Expression of the Aeluropus littoralis AlSAP Gene Enhances Rice Yield under Field Drought at the Reproductive Stage

De novo, high-quality assembly and annotation of the halophyte grass Aeluropus littoralis draft genome and identification of A20/AN1 zinc finger protein family

BACKGROUND

Aeluropus littoralis is considered a valuable natural forage plant for ruminant livestock and is highly tolerant to extreme abiotic stresses, especially salinity, drought, and heat. It is a monocotyledonous halophyte, has salt glands, performs C4-type photosynthesis and has a close genetic relationship with cereal crops. Moreover, previous studies have shown its huge potential as a reservoir of genes and promoters to understand and improve abiotic stress tolerance in crops.

RESULTS

The sequencing and hybrid assembly of the A. littoralis genome (2n = 2X = 20) using short and long reads from the BGISeq-500 and PacBio high-fidelity (HiFi) sequencing platforms, respectively. Using the k-mer analysis method, the haploid genome size of A. littoralis was estimated to be 360 Mb (with a heterozygosity rate of 1.88%). The hybrid assembled genome included 4,078 contigs with a GC content of 44% and covered 348 Mb. The longest contig and the N50 values were 5.1 Mb and 133.77 kb, respectively. The Benchmarking Universal Single Copy Ortholog (BUSCO) value was 91.1%, indicating good integrity of the assembled genome. The discovered repetitive elements accounted for 90.6 Mb, representing 26.03% of the total genome, and included a significant component of transposable elements (11.48%, ~40 Mb). Using a homology-based approach, 35,147 genes were predicted from the genome assembly. We next focused our analysis on the zinc-finger A20/AN1 gene family, a member of which (AlSAP) was previously shown to confer increased tolerance to osmotic and salt stresses when it was over-expressed in tobacco, wheat, and rice. Here, we identified the complete set of members of this family in the Aeluropus littoralis genome, thereby laying the foundation for their future functional analysis in cereal crops. In addition, the expression patterns of four novel genes from this family were analyzed by qPCR.

CONCLUSION

This resource and our findings will contribute to improve the current understanding of salinity tolerance in halophytes while providing useful genes and allelic variation to improve salinity and drought tolerance in cereals through genetic engineering and gene editing, respectively.

Aeluropus lagopoides: an important halophyte with key physiological and molecular mechanisms for salinity tolerance and a unique genetic resource for developing climate resilient crops

Aeluropus lagopoides is salt secreting halophytic perennial grass that commonly grows in coastal regions. Under excessive saline conditions, A. lagopoides is able to thrive and completes its life cycle. It has developed various adaptive mechanisms to tolerate harsh environmental conditions. Aeluropus follow the novel mechanism of salt secretion by excreting Na+ from the leaf sheath and stem of the plant in the form of salt crystals. Various salt responsive genes and transcription factors have been studied under salinity stress in A. lagopoides. Economically important phytochemicals are also present in this plant, thus, making it industrially important. Utilization of salt stress responsive genes and transcription factors in developing salt tolerant transgenics crops can also provide significant benefits, and potentially boost the agricultural industry for sustainable growth and production.

Research progress on plant stress-associated protein (SAP) family: Master regulators to deal with environmental stresses

Every year, unfavorable environmental factors significantly affect crop productivity and threaten food security. Plants are sessile; they cannot move to escape unfavorable environmental conditions, and therefore, they activate a variety of defense pathways. Among them are processes regulated by stress-associated proteins (SAPs). SAPs have a specific zinc finger domain (A20) at the N-terminus and either AN1 or C2H2 at the C-terminus. SAP proteins are involved in many biological processes and in response to various abiotic or biotic constraints. Most SAPs play a role in conferring transgenic stress resistance and are stress-inducible. The emerging field of SAPs in abiotic or biotic stress response regulation has attracted the attention of researchers. Although SAPs interact with various proteins to perform their functions, the exact mechanisms of these interactions remain incompletely understood. This review aims to provide a comprehensive understanding of SAPs, covering their diversity, structure, expression, and subcellular localization. SAPs play a pivotal role in enabling crosstalk between abiotic and biotic stress signaling pathways, making them essential for developing stress-tolerant crops without yield penalties. Collectively, understanding the complex regulation of SAPs in stress responses can contribute to enhancing tolerance against various environmental stresses through several techniques such as transgenesis, classical breeding, or gene editing.

Rice A20/AN1 protein, OsSAP10, confers water-deficit stress tolerance via proteasome pathway and positive regulation of ABA signaling in Arabidopsis

KEY MESSAGE

Overexpression of rice A20/AN1 zinc-finger protein, OsSAP10, improves water-deficit stress tolerance in Arabidopsis via interaction with multiple proteins. Stress-associated proteins (SAPs) constitute a class of A20/AN1 zinc-finger domain containing proteins and their genes are induced in response to multiple abiotic stresses. The role of certain SAP genes in conferring abiotic stress tolerance is well established, but their mechanism of action is poorly understood. To improve our understanding of SAP gene functions, OsSAP10, a stress-inducible rice gene, was chosen for the functional and molecular characterization. To elucidate its role in water-deficit stress (WDS) response, we aimed to functionally characterize its roles in transgenic Arabidopsis, overexpressing OsSAP10. OsSAP10 transgenics showed improved tolerance to water-deficit stress at seed germination, seedling and mature plant stages. At physiological and biochemical levels, OsSAP10 transgenics exhibited a higher survival rate, increased relative water content, high osmolyte accumulation (proline and soluble sugar), reduced water loss, low ROS production, low MDA content and protected yield loss under WDS relative to wild type (WT). Moreover, transgenics were hypersensitive to ABA treatment with enhanced ABA signaling and stress-responsive genes expression. The protein-protein interaction studies revealed that OsSAP10 interacts with proteins involved in proteasomal pathway, such as OsRAD23, polyubiquitin and with negative and positive regulators of stress signaling, i.e., OsMBP1.2, OsDRIP2, OsSCP and OsAMTR1. The A20 domain was found to be crucial for most interactions but insufficient for all interactions tested. Overall, our investigations suggest that OsSAP10 is an important candidate for improving water-deficit stress tolerance in plants, and positively regulates ABA and WDS signaling via protein-protein interactions and modulation of endogenous genes expression in ABA-dependent manner.

Aeluropus littoralis stress-associated protein promotes water deficit resilience in engineered durum wheat

Global climate change-related water deficit negatively affect the growth, development and yield performance of multiple cereal crops, including durum wheat. Therefore, the improvement of water-deficit stress tolerance in durum wheat varieties in arid and semiarid areas has become imperative for food security. Herein, we evaluated the water deficiency resilience potential of two marker-free transgenic durum wheat lines (AlSAP-lines: K9.3 and K21.3) under well-watered and water-deficit stress conditions at both physiological and agronomic levels. These two lines overexpressed the AlSAP gene, isolated from the halophyte grass Aeluropus littoralis, encoding a stress-associated zinc finger protein containing the A20/AN1 domains. Under well-watered conditions, the wild-type (WT) and both AlSAP-lines displayed comparable performance concerning all the evaluated parameters. Ectopic transgene expression exerted no adverse effects on growth and yield performance of the durum wheat plants. Under water-deficit conditions, no significant differences in the plant height, leaf number, spike length, and spikelet number were observed between AlSAP-lines and WT plants. However, compared to WT, the AlSAP-lines exhibited greater dry matter production, greater flag leaf area, improved net photosynthetic rate, stomatal conductance, and water use efficiency. Notably, the AlSAP-lines displayed 25 % higher grain yield (GY) than the WT plants under water-deficit conditions. The RT-qPCR-based selected stress-related gene (TdDREB1, TdLEA, TdAPX1, and TdBlt101-2) expression analyses indicated stress-related genes enhancement in AlSAP-durum wheat plants under both well-watered and water-deficit conditions, potentially related to the water-deficit resilience. Collectively, our findings support that the ectopic AlSAP expression in durum wheat lines enhances water-deficit resilience ability, thereby potentially compensate for the GY loss in arid and semi-arid regions.

Evaluation of Halophyte Biopotential as an Unused Natural Resource: The Case of Lobularia maritima

Halophytes are plant species widely distributed in saline habitats, such as beaches, postindustrial wastelands, irrigated lands, salt flats, and others. Excessive salt level, known to limit plant growth, is not harmful to halophytes, which have developed a variety of defense mechanisms allowing them to colonize harsh environments. Plants under stress are known to respond with several morpho-anatomical adaptations, but also to enhance the production of secondary metabolites to better cope with difficult conditions. Owing to these adaptations, halophytes are an interesting group of undemanding plants with a high potential for application in the food and pharmaceutical industries. Therefore, this review aims to present the characteristics of halophytes, describe changes in their gene expression, and discuss their synthesized metabolites of pharmacognostic and pharmacological significance. Lobularia maritima is characterized as a widely spread halophyte that has been shown to exhibit various pharmacological properties in vitro and in vivo. It is concluded that halophytes may become important sources of natural products for the treatment of various ailments and for supplementing the human diet with necessary non-nutrients and minerals. However, extensive studies are needed to deepen the knowledge of their biological potential in vivo, so that they can be introduced to the pharmaceutical and food industries.

Initial Description of the Genome of Aeluropus littoralis, a Halophile Grass

The use of wild plant species or their halophytic relatives has been considered in plant breeding programs to improve salt and drought tolerance in crop plants. Aeluropus littoralis serves as halophyte model for identification and isolation of novel stress adaptation genes. A. littoralis, a perennial monocot grass, grows in damp or arid areas, often salt-impregnated places and wasteland in cultivated areas, can survive periodically high water salinity, and tolerate high salt concentrations in the soil up to 1,100 mM sodium chloride. Therefore, it serves as valuable genetic resource to understand molecular mechanisms of stress-responses in monocots. The knowledge can potentially be used for improving tolerance to abiotic stresses in economically important crops. Several morphological, anatomical, ecological, and physiological traits of A. littoralis have been investigated so far. After watering with salt water the grass is able to excrete salt via its salt glands. Meanwhile, a number of ESTs (expressed sequence tag), genes and promoters induced by the salt and drought stresses were isolated, sequenced and annotated at a molecular level. Transfer of stress related genes to other species resulted in enhanced stress resistance. Here we describe the genome sequence and structure of A. littoralis analyzed by whole genome sequencing and histological analysis. The chromosome number was determined to be 20 (2n = 2x = 20). The genome size was calculated to be 354 Mb. This genomic information provided here, will support the functional investigation and application of novel genes improving salt stress resistance in crop plants. The utility of the sequence information is exemplified by the analysis of the DREB-transcription factor family.

Identification of Candidate Genes Regulating Drought Tolerance in Pearl Millet

Pearl millet is an important crop of the arid and semi-arid ecologies to sustain food and fodder production. The greater tolerance to drought stress attracts us to examine its cellular and molecular mechanisms via functional genomics approaches to augment the grain yield. Here, we studied the drought response of 48 inbreds representing four different maturity groups at the flowering stage. A set of 74 drought-responsive genes were separated into five major phylogenic groups belonging to eight functional groups, namely ABA signaling, hormone signaling, ion and osmotic homeostasis, TF-mediated regulation, molecular adaptation, signal transduction, physiological adaptation, detoxification, which were comprehensively studied. Among the conserved motifs of the drought-responsive genes, the protein kinases and MYB domain proteins were the most conserved ones. Comparative in-silico analysis of the drought genes across millet crops showed foxtail millet had most orthologs with pearl millet. Of 698 haplotypes identified across millet crops, MyC2 and Myb4 had maximum haplotypes. The protein–protein interaction network identified ABI2, P5CS, CDPK, DREB, MYB, and CYP707A3 as major hub genes. The expression assay showed the presence of common as well as unique drought-responsive genes across maturity groups. Drought tolerant genotypes in respective maturity groups were identified from the expression pattern of genes. Among several gene families, ABA signaling, TFs, and signaling proteins were the prospective contributors to drought tolerance across maturity groups. The functionally validated genes could be used as promising candidates in backcross breeding, genomic selection, and gene-editing schemes in pearl millet and other millet crops to increase the yield in drought-prone arid and semi-arid ecologies.

Genome-Wide Analyses of Tea Plant Stress-Associated Proteins (SAPs) Reveal the Role of CsSAP12 in Increased Drought Tolerance in Transgenic Tomatoes

Plant stress-associated proteins (SAPs) contain A20/AN1 zinc finger domains and are involved in plant response to abiotic stresses. In this study, we aimed to explore the biological function of tea plant CsSAPs. A total of 14 CsSAP genes were identified in the tea plant genome using a reference genome database (Camellia sinensis var. sinensis). The CsSAPs were divided into the following two groups: Group I, containing one AN1 domain and/or one A20 domain; and Group II, containing two AN1 domains and/or two C2H2 domains. The sequence alignments and conserved domains analysis indicated that the CsSAPs were highly structurally conserved in terms of amino acid sequence and protein structure. The CsSAPs showed different transcript levels in spatio-temporal expression and in response to cold and drought stress in tea plants. Furthermore, the expression of CsSAP12 was considerably upregulated under drought stress. The overexpression of CsSAP12 in transgenic tomatoes showed increased tolerance to drought stress compared with the wild type. Altogether, the results showed that CsSAP12 might be involved in drought stress. Thus, CsSAP12 might be a target gene in genetic engineering to improve drought tolerance in tea plants.

Expression of the CCCH-tandem zinc finger protein gene OsTZF5 under a stress-inducible promoter mitigates the effect of drought stress on rice grain yield under field conditions

Increasing drought resistance without sacrificing grain yield remains an ongoing challenge in crop improvement. In this study, we report that Oryza sativa CCCH-tandem zinc finger protein 5 (OsTZF5) can confer drought resistance and increase grain yield in transgenic rice plants. Expression of OsTZF5 was induced by abscisic acid, dehydration and cold stress. Upon stress, OsTZF5-GFP localized to the cytoplasm and cytoplasmic foci. Transgenic rice plants overexpressing OsTZF5 under the constitutive maize ubiquitin promoter exhibited improved survival under drought but also growth retardation. By introducing OsTZF5 behind the stress-responsive OsNAC6 promoter in two commercial upland cultivars, Curinga and NERICA4, we obtained transgenic plants that showed no growth retardation. Moreover, these plants exhibited significantly increased grain yield compared to non-transgenic cultivars in different confined field drought environments. Physiological analysis indicated that OsTZF5 promoted both drought tolerance and drought avoidance. Collectively, our results provide strong evidence that OsTZF5 is a useful biotechnological tool to minimize yield losses in rice grown under drought conditions.

A Stress-Associated Protein, PtSAP13, From Populus trichocarpa Provides Tolerance to Salt Stress

The growth and production of poplars are usually affected by unfavorable environmental conditions such as soil salinization. Thus, enhancing salt tolerance of poplars will promote their better adaptation to environmental stresses and improve their biomass production. Stress-associated proteins (SAPs) are a novel class of A20/AN1 zinc finger proteins that have been shown to confer plants' tolerance to multiple abiotic stresses. However, the precise functions of SAP genes in poplars are still largely unknown. Here, the expression profiles of Populus trichocarpa SAPs in response to salt stress revealed that PtSAP13 with two AN1 domains was up-regulated dramatically during salt treatment. The β-glucuronidase (GUS) staining showed that PtSAP13 was accumulated dominantly in leaf and root, and the GUS signal was increased under salt condition. The Arabidopsis transgenic plants overexpressing PtSAP13 exhibited higher seed germination and better growth than wild-type (WT) plants under salt stress, demonstrating that overexpression of PtSAP13 increased salt tolerance. Higher activities of antioxidant enzymes were found in PtSAP13-overexpressing plants than in WT plants under salt stress. Transcriptome analysis revealed that some stress-related genes, including Glutathione peroxidase 8, NADP-malic enzyme 2, Response to ABA and Salt 1, WRKYs, Glutathione S-Transferase, and MYBs, were induced by salt in transgenic plants. Moreover, the pathways of flavonoid biosynthesis and metabolic processes, regulation of response to stress, response to ethylene, dioxygenase activity, glucosyltransferase activity, monooxygenase activity, and oxidoreductase activity were specially enriched in transgenic plants under salt condition. Taken together, our results demonstrate that PtSAP13 enhances salt tolerance through up-regulating the expression of stress-related genes and mediating multiple biological pathways.

Source-Sink Regulation in Crops under Water Deficit

To meet the food demands of an increasing world population, it is necessary to improve crop production; a task that is made more challenging by the changing climate. Several recent reports show that increasing the capacity of plants to assimilate carbon (source strength), or to tap into the internal carbon reservoir (sink strength), has the potential to improve plant productivity in the field under water-deficit conditions. Here, we review the effects of water deficit on the source-sink communication, as well as the respective regulatory mechanisms underpinning plant productivity. We also highlight stress-tolerant traits that can contribute to harness source and sink strengths towards producing high-yielding and drought-tolerant crops, depending on the drought scenario.

Drought and heat stress-related proteins: an update about their functional relevance in imparting stress tolerance in agricultural crops

We describe here the recent developments about the involvement of diverse stress-related proteins in sensing, signaling, and defending the cells in plants in response to drought or/and heat stress. In the current era of global climate drift, plant growth and productivity are often limited by various environmental stresses, especially drought and heat. Adaptation to abiotic stress is a multigenic process involving maintenance of homeostasis for proper survival under adverse environment. It has been widely observed that a series of proteins respond to heat and drought conditions at both transcriptional and translational levels. The proteins are involved in various signaling events, act as key transcriptional activators and saviors of plants under extreme environments. A detailed insight about the functional aspects of diverse stress-responsive proteins may assist in unraveling various stress resilience mechanisms in plants. Furthermore, by identifying the metabolic proteins associated with drought and heat tolerance, tolerant varieties can be produced through transgenic/recombinant technologies. A large number of regulatory and functional stress-associated proteins are reported to participate in response to heat and drought stresses, such as protein kinases, phosphatases, transcription factors, and late embryogenesis abundant proteins, dehydrins, osmotins, and heat shock proteins, which may be similar or unique to stress treatments. Few studies have revealed that cellular response to combined drought and heat stresses is distinctive, compared to their individual treatments. In this review, we would mainly focus on the new developments about various stress sensors and receptors, transcription factors, chaperones, and stress-associated proteins involved in drought or/and heat stresses, and their possible role in augmenting stress tolerance in crops.

Comprehensive metabolomic and proteomic analysis in biochemical metabolic pathways of rice spikes under drought and submergence stress

Drought and submergence are the main adverse factors affecting plant growth and yield formation in parts of China, especially in the Yangtze River region. In this study, T1 (drought duration: 10 d), T2 (submergence duration: 8 d) and CK (control) treatments were applied. This work aimed to study the changes in metabolic pathways of rice under drought and submergence stress during the panicle differentiation stage. The identification and analysis of differential metabolites and differentially expressed proteins functions indicate that drought and submergence mainly promoted the energy metabolism pathway, carbon fixation in photosynthetic organism pathway, carbohydrate metabolic process, and reactive oxygen species (ROS) metabolic process functions. Under drought stress, the inhibition of photosynthetic rate is mainly through stomatal conductance restriction, and flavonoid pathway regulates the metabolic process of ROS. Under submergence stress, the electron transfer chain was destroyed to inhibit the photosynthetic rate, and the antioxidant system was activated to regulate the metabolism of ROS. The changes in related enzymes or proteins in metabolic regulatory networks are analyzed, which will be conducive to understanding the response mechanism of rice drought and submergence more deeply and provide a scientific basis for rice drought and submergence prevention and mitigation, and the breeding of drought- and submergence-resistant varieties.

A stress-associated protein, AtSAP13, from Arabidopsis thaliana provides tolerance to multiple abiotic stresses

Members of Stress-Associated Protein (SAP) family in plants have been shown to impart tolerance to multiple abiotic stresses, however, their mode of action in providing tolerance to multiple abiotic stresses is largely unknown. There are 14 SAP genes in Arabidopsis thaliana containing A20, AN1, and Cys2-His2 zinc finger domains. AtSAP13, a member of the SAP family, carries two AN1 zinc finger domains and an additional Cys2-His2 domain. AtSAP13 transcripts showed upregulation in response to Cd, ABA, and salt stresses. AtSAP13 overexpression lines showed strong tolerance to toxic metals (AsIII, Cd, and Zn), drought, and salt stress. Further, transgenic lines accumulated significantly higher amounts of Zn, but less As and Cd accumulation in shoots and roots. AtSAP13 promoter-GUS fusion studies showed GUS expression predominantly in the vascular tissue, hydathodes, and the apical meristem and region of root maturation and elongation as well as the root hairs. At the subcellular level, the AtSAP13-eGFP fusion protein was found to localize in both nucleus and cytoplasm. Through yeast one-hybrid assay, we identified several AP2/EREBP family transcription factors that interacted with the AtSAP13 promoter. AtSAP13 and its homologues will be highly useful for developing climate resilient crops.

The LmSAP gene isolated from the halotolerant Lobularia maritima improves salt and ionic tolerance in transgenic tobacco lines

The A20/AN1 zinc-finger domain-containing proteins of the stress-associated proteins (SAPs) family are fast emerging as potential candidates for biotechnological approaches to improve abiotic stress tolerance in plants. We identified LmSAP, one of the SAPs genes in Lobularia maritima (L.) Desv., a halophyte brassicaceae, through its transcript accumulation in response to salinity and ionic stresses. Sequence homology analysis revealed that LmSAP contains two conserved zinc-finger domains A20 and AN1. Phylogeny analyses showed that LmSAP exhibited high amino acid sequence identity to other plant SAPs. Heterologous expression of LmSAP in yeast increased cell tolerance to salt and osmotic stress. In addition, the overexpression of LmSAP conferred high salt and ionic tolerance to transgenic tobacco plants. Transgenic tobacco seedlings showed higher survival rates and antioxidant activities under salt and ionic stresses. Enhanced antioxidant activities paralleled lower malondialdehyde and superoxide anion O2- levels in the LmSAP transgenic seedlings. Overall, our results suggest that overexpression of LmSAP enhanced salt tolerance by maintaining ionic balance and limiting oxidative and osmotic stresses.