Microarray analysis of transcriptional responses to abscisic acid and osmotic, salt, and drought stress in the moss, Physcomitrella patens

The bryophyte rhizoid-sphere microbiome responds to water deficit

The roots of vascular plants are colonised by a multitude of microbes, which play an important role in plant health and stress resilience. Drought stress in particular is devastating for crop yield and causes major shifts in the rhizosphere microbial communities. However, the microbiome associated to the rhizoids (hereafter termed rhizoid-sphere) of the nonvascular bryophytes remains largely unexplored. Here, we use amplicon sequencing to explore the rhizoid-sphere microbiome of three bryophyte species under drought and well-watered conditions. Comparing rhizoid-sphere microbial communities associated with the two liverworts Marchantia polymorpha and Marchantia paleacea and the moss Physcomitrium patens showed characteristic differences in composition between host species and both conserved and unique changes under drought. At phylum level, these changes were similar to changes in the rhizosphere of angiosperms under drought. Furthermore, we observed strong differences in rhizoid-sphere colonisation between bryophyte species for taxa known for nitrogen fixation and plant growth promotion. Interestingly, M. polymorpha prioritised the growth of belowground organs under osmotic stress, as is the case for angiosperms under drought. Taken together, our results show interesting parallels between bryophytes and angiosperms in the relation with their rhizo(id-)sphere, suggesting evolutionary conservation among land plants in their response to drought stress.

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.

Molecular Mechanisms for Regulating Stomatal Formation across Diverse Plant Species

Plant stomata play a crucial role in photosynthesis by regulating transpiration and gas exchange. Meanwhile, environmental cues can also affect the formation of stomata. Stomatal formation, therefore, is optimized for the survival and growth of the plant despite variable environmental conditions. To adapt to environmental conditions, plants open and close stomatal pores and even regulate the number of stomata that develop on the epidermis. There are great differences in the leaf structure and developmental origin of the cell in the leaf between Arabidopsis and grass plants. These differences affect the fine regulation of stomatal formation due to different plant species. In this paper, a comprehensive overview of stomatal formation and the molecular networks and genetic mechanisms regulating the polar division and cell fate of stomatal progenitor cells in dicotyledonous plants such as Arabidopsis and Poaceae plants such as Oryza sativa and Zea mays is provided. The processes of stomatal formation mediated by plant hormones and environmental factors are summarized, and a model of stomatal formation in plants based on the regulation of multiple signaling pathways is outlined. These results contribute to a better understanding of the mechanisms of stomatal formation and epidermal morphogenesis in plants and provide a valuable theoretical basis and gene resources for improving crop resilience and yield traits.

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.

Genome-wide identification of CaARR-Bs transcription factor gene family in pepper and their expression patterns under salinity stress

In plants, ARRs-B transcription factors play a crucial role in regulating cytokinin signal transduction, abiotic stress resistance, and plant development. A number of adverse environmental conditions have caused severe losses for the pepper (Capsicum annuum L.)-a significant and economically important vegetable. Among the transcription factors of the type B-ARRs family, multiple members have different functions. In pepper, only a few members of the ARRs-B family have been reported and characterized. The current study aimed to characterize ARRs-B transcription factors in C. annuum, including phylogenetic relationships, gene structures, protein motif arrangement, and RT-qPCR expression analyses and their role in salinity stress. In total, ten genes encode CaARRs-B transcription factors (CaARR1 to CaARR10) from the largest subfamily of type-B ARRs were identified in C. annum. The genome-wide analyses of the CaARRs-B family in C. annuum were performed based on the reported ARRs-B genes in Arabidopsis. An analysis of homologous alignments of candidate genes, including their phylogenetic relationships, gene structures, conserved domains, and qPCR expression profiles, was conducted. In comparison with other plant ARRs-B proteins, CaARRs-B proteins showed gene conservation and potentially specialized functions. In addition, tissue-specific expression profiles showed that CaARRs-B genes were differentially expressed, suggesting functionally divergent. CaARRs-B proteins had a typical conserved domain, including AAR-like (pfam: PF00072) and Myb DNA binding (pfam: PF00249) domains. Ten of the CaARRs-B genes were asymmetrically mapped on seven chromosomes in Pepper. Additionally, the phylogenetic tree of CaARRs-B genes from C. annuum and other plant species revealed that CaARRs-B genes were classified into four clusters, which may have evolved conservatively. Further, using quantitative real-time qRT-PCR, the study assessed the expression patterns of CaARRs-B genes in Capsicum annuum seedlings subjected to salt stress. The study used quantitative real-time qRT-PCR to examine CaARRs-B gene expression in Capsicum annuum seedlings under salt stress. Roots exhibited elevated expression of CaARR2 and CaARR9, while leaves showed decreased expression for CaARR3, CaARR4, CaARR7, and CaARR8. Notably, no amplification was observed for CaARR10. This research sheds light on the roles of CaARRs-B genes in pepper's response to salinity stress. These findings enrich our comprehension of the functional implications of CaARRs-B genes in pepper, especially in responding to salinity stress, laying a solid groundwork for subsequent in-depth studies and applications in the growth and development of Capsicum annuum.

Role of TRDMT1/DNMT2 in stress adaptation and its influence on transcriptome and proteome dynamics under osmotic stress in Physcomitrium patens

Early land plants such as the moss Physcomitrium patens lack several morphological traits that offer protection to tracheophytes from environmental stresses. These plants instead have evolved several physiological and biochemical mechanisms that facilitate them to adapt to terrestrial stresses such as drought. We have previously shown that loss-of-function mutants of tRNA (cytosine(38)-C(5))-methyltransferase TRDMT1/DNMT2 in P. patens are highly sensitive to oxidative and osmotic stress. To gain insight into the role of PpTRDMT1/PpDNMT2 in modulating genetic networks under osmotic stress, genome-wide transcriptome and proteome studies were undertaken in wild-type and ppdnmt2 plants. Transcriptome analysis revealed 375 genes to be differentially expressed in the ppdnmt2 under stress compared to the WT. Most of these genes are affiliated with carbohydrate metabolic pathways, photosynthesis, cell wall biogenesis, pathways related to isotropic and polarised cell growth and transcription factors among others. Histochemical staining showed elevated levels of reactive oxygen species in ppdnmt2 while transmission electron microscopy revealed no distinct defects in the ultrastructure of chloroplasts. Immunoprecipitation using PpDNMT2-specific antibody coupled with mass spectrometry revealed core proteins of the glycolytic pathway, antioxidant enzymes, proteins of amino acid biosynthetic pathways and photosynthesis-related proteins among others to co-purify with PpTRDMT1/PpDNMT2 under osmotic stress. Yeast two-hybrid assays, protein deletion and α-galactosidase assays showed the cytosol glycolytic protein glyceraldehyde 3-phosphate dehydrogenase to bind to the catalytic motifs in PpTRDMT1/PpDNMT2. Results presented in this study allow us to better understand genetic networks linking enzymes of energy metabolism, epigenetic processes and RNA pol II-mediated transcription during osmotic stress tolerance in P. patens.

Genome-Wide Characterization and Expression Profiling of ABA Biosynthesis Genes in a Desert Moss Syntrichia caninervis

Syntrichia caninervis can survive under 80-90% protoplasmic water losses, and it is a model plant in desiccation tolerance research. A previous study has revealed that S. caninervis would accumulate ABA under dehydration stress, while the ABA biosynthesis genes in S. caninervis are still unknown. This study identified one ScABA1, two ScABA4s, five ScNCEDs, twenty-nine ScABA2s, one ScABA3, and four ScAAOs genes, indicating that the ABA biosynthesis genes were complete in S. caninervis. Gene location analysis showed that the ABA biosynthesis genes were evenly distributed in chromosomes but were not allocated to sex chromosomes. Collinear analysis revealed that ScABA1, ScNCED, and ScABA2 had homologous genes in Physcomitrella patens. RT-qPCR detection found that all of the ABA biosynthesis genes responded to abiotic stress; it further indicated that ABA plays an important role in S. caninervis. Moreover, the ABA biosynthesis genes in 19 representative plants were compared to study their phylogenetic and conserved motifs; the results suggested that the ABA biosynthesis genes were closely associated with plant taxa, but these genes had the same conserved domain in each plant. In contrast, there is a huge variation in the exon number between different plant taxa; it revealed that ABA biosynthesis gene structures are closely related to plant taxa. Above all, this study provides strong evidence demonstrating that ABA biosynthesis genes were conserved in the plant kingdom and deepens our understanding of the evolution of the phytohormone ABA.

Analysis of the Qualitative and Quantitative Content of the Phenolic Compounds of Selected Moss Species under NaCl Stress

The response to salt stress analysed by quantitative and qualitative analyses in three selected moss species was studied. Non-halophytic funaroid Physcomitrium patens and two halophytic mosses, funaroid Entosthodon hungaricus and pottioid Hennediella heimii were exposed to salt stress under controlled in vitro conditions. The results clearly showed various phenolics to be present and included to some extent as a non-enzymatic component of oxidative, i.e., salt stress. The common pattern of responses characteristic of phenolic compounds was not present in these moss species, but in all three species the role of phenolics to stress tolerance was documented. The phenolic p-coumaric acid detected in all three species is assumed to be a common phenolic included in the antioxidative response and salt-stress tolerance. Although the stress response in each species also included other phenolics, the mechanisms were different, and also dependent on the stress intensity and duration.

Genome-wide identification of drought-responsive microRNAs and their target genes in Chinese jujube by deep sequencing

BACKGROUND

MicroRNAs (miRNAs) are about 21 snucleotide (nt) long, non-coding RNAs that play an important role in plant abiotic stress responses. Chinese jujube is a native fruit tree in China, which is also an admittedly drought-resistant plant. But the drought-related miRNAs have little been reported in jujube.

OBJECTIVE

To identify possibly drought-responsive microRNAs and their target genes in Chinese Jujube.

METHODS

Twelve small RNA libraries were constructed from two jujube genotypes both drought treated and control samples with three replicates to identify known and novel miRNAs in Chinese Jujube, DESeq2 was used to identify expression pattern of miRNAs between drought treatment and control samples, TargetFinder program was used to predict potential target genes of conserved and novel miRNAs, RT-qPCR were used to analysis the expression levels of drought-related miRNAs and their potential targets. The RNA ligase-mediated RLM-5' RACE experiments were performed to validate predicted target genes of drought-related miRNAs.

RESULTS

43 known miRNAs and 431 novel miRNAs were identified in Chinese jujube. Expression analysis showed that 28 miRNAs were differential expressed under drought stress in jujube variety "Dongzao", including 21 up-regulated miRNAs and 7 down-regulated miRNAs, 61 miRNAs were differential expressed under drought stress in Chinese jujube variety "Zanhuangdazao", including 23 up-regulated miRNAs and 37 down-regulated miRNAs. Depend on miRNAs target prediction, functional annotation and expression analysis, we identified 9 drought-related miRNAs, and 7 target genes of 6 miRNAs were confirmed using the modified 5'-RACE method. Also, RT-qPCR analyses revealed that relative expression of those miRNAs and their targets have negative tendency.

CONCLUSION

We identified 6 drought-related miRNAs by high-throughout sequencing and target gene annotation from Chinese jujube, and targets of those miRNAs were confirmed by the modified 5'-RACE method. These findings provide molecular evidence for enhancing drought tolerance in Chinese jujube and other plants.

Transcriptome analysis of response strategy in Hemerocallis fulva under drought stress

BACKGROUND

Hemerocallis fulva is an important ground cover plant widely used in urban greening. The analysis of the molecular mechanism underlying the drought response of H. fulva can lay a foundation for improving its adaptability and expanding its planting area.

OBJECTIVE

To reveal the drought response mechanisms of H. fulva, identify candidate unigenes associated with drought response, and lay a foundation for further unigenes functional study and drought resistance improvement of H. fulva via genetic engineering.

METHODS

RNA was isolated from H. fulva under different experimental conditions. De novo transcriptomic analysis of the samples was performed to screen drought response unigenes. The transcriptional changes of candidate drought response unigenes were verified by quantitative real-time PCR.

RESULTS

The differentially expressed unigenes and their functions were analyzed after H. fulva treated by PEG-simulated drought stress and rewatering. The candidate unigenes, associated with H. fulva drought response, were identified after transcriptome analysis. Then, the transcription level of drought response unigenes of H. fulva under different conditions was further verified. Abscisic acid, protein phosphorylation, sterol biosynthesis and ion transport were involved in drought response with quick restore in H. fulva. The response unigenes, involved in hormone (ABA, JA, CK and GA) signaling pathways, defense response, high light response, karrikin response and leaf shaping, can maintain at changed expression levels even after stress withdraw.

CONCLUSION

Hemerocallis fulva has unique drought response mechanism. Negative regulation mechanism may play more important roles in drought response of H. fulva. The analysis of candidate unigenes, associated with drought response, lays a foundation for further drought resistance improvement of H. fulva.

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.

Moss transcription factors regulating development and defense responses to stress

Transcription factors control gene expression, leading to regulation of biological processes that determine plant development and adaptation to the environment. Land colonization by plants occurred 450-470 million years ago and was accompanied by an increase in the complexity of transcriptional regulation associated to transcription factor gene expansions. AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY transcription factor families increased in land plants compared with algae. In angiosperms, they play crucial roles in regulating plant growth and responses to environmental stressors. However, less information is available in bryophytes and only in a few cases is the functional role of moss transcription factors in stress mechanisms known. In this review, we discuss current knowledge of the transcription factor families involved in development and defense responses to stress in mosses and other bryophytes. By exploring and analysing the Physcomitrium patens public database and published transcriptional profiles, we show that a high number of AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY genes are differentially expressed in response to abiotic stresses and during biotic interactions. Expression profiles together with a comprehensive analysis provide insights into relevant transcription factors involved in moss defenses, and hint at distinct and conserved biological roles between bryophytes and angiosperms.

Desiccation-rehydration measurements in bryophytes: current status and future insights

Desiccation-rehydration experiments have been employed over the years to evaluate desiccation tolerance of bryophytes (Bryophyta, Marchantiophyta, and Anthocerotophyta). Researchers have applied a spectrum of protocols to induce desiccation and subsequent rehydration, and a wide variety of techniques have been used to study desiccation-dependent changes in bryophyte molecular, cellular, physiological, and structural traits, resulting in a multifaceted assortment of information that is challenging to synthesize. We analysed 337 desiccation-rehydration studies, providing information for 351 species, to identify the most frequent methods used, analyse the advances in desiccation studies over the years, and characterize the taxonomic representation of the species assessed. We observed certain similarities across methodologies, but the degree of convergence among the experimental protocols was surprisingly low. Out of 52 bryophyte orders, 40% have not been studied, and data are lacking for multiple remote or difficult to access locations. We conclude that for quantitative interspecific comparisons of desiccation tolerance, rigorous standardization of experimental protocols and measurement techniques, and simultaneous use of an array of experimental techniques are required for a mechanistic insight into the different traits modified in response to desiccation. New studies should also aim to fill gaps in taxonomic, ecological, and spatial coverage of bryophytes.

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.

Role of the type-B authentic response regulator gene family in fragrant rice under alkaline salt stress

Globally, rice is being consumed as a main staple food and faces different kinds of biotic and abiotic stresses such drought, salinity, and pest attacks. Through the cytokinin signaling, Type-B authentic response regulators (ARR-Bs) respond positively towards the environmental stimuli. ARR-Bs are involved in abiotic stress tolerance and plant development but their molecular mechanisms in fragrant rice are still not fully explored. The current study showed the genome-wide characterization of OsARR-B genes under alkaline salt stress. Results showed that in total, 24 OsARR-B genes were found and divided into four subgroups on the basis of a phylogenetic analysis. These genes were located on all rice chromosomes except 8 and 10. Analysis of gene duplications, gene structure, cis-elements, protein-protein interactions, and miRNA were performed. Gene ontology analysis showed that OsARR-B genes are involved in plant development through the regulation of molecular functions, biological processes, and cellular components. Furthermore, 117 and 192 RNA editing sites were detected in chloroplast and mitochondrial genes, respectively, encoding proteins of OsARR-B. In chloroplast and mitochondrial genes, six and nine types of amino acid changes, respectively, were caused by RNA editing, showing that RNA editing has a role in the alkaline salt stress tolerance in fragrant rice. We also used a comparative transcriptome approach to study the gene expression changes in alkaline tolerant and susceptible genotypes. Under alkaline salt stress, OsARR-B5, OsARR-B7, OsARR-B9, OsARR-B10, OsARR-B16, OsARR-B22, and OsARR-B23 showed higher transcript levels in alkaline salt tolerant genotypes as compared to susceptible ones. Quantitative RT-PCR showed upregulation of gene expression in the alkaline tolerant genotypes under alkaline stress. Our study explored the gene expression profiling and RESs of two rice contrasting genotypes, which will help to understand the molecular mechanisms of alkaline salt tolerance in fragrant rice.

The specific glycerolipid composition is responsible for maintaining the membrane stability of Physcomitrella patens under dehydration stress

Land colonization is a major event in plant evolution. Little is known about the evolutionary characteristics of lipids during this process. Here, we proved that Physcomitrella patens, a bryophyte that appeared in the early evolution of terrestrial plants, has short-term desiccation resistance. The maintenance of membrane integrity is related to its specific glycerolipid composition and key genes for lipid metabolism. We analyzed 414 types of lipid molecules, and found that phospholipids accounted for 61.7%, mainly PC and PI; glycolipids accounted for only 26.5%, with a special MGDG molecular map. The most abundant MDGD, that is, MGDG34:6, contained rare 15- and 19-carbon acyl chains; the level of neutral lipids was higher. This was consistent with the results observed by TEM, with fewer lamellae and obvious lipid droplets. Slight dehydration accumulated a large number of TAG molecules, and severe dehydration degraded phospholipids and caused membrane leakage, but PA and MGDG fluctuated less. The key genes of lipid metabolism, DGAT and PAP, were actively transcribed, suggesting that PA was one of the main DAG sources for TAG synthesis. This work proves that Physcomitrella patens adopts high-constitutive PC and PI similar to plant seeds, abundant TAG, and its own specific MGDG to resist extreme dehydration. This result provides a new insight into the lipid evolution of early terrestrial plants against unfavorable terrestrial environments.

DICER-LIKE1a autoregulation based on intronic microRNA processing is required for stress adaptation in Physcomitrium patens

The Physcomitrium patens DICER-LIKE1a (PpDCL1a) mRNA encoding the essential Dicer protein for microRNA (miRNA) biogenesis harbors an intronic miRNA (miR1047). An autoregulatory mechanism to control PpDCL1a abundance that is based on competitive processing of the intronic miRNA and proper PpDCL1a mRNA splicing has previously been proposed. If intron splicing occurs first the mRNA can be translated into the functional PpDCL1a protein, whereas the processing of the intronic miRNA catalyzed by PpDCL1a itself, prior to pre-mRNA splicing, generates a truncated transcript unable to produce a functional protein. This proposed autoregulation of DCL1 has not been functionally analyzed in any plant species, and the existence of this autoregulatory control is expected to have a general impact on the overall miRNA biogenesis pathway and the transcriptome that is under miRNA control. We abolished PpDCL1a autoregulatory feedback control by the precise deletion of the MIR1047-containing intron. The generated line displayed hypersensitivity to salt stress and hyposensitivity to the plant hormone ABA, accompanied by the disturbed expression of miRNAs and mRNAs, revealed by transcriptome analyses. The feedback control together with the phenotypic abnormalities and molecular changes in the intron-less line can be rescued by the re-insertion of a modified intron harboring a sequence-unrelated artificial miRNA. Our findings indicate the physiological importance of miR1047-based feedback control of PpDCL1a transcript abundance, which controls the expression of miRNAs, and their cognate target RNAs during salt stress adaptation, and suggests a key role for this autoregulation in the molecular adaptation of land plants to terrestrial habitats.

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.

Characterization of Vascular plant One-Zinc finger (VOZ) in soybean (Glycine max and Glycine soja) and their expression analyses under drought condition

Vascular plant one-zinc-finger (VOZ) transcription factors regulate plant growth and development under drought conditions. Six VOZ transcription factors encoding genes exist in soybean genome (both in Glycine max and Glycine soja). Herein, GmVOZs and GsVOZs were identified through in silico analysis and characterized with different bioinformatics tools and expression analysis. Phylogenetic analysis classified VOZ genes in four groups. Sequence logos analysis among G. max and G. soja amino acid residues revealed higher conservation. Presence of stress related cis-elements in the upstream regions of GmVOZs and GsVOZs highlights their role in tolerance against abiotic stresses. The collinearity analysis identified 14 paralogous/orthologous gene pairs within and between G. max and G. soja. The Ka/Ks values showed that soybean VOZ genes underwent selection pressure with limited functional deviation arising from whole genome and segmental duplication. The GmVOZs and GsVOZs were found to express in roots and leaves at seedling stage. The qRT-PCR revealed that GmVOZs and GsVOZs transcripts can be regulated by abiotic stresses such as polyethylene glycol (PEG). The findings of this study will provide a reference to decipher physiological and molecular functions of VOZ genes in soybean.

Morpho-Physiological, Biochemical, and Genetic Responses to Salinity in Medicago truncatula

We used an integrated morpho-physiological, biochemical, and genetic approach to investigate the salt responses of four lines (TN1.11, TN6.18, JA17, and A10) of Medicago truncatula. Results showed that TN1.11 exhibited a high tolerance to salinity, compared with the other lines, recording a salinity induced an increase in soluble sugars and soluble proteins, a slight decrease in malondialdehyde (MDA) accumulation, and less reduction in plant biomass. TN6.18 was the most susceptible to salinity as it showed less plant weight, had elevated levels of MDA, and lower levels of soluble sugars and soluble proteins under salt stress. As transcription factors of the APETALA2/ethylene responsive factor (AP2/ERF) family play important roles in plant growth, development, and responses to biotic and abiotic stresses, we performed a functional characterization of MtERF1 gene. Real-time PCR analysis revealed that MtERF1 is mainly expressed in roots and is inducible by NaCl and low temperature. Additionally, under salt stress, a greater increase in the expression of MtERF1 was found in TN1.11 plants than that in TN6.18. Therefore, the MtERF1 pattern of expression may provide a useful marker for discriminating among lines of M. truncatula and can be used as a tool in breeding programs aiming at obtaining Medicago lines with improved salt tolerance.

Ties between Stress and Lipid Droplets Pre-date Seeds

Seeds were a key evolutionary innovation. These durable structures provide a concerted solution to two challenges on land: dispersal and stress. Lipid droplets (LDs) that act as nutrient storage reservoirs are one of the main cell-biological reasons for seed endurance. Although LDs are key structures in spermatophytes and are especially abundant in seeds, they are found across plants and algae, and increase during stress. Further, the proteins that underpin their form and function often have deep homologs. We propose an evolutionary scenario in which (i) the generation of LDs arose as a mechanism to mediate general drought and desiccation resilience, and (ii) the required protein framework was co-opted by spermatophytes for a seed-specific program.

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.

Evo-physio: on stress responses and the earliest land plants

Embryophytes (land plants) can be found in almost any habitat on the Earth's surface. All of this ecologically diverse embryophytic flora arose from algae through a singular evolutionary event. Traits that were, by their nature, indispensable for the singular conquest of land by plants were those that are key for overcoming terrestrial stressors. Not surprisingly, the biology of land plant cells is shaped by a core signaling network that connects environmental cues, such as stressors, to the appropriate responses-which, thus, modulate growth and physiology. When did this network emerge? Was it already present when plant terrestrialization was in its infancy? A comparative approach between land plants and their algal relatives, the streptophyte algae, allows us to tackle such questions and resolve parts of the biology of the earliest land plants. Exploring the biology of the earliest land plants might shed light on exactly how they overcame the challenges of terrestrialization. Here, we outline the approaches and rationale underlying comparative analyses towards inferring the genetic toolkit for the stress response that aided the earliest land plants in their conquest of land.

Transcriptomic analysis of poco1, a mitochondrial pentatricopeptide repeat protein mutant in Arabidopsis thaliana

BACKGROUND

Flowering is a crucial stage during plant development. Plants may respond to unfavorable conditions by accelerating reproductive processes like flowering. In a recent study, we showed that PRECOCIOUS1 (POCO1) is a mitochondrial pentatricopeptide repeat (PPR) protein involved in flowering time and abscisic acid (ABA) signaling in Arabidopsis thaliana. Here, we use RNA-seq data to investigate global gene expression alteration in the poco1 mutant.

RESULTS

RNA-seq analysis was performed during different developmental stages for wild-type and poco1 plants. The most profound differences in gene expression were found when wild-type and poco1 plants of the same developmental stage were compared. Coverage analysis confirmed the T-DNA insertion in POCO1, which was concomitant with truncated transcripts. Many biological processes were found to be enriched. Several flowering-related genes such as FLOWERING LOCUS T (FT), which may be involved in the early-flowering phenotype of poco1, were differentially regulated. Numerous ABA-associated genes, including the core components of ABA signaling such as ABA receptors, protein phosphatases, protein kinases, and ABA-responsive element (ABRE) binding proteins (AREBs)/ABRE-binding factors (ABFs) as well as important genes for stomatal function, were mostly down-regulated in poco1. Drought and oxidative stress-related genes, including ABA-induced stress genes, were differentially regulated. RNA-seq analysis also uncovered differentially regulated genes encoding various classes of transcription factors and genes involved in cellular signaling. Furthermore, the expression of stress-associated nuclear genes encoding mitochondrial proteins (NGEMPs) was found to be altered in poco1. Redox-related genes were affected, suggesting that the redox state in poco1 might be altered.

CONCLUSION

The identification of various enriched biological processes indicates that complex regulatory mechanisms underlie poco1 development. Differentially regulated genes associated with flowering may contribute to the early-flowering phenotype of poco1. Our data suggest the involvement of POCO1 in the early ABA signaling process. The down-regulation of many ABA-related genes suggests an association of poco1 mutation with the ABA signaling deficiency. This condition further affects the expression of many stress-related, especially drought-associated genes in poco1, consistent with the drought sensitivity of poco1. poco1 mutation also affects the expression of genes associated with the cellular regulation, redox, and mitochondrial perturbation.

A Na+/H+ antiporter, K2-NhaD, improves salt and drought tolerance in cotton (Gossypium hirsutum L.)

Overexpression of K2-NhaD in transgenic cotton resulted in phenotypes with strong salinity and drought tolerance in greenhouse and field experiments, increased expression of stress-related genes, and improved regulation of metabolic pathways, such as the SOS pathway. Drought and salinity are major abiotic stressors which negatively impact cotton yield under field conditions. Here, a plasma membrane Na⁺/H⁺ antiporter gene, K2-NhaD, was introduced into upland cotton R15 using an Agrobacterium tumefaciens-mediated transformation system. Homozygous transgenic lines K9, K17, and K22 were identified by PCR and glyphosate-resistance. TAIL-PCR confirmed that T-DNA carrying the K2-NhaD gene in transgenic lines K9, K17 and K22 was inserted into chromosome 3, 19 and 12 of the cotton genome, respectively. Overexpression of K2-NhaD in transgenic cotton plants grown in greenhouse conditions and subjected to drought and salinity stress resulted in significantly higher relative water content, chlorophyll, soluble sugar, proline levels, and SOD, CAT, and POD activity, relative to non-transgenic plants. The expression of stress-related genes was significantly upregulated, and this resulted in improved regulation of metabolic pathways, such as the salt overly sensitive pathway. K2-NhaD transgenic plants growing under field conditions displayed strong salinity and drought tolerance, especially at high levels of soil salinity and drought. Seed cotton yields in transgenic line were significantly higher than in wild-type plants. In conclusion, the data indicate that K2-NhaD transgenic lines have great potential for the production of stress-tolerant cotton under field conditions.

Dynamics of the Transcriptome Response to Heat in the Moss, Physcomitrella patens

Thermal stress negatively impacts crop yields, and as the overall temperature of the earth's atmosphere is gradually increasing, the identification of the temperature transduction pathway of the heat signal is essential in developing new strategies in order to adapt plant breeding to warmer climates. Heat stress damages the molecular structures and physiological processes in plants in proportion to the level and duration of the stress, which leads to different types of responses. In general, plants respond more efficiently when they are first subjected to a moderate temperature increase before being subjected to a higher temperature stress. This adaptive response is called the acclimation period and has been investigated in several plant species. However, there is a lack of information on the dynamic of the Heat Shock Response (HSR) over a continuous period of temperature rise without an acclimation period. In this paper, we investigated the effects of mild (30 °C) and high (37 °C) continuous heat stress over a 24-h period. Through RNA-Seq analysis, we assessed the remodeling of the transcriptome in the moss Physcomitrella patens. Our results showed that the 30 °C treatment particularly affected the expression of a few genes at 1 and 24 h, suggesting a biphasic response. Up-regulated genes at 1 h encode mainly HSR proteins (protein folding and endoplasmic reticulum stress), indicating an early heat response; while the up-regulated genes at 24 h belong to the thiamine biosynthesis pathway. In contrast, the genes involved in photosynthesis and carbon partitioning were repressed by this treatment. Under a higher temperature stress (37 °C), the induction of the HSR occurred rapidly (1 h) and was then attenuated throughout the time points investigated. A network approach (Weighted Gene Correlation Network Analysis, WGCNA) was used to identify the groups of genes expressing similar profiles, highlighting a HsfA1E binding motif within the promoters of some unrelated genes which displayed rapid and transient heat-activation. Therefore, it could be suggested that these genes could be direct targets of activation by a HsfA1E transcription factors.

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.

Different Families of Retrotransposons and DNA Transposons Are Actively Transcribed and May Have Transposed Recently in Physcomitrium (Physcomitrella) patens

Similarly to other plant genomes of similar size, more than half of the genome of P. patens is covered by Transposable Elements (TEs). However, the composition and distribution of P. patens TEs is quite peculiar, with Long Terminal Repeat (LTR)-retrotransposons, which form patches of TE-rich regions interleaved with gene-rich regions, accounting for the vast majority of the TE space. We have already shown that RLG1, the most abundant TE in P. patens, is expressed in non-stressed protonema tissue. Here we present a non-targeted analysis of the TE expression based on RNA-Seq data and confirmed by qRT-PCR analyses that shows that, at least four LTR-RTs (RLG1, RLG2, RLC4 and tRLC5) and one DNA transposon (PpTc2) are expressed in P. patens. These TEs are expressed during development or under stresses that P. patens frequently faces, such as dehydratation/rehydratation stresses, suggesting that TEs have ample possibilities to transpose during P. patens life cycle. Indeed, an analysis of the TE polymorphisms among four different P. patens accessions shows that different TE families have recently transposed in this species and have generated genetic variability that may have phenotypic consequences, as a fraction of the TE polymorphisms are within or close to genes. Among the transcribed and mobile TEs, tRLC5 is particularly interesting as it concentrates in a single position per chromosome that could coincide with the centromere, and its expression is specifically induced in young sporophyte, where meiosis takes place.

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.

Dissecting the Genomic Diversification of Late Embryogenesis Abundant (LEA) Protein Gene Families in Plants

Late embryogenesis abundant (LEA) proteins include eight multigene families that are expressed in response to water loss during seed maturation and in vegetative tissues of desiccation tolerant species. To elucidate LEA proteins evolution and diversification, we performed a comprehensive synteny and phylogenetic analyses of the eight gene families across 60 complete plant genomes. Our integrated comparative genomic approach revealed that synteny conservation and diversification contributed to LEA family expansion and functional diversification in plants. We provide examples that: 1) the genomic diversification of the Dehydrin family contributed to differential evolution of amino acid sequences, protein biochemical properties, and gene expression patterns, and led to the appearance of a novel functional motif in angiosperms; 2) ancient genomic diversification contributed to the evolution of distinct intrinsically disordered regions of LEA_1 proteins; 3) recurrent tandem-duplications contributed to the large expansion of LEA_2; and 4) dynamic synteny diversification played a role on the evolution of LEA_4 and its function on plant desiccation tolerance. Taken together, these results show that multiple evolutionary mechanisms have not only led to genomic diversification but also to structural and functional plasticity among LEA proteins which have jointly contributed to the adaptation of plants to water-limiting environments.

ABA-Induced Vegetative Diaspore Formation in Physcomitrella patens

The phytohormone abscisic acid (ABA) is a pivotal regulator of gene expression in response to various environmental stresses such as desiccation, salt and cold causing major changes in plant development and physiology. Here we show that in the moss Physcomitrella patens exogenous application of ABA triggers the formation of vegetative diaspores (brachycytes or brood cells) that enable plant survival in unfavorable environmental conditions. Such diaspores are round-shaped cells characterized by the loss of the central vacuole, due to an increased starch and lipid storage preparing these cells for growth upon suitable environmental conditions. To gain insights into the gene regulation underlying these developmental and physiological changes, we analyzed early transcriptome changes after 30, 60, and 180 min of ABA application and identified 1,030 differentially expressed genes. Among these, several groups can be linked to specific morphological and physiological changes during diaspore formation, such as genes involved in cell wall modifications. Furthermore, almost all members of ABA-dependent signaling and regulation were transcriptionally induced. Network analysis of transcription-associated genes revealed a large overlap of our study with ABA-dependent regulation in response to dehydration, cold stress, and UV-B light, indicating a fundamental function of ABA in diverse stress responses in moss. We also studied the evolutionary conservation of ABA-dependent regulation between moss and the seed plant Arabidopsis thaliana pointing to an early evolution of ABA-mediated stress adaptation during the conquest of the terrestrial habitat by plants.

Abscisic acid, cold and salt stimulate conserved metabolic regulation in the moss Physcomitrella patens

Salt and cold are major abiotic stresses that have adverse effects on plant growth and development. To cope with these stresses and their detrimental effects plants have evolved several metabolic, biochemical and physiological processes that are mainly triggered and mediated by the plant hormone abscisic acid (ABA). To elucidate the metabolic responses of the moss Physcomitrella patens, which serves as a model plant for abiotic stress adaptation, we performed GC-MS-based metabolic profiling of plants challenged for 5 and 28 h with either salt, cold or ABA. Our results indicate significant changes in the accumulation of several sugars including maltose, isomaltose and trehalose, amino acids including arginine, histidine, ornithine, tryptophan and tyrosine, and organic acids mainly citric acid and malonic acid. The metabolic responses provoked by ABA, cold and salt show considerable similarities. The accumulation of certain metabolites positively correlates with gene expression data whereas some metabolites do not show correlation with cognate transcript abundance. To place our results into an evolutionary context we compared the ABA- and stress-induced metabolic changes in moss to available metabolic profiles of the seed plant Arabidopsis thaliana. We detected considerable conservation between the species, indicating early evolution of stress-associated metabolic adaptations that probably occurred at the plant water-to-land transition.

Overexpression of Arabidopsis ubiquitin ligase AtPUB46 enhances tolerance to drought and oxidative stress

The U-Box E3 ubiquitin ligase, AtPUB46, functions in the drought response: T-DNA insertion mutants of this single paralogous gene are hypersensitive to water- and oxidative stress (Adler et al. BMC Plant Biology 17:8, 2017). Here we analyze the phenotype of AtPUB46 overexpressing (OE) plants. AtPUB46-OE show increased tolerance to water stress and have smaller leaf blades and reduced stomatal pore area and stomatal index compared with wild type (WT). Despite this, the rate of water loss from detached rosettes is similar in AtPUB46-OE and WT plants. Germination of AtPUB46-OE seeds was less sensitive to salt than WT whereas seedling greening was more sensitive. We observed a complex response to oxidative stress applied by different agents: AtPUB46-OE plants were hypersensitive to H₂O₂ but hyposensitive to methyl viologen. AtPUB46-GFP fusion protein is cytoplasmic, however, in response to H₂O₂ a considerable proportion translocates to the nucleus. We conclude that the differential stress phenotype of the AtPUB46-OE does not result from its smaller leaf size but from a change in the activity of a stress pathway(s) regulated by a degradation substrate of the AtPUB46 E3 and also from a reduction in stomatal pore size and index.

Conserved and differential transcriptional responses of peroxisome associated pathways to drought, dehydration and ABA

Plant peroxisomes are important components of cellular antioxidant networks, dealing with ROS generated by multiple metabolic pathways. Peroxisomes respond to environmental and cellular conditions by changing their size, number, and proteomic content. To investigate the role of peroxisomes in response to drought, dehydration and ABA treatment we took an evolutionary and comparative genomics approach. Colonisation of land required evolution of dehydration tolerance in the absence of subsequent anatomical adaptations. Therefore, the model bryophyte Physcomitrella patens, the model dicot Arabidopsis thaliana and wheat (Tricitcum aestivum), a globally important cereal crop were compared. Three sets of genes namely 'PTS1 genes' (a proxy for genes encoding peroxisome targeted proteins), PEX genes (involved in peroxisome biogenesis) and genes involved in plant antioxidant networks were identified in all 3 species and their expression compared under drought (dehydration) and ABA treatment. Genes encoding enzymes of β-oxidation and gluconeogenesis, antioxidant enzymes including catalase and glutathione reductase and PEX3 and PEX11 isoforms showed conserved up-regulation, and peroxisome proliferation was induced by ABA in moss. Interestingly, expression of some of these genes differed between drought sensitive and resistant genotypes of wheat in line with measured photosynthetic and biochemical differences. These results point to an underappreciated role for peroxisomes in drought response.

Phosphoproteomic profiling reveals ABA-responsive phosphosignaling pathways in Physcomitrella patens

Abscisic acid (ABA) and its signaling system are important for land plants to survive in terrestrial conditions. Here, we took a phosphoproteomic approach to elucidate the ABA signaling network in Physcomitrella patens, a model species of basal land plants. Our phosphoproteomic analysis detected 4630 phosphopeptides from wild-type P. patens and two ABA-responsive mutants, a disruptant of group-A type-2C protein phosphatase (PP2C; ppabi1a/b) and AR7, a defective mutant in ARK, identified as an upstream regulator of SnRK2. Quantitative analysis detected 143 ABA-responsive phosphopeptides in P. patens. The analysis indicated that SnRK2-mediated phosphorylation and target motifs were partially conserved in bryophytes. Our data demonstrate that the PpSnRK2B and AREB/ABF-type transcription factors are phosphorylated in vivo in response to ABA under the control of ARK. On the other hand, our data also revealed the following: (i) the entire ABA-responsive phosphoproteome in P. patens is quite diverse; (ii) P. patens PP2C affects additional pathways other than the known ABA signaling pathway; and (iii) ARK is mainly involved in ABA signaling. Taken together, we propose that the core ABA signaling pathway is essential in all land plants; however, some ABA-responsive phosphosignaling uniquely developed in bryophytes during the evolutionary process.

Embryophyte stress signaling evolved in the algal progenitors of land plants

The evolution of land plants from algae is an age-old question in biology. The entire terrestrial flora stems from a grade of algae, the streptophyte algae. Recent phylogenomic studies have pinpointed the Zygnematophyceae as the modern-day streptophyte algal lineage that is most closely related to the algal land plant ancestor. Here, we provide insight into the biology of this ancestor that might have aided in its conquest of land. Specifically, we uncover the existence of stress-signaling pathways and the potential for intimate plastid-nucleus communication. Plastids act as environmental sensors in land plants; our data suggest that this feature was present in a common ancestor they shared with streptophyte algae.

Streptophytes are unique among photosynthetic eukaryotes in having conquered land. As the ancestors of land plants, streptophyte algae are hypothesized to have possessed exaptations to the environmental stressors encountered during the transition to terrestrial life. Many of these stressors, including high irradiance and drought, are linked to plastid biology. We have investigated global gene expression patterns across all six major streptophyte algal lineages, analyzing a total of around 46,000 genes assembled from a little more than 1.64 billion sequence reads from six organisms under three growth conditions. Our results show that streptophyte algae respond to cold and high light stress via expression of hallmark genes used by land plants (embryophytes) during stress–response signaling and downstream responses. Among the strongest differentially regulated genes were those associated with plastid biology. We observed that among streptophyte algae, those most closely related to land plants, especially Zygnema, invest the largest fraction of their transcriptional budget in plastid-targeted proteins and possess an array of land plant-type plastid-nucleus communication genes. Streptophyte algae more closely related to land plants also appear most similar to land plants in their capacity to respond to plastid stressors. Support for this notion comes from the detection of a canonical abscisic acid receptor of the PYRABACTIN RESISTANCE (PYR/PYL/RCAR) family in Zygnema, the first found outside the land plant lineage. We conclude that a fine-tuned response toward terrestrial plastid stressors was among the exaptations that allowed streptophytes to colonize the terrestrial habitat on a global scale.

Transcriptome profiling during mangrove viviparity in response to abscisic acid

Mangrove plants adapt to coastal tidal mudflats with specially evolved viviparity seed development. However, very little is known about the genetic and molecular mechanisms of mangrove viviparity. Here, we tested a hypothesis that plant hormone abscisic acid (ABA) plays a significant role in precocious germination of viviparous Kandelia obovata seeds by exogenous applications. Through transcriptome analysis of ABA treated seeds, it was found that ABA repressed mangrove fruit growth and development, and there were thousands of genes differentially expressed. As a result, dynamics of the pathways were dramatically altered. In particular, "Plant hormone signal transduction" and "MAPK signaling pathway" were represented significantly. Among differentially expressed genes, some key genes of ABA signal transduction were induced, while ABA biosynthesis genes were repressed. Take ABI1 and ABI2, key negative regulators in ABA signal pathway, as examples, homologous alignment and a phylogenetic tree in various species showed that ABI1 and ABI2 are highly conserved among various species. The functional similarity of these genes was confirmed by transgenic work in Arabidopsis. Taken together, ABA inhibited mangrove viviparity, but mangroves developed a mechanism to prevent accidently increase of ABA in the harsh environment for maintaining viviparous reproductive strategy.

Genome-wide analysis and expression profiles of NTMC2 family genes in Oryza sativa

N-terminal-TM-C2 domain proteins (NTMC2), which share domain architecture and sequence similarity to synaptotagmins (Syts) in mammals and FAM62 (extended Syts) in metazoans, form a small gene family in plants. Previous studies showed that the Arabidopsis thaliana NTMC2 type 1.1 protein (NTMC2T1.1, named AtSyt1) possesses calcium- and membrane-binding activities that allow it to function in a plasma membrane repair pathway induced by stress. However, we lack understanding of the diverse biological roles of plant NTMC2 family genes. In this study, a total of 13 OsNTMC2 genes was identified through a comprehensive bioinformatics analysis of the rice (Oryza sativa L.) genome and classified into six OsNTMC2 groups (OsNTMC2T1 to OsNTMC2T6) based on phylogeny and motif constitution. OsNTMC2T1 to OsNTMC2T3 have two calcium-binding domains (C2A and C2B), but OsNTMC2T4 to OsNTMC2T6 have single C2 domain. The expression profiles of OsNTMC2 genes were analysed at different stages of vegetative and reproductive development. This analysis revealed that at least one OsNTMC2 gene was abundantly expressed at each stage of development. These results should facilitate research on this gene family and provide new insights elucidating their functions in higher plants.

A novel family of transcription factors conserved in angiosperms is required for ABA signalling

The plant hormone abscisic acid (ABA) plays a crucial role in regulating plant responses to environmental stresses. Interplay of several different proteins including the PYR/PYL/RCAR receptors, A-group PP2C protein phosphatases, SnRK2 protein kinases, and downstream transcription factors regulates ABA signalling. We report here the identification of a family of ABA-induced transcription repressors (AITRs) that act as feedback regulators in ABA signalling. We found that the expression of all the 6 Arabidopsis AITR genes was induced by exogenously ABA, and their expression levels were decreased in ABA biosynthesis mutant aba1-5. BLAST searches showed that AITRs are exclusively present in angiosperms. When recruited to the promoter region of a reporter gene by a fused DNA binding domain, all AITRs inhibited reporter gene expression in transfected protoplasts. In Arabidopsis, aitr mutants showed reduced sensitivity to ABA and to stresses such as salt and drought. Quantitative RT-PCR analysis demonstrated that the ABA-induced response of PP2C and some PYR/PYL/RCAR genes was reduced in AITR5 transgenic plants but increased in an aitr2 aitr5 aitr6 triple mutant. These results provide important new insights into the regulation of ABA signalling in plants, and such information may lead to the production of plants with enhanced resistance to environmental stresses.

Surviving a Dry Future: Abscisic Acid (ABA)-Mediated Plant Mechanisms for Conserving Water under Low Humidity

Angiosperms are able to respond rapidly to the first sign of dry conditions, a decrease in air humidity, more accurately described as an increase in the vapor pressure deficit between the leaf and the atmosphere (VPD), by abscisic acid (ABA)-mediated stomatal closure. The genes underlying this response offer valuable candidates for targeted selection of crop varieties with improved drought tolerance, a critical goal for current plant breeding programs, to maximize crop production in drier and increasingly marginalized environments, and meet the demands of a growing population in the face of a changing climate. Here, we review current understanding of the genetic mechanisms underpinning ABA-mediated stomatal closure, a key means for conserving water under dry conditions, examine how these mechanisms evolved, and discuss what remains to be investigated.

Desiccation tolerance in bryophytes: The dehydration and rehydration transcriptomes in the desiccation-tolerant bryophyte Bryum argenteum

The desiccation tolerant bryophyte Bryum argenteum is an important component of desert biological soil crusts (BSCs) and is emerging as a model system for studying vegetative desiccation tolerance. Here we present and analyze the hydration-dehydration-rehydration transcriptomes in B. argenteum to establish a desiccation-tolerance transcriptomic atlas. B. argenteum gametophores representing five different hydration stages (hydrated (H0), dehydrated for 2 h (D2), 24 h (D24), then rehydrated for 2 h (R2) and 48 h (R48)), were sampled for transcriptome analyses. Illumina high throughput RNA-Seq technology was employed and generated more than 488.46 million reads. An in-house de novo transcriptome assembly optimization pipeline based on Trinity assembler was developed to obtain a reference Hydration-Dehydration-Rehydration (H-D-R) transcriptome comprising of 76,206 transcripts, with an N50 of 2,016 bp and average length of 1,222 bp. Comprehensive transcription factor (TF) annotation discovered 978 TFs in 62 families, among which 404 TFs within 40 families were differentially expressed upon dehydration-rehydration. Pfam term enrichment analysis revealed 172 protein families/domains were significantly associated with the H-D-R cycle and confirmed early rehydration (i.e. the R2 stage) as exhibiting the maximum stress-induced changes in gene expression.

Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens: introducing the ecotype Reute

Rich ecotype collections are used for several plant models to unravel the molecular causes of phenotypic differences, and to investigate the effects of environmental adaption and acclimation. For the model moss Physcomitrella patens collections of accessions are available, and have been used for phylogenetic and taxonomic studies, for example, but few have been investigated further for phenotypic differences. Here, we focus on the Reute accession and provide expression profiling and comparative developmental data for several stages of sporophyte development, as well as information on genetic variation via genomic sequencing. We analysed cross-technology and cross-laboratory data to define a confident set of 15 mature sporophyte-specific genes. We find that the standard laboratory strain Gransden produces fewer sporophytes than Reute or Villersexel, although gametangia develop with the same time course and do not show evident morphological differences. Reute exhibits less genetic variation relative to Gransden than Villersexel, yet we found variation between Gransden and Reute in the expression profiles of several genes, as well as variation hot spots and genes that appear to evolve under positive Darwinian selection. We analyzed expression differences between the ecotypes for selected candidate genes in the GRAS transcription factor family, the chalcone synthase family and in genes involved in cell wall modification that are potentially related to phenotypic differences. We confirm that Reute is a P. patens ecotype, and suggest its use for reverse-genetics studies that involve progression through the life cycle and multiple generations.

What are the evolutionary origins of stomatal responses to abscisic acid in land plants?

The evolution of active stomatal closure in response to leaf water deficit, mediated by the hormone abscisic acid (ABA), has been the subject of recent debate. Two different models for the timing of the evolution of this response recur in the literature. A single-step model for stomatal control suggests that stomata evolved active, ABA-mediated control of stomatal aperture, when these structures first appeared, prior to the divergence of bryophyte and vascular plant lineages. In contrast, a gradualistic model for stomatal control proposes that the most basal vascular plant stomata responded passively to changes in leaf water status. This model suggests that active ABA-driven mechanisms for stomatal responses to water status instead evolved after the divergence of seed plants, culminating in the complex, ABA-mediated responses observed in modern angiosperms. Here we review the findings that form the basis for these two models, including recent work that provides critical molecular insights into resolving this intriguing debate, and find strong evidence to support a gradualistic model for stomatal evolution.

Molecular Evolution of Grass Stomata

Grasses began to diversify in the late Cretaceous Period and now dominate more than one third of global land area, including three-quarters of agricultural land. We hypothesize that their success is likely attributed to the evolution of highly responsive stomata capable of maximizing productivity in rapidly changing environments. Grass stomata harness the active turgor control mechanisms present in stomata of more ancient plant lineages, maximizing several morphological and developmental features to ensure rapid responses to environmental inputs. The evolutionary development of grass stomata appears to have been a gradual progression. Therefore, understanding the complex structures, developmental events, regulatory networks, and combinations of ion transporters necessary to drive rapid stomatal movement may inform future efforts towards breeding new crop varieties.

The evolution of the role of ABA in the regulation of water-use efficiency: From biochemical mechanisms to stomatal conductance

Abscisic acid is found in a wide variety of organisms. In the plant kingdom, ABA's role in mediating responses to abiotic stress has been conserved and enhanced throughout evolution. The emergence of plants to terrestrial environments required the development of mechanisms to cope with ongoing and severe abiotic stress such as drought and rapid changes in humidity and temperature. The common understanding is that terrestrial plants evolved strategies ranging from desiccation-tolerance mechanisms (mosses) to drought tolerance (CAM plants), to better exploit different ecological niches. In between these divergent water regulation strategies, ABA plays a significant role in managing plants' adaptation to new environments by optimizing water-use efficiency (WUE) under particular environmental conditions. ABA plays some very different roles in the regulation of WUE. ABA's role in the regulation of guard cells and transpiration has yielded a wide variety of WUE-regulation mechanisms, ranging from no sensitivity (ferns) to low sensitivity (anisohydric behavior) to hypersensitivity to ABA (isohydric behavior and putatively CAM plants). ABA also plays a role in the regulation of non-stomatal, biochemical mechanisms of WUE regulation. In angiosperms, this includes the control of osmotic adjustment and morphological changes, including changes in leaf size, stomatal density, stomatal size and root development. Under severe stress, ABA also appears to initiate leaf senescence via transcriptional regulation, to directly inhibit photosynthesis.

The Transcriptional Response to DNA-Double-Strand Breaks in Physcomitrella patens

The model bryophyte Physcomitrella patens is unique among plants in supporting the generation of mutant alleles by facile homologous recombination-mediated gene targeting (GT). Reasoning that targeted transgene integration occurs through the capture of transforming DNA by the homology-dependent pathway for DNA double-strand break (DNA-DSB) repair, we analysed the genome-wide transcriptomic response to bleomycin-induced DNA damage and generated mutants in candidate DNA repair genes. Massively parallel (Illumina) cDNA sequencing identified potential participants in gene targeting. Transcripts encoding DNA repair proteins active in multiple repair pathways were significantly up-regulated. These included Rad51, CtIP, DNA ligase 1, Replication protein A and ATR in homology-dependent repair, Xrcc4, DNA ligase 4, Ku70 and Ku80 in non-homologous end-joining and Rad1, Tebichi/polymerase theta, PARP in microhomology-mediated end-joining. Differentially regulated cell-cycle components included up-regulated Rad9 and Hus1 DNA-damage-related checkpoint proteins and down-regulated D-type cyclins and B-type CDKs, commensurate with the imposition of a checkpoint at G2 of the cell cycle characteristic of homology-dependent DNA-DSB repair. Candidate genes, including ATP-dependent chromatin remodelling helicases associated with repair and recombination, were knocked out and analysed for growth defects, hypersensitivity to DNA damage and reduced GT efficiency. Targeted knockout of PpCtIP, a cell-cycle activated mediator of homology-dependent DSB resection, resulted in bleomycin-hypersensitivity and greatly reduced GT efficiency.

The decision to germinate is regulated by divergent molecular networks in spores and seeds

Dispersal is a key step in land plant life cycles, usually via formation of spores or seeds. Regulation of spore- or seed-germination allows control over the timing of transition from one generation to the next, enabling plant dispersal. A combination of environmental and genetic factors determines when seed germination occurs. Endogenous hormones mediate this decision in response to the environment. Less is known about how spore germination is controlled in earlier-evolving nonseed plants. Here, we present an in-depth analysis of the environmental and hormonal regulation of spore germination in the model bryophyte Physcomitrella patens (Aphanoregma patens). Our data suggest that the environmental signals regulating germination are conserved, but also that downstream hormone integration pathways mediating these responses in seeds were acquired after the evolution of the bryophyte lineage. Moreover, the role of abscisic acid and diterpenes (gibberellins) in germination assumed much greater importance as land plant evolution progressed. We conclude that the endogenous hormone signalling networks mediating germination in response to the environment may have evolved independently in spores and seeds. This paves the way for future research about how the mechanisms of plant dispersal on land evolved.

An ancient and conserved function for Armadillo-related proteins in the control of spore and seed germination by abscisic acid

Armadillo-related proteins regulate development throughout eukaryotic kingdoms. In the flowering plant Arabidopsis thaliana, Armadillo-related ARABIDILLO proteins promote multicellular root branching. ARABIDILLO homologues exist throughout land plants, including early-diverging species lacking true roots, suggesting that early-evolving ARABIDILLOs had additional biological roles. Here we investigated, using molecular genetics, the conservation and diversification of ARABIDILLO protein function in plants separated by c. 450 million years of evolution. We demonstrate that ARABIDILLO homologues in the moss Physcomitrella patens regulate a previously undiscovered inhibitory effect of abscisic acid (ABA) on spore germination. Furthermore, we show that A. thaliana ARABIDILLOs function similarly during seed germination. Early-diverging ARABIDILLO homologues from both P. patens and the lycophyte Selaginella moellendorffii can substitute for ARABIDILLO function during A. thaliana root development and seed germination. We conclude that (1) ABA was co-opted early in plant evolution to regulate functionally analogous processes in spore- and seed-producing plants and (2) plant ARABIDILLO germination functions were co-opted early into both gametophyte and sporophyte, with a specific rooting function evolving later in the land plant lineage.

The mitochondrial proteome of the moss Physcomitrella patens

Extant basal land plants are routinely used to trace plant evolution and to track strategies for high abiotic stress resistance. Whereas the structure of mitochondrial genomes and RNA editing are already well studied, mitochondrial proteome research is restricted to a few data sets. While the mitochondrial proteome of the model moss Physcomitrella patens is covered to an estimated 15-25% by proteomic evidence to date, the available data have already provided insights into the evolution of metabolic compartmentation, dual targeting and mitochondrial heterogeneity. This review summarizes the current knowledge about the mitochondrial proteome of P. patens, and gives a perspective on its use as a mitochondrial model system. Its amenability to gene editing, metabolic labelling as well as fluorescence microscopy provides a unique platform to study open questions in mitochondrial biology, such as regulation of protein stability, responses to stress and connectivity to other organelles. Future challenges will include improving the proteomic resources for P. patens, and to link protein inventories and modifications as well as evolutionary differences to the functional level.