redox homeostasis (15%), amino acid and nitrogen metabolism (4%), carbohydrate metabolism (5%), protein folding and assembly (10%), protein hydrolysis (9%), protein synthesis (12%), and other unknown functions (4%). Specifically, we demonstrated that exogenous treatment with salicylic acid promoted recovery in both rice cultivars from Magnaporthe grisea infection by enhancing: the regulation of signal transduction, increasing energy conversion and production through the regulation of the glycolytic pathway, and other various biochemical processes. These findings may facilitate future studies of the molecular mechanisms of rice blast resistance.

ICE-CBF-COR Signaling Cascade and Its Regulation in Plants Responding to Cold Stress

Cold stress limits plant geographical distribution and influences plant growth, development, and yields. Plants as sessile organisms have evolved complex biochemical and physiological mechanisms to adapt to cold stress. These mechanisms are regulated by a series of transcription factors and proteins for efficient cold stress acclimation. It has been established that the ICE-CBF-COR signaling pathway in plants regulates how plants acclimatize to cold stress. Cold stress is perceived by receptor proteins, triggering signal transduction, and Inducer of CBF Expression (ICE) genes are activated and regulated, consequently upregulating the transcription and expression of the C-repeat Binding Factor (CBF) genes. The CBF protein binds to the C-repeat/Dehydration Responsive Element (CRT/DRE), a homeopathic element of the Cold Regulated genes (COR gene) promoter, activating their transcription. Transcriptional regulations and post-translational modifications regulate and modify these entities at different response levels by altering their expression or activities in the signaling cascade. These activities then lead to efficient cold stress tolerance. This paper contains a concise summary of the ICE-CBF-COR pathway elucidating on the cross interconnections with other repressors, inhibitors, and activators to induce cold stress acclimation in plants.

The bZIP transcription factors in Liriodendron chinense: Genome-wide recognition, characteristics and cold stress response

The basic leucine zipper (bZIP) is a transcription factor family that plays critical roles in abiotic and biotic stress responses as well as plant development and growth. A comprehensive genome-wide study in Liriodendron chinense was conducted to identify 45 bZIP transcription factors (LchibZIPs), which were divided into 13 subgroups according the phylogenetic analysis. Proteins in the same subgroup shared similar gene structures and conserved domains, and a total of 20 conserved motifs were revealed in LchibZIP proteins. Gene localization analysis revealed that LchibZIP genes were unequally distributed across 16 chromosomes, and that 4 pairs of tandem and 9 segmental gene duplications existed. Concluding that segmental duplication events may be strongly associated with the amplification of the L. chinense bZIP gene family. We also assessed the collinearity of LchibZIPs between the Arabidopsis and Oryza and showed that the LchibZIP is evolutionarily closer to O. sativa as compared to the A. thaliana. The cis-regulatory element analysis showed that LchibZIPs clustered in one subfamily are involved in several functions. In addition, we gathered novel research suggestions for further exploration of the new roles of LchibZIPs from protein-protein interactions and gene ontology annotations of the LchibZIP proteins. Using the RNA-seq data and qRT-PCR we analyzed the gene expression patterns of LchibZIP genes, and showed that LchibZIP genes regulate cold stress, especially LchibZIP4 and LchibZIP7; and LchibZIP2 and LchibZIP28 which were up-regulated and down-regulated by cold stress, respectively. Studies of genetic engineering and gene function in L. chinense can benefit greatly from the thorough investigation and characterization of the L. chinense bZIP gene family.