OsPFA-DSP1, a rice protein tyrosine phosphatase, negatively regulates drought stress responses in transgenic tobacco and rice plants

Transcriptome and Small RNA Sequencing Reveals the Basis of Response to Salinity, Alkalinity and Hypertonia in Quinoa (Chenopodium quinoa Willd.)

Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous cereal that is rich in nutrients. This important crop has been shown to have significant tolerance to abiotic stresses such as salinization and drought. Understanding the underlying mechanism of stress response in quinoa would be a significant advantage for breeding crops with stress tolerance. Here, we treated the low-altitude quinoa cultivar CM499 with either NaCl (200 mM), Na₂CO₃/NaHCO₃ (100 mM, pH 9.0) or PEG6000 (10%) to induce salinity, alkalinity and hypertonia, respectively, and analyzed the subsequent expression of genes and small RNAs via high-throughput sequencing. A list of known/novel genes were identified in quinoa, and the ones responding to different stresses were selected. The known/novel quinoa miRNAs were also identified, and the target genes of the stress response ones were predicted. Both the differently expressed genes and the targets of differently expressed miRNAs were found to be enriched for reactive oxygen species homeostasis, hormone signaling, cell wall synthesis, transcription factors and some other factors. Furthermore, we detected changes in reactive oxygen species accumulation, hormone (auxin and ethylene) responses and hemicellulose synthesis in quinoa seedlings treated with stresses, indicating their important roles in the response to saline, alkaline or hyperosmotic stresses in quinoa. Thus, our work provides useful information for understanding the mechanism of abiotic stress responses in quinoa, which would provide clues for improving breeding for quinoa and other crops.

Targeted and untargeted metabolomics reveals deep analysis of drought stress responses in needles and roots of Pinus taeda seedlings

Drought stress is one of major environmental stresses affecting plant growth and yield. Although Pinus taeda trees are planted in rainy southern China, local drought sometime occurs and can last several months, further affecting their growth and resin production. In this study, P. taeda seedlings were treated with long-term drought (42 d), and then targeted and untargeted metabolomics analysis were carried out to evaluate drought tolerance of P. taeda. Targeted metabolomics analysis showed that levels of some sugars, phytohormones, and amino acids significantly increased in the roots and needles of water-stressed (WS) P. taeda seedlings, compared with well-watered (WW) pine seedlings. These metabolites included sucrose in pine roots, the phytohormones abscisic acid and sacylic acid in pine needles, the phytohormone gibberellin (GA4) and the two amino acids, glycine and asparagine, in WS pine roots. Compared with WW pine seedlings, the neurotransmitter acetylcholine significantly increased in needles of WS pine seedlings, but significantly reduced in their roots. The neurotransmitters L-glutamine and hydroxytyramine significantly increased in roots and needles of WS pine seedlings, respectively, compared with WW pine seedlings, but the neurotransmitter noradrenaline significantly reduced in needles of WS pine seedlings. Levels of some unsaturated fatty acids significantly reduced in roots or needles of WS pine seedlings, compared with WW pine seedlings, such as linoleic acid, oleic acid, myristelaidic acid, myristoleic acid in WS pine roots, and palmitelaidic acid, erucic acid, and alpha-linolenic acid in WS pine needles. However, three saturated fatty acids significantly increased in WS pine seedlings, i.e., dodecanoic acid in WS pine needles, tricosanoic acid and heptadecanoic acid in WS pine roots. Untargeted metabolomics analysis showed that levels of some metabolites increased in WS pine seedlings, especially sugars, long-chain lipids, flavonoids, and terpenoids. A few of specific metabolites increased greatly, such as androsin, piceatanol, and panaxatriol in roots and needles of WS pine seedlings. Comparing with WW pine seedlings, it was found that the most enriched pathways in WS pine needles included flavone and flavonol biosynthesis, ABC transporters, diterpenoid biosynthesis, plant hormone signal transduction, and flavonoid biosynthesis; in WS pine roots, the most enriched pathways included tryptophan metabolism, caffeine metabolism, sesquiterpenoid and triterpenoid biosynthesis, plant hormone signal transduction, biosynthesis of phenylalanine, tyrosine, and tryptophan. Under long-term drought stress, P. taeda seedlings showed their own metabolomics characteristics, and some new metabolites and biosynthesis pathways were found, providing a guideline for breeding drought-tolerant cultivars of P. taeda.

Importance of Tyrosine Phosphorylation in Hormone-Regulated Plant Growth and Development

Protein phosphorylation is the most frequent post-translational modification (PTM) that plays important regulatory roles in a wide range of biological processes. Phosphorylation mainly occurs on serine (Ser), threonine (Thr), and tyrosine (Tyr) residues, with the phosphorylated Tyr sites accounting for ~1–2% of all phosphorylated residues. Tyr phosphorylation was initially believed to be less common in plants compared to animals; however, recent investigation indicates otherwise. Although they lack typical protein Tyr kinases, plants possess many dual-specificity protein kinases that were implicated in diverse cellular processes by phosphorylating Ser, Thr, and Tyr residues. Analyses of sequenced plant genomes also identified protein Tyr phosphatases and dual-specificity protein phosphatases. Recent studies have revealed important regulatory roles of Tyr phosphorylation in many different aspects of plant growth and development and plant interactions with the environment. This short review summarizes studies that implicated the Tyr phosphorylation in biosynthesis and signaling of plant hormones.

A structural exposé of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop

Structural snapshots of protein/ligand complexes are a prerequisite for gaining atomic level insight into enzymatic reaction mechanisms. An important group of enzymes has been deprived of this analytical privilege: members of the protein tyrosine phosphatase (PTP) superfamily with catalytic WPD-loops lacking the indispensable general-acid/base within a tryptophan-proline-aspartate/glutamate context. Here, we provide the ligand/enzyme crystal complexes for one such PTP outlier: Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1 (AtPFA-DSP1), herein unveiled as a regioselective and efficient phosphatase towards inositol pyrophosphate (PP-InsP) signaling molecules. Although the WPD loop is missing its canonical tripeptide motif, this structural element contributes to catalysis by assisting PP-InsP delivery into the catalytic pocket, for a choreographed exchange with phosphate reaction product. Subsequently, an intramolecular proton donation by PP-InsP substrate is posited to substitute functionally for the absent aspartate/glutamate general-acid. Overall, we expand mechanistic insight into adaptability of the conserved PTP structural elements.

AtPFA-DSP5 interacts with MPK3/MPK6 and negatively regulates plant salt responses

Protein tyrosine phosphatases play essential roles in plant growth and development and in plant responses to biotic or abiotic stresses. We recently demonstrated that an atypical dual-specificity protein tyrosine phosphatase in plants, AtPFA-DSP3 (DSP3), negatively regulates plant salt tolerance. Here, we report that a homolog of DSP3, AtPFA-DSP5 (DSP5), affects the response of plants to high-salt conditions. A loss-of-function mutant of DSP5 showed reduced sensitivity to salt treatment at the seed germination and vegetative stages of development while a gain-of-function mutant of DSP5 showed increased sensitivity to salt stress. The salt responses of dsp3dsp5 double-mutant plants were similar to those of dsp3 and dsp5 single-mutant plants. Gel overlay and firefly luciferase complementation assays showed that DSP5 interacts with MPK3 and MPK6 in vitro and in vivo. These results indicate that DSP5 is a novel negative regulator of salt responses in Arabidopsis that interacts directly with MPK3 and MPK6.

Molecular mapping and characterization of QBp.caas-3BL for black point resistance in wheat (Triticum aestivum L.)

We fine-mapped QBp.caas-3BL for black point resistance in an interval of 1.7 Mb containing five high-confidence annotated genes and developed a KASP marker suitable for selection of QBp.caas-3BL. Wheat black point, which occurs in most wheat-growing regions of the world, is detrimental to grain appearance, processing and nutrient quality. Mining and characterization of genetic loci for black point resistance are helpful for breeding resistant wheat cultivars. We previously identified a major QTL QBp.caas-3BL in a recombinant inbred line (RIL) population of Linmai 2/Zhong 892 across five environments. Here we confirmed the QTL in two additional environments. The genetic region of QBp.caas-3BL was enriched with newly developed markers. Using four sets of near isogenic lines, QBp.caas-3BL was narrowed down to a physical interval of approximately 1.7 Mb, including five annotated genes according to IWGSC reference genome. TraesCS3B02G404300, TraesCS3B02G404600 and TraesCS3B02G404700 were predicted as candidate genes based on the analyses of sequence polymorphisms and differential expression. We also converted a SNP of TraesCS3B02G404700 into a breeding-applicable KASP marker and verified its efficacy for marker-assisted breeding in a panel of germplasm. The findings not only lay a foundation for map-based cloning of QBp.caas-3BL but also provide a useful marker for selection of resistant cultivars genotypes in wheat breeding.

Dry cultivation and cultivar affect starch synthesis and traits to define rice grain quality in various panicle parts

A pot experiment was conducted to explore the effects of high-quality (Huanghuazhan, HH), drought-resistant (IR, IRAT109) and drought-susceptible cultivars (ZS, Zhenshan97) under flooding irrigation and dry cultivation (D) on the starch accumulation and synthesis, physicochemical traits of starch granules and rice grain quality at the upper (U) and lower panicle. Under D treatment, IR and ZS had lower rice quality, especially the appearance and cooking quality. DHH-U had the highest appearance, nutritional and cooking quality among all cultivars under D treatment, which could be ascribed to the synthesis of more short-branch chain amylopectin and correspondingly higher starch granule tightness. DHH-U also maintained ordered carbohydrate structure, crystalline regions, and many hydrophilic and hydrophobic functional groups in starch granules before pasting. It could prevent the polymerization of small molecules to avoid the formation of macromolecules after pasting. Overall, these findings may facilitate the improvement of grain quality in rice dry cultivation.

AtPFA-DSP3, an atypical dual-specificity protein tyrosine phosphatase, affects salt stress response by modulating MPK3 and MPK6 activity

Protein phosphorylation, especially serine/threonine and tyrosine phosphorylation, plays significant roles in signalling during plant growth and development as well as plant responses to biotic or abiotic stresses. Dual-specificity protein tyrosine phosphatases dephosphorylate components of these signalling pathways. Here, we report that an atypical dual-specificity protein tyrosine phosphatase, AtPFA-DSP3 (DSP3), negatively affects the response of plants to high-salt conditions. A DSP3 loss-of-function mutant showed reduced sensitivity to salt treatment. DSP3 was primarily localized in nuclei and was degraded during salt treatment. Compared to wild type, the level of ROS was lower in the dsp3 mutant and higher in plants ectopically expressing DSP3, indicating that higher DSP3 level was associated with increased ROS production. DSP3 interacted with and dephosphorylated MPK3 and MPK6. Genetic analyses of a dsp3mpk3 double mutant revealed that DSP3's effect on salt stress depends on MPK3. Moreover, the phosphatase activity of DSP3 was required for its role in salt signalling. These results indicate that DSP3 is a negative regulator of salt responses in Arabidopsis by directly modulating the accumulation of phosphorylated MPK3 and MPK6.

Metabolic profiles of moso bamboo in response to drought stress in a field investigation

An increasing number of moso bamboo habitats are suffering severe drought events. The improvement in our understanding of the mechanisms of drought-resistance in moso bamboo benefits their genetic improvement and maintenance of forest sustainability. Here, we investigated the metabolic changes across the annual growth cycle of moso bamboo in the field under drought stress using liquid chromatography coupled to mass spectrometry (LC-MS) based on untargeted metabolomic profiling. Our results showed that the metabolic profiles induced by drought stress were relatively consistent among the three growth stages. Specifically, most responsive metabolites exhibited enhanced accumulation under drought stress, including anthocyanins, glycosides, organic acids, amino acids, and sugars and sugar alcohols. The potential metabolism pathways involved in the response to drought stress were mainly included into amino acid metabolism and sugar metabolism pathways. Five common responsive metabolic pathways were found among three growth stages, including linoleic acid metabolism, ubiquinone and other terpenoid-quinone biosynthesis, tyrosine metabolism, starch and sucrose metabolism and isoquinoline alkaloid biosynthesis. Overall, our findings provide new insights into the responsive mechanisms of the moso bamboo under drought stress in terms of metabolic profiles.

Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress

The efficiency of stress-induced adaptive responses of plants depends on intricate coordination of multiple signal transduction pathways that act coordinately or, in some cases, antagonistically. Protein post-translational modifications (PTMs) can regulate protein activity and localization as well as protein-protein interactions in numerous cellular processes, thus leading to elaborate regulation of plant responses to various external stimuli. Understanding responses of crop plants under field conditions is crucial to design novel stress-tolerant cultivars that maintain robust homeostasis even under extreme conditions. In this review, proteomic studies of PTMs in crops are summarized. Although the research on the roles of crop PTMs in regulating stress response mechanisms is still in its early stage, several novel insights have been retrieved so far. This review covers techniques for detection of PTMs in plants, representative PTMs in plants under abiotic stress, and how PTMs control functions of representative proteins. In addition, because PTMs under abiotic stresses are well described in soybeans under submergence, recent findings in PTMs of soybean proteins under flooding stress are introduced. This review provides information on advances in PTM study in relation to plant adaptations to abiotic stresses, underlining the importance of PTM study to ensure adequate agricultural production in the future.

Rubisco Activase Is Also a Multiple Responder to Abiotic Stresses in Rice

Ribulose-1,5-bisphosphate carboxylase/oxygenase activase (RCA) is a nuclear gene that encodes a chloroplast protein that plays an important role in photosynthesis. Some reports have indicated that it may play a role in acclimation to different abiotic stresses. In this paper, we analyzed the stress-responsive elements in the 2.0 kb 5’-upstream regions of the RCA gene promoter and the primary, secondary and tertiary structure of the protein. We identified some cis-elements of multiple stress-related components in the RCA promoter. Amino acid and evolution analyses showed that the RCA protein had conserved regions between different species; however, the size and type varied. The secondary structures, binding sites and tertiary structures of the RCA proteins were also different. This might reflect the differences in the transcription and translation levels of the two RCA isoforms during adaptation to different abiotic stresses. Although both the transcription and translation levels of RCA isoforms in the rice leaves increased under various stresses, the large isoform was increased more significantly in the chloroplast stroma and thylakoid. It can be concluded that RCA, especially RCA_L, is also a multiple responder to abiotic stresses in rice, which provides new insights into RCA functions.

Role of Protein Tyrosine Phosphatases in Plants

Reversible protein phosphorylation is a crucial regulatory mechanism that controls many biological processes in eukaryotes. In plants, phosphorylation events primarily occur on serine (Ser) and threonine (Thr) residues, while in certain cases, it was also discovered on tyrosine (Tyr) residues. In contrary to plants, extensive reports on Tyr phosphorylation regulating a large numbers of biological processes exist in animals. Despite of such prodigious function in animals, Tyr phosphorylation is a least studied mechanism of protein regulation in plants. Recently, various chemical analytical procedures have strengthened the view that Tyr phosphorylation is equally prevalent in plants as in animals. However, regardless of Tyr phosphorylation events occuring in plants, no evidence could be found for the existence of gene encoding for Tyr phosphorylation i.e. the typical Tyr kinases. Various methodologies have suggested that plant responses to stress signals and developmental processes involved modifications in protein Tyr phosphorylation. Correspondingly, various reports have established the role of PTPs (Protein Tyrosine Phosphatases) in the dephosphorylation and inactivation of mitogen activated protein kinases (MAPKs) hence, in the regulation of MAPK signaling cascade. Besides this, many dual specificity protein phosphatases (DSPs) are also known to bind starch and regulate starch metabolism through reversible phosphorylation. Here, we are emphasizing the significant progress on protein Tyr phosphatases to understand the role of these enzymes in the regulation of post-translational modification in plant physiology and development.

Diurnal oscillations of soybean circadian clock and drought responsive genes

Rhythms produced by the endogenous circadian clock play a critical role in allowing plants to respond and adapt to the environment. While there is a well-established regulatory link between the circadian clock and responses to abiotic stress in model plants, little is known of the circadian system in crop species like soybean. This study examines how drought impacts diurnal oscillation of both drought responsive and circadian clock genes in soybean. Drought stress induced marked changes in gene expression of several circadian clock-like components, such as LCL1-, GmELF4- and PRR-like genes, which had reduced expression in stressed plants. The same conditions produced a phase advance of expression for the GmTOC1-like, GmLUX-like and GmPRR7-like genes. Similarly, the rhythmic expression pattern of the soybean drought-responsive genes DREB-, bZIP-, GOLS-, RAB18- and Remorin-like changed significantly after plant exposure to drought. In silico analysis of promoter regions of these genes revealed the presence of cis-elements associated both with stress and circadian clock regulation. Furthermore, some soybean genes with upstream ABRE elements were responsive to abscisic acid treatment. Our results indicate that some connection between the drought response and the circadian clock may exist in soybean since (i) drought stress affects gene expression of circadian clock components and (ii) several stress responsive genes display diurnal oscillation in soybeans.

Two homologous putative protein tyrosine phosphatases, OsPFA-DSP2 and AtPFA-DSP4, negatively regulate the pathogen response in transgenic plants

Protein phosphatases, together with protein kinases, regulate protein phosphorylation and dephosphorylation, and play critical roles in plant growth and biotic stress responses. However, little is known about the biological functions of plant protein tyrosine dual-specificity phosphatase (PFA-DSP) in biotic stresses. Here, we found that OsPFA-DSP2 was mainly expressed in calli, seedlings, roots, and young panicles, and localized in cytoplasm and nucleus. Ectopic overexpression of OsPFA-DSP2 in rice increased sensitivity to Magnaporthe grisea (M. grisea Z1 strain), inhibited the accumulation of hydrogen peroxide (H₂O₂) and suppressed the expression of pathogenesis-related (PR) genes after fungal infection. Interestingly, transgenic Arabidopsis plants overexpressing AtPFA-DSP4, which is homologous to OsPFA-DSP2, also exhibited sensitivity to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), reduced accumulation of H₂O₂ and decreased photosynthesic capacity after infection compared with Col-0. These results indicate that OsPFA-DSP2 and AtPFA-DSP4 act as negative regulators of the pathogen response in transgenic plants.