OsiSAP1 overexpression improves water-deficit stress tolerance in transgenic rice by affecting expression of endogenous stress-related genes

Genome-wide identification of SAP family genes and characterization of TaSAP6-A1 to improve Cd tolerance in Triticum aestivum L

Stress Associated Proteins (SAPs) contain A20/AN1 zinc finger domains and, have been proposed to function in various physiological processes such as cold, salinity, drought, heavy metals, damage, and flooding resistance in plants. Here, a total of 131 SAP genes were identified, including T. aestivum (60), T. urartu (10), Ae. Tauschii (16), T. dicoccoides (13), O. sativa (18), and A. thaliana (14). A phylogenetic analysis revealed that the SAPs are clustered into two subfamilies. The TaSAP genes in the collinear region comprised 34 pairs of duplicated genes formed through segmental duplication events. Overexpressing TaSAP6-A1 in wheat enhanced Cd tolerance, whereas knock-down of this gene increased Cd sensitivity. Yeast two-hybrid (Y2H) and bimolecular fluorescent complementation assays (BiFC) demonstrated interaction between TaSAP6-A1 and phenylalanine ammonia-lyase (TaPAL), the first enzyme in the phenylpropanoid pathway. This study provides a valuable reference for further investigations into the functional and molecular mechanisms of the SAP gene family.

Exploring and exploiting the rice phytobiome to tackle climate change challenges

The future of agriculture is uncertain under the current climate change scenario. Climate change directly and indirectly affects the biotic and abiotic elements that control agroecosystems, jeopardizing the safety of the world's food supply. A new area that focuses on characterizing the phytobiome is emerging. The phytobiome comprises plants and their immediate surroundings, involving numerous interdependent microscopic and macroscopic organisms that affect the health and productivity of plants. Phytobiome studies primarily focus on the microbial communities associated with plants, which are referred to as the plant microbiome. The development of high-throughput sequencing technologies over the past 10 years has dramatically advanced our understanding of the structure, functionality, and dynamics of the phytobiome; however, comprehensive methods for using this knowledge are lacking, particularly for major crops such as rice. Considering the impact of rice production on world food security, gaining fresh perspectives on the interdependent and interrelated components of the rice phytobiome could enhance rice production and crop health, sustain rice ecosystem function, and combat the effects of climate change. Our review re-conceptualizes the complex dynamics of the microscopic and macroscopic components in the rice phytobiome as influenced by human interventions and changing environmental conditions driven by climate change. We also discuss interdisciplinary and systematic approaches to decipher and reprogram the sophisticated interactions in the rice phytobiome using novel strategies and cutting-edge technology. Merging the gigantic datasets and complex information on the rice phytobiome and their application in the context of regenerative agriculture could lead to sustainable rice farming practices that are resilient to the impacts of climate change.

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.

Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress

Stress-associated proteins (SAPs) are known to play an important role in plant responses to abiotic stresses. This study systematically identified members of the sunflower SAP gene family using sunflower genome data. The genes of the sunflower SAP gene family were analyzed using bioinformatic methods, and gene expression was assessed through fluorescence quantification (qRT-PCR) under salt and drought stress. A comprehensive analysis was also performed on the number, structure, collinearity, and phylogeny of seven Compositae species and eight other plant SAP gene families. The sunflower genome was found to have 27 SAP genes, distributed across 14 chromosomes. The evolutionary analysis revealed that the SAP family genes could be divided into three subgroups. Notably, the annuus variety exhibited amplification of the SAP gene for Group 3. Among the Compositae species, C. morifolium demonstrated the highest number of collinearity gene pairs and the closest distance on the phylogenetic tree, suggesting relative conservation in the evolutionary process. An analysis of gene structure revealed that Group 1 exhibited the most complex gene structure, while the majority of HaSAP genes in Group 2 and Group 3 lacked introns. The promoter analysis revealed the presence of cis-acting elements related to ABA, indicating their involvement in stress responses. The expression analysis indicated the potential involvement of 10 genes (HaSAP1, HaSAP3, HaSAP8, HaSAP10, HaSAP15, HaSAP16, HaSAP21, HaSAP22, HaSAP23, and HaSAP26) in sunflower salt tolerance. The expression of these 10 genes were then examined under salt and drought stress using qRT-PCR, and the tissue-specific expression patterns of these 10 genes were also analyzed. HaSAP1, HaSAP21, and HaSAP23 exhibited consistent expression patterns under both salt and drought stress, indicating these genes play a role in both salt tolerance and drought resistance in sunflower. The findings of this study highlight the significant contribution of the SAP gene family to salt tolerance and drought resistance in sunflower.

Molecular Mechanisms and Regulatory Pathways Underlying Drought Stress Response in Rice

Rice is a staple food for 350 million people globally. Its yield thus affects global food security. Drought is a serious environmental factor affecting rice growth. Alleviating the inhibition of drought stress is thus an urgent challenge that should be solved to enhance rice growth and yield. This review details the effects of drought on rice morphology, physiology, biochemistry, and the genes associated with drought stress response, their biological functions, and molecular regulatory pathways. The review further highlights the main future research directions to collectively provide theoretical support and reference for improving drought stress adaptation mechanisms and breeding new drought-resistant rice varieties.

Delineating the tissue-mediated drought stress governed tuning of conserved miR408 and its targets in rice

Engineering drought tolerance in rice needs to focus on regulators that enhance tolerance while boosting plant growth and vigor. The present study delineated the concealed function and tissue-mediated interplay of the miR408/target module in imparting drought stress tolerance in rice. The plant miR408 family comprises three dominant mature forms (21 nt), including a distinct monocot variant (F-7 with 5' C) and is divided into six groups. miR408 majorly cleaves genes belonging to the blue copper protein in addition to several other species-specific targets in plants. Comparative sequence analysis in 4726 rice accessions identified 22 sequence variants (SNP and InDELs) in its promoter (15) and pre-miR408 region. Haplotype analysis of the sequence variants indicated eight haplotypes (three: Japonica-specific and five: Indica-specific) of the miR408 promoter. In drought-tolerant Nagina 22, miR408 follows flag leaf preferential expression. Under drought conditions, its levels are upregulated in flag leaf and roots which seems to be regulated by a differential fraction of methylated cytosines (mCs) in the precursor region. The active pool of miR408 regulated targets under control and drought conditions is impacted by the tissue type. Comparative expression analysis of the miR408/target module under different sets of conditions features 83 targets exhibiting antagonistic expression in rice, out of which 12 genes, including four PLANTACYANINS (OsUCL6, 7, 9 and 30), PIRIN, OsLPR1, OsCHUP1, OsDOF12, OsBGLU1, glycine-rich cell wall gene, OsDUT, and OsERF7, are among the high confidence targets. Further, overexpression of MIR408 in drought-sensitive rice cultivar (PB1) leads to the massive enhancement of vegetative growth in rice with improved ETR and Y(II) and enhanced dehydration stress tolerance. The above results suggest that miR408 is likely to act as a positive regulator of growth and vigor, as well as dehydration stress, making it a potential candidate for engineering drought tolerance in rice.

OsSAP6 Positively Regulates Soda Saline-Alkaline Stress Tolerance in Rice

BACKGROUND

Soil salinization is a worldwide environmental problem, especially in the arid and semiarid regions of northeastern China, which are heavily affected by soda saline-alkaline stress. At present, there is an urgent need to improve the soda saline-alkaline stress tolerance of rice.

RESULTS

Stress-associated proteins are involved in regulating the abiotic stresses in plants. There are 18 members of the rice stress-associated protein (OsSAP) gene family. In this study, the expression levels of OsSAP6 in leaves and roots were upregulated with increasing NaHCO₃ stress duration. OsSAP6 was located in nucleus and cytoplasm. The bud length and total root length of OsSAP6 overexpression rice were significantly longer than those of Lj11 (Oryza sativa longjing11) during germination stage, and the survival rates, plant height and malondialdehyde content at the seedling stage showed tolerance growth of saline-alkaline stress. The expression of OsCu/Zn-SOD, OsAPX2, and OsCAT1 in transgenic lines was increased significantly under SAE (soda saline-alkali soil eluent) stress. OsSAP6 interacts with OsPK5 according to yeast two-hybrid screening and luciferase complementation experiments. The expression of OsPK5 increased under NaHCO₃ and H₂O₂ stress, and the overexpression of OsPK5 in rice improved soda saline-alkaline tolerance.

CONCLUSION

Overexpression of OsSAP6 in rice significantly enhanced saline-alkaline tolerance compared with the wild type. It is speculated that OsSAP6 responds to soda salinity stress and interacts with OsPK5 to positively regulate soda saline-alkaline tolerance through ROS homeostasis. This study revealed the features of OsSAP6 involved in response to soda saline-alkaline stress and the interaction with OsPK5, which provided resources for breeding aimed at improving the soda saline-alkaline stress tolerance of rice.

Comprehensive Identification and Functional Analysis of Stress-Associated Protein (SAP) Genes in Osmotic Stress in Maize

Stress-associated proteins (SAPs) are a kind of zinc finger protein with an A20/AN1 domain and contribute to plants' adaption to various abiotic and biological stimuli. However, little is known about the SAP genes in maize (Zea mays L.). In the present study, the SAP genes were identified from the maize genome. Subsequently, the protein properties, gene structure and duplication, chromosomal location, and cis-acting elements were analyzed by bioinformatic methods. Finally, their expression profiles under osmotic stresses, including drought and salinity, as well as ABA, and overexpression in Saccharomyces cerevisiae W303a cells, were performed to uncover the potential function. The results showed that a total of 10 SAP genes were identified and named ZmSAP1 to ZmSAP10 in maize, which was unevenly distributed on six of the ten maize chromosomes. The ZmSAP1, ZmSAP4, ZmSAP5, ZmSAP6, ZmSAP7, ZmSAP8 and ZmSAP10 had an A20 domain at N terminus and AN1 domain at C terminus, respectively. Only ZmSAP2 possessed a single AN1 domain at the N terminus. ZmSAP3 and ZmSAP9 both contained two AN1 domains without an A20 domain. Most ZmSAP genes lost introns and had abundant stress- and hormone-responsive cis-elements in their promoter region. The results of quantitative real-time PCR showed that all ZmSAP genes were regulated by drought and saline stresses, as well as ABA induction. Moreover, heterologous expression of ZmSAP2 and ZmSAP7 significantly improved the saline tolerance of yeast cells. The study provides insights into further underlying the function of ZmSAPs in regulating stress response in maize.

Genome-Wide Identification of the A20/AN1 Zinc Finger Protein Family Genes in Ipomoea batatas and Its Two Relatives and Function Analysis of IbSAP16 in Salinity Tolerance

Stress-associated protein (SAP) genes—encoding A20/AN1 zinc-finger domain-containing proteins—play pivotal roles in regulating stress responses, growth, and development in plants. They are considered suitable candidates to improve abiotic stress tolerance in plants. However, the SAP gene family in sweetpotato (Ipomoea batatas) and its relatives is yet to be investigated. In this study, 20 SAPs in sweetpotato, and 23 and 26 SAPs in its wild diploid relatives Ipomoea triloba and Ipomoea trifida were identified. The chromosome locations, gene structures, protein physiological properties, conserved domains, and phylogenetic relationships of these SAPs were analyzed systematically. Binding motif analysis of IbSAPs indicated that hormone and stress responsive cis-acting elements were distributed in their promoters. RT-qPCR or RNA-seq data revealed that the expression patterns of IbSAP, ItbSAP, and ItfSAP genes varied in different organs and responded to salinity, drought, or ABA (abscisic acid) treatments differently. Moreover, we found that IbSAP16 driven by the 35 S promoter conferred salinity tolerance in transgenic Arabidopsis. These results provided a genome-wide characterization of SAP genes in sweetpotato and its two relatives and suggested that IbSAP16 is involved in salinity stress responses. Our research laid the groundwork for studying SAP-mediated stress response mechanisms in sweetpotato.

Genome-wide in silico identification and characterization of the stress associated protein (SAP) gene family encoding A20/AN1 zinc-finger proteins in potato (Solanum tuberosum L.)

Stress associated proteins (SAPs) in plants have a key role in providing tolerance to multiple abiotic stresses. SAP gene family in Solanum tuberosum has not been fully studied before. This study identified 17 StSAP genes in S. tuberosum which code for A20/AN1 zinc-finger proteins. All the genes were distributed on ten different chromosomes and six segmental duplication events were identified. The SAPs in S. tuberosum and its orthologs in Arabidopsis thaliana were classified into six groups through the phylogenetic analysis. Introns across StSAP genes were identified in four genes. The promotor study of the StSAP genes showed different hormone and stress-related cis-elements that could potentially have a role in environmental stress response. The expression of StSAP genes in response to heat, mannitol, and salt were analyzed through in silico transcriptomic analysis. This study could potentially help in further understanding the functions of SAP genes in S. tuberosum.

Yield-associated putative gene regulatory networks in Oryza sativa L. subsp. indica and their association with high-yielding genotypes

BACKGROUND

With the increase in population and economies of developing countries in Asia and Africa, the research towards securing future food demands is an imminent need. Among japonica and indica genotypes, indica rice varieties are largely cultivated across the globe. However, our present understanding of yield-contributing gene information stems mainly from japonica and studies on the yield potential of indica genotypes are limited.

METHODS AND RESULTS

In the present study, yield contributing orthologous genes previously characterized from japonica varieties were identified in the indica genome and analysed with binGO tool for GO biological processes categorization. Transcription factor binding site enrichment analysis in the promoters of yield-related genes of indica was performed with MEME-AME tool that revealed putative common TF regulators are enriched in flower development, two-component signalling and water deprivation biological processes. Gene regulatory networks revealed important TF-target interactions that might govern yield-related traits. Some of the identified candidate genes were validated by qRT-PCR analysis for their expression and association with yield-related traits among 16 widely cultivated popular indica genotypes. Further, SNP-metabolite-trait association analysis was performed using high-yielding indica variety Rasi. This resulted in the identification of putative SNP variations in TF regulators and targeted yield genes significantly linked with metabolite accumulation.

CONCLUSIONS

The study suggests some of the high yielding indica genotypes such as Ravi003, Rasi and Kavya could be used as potential donors in breeding programs based on yield gene expression analysis and SNP-metabolites associations.

A stress-associated protein OsSAP8 modulates gibberellic acid biosynthesis by reducing the promotive effect of transcription factor OsbZIP58 on OsKO2

Gibberellic acid (GA) is a vital phytohormone for plant growth and development. GA biosynthesis is a complex pathway regulated by various transcription factors. Here we report a stress-associated protein 8 (OsSAP8), negatively involved in GA biosynthesis. Overexpression of OsSAP8 in rice resulted in a semi-dwarfism phenotype and reduced endogenous GA3 content. In contrast, an OsSAP8 knockout mutant exhibited higher endogenous GA3 content and slightly increased plant height. Sub-cellular localization analysis of OsSAP8 showed that it could enter the nucleus. Based on electrophoretic mobility shift assay and yeast one hybrid experiments, OsSAP8 was found to bind to the cis-acting regulatory element GADOWNAT of ent-kaurene oxidases (KO2, KO3, KO5). The results from dual-luciferase reporter assays showed that OsSAP8 does not activate LUC reporter gene expression. However, it could interact with basic leucine zipper 58 (OsbZIP58), which has strong transcriptional activation potential on OsKO2. Moreover, the interaction between OsSAP8, rice lesion simulating disease 1-like 1 (OsLOL1), and OsbZIP58 could reduce the promotive effect of transcription factor OsbZIP58 on OsKO2. These results provide some new insights on the regulation of GA biosynthesis in rice.

Identification and Expression Analysis of Zinc Finger A20/AN1 Stress-Associated Genes SmSAP Responding to Abiotic Stress in Eggplant

Stress-associated proteins (SAP), a class of zinc-finger proteins, have been identified as novel stress regulatory proteins in stress responses. However, SAP genes in eggplant (SmSAP) have been little reported. It has important significance in identifying SAP members, understanding the molecular mechanisms underlying stress responses, and tolerance. We performed a comprehensive study of the A20/AN1 domains, motifs, gene structures, phylogenetic relationships, chromosomal locations, gene replications, collinearity, cis-acting elements, and expression pattern responses to various abiotic stresses. Twenty-one SAP genes were identified in eggplant (SmSAP) and were localized on 10 chromosomes. A phylogenetic analysis revealed that most of the SmSAP proteins showed a high homology with the tomato SAP members, and 21 members were divided into four groups based on the homology of the SAP members in eggplant, tomato, rice, and Arabidopsis. Further analysis revealed that SmSAP proteins contain the characteristic A20/AN1 domains, the A20 domain composed of motif 2 (ILCINNCGFFGSPATMNLCSKCYKDMJLK). Four pairs of tandem duplications were found in eggplant, and 10 SmSAP genes had collinearity with SAP genes from Arabidopsis, potato, or tomato, but only four SmSAP genes were collinear with SAP genes in the three species mentioned above. Moreover, the promoters of SmSAP genes were predicted to contain many cis-acting elements that respond to abiotic stress and hormones. A qRT-PCR analysis of the four selected SmSAP genes exhibited diverse expression levels in response to various environmental stresses. These results provided a comprehensive analysis of the SmSAP genes and lay a solid foundation for improving the understanding of the functional diversification of SAP genes under various environmental stresses in eggplant.

Comprehensive analysis of the stress associated protein (SAP) gene family in Tamarix hispida and the function of ThSAP6 in salt tolerance

Stress associated proteins (SAPs), a class of A20/AN1 zinc finger domain-containing proteins, are involved in a variety of biotic and abiotic stress responses in plants. However, little is known about the SAP gene family and their functions in Tamarix hispida. In this study, we isolated and characterized 11 SAPs from T. hispida. The expression patterns of ThSAPs were analyzed under various stresses (salt and drought) and phytohormone treatment (SA, ABA and MeJA) using real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR). Most ThSAPs exhibited transcriptional responses to abiotic stresses and phytohormones. Among these ThSAPs, ThSAP6 was significantly induced by salt stress. Gain-and loss-of-function analyses revealed that ThSAP6 was a positive regulator of salt stress response. Overexpression of ThSAP6 in T. hispida increased antioxidant enzymes activity and proline content and decreased reactive oxygen species (ROS) accumulation and cell membrane damage under salt stress, while the opposite physiological changes were observed in ThSAP6-RNAi (RNA interference) lines. This study provides a comprehensive description of the SAP gene family in T. hispida, and demonstrates that ThSAP6 is a potential candidate for biotechnological approaches to improve salt tolerance in plants.

Genomic characterization and expression profiles of stress-associated proteins (SAPs) in castor bean (Ricinus communis)

Stress-associated proteins (SAPs) are known as response factors to multiple abiotic and biotic stresses in plants. However, the potential physiological and molecular functions of SAPs remain largely unclear. Castor bean (Ricinus communis L.) is one of the most economically valuable non-edible woody oilseed crops, able to be widely cultivated in marginal lands worldwide because of its broad adaptive capacity to soil and climate conditions. Whether SAPs in castor bean plays a key role in adapting diverse soil conditions and stresses remains unknown. In this study, we used the castor bean genome to identify and characterize nine castor bean SAP genes (RcSAP). Structural analysis showed that castor bean SAP gene structures and functional domain types vary greatly, differing in intron number, protein sequence, and functional domain type. Notably, the AN1-C2H2-C2H2 zinc finger domain within RcSAP9 has not been often observed in other plant families. High throughput RNA-seq data showed that castor bean SAP gene profiles varied among different tissues. In addition, castor bean SAP gene expression varied in response to different stresses, including salt, drought, heat, cold and ABA and MeJA, suggesting that the transcriptional regulation of castor bean SAP genes might operate independently of each other, and at least partially independent from ABA and MeJA signal pathways. Cis-element analyses for each castor bean SAP gene showed that no common cis-elements are shared across the nine castor bean SAP genes. Castor bean SAPs were localized to different regions of cells, including the cytoplasm, nucleus, and cytomembrane. This study provides a comprehensive profile of castor bean SAP genes that advances our understanding of their potential physiological and molecular functions in regulating growth and development and their responses to different abiotic stresses.

Genome-Wide Association Study and Identification of Candidate Genes for Nitrogen Use Efficiency in Barley (Hordeum vulgare L.)

Nitrogen (N) fertilizer is largely responsible for barley grain yield potential and quality, yet excessive application leads to environmental pollution and high production costs. Therefore, efficient use of N is fundamental for sustainable agriculture. In the present study, we investigated the performance of 282 barley accessions through hydroponic screening using optimal and low NH4NO3 treatments. Low-N treatment led to an average shoot dry weight reduction of 50%, but there were significant genotypic differences among the accessions. Approximately 20% of the genotypes showed high (>75%) relative shoot dry weight under low-N treatment and were classified as low-N tolerant, whereas 20% were low-N sensitive (≤55%). Low-N tolerant accessions exhibited well-developed root systems with an average increase of 60% in relative root dry weight to facilitate more N absorption. A genome-wide association study (GWAS) identified 66 significant marker trait associations (MTAs) conferring high nitrogen use efficiency, four of which were stable across experiments. These four MTAs were located on chromosomes 1H(1), 3H(1), and 7H(2) and were associated with relative shoot length, relative shoot and root dry weight. Genes corresponding to the significant MTAs were retrieved as candidate genes, including members of the asparagine synthetase gene family, several transcription factor families, protein kinases, and nitrate transporters. Most importantly, the high-affinity nitrate transporter 2.7 (HvNRT2.7) was identified as a promising candidate on 7H for root and shoot dry weight. The identified candidate genes provide new insights into our understanding of the molecular mechanisms driving nitrogen use efficiency in barley and represent potential targets for genetic improvement.

Global transcriptome analysis of novel stress associated protein (SAP) genes expression dynamism of combined abiotic stresses in Oryza sativa (L.)

Genes encoding proteins with A20/AN1 zinc-finger domains, belonging to the stress associated protein (SAP) gene family, are present in all eukaryotes and play a decisive role in plant response to diverse physiological and molecular activities particularly on biotic and abiotic stresses (AbS). In this first and foremost study, global transcriptome analysis of members of the SAP gene family was carried out in C3 model-Oryza sativa (OsSAP) aiming at the identification of OsSAP genes activated in response to unique or Combined AbS (CAbS). Based on the available spatio-temporal and phytohormonal RNA-Seq expression profile datasets, nine OsSAP genes were filtered out and identified by a differential expression signature noted in various tissues as well as plant hormones. Comparative genome ideogram of OsSAP genes confirmed the orthologous collinearity with C4 panicoid genomes. Interactome of these genes, revealed the molecular cross-talks of OsSAP. Thus, the computational expression signature of OsSAP genes led to a better understanding of gene dynamism in diverse developmental tissues/organs. Transcriptional regulation analysis of key OsSAP genes in response to stress (drought and salinity) suggested the novel role of OsSAP1, OsSAP2, OsSAP5, OsSAP7, OsSAP8 and OsSAP11 in AbS. Altogether, the study provides deeper insights on molecular characteristics of OsSAP genes, which could be deployed further to decipher their precise functional roles in AbS responses.Communicated by Ramaswamy H. Sarma.

Identification and Expression Analysis of Stress-Associated Proteins (SAPs) Containing A20/AN1 Zinc Finger in Cucumber

Stress-associated proteins (SAPs) are a class of zinc finger proteins that confer tolerance to a variety of abiotic and biotic stresses in diverse plant species. However, in cucumber (Cucumis sativus L.), very little is known about the roles of SAP gene family members in regulating plant growth, development, and stress responses. In this study, a total of 12 SAP genes (named as CsSAP1-CsSAP12) were identified in the cucumber genome, which were unevenly distributed on six chromosomes. Gene duplication analysis detected one tandem duplication and two segmental duplication events. Phylogenetic analysis of SAP proteins from cucumber and other plants suggested that they could be divided into seven groups (sub-families), and proteins in the same group generally had the same arrangement of AN1 (ZnF-AN1) and A20 (ZnF-A20) domains. Most of the CsSAP genes were intronless and harbored a number of stress- and hormone-responsive cis-elements in their promoter regions. Tissue expression analysis showed that the CsSAP genes had a broad spectrum of expression in different tissues, and some of them displayed remarkable alteration in expression during fruit development. RT-qPCR results indicated that all the selected CsSAP genes displayed transcriptional responses to cold, drought, and salt stresses. These results enable the first comprehensive description of the SAP gene family in cucumber and lay a solid foundation for future research on the biological functions of CsSAP genes.

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.

Functional domain analysis of LmSAP protein reveals the crucial role of the zinc-finger A20 domain in abiotic stress tolerance

Stress-associated proteins (SAPs), such as A20/AN1 zinc-finger domain-containing proteins, have emerged as a novel class of proteins involved in abiotic stress signaling, and they are important candidates for preventing the loss of yield caused by exposure to environmental stresses. In a previous report, it was found that the ectopic-expression of Lobularia maritima stress-associated protein, LmSAP, conferred tolerance to abiotic and heavy metal stresses in transgenic tobacco plants. This study aimed to investigate the functions of the A20 and AN1 domains of LmSAP in salt and osmotic stress tolerance. To this end, in addition to the full-length LmSAP gene, we have generated three LmSAP-truncated forms (LmSAPΔA20, LmSAPΔAN1, and LmSAPΔA20-ΔAN1). Heterologous expression in Saccharomyces cerevisiae of different truncated forms of LmSAP revealed that the A20 domain is essential to increase cell tolerance to salt, ionic, and osmotic stresses. Transgenic tobacco plants overexpressing LmSAP and LmSAPΔAN1 constructs exhibited higher tolerance to salt and osmotic stresses in comparison to the non-transgenic plants (NT) and lines transformed with LmSAPΔA20 and LmSAPΔA20-ΔAN1 constructs. Similarly, transgenic plants overexpressing the full-length LmSAP gene and LmSAPΔAN1 truncated domain maintained higher superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) enzymatic activities due to the high expression levels of the genes encoding these key antioxidant enzymes, MnSOD, POD, and CAT1, as well as accumulated lower levels of malondialdehyde (MDA) under salt and osmotic stresses compared to NT and LmSAPΔA20 and LmSAPΔA20-ΔAN1 forms. These findings provide insights into the pivotal role of A20 and AN1 domains of LmSAP protein in salt and osmotic stress tolerance.

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.

Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

Stress-associated proteins (SAPs) are novel A20/AN1 zinc finger domain-containing proteins that are now favorable targets to improve abiotic stress tolerance in plants. However, the SAP gene family and their biological functions have not been identified in the important fruit crop apple (Malus × domestica Borkh.). We conducted a genome-wide analysis and cloning of this gene family in apple and determined that the overexpression of MdSAP15 enhances drought tolerance in Arabidopsis plants. We identified 30 SAP genes in the apple genome. Phylogenetic analysis revealed two major groups within that family. Results from sequence alignments and analyses of 3D structures, phylogenetics, genomics structure, and conserved domains indicated that apple SAPs are highly and structurally conserved. Comprehensive qRT-PCR analysis found various expression patterns for MdSAPs in different tissues and in response to a water deficit. A transgenic analysis showed that the overexpression of MdSAP15 in transgenic Arabidopsis plants markedly enhanced their tolerance to osmotic and drought stresses. Our results demonstrate that the SAP genes are highly conserved in plant species, and that MdSAP15 can be used as a target gene in genetic engineering approaches to improve drought tolerance.

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.

Comparative Transcriptome Analyses Reveal Potential Mechanisms of Enhanced Drought Tolerance in Transgenic Salvia Miltiorrhiza Plants Expressing AtDREB1A from Arabidopsis

In our previous study, drought-resistant transgenic plants of Salvia miltiorrhiza were produced via overexpression of the transcription factor AtDREB1A. To unravel the molecular mechanisms underpinning elevated drought tolerance in transgenic plants, in the present study we compared the global transcriptional profiles of wild-type (WT) and AtDREB1A-expressing transgenic plants using RNA-sequencing (RNA-seq). Using cluster analysis, we identified 3904 differentially expressed genes (DEGs). Compared with WT plants, 423 unigenes were up-regulated in pRD29A::AtDREB1A-31 before drought treatment, while 936 were down-regulated and 1580 and 1313 unigenes were up- and down-regulated after six days of drought. COG analysis revealed that the 'signal transduction mechanisms' category was highly enriched among these DEGs both before and after drought stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation, DEGs associated with "ribosome", "plant hormone signal transduction", photosynthesis", "plant-pathogen interaction", "glycolysis/gluconeogenesis" and "carbon fixation" are hypothesized to perform major functions in drought resistance in AtDREB1A-expressing transgenic plants. Furthermore, the number of DEGs associated with different transcription factors increased significantly after drought stress, especially the AP2/ERF, bZIP and MYB protein families. Taken together, this study substantially expands the transcriptomic information for S. miltiorrhiza and provides valuable clues for elucidating the mechanism of AtDREB1A-mediated drought tolerance in transgenic plants.

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.

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

We evaluated the yields of Oryza sativa L. 'Nipponbare' rice lines expressing a gene encoding an A20/AN1 domain stress-associated protein, AlSAP, from the halophyte grass Aeluropus littoralis under the control of different promoters. Three independent field trials were conducted, with drought imposed at the reproductive stage. In all trials, the two transgenic lines, RN5 and RN6, consistently out-performed non-transgenic (NT) and wild-type (WT) controls, providing 50-90% increases in grain yield (GY). Enhancement of tillering and panicle fertility contributed to this improved GY under drought. In contrast with physiological records collected during previous greenhouse dry-down experiments, where drought was imposed at the early tillering stage, we did not observe significant differences in photosynthetic parameters, leaf water potential, or accumulation of antioxidants in flag leaves of AlSAP-lines subjected to drought at flowering. However, AlSAP expression alleviated leaf rolling and leaf drying induced by drought, resulting in increased accumulation of green biomass. Therefore, the observed enhanced performance of the AlSAP-lines subjected to drought at the reproductive stage can be tentatively ascribed to a primed status of the transgenic plants, resulting from a higher accumulation of biomass during vegetative growth, allowing reserve remobilization and maintenance of productive tillering and grain filling. Under irrigated conditions, the overall performance of AlSAP-lines was comparable with, or even significantly better than, the NT and WT controls. Thus, AlSAP expression inflicted no penalty on rice yields under optimal growth conditions. Our results support the use of AlSAP transgenics to reduce rice GY losses under drought conditions.

Expression of cold and drought regulatory protein (CcCDR) of pigeonpea imparts enhanced tolerance to major abiotic stresses in transgenic rice plants

Transgenic rice expressing pigeonpea Cc CDR conferred high-level tolerance to different abiotic stresses. The multiple stress tolerance observed in CcCDR -transgenic lines is attributed to the modulation of ABA-dependent and-independent signalling-pathway genes. Stable transgenic plants expressing Cajanus cajan cold and drought regulatory protein encoding gene (CcCDR), under the control of CaMV35S and rd29A promoters, have been generated in indica rice. Different transgenic lines of CcCDR, when subjected to drought, salt, and cold stresses, exhibited higher seed germination, seedling survival rates, shoot length, root length, and enhanced plant biomass when compared with the untransformed control plants. Furthermore, transgenic plants disclosed higher leaf chlorophyll content, proline, reducing sugars, SOD, and catalase activities, besides lower levels of MDA. Localization studies revealed that the CcCDR-GFP fusion protein was mainly present in the nucleus of transformed cells of rice. The CcCDR transgenics were found hypersensitive to abscisic acid (ABA) and showed reduced seed germination rates as compared to that of control plants. When the transgenic plants were exposed to drought and salt stresses at vegetative and reproductive stages, they revealed larger panicles and higher number of filled grains compared to the untransformed control plants. Under similar stress conditions, the expression levels of P5CS, bZIP, DREB, OsLEA3, and CIPK genes, involved in ABA-dependent and-independent signal transduction pathways, were found higher in the transgenic plants than the control plants. The overall results amply demonstrate that the transgenic rice expressing CcCDR bestows high-level tolerance to drought, salt, and cold stress conditions. Accordingly, the CcCDR might be deployed as a promising candidate gene for improving the multiple stress tolerance of diverse crop plants.

Dual regulation of water retention and cell growth by a stress-associated protein (SAP) gene in Prunus

We have identified a gene (PpSAP1) of Prunus persica coding for a stress-associated protein (SAP) containing Zn-finger domains A20 and AN1. SAPs have been described as regulators of the abiotic stress response in plant species, emerging as potential candidates for improvement of stress tolerance in plants. PpSAP1 was highly expressed in leaves and dormant buds, being down-regulated before bud dormancy release. PpSAP1 expression was moderately induced by water stresses and heat in buds. In addition, it was found that PpSAP1 strongly interacts with polyubiquitin proteins in the yeast two-hybrid system. The overexpression of PpSAP1 in transgenic plum plants led to alterations in leaf shape and an increase of water retention under drought stress. Moreover, we established that leaf morphological alterations were concomitant with a reduced cell size and down-regulation of genes involved in cell growth, such as GROWTH-REGULATING FACTOR (GRF)1-like, TONOPLAST INTRINSIC PROTEIN (TIP)-like, and TARGET OF RAPAMYCIN (TOR)-like. Especially, the inverse expression pattern of PpSAP1 and TOR-like in transgenic plum and peach buds suggests a role of PpSAP1 in cell expansion through the regulation of TOR pathway.

bHLH142 regulates various metabolic pathway-related genes to affect pollen development and anther dehiscence in rice

Apposite development of anther and its dehiscence are important for the reproductive success of the flowering plants. Recently, bHLH142, a bHLH transcription factor encoding gene of rice has been found to show anther-specific expression and mutant analyses suggest its functions in regulating tapetum differentiation and degeneration during anther development. However, our study on protein level expression and gain-of-function phenotype revealed novel aspects of its regulation and function during anther development. Temporally dissimilar pattern of bHLH142 transcript and polypeptide accumulation suggested regulation of its expression beyond transcriptional level. Overexpression of bHLH142 in transgenic rice resulted in indehiscent anthers and aborted pollen grains. Defects in septum and stomium rupture caused anther indehiscence while pollen abortion phenotype attributed to abnormal degeneration of the tapetum. Furthermore, RNA-Seq-based transcriptome analysis of tetrad and mature pollen stage anthers of wild type and bHLH142OEplants suggested that it might regulate carbohydrate and lipid metabolism, cell wall modification, reactive oxygen species (ROS) homeostasis and cell death-related genes during rice anther development. Thus, bHLH142 is an anther-specific gene whose expression is regulated at transcriptional and post-transcriptional/translational levels. It plays a role in pollen maturation and anther dehiscence by regulating expression of various metabolic pathways-related genes.

Over-Expression of OsHOX24 Confers Enhanced Susceptibility to Abiotic Stresses in Transgenic Rice via Modulating Stress-Responsive Gene Expression

Homeobox transcription factors play critical roles in plant development and abiotic stress responses. In the present study, we raised rice transgenics over-expressing stress-responsive OsHOX24 gene (rice homeodomain-leucine zipper I sub-family member) and analyzed their response to various abiotic stresses at different stages of development. At the seed germination stage, rice transgenics over-expressing OsHOX24 exhibited enhanced sensitivity to abiotic stress conditions and abscisic acid as compared to wild-type (WT). OsHOX24 over-expression rice seedlings showed reduced root and shoot growth under salinity and desiccation stress (DS) conditions. Various physiological and phenotypic assays confirmed higher susceptibility of rice transgenics toward abiotic stresses as compared to WT at mature and reproductive stages of rice development too. Global gene expression profiling revealed differential regulation of several genes in the transgenic plants under control and DS conditions. Many of these differentially expressed genes were found to be involved in transcriptional regulatory activities, besides carbohydrate, nucleic acid and lipid metabolic processes and response to abiotic stress and hormones. Taken together, our findings highlighted the role of OsHOX24 in regulation of abiotic stress responses via modulating the expression of stress-responsive genes in rice.

Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India

Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.

Isolation and characterization of LcSAP, a Leymus chinensis gene which enhances the salinity tolerance of Saccharomyces cerevisiae

A number of members of the SAP ("stress-associated protein") gene family have been implicated in the plant stress response. Here, a SAP gene has been isolated using PCR RACE from the perennial grass Leymus chinensis, a species which has reputation for ecological adaptability. The 17.6 kDa LcSAP product comprised 161 residues, including both an A20 domain and an AN1 domain, a feature of type I SAPs. Using a semi-quantitative RT-PCR assay to profile its transcription, it was shown that LcSAP was more strongly transcribed in the leaf than in the root under control conditions. The level of LcSAP transcription began to rise 6 h after the plant's exposure to 400 mM NaCl, and the abundance of transcript remained stable for at least 24 h. Exposing the plant to 100 mM Na₂CO₃ also induced LcSAP transcription, but the abundance of SAP transcript faded after 6 h. When LcSAP was introduced into yeast cells, the transgenic cells grew better than wild type ones when the medium contained 1.4 M NaCl. The ability of LcSAP to respond to salinity stress in yeast suggests that it also makes a contribution to the stress tolerance shown by L. chinensis.

Overexpression of OsSAP16 Regulates Photosynthesis and the Expression of a Broad Range of Stress Response Genes in Rice (Oryza sativa L.)

This study set out to identify and characterize transcription factors regulating photosynthesis in rice. Screening populations of rice T-DNA activation lines led to the identification of a T-DNA mutant with an increase in intrinsic water use efficiency (iWUE) under well-watered conditions. Flanking sequence analysis showed that the T-DNA construct was located upstream of LOC_Os07g38240 (OsSAP16) encoding for a stress-associated protein (SAP). A second mutant identified with activation in the same gene exhibited the same phenotype; expression of OsSAP16 was shown to be enhanced in both lines. There were no differences in stomatal development or morphology in either of these mutants, although overexpression of OsSAP16 reduced stomatal conductance. This phenotype limited CO2 uptake and the rate of photosynthesis, which resulted in the accumulation of less biomass in the two mutants. Whole transcriptome analysis showed that overexpression of OsSAP16 led to global changes in gene expression consistent with the function of zinc-finger transcription factors. These results show that the gene is involved in modulating the response of rice to drought stress through regulation of the expression of a set of stress-associated genes.

Silicon-induced reversibility of cadmium toxicity in rice

Silicon (Si) modulates tolerance to abiotic stresses, but little is known about the reversibility of stress effects by supplementing previously stressed plants with Si. This is surprising since recovery experiments might allow mechanisms of Si-mediated amelioration to be addressed. Rice was exposed to 10 µM CdCl2 for 4 d in hydroponics, followed by 0.6mM Si(OH)4 supplementation for 4 d. Si reversed the effects of Cd, as reflected in plant growth, photosynthesis, elemental composition, and some biochemical parameters. Cd-dependent deregulation of nutrient homeostasis was partially reversed by Si supply. Photosynthetic recovery within 48h following Si supply, coupled with strong stimulation of the ascorbate-glutathione system, indicates efficient activation of defense. The response was further verified by transcript analyses with emphasis on genes encoding members of the stress-associated protein (SAP) family. The transcriptional response to Cd was mostly reversed following Si supply. Reprogramming of the Cd response was obvious for Phytochelatin synthase 1, SAP1 , SAP14, and the transcription factor genes AP2/Erf020, Hsf31, and NAC6 whose transcript levels were strongly activated in roots of Cd-stressed rice, but down-regulated in the presence of Si. These findings, together with changes in biochemical parameters, highlight the significance of Si in growth recovery of Cd-stressed rice and indicate a decisive role for readjusting cell redox homeostasis.

Advances in Agrobacterium tumefaciens-mediated genetic transformation of graminaceous crops

Steady increase in global population poses several challenges to plant science research, including demand for increased crop productivity, grain yield, nutritional quality and improved tolerance to different environmental factors. Transgene-based approaches are promising to address these challenges by transferring potential candidate genes to host organisms through different strategies. Agrobacterium-mediated gene transfer is one such strategy which is well known for enabling efficient gene transfer in both monocot and dicots. Due to its versatility, this technique underwent several advancements including development of improved in vitro plant regeneration system, co-cultivation and selection methods, and use of hyper-virulent strains of Agrobacterium tumefaciens harbouring super-binary vectors. The efficiency of this method has also been enhanced by the use of acetosyringone to induce the activity of vir genes, silver nitrate to reduce the Agrobacterium-induced necrosis and cysteine to avoid callus browning during co-cultivation. In the last two decades, extensive efforts have been invested towards achieving efficient Agrobacterium-mediated transformation in cereals. Though high-efficiency transformation systems have been developed for rice and maize, comparatively lesser progress has been reported in other graminaceous crops. In this context, the present review discusses the progress made in Agrobacterium-mediated transformation system in rice, maize, wheat, barley, sorghum, sugarcane, Brachypodium, millets, bioenergy and forage and turf grasses. In addition, it also provides an overview of the genes that have been recently transferred to these graminaceous crops using Agrobacterium, bottlenecks in this technique and future possibilities for crop improvement.

MsZEP, a novel zeaxanthin epoxidase gene from alfalfa (Medicago sativa), confers drought and salt tolerance in transgenic tobacco

KEY MESSAGE

The zeaxanthin epoxidase gene ( MsZEP ) was cloned and characterized from alfalfa and validated for its function of tolerance toward drought and salt stresses by heterologous expression in Nicotiana tabacum. Zeaxanthin epoxidase (ZEP) plays important roles in plant response to various environment stresses due to its functions in ABA biosynthetic and the xanthophyll cycle. To understand the expression characteristics and the biological functions of ZEP in alfalfa (Medicago sativa), a novel gene, designated as MsZEP (KM044311), was cloned, characterized and overexpressed in Nicotiana tabacum. The open reading frame of MsZEP contains 1992 bp nucleotides and encodes a 663-amino acid polypeptide. Amino acid sequence alignment indicated that deduced MsZEP protein was highly homologous to other plant ZEP sequences. Phylogenetic analysis showed that MsZEP was grouped into a branch with other legume plants. Real-time quantitative PCR revealed that MsZEP gene expression was clearly tissue-specific, and the expression levels were higher in green tissues (leaves and stems) than in roots. MsZEP expression decreased in shoots under drought, cold, heat and ABA treatment, while the expression levels in roots showed different trends. Besides, the results showed that nodules could up-regulate the MsZEP expression under non-stressful conditions and in the earlier stage of different abiotic stress. Heterologous expression of the MsZEP gene in N. tabacum could confer tolerance to drought and salt stress by affecting various physiological pathways, ABA levels and stress-responsive genes expression. Taken together, these results suggested that the MsZEP gene may be involved in alfalfa responses to different abiotic stresses and nodules, and could enhance drought and salt tolerance of transgenic tobacco by heterologous expression.

Rice Stress Associated Protein 1 (OsSAP1) Interacts with Aminotransferase (OsAMTR1) and Pathogenesis-Related 1a Protein (OsSCP) and Regulates Abiotic Stress Responses

Stress associated proteins (SAPs) are the A20/AN1 zinc-finger containing proteins which can regulate the stress signaling in plants. The rice SAP protein, OsSAP1 has been shown to confer abiotic stress tolerance to plants, when overexpressed, by modulating the expression of endogenous stress-related genes. To further understand the mechanism of OsSAP1-mediated stress signaling, OsSAP1 interacting proteins were identified using yeast two-hybrid analysis. Two novel proteins, aminotransferase (OsAMTR1) and a SCP/TAPS or pathogenesis-related 1 class of protein (OsSCP) were found to interact with OsSAP1. The genes encoding OsAMTR1 and OsSCP were stress-responsive and showed higher expression upon abiotic stress treatments. The role of OsAMTR1 and OsSCP under stress was analyzed by overexpressing them constitutively in Arabidopsis and responses of transgenic plants were assessed under salt and water-deficit stress. The OsAMTR1 and OsSCP overexpressing plants showed higher seed germination, root growth and fresh weight than wild-type plants under stress conditions. Overexpression of OsAMTR1 and OsSCP affected the expression of many known stress-responsive genes which were not affected by the overexpression of OsSAP1. Moreover, the transcript levels of OsSCP and OsAMTR1 were also unaffected by the overexpression of OsSAP1. Hence, it was concluded that OsSAP1 regulates the stress responsive signaling by interacting with these proteins which further regulate the downstream stress responsive gene expression.

An A20/AN1-type zinc finger protein modulates gibberellins and abscisic acid contents and increases sensitivity to abiotic stress in rice (Oryza sativa)

The plant hormones gibberellins (GA) and abscisic acid (ABA) play important roles in plant development and stress responses. Here we report a novel A20/AN1-type zinc finger protein ZFP185 involved in GA and ABA signaling in the regulation of growth and stress response. ZFP185 was constitutively expressed in various rice tissues. Overexpression of ZFP185 in rice results in a semi-dwarfism phenotype, reduced cell size, and the decrease of endogenous GA3 content. By contrast, higher GA3 content was observed in RNAi plants. The application of exogenous GA3 can fully rescue the semi-dwarfism phenotype of ZFP185 overexpressing plants, suggesting the negative role of ZFP185 in GA biosynthesis. Besides GA, overexpression of ZFP185 decreased ABA content and expression of several ABA biosynthesis-related genes. Moreover, it was found that ZFP185, unlike previously known A20/AN1-type zinc finger genes, increases sensitivity to drought, cold, and salt stresses, implying the negative role of ZFP185 in stress tolerance. ZFP185 was localized in the cytoplasm and lacked transcriptional activation potential. Our study suggests that ZFP185 regulates plant growth and stress responses by affecting GA and ABA biosynthesis in rice.

Rice OsiSAP7 negatively regulates ABA stress signalling and imparts sensitivity to water-deficit stress in Arabidopsis

Stress associated protein (SAP) genes in plants regulate abiotic stress responses. SAP gene family consists of 18 members in rice. Although their abiotic stress responsiveness is well established, the mechanism of their action is poorly understood. OsiSAP7 was chosen to investigate the mechanism of its action based on the dual nature of its sub-cellular localization preferentially in the nucleus or sub-nuclear speckles upon transient expression in onion epidermal cells. Its expression was down-regulated in rice seedlings under abiotic stresses. OsiSAP7 was localized evenly in the nucleus under unstressed conditions and in sub-nuclear speckles on MG132 treatment. OsiSAP7 exhibits E3 ubiquitin ligase activity in vitro. Abiotic stress responses of OsiSAP7 were assessed by its overexpression in Arabidopsis under the control of a stress inducible promoter rd29A. Stress response assessment was done at seed germination and advanced stages of development. Transgenics were ABA insensitive at seed germination stage and sensitive to water-deficit stress at advanced stage as compared to wild type (WT). They were also impaired in ABA and stress-responsive gene expression. Our study suggests that OsiSAP7 acts as a negative regulator of ABA and water-deficit stress signalling by acting as an E3 ubiquitin ligase.