METALLOTHIONEIN genes encoding ROS scavenging enzymes are down-regulated in the root cortex during inducible aerenchyma formation in rice

CDPK5 and CDPK13 play key roles in acclimation to low oxygen through the control of RBOH-mediated ROS production in rice

CALCIUM-DEPENDENT PROTEIN KINASE (CDPK) stimulates reactive oxygen species (ROS)-dependent signaling by activating RESPIRATORY BURST OXIDASE HOMOLOG (RBOH). The lysigenous aerenchyma is a gas space created by cortical cell death that facilitates oxygen diffusion from the shoot to the root tips. Previously, we showed that RBOHH is indispensable for the induction of aerenchyma formation in rice (Oryza sativa) roots under low-oxygen conditions. Here, we showed that CDPK5 and CDPK13 localize to the plasma membrane where RBOHH functions. Mutation analysis of the serine at residues 92 and 107 of RBOHH revealed that these residues are required for CDPK5- and CDPK13-mediated activation of ROS production. The requirement of Ca2+ for CDPK5 and CDPK13 function was confirmed using in vitro kinase assays. CRISPR/Cas9-based mutagenesis of CDPK5 and/or CDPK13 revealed that the double knockout almost completely suppressed inducible aerenchyma formation, whereas the effects were limited in the single knockout of either CDPK5 or CDPK13. Interestingly, the double knockout almost suppressed the induction of adventitious root formation, which is widely conserved in vascular plants, under low-oxygen conditions. Our results suggest that CDPKs are essential for the acclimation of rice to low-oxygen conditions and also for many other plant species conserving CDPK-targeted phosphorylation sites in RBOH homologs.

PagMYB180 regulates adventitious rooting via a ROS/PCD-dependent pathway in poplar

The formation of adventitious roots (AR) is an essential step in the vegetative propagation of economically woody species. Reactive oxygen species (ROS) function as signaling molecules in regulating root growth and development. Here, we identified an R2R3-MYB transcription factor PagMYB180 as a regulator of AR formation in hybrid poplar (Populus alba × Populus glandulosa). PagMYB180 was specifically expressed in the vascular tissues of poplar roots, stems and leaves, and its protein was localized in the nucleus and acted as a transcriptional repressor. Both dominant repression and overexpression of PagMYB180 resulted in a significant reduction of AR quantity, a substantial increase of AR length, and an elevation of both the quantity and length of lateral roots (LR) compared to the wild type (WT) plants. Furthermore, PagMYB180 regulates programmed cell death (PCD) in root cortex cells, which is associated with elevated levels of ROS. Transcriptome and reverse transcription-quantitative PCR (RT-qPCR) analyses revealed that a series of differentially expressed genes are related to ROS, PCD and ethylene synthesis. Taken together, these results suggest that PagMYB180 may regulate AR development via a ROS/PCD-dependent pathway in poplar.

Understanding plant responses to saline waterlogging: insights from halophytes and implications for crop tolerance

MAIN CONCLUSION

Saline and wet environments stress most plants, reducing growth and yield. Halophytes adapt with ion regulation, energy maintenance, and antioxidants. Understanding these mechanisms aids in breeding resilient crops for climate change. Waterlogging and salinity are two abiotic stresses that have a major negative impact on crop growth and yield. These conditions cause osmotic, ionic, and oxidative stress, as well as energy deprivation, thus impairing plant growth and development. Although few crop species can tolerate the combination of salinity and waterlogging, halophytes are plant species that exhibit high tolerance to these conditions due to their morphological, anatomical, and metabolic adaptations. In this review, we discuss the main mechanisms employed by plants exposed to saline waterlogging, intending to understand the mechanistic basis of their ion homeostasis. We summarize the knowledge of transporters and channels involved in ion accumulation and exclusion, and how they are modulated to prevent cytosolic toxicity. In addition, we discuss how reactive oxygen species production and cell signaling enhance ion transport and aerenchyma formation, and how plants exposed to saline waterlogging can control oxidative stress. We also address the morphological and anatomical modifications that plants undergo in response to combined stress, including aerenchyma formation, root porosity, and other traits that help to mitigate stress. Furthermore, we discuss the peculiarities of halophyte plants and their features that can be leveraged to improve crop yields in areas prone to saline waterlogging. This review provides valuable insights into the mechanisms of plant adaptation to saline waterlogging thus paving the path for future research on crop breeding and management strategies.

Where the wild things are: genetic associations of environmental adaptation in the Oryza rufipogon species complex

Crop wild relatives host unique adaptation strategies that enable them to thrive across a wide range of habitats. As pressures from a changing climate mount, a more complete understanding of the genetic variation that underlies this adaptation could enable broader utilization of wild materials for crop improvement. Here, we carry out environmental association analyses (EAA) in the Oryza rufipogon species complex (ORSC), the wild progenitor of cultivated Asian rice, to identify genomic regions associated with environmental adaptation characterized by variation in bioclimatic and soil variables. We further examine regions for colocalizations with phenotypic associations within the same collection. EAA results indicate that significant regions tend to associate with single environmental variables, although 2 significant loci on chromosomes 3 and 5 are detected as common across multiple variable types (i.e. precipitation, temperature, and/or soil). Distributions of allele frequencies at significant loci across subpopulations of cultivated Oryza sativa indicate that, in some cases, adaptive variation may already be present among cultivars, although evaluation in cultivated populations is needed to empirically test this. This work has implications for the potential utility of wild genetic resources in pre-breeding efforts for rice improvement.

Emerging role of small GTPases and their interactome in plants to combat abiotic and biotic stress

Plants are frequently subjected to abiotic and biotic stress which causes major impediments in their growth and development. It is emerging that small guanosine triphosphatases (small GTPases), also known as monomeric GTP-binding proteins, assist plants in managing environmental stress. Small GTPases function as tightly regulated molecular switches that get activated with the aid of guanosine triphosphate (GTP) and deactivated by the subsequent hydrolysis of GTP to guanosine diphosphate (GDP). All small GTPases except Rat sarcoma (Ras) are found in plants, including Ras-like in brain (Rab), Rho of plant (Rop), ADP-ribosylation factor (Arf) and Ras-like nuclear (Ran). The members of small GTPases in plants interact with several downstream effectors to counteract the negative effects of environmental stress and disease-causing pathogens. In this review, we describe processes of stress alleviation by developing pathways involving several small GTPases and their associated proteins which are important for neutralizing fungal infections, stomatal regulation, and activation of abiotic stress-tolerant genes in plants. Previous reviews on small GTPases in plants were primarily focused on Rab GTPases, abiotic stress, and membrane trafficking, whereas this review seeks to improve our understanding of the role of all small GTPases in plants as well as their interactome in regulating mechanisms to combat abiotic and biotic stress. This review brings to the attention of scientists recent research on small GTPases so that they can employ genome editing tools to precisely engineer economically important plants through the overexpression/knock-out/knock-in of stress-related small GTPase genes.

Walking through crossroads-rice responses to heat and biotic stress interactions

Rice, the most important source of calories for humans is prone to severe yield loss due to changing climate including heat stress. Additionally, rice encounters biotic stresses in conjunction with heat stress, which exacerbates the adverse effects, and exponentially increase such losses. Several investigations have identified biotic and heat stress-related quantitative trait loci (QTLs) that may contribute to improved tolerance to these stresses. However, a significant knowledge gap exists in identifying the genomic regions imparting tolerance against combined biotic and heat stress. Hereby, we are presenting a conceptual meta-analysis identifying genomic regions that may be promising candidates for enhancing combined biotic and heat stress tolerance in rice. Fourteen common genomic regions were identified along chromosomes 1, 2, 3, 4, 6, 10 and 12, which harbored 1265 genes related to heat stress and defense responses in rice. Further, the meta expression analysis revealed 24 differentially expressed genes (DEGs) involved in calcium-mediated stress signaling including transcription factors Myb, bHLH, ROS signaling, molecular chaperones HSP110 and pathogenesis related proteins. Additionally, we also proposed a hypothetical model based on GO and MapMan analysis representing the pathways intersecting heat and biotic stresses. These DEGs can be potential candidate genes for improving tolerance to combined biotic and heat stress in rice. We present a framework highlighting plausible connecting links (QTLs/genes) between rice response to heat stress and different biotic factors associated with yield, that can be extended to other crops.

Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia

Hypoxia is an abiotic stress in plants. Flooding resulting from climate change is a major crop threat that increases the risk of hypoxic stress. The molecular mechanisms underlying hypoxia in plants were elucidated in recent years, but new genes related to this stress remain to be discovered. Thus, we aimed to perform a meta-analysis of the RNA sequencing (RNA-Seq) data of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) under hypoxia. We collected 29 (Arabidopsis) and 26 (rice) pairs of RNA-Seq data involving hypoxic (including submergence) and normoxic (control) treatments and extracted the genes that were commonly upregulated or downregulated in the majority of the experiments. The meta-analysis revealed 40 and 19 commonly upregulated and downregulated genes, respectively, in the two species. Several WRKY transcription factors and cinnamate-4-hydroxylase were commonly upregulated, but their involvement in hypoxia remains unclear. Our meta-analysis identified candidate genes for novel molecular mechanisms in plants under hypoxia.

CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice

In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.

Preformed aerenchyma determines the differential tolerance response under partial submergence imposed by fresh and saline water flooding in rice

Plant's response to fresh- and saline-water flooding and the resulting partial submergence, seems different due to the added complexities of element toxicity of salinity. We identified a few rice genotypes which can tolerate combined stresses of partial submergence and salinity during saline water flooding. To gain mechanistic insights, we compared two rice genotypes: Varshadhan (freshwater-flooding tolerant) and Rashpanjor (both fresh- and saline-water flooding tolerant). We found greater ethylene production and increased "respiratory burst oxidase homolog" (RBOH)-mediated reactive oxygen species (ROS) production led to well-developed constitutive aerenchyma formation in Rashpanjor, which makes it preadapted to withstand fresh- and saline-water flooding. On the contrary, an induced aerenchyma formation-dependent tolerance mechanism of Varshadhan worked well for freshwater flooding but failed to provide tolerance to saline-water flooding. Additional salt stress was found to significantly inhibit the induced aerenchyma formation process due to the dampening of ROS signaling by the action of metallothionein in Varshadhan. Besides, inconspicuous changes in ionic regulation processes in these two genotypes under saline-water flooding suggest preadapted constitutive aerenchyma formation plays a more significant role than elemental toxicity per se in tolerating combined stresses encountered during saline water flooding in rice. Overall, our study indicated that well-developed constitutive aerenchyma provide an adaptive advantage during partial submergence due to saline water flooding in rice as the key process of induced aerenchyma formation is hampered in the presence of salinity stress coupled with partial submergence.

Heterotrimeric G protein γ subunit DEP1 is involved in hydrogen peroxide signaling and promotes aerenchyma formation in rice roots

Heterotrimeric G-protein α and β-subunits regulate H₂O₂-mediated aerenchyma formation. The rice G-protein γ-subunit, dense and erect panicle 1 (DEP1), is known to interact with the α-subunit and regulate nitrogen utilization and yield. However, it is unclear whether DEP1 regulates cell death for aerenchyma formation in rice roots. Using wild-type WYJ8 and its transgenic line WYJ8(DEP1), we confirmed that DEP1 is involved in H₂O₂-mediated aerenchyma formation. The rates of aerenchyma formation varied in different parts of the roots in both varieties, with the highest rate in the 4-7 cm segments, reaching a plateau in the 7-8 cm segments. Compared with WYJ8, the aerenchyma area and H₂O₂ content in WYJ8(DEP1) were increased by 55.98% and 53.37%, respectively; however, the responses of aerenchyma formation to exogenous H₂O₂ were basically the same in the two varieties. Diphenylene iodonium (DPI) treatment had no effect on H₂O₂ production and elimination processes in WYJ8, but significantly reduced the activity of the key enzyme that catalyzes H₂O₂ biosynthesis in WYJ8(DEP1). Importantly, exogenous H₂O₂ treatment did not offset the effect of the decrease in endogenous H₂O₂ level caused by DPI on aerenchyma formation. These results indicated that DEP1 enhanced H₂O₂ biosynthesis and promoted the cell death of the root cortex, thus contributing to aerenchyma development in WYJ8(DEP1).

Domestication of High-Copy Transposons Underlays the Wheat Small RNA Response to an Obligate Pathogen

Plant genomes have evolved several evolutionary mechanisms to tolerate and make use of transposable elements (TEs). Of these, transposon domestication into cis-regulatory and microRNA (miRNA) sequences is proposed to contribute to abiotic/biotic stress adaptation in plants. The wheat genome is derived at 85% from TEs, and contains thousands of miniature inverted-repeat transposable elements (MITEs), whose sequences are particularly prone for domestication into miRNA precursors. In this study, we investigate the contribution of TEs to the wheat small RNA immune response to the lineage-specific, obligate powdery mildew pathogen. We show that MITEs of the Mariner superfamily contribute the largest diversity of miRNAs to the wheat immune response. In particular, MITE precursors of miRNAs are wide-spread over the wheat genome, and highly conserved copies are found in the Lr34 and QPm.tut-4A mildew resistance loci. Our work suggests that transposon domestication is an important evolutionary force driving miRNA functional innovation in wheat immunity.

RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root

Due to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. This may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RNA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar 'Moneymaker', in response to short- (6 h) and long-term (48 h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short- and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes with a potential role in aerenchyma formation which facilitates oxygen transport and may act as an escape mechanism enabling hypoxia tolerance. Moreover, we identified differentially regulated genes related to carbon and amino acid metabolism and redox homeostasis. Of particular interest were the differentially regulated transcription factors, which act as master regulators of downstream target genes involved in responses to short and/or long-term hypoxia. Our data suggest a temporal metabolic and anatomic adjustment to hypoxia in tomato root which requires further investigation. We propose that the regulated genes identified in this study are good candidates for further studies regarding hypoxia tolerance in tomato or other crops.

Modulatory Role of Reactive Oxygen Species in Root Development in Model Plant of Arabidopsis thaliana

Reactive oxygen species (ROS), a type of oxygen monoelectronic reduction product, have a higher chemical activity than O₂. Although ROS pose potential risks to all organisms via inducing oxidative stress, indispensable role of ROS in individual development cannot be ignored. Among them, the role of ROS in the model plant Arabidopsis thaliana is deeply studied. Mounting evidence suggests that ROS are essential for root and root hair development. In the present review, we provide an updated perspective on the latest research progress pertaining to the role of ROS in the precise regulation of root stem cell maintenance and differentiation, redox regulation of the cell cycle, and root hair initiation during root growth. Among the different types of ROS, O₂ ^•- and H₂O₂ have been extensively investigated, and they exhibit different gradient distributions in the roots. The concentration of O₂ ^•- decreases along a gradient from the meristem to the transition zone and the concentration of H₂O₂ decreases along a gradient from the differentiation zone to the elongation zone. These gradients are regulated by peroxidases, which are modulated by the UPBEAT1 (UPB1) transcription factor. In addition, multiple transcriptional factors, such as APP1, ABO8, PHB3, and RITF1, which are involved in the brassinolide signaling pathway, converge as a ROS signal to regulate root stem cell maintenance. Furthermore, superoxide anions (O₂ ^•-) are generated from the oxidation in mitochondria, ROS produced during plasmid metabolism, H₂O₂ produced in apoplasts, and catalysis of respiratory burst oxidase homolog (RBOH) in the cell membrane. Furthermore, ROS can act as a signal to regulate redox status, which regulates the expression of the cell-cycle components CYC2;3, CYCB1;1, and retinoblastoma-related protein, thereby controlling the cell-cycle progression. In the root maturation zone, the epidermal cells located in the H cell position emerge to form hair cells, and plant hormones, such as auxin and ethylene regulate root hair formation via ROS. Furthermore, ROS accumulation can influence hormone signal transduction and vice versa. Data about the association between nutrient stress and ROS signals in root hair development are scarce. However, the fact that ROBHC/RHD2 or RHD6 is specifically expressed in root hair cells and induced by nutrients, may explain the relationship. Future studies should focus on the regulatory mechanisms underlying root hair development via the interactions of ROS with hormone signals and nutrient components.

Identification of the metallothionein gene family from cucumber and functional characterization of CsMT4 in Escherichia coli under salinity and osmotic stress

Metallothionein (MT) proteins are low-molecular-weight, cysteine-rich and metal-binding proteins that play important roles in the maintenance of metal homeostasis and detoxification, but their roles in abiotic stress tolerance remain largely unknown. In this study, three MT family genes (CsMT2, CsMT3 and CsMT4) were identified in the cucumber genome. CsMT2, CsMT3 and CsMT4 possessed 14, 10, and 18 Cys residues, which were clustered into 2, 2, and 3 Cys-rich regions, respectively. Phylogenetic analysis of MTs from cucumber, Arabidopsis and soybean revealed that these MTs were clustered into four groups in accordance with the MT types (types 1-4). An analysis of the cis-acting regulatory elements revealed that a series of hormone-, stress-, and development-related cis-elements were present in the promoter regions of CsMT genes. Expression pattern analysis by RT-PCR showed that the CsMT genes exhibited different tissue expression patterns. CsMT2 showed relatively higher expression in stem, leaf, and flower; CsMT3 was mainly expressed in leaf, flower, and fruit, while CsMT4 was highly expressed in fruit and leaf. The qRT-PCR results showed that the CsMT genes were induced by various stress treatments including NaCl, PEG, and ABA, while CsMT4 displayed much higher expression levels in response to these stresses than CsMT2 and CsMT3. Escherichia coli cells expressing CsMT4 exhibited higher salinity and osmotic tolerance compared with control cells, indicating the significant function of CsMT4 to confer tolerance to these stresses. These results lay a foundation for further research on the function of MT family genes in plant stress responses.

Comparative expression analysis of genes encoding metallothioneins in response to heavy metals and abiotic stresses in rice (Oryza sativa) and Arabidopsis thaliana

To get insights into the functions of metallothionein (MT) in plant response to multiple stresses, expressions of 10 rice MT genes (OsMTs) and 7 Arabidopsis MT genes (AtMTs) were comprehensively analyzed under combined heavy metal and salt stress. OsMT1a, OsMT1b, OsMT1c, OsMT1g, and OsMT2a were increased by different heavy metals. Notably, ABA remarkably increased OsMT4 up to 80-fold. Combined salt and heavy metals (Cd, Pb, Cu) synergistically increased OsMT1a, OsMT1c, and OsMT1g, whereas combined salt and H₂O₂ or ABA synergistically increased OsMT1a and OsMT4. Heavy metals decreased AtMT1c, AtMT2b, and AtMT3 but cold or ABA increased AtMT1a, AtMT1c, and AtMT2a. AtMT4a was markedly increased by salt stress. Combined salt and other stresses (Pb, Cd, H₂O₂) synergistically increased AtMT4a. Taken together, these findings suggest that MTs in monocot and dicot respond differently to combined stresses, which provides a valuable basis to further determine the roles of MTs in broad stress tolerance.