Role of ABA and ABI3 in desiccation tolerance

Drought Stress Inhibits the Accumulation of Rotenoids and the Biosynthesis of Drought-Responsive Phytohormones in Mirabilis himalaica (Edgew.) Heim Calli

Background:Mirabilis himalaica, distributed in the high-altitude, arid, and semi-arid regions of Xizang, exhibits great tolerance to drought, which is rich in rotenoids and other secondary metabolites. It is still unknown, though, how drought stress influences rotenoid synthesis in M. himalaica. Methods: In this study, the calli of M. himalaica were subjected to 5% PEG6000 for 0, 20, and 40 h and divided into control group (CK), mild-drought-treated group (M), and high-drought-treated group (H), respectively. We then analyzed the relative content of three main rotenoids in M. himalaica using high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS). Results: Our findings demonstrated that the content of rotenoids was significantly reduced under drought stress. Transcriptome analysis subsequently revealed 14,525 differentially expressed genes (DEGs) between the different treatments. Furthermore, these DEGs exhibited enrichment in pathways associated with isoflavone biosynthesis and hormone signaling pathways. Key genes with decreased expression patterns during drought stress were also found to be involved in rotenoid accumulation and drought-responsive phytohormone signaling, including abscisic acid (ABA), auxin (IAA), and jasmonic acid (JA). Conclusions: These findings elucidate the molecular processes of drought resistance in M. himalaica and shed light on the relationship between rotenoid production and drought stress in M. himalaica.

ABI3 regulates ABI1 function to control cell length in primary root elongation zone

Post-embryonic primary root growth is effectively an interplay of several hormone signalling pathways. Here, we show that the ABA-responsive transcription factor ABI3 controls primary root growth through the regulation of JA signalling molecule JAZ1 along with ABA-responsive factor ABI1. In the absence of ABI3, the primary root elongation zone is shortened with significantly reduced cell length. Expression analyses and ChIP-based assays indicate that ABI3 negatively regulates JAZ1 expression by occupying its upstream regulatory sequence and enriching repressive histone modification mark H3K27 trimethylation, thereby occluding RNAPII occupancy. Previous studies have shown that JAZ1 interacts with ABI1, the protein phosphatase 2C, that works during ABA signalling. Our results indicate that in the absence of ABI3, when JAZ1 expression levels are high, the ABI1 protein shows increased stability, compared to when JAZ1 is absent, or ABI3 is overexpressed. Consequently, in the abi3-6 mutant, due to the higher stability of ABI1, reduced phosphorylation of plasma membrane H+-ATPase (AHA2) occurs. HPTS staining further indicated that abi3-6 root cell apoplasts show reduced protonation, compared to wild-type and ABI3 overexpressing seedlings. Such impeded proton extrusion negatively affects cell length in the primary root elongation zone. ABI3 therefore controls cell elongation in the primary root by affecting the ABI1-dependent protonation of root cell apoplasts. In summary, ABI3 controls the expression of JAZ1 and in turn modulates the function of ABI1 to regulate cell length in the elongation zone during primary root growth.

Gaining or cutting SLAC: the evolution of plant guard cell signalling pathways

The evolution of adjustable stomatal pores, enabling CO2 acquisition, was one of the most significant events in the development of life on land. Here, we investigate how the guard cell signalling pathways that regulate stomatal movements evolved. We compare fern and angiosperm guard cell transcriptomes and physiological responses, and examine the functionality of ion channels from diverse plant species. We find that, despite conserved expression in guard cells, fern anion channels from the SLAC/SLAH family are not activated by the same abscisic acid (ABA) pathways that provoke stomatal closure in angiosperms. Accordingly, we find an insensitivity of fern stomata to ABA. Moreover, our analysis points to a complex evolutionary history, featuring multiple gains and/or losses of SLAC activation mechanisms, as these channels were recruited to a role in stomatal closure. Our results show that the guard cells of flowering and nonflowering plants share similar core features, with lineage-specific and ecological niche-related adaptations, likely underlying differences in behaviour.

Identification of a novel gene, Bryophyte Co-retained Gene 1, that has a positive role in desiccation tolerance in the moss Physcomitrium patens

The moss Physcomitrium patens is a model system for the evolutionary study of land plants, and as such, it may contain as yet unannotated genes with functions related to the adaptation to water deficiency that was required during the water-to-land transition. In this study, we identified a novel gene, Bryophyte Co-retained Gene 1 (BCG1), in P. patens that is responsive to dehydration and rehydration. Under de- and rehydration treatments, BCG1 was significantly co-expressed with DHNA, which encodes a dehydrin (DHN). Examination of previous microarray data revealed that BCG1 is highly expressed in spores, archegonia (female reproductive organ), and mature sporophytes. In addition, the bcg1 mutant showed reduced dehydration tolerance, and this was accompanied by a relatively low level of chlorophyll content during recovery. Comprehensive transcriptomics uncovered a detailed set of regulatory processes that were affected by the disruption to BCG1. Experimental evidence showed that BCG1 might function in antioxidant activity, the abscisic acid pathway, and in intracellular Ca2+ homeostasis to resist desiccation. Overall, our results provide insights into the role of a bryophyte co-retained gene in desiccation tolerance.

Environmental Pollutant Anthracene Induces ABA-Dependent Transgenerational Effects on Gemmae Dormancy in Marchantia polymorpha

Anthracene, a polycyclic aromatic hydrocarbon (PAH) from fossil fuel combustion, poses significant environmental threats. This study investigates the role of abscisic acid (ABA) in the anthracene tolerance of the liverwort Marchantia polymorpha using mutants deficient in ABA perception (Mppyl1) or biosynthesis (Mpaba1). In this study, we monitored the role of ABA in the anthracene tolerance response by tracking two ABA-controlled traits: plant growth inhibition and gemmae dormancy. We found that the anthracene-induced inhibition of plant growth is dose-dependent, similar to the growth-inhibiting effect of ABA, but independent of ABA pathways. However, gemmae dormancy was differentially affected by anthracene in ABA-deficient mutants. We found that gemmae from anthracene-exposed WT plants exhibited reduced germination compared to those from mock-treated plants. This suggests that the anthracene exposure of mother plants induces a transgenerational effect, resulting in prolonged dormancy in their asexual propagules. While Mppyl1 gemmae retained a dormancy delay when derived from anthracene-exposed thalli, the ABA biosynthesis mutant Mpaba1 did not display any significant dormancy delay as a consequence of anthracene exposure. These results, together with the strong induction of ABA marker genes upon anthracene treatment, imply that anthracene-induced germination inhibition relies on ABA synthesis in the mother plant, highlighting the critical role of MpABA1 in the tolerance response. These findings reveal a complex interplay between anthracene stress and ABA signaling, where anthracene triggers ABA-mediated responses, influencing reproductive success and highlighting the potential for leveraging genetic and hormonal pathways to enhance plant resilience in contaminated habitats.

ABSCISIC ACID INSENSITIVE 3 promotes auxin signalling by regulating SHY2 expression to control primary root growth in response to dehydration stress

Plants combat dehydration stress through different strategies including root architectural changes. Here we show that when exposed to varying levels of dehydration stress, primary root growth in Arabidopsis is modulated by regulating root meristem activity. Abscisic acid (ABA) in concert with auxin signalling adjust primary root growth according to stress levels. ABSCISIC ACID INSENSITIVE 3 (ABI3), an ABA-responsive transcription factor, stands at the intersection of ABA and auxin signalling and fine-tunes primary root growth in response to dehydration stress. Under low ABA or dehydration stress, induction of ABI3 expression promotes auxin signalling by decreasing expression of SHY2, a negative regulator of auxin response. This further enhances the expression of auxin transporter gene PIN1 and cell cycle gene CYCB1;1, resulting in an increase in primary root meristem size and root length. Higher levels of dehydration stress or ABA repress ABI3 expression and promote ABSCISIC ACID INSENSITIVE 5 (ABI5) expression. This elevates SHY2 expression, thereby impairing primary root meristem activity and retarding root growth. Notably, ABI5 can promote SHY2 expression only in the absence of ABI3. Such ABA concentration-dependent expression of ABI3 therefore functions as a regulatory sensor of dehydration stress levels and orchestrates primary root growth by coordinating its downstream regulation.

Drying without dying: A genome database for desiccation-tolerant plants and evolution of desiccation tolerance

Desiccation is typically fatal, but a small number of land plants have evolved vegetative desiccation tolerance (VDT), allowing them to dry without dying through a process called anhydrobiosis. Advances in sequencing technologies have enabled the investigation of genomes for desiccation-tolerant plants over the past decade. However, a dedicated and integrated database for these valuable genomic resources has been lacking. Our prolonged interest in VDT plant genomes motivated us to create the "Drying without Dying" database, which contains a total of 16 VDT-related plant genomes (including 10 mosses) and incorporates 10 genomes that are closely related to VDT plants. The database features bioinformatic tools, such as blast and homologous cluster search, sequence retrieval, Gene Ontology term and metabolic pathway enrichment statistics, expression profiling, co-expression network extraction, and JBrowser exploration for each genome. To demonstrate its utility, we conducted tailored PFAM family statistical analyses, and we discovered that the drought-responsive ABA transporter AWPM-19 family is significantly tandemly duplicated in all bryophytes but rarely so in tracheophytes. Transcriptomic investigations also revealed that response patterns following desiccation diverged between bryophytes and angiosperms. Combined, the analyses provided genomic and transcriptomic evidence supporting a possible divergence and lineage-specific evolution of VDT in plants. The database can be accessed at http://desiccation.novogene.com. We expect this initial release of the "Drying without Dying" plant genome database will facilitate future discovery of VDT genetic resources.

Proteome plasticity during Physcomitrium patens spore germination - from the desiccated phase to heterotrophic growth and reconstitution of photoautotrophy

The establishment of moss spores is considered a milestone in plant evolution. They harbor protein networks underpinning desiccation tolerance and accumulation of storage compounds that can be found already in algae and that are also utilized in seeds and pollen. Furthermore, germinating spores must produce proteins that drive the transition through heterotrophic growth to the autotrophic plant. To get insight into the plasticity of this proteome, we investigated it at five timepoints of moss (Physcomitrium patens) spore germination and in protonemata and gametophores. The comparison to previously published Arabidopsis proteome data of seedling establishment showed that not only the proteomes of spores and seeds are functionally related, but also the proteomes of germinating spores and young seedlings. We observed similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and β-oxidation and the glyoxylate cycle. However, there were also striking differences. For example, spores lacked any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis seeds, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss. The comparison of spores to Nicotiana tabacum pollen indicated similarities for example in regards to resistance to desiccation and hypoxia, but the overall developmental pattern did not align as in the case of seedling establishment and spore germination.

Development of PEG-mediated genetic transformation and gene editing system of Bryum argenteum as an abiotic stress tolerance model plant

KEY MESSAGE

To establish a sterile culture system and protoplast regeneration system for Bryum argenteum, and to establish and apply CRISPR/Cas9 system in Bryum argenteum. Bryum argenteum is a fascinating, cosmopolitan, and versatile moss species that thrives in various disturbed environments. Because of its comprehensive tolerance to the desiccation, high UV and extreme temperatures, it is emerging as a model moss for studying the molecular mechanisms underlying plant responses to abiotic stresses. However, the lack of basic tools such as gene transformation and targeted genome modification has hindered the understanding of the molecular mechanisms underlying the survival of B. argenteum in different environments. Here, we reported the protonema of B. argenteum can survive up to 95.4% water loss. In addition, the genome size of B. argenteum is approximately 313 Mb by kmer analysis, which is smaller than the previously reported 700 Mb. We also developed a simple method for protonema induction and an efficient protoplast isolation and regeneration protocol for B. argenteum. Furthermore, we established a PEG-mediated protoplast transient transfection and stable transformation system for B. argenteum. Two homologues of ABI3(ABA-INSENSITIVE 3) gene were successfully cloned from B. argenteum. To further investigate the function of the ABI3 gene in B. argenteum, we used the CRISPR/Cas9 genetic editing system to target the BaABI3A and BaABI3B gene in B. argenteum protoplasts. This resulted in mutagenesis at the target in about 2-5% of the regenerated plants. The isolated abi3a and abi3b mutants exhibited increased sensitivity to desiccation, suggesting that BaABI3A and BaABI3B play redundant roles in desiccation stress. Overall, our results provide a rapid and simple approach for molecular genetics in B. argenteum. This study contributes to a better understanding of the molecular mechanisms of plant adaptation to extreme environmental.

Enhancement of salt tolerance of alfalfa: Physiological and molecular responses of transgenic alfalfa plants expressing Syntrichia caninervis-derived ScABI3

Alfalfa (Medicago sativa L.), a perennial forage plant, is a rich source of nutrients such as vitamins, minerals, and proteins. Salt stress, however, impedes its growth. The plant-specific transcription factor abscisic acid insensitive 3 (ABI3) has a critical contribution to the control of abscisic acid (ABA) signaling pathway and abiotic stress response. The gene ScABI3 from Syntrichia caninervis, a moss species tolerant to desiccation, could be considered a potential candidate gene to modify alfalfa's nutritional and growth aspects. However, it remains unclear how ScABI3 affects the salt stress response of transgenic alfalfa. Therefore, we elucidated the role and molecular mechanism of ScABI3 from S. caninervis as an ABA signaling factor in transgenic alfalfa. Our findings demonstrate that ScABI3 overexpression in transgenic alfalfa improves salt tolerance by promoting relative water content, antioxidant enzyme activity, and photosynthetic parameters. Furthermore, the key genes of plant hormone signaling and the classical salt tolerance pathway were activated in ScABI3 transgenic lines under salt stress. Based on these results, ScABI3 could be considered a potentially critical candidate gene to alleviate salt stress in alfalfa. The present study provides valuable insights for developing transgenic crop breeding strategies for saline-alkaline soils.

Genome-wide identification of the B3 transcription factor family in pepper (Capsicum annuum) and expression patterns during fruit ripening

In plants, B3 transcription factors play important roles in a variety of aspects of their growth and development. While the B3 transcription factor has been extensively identified and studied in numerous species, there is limited knowledge regarding its B3 superfamily in pepper. Through the utilization of genome-wide sequence analysis, we identified a total of 106 B3 genes from pepper (Capsicum annuum), they are categorized into four subfamilies: RAV, ARF, LAV, and REM. Chromosome distribution, genetic structure, motif, and cis-acting element of the pepper B3 protein were analyzed. Conserved gene structure and motifs outside the B3 domain provided strong evidence for phylogenetic relationships, allowing potential functions to be deduced by comparison with homologous genes from Arabidopsis. According to the high-throughput transcriptome sequencing analysis, expression patterns differ during different phases of fruit development in the majority of the 106 B3 pepper genes. By using qRT-PCR analysis, similar expression patterns in fruits from various time periods were discovered. In addition, further analysis of the CaRAV4 gene showed that its expression level decreased with fruit ripening and located in the nucleus. B3 transcription factors have been genome-wide characterized in a variety of crops, but the present study is the first genome-wide analysis of the B3 superfamily in pepper. More importantly, although B3 transcription factors play key regulatory roles in fruit development, it is uncertain whether B3 transcription factors are involved in the regulation of the fruit development and ripening process in pepper and their specific regulatory mechanisms because the molecular mechanisms of the process have not been fully explained. The results of the study provide a foundation and new insights into the potential regulatory functions and molecular mechanisms of B3 genes in the development and ripening process of pepper fruits, and provide a solid theoretical foundation for the enhancement of the quality of peppers and their selection and breeding of high-yield varieties.

Metabolomic Analysis of the Desert Moss Syntrichia caninervis Provides Insights into Plant Dehydration and Rehydration Response

Desiccation-tolerant (DT) plants can survive extreme dehydration and tolerate the loss of up to 95% of their water content, making them ideal systems to determine the mechanism behind extreme drought stress and identify potential approaches for developing drought-tolerant crops. The desert moss Syntrichia caninervis is an emerging model for extreme desiccation tolerance that has benefited from high-throughput sequencing analyses, allowing identification of stress-tolerant genes; however, its metabolic response to desiccation is unknown. A liquid chromatography-mass spectrometry analysis of S. caninervis at six dehydration-rehydration stages revealed 912 differentially abundant compounds, belonging to 93 metabolic classes. Many (256) metabolites accumulated during rehydration in S. caninervis, whereas only 71 accumulated during the dehydration period, in contrast to the pattern observed in vascular DT plants. During dehydration, nitrogenous amino acids (l-glutamic acid and cysteinylglycine), alkaloids (vinleurosine) and steroids (physalin D) accumulated, whereas glucose 6-phosphate decreased. During rehydration, γ-aminobutyric acid, glucose 6-phosphate and flavonoids (karanjin and aromadendrin) accumulated, as did the plant hormones 12-oxo phytodienoic acid (12-OPDA) and trans-zeatin riboside. The contents ofl-arginine, maltose, turanose, lactulose and sucrose remained high throughout dehydration-rehydration. Syntrichia caninervis thus accumulates antioxidants to scavenge reactive oxygen species, accumulating nitrogenous amino acids and cytoprotective metabolites and decreasing energy metabolism to enter a protective state from dehydration-induced damage. During subsequent rehydration, many metabolites rapidly accumulated to prevent oxidative stress and restore physiological activities while repairing cells, representing a more elaborate rehydration repair mechanism than vascular DT plants, with a faster and greater accumulation of metabolites. This metabolic kinetics analysis in S. caninervis deepens our understanding of its dehydration mechanisms and provides new insights into the different strategies of plant responses to dehydration and rehydration.

Exogenous preculture with sucrose and abscisic acid improves post-cryopreservation survival of eastern bracken fern gametophytes

Cryopreservation is an important technique used in the conservation of various plant tissues. This study proposes a cryopreservation method for the long-term conservation of eastern bracken fern gametophytes (Pteridium aquilinum var. latiusculum). Encapsulation-dehydration of the gametophytes was performed, and the exogenous sucrose and abscisic acid (ABA) preculture conditions were investigated. Gametophytes are sensitive to dehydration and drying, and the following treatment conditions were applied: encapsulation by alginate containing 0.75 M sucrose, 18-h loading treatment with 0.75 M sucrose, and 6-h drying treatment. The survival rate following cryopreservation was determined. The water content of < 27.5% in the alginate beads after dehydration and drying was found to be appropriate for ensuring survival. Additionally, performing an exogenous sucrose and ABA preculture was essential before encapsulation to achieve a survival of ≥ 90%. The high stress induced by cryopreservation and exogenous preculture regulated the expression of PaSuSy, PaLEA14, and PaABI1b and the endogenous ABA content. In eastern bracken gametophytes, ABI1 appears to be a negative regulator of ABA signaling. These results indicate that the encapsulation-dehydration method is effective for the long-term conservation of eastern bracken fern gametophytes, and exogenous preculture alleviates abiotic stress and increases the survival rate.

A Medicago truncatula lncRNA MtCIR1 negatively regulates response to salt stress

A lncRNA MtCIR1 negatively regulates the response to salt stress in Medicago truncatula seed germination by modulating seedling growth and ABA metabolism and signaling by enhancing Na⁺ accumulation. Increasing evidence suggests that long non-coding RNAs (lncRNAs) are involved in the regulation of plant tolerance to varying abiotic stresses. A large number of lncRNAs that are responsive to abiotic stress have been identified in plants; however, the mechanisms underlying the regulation of plant responses to abiotic stress by lncRNAs are largely unclear. Here, we functionally characterized a salt stress-responsive lncRNA derived from the leguminous model plant M. truncatula, referred to as MtCIR1, by expressing MtCIR1 in Arabidopsis thaliana in which no such homologous sequence was observed. Expression of MtCIR1 rendered seed germination more sensitive to salt stress by enhanced accumulation of abscisic acid (ABA) due to suppressing the expression of the ABA catabolic enzyme CYP707A2. Expression of MtCIR1 also suppressed the expression of genes associated with ABA receptors and signaling. The ABA-responsive gene AtPGIP2 that was involved in degradation of cell wall during seed germination was up-regulated by expressing MtCIR1. On the other hand, expression of MtCIR1 in Arabidopsis thaliana enhanced foliar Na⁺ accumulation by down-regulating genes encoding Na⁺ transporters, thus rendering the transgenic plants more sensitive to salt stress. These results demonstrate that the M. truncatula lncRNA MtCIR1 negatively regulates salt stress response by targeting ABA metabolism and signaling during seed germination and foliar Na⁺ accumulation by affecting Na⁺ transport under salt stress during seedling growth. These novel findings would advance our knowledge on the regulatory roles of lncRNAs in response of plants to salt stress.

Integrated transcriptome and metabolome analyses reveal the adaptation of Antarctic moss Pohlia nutans to drought stress

Most regions of the Antarctic continent are experiencing increased dryness due to global climate change. Mosses and lichens are the dominant vegetation of the ice-free areas of Antarctica. However, the molecular mechanisms of these Antarctic plants adapting to drought stress are less documented. Here, transcriptome and metabolome analyses were employed to reveal the responses of an Antarctic moss (Pohlia nutans subsp. LIU) to drought stress. We found that drought stress made the gametophytes turn yellow and curled, and enhanced the contents of malondialdehyde and proline, and the activities of antioxidant enzymes. Totally, 2,451 differentially expressed genes (DEGs) were uncovered under drought treatment. The representative DEGs are mainly involved in ROS-scavenging and detoxification, flavonoid metabolism pathway, plant hormone signaling pathway, lipids metabolism pathway, transcription factors and signal-related genes. Meanwhile, a total of 354 differentially changed metabolites (DCMs) were detected in the metabolome analysis. Flavonoids and lipids were the most abundant metabolites and they accounted for 41.53% of the significantly changed metabolites. In addition, integrated transcriptome and metabolome analyses revealed co-expression patterns of flavonoid and long-chain fatty acid biosynthesis genes and their metabolites. Finally, qPCR analysis demonstrated that the expression levels of stress-related genes were significantly increased. These genes included those involved in ABA signaling pathway (NCED3, PP2C, PYL, and SnAK2), jasmonate signaling pathway (AOC, AOS, JAZ, and OPR), flavonoid pathway (CHS, F3',5'H, F3H, FLS, FNS, and UFGT), antioxidant and detoxifying functions (POD, GSH-Px, Prx and DTX), and transcription factors (ERF and DREB). In summary, we speculated that P. nutans were highly dependent on ABA and jasmonate signaling pathways, ROS scavenging, flavonoids and fatty acid metabolism in response to drought stress. These findings present an important knowledge for assessing the impact of coastal climate change on Antarctic basal plants.

Molecular and physiological responses to desiccation indicate the abscisic acid pathway is conserved in the peat moss, Sphagnum

Mosses of the genus Sphagnum are the main components of peatlands, a major carbon-storing ecosystem. Changes in precipitation patterns are predicted to affect water relations in this ecosystem, but the effect of desiccation on the physiological and molecular processes in Sphagnum is still largely unexplored. Here we show that different Sphagnum species have differential physiological and molecular responses to desiccation but, surprisingly, this is not directly correlated with their position in relation to the water table. In addition, the expression of drought responsive genes is increased upon water withdrawal in all species. This increase in gene expression is accompanied by an increase in abscisic acid (ABA), supporting a role for ABA during desiccation responses in Sphagnum. Not only do ABA levels increase upon desiccation, but Sphagnum plants pre-treated with ABA display increased tolerance to desiccation, suggesting that ABA levels play a functional role in the response. In addition, many of the ABA signalling components are present in Sphagnum and we demonstrate, by complementation in Physcomitrium patens, that Sphagnum ABI3 is functionally conserved. The data presented here, therefore, support a conserved role for ABA in desiccation responses in Sphagnum.

Biocompatible Abscisic Acid-Sensing Supramolecular Hybridization Probe for Spatiotemporal Fluorescence Imaging in Plant Tissues

Achieving detection of the phytohormone abscisic acid (ABA) is of critical importance for understanding plant growth and development. We report a hybrid supramolecular fluorescent probe that uses bovine serum albumin (BSA) as a host. Aggregation-induced emission of fluorescent chromophores (AIEgens) enables luminescence in the presence of BSA. ABA and its aptamer act as a switch to trigger this fluorescent system, the strategy that exhibits high sensitivity to abscisic acid with a detection limit of 0.098 nM. The probe test strip also enables visualization of ABA content from plants by colorimetric observation with the naked eye. In particular, the high biocompatibility and small molecular size of the prepared fluorescent probe allow for effective monitoring of ABA in plant tissues by fluorescence imaging. This strategy provides a new perspective to achieve the detection of endogenous and exogenous ABA in plants and has important implications for plant biology research.

Orphan gene PpARDT positively involved in drought tolerance potentially by enhancing ABA response in Physcomitrium (Physcomitrella) patens

Almost all genomes have orphan genes, the majority of which are not functionally annotated. There is growing evidence showed that orphan genes may play important roles in the environmental stress response of Physcomitrium patens. We identified PpARDT (ABA-responsive drought tolerance) as a moss-specific and ABA-responsive orphan gene in P. patens. PpARDT is mainly expressed during the gametophytic stage of the life cycle, and the expression was induced by different abiotic stresses. A PpARDT knockout (Ppardt) mutant showed reduced dehydration-rehydration tolerance, and the phenotype could be rescued by exogenous ABA. Meanwhile, transgenic Arabidopsis lines exhibiting heterologous expression of PpARDT were more sensitive to exogenous ABA than wild-type (Col-0) plants and showed enhanced drought tolerance. These indicate that PpARDT confers drought tolerance among land plants potentially by enhancing ABA response. Further, we identified genes encoding abscisic acid receptor PYR/PYL family proteins, and ADP-ribosylation factors (Arf) as hub genes associated with the Ppardt phenotype. Given the lineage-specific characteristics of PpARDT, our results provide insights into the roles of orphan gene in shaping lineage-specific adaptation possibly by recruiting common pre-existed pathway components.

Exploring the High Variability of Vegetative Desiccation Tolerance in Pteridophytes

In the context of plant evolution, pteridophytes, which is comprised of lycophytes and ferns, occupy an intermediate position between bryophytes and seed plants, sharing characteristics with both groups. Pteridophytes is a highly diverse group of plant species that occupy a wide range of habitats including ecosystems with extreme climatic conditions. There is a significant number of pteridophytes that can tolerate desiccation by temporarily arresting their metabolism in the dry state and reactivating it upon rehydration. Desiccation-tolerant pteridophytes exhibit a strategy that appears to be intermediate between the constitutive and inducible desiccation tolerance (DT) mechanisms observed in bryophytes and angiosperms, respectively. In this review, we first describe the incidence and anatomical diversity of desiccation-tolerant pteridophytes and discuss recent advances on the origin of DT in vascular plants. Then, we summarize the highly diverse adaptations and mechanisms exhibited by this group and describe how some of these plants could exhibit tolerance to multiple types of abiotic stress. Research on the evolution and regulation of DT in different lineages is crucial to understand how plants have adapted to extreme environments. Thus, in the current scenario of climate change, the knowledge of the whole landscape of DT strategies is of vital importance as a potential basis to improve plant abiotic stress tolerance.

The ABI3 Transcription Factor Interaction and Antagonism with Ubiquitin E3 Ligase ScPRT1 in Syntrichia caninervis

The ubiquitination pathway has been found to regulate plant responses to environmental stress. However, the role of E3 ubiquitin ligase in desiccation tolerant moss has not yet been elucidated. Previous research has shown that the abscisic acid (ABA) signaling factor ScABI3 can significantly increase desiccation tolerance and reduce ABA sensitivity in the desert moss Syntrichia caninervis. In this study, we identified a RING-type E3 ubiquitin ligase, ScPRT1, and showed that ScABI3 can directly interact with ScPRT1 in vitro and in vivo. Furthermore, we found that the high expression of ScPRT1 can interfere with the transcription of ScABI3 under ABA treatment. Therefore, we speculate that ScPRT1 may degrade ScABI3 through the ubiquitin-26S proteasome system and participate in ABA-dependent signaling in response to ABA-insensitivity or desiccation tolerance in S. caninervis. The findings from our study may enrich our knowledge of the role of E3 ubiquitin ligase in desiccation tolerance and lay a theoretical foundation for an in-depth study of the relationship between ubiquitination modification and ABA signal transduction under environmental stress.

Targeted Gene Knockouts by Protoplast Transformation in the Moss Physcomitrella patens

Targeted gene knockout is particularly useful for analyzing gene functions in plant growth, signaling, and development. By transforming knockout cassettes consisting of homologous sequences of the target gene into protoplasts, the classical gene targeting method aims to obtain targeted gene replacement, allowing for the characterization of gene functions in vivo. The moss Physcomitrella patens is a known model organism for a high frequency of homologous recombination and thus harbors a remarkable rate of gene targeting. Other moss features, including easy to culture, dominant haploidy phase, and sequenced genome, make gene targeting prevalent in Physcomitrella patens. However, even gene targeting was powerful to generate knockouts, researchers using this method still experienced technical challenges. For example, obtaining a good number of targeted knockouts after protoplast transformation and regeneration disturbed the users. Off-target mutations such as illegitimate random integration mediated by nonhomologous end joining and targeted insertion wherein one junction on-target but the other end off-target is commonly present in the knockouts. Protoplast fusion during transformation and regeneration was also a problem. This review will discuss the advantages and technical challenges of gene targeting. Recently, CRISPR-Cas9 is a revolutionary technology and becoming a hot topic in plant gene editing. In the second part of this review, CRISPR-Cas9 technology will be focused on and compared to gene targeting regarding the practical use in Physcomitrella patens. This review presents an updated perspective of the gene targeting and CRISPR-Cas9 techniques to plant biologists who may consider studying gene functions in the model organism Physcomitrella patens.

TMT-Based Quantitative Proteomic Analysis Reveals the Physiological Regulatory Networks of Embryo Dehydration Protection in Lotus (Nelumbo nucifera)

Lotus is an aquatic plant that is sensitive to water loss, but its seeds are longevous after seed embryo dehydration and maturation. The great difference between the responses of vegetative organs and seeds to dehydration is related to the special protective mechanism in embryos. In this study, tandem mass tags (TMT)-labeled proteomics and parallel reaction monitoring (PRM) technologies were used to obtain novel insights into the physiological regulatory networks during lotus seed dehydration process. Totally, 60,266 secondary spectra and 32,093 unique peptides were detected. A total of 5,477 proteins and 815 differentially expressed proteins (DEPs) were identified based on TMT data. Of these, 582 DEPs were continuously downregulated and 228 proteins were significantly up-regulated during the whole dehydration process. Bioinformatics and protein-protein interaction network analyses indicated that carbohydrate metabolism (including glycolysis/gluconeogenesis, galactose, starch and sucrose metabolism, pentose phosphate pathway, and cell wall organization), protein processing in ER, DNA repair, and antioxidative events had positive responses to lotus embryo dehydration. On the contrary, energy metabolism (metabolic pathway, photosynthesis, pyruvate metabolism, fatty acid biosynthesis) and secondary metabolism (terpenoid backbone, steroid, flavonoid biosynthesis) gradually become static status during lotus embryo water loss and maturation. Furthermore, non-enzymatic antioxidants and pentose phosphate pathway play major roles in antioxidant protection during dehydration process in lotus embryo. Abscisic acid (ABA) signaling and the accumulation of oligosaccharides, late embryogenesis abundant proteins, and heat shock proteins may be the key factors to ensure the continuous dehydration and storage tolerance of lotus seed embryo. Stress physiology detection showed that H2O2 was the main reactive oxygen species (ROS) component inducing oxidative stress damage, and glutathione and vitamin E acted as the major antioxidant to maintain the REDOX balance of lotus embryo during the dehydration process. These results provide new insights to reveal the physiological regulatory networks of the protective mechanism of embryo dehydration in lotus.

Influence of Drought Stress and Rehydration on Moisture and Photosynthetic Physiological Changes in Three Epilithic Moss Species in Areas of Karst Rocky Desertification

The drought resistance mechanism of typical mosses in the karst area was studied, and the water and photosynthetic physiological adaptation of mosses to karst environmental change was analyzed in this paper, which provided the basis for the restoration and control of karst rocky desertification ecological environment. Three superior plants in the rocky desertification area of Guizhou province were selected; they are, respectively, Erythrodontium julaceum (Schwaegr.) Par., Barbula unguiculata Hedw., and Bryum argenteum Hedw. Results show that the three kinds of plant rock mosses of leaf water potential (Ψs), free water content ( $V_a$ ), total water content, and relative water content (RWC) decreased; bound water ( $V_s$ ), water saturation deficit (WSD), and $V_s$ / $V_a$ ratio increased; transpiration rate (Tr) fell slightly, under drought stress. The physiological indexes of water have different degrees of recovery after rehydration. The total chlorophyll content shows a trend of first increasing followed by falling and then rising. RWC was negatively related to qN and positively related to $F_v$ / $F_m$ , yield, ETR, and qP. After rewetting, the fluorescence parameters are returned to average level under mild-to-moderate stress. At the same time, it is hard to get back to the control level under severe pressure. The water use efficiency (WUE) decreased with stress and recovered to different degrees after rehydration.

Pseudocrossidium replicatum (Taylor) R.H. Zander is a fully desiccation-tolerant moss that expresses an inducible molecular mechanism in response to severe abiotic stress

KEY MESSAGE

The moss Pseudocrossidium replicatum is a desiccation-tolerant species that uses an inducible system to withstand severe abiotic stress in both protonemal and gametophore tissues. Desiccation tolerance (DT) is the ability of cells to recover from an air-dried state. Here, the moss Pseudocrossidium replicatum was identified as a fully desiccation-tolerant (FDT) species. Its gametophores rapidly lost more than 90% of their water content when exposed to a low-humidity atmosphere [23% relative humidity (RH)], but abscisic acid (ABA) pretreatment diminished the final water loss after equilibrium was reached. P. replicatum gametophores maintained good maximum photosystem II (PSII) efficiency (Fv/Fm) for up to two hours during slow dehydration; however, ABA pretreatment induced a faster decrease in the Fv/Fm. ABA also induced a faster recovery of the Fv/Fm after rehydration. Protein synthesis inhibitor treatment before dehydration hampered the recovery of the Fv/Fm when the gametophores were rehydrated after desiccation, suggesting the presence of an inducible protective mechanism that is activated in response to abiotic stress. This observation was also supported by accumulation of soluble sugars in gametophores exposed to ABA or NaCl. Exogenous ABA treatment delayed the germination of P. replicatum spores and induced morphological changes in protonemal cells that resembled brachycytes. Transcriptome analyses revealed the presence of an inducible molecular mechanism in P. replicatum protonemata that was activated in response to dehydration. This study is the first RNA-Seq study of the protonemal tissues of an FDT moss. Our results suggest that P. replicatum is an FDT moss equipped with an inducible molecular response that prepares this species for severe abiotic stress and that ABA plays an important role in this response.

Freeze-thaw cycles change the physiological sensitivity of Syntrichia caninervis to snow cover

Spring, especially the freeze-thaw season, is considered the key period for the growth and carbon sequestration of desert mosses. It is not clear how the change in environment water and temperature affects the physiological characteristics of desert mosses in freeze-thaw season. In this study, the effects of water and freeze-thaw cycles on the physiological characteristics of Syntrichia caninervis were assessed by manipulating the increase or removal of 65% snow and changes in the freeze-thaw cycles. The results showed that the changes in snow depth, freeze-thaw cycles, and their interaction significantly affected the plant water content, osmoregulatory substances content, antioxidant substance, and antioxidant enzyme activities. The contents of free proline, soluble sugar, ascorbic acid (AsA), reduced glutathione (GSH), and malondialdehyde (MDA), and superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities increased significantly with the decrease in snow depth and freeze-thaw cycles. POD and free proline were the most sensitive to the snow depth and freeze-thaw cycles, while SOD and CAT were the least sensitive. Therefore, compared with the increase in freeze-thaw cycles, the reduction in freeze-thaw cycles weakened the physiological sensitivity of S. caninervis to snow depth changes.

Phytohormone biosynthesis and signaling pathways of mosses

Most known phytohormones regulate moss development. We present a comprehensive view of the synthesis and signaling pathways for the most investigated of these compounds in mosses, focusing on the model Physcomitrium patens. The last 50 years of research have shown that most of the known phytohormones are synthesized by the model moss Physcomitrium patens (formerly Physcomitrella patens) and regulate its development, in interaction with responses to biotic and abiotic stresses. Biosynthesis and signaling pathways are best described in P. patens for the three classical hormones auxins, cytokinins and abscisic acid. Furthermore, their roles in almost all steps of development, from early filament growth to gametophore development and sexual reproduction, have been the focus of much research effort over the years. Evidence of hormonal roles exist for ethylene and for CLE signaling peptides, as well as for salicylic acid, although their possible effects on development remain unclear. Production of brassinosteroids by P. patens is still debated, and modes of action for these compounds are even less known. Gibberellin biosynthesis and signaling may have been lost in P. patens, while gibberellin precursors such as ent-kaurene derivatives could be used as signals in a yet to discover pathway. As for jasmonic acid, it is not used per se as a hormone in P. patens, but its precursor OPDA appears to play a corresponding role in defense against abiotic stress. We have tried to gather a comprehensive view of the biosynthesis and signaling pathways for all these compounds in mosses, without forgetting strigolactones, the last class of plant hormones to be reported. Study of the strigolactone response in P. patens points to a novel signaling compound, the KAI2-ligand, which was likely employed as a hormone prior to land plant emergence.

Systems biology of resurrection plants

Plant species that exhibit vegetative desiccation tolerance can survive extreme desiccation for months and resume normal physiological activities upon re-watering. Here we survey the recent knowledge gathered from the sequenced genomes of angiosperm and non-angiosperm desiccation-tolerant plants (resurrection plants) and highlight some distinct genes and gene families that are central to the desiccation response. Furthermore, we review the vast amount of data accumulated from analyses of transcriptomes and metabolomes of resurrection species exposed to desiccation and subsequent rehydration, which allows us to build a systems biology view on the molecular and genetic mechanisms of desiccation tolerance in plants.

Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds

Chinese cork oak (Quercus variabilis) is a widely distributed and highly valuable deciduous broadleaf tree from both ecological and economic perspectives. Seeds of this species are recalcitrant, i.e., sensitive to desiccation, which affects their storage and long-term preservation of germplasm. However, little is known about the underlying molecular mechanism of desiccation sensitivity of Q. variabilis seeds. In this study, the seeds were desiccated with silica gel for certain days as different treatments from 0 (Control) to 15 days (T15) with a gradient of 1 day. According to the seed germination percentage, four key stages (Control, T2, T4, and T11) were found. Then the transcriptomic profiles of these four stages were compared. A total of 4,405, 4,441, and 5,907 differentially expressed genes (DEGs) were identified in T2 vs. Control, T4 vs. Control, and T11 vs. Control, respectively. Among them, 2,219 DEGs were overlapped in the three comparison groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these DEGs were enriched into 124 pathways, such as "Plant hormone signal transduction" and "Glycerophospholipid metabolism". DEGs related to hormone biosynthesis and signal transduction (ZEP, YUC, PYR, ABI5, ERF1B, etc.), stress response proteins (LEA D-29, HSP70, etc.), and phospholipase D (PLD1) were detected during desiccation. These genes and their interactions may determine the desiccation sensitivity of seeds. In addition, group specific DEGs were also identified in T2 vs. Control (PP2C62, UNE12, etc.), T4 vs. Control (WRKY1-like, WAK10, etc.), and T11 vs. Control (IBH1, bZIP44, etc.), respectively. Finally, a possible work model was proposed to show the molecular regulation mechanism of desiccation sensitivity in Q. variabilis seeds. This is the first report on the molecular regulation mechanism of desiccation sensitivity of Q. variabilis seeds using RNA-Seq. The findings could make a great contribution to seed storage and long-term conservation of recalcitrant seeds in the future.

Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

BACKGROUND

The B3 superfamily (B3s) represents a class of large plant-specific transcription factors, which play diverse roles in plant growth and development process including flowering induction. However, identification and functional surveys of B3 superfamily have not been reported in ethylene-induced pineapple flowering (Ananas comosus).

RESULTS

57 B3 genes containing B3 domain were identified and phylogenetically classified into five subfamilies. Chromosomal localization analysis revealed that 54 of 57 AcB3s were located on 21 Linkage Groups (LG). Collinearity analysis demonstrated that the segmental duplication was the main event in the evolution of B3 gene superfamily, and most of them were under purifying selection. The analysis of cis-element composition suggested that most of these genes may have function in response to abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR analysis of 40 AcB3s containing ethylene responsive elements exhibited that the expression levels of 35 genes were up-regulated within 1 d after ethephon treatment and some were highly expressed in flower bud differentiation period in stem apex, such as Aco012003, Aco019552 and Aco014401.

CONCLUSION

This study provides a basic information of AcB3s and clues for involvement of some AcB3s in ethylene-induced flowering in pineapple.

Physcomitrium patens Mutants in Auxin Conjugating GH3 Proteins Show Salt Stress Tolerance but Auxin Homeostasis Is Not Involved in Regulation of Oxidative Stress Factors

Salt stress is among the most challenging abiotic stress situations that a plant can experience. High salt levels do not only occur in areas with obvious salty water, but also during drought periods where salt accumulates in the soil. The moss Physcomitrium patens became a model for studying abiotic stress in non-vascular plants. Here, we show that high salt concentrations can be tolerated in vitro, and that auxin homeostasis is connected to the performance of P. patens under these stress conditions. The auxin levels can be regulated by conjugating IAA to amino acids by two members of the family of GH3 protein auxin amino acid-synthetases that are present in P. patens. Double GH3 gene knock-out mutants were more tolerant to high salt concentrations. Furthermore, free IAA levels were differentially altered during the time points investigated. Since, among the mutant lines, an increase in IAA on at least one NaCl concentration tested was observed, we treated wild type (WT) plants concomitantly with NaCl and IAA. This experiment showed that the salt tolerance to 100 mM NaCl together with 1 and 10 µM IAA was enhanced during the earlier time points. This is an additional indication that the high IAA levels in the double GH3-KO lines could be responsible for survival in high salt conditions. While the high salt concentrations induced several selected stress metabolites including phenols, flavonoids, and enzymes such as peroxidase and superoxide dismutase, the GH3-KO genotype did not generally participate in this upregulation. While we showed that the GH3 double KO mutants were more tolerant of high (250 mM) NaCl concentrations, the altered auxin homeostasis was not directly involved in the upregulation of stress metabolites.

A fundamental developmental transition in Physcomitrium patens is regulated by evolutionarily conserved mechanisms

One of the most defining moments in history was the colonization of land by plants approximately 470 million years ago. The transition from water to land was accompanied by significant changes in the plant body plan, from those than resembled filamentous representatives of the charophytes, the sister group to land plants, to those that were morphologically complex and capable of colonizing harsher habitats. The moss Physcomitrium patens (also known as Physcomitrella patens) is an extant representative of the bryophytes, the earliest land plant lineage. The protonema of P. patens emerges from spores from a chloronemal initial cell, which can divide to self-renew to produce filaments of chloronemal cells. A chloronemal initial cell can differentiate into a caulonemal initial cell, which can divide and self-renew to produce filaments of caulonemal cells, which branch extensively and give rise to three-dimensional shoots. The process by which a chloronemal initial cell differentiates into a caulonemal initial cell is tightly regulated by auxin-induced remodeling of the actin cytoskeleton. Studies have revealed that the genetic mechanisms underpinning this transition also regulate tip growth and differentiation in diverse plant taxa. This review summarizes the known cellular and molecular mechanisms underpinning the chloronema to caulonema transition in P. patens.

Activation of SnRK2 by Raf-like kinase ARK represents a primary mechanism of ABA and abiotic stress responses

The Raf-like protein kinase abscisic acid (ABA) and abiotic stress-responsive Raf-like kinase (ARK) previously identified in the moss Physcomitrium (Physcomitrella) patens acts as an upstream regulator of subgroup III SNF1-related protein kinase2 (SnRK2), the key regulator of ABA and abiotic stress responses. However, the mechanisms underlying activation of ARK by ABA and abiotic stress for the regulation of SnRK2, including the role of ABA receptor-associated group A PP2C (PP2C-A), are not understood. We identified Ser1029 as the phosphorylation site in the activation loop of ARK, which provided a possible mechanism for regulation of its activity. Analysis of transgenic P. patens ark lines expressing ARK-GFP with Ser1029-to-Ala mutation indicated that this replacement causes reductions in ABA-induced gene expression, stress tolerance, and SnRK2 activity. Immunoblot analysis using an anti-phosphopeptide antibody indicated that ABA treatments rapidly stimulate Ser1029 phosphorylation in the wild type (WT). The phosphorylation profile of Ser1029 in ABA-hypersensitive ppabi1 lacking protein phosphatase 2C-A (PP2C-A) was similar to that in the WT, whereas little Ser1029 phosphorylation was observed in ABA-insensitive ark missense mutant lines. Furthermore, newly isolated ppabi1 ark lines showed ABA-insensitive phenotypes similar to those of ark lines. Therefore, ARK is a primary activator of SnRK2, preceding negative regulation by PP2C-A in bryophytes, which provides a prototype mechanism for ABA and abiotic stress responses in plants.

Unexplored dimensions of variability in vegetative desiccation tolerance

Desiccation tolerance has evolved recurrently across diverse land plant lineages as an adaptation for survival in regions where seasonal rainfall drives periodic drying of vegetative tissues. Growing interest in this phenomenon has fueled recent physiological, biochemical, and genomic insights into the mechanistic basis of desiccation tolerance. Although, desiccation tolerance is often viewed as binary and monolithic, substantial variation exists in the phenotype and underlying mechanisms across diverse lineages, heterogeneous populations, and throughout the development of individual plants. Most studies have focused on conserved responses in a subset desiccation-tolerant plants under laboratory conditions. Consequently, the variability and natural diversity of desiccation-tolerant phenotypes remains largely uncharacterized. Here, we discuss the natural variation in desiccation tolerance and argue that leveraging this diversity can improve our mechanistic understanding of desiccation tolerance. We summarize information collected from ~600 desiccation-tolerant land plants and discuss the taxonomic distribution and physiology of desiccation responses. We point out the need to quantify natural diversity of desiccation tolerance on three scales: variation across divergent lineages, intraspecific variation across populations, and variation across tissues and life stages of an individual plant. We conclude that this variability should be accounted for in experimental designs and can be leveraged for deeper insights into the intricacies of desiccation tolerance.

Decoding ABA and osmostress signalling in plants from an evolutionary point of view

The plant hormone abscisic acid (ABA) is fundamental for land plant adaptation to water-limited conditions. Osmostress, such as drought, induces ABA accumulation in angiosperms, triggering physiological responses such as stomata closure. The core components of angiosperm ABA signalling are soluble ABA receptors, group A protein phosphatase type 2C and SNF1-related protein kinase2 (SnRK2). ABA also has various functions in non-angiosperms, however, suggesting that its role in adaptation to land may not have been angiosperm-specific. Indeed, among land plants, the core ABA signalling components are evolutionarily conserved, implying their presence in a common ancestor. Results of ongoing functional genomics studies of ABA signalling components in bryophytes and algae have expanded our understanding of the evolutionary role of ABA signalling, with genome sequencing uncovering the ABA core module even in algae. In this review, we describe recent discoveries involving the ABA core module in non-angiosperms, tracing the footprints of how ABA evolved as a phytohormone. We also cover the latest findings on Raf-like kinases as upstream regulators of the core ABA module component SnRK2. Finally, we discuss the origin of ABA signalling from an evolutionary perspective.

Reconstructing trait evolution in plant evo-devo studies

Our planet is teeming with an astounding diversity of plants. In a mere single group of closely related species, tremendous diversity can be observed in their form and function - the colour of petals in flowering plants, the shape of the fronds in ferns, and the branching pattern of the gametophyte in mosses. Diversity can also be found in subtler traits, such as the resistance to pathogens or the ability to recruit symbiotic microbes from the environment. Plant traits can also be highly conserved - at the cellular and metabolic levels, entire biosynthetic pathways are present in all plant groups, and morphological characteristics such as vascular tissues have been conserved for hundreds of millions of years. The research community that seeks to understand these traits - both the diverse and the conserved - by taking an evolutionary point-of-view on plant biology is growing. Here, we summarize a subset of the different aspects of plant evolutionary biology, provide a guide for structuring comparative biology approaches and discuss the pitfalls that (plant) researchers should avoid when embarking on such studies.

The evolving role of abscisic acid in cell function and plant development over geological time

Abscisic acid (ABA) is found in a wide diversity of organisms, yet we know most about the hormonal action of this compound in the ecologically dominant and economically important angiosperms. In angiosperms, ABA regulates a suite of critical responses from desiccation tolerance through to seed dormancy and stomatal closure. Work exploring the function of key genes in the ABA signalling pathway of angiosperms has revealed that this signal transduction pathway is ancient, yet considerable change in the physiological roles of this hormone have occurred over geological time. With recent advances in our capacity to characterise gene function in non-angiosperms we are on the cusp of revealing the origins of this critical hormonal signalling pathway in plants, and understanding how a simple hormone may have shaped land plant diversity, ecology and adaptation over the past 500 million years.

A Chloroplast COR413 Protein From Physcomitrella patens Is Required for Growth Regulation Under High Light and ABA Responses

COR413 genes belong to a poorly characterized group of plant-specific cold-regulated genes initially identified as part of the transcriptional activation machinery of plants during cold acclimation. They encode multispanning transmembrane proteins predicted to target the plasma membrane or the chloroplast inner membrane. Despite being ubiquitous throughout the plant kingdom, little is known about their biological function. In this study, we used reverse genetics to investigate the relevance of a predicted chloroplast localized COR413 protein (PpCOR413im) from the moss Physcomitrella patens in developmental and abiotic stress responses. Expression of PpCOR413im was strongly induced by abscisic acid (ABA) and by various environmental stimuli, including low temperature, hyperosmosis, salinity and high light. In vivo subcellular localization of PpCOR413im-GFP fusion protein revealed that this protein is localized in chloroplasts, confirming the in silico predictions. Loss-of-function mutants of PpCOR413im exhibited growth and developmental alterations such as growth retardation, reduced caulonema formation and hypersensitivity to ABA. Mutants also displayed altered photochemistry under various abiotic stresses, including dehydration and low temperature, and exhibited a dramatic growth inhibition upon exposure to high light. Disruption of PpCOR413im also caused altered chloroplast ultrastructure, increased ROS accumulation, and enhanced starch and sucrose levels under high light or after ABA treatment. In addition, loss of PpCOR413im affected both nuclear and chloroplast gene expression in response to ABA and high light, suggesting a role for this gene downstream of ABA in the regulation of growth and environmental stress responses. Developmental alterations exhibited by PpCOR413im knockout mutants had remarkable similarities to those exhibited by hxk1, a mutant lacking a major chloroplastic hexokinase, an enzyme involved in energy homeostasis. Based on these findings, we propose that PpCOR413im is involved in coordinating energy metabolism with ABA-mediated growth and developmental responses.

Quantitative Imaging Reveals Distinct Contributions of SnRK2 and ABI3 in Plasmodesmatal Permeability in Physcomitrella patens

Cell-to-cell communication is tightly regulated in response to environmental stimuli in plants. We previously used a photoconvertible fluorescent protein Dendra2 as a model reporter to study this process. This experiment revealed that macromolecular trafficking between protonemal cells in Physcomitrella patens is suppressed in response to abscisic acid (ABA). However, it remains unknown which ABA signaling components contribute to this suppression and how. Here, we show that ABA signaling components SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 2 (PpSnRK2) and ABA INSENSITIVE 3 (PpABI3) play roles as an essential and promotive factor, respectively, in regulating ABA-induced suppression of Dendra2 diffusion between cells (ASD). Our quantitative imaging analysis revealed that disruption of PpSnRK2 resulted in defective ASD onset itself, whereas disruption of PpABI3 caused an 81-min delay in the initiation of ASD. Live-cell imaging of callose deposition using aniline blue staining showed that, despite this onset delay, callose deposition on cross walls remained constant in the PpABI3 disruptant, suggesting that PpABI3 facilitates ASD in a callose-independent manner. Given that ABA is an important phytohormone to cope with abiotic stresses, we further explored cellular physiological responses. We found that the acquisition of salt stress tolerance is promoted by PpABI3 in a quantitative manner similar to ASD. Our results suggest that PpABI3-mediated ABA signaling may effectively coordinate cell-to-cell communication during the acquisition of salt stress tolerance. This study will accelerate the quantitative study for ABA signaling mechanism and function in response to various abiotic stresses.

Desiccation Tolerance: Avoiding Cellular Damage During Drying and Rehydration

Desiccation of plants is often lethal but is tolerated by the majority of seeds and by vegetative tissues of only a small number of land plants. Desiccation tolerance is an ancient trait, lost from vegetative tissues following the appearance of tracheids but reappearing in several lineages when selection pressures favored its evolution. Cells of all desiccation-tolerant plants and seeds must possess a core set of mechanisms to protect them from desiccation- and rehydration-induced damage. This review explores how desiccation generates cell damage and how tolerant cells assuage the complex array of mechanical, structural, metabolic, and chemical stresses and survive.Likewise, the stress of rehydration requires appropriate mitigating cellular responses. We also explore what comparative genomics, both structural and responsive, have added to our understanding of cellular protection mechanisms induced by desiccation, and how vegetative desiccation tolerance circumvents destructive, stress-induced cell senescence.

Contrasted evolutionary trajectories of plant transcription factors

Because of their prominent roles in plant development, transcription factors (TF) play central roles as drivers of innovation in the evolution of the green lineage (viridiplantae). The advent of massive sequencing combined with comparative genetics/genomics allows a rigorous investigation of how TF families have contributed to plant diversification from charophyte algae to bryophytes to angiosperms. Here, we review recent progress on TF family reconstruction and the identification of distantly related TFs present throughout the evolutionary timeline from algae to angiosperms. These data provide examples of contrasting evolutionary trajectories of TF families and illustrate how conserved TFs adopt diverse roles over the course of evolution.

Vegetative desiccation tolerance in the resurrection plant Xerophyta humilis has not evolved through reactivation of the seed canonical LAFL regulatory network

It has been hypothesised that vegetative desiccation tolerance in resurrection plants evolved via reactivation of the canonical LAFL (i.e. LEC1, ABI3, FUS3 and LEC2) transcription factor (TF) network that activates the expression of genes during the maturation of orthodox seeds leading to desiccation tolerance of the plant embryo in most angiosperms. There is little direct evidence to support this, however, and the transcriptional changes that occur during seed maturation in resurrection plants have not previously been studied. Here we performed de novo transcriptome assembly for Xerophyta humilis, and analysed gene expression during seed maturation and vegetative desiccation. Our results indicate that differential expression of a set of 4205 genes is common to maturing seeds and desiccating leaves. This shared set of genes is enriched for gene ontology terms related to abiotic stress, including water stress and abscisic acid signalling, and includes many genes that are seed-specific in Arabidopsis thaliana and targets of ABI3. However, while we observed upregulation of orthologues of the canonical LAFL TFs and ABI5 during seed maturation, similar to what is seen in A. thaliana, this did not occur during desiccation of leaf tissue. Thus, reactivation of components of the seed desiccation program in X. humilis vegetative tissues likely involves alternative transcriptional regulators.

From reproduction to production, stomata are the master regulators

The best predictor of leaf level photosynthetic rate is the porosity of the leaf surface, as determined by the number and aperture of stomata on the leaf. This remarkable correlation between stomatal porosity (or diffusive conductance to water vapour g_s ) and CO₂ assimilation rate (A) applies to all major lineages of vascular plants (Figure 1) and is sufficiently predictable that it provides the basis for the model most widely used to predict water and CO₂ fluxes from leaves and canopies. Yet the Ball-Berry formulation is only a phenomenological approximation that captures the emergent character of stomatal behaviour. Progressing to a more mechanistic prediction of plant gas exchange is challenging because of the diversity of biological components regulating stomatal action. These processes are the product of more than 400 million years of co-evolution between stomatal, vascular and photosynthetic tissues. Both molecular and structural components link the abiotic world of the whole plant with the turgor pressure of the epidermis and guard cells, which ultimately determine stomatal pore size and porosity to water and CO₂ exchange (New Phytol., 168, 2005, 275). In this review we seek to simplify stomatal behaviour by using an evolutionary perspective to understand the principal selective pressures involved in stomatal evolution, thus identifying the primary regulators of stomatal aperture. We start by considering the adaptive process that has locked together the regulation of water and carbon fluxes in vascular plants, finally examining specific evidence for evolution in the proteins responsible for regulating guard cell turgor.

Evolution of Abscisic Acid Signaling Module and Its Perception

We hereby review the perception and responses to the stress hormone Abscisic acid (ABA), along the trajectory of 500M years of plant evolution, whose understanding may resolve how plants acquired this signaling pathway essential for the colonization of land. ABA levels rise in response to abiotic stresses, coordinating physiological and metabolic responses, helping plants survive stressful environments. In land plants, ABA signaling cascade leads to growth arrest and large-scale changes in transcript levels, required for coping with environmental stressors. This response is regulated by a PYRABACTIN RESISTANCE 1-like (PYL)-PROTEIN PHOSPHATASE 2C (PP2C)-SNF1-RELATED PROTEIN KINASE 2 (SnRK2) module, that initiates phosphor-activation of transcription factors and ion channels. The enzymatic portions of this module (phosphatase and kinase) are functionally conserved from streptophyte algae to angiosperms, whereas the regulatory component -the PYL receptors, putatively evolved in the common ancestor of Zygnematophyceae and embryophyte as a constitutive, ABA-independent protein, further evolving into a ligand-activated receptor at the embryophyta. This evolutionary process peaked with the appearance of the strictly ABA-dependent subfamily III stress-triggered angiosperms' dimeric PYL receptors. The emerging picture is that the ancestor of land plants and its predecessors synthesized ABA, as its biosynthetic pathway is conserved between ancestral and current day algae. Despite this ability, it was only the common ancestor of land plants which acquired the hormonal-modulation of PYL activity by ABA. This raises several questions regarding both ABA's function in ABA-non-responsive organisms, and the evolutionary aspects of the ABA signal transduction pathway.

Gene gains paved the path to land

Two genomes of the closest algal sisters to land plants were sequenced, providing potential evidence that bacterial genes were key in adapting to terrestrial stresses.

The poplar R2R3 MYB transcription factor PtrMYB94 coordinates with abscisic acid signaling to improve drought tolerance in plants

In plants, R2R3 MYB transcription factors (TFs) consist of one large gene family and are involved in the regulation of many developmental processes and various stresses. However, the functions of most of MYB TFs in woody plants remain unknown. Here, PtrMYB94, an R2R3 MYB TF from Populus trichocarpa, is characterized to be involved in the regulation of drought responses and abscisic acid (ABA) signaling. PtrMYB94 encodes a nuclear-localized R2R3 MYB TF. RT-PCR results showed that the PtrMYB94 transcripts were relatively abundant in leaves and stems, and were induced rapidly in response to dehydration stress. Overexpression of PtrMYB94 improved plant drought responses, suggesting that this MYB TF may functionally regulate poplar adaptability to drought stress. Furthermore, the analysis of transcriptional expression and PtrMYB94 promoter: GUS activity showed that PtrMYB94 responded to ABA induction. PtrMYB94-overexpressing plants exhibited the inhibition of seed germination compared with the wild-type (WT) control under ABA exposure condition. The ABA content was evidently increased in the PtrMYB94-overexpressing plants relative to the WT plants. In addition, transcript levels of several ABA- and drought-responsive genes, such as ABA1 and DREB2B, were up-regulated. Taken together, our results suggest that PtrMYB94 is involved in an ABA-dependent drought stress regulation in Populus.

Physcomitrella as a model system for plant cell biology and organelle-organelle communication

In multicellular eukaryotic cells, metabolism and growth are sustained by the cooperative functioning of organelles in combination with cell-to-cell communication at the organism level. In land plants, multiple strategies have evolved to adapt to life outside water. As basal land plant, the moss Physcomitrella patens is used for comparative genomics, allowing to study lineage-specific features, as well as to track the evolution of fundamental parameters of plant cell organisation and physiology. P. patens is a versatile model for cell biology research, especially to investigate adaptive growth, stress biology as well as organelle dynamics and interactions. Recent advances include the use of genetically encoded biosensors for in vivo imaging of physiological parameters.

PpAKR1A, a Novel Aldo-Keto Reductase from Physcomitrella Patens, Plays a Positive Role in Salt Stress

The moss Physcomitrella patens is tolerant of highly saline environments. In plants, salinity stress may induce the production of toxic reactive carbonyl species (RCS) and oxidative damage. Aldo-keto reductases (AKRs) are a large group of NADP-dependent oxidoreductases involved in RCS detoxification. However, many members in this superfamily remain uncharacterized. In this study, we cloned and characterised a putative AKR1 from P. patens, named PpAKR1A. Notably, the transcription level of PpAKR1A was induced by salt and methylglyoxal (MG) stress, and the recombinant PpAKR1A protein catalysed the reduction of toxic aldehydes. PpAKR1A knockout mutants of P. patens (ppakr1a) were sensitive to NaCl and MG treatment, as indicated by much lower concentrations of chlorophyll and much higher concentrations of MG and H₂O₂ than those in WT plants. Meanwhile, ppakr1a plants exhibited decreases in the MG-reducing activity and reactive oxygen species-scavenging ability in response to salt stress, possibly due to decreases in the activities of antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD). Our results indicate that PpAKR1A is an aldo-keto reductase that detoxifies MG and thus plays an important role in salt stress tolerance in P. patens.

Acclimation and endogenous abscisic acid in the moss Physcomitrella patens during acquisition of desiccation tolerance

The moss Physcomitrella patens has been used as a model organism to study the induction of desiccation tolerance (DT), but links between dehydration rate, the accumulation of endogenous abscisic acid (ABA) and DT remain unclear. In this study, we show that prolonged acclimation of P. patens at 89% relative humidity (RH) [-16 MPa] can induce tolerance of desiccation at 33% RH (-153 MPa) in both protonema and gametophore stages. During acclimation, significant endogenous ABA accumulation occurred after 1 day in gametophores and after 2 days in protonemata. Physcomitrella patens expressing the ABA-inducible EARLY METHIONINE promoter fused to a cyan fluorescent protein (CFP) reporter gene revealed a mostly uniform distribution of the CFP increasing throughout the tissues during acclimation. DT was measured by day 6 of acclimation in gametophores, but not until 9 days of acclimation for protonemata. These results suggest that endogenous ABA accumulating when moss cells experience moderate water loss requires sufficient time to induce the changes that permit cells to survive more severe desiccation. These results provide insight for ongoing studies of how acclimation induces metabolic changes to enable DT in P. patens.

Involvement of abscisic acid-responsive element-binding factors in cassava (Manihot esculenta) dehydration stress response

Cassava (Manihot esculenta) is a major staple food, animal feed and energy crop in the tropics and subtropics. It is one of the most drought-tolerant crops, however, the mechanisms of cassava drought tolerance remain unclear. Abscisic acid (ABA)-responsive element (ABRE)-binding factors (ABFs) are transcription factors that regulate expression of target genes involved in plant tolerance to drought, high salinity, and osmotic stress by binding ABRE cis-elements in the promoter regions of these genes. However, there is little information about ABF genes in cassava. A comprehensive analysis of Manihot esculenta ABFs (MeABFs) described the phylogeny, genome location, cis-acting elements, expression profiles, and regulatory relationship between these factors and Manihot esculenta betaine aldehyde dehydrogenase genes (MeBADHs). Here we conducted genome-wide searches and subsequent molecular cloning to identify seven MeABFs that are distributed unevenly across six chromosomes in cassava. These MeABFs can be clustered into three groups according to their phylogenetic relationships to their Arabidopsis (Arabidopsis thaliana) counterparts. Analysis of the 5′-upstream region of MeABFs revealed putative cis-acting elements related to hormone signaling, stress, light, and circadian clock. MeABF expression profiles displayed clear differences among leaf, stem, root, and tuberous root tissues under non-stress and drought, osmotic, or salt stress conditions. Drought stress in cassava leaves and roots, osmotic stress in tuberous roots, and salt stress in stems induced expression of the highest number of MeABFs showing significantly elevated expression. The glycine betaine (GB) content of cassava leaves also was elevated after drought, osmotic, or salt stress treatments. BADH1 is involved in GB synthesis. We show that MeBADH1 promoter sequences contained ABREs and that MeBADH1 expression correlated with MeABF expression profiles in cassava leaves after the three stress treatments. Taken together, these results suggest that in response to various dehydration stresses, MeABFs in cassava may activate transcriptional expression of MeBADH1 by binding the MeBADH1 promoter that in turn promotes GB biosynthesis and accumulation via an increase in MeBADH1 gene expression levels and MeBADH1 enzymatic activity. These responses protect cells against dehydration stresses by preserving an osmotic balance that enhances cassava tolerance to dehydration stresses.