Role of HKT1 in Thellungiella salsuginea, a model extremophile plant

The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions

Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.

Adaptative Mechanisms of Halophytic Eutrema salsugineum Encountering Saline Environment

Salt cress (Eutrema salsugineum), an Arabidopsis-related halophyte, can naturally adapt to various harsh climates and soil conditions; thus, it is considered a desirable model plant for deciphering mechanisms of salt and other abiotic stresses. Accumulating evidence has revealed that compared with Arabidopsis, salt cress possesses stomata that close more tightly and more succulent leaves during extreme salt stress, a noticeably higher level of proline, inositols, sugars, and organic acids, as well as stress-associated transcripts in unstressed plants, and they are induced rapidly under stress. In this review, we systematically summarize the research on the morphology, physiology, genome, gene expression and regulation, and protein and metabolite profile of salt cress under salt stress. We emphasize the latest advances in research on the genome adaptive evolution encountering saline environments, and epigenetic regulation, and discuss the mechanisms underlying salt tolerance in salt cress. Finally, we discuss the existing questions and opportunities for future research in halophytic Eutrema. Together, the review fosters a better understanding of the mechanism of plant salt tolerance and provides a reference for the research and utilization of Eutrema as a model extremophile in the future. Furthermore, the prospects for salt cress applied to explore the mechanism of salt tolerance provide a theoretical basis to develop new strategies for agricultural biotechnology.

HKT sodium and potassium transporters in Arabidopsis thaliana and related halophyte species

High salinity induces osmotic stress and often leads to sodium ion-specific toxicity, with inhibitory effects on physiological, biochemical and developmental pathways. To cope with increased Na⁺ in soil water, plants restrict influx, compartmentalize ions into vacuoles, export excess Na⁺ from the cell, and distribute ions between the aerial and root organs. In this review, we discuss our current understanding of how high-affinity K⁺ transporters (HKT) contribute to salinity tolerance, focusing on HKT1-like family members primarily involved in long-distance transport, and in the recent research in the model plant Arabidopsis and its halophytic counterparts of the Eutrema genus. Functional characterization of the salt overly sensitive (SOS) pathway and HKT1-type transporters in these species indicate that they utilize similar approaches to deal with salinity, regardless of their tolerance.

Natural Genetic Resources from Diverse Plants to Improve Abiotic Stress Tolerance in Plants

The current agricultural system is biased for the yield increase at the cost of biodiversity. However, due to the loss of precious genetic diversity during domestication and artificial selection, modern cultivars have lost the adaptability to cope with unfavorable environments. There are many reports on variations such as single nucleotide polymorphisms (SNPs) and indels in the stress-tolerant gene alleles that are associated with higher stress tolerance in wild progenitors, natural accessions, and extremophiles in comparison with domesticated crops or model plants. Therefore, to gain a better understanding of stress-tolerant traits in naturally stress-resistant plants, more comparative studies between the modern crops/model plants and crop progenitors/natural accessions/extremophiles are required. In this review, we discussed and summarized recent progress on natural variations associated with enhanced abiotic stress tolerance in various plants. By applying the recent biotechniques such as the CRISPR/Cas9 gene editing tool, natural genetic resources (i.e., stress-tolerant gene alleles) from diverse plants could be introduced to the modern crop in a non-genetically modified way to improve stress-tolerant traits.

Role and Functional Differences of HKT1-Type Transporters in Plants under Salt Stress

Abiotic stresses generally cause a series of morphological, biochemical and molecular changes that unfavorably affect plant growth and productivity. Among these stresses, soil salinity is a major threat that can seriously impair crop yield. To cope with the effects of high salinity on plants, it is important to understand the mechanisms that plants use to deal with it, including those activated in response to disturbed Na⁺ and K⁺ homeostasis at cellular and molecular levels. HKT1-type transporters are key determinants of Na⁺ and K⁺ homeostasis under salt stress and they contribute to reduce Na⁺-specific toxicity in plants. In this review, we provide a brief overview of the function of HKT1-type transporters and their importance in different plant species under salt stress. Comparison between HKT1 homologs in different plant species will shed light on different approaches plants may use to cope with salinity.

Halophytism: What Have We Learnt From Arabidopsis thaliana Relative Model Systems?

Halophytes are able to thrive in salt concentrations that would kill 99% of other plant species, and identifying their salt-adaptive mechanisms has great potential for improving the tolerance of crop plants to salinized soils. Much research has focused on the physiological basis of halophyte salt tolerance, whereas the elucidation of molecular mechanisms has traditionally lagged behind due to the absence of a model halophyte system. However, over the last decade and a half, two Arabidopsis (Arabidopsis thaliana) relatives, Eutrema salsugineum and Schrenkiella parvula, have been established as transformation-competent models with various genetic resources including high-quality genome assemblies. These models have facilitated powerful comparative analyses with salt-sensitive Arabidopsis to unravel the genetic adaptations that enable a halophytic lifestyle. The aim of this review is to explore what has been learned about halophytism using E. salsugineum and S. parvula We consider evidence from physiological and molecular studies suggesting that differences in salt tolerance between related halophytes and salt-sensitive plants are associated with alterations in the regulation of basic physiological, biochemical, and molecular processes. Furthermore, we discuss how salt tolerance mechanisms of the halophytic models are reflected at the level of their genomes, where evolutionary processes such as subfunctionalization and/or neofunctionalization have altered the expression and/or functions of genes to facilitate adaptation to saline conditions. Lastly, we summarize the many areas of research still to be addressed with E. salsugineum and S. parvula as well as obstacles hindering further progress in understanding halophytism.

The High-Affinity Potassium Transporter EpHKT1;2 From the Extremophile Eutrema parvula Mediates Salt Tolerance

To survive salt stress, plants must maintain a balance between sodium and potassium ions. High-affinity potassium transporters (HKTs) play a key role in reducing Na+ toxicity through K+ uptake. Eutrema parvula (formerly known as Thellungiella parvula), a halophyte closely related to Arabidopsis, has two HKT1 genes that encode EpHKT1;1 and EpHKT1;2. In response to high salinity, the EpHKT1;2 transcript level increased rapidly; by contrast, the EpHKT1;1 transcript increased more slowly in response to salt treatment. Yeast cells expressing EpHKT1;2 were able to tolerate high concentrations of NaCl, whereas EpHKT1;1-expressing yeast cells remained sensitive to NaCl. Amino acid sequence alignment with other plant HKTs showed that EpHKT1;1 contains an asparagine residue (Asn-213) in the second pore-loop domain, but EpHKT1;2 contains an aspartic acid residue (Asp-205) at the same position. Yeast cells expressing EpHKT1;1, in which Asn-213 was substituted with Asp, were able to tolerate high concentrations of NaCl. In contrast, substitution of Asp-205 by Asn in EpHKT1;2 did not enhance salt tolerance and rather resulted in a similar function to that of AtHKT1 (Na+ influx but no K+ influx), indicating that the presence of Asn or Asp determines the mode of cation selectivity of the HKT1-type transporters. Moreover, Arabidopsis plants (Col-gl) overexpressing EpHKT1;2 showed significantly higher tolerance to salt stress and accumulated less Na+ and more K+ compared to those overexpressing EpHKT1;1 or AtHKT1. Taken together, these results suggest that EpHKT1;2 mediates tolerance to Na+ ion toxicity in E. parvula and is a major contributor to its halophytic nature.

De novo sequencing, assembly, and analysis of Iris lactea var. chinensis roots' transcriptome in response to salt stress

As a halophyte, Iris lactea var. chinensis (I. lactea var. chinensis) is widely distributed and has good drought and heavy metal resistance. Moreover, it is an excellent ornamental plant. I. lactea var. chinensis has extensive application prospects owing to the global impacts of salinization. To better understand its molecular mechanism involved in salt resistance, the de novo sequencing, assembly, and analysis of I. lactea var. chinensis roots' transcriptome in response to salt-stress conditions was performed. On average, 74.17% of the clean reads were mapped to unigenes. A total of 121,093 unigenes were constructed and 56,398 (46.57%) were annotated. Among these, 13,522 differentially expressed genes (DEGs) were identified between salt-treated and control samples Compared to the transcriptional level of control, 7037 DEGs were up-regulated and 6539 down-regulated. In addition, 129 up-regulated and 1609 down-regulated genes were simultaneously detected in all three pairwise comparisons between control and salt-stressed libraries. At least 247 and 250 DEGs encoding transcription factors and transporter proteins were identified. Meanwhile, 130 DEGs regarding reactive oxygen species (ROS) scavenging system were also summarized. Based on real-time quantitative RT-PCR, we verified the changes in the expression patterns of 10 unigenes. Our study identified potential salt-responsive candidate genes and increased the understanding of halophyte responses to salinity stress.

GWAS Uncovers Differential Genetic Bases for Drought and Salt Tolerances in Sesame at the Germination Stage

Sesame has great potential as an industrial crop but its production is challenged by drought and salt stresses. To unravel the genetic variants leading to salinity and drought tolerances at the germination stage, genome-wide association studies of stress tolerance indexes related to NaCl-salt and polyethylene glycol-drought induced stresses were performed with a diversity panel of 490 sesame accessions. An extensive variation was observed for drought and salt responses in the population and most of the accessions were moderately tolerant to both stresses. A total of 132 and 120 significant Single Nucleotide Polymorphisms (SNPs) resolved to nine and 15 Quantitative trait loci (QTLs) were detected for drought and salt stresses, respectively. Only two common QTLs for drought and salt responses were found located on linkage groups 5 and 7, respectively. This indicates that the genetic bases for drought and salt responses in sesame are different. A total of 13 and 27 potential candidate genes were uncovered for drought and salt tolerance indexes, respectively, encoding transcription factors, antioxidative enzymes, osmoprotectants and involved in hormonal biosynthesis, signal transduction or ion sequestration. The identified SNPs and potential candidate genes represent valuable resources for future functional characterization towards the enhancement of sesame cultivars for drought and salt tolerances.

TsNAC1 Is a Key Transcription Factor in Abiotic Stress Resistance and Growth

NAC proteins constitute one of the largest families of plant-specific transcription factors, and a number of these proteins participate in the regulation of plant development and responses to abiotic stress. T. HALOPHILA STRESS RELATED NAC1 (TsNAC1), cloned from the halophyte Thellungiella halophila, is a NAC transcription factor gene, and its overexpression can improve abiotic stress resistance, especially in salt stress tolerance, in both T. halophila and Arabidopsis (Arabidopsis thaliana) and retard the growth of these plants. In this study, the transcriptional activation activity of TsNAC1 and RD26 from Arabidopsis was compared with the target genes' promoter regions of TsNAC1 from T. halophila, and the results showed that the transcriptional activation activity of TsNAC1 was higher in tobacco (Nicotiana tabacum) and yeast. The target sequence of the promoter from the target genes also was identified, and TsNAC1 was shown to target the positive regulators of ion transportation, such as T. HALOPHILA H⁺-PPASE1, and the transcription factors MYB HYPOCOTYL ELONGATION-RELATED and HOMEOBOX12 In addition, TsNAC1 negatively regulates the expansion of cells, inhibits LIGHT-DEPENDENT SHORT HYPOCOTYLS1 and UDP-XYLOSYLTRANSFERASE2, and directly controls the expression of MULTICOPY SUPPRESSOR OF IRA14 Based on these results, we propose that TsNAC1 functions as an important upstream regulator of plant abiotic stress responses and vegetative growth.

Differential selection of sodium and potassium ions by TsHKT1;2

Among abiotic stresses, soil salinity is a major threat to agriculture. To address and control the effects of high salinity on plants, it is important to understand their responses to salt stress that disturbs the homeostatic equilibrium at cellular and molecular levels. To deal and control effects of high salinity on plants, it is important to understand their responses to salt stress that disturbs the homeostatic equilibrium at cellular and molecular levels. In this regard, halophytes (salt tolerant plants) can provide superior models for the study of salt stress defense parameters compared to glycophytes (salt sensitive species). TsHKT1;2 one of the 3 copies of HKT1 in the Arabidopsis relative halophyte, Thellungiella salsuginea acts as a potassium transporter, even under salt stress. TsHKT1;2 includes a conserved Asp (D) residue in the 2(nd) pore-loop domain. Most other HKT1 sequences, including AtHKT1, contain Asn (N) in this position. We found that athkt1-1 plants complemented by TsHKT1;2 under native AtHKT1 promoter were more tolerant to salt stress, while substitution of Asp (D207) by Asn (N) significantly reduced resistance to salinity. We suggest that the presence of Asn or Asp is the essential feature that defines and establishes cation selectivity in dicot HKT1-type transporters.

A Single Amino-Acid Substitution in the Sodium Transporter HKT1 Associated with Plant Salt Tolerance

A crucial prerequisite for plant growth and survival is the maintenance of potassium uptake, especially when high sodium surrounds the root zone. The Arabidopsis HIGH-AFFINITY K(+) TRANSPORTER1 (HKT1), and its homologs in other salt-sensitive dicots, contributes to salinity tolerance by removing Na(+) from the transpiration stream. However, TsHKT1;2, one of three HKT1 copies in Thellungiella salsuginea, a halophytic Arabidopsis relative, acts as a K(+) transporter in the presence of Na(+) in yeast (Saccharomyces cerevisiae). Amino-acid sequence comparisons indicated differences between TsHKT1;2 and most other published HKT1 sequences with respect to an Asp residue (D207) in the second pore-loop domain. Two additional T salsuginea and most other HKT1 sequences contain Asn (n) in this position. Wild-type TsHKT1;2 and altered AtHKT1 (AtHKT1(N-D)) complemented K(+)-uptake deficiency of yeast cells. Mutant hkt1-1 plants complemented with both AtHKT1(N) (-) (D) and TsHKT1;2 showed higher tolerance to salt stress than lines complemented by the wild-type AtHKT1 Electrophysiological analysis in Xenopus laevis oocytes confirmed the functional properties of these transporters and the differential selectivity for Na(+) and K(+) based on the n/d variance in the pore region. This change also dictated inward-rectification for Na(+) transport. Thus, the introduction of Asp, replacing Asn, in HKT1-type transporters established altered cation selectivity and uptake dynamics. We describe one way, based on a single change in a crucial protein that enabled some crucifer species to acquire improved salt tolerance, which over evolutionary time may have resulted in further changes that ultimately facilitated colonization of saline habitats.

Functional characterisation of an intron retaining K(+) transporter of barley reveals intron-mediated alternate splicing

Intron retention in transcripts and the presence of 5' and 3' splice sites within these introns mediate alternate splicing, which is widely observed in animals and plants. Here, functional characterisation of the K(+) transporter, HvHKT2;1, with stably retained introns from barley (Hordeum vulgare) in yeast (Saccharomyces cerevisiae), and transcript profiling in yeast and transgenic tobacco (Nicotiana tabacum) is presented. Expression of intron-retaining HvHKT2;1 cDNA (HvHKT2;1-i) in trk1, trk2 yeast strain defective in K(+) uptake restored growth in medium containing hygromycin in the presence of different concentrations of K(+) and mediated hypersensitivity to Na(+) . HvHKT2;1-i produces multiple transcripts via alternate splicing of two regular introns and three exons in different compositions. HKT isoforms with retained introns and exon skipping variants were detected in relative expression analysis of (i) HvHKT2;1-i in barley under native conditions, (ii) in transgenic tobacco plants constitutively expressing HvHKT2;1-i, and (iii) in trk1, trk2 yeast expressing HvHKT2;1-i under control of an inducible promoter. Mixed proportions of three HKT transcripts: HvHKT2;1-e (first exon region), HvHKT2;1-i1 (first intron) and HvHKT2;1-i2 (second intron) were observed. The variation in transcript accumulation in response to changing K(+) and Na(+) concentrations was observed in both heterologous and plant systems. These findings suggest a link between intron-retaining transcripts and different splice variants to ion homeostasis, and their possible role in salt stress.

Substantial reprogramming of the Eutrema salsugineum (Thellungiella salsuginea) transcriptome in response to UV and silver nitrate challenge

BACKGROUND

Cruciferous plants synthesize a large variety of tryptophan-derived phytoalexins in response to pathogen infection, UV irradiation, or high dosages of heavy metals. The major phytoalexins of Eutrema salsugineum (Thellungiella salsuginea), which has recently been established as an extremophile model plant, are probably derivatives of indole glucosinolates, in contrast to Arabidopsis, which synthesizes characteristic camalexin from the glucosinolate precursor indole-3-acetaldoxime.

RESULTS

The transcriptional response of E. salsugineum to UV irradiation and AgNO3 was monitored by RNAseq and microarray analysis. Most transcripts (respectively 70% and 78%) were significantly differentially regulated and a large overlap between the two treatments was observed (54% of total). While core genes of the biosynthesis of aliphatic glucosinolates were repressed, tryptophan and indole glucosinolate biosynthetic genes, as well as defence-related WRKY transcription factors, were consistently upregulated. The putative Eutrema WRKY33 ortholog was functionally tested and shown to complement camalexin deficiency in Atwrky33 mutant.

CONCLUSIONS

In E. salsugineum, UV irradiation or heavy metal application resulted in substantial transcriptional reprogramming. Consistently induced genes of indole glucosinolate biosynthesis and modification will serve as candidate genes for the biosynthesis of Eutrema-specific phytoalexins.

Model of Cation Transportation Mediated by High-Affinity Potassium Transporters (HKTs) in Higher Plants

Trk/Ktr/HKT transporters probably were evolved from simple K⁺ channels KcsA. HKT transporters, which mediate Na⁺-uniport or Na⁺/K⁺-symport, maintain K⁺/Na⁺ homeostasis and increase salinity tolerance, can be classified into three subfamilies in higher plants. In this review, we systematically analyzed the characteristics of amino acids sequences and physiological functions of HKT transporters in higher plant. Furthermore, we depicted the hypothetical models of cations selection and transportation mediated by HKT transporters according to the highly conserved structure for the goal of better understanding the cations transportation processes.

Comparative 2D-DIGE analysis of salinity responsive microsomal proteins from leaves of salt-sensitive Arabidopsis thaliana and salt-tolerant Thellungiella salsuginea

Halophytes have evolved unique molecular strategies to overcome high soil salinity but we still know very little about the main mechanisms that these plants use to complete their lifecycle under salinity stress. One useful approach to further our understanding in this area is to directly compare the response to salinity of two closely related species which show diverse levels of salt tolerance. Here we present a comparative proteomic study using DIGE of leaf microsomal proteins to identify salt-responsive membrane associated proteins in Arabidopsis thaliana (a glycophyte) and Thellungiella salsuginea (a halophyte). While a small number of distinct protein abundance changes were observed upon salt stress in both species, the most notable differences were observed between species and specifically, in untreated plants with a total of 36 proteins displaying significant abundance changes. Gene ontology (GO) term enrichment analysis showed that the majority of these proteins were distributed into two functional categories; transport (31%) and carbohydrate metabolism (17%). Results identify several novel salt responsive proteins in this system and support the theory that T. salsuginea shows a high degree of salt-tolerance because molecular mechanisms are primed to deal with the stress. This intrinsic ability to anticipate salinity stress distinguishes it from the glycophyte A. thaliana.

BIOLOGICAL SIGNIFICANCE

There is significant interest in understanding the molecular mechanisms that plants use to tolerate salinity as soil salinization is becoming an increasing concern for agriculture with high soil Na(+) levels leading to reduced yields and economic loss. Much of our knowledge on the molecular mechanisms employed by plants to combat salinity stress has come from work on salt-sensitive plants, but studies on naturally occurring highly salt-resistant plants, halophytes, and direct comparisons between closely related glycophytes and halophytes, could help to further our understanding of salinity tolerance mechanisms. In this study, employing two closely related species which differ markedly in their salt-tolerance, we carried out a quantitative proteomic approach using 2D-DIGE to identify salt-responsive proteins and compare and contrast the differences between the two plant species. Our work complements a previous study using iTRAQ technology (34) and highlights the benefits of using alternative technologies and approaches to gain a broader representation of the salt-responsive proteome in these species.