Global transcriptome analysis provides new insights in Thellungiella salsuginea stress response

PLATZ transcription factors and their emerging roles in plant responses to environmental stresses

Plant A/T-rich sequence- and zinc-binding (PLATZ) family proteins represent a novel class of plant-specific transcription factors that bind to A/T-rich sequences. Advances in high-throughput sequencing and bioinformatics analyses have facilitated the identification of numerous PLATZ proteins across various plant species. Over the last decade, accumulating evidence from omics analyses, genetics studies, and gain- and loss-of function investigations has indicated that PLATZ proteins play crucial roles in the complex regulatory networks governing plant development and adaptation to environmental stress. Recently, an excellent review has been published highlighting the roles of PLATZ proteins in controlling plant developmental processes. However, a comprehensive review specifically addressing the molecular mechanisms by which these proteins drive their functions in plant responses to environmental cues is currently lacking. In this review, we summarize the characteristics and identification of PLATZ proteins, emphasizing their significance in stress responses. We also highlight the crosstalk between PLATZ proteins and phytohormones. Furthermore, we discuss the downstream target genes, interacting partners, and upstream regulatory mechanisms associated with PLATZ proteins, providing a thorough understanding of their multifaceted roles in plants.

Genome-wide identification of the bZIP family in Eutrema salsugineum and functional analysis of EsbZIP51 in regulating salt tolerance

The halophyte Eutrema salsugineum is naturally distributed in saline-alkali soil and has been proposed as a model plant for understanding plant salt tolerance. As one of the largest and most diverse TF families, basic leucine zipper motif (bZIP) TFs perform robust functions in plant growth and environmental response, however the generalized information of EsbZIP genes and its regulatory role in salt tolerance has not been systematically studied to date. Here, we identified and characterized the bZIP members in E. salsugineum, the sequence feature and phylogeny of EsbZIPs have been exhaustively described. Through the global detection on the transcriptional pattern of EsbZIPs under salt stress, it was found that EsbZIP51 is potentially involved in the positive regulation of salt response. The transgenic plants with heterologous expression of EsbZIP51 exhibited enhanced salt tolerance, as manifested by the healthier growth phenotype and increased capacity in maintaining ion and ROS homeostasis upon salt stress. DNA affinity purification sequencing revealed that a set of candidate genes targeted by EsbZIP51, and functional validation by dual-LUC assays showed EsbZIP51 can specifically bind to the promoter of EsNHX4 and regulates the gene expression, which is required for the modulation of ion balance under salt stress. Together, this study provides insight into the genomic information of EsbZIPs and uncovers a previously uncharacterized functional genes involved in plant salt tolerance.

Identification and Functional Characterization of Abiotic Stress Tolerance-Related PLATZ Transcription Factor Family in Barley (Hordeum vulgare L.)

Plant AT-rich sequence and zinc-binding proteins (PLATZs) are a novel category of plant-specific transcription factors involved in growth, development, and abiotic stress responses. However, the PLATZ gene family has not been identified in barley. In this study, a total of 11 HvPLATZs were identified in barley, and they were unevenly distributed on five of the seven chromosomes. The phylogenetic tree, incorporating PLATZs from Arabidopsis, rice, maize, wheat, and barley, could be classified into six clusters, in which HvPLATZs are absent in Cluster VI. HvPLATZs exhibited conserved motif arrangements with a characteristic PLATZ domain. Two segmental duplication events were observed among HvPLATZs. All HvPLATZs were core genes present in 20 genotypes of the barley pan-genome. The HvPLATZ5 coding sequences were conserved among 20 barley genotypes, whereas HvPLATZ4/9/10 exhibited synonymous single nucleotide polymorphisms (SNPs); the remaining ones showed nonsynonymous variations. The expression of HvPLATZ2/3/8 was ubiquitous in various tissues, whereas HvPLATZ7 appeared transcriptionally silent; the remaining genes displayed tissue-specific expression. The expression of HvPLATZs was modulated by salt stress, potassium deficiency, and osmotic stress, with response patterns being time-, tissue-, and stress type-dependent. The heterologous expression of HvPLATZ3/5/6/8/9/10/11 in yeast enhanced tolerance to salt and osmotic stress, whereas the expression of HvPLATZ2 compromised tolerance. These results advance our comprehension and facilitate further functional characterization of HvPLATZs.

Genome-wide identification of PYL/PYR-PP2C (A)-SnRK2 genes in Eutrema and their co-expression analysis in response to ABA and abiotic stresses

ABA signaling core components PYR/PYL, group A PP2C and SnRK2 play important roles in various environmental stress responses of plants. This study identified 14 PYR/PYL, 9 PP2C (A), and 10 SnRK2 genes from halophytic Eutrema. Phylogenetic analysis showed 4 EsPYR/PYL, 4 EsPP2C (A) and 3 EsSnRK2 subfamilies characterized, which was supported by their gene structures and protein motifs. Large-scale segmental duplication event was demonstrated to be a major contributor to expansion of the EsPYL-PP2C (A)-SnRK2 gene families. Synteny relationship analysis revealed more orthologous PYL-PP2C (A)-SnRK2 gene pairs located in collinear blocks between Eutrema and Brassica than that between Eutrema and Arabidopsis. RNA-seq and qRT-PCR revealed EsABI1, EsABI2 and EsHAL2 showed a significantly up-regulated expression in leaves and roots in response to ABA, NaCl or cold stress. Three markedly co-expression modules of ABA/R-brown, NaCl/L-lightsteelblue1 and Cold/R-lightgreen were uncovered to contain EsPYL-PP2C (A)-SnRK2 genes by WGCNA analysis. GO and KEGG analysis indicated that the genes of ABA/R-brown module containing EsHAB1, EsHAI2 and EsSnRK2.6 were enriched in proteasome pathway. Further, EsHAI2-OE transgenic Arabidopsis lines showed significantly enhanced seeds germination and seedlings growth. This work provides a new insight for elucidating potential molecular functions of PYL-PP2C (A)-SnRK2 responding to ABA and abiotic stresses.

Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum)

BACKGROUND

Plant AT-rich sequence and zinc-binding (PLATZ) proteins belong to a novel class of plant-specific zinc-finger-dependent DNA-binding proteins that play essential roles in plant growth and development. Although the PLATZ gene family has been identified in several species, systematic identification and characterization of this gene family has not yet been carried out for Tartary buckwheat, which is an important medicinal and edible crop with high nutritional value. The recent completion of Tartary buckwheat genome sequencing has laid the foundation for this study.

RESULTS

A total of 14 FtPLATZ proteins were identified in Tartary buckwheat and were classified into four phylogenetic groups. The gene structure and motif composition were similar within the same group, and evident distinctions among different groups were detected. Gene duplication, particularly segmental duplication, was the main driving force in the evolution of FtPLATZs. Synteny analysis revealed that Tartary buckwheat shares more orthologous PLATZ genes with dicotyledons, particularly soybean. In addition, the expression of FtPLATZs in different tissues and developmental stages of grains showed evident specificity and preference. FtPLATZ3 may be involved in the regulation of grain size, and FtPLATZ4 and FtPLATZ11 may participate in root development. Abundant and variable hormone-responsive cis-acting elements were distributed in the promoter regions of FtPLATZs, and almost all FtPLATZs were significantly regulated after exogenous hormone treatments, particularly methyl jasmonate treatment. Moreover, FtPLATZ6 was significantly upregulated under all exogenous hormone treatments, which may indicate that this gene plays a critical role in the hormone response of Tartary buckwheat.

CONCLUSIONS

This study lays a foundation for further exploration of the function of FtPLATZ proteins and their roles in the growth and development of Tartary buckwheat and contributes to the genetic improvement of Tartary buckwheat.

Transcriptome profiling of Malus sieversii under freezing stress after being cold-acclimated

Background

Freezing temperatures are an abiotic stress that has a serious impact on plant growth and development in temperate regions and even threatens plant survival. The wild apple tree (Malus sieversii) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in wild apple trees.

Results

Phytohormone and physiology profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that JA, IAA, and ABA accumulated in the cold acclimation stage and decreased during freezing stress in response to freezing stress. To elucidate the molecular mechanisms of freezing stress after cold acclimation, we employed single molecular real-time (SMRT) and RNA-seq technologies to study genome-wide expression profiles in wild apple. Using the PacBio and Illumina platform, we obtained 20.79G subreads. These reads were assembled into 61,908 transcripts, and 24,716 differentially expressed transcripts were obtained. Among them, 4410 transcripts were differentially expressed during the whole process of freezing stress, and these were examined for enrichment via GO and KEGG analyses. Pathway analysis indicated that “plant hormone signal transduction”, “starch and sucrose metabolism”, “peroxisome” and “photosynthesis” might play a vital role in wild apple responses to freezing stress. Furthermore, the transcription factors DREB1/CBF, MYC2, WRKY70, WRKY71, MYB4 and MYB88 were strongly induced during the whole stress period.

Conclusions

Our study presents a global survey of the transcriptome profiles of wild apple trees in dynamic response to freezing stress after two days cold acclimation and provides insights into the molecular mechanisms of freezing adaptation of wild apple plants for the first time. The study also provides valuable information for further research on the antifreezing reaction mechanism and genetic improvement of M. sieversii after cold acclimation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07998-0.

Increased expression of ANAC017 primes for accelerated senescence

Recent studies in Arabidopsis (Arabidopsis thaliana) have reported conflicting roles for NAC DOMAIN CONTAINING PROTEIN 17 (ANAC017), a transcription factor regulating mitochondria-to-nuclear signaling, and its closest paralog NAC DOMAIN CONTAINING PROTEIN 16 (ANAC016), in leaf senescence. By synchronizing senescence in individually darkened leaves of knockout and overexpressing mutants from these contrasting studies, we demonstrate that elevated ANAC017 expression consistently causes accelerated senescence and cell death. A time-resolved transcriptome analysis revealed that senescence-associated pathways such as autophagy are not constitutively activated in ANAC017 overexpression lines, but require a senescence-stimulus to trigger accelerated induction. ANAC017 transcript and ANAC017-target genes are constitutively upregulated in ANAC017 overexpression lines, but surprisingly show a transient "super-induction" 1 d after senescence induction. This induction of ANAC017 and its target genes is observed during the later stages of age-related and dark-induced senescence, indicating the ANAC017 pathway is also activated in natural senescence. In contrast, knockout mutants of ANAC017 showed lowered senescence-induced induction of ANAC017 target genes during the late stages of dark-induced senescence. Finally, promoter binding analyses show that the ANAC016 promoter sequence is directly bound by ANAC017, so ANAC016 likely acts downstream of ANAC017 and is directly transcriptionally controlled by ANAC017 in a feed-forward loop during late senescence.

How soil ion stress and type influence the flooding adaptive strategies of Phragmites australis and Bolboschoenus planiculmis in temperate saline-alkaline wetlands?

Soil saline-alkaline stress and flooding extremes have been projected to be the main factors influencing the degradation of marsh plants in wetlands worldwide, which would affect their ecological functions (i.e. food source for migrating birds). Plants cope with flooding either by escaping from below water through shoot elongation or by remaining quiescent until water subsides. However, little is known about the adaptive strategies of Phragmites australis and Bolboschoenus planiculmis to flooding combined with salinity-alkalinity, which are the key environmental filters in Western Songnen Plain, China. Accordingly, this study investigated the adaptive strategies of P. australis and B. planiculmis subjected to the interacting effects of flooding and soil ion stress under field and greenhouse conditions. Results showed that the two species adopted different strategies to survive flooding. P. australis exhibited an escape strategy because of leaf and shoot elongation with increasing flooding depth whereas B. planiculmis became quiescent with no or deceased leaf and shoot elongation and biomass accumulation. High soil ion stress changed the flooding adaptive strategy of P. australis to a quiescence strategy, whereas B. planiculmis remained quiescent with increasing flooding depth at each soil ion content. The strategies of the two species were changed by alkaline ion stress but not by saline ion stress, and they exhibited different adaptive responses. High alkaline ion stress induced P. australis to remain quiescent with increasing flooding depth, whereas low alkaline ion stress promoted B. planicumis to escape from below water, probably due to the buffer effect of low alkaline ion contents outside the roots probably. Hence, P. australis and B. planicumis might adopt the quiescence strategy with increasing degree of soil salinization and alkalization under high greenhouse gas emissions scenarios in Western Songnen Plain, which may lead to severe degradation of the two kinds of marshes in the future.

Function and application of the Eutrema salsugineum PHT1;1 gene in phosphate deficiency stress

Low availability of inorganic phosphate (Pi) in soil is often a limiting factor for plant growth and productivity. The Pi transporter plays an important role in the absorption and utilization of phosphorus in plants. Eutrema salsugineum shows strong tolerance under Pi stress conditions, but the function of the E. salsugineum PHT1 genes has not yet been systematically studied. This study isolated a phosphate transporter gene (EsPHT1;1) from the halophyte E. salsugineum and functionally characterized it in the herbaceous model plant, Arabidopsis thaliana, and in an important oil crop species, soybean (Glycine max (L.) Merr.). Under Pi deficient conditions, transgenic Arabidopsis and transgenic soybean grew better and exhibited significant improvement in root growth, biomass accumulation and seed yield compared with wild-type (WT) plants. These phenotypic enhancements were more apparent under inadequate Pi conditions than under sufficient or no Pi conditions, which is in agreement with the observation that the transgenic plants accumulated higher amounts of Pi and total P in shoots and roots than WT plants only when inadequate Pi was supplied. The results of the present study indicate that overexpression of EsPHT1;1 can efficiently enhance the growth and reproductive performance of both Arabidopsis and soybean plants challenged by low P stress, which results confirm the important role of PHT1;1 in dealing with Pi deficiency.

Abiotic stress signalling in extremophile land plants

Plant life relies on complex arrays of environmental stress sensing and signalling mechanisms. Extremophile plants develop and grow in harsh environments with extremes of cold, heat, drought, desiccation, or salinity, which have resulted in original adaptations. In accordance with their polyphyletic origins, extremophile plants likely possess core mechanisms of plant abiotic stress signalling. However, novel properties or regulations may have emerged in the context of extremophile adaptations. Comparative omics of extremophile genetic models, such as Arabidopsis lyrata, Craterostigma plantagineum, Eutrema salsugineum, and Physcomitrella patens, reveal diverse strategies of sensing and signalling that lead to a general improvement in abiotic stress responses. Current research points to putative differences of sensing and emphasizes significant modifications of regulatory mechanisms, at the level of secondary messengers (Ca2+, phospholipids, reactive oxygen species), signal transduction (intracellular sensors, protein kinases, transcription factors, ubiquitin-mediated proteolysis) or signalling crosstalk. Involvement of hormone signalling, especially ABA signalling, cell homeostasis surveillance, and epigenetic mechanisms, also shows that large-scale gene regulation, whole-plant integration, and probably stress memory are important features of adaptation to extreme conditions. This evolutionary and functional plasticity of signalling systems in extremophile plants may have important implications for plant biotechnology, crop improvement, and ecological risk assessment under conditions of climate change.

Genetic mechanisms of salt stress responses in halophytes

Abiotic stress is a major threat to plant growth and development, resulting in extensive crop loss worldwide. Plants react to abiotic stresses through physiological, biochemical, molecular, and genetic adaptations that promote survival. Exploring the molecular mechanisms involved in abiotic stress responses across various plant species is essential for improving crop yields in unfavorable environments. Halophytes are characterized as plants that survive to reproduce in soils containing high salt concentrations, and thus act as an ideal model to comprehend complicated genetic and physiological mechanisms of salinity stress tolerance. Plant ecologists classify halophytes into three main groups: euhalophytes, recretohalophytes, and pseudo-halophytes. Recent genetic and molecular research has showed complicated regulatory networks by which halophytes coordinate stress adaptation and tolerance. Furthermore, investigation of natural variations in these stress responses has supplied new perspectives on the evolution of mechanisms that regulate tolerance and adaptation. This review discusses the current understanding of the genetic mechanisms that contribute to salt-stress tolerance among different classes of halophytes.