A P4-ATPase gene GbPATP of cotton confers chilling tolerance in plants

Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals

At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.

Applications of Virus-Induced Gene Silencing in Cotton

Virus-induced gene silencing (VIGS) is an RNA-mediated reverse genetics technique that has become an effective tool to investigate gene function in plants. Cotton is one of the most important economic crops globally. In the past decade, VIGS has been successfully applied in cotton functional genomic studies, including those examining abiotic and biotic stress responses and vegetative and reproductive development. This article summarizes the traditional vectors used in the cotton VIGS system, the visible markers used for endogenous gene silencing, the applications of VIGS in cotton functional genomics, and the limitations of VIGS and how they can be addressed in cotton.

Calcium-dependent protein kinase GhCDPK4 plays a role in drought and abscisic acid stress responses

Drought is an important factor limiting the yield and quality of cotton. In the present study, the gene encoding the cotton calcium-dependent protein kinase GhCDPK4 was identified and characterized in the transcriptome of cotton under PEG-induced drought stress. In RT-qPCR experiments, GhCDPK4 expression was found to be up-regulated under drought and abscisic acid (ABA) stress. Under drought conditions, heterologous overexpression of GhCDPK4 in tobacco showed a better phenotypic status, higher antioxidant enzyme activity, and lower relative electrolyte leakage (REL) and malondialdehyde (MDA) content. Meanwhile, ghcdpk4-silenced cotton plants, which were extremely sensitive to drought, exhibited higher levels of O^2-，H₂O₂, and MDA contents compared to the control. Meanwhile, silenced lines showed impaired stomatal closure under drought stress, resulting in increased water loss from transpiration in silenced lines. GhCDPK4 expression was induced by ABA, and there are five ABA-responsive elements in its promoter. and C2-DOMAIN ABA-RELATED 4(CAR4, Gh_D09G1653) were found to interact and be co-expressed in the GhCDPK4 interaction network. Therefore, GhCDPK4 may reduce the extent of water loss and oxidative damage in cotton under drought by positively regulating ABA-controlled stomatal closure and reactive oxygen species (ROS) scavenging systems. This study demonstrates the great potential of GhCDPK4 in improving drought resistance in crops.

Genome-wide identification and functional analysis of ICE genes reveal that Gossypium thurberi "GthICE2" is responsible for cold and drought stress tolerance

Cold stress has been found to have a negative impact on cotton growth and annual production. To address this issue, the utilization of cold-tolerant gene resources from wild species of Gossypium is crucial for genetic improvements in cultivated cotton. ICE (inducer of CBF expression) are the key regulators of cold tolerance in plants, however, there is relatively little information on ICE genes in cotton. Herein, we performed comprehensive bioinformatics analyses of the ICE gene family in eight cotton species. Phylogenetic analysis showed that 52 ICE genes were clustered into four subgroups. Cis-regulatory elements analysis suggests that the expression of ICE genes might be regulated by light, plant hormones, and various environment stresses. Higher expression of GthICE2 was observed in leaves as compared to roots and stems, in response to cold, drought, and exogenous hormone ABA. Furthermore, overexpression of GthICE2 in A. thaliana led to higher germination and survival rates, longer root length, lower ion leakage, and induction under cold and drought stress. Histochemical staining showed that oxidative damage in transgenic lines was much lower compared to wild-type plants. Lower MDA contents and higher SOD and POD activities were observed in overexpressed plants. Y1H and LUC assays revealed that GthICE2 might activate the expression of GthCBF4, a cold-responsive gene, by connecting with the MYC cis-element present in the promoter of GthCBF4. GthICE2 confers cold and drought stress tolerance in cotton. Our findings add significantly to the existing knowledge regarding cold stress tolerance and helps to elucidate cold response mechanisms in cotton.

Mini-review: Lipid flippases as putative targets for biotechnological crop improvement

An increasing world population and drastic changes in weather conditions are challenging agricultural production. To face these challenges and ensure sustainable food production in the future, crop plants need to be improved to withstand several different biotic and abiotic stresses. Commonly, breeders select varieties that can tolerate a specific type of stress and then cross these varieties to stack beneficial traits. This strategy is time-consuming and strictly dependent on the stacked traits been genetically unlinked. Here, we revise the role of plant lipid flippases of the P4 ATPase family in stress-related responses with a special focus on the pleiotropic nature of their functions and discuss their suitability as biotechnological targets for crop improvement.

Plant transbilayer lipid asymmetry and the role of lipid flippases

Many biological membranes present an asymmetric lipid distribution between the two leaflets that is known as the transbilayer lipid asymmetry. This asymmetry is essential for cell survival and its loss is related to apoptosis. In mammalian and yeast cells, ATP-dependent transport of lipids to the cytosolic side of the biological membranes, carried out by so-called lipid flippases, contributes to the transbilayer lipid asymmetry. Most of these lipid flippases belong to the P4-ATPase protein family, which is also present in plants. In this review, we summarize the relatively scarce literature concerning the presence of transbilayer lipid asymmetry in different plant cell membranes and revise the potential role of lipid flippases of the P4-ATPase family in generation and/or maintenance of this asymmetry.

Assessment of Salt Stress to Arabidopsis Based on the Detection of Hydrogen Peroxide Released by Leaves Using an Electrochemical Sensor

Salt stress will have a serious inhibitory effect on various metabolic processes of plant cells, this will lead to the excessive accumulation of reactive oxygen species (ROS). Hydrogen peroxide (H2O2) is a type of ROS that can severely damage plant cells in large amounts. Existing methods for assessing the content of H2O2 released from leaves under salt stress will cause irreversible damage to plant leaves and are unable to detect H2O2 production in real time. In this study, on the strength of a series of physiological indicators to verify the occurrence of salt stress, an electrochemical sensor for the detection of H2O2 released from leaves under salt stress was constructed. The sensor was prepared by using multi-walled carbon nanotube-titanium carbide-palladium (MWCNT-Ti3C2Tx-Pd) nanocomposite as substrate material and showed a linear response to H2O2 detection in the range 0.05-18 mM with a detection limit of 3.83 μM. Moreover, we measured the determination of H2O2 released from Arabidopsis leaves at different times of salt stress by the sensor, which was consistent with conventional method. This study demonstrates that electrochemical sensing is a desirable technology for the dynamic determination of H2O2 released by leaves and the assessment of salt stress to plants.

Visible gland constantly traces virus-induced gene silencing in cotton

A virus-induced gene silencing (VIGS) system was established to induce endogenous target gene silencing by post-transcriptional gene silencing (PTGS), which is a powerful tool for gene function analysis in plants. Compared with stable transgenic plant via Agrobacterium-mediated gene transformation, phenotypes after gene knockdown can be obtained rapidly, effectively, and high-throughput through VIGS system. This approach has been successfully applied to explore unknown gene functions involved in plant growth and development, physiological metabolism, and biotic and abiotic stresses in various plants. In this system, GhCLA1 was used as a general control, however, silencing of this gene leads to leaf albino, wilting, and plant death ultimately. As such, it cannot indicate the efficiency of target gene silencing throughout the whole plant growth period. To address this question, in this study, we developed a novel marker gene, Gossypium PIGMENT GLAND FORMATION GENE (GoPGF), as the control to trace the efficiency of gene silencing in the infected tissues. GoPGF has been proved a key gene in gland forming. Suppression of GoPGF does not affect the normal growth and development of cotton. The number of gland altered related to the expression level of GoPGF gene. So it is a good marker that be used to trace the whole growth stages of plant. Moreover, we further developed a method of friction inoculation to enhance and extend the efficiency of VIGS, which facilitates the analysis of gene function in both the vegetative stage and reproductive stage. This improved VIGS technology will be a powerful tool for the rapid functional identification of unknown genes in genomes.

The GhMYB36 transcription factor confers resistance to biotic and abiotic stress by enhancing PR1 gene expression in plants

Drought and Verticillium wilt disease are two main factors that limit cotton production, which necessitates the identification of key molecular switch to simultaneously improve cotton resistance to Verticillium dahliae and tolerance to drought stress. R2R3-type MYB proteins could play such a role because of their conserved functions in plant development, growth, and metabolism regulation, however, till date a MYB gene conferring the desired resistance to both biotic and abiotic stresses has not been found in cotton. Here, we describe the identification of GhMYB36, a gene encoding a R2R3-type MYB protein in Gossypium hirsutum, which confers drought tolerance and Verticilium wilt resistance in both Arabidopsis and cotton. GhMYB36 was highly induced by PEG-simulated drought stress in G. hirsutum. GhMYB36-silenced cotton plants were more sensitive to both drought stress and Verticillium wilt. GhMYB36 overexpression in transgenic Arabidopsis and cotton plants gave rise to improved drought tolerance and Verticillium wilt resistance. Transient expression of fused GhMYB36-GFP in tobacco cells was able to localize GhMYB36 in the cell nucleus. In addition, RNA-seq analysis together with qRT-PCR validation in transgenic Arabidopsis overexpressing GhMYB36 revealed significantly enhanced PR1 expression. Luciferase interaction assays indicated that GhMYB36 are probably bound to the promoter of PR1 to activate its expression and the interaction, which was further verified by Yeast one hybrid assay. Taken together, our results suggest that GhMYB36 functions as a transcription factor that is involved in drought tolerance and Verticillium wilt resistance in Arabidopsis and cotton by enhancing PR1 expression.

A Putative P-Type ATPase Regulates the Secretion of Hydrolytic Enzymes, Phospholipid Transport, Morphogenesis, and Pathogenesis in Phytophthora capsici

Phytophthora capsici is an important plant pathogenic oomycete with multiple hosts. The P4-ATPases, aminophospholipid translocases (APTs), play essential roles in the growth and pathogenesis of fungal pathogens. However, the function of P4-ATPase in P. capsici remains unclear. This study identified and characterized PcApt1, a P4-ATPase Drs2 homolog, in P. capsici. Deletion of PcAPT1 by CRISPR/Cas9 knock-out strategy impaired hyphal growth, extracellular laccase activity. Cytological analyses have shown that PcApt1 participates in phosphatidylserine (PS) transport across the plasma membrane. Also, we showed that targeted deletion of PcAPT1 triggered a significant reduction in the virulence of P. capsici. Secretome analyses have demonstrated that secretion of hydrolytic enzymes decreased considerably in the PcAPT1 gene deletion strains compared to the wild-type. Overall, our results showed that PcApt1 plays a pivotal role in promoting morphological development, phospholipid transport, secretion of hydrolytic enzymes, and the pathogenicity of the polycyclic phytopathogenic oomycete P. capsici. This study underscores the need for comprehensive evaluation of subsequent members of the P-type ATPase family to provide enhanced insights into the dynamic contributions to the pathogenesis of P. capsici and their possible deployment in the formulation of effective control strategies.

Comparative transcriptome, physiological and biochemical analyses reveal response mechanism mediated by CBF4 and ICE2 in enhancing cold stress tolerance in Gossypium thurberi

Low temperature is one of the key environmental stresses that impair plant growth and significantly restricts the productivity and spatial distribution of crop plants. Gossypium thurberi, a wild diploid cotton species, has adapted to a wide range of temperatures and exhibits a better tolerance to chilling stress. Here, we compared phenotypes and physiochemical changes in G. thurberi under cold stress and found this species indeed showed better cold tolerance. Therefore, to understand the molecular mechanisms of the cold tolerance in G. thurberi, we compared transcription changes in leaves of G. thurberi under cold stress by high-throughput transcriptome sequencing. In total, 35 617 unigenes were identified in the whole-genome transcription profile, and 4226 differentially expressed genes (DEGs) were discovered in the leaves upon cold treatment. Gene Ontology (GO) classification analyses showed that the majority of DEGs belonged to categories of signal transduction, transcription factors (TFs) and carbohydrate transport and metabolism. The expression of several cold-responsive genes such as ICE1, CBF4, RAP2-7 and abscisic acid (ABA) biosynthesis genes involved in different signalling pathways were induced after G. thurberi seedlings were exposed to cold stress. Furthermore, cold sensitivity was increased in CBF4 and ICE2 virus-induced gene silencing (VIGS) plants, and high level of malondialdehyde (MDA) showed that the CBF4 and ICE2 silenced plants were under oxidative stress compared to their wild types, which relatively had higher levels of antioxidant enzyme activity, as evident by high levels of proline and superoxide dismutase (SOD) content. In conclusion, our findings reveal a new regulatory network of cold stress response in G. thurberi and broaden our understanding of the cold tolerance mechanism in cotton, which might accelerate functional genomics studies and genetic improvement for cold stress tolerance in cultivated cotton.

Catch You on the Flip Side: A Critical Review of Flippase Mutant Phenotypes

Lipid flippases are integral membrane proteins that use ATP hydrolysis to power the generation of phospholipid asymmetry between the two leaflets of biological membranes, a process essential for cell survival. Although the first report of a plant lipid flippase was published in 2000, progress in the field has been slow, partially due to the high level of redundancy in this gene family. However, recently an increasing number of reports have examined the physiological function of lipid flippases, mainly in Arabidopsis thaliana. In this review we aim to summarize recent findings on the physiological relevance of lipid flippases in plant adaptation to a changing environment and caution against misinterpretation of pleiotropic effects in genetic studies of flippases.

Genome-wide identification of lectin receptor kinases in pear: Functional characterization of the L-type LecRLK gene PbLRK138

Lectin receptor-like kinases (LecRLKs) are membrane-bound receptors that are believed to be involved in biotic and abiotic stress responses. However, little is known about the LecRLK family in pear. In this study, a total of 172 LecRLK genes were first identified in the entire pear genome. The 172 LecRLKs were divided into three types (111 G-, 59 L- and two C-types) based on their structure and phylogenetic relationships. LecRLKs gene expressions were detected in different pear tissues including roots, stems, leaves, flowers and fruits, and the most of the 11 selected LecRLKs exhibited similar expression patterns. Furthermore, six selected LecRLKs were shown to be involved in salt stress response. Overexpression of PbLRK138, an L-type LecRLK, caused cell death and induced expression of defense-related genes in Nicotiana benthamiana. Two deletion mutants containing lectin or transmembrane and serine/threonine kinase domains did not trigger cell death. In addition, only the mutant with the transmembrane domain was localized to the plasma membrane.

Heterologous expression of GmSIP1;3 from soybean in tobacco showed and growth retardation and tolerance to hydrogen peroxide

Aquaporins (AQPs) are transmembrane protein channels that are members of Major Intrinsic Proteins (MIP) superfamily. AQPs play important roles in plant reproduction, cell elongation, osmoregulation, influence leaf physiology and are responsive to drought and salt tolerance. Small intrinsic proteins (SIPs)belongs to one of the groups of AQPs, which are mainly localized to endoplasmic reticulum(ER). While this group of aquaporin is being well studied in Arabidopsis, grape and other plant species, not much is known about the molecular regulatory mechanisms driven by ER-type AQPs in Glycine Max. In this study, the function of GmSIP1;3 is studied in detail by using both yeast and plant systems. GmSIP1;3 showed a ubiquitous expression pattern in all different tissues in Glycine Max. Heterologous expression of GmSIP1;3 in Nicotiana tabacum conferred a short root phenotype,growth retardation at seedling stage and significant tolerance to oxidative stress (H2O2) both in yeast and plant systems. Auxin (IAA) content significantly increased in transgenic plants compared with that of wild type, however, the abscisic acid (ABA) content was significantly reduced. Subcellular localization and colocalization analyses showed GmSIP1;3 localized to ER plasma membrane. On the basis of these observations, we postulate that GmSIP1;3 is involved in oxidative stress pathways.

Two Lysin-Motif Receptor Kinases, Gh-LYK1 and Gh-LYK2, Contribute to Resistance against Verticillium wilt in Upland Cotton

Lysin-motif (LysM) receptor kinases (LYKs) play essential roles in recognition of chitin and activation of defense responses against pathogenic fungi in the model plants Arabidopsis and rice. The function of LYKs in non-model plants, however, remains elusive. In the present work, we found that the transcription of two LYK-encoding genes from cotton, Gh-LYK1 and Gh-LYK2, was induced after Verticillium dahliae infection. Virus-induced gene silencing (VIGS) of Gh-LYK1 and Gh-LYK2 in cotton plants compromises resistance to V. dahliae. As putative pattern recognition receptors (PRRs), both Gh-LYK1 and Gh-LYK2 are membrane-localized, and all three LysM domains of Gh-LYK1 and Gh-LYK2 are required for their chitin-binding ability. However, since Gh-LYK2, but not Gh-LYK1, is a pseudo-kinase and, on the other hand, the ectodomain (ED) of Gh-LYK2 can induce reactive oxygen species (ROS) burst in planta, Gh-LYK2 and Gh-LYK1 may contribute differently to cotton defense. Taken together, our results establish that both Gh-LYK1 and Gh-LYK12 are required for defense against V. dahliae in cotton, possibly through different mechanisms.