A Membrane-Bound NAC-Like Transcription Factor OsNTL5 Represses the Flowering in Oryza sativa

Stress-induced nuclear translocation of ONAC023 improves drought and heat tolerance through multiple processes in rice

Drought and heat are major abiotic stresses frequently coinciding to threaten rice production. Despite hundreds of stress-related genes being identified, only a few have been confirmed to confer resistance to multiple stresses in crops. Here we report ONAC023, a hub stress regulator that integrates the regulations of both drought and heat tolerance in rice. ONAC023 positively regulates drought and heat tolerance at both seedling and reproductive stages. Notably, the functioning of ONAC023 is obliterated without stress treatment and can be triggered by drought and heat stresses at two layers. The expression of ONAC023 is induced in response to stress stimuli. We show that overexpressed ONAC23 is translocated to the nucleus under stress and evidence from protoplasts suggests that the dephosphorylation of the remorin protein OSREM1.5 can promote this translocation. Under drought or heat stress, the nuclear ONAC023 can target and promote the expression of diverse genes, such as OsPIP2;7, PGL3, OsFKBP20-1b, and OsSF3B1, which are involved in various processes including water transport, reactive oxygen species homeostasis, and alternative splicing. These results manifest that ONAC023 is fine-tuned to positively regulate drought and heat tolerance through the integration of multiple stress-responsive processes. Our findings provide not only an underlying connection between drought and heat responses, but also a promising candidate for engineering multi-stress-resilient rice.

Advances in membrane-tethered NAC transcription factors in plants

Transcription factors are central components in cell signal transduction networks and are critical regulators for gene expression. It is estimated that approximately 10% of all transcription factors are membrane-tethered. MTFs (membrane-bound transcription factors) are latent transcription factors that are inherently anchored in the cellular membrane in a dormant form. When plants encounter environmental stimuli, they will be released from the membrane by intramembrane proteases or by the ubiquitin proteasome pathway and then were translocated to the nucleus. The capacity to instantly activate dormant transcription factors is a critical strategy for modulating diverse cellular functions in response to external or internal signals, which provides an important transcriptional regulatory network in response to sudden stimulus and improves plant survival. NTLs (NTM1-like) are a small subset of NAC (NAM, ATAF1/2, CUC2) transcription factors, which contain a conserved NAC domain at the N-terminus and a transmembrane domain at the C-terminus. In the past two decades, several NTLs have been identified from several species, and most of them are involved in both development and stress response. In this review, we review the reports and findings on NTLs in plants and highlight the mechanism of their nuclear import as well as their functions in regulating plant growth and stress response.

Isolation, Characterization, and Expression Analysis of NAC Transcription Factor from Andrographis paniculata (Burm. f.) Nees and Their Role in Andrographolide Production

Andrographis paniculata (Burm. f.) Nees is an important medicinal plant known for its bioactive compound andrographolide. NAC transcription factors (NAM, ATAF1/2, and CUC2) play a crucial role in secondary metabolite production, stress responses, and plant development through hormonal signaling. In this study, a putative partial transcript of three NAC family genes (ApNAC83, ApNAC21 22 and ApNAC02) was used to isolate full length genes using RACE. Bioinformatics analyses such as protein structure prediction, cis-acting regulatory elements, and gene ontology analysis were performed. Based on in silico predictions, the diterpenoid profiling of the plant's leaves (five-week-old) and the real-time PCR-based expression analysis of isolated NAC genes under abscisic acid (ABA) treatment were performed. Additionally, the expression analysis of isolated NAC genes under MeJA treatment and transient expression in Nicotiana tabacum was performed. Full-length sequences of three members of the NAC transcription factor family, ApNAC83 (1102 bp), ApNAC21 22 (996 bp), and ApNAC02 (1011 bp), were isolated and subjected to the promoter and gene ontology analysis, which indicated their role in transcriptional regulation, DNA binding, ABA-activated signaling, and stress management. It was observed that ABA treatment leads to a higher accumulation of andrographolide and 14-deoxyandrographolide content, along with the upregulation of ApNAC02 (9.6-fold) and the downregulation of ApNAC83 and ApNAC21 22 in the leaves. With methyl jasmonate treatment, ApNAC21 22 expression decreased, while ApNAC02 increased (1.9-fold), with no significant change being observed in ApNAC83. The transient expression of the isolated NAC genes in a heterologous system (Nicotiana benthamiana) demonstrated their functional transcriptional activity, leading to the upregulation of the NtHMGR gene, which is related to the terpene pathway in tobacco. The expression analysis and heterologous expression of ApNAC21 22 and ApNAC02 indicated their role in andrographolide biosynthesis.

Functional characterization of GhNAC2 promoter conferring hormone- and stress-induced expression: a potential tool to improve growth and stress tolerance in cotton

The GhNAC2 transcription factor identified from G. herbaceum improves root growth and drought tolerance through transcriptional reprogramming of phytohormone signaling. The promoter of such a versatile gene could serve as an important genetic engineering tool for biotechnological application. In this study, we identified and characterized the promoter of GhNAC2 to understand its regulatory mechanism. GhNAC2 transcription factor increased in root tissues in response to GA, ethylene, auxin, ABA, mannitol, and NaCl. In silico analysis revealed an overrepresentation of cis-regulatory elements associated with hormone signaling, stress responses and root-, pollen-, and seed-specific promoter activity. To validate their role in GhNAC2 function/regulation, an 870-bp upstream regulatory sequence was fused with the GUS reporter gene (uidA) and expressed in Arabidopsis and cotton hairy roots for in planta characterization. Histochemical GUS staining indicated localized expression in root tips, root elongation zone, root primordia, and reproductive tissues under optimal growth conditions. Mannitol, NaCl, auxin, GA, and ABA, induced the promoter-driven GUS expression in all tissues while ethylene suppressed the promoter activity. The results show that the 870 nt fragment of the GhNAC2 promoter drives root-preferential expression and responds to phytohormonal and stress signals. In corroboration with promoter regulation, GA and ethylene pathways differentially regulated root growth in GhNAC2-expressing Arabidopsis. The findings suggest that differential promoter activity governs the expression of GhNAC2 in root growth and stress-related functions independently through specific promoter elements. This multifarious promoter can be utilized to develop yield and climate resilience in cotton by expanding the options to control gene regulation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01411-2.

Flowering repressor CmSVP recruits the TOPLESS corepressor to control flowering in chrysanthemum

Plant flowering time is induced by environmental and endogenous signals perceived by the plant. The MCM1-AGAMOUSDEFICIENS-Serum Response Factor-box (MADS-box) protein SHORT VEGETATIVE PHASE (SVP) is a pivotal repressor that negatively regulates the floral transition during the vegetative phase; however, the transcriptional regulatory mechanism remains poorly understood. Here, we report that CmSVP, a chrysanthemum (Chrysanthemum morifolium Ramat.) homolog of SVP, can repress the expression of a key flowering gene, a chrysanthemum FLOWERING LOCUS T-like gene (CmFTL3), by binding its promoter CArG element to delay flowering in the ambient temperature pathway in chrysanthemum. Protein-protein interaction assays identified an interaction between CmSVP and CmTPL1-2, a chrysanthemum homologue of TOPLESS (TPL) that plays critical roles as transcriptional corepressor in many aspects of plant life. Genetic analyses revealed the CmSVP-CmTPL1-2 transcriptional complex is a prerequisite for CmSVP to act as a floral repressor. Furthermore, overexpression of CmSVP rescued the phenotype of the svp-31 mutant in Arabidopsis (Arabidopsis thaliana), overexpression of AtSVP or CmSVP in the Arabidopsis dominant-negative mutation tpl-1 led to ineffective late flowering, and AtSVP interacted with AtTPL, confirming the conserved function of SVP in chrysanthemum and Arabidopsis. We have validated a conserved machinery wherein SVP partially relies on TPL to inhibit flowering via a thermosensory pathway.

Genome-wide identification and molecular evolution of NAC gene family in Dendrobium nobile

NAC transcription factors are an important genes that regulate plant growth and development, and can regulate functions such as fruit ripening in plants. Based on genome data of Dendrobium nobile, the NAC gene family was identified and analyzed by bioinformatics methods. In this study, we identified 85 NAC genes in Dendrobium nobile genome, and systematically analyzed the NAC gene family. We found that they were distributed unevenly in the nineteen chromosomes. The amino acid length of D. nobile NAC gene family (DnoNACs) ranged from 80 to 1065, molecular weight ranged from 22.17 to 119.02 kD, and isoelectric point ranged from 4.61~9.26. Its promoter region contains multiple stress responsive elements, including light responsive, gibberellin-responsive, abscisic acid responsiveness, MeJA-responsiveness and drought-inducibility elements. Phylogenetic analysis indicates that the D. nobile NAC gene family is most closely related to Dendrobium catenatum and Dendrobium chrysotoxum. Analysis of SSR loci indicates that the fraction of mononucleotide repeats was the largest, as was the frequency of A/T. Non-coding RNA analysis showed that these 85 NAC genes contain 397 miRNAs. The collinearity analysis shows that 9 collinear locis were found on the chromosomes of D. nobile with Arabidopsis thaliana, and 75 collinear locis with D.chrysotoxum. QRT-PCR experiment under different salt concentration and temperature conditions verified the response mechanism of DnoNAC gene family under stress conditions. Most DnoNAC genes are sensitive to salt stress and temperature stress. The results of this study provide a reference for further understanding the function of NAC gene in D. nobile.

Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field

Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6% to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly.

Understanding Transcription Factors and How They Affect Processes in Cucumber Sex Determination

Plant reproduction is a fundamental process on Earth from the perspective of biodiversity, biomass gain, and crop productivity. It is therefore important to understand the sex determination process, and many researchers are investigating the molecular basis of this phenomenon. However, information on the influence of transcription factors (TFs), genes that encode DNA-binding proteins, on this process is limited, although cucumber is a model plant in this regard. In the present study, based on RNA-seq data for differentially expressed genes (DEGs), we aimed to investigate the regulatory TFs that may influence the metabolic processes in the shoot apex containing the forming flower buds. Therefore, the annotation of the genome of the B10 cucumber line was supplemented with the assigned families of transcription factors. By performing ontology analyses of the DEGs, the processes they participate in were identified, and TFs were located among the results. In addition, TFs that have significantly overrepresented targets among DEGs were detected, and sex-specific interactome network maps were generated, indicating the regulatory TFs based on their effects on DEGs and furthermore, on the processes leading to the formation of different-sex flowers. Among the most overrepresented TF families in the sex comparisons were the NAC, bHLH, MYB, and bZIP families. An interaction network analysis indicated the most abundant families among DEGs' regulatory TFs were MYB, AP2/ERF, NAC, and bZIP, and those with the most significant impact on developmental processes were identified, namely the AP/ERF family, followed by DOF, MYB, MADS, and others. Thus, the networks' central nodes and key regulators were identified with respect to male, female, and hermaphrodite forms. Here, we proposed the first model of the regulatory network of TFs that influences the metabolism of sex development in cucumber. These findings may help us to understand the molecular genetics and functional mechanisms underlying sex determination processes.

UDP-glucose epimerase 1, moonlighting as a transcriptional activator, is essential for tapetum degradation and male fertility in rice

Multiple enzymes perform moonlighting functions distinct from their main roles. UDP-glucose epimerases (UGEs), a subclass of isomerases, catalyze the interconversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal). We identified a rice male-sterile mutant, osuge1, with delayed tapetum degradation and abortive pollen. The mutant osuge1 protein lacked UDP-glucose epimerase activity, resulting in higher UDP-Gal content and lower UDP-Glc levels in the osuge1 mutant compared with the wild type. Interestingly, we discovered that OsUGE1 participates in the TIP2/bHLH142-TDR-EAT1/DTD transcriptional regulatory cascade involved in tapetum degradation, in which TIP2 and TDR regulate the expression of OsUGE1 while OsUGE1 regulates the expression of EAT1. In addition, we found that OsUGE1 regulates the expression of its own gene by directly binding to an E-box element in the OsUGE1 promoter. Collectively, our results indicate that OsUGE1 not only functions as a UDP-glucose epimerase but also moonlights as a transcriptional activator to promote tapetum degradation, revealing a novel regulatory mechanism of rice reproductive development.

POLLEN WALL ABORTION 1 is essential for pollen wall development in rice

The integrity of pollen wall structures is essential for pollen development and maturity in rice (Oryza sativa L.). In this study, we isolated and characterized the rice male-sterile mutant pollen wall abortion 1 (pwa1), which exhibits a defective pollen wall (DPW) structure and has sterile pollen. Map-based cloning, genetic complementation, and gene knockout experiments revealed that PWA1 corresponds to the gene LOC_Os01g55094 encoding a coiled-coil domain-containing protein. PWA1 localized to the nucleus, and PWA1 was expressed in the tapetum and microspores. PWA1 interacted with the transcription factor TAPETUM DEGENERATION RETARDATION (TDR)-INTERACTING PROTEIN2 (TIP2, also named bHLH142) in vivo and in vitro. The tip2-1 mutant, which we obtained by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated gene editing, showed delayed tapetum degradation, sterile pollen, and DPWs. We determined that TIP2/bHLH142 regulates PWA1 expression by binding to its promoter. Analysis of the phenotype of the tip2-1 pwa1 double mutant indicated that TIP2/bHLH142 functions upstream of PWA1. Further studies suggested that PWA1 has transcriptional activation activity and participates in pollen intine development through the β-glucosidase Os12BGlu38. Therefore, we identified a sterility factor, PWA1, and uncovered a regulatory network underlying the formation of the pollen wall and mature pollen in rice.

Transcriptome Analysis of Lycoris chinensis Bulbs Reveals Flowering in the Age-Mediated Pathway

Lycoris is a summer bulbous flower that commonly needs to go through a long period of vegetative growth for 3 to 5 years before flowering. Plant flowering is regulated by a complex genetic network. Compared with most perennial flowers, knowledge on the molecular mechanism responsible for floral transition in bulbous flowers is lacking, and only a few genes that regulate flowering have been identified with few reports on the floral transition in Lycoris. In this study, we identified many differentially expressed genes (DEGs) and transcription factors (TFs) by RNA-Seq in L. chinensis bulbs of different ages, including one- to four-year-old nonflowering bulbs and four-year-old flowering bulbs. Some DEGs were enriched in Gene Ontology (GO) terms between the three- and four-year-old bulbs, and there most genes were enriched in terms of metabolic process and catalytic activity. In the four-year old bulbs, most of the DEGs that may be involved in flowering were classified under the GO term biological process, which was a totally different result from the vegetative bulbs. Some DEGs between flowering and nonflowering bulbs were enriched in plant hormone signal transduction, including the hormones auxin, cytokinin, abscisic acid, and ethylene, but no DEGs were enriched in the gibberellin pathway. Auxin is the main endogenous phytohormone involved in bulb growth and development, but cytokinin, abscisic acid, and ethylene were shown to increase in flowering bulbs. In addition, energy-metabolism-related genes maintain a high expression level in large bulbs, and some positive regulators (SPL, COL, and AP1) and early flowering genes were also shown to be highly expressed in the meristems of flowering bulbs. It suggested that sugar molecules may be the energy source that regulates the signal transduction of flowering by connecting with phytohormone signaling in Lycoris. A total of 1911 TFs were identified and classified into 89 categories, where the top six families with the largest gene numbers were C2H2, NAC, AP2/ERF-ERF, C3H, MYB-related, and WRKY. Most DEGs were in the AP2/ERF-ERF family, and most of them were downregulated in 4-year-old flowering bulbs. A number of families were reported to be involved in plant flowering, including NAC, AP2/ERF, MYB, WRKY, bZIP, MADS, and NF-Y. These results can act as a genetic resource to aid in the explanation of the genetic mechanism responsible for the flowering of Lycoris and other bulbous flowers.

Proteolytic Activation of Plant Membrane-Bound Transcription Factors

Due to the presence of a transmembrane domain, the subcellular mobility plan of membrane-bound or membrane-tethered transcription factors (MB-TFs) differs from that of their cytosolic counterparts. The MB-TFs are mostly locked in (sub)cellular membranes, until they are released by a proteolytic cleavage event or when the transmembrane domain (TMD) is omitted from the transcript due to alternative splicing. Here, we review the current knowledge on the proteolytic activation mechanisms of MB-TFs in plants, with a particular focus on regulated intramembrane proteolysis (RIP), and discuss the analogy with the proteolytic cleavage of MB-TFs in animal systems. We present a comprehensive inventory of all known and predicted MB-TFs in the model plant Arabidopsis thaliana and examine their experimentally determined or anticipated subcellular localizations and membrane topologies. We predict proteolytically activated MB-TFs by the mapping of protease recognition sequences and structural features that facilitate RIP in and around the TMD, based on data from metazoan intramembrane proteases. Finally, the MB-TF functions in plant responses to environmental stresses and in plant development are considered and novel functions for still uncharacterized MB-TFs are forecasted by means of a regulatory network-based approach.

Overexpression of AHL9 accelerates leaf senescence in Arabidopsis thaliana

BACKGROUND

Leaf senescence, the final stage of leaf growth and development, is regulated by numerous internal factors and environmental cues. Ethylene is one of the key senescence related hormones, but the underlying molecular mechanism of ethylene-induced leaf senescence remains poorly understood.

RESULTS

In this study, we identified one AT-hook like (AHL) protein, AHL9, as a positive regulator of leaf senescence in Arabidopsis thaliana. Overexpression of AHL9 significantly accelerates age-related leaf senescence and promotes dark-induced leaf chlorosis. The early senescence phenotype observed in AHL9 overexpressing lines is inhibited by the ethylene biosynthesis inhibitor aminooxyacetic acid suggesting the involvement of ethylene in the AHL9-associated senescence. RNA-seq and quantitative reverse transcription PCR (qRT-PCR) data identified numerous senescence-associated genes differentially expressed in leaves of AHL9 overexpressing transgenic plants.

CONCLUSIONS

Our investigation demonstrates that AHL9 functions in accelerating the leaf senescence process via ethylene synthesis or signalling.

PaNAC089 is a membrane-tethered transcription factor (MTTF) that modulates flowering, chlorophyll breakdown and trichome initiation

Flowering and senescence are essential developmental stages of green plants, which are governed by complex molecular regulatory networks. However, the connection between flowering regulation and senescence regulation in London plane tree (Platanus acerifolia ) remains unknown. In this study, we identified a gene PaNAC089 from London plane tree, which encodes a membrane-tethered transcription factor (MTTF) belonging to the NAC (NAM, ATAF1/2, CUC2) transcription factor family. We investigated the functions of PaNAC089 in the regulation of flowering and senescence through the analysis of expression profiles and transgenic phenotypes. Heterologous overexpression of ΔPaNAC089 delayed flowering and inhibited chlorophyll breakdown to produce dark green rosette leaves in Arabidopsis . In addition, the trichome density of rosette leaves was decreased in transgenic lines. In ΔPaNAC089 overexpression plants, a series of functional genes with inhibited expression were identified by quantitative real-time polymerase chain reaction (qRT-PCR), including genes that regulate flowering, chlorophyll decomposition, and trichome initiation. Furthermore, Δ PaNAC089 directly binds to the promoter of CONSTANS (CO ) and NON-YELLOWING2 (NYE2 ) in the yeast one-hybrid assay. Consistent with this, luciferase (LUC) transient expression assays also showed that Δ PaNAC089 could inhibit the activity of NYE2 . To summarise, our data suggests that PaNAC089 is an MTTF that modulates flowering, chlorophyll breakdown and trichome initiation.

OsMYB103 is essential for tapetum degradation in rice

OsMYB103 positively regulates tapetum degradation, and functions downstream of TDR and upstream of EAT1 and PTC1. The precise regulation of programmed cell death (PCD) of the tapetum is crucial for the development of anthers and pollen in rice. In this study, we isolated and identified a male-sterile mutant of rice, osmyb103, which exhibited delayed tapetum degradation and defective mature pollen. Map-based cloning and genetic complementation revealed that OsMYB103 corresponded to the gene LOC_Os04g39470 and encoded a R2R3 MYB transcription factor. OsMYB103 was localized in the nucleus and was expressed preferentially in the tapetal cells and microspores of the anther. OsMYB103 regulated the expression of two transcription factors, ETERNAL TAPETUM 1 (EAT1) and PERSISTENT TAPETAL CELL 1 (PTC1), both of which regulated tapetum degradation positively. Moreover, the expression of OsMYB103 was directly regulated by the additional positive regulator of tapetum degradation TAPETUM DEGENERATION RETARDATION (TDR) and was able to interact with it. Genetic evidence confirmed that OsMYB103 acted upstream of EAT1. The results show that OsMYB103 is a positive regulator of tapetum degradation in rice. These findings provide a better understanding of the regulatory network that underlies degradation of the tapetum in rice.

HuNAC20 and HuNAC25, Two Novel NAC Genes from Pitaya, Confer Cold Tolerance in Transgenic Arabidopsis

NAC transcription factors are one of the largest families of transcriptional regulators in plants, and members of the gene family play vital roles in regulating plant growth and development processes including biotic/abiotic stress responses. However, little information is available about the NAC family in pitaya. In this study, we conducted a genome-wide analysis and a total of 64 NACs (named HuNAC1-HuNAC64) were identified in pitaya (Hylocereus). These genes were grouped into fifteen subgroups with diversities in gene proportions, exon–intron structures, and conserved motifs. Genome mapping analysis revealed that HuNAC genes were unevenly scattered on all eleven chromosomes. Synteny analysis indicated that the segmental duplication events played key roles in the expansion of the pitaya NAC gene family. Expression levels of these HuNAC genes were analyzed under cold treatments using qRT-PCR. Four HuNAC genes, i.e., HuNAC7, HuNAC20, HuNAC25, and HuNAC30, were highly induced by cold stress. HuNAC7, HuNAC20, HuNAC25, and HuNAC30 were localized exclusively in the nucleus. HuNAC20, HuNAC25, and HuNAC30 were transcriptional activators while HuNAC7 was a transcriptional repressor. Overexpression of HuNAC20 and HuNAC25 in Arabidopsis thaliana significantly enhanced tolerance to cold stress through decreasing ion leakage, malondialdehyde (MDA), and H₂O₂ and O₂⁻ accumulation, accompanied by upregulating the expression of cold-responsive genes (AtRD29A, AtCOR15A, AtCOR47, and AtKIN1). This study presents comprehensive information on the understanding of the NAC gene family and provides candidate genes to breed new pitaya cultivars with tolerance to cold conditions through genetic transformation.

ZmSNAC13, a maize NAC transcription factor conferring enhanced resistance to multiple abiotic stresses in transgenic Arabidopsis

Abiotic stress is the main factor that severely limits crop growth and yield. NAC (NAM, ATAF1/2 and CUC2) transcription factors play an important role in dealing with various abiotic stresses. Here, we discovered the ZmSNAC13 gene in drought-tolerant maize lines by RNA-seq analysis and verified its function in Arabidopsis thaliana. First, its gene structure showed that ZmSNAC13 had a typical NAC domain and a highly variable C-terminal. There were multiple cis-acting elements related to stress in its promoter region. Overexpression of ZmSNAC13 resulted in enhanced tolerances to drought and salt stresses in Arabidopsis, characterized by a reduction in the water loss rate, a sustained effective photosynthesis rate, and increased cell membrane stability in leaves under drought conditions. Transcriptome analysis showed that a large number of differentially expressed genes regulated by overexpression of ZmSNAC13 were identified, and the main drought tolerance regulatory pathways involved were the ABA pathway and MAPK cascade signaling pathway. Overexpression of ZmSNAC13 promoted the expression of genes, such as PYL9 and DREB3, thereby enhancing tolerance to adverse environments. Adaptability, while restraining genes expression such as WRKY53 and MPK3, facilitates regulation of senescence in Arabidopsis and improves plant responses to adversity. Therefore, ZmSNAC13 is promising gene of interest for use in transgenic breeding to improve abiotic stress tolerance in crops.

Identification and functional characterization of Gh_D01G0514 (GhNAC072) transcription factor in response to drought stress tolerance in cotton

Cotton encounters long-term drought stress problems resulting in major yield losses. Transcription factors (TFs) plays an important role in response to biotic and abiotic stresses. The coexpression patterns of gene networks associated with drought stress tolerance were investigated using transcriptome profiles. Applying a weighted gene coexpression network analysis, we discovered a salmon module with 144 genes strongly linked to drought stress tolerance. Based on coexpression and RT-qPCR analysis GH_D01G0514 was selected as the candidate gene, as it was also identified as a hub gene in both roots and leaves with a consistent expression in response to drought stress in both tissues. For validation of GH_D01G0514, Virus Induced Gene Silencing was performed and VIGS plants showed significantly higher excised leaf water loss and ion leakage, while lower relative water and chlorophyll contents as compared to WT (Wild type) and positive control plants. Furthermore, the WT and positive control seedlings showed higher CAT and SOD activities, and lower activities of hydrogen peroxide and MDA enzymes as compared to the VIGS plants. Gh_D01G0514 (GhNAC072) was localized in the nucleus and cytoplasm. Y2H assay demonstrates that Gh_D01G0514 has a potential of auto activation. It was observed that the Gh_D01G0514 was highly upregulated in both tissues based on RNA Seq and RT-qPCR analysis. Thus, we inferred that, this candidate gene might be responsible for drought stress tolerance in cotton. This finding adds significantly to the existing knowledge of drought stress tolerance in cotton and deep molecular analysis are required to understand the molecular mechanisms underlying drought stress tolerance in cotton.

CHYR1 ubiquitinates the phosphorylated WRKY70 for degradation to balance immunity in Arabidopsis thaliana

It is critically important for plants to control the trade-off between normal growth and pathogen immunity. However, the underlying molecular mechanism remains largely unknown. Here we report such a mechanism controlled by WRKY70 and its partner CHYR1 in Arabidopsis. We found that both levels of the WRKY70 target gene SARD1 and the phosphorylated forms of WRKY70 were increased in WRKY70OE plants upon Pst DC3000 infection. Mechanistically, phosphorylation of WRKY70 at Thr22 and Ser34 occurs, which then activates SARD1 expression through binding to a WT box. Phosphorylated WRKY70 is degraded by 26S proteasome via CHYR1 when resuming normal growth after infection. In addition, nonphosphorylated WRKY70 represses SARD1 expression by binding to both W (inhibitory activity site) and WT (active activity site) boxes. The binding of WRKY70 to alternative cis-elements of SARD1 through a phosphorylation-mediated switch controlled by CHYR1 contributes to modulating the balance between immunity and growth.

Interactions between ScNAC23 and ScGAI regulate GA-mediated flowering and senescence in sugarcane

Control of gene transcription is crucial to regulate plant growth and development events, such as flowering, leaf senescence, and seed germination. Here we identified a NAC transcription factor (ScNAC23) isolated from sugarcane (cv. ROC22). Analysis by qRT-PCR indicated that ScNAC23 expression was strongly induced in mature leaves and flowering varieties and was also responsive to exogenous treatment with the hormone gibberellin (GA). Ectopic expression of ScNAC23 in Arabidopsis accelerated bolting, flowering, and leaf senescence compared to wild type plants. Furthermore, Arabidopsis overexpressed ScNAC23 were more sensitive to GA than the wild type, and exogenous GA significantly accelerated flowering and senescence in the ScNAC23-overexpressed ones. A direct interaction between ScNAC23 and ScGAI, an inhibitor of GA signaling, was confirmed by yeast-two hybrid, bimolecular fluorescence complementation, and GST-pull down assay. The putative GA-ScNAC23-LFY/SAGs regulator module might provide a new sight into the molecular action of GA to accelerating flowering and leaf senescence in sugarcane.

The transcription factor ZmNAC49 reduces stomatal density and improves drought tolerance in maize

Drought stress severely limits the growth, development, and productivity of crops, and therefore understanding the mechanisms by which plants respond to drought is crucial. In this study, we cloned a maize NAC transcription factor, ZmNAC49, and identified its function in response to drought stress. We found that ZmNAC49 is localized in the nucleus and has transcriptional activation activity. ZmNAC49 expression is rapidly and strongly induced by drought stress, and overexpression enhances stress tolerance in maize. Overexpression also significant decreases the transpiration rate, stomatal conductance, and stomatal density in maize. Detailed study showed that ZmNAC49 overexpression affects the expression of genes related to stomatal development, namely ZmTMM, ZmSDD1, ZmMUTE, and ZmFAMA. In addition, we found that ZmNAC49 can directly bind to the promoter of ZmMUTE and suppress its expression. Taken together, our results show that the transcription factor ZmNAC49 represses ZmMUTE expression, reduces stomatal density, and thereby enhances drought tolerance in maize.

COP1 promotes ABA-induced stomatal closure by modulating the abundance of ABI/HAB and AHG3 phosphatases

Plant stomata play a crucial role in leaf function, controlling water transpiration in response to environmental stresses and modulating the gas exchange necessary for photosynthesis. The phytohormone abscisic acid (ABA) promotes stomatal closure and inhibits light-induced stomatal opening. The Arabidopsis thaliana E3 ubiquitin ligase COP1 functions in ABA-mediated stomatal closure. However, the underlying molecular mechanisms are still not fully understood. Yeast two-hybrid assays were used to identify ABA signaling components that interact with COP1, and biochemical, molecular and genetic studies were carried out to elucidate the regulatory role of COP1 in ABA signaling. The cop1 mutants are hyposensitive to ABA-triggered stomatal closure under light and dark conditions. COP1 interacts with and ubiquitinates the Arabidopsis clade A type 2C phosphatases (PP2Cs) ABI/HAB group and AHG3, thus triggering their degradation. Abscisic acid enhances the COP1-mediated degradation of these PP2Cs. Mutations in ABI1 and AHG3 partly rescue the cop1 stomatal phenotype and the phosphorylation level of OST1, a crucial SnRK2-type kinase in ABA signaling. Our data indicate that COP1 is part of a novel signaling pathway promoting ABA-mediated stomatal closure by regulating the stability of a subset of the Clade A PP2Cs. These findings provide novel insights into the interplay between ABA and the light signaling component in the modulation of stomatal movement.

Decreased Vascular Bundle 1 affects mitochondrial and plant development in rice

BACKGROUND

Mitochondria are vital regulators of plant growth and development, constitute the predominant source of ATP, and participate in multiple anabolic and catabolic metabolic pathways. But the mechanism by which dysfunctional mitochondria affect plant growth remains unknown, and more mitochondria-defective mutants need to be identified.

RESULTS

A mitochondria-defective mutant decreased vascular bundle 1 (dvb1) was isolated from rice mutant library mutagenized by EMS (ethylmethane sulfonate), which shows dwarfism, narrow leaves, short branches, few vascular bundles, and low fertility. Map-based cloning, genetic complementation, and phylogenetic analysis revealed that DVB1 encodes a structural protein classified in the Mic10 family and is required for the formation of cristae in mitochondria, and was primarily expressed in vascular bundles. The DVB1 protein is partially localized in the mitochondria and capable of forming dimers and polymers. Comparing with the wild type, disruption of amino acid metabolism and increased auxin synthesis were observed in dvb1 mutant which also showed increased sensitivity to the mitochondrial electron transport inhibitors.

CONCLUSIONS

DVB1 belongs to Mic10 family and DVB1 is partially localized in the mitochondria. Further studies indicated that DVB1 is important for mitochondrial and plant development in rice.

Time-course effects of Tris(1,3-dichloro-2-propyl) phosphate (TDCPP) on Chlorella pyrenoidosa: Growth inhibition and adaptability mechanisms

Tris(1,3-dichloro-2-propyl) phosphate (TDCPP), a widely used chlorinated organophosphorus flame retardant, is an increasingly widespread contaminant of aquatic environment. In this study, time-dependent effect of TDCPP on the freshwater green-algae Chlorella pyrenoidosa was investigated and its underlying mechanisms were explored. We show that TDCPP lower than 10 ppm caused a reversible inhibition of algal growth, with complete inhibition occurring at 15 ppm. This inhibition was not caused by damage from reactive oxygen species, but rather resulted from the impairment of photosynthetic function, with PSII reaction center as the primary target, as indicated by Chl a fluorescence induction, Q_A^- reoxidation, S-state distribution and immunoblot analysis. The reversal of damage caused by TDCPP concentrations under 10 ppm might be attributable to the repair of photosynthetic function by de novo protein biosynthesis in the chloroplast, with the most likely explanation being the replacement of the damaged PSII D1 protein. The results provide novel insights into mechanisms of TDCPP toxicity toward freshwater microalgae and better understanding of ecological consequences of TDCPP in the environment.

SlEAD1, an EAR motif-containing ABA down-regulated novel transcription repressor regulates ABA response in tomato

EAR motif-containing proteins are able to repress gene expression, therefore play important roles in regulating plants growth and development, plant response to environmental stimuli, as well as plant hormone signal transduction. ABA is a plant hormone that regulates abiotic stress tolerance in plants via signal transduction. ABA signaling via the PYR1/PYLs/RCARs receptors, the PP2Cs phosphatases, and SnRK2s protein kinases activates the ABF/AREB/ABI5-type bZIP transcription factors, resulting in the activation/repression of ABA response genes. However, functions of many ABA response genes remained largely unknown. We report here the identification of the ABA-responsive gene SlEAD1 (Solanum lycopersicum EAR motif-containing ABA down-regulated 1) as a novel EAR motif-containing transcription repressor gene in tomato. We found that the expression of SlEAD1 was down-regulated by ABA treatment, and SlEAD1 repressed reporter gene expression in transfected protoplasts. By using CRISPR gene editing, we generated transgene-free slead1 mutants and found that the mutants produced short roots. By using seed germination and root elongation assays, we examined ABA response of the slead1 mutants and found that ABA sensitivity in the mutants was increased. By using qRT-PCR, we further show that the expression of some of the ABA biosynthesis and signaling component genes were increased in the slead1 mutants. Taken together, our results suggest that SlEAD1 is an ABA response gene, that SlEAD1 is a novel EAR motif-containing transcription repressor, and that SlEAD1 negatively regulates ABA responses in tomato possibly by repressing the expression of some ABA biosynthesis and signaling genes.

Global analysis of expression profile of members of DnaJ gene families involved in capsaicinoids synthesis in pepper (Capsicum annuum L)

BACKGROUND

The DnaJ proteins play critical roles in plant development and stress responses. Recently, seventy-six DnaJ genes were identified through a comprehensive bioinformatics analysis in the pepper genome. However, there were no reports on understanding of phylogenetic relationships and diverse expression profile of pepper DnaJ genes to date. Herein, we performed the systemic analysis of the phylogenetic relationships and expression profile of pepper DnaJ genes in different tissues and in response to both abiotic stress and plant hormones.

RESULTS

Phylogenetic analysis showed that all the pepper DnaJ genes were grouped into 7 sub-families (sub-family I, II, III, IV, V, VI and VII) according to sequence homology. The expression of pepper DnaJs in different tissues revealed that about 38% (29/76) of pepper DnaJs were expressed in at least one tissue. The results demonstrate the potentially critical role of DnaJs in pepper growth and development. In addition, to gain insight into the expression difference of pepper DnaJ genes in placenta between pungent and non-pungent, their expression patterns were also analyzed using RNA-seq data and qRT-PCR. Comparison analysis revealed that eight genes presented distinct expression profiles in pungent and non-pungent pepper. The CaDnaJs co-expressed with genes involved in capsaicinoids synthesis during placenta development. What is more, our study exposed the fact that these eight DnaJ genes were probably regulated by stress (heat, drought and salt), and were also regulated by plant hormones (ABA, GA3, MeJA and SA).

CONCLUSIONS

In summary, these results showed that some DnaJ genes expressed in placenta may be involved in plant response to abiotic stress during biosynthesis of compounds related with pungency. The study provides wide insights to the expression profiles of pepper DanJ genes and contributes to our knowledge about the function of DnaJ genes in pepper.

Screening of abiotic stress-responsive cotton genes using a cotton full-length cDNA overexpressing Arabidopsis library

Cotton (Gossypium hirsutum L.) is a major crop and the main source of natural fiber worldwide. Because various abiotic and biotic stresses strongly influence cotton fiber yield and quality, improved stress resistance of this crop plant is urgently needed. In this study, we used Gateway technology to construct a normalized full-length cDNA overexpressing (FOX) library from upland cotton cultivar ZM12 under various stress conditions. The library was transformed into Arabidopsis to produce a cotton-FOX-Arabidopsis library. Screening of this library yielded 6,830 transgenic Arabidopsis lines, of which 757 were selected for sequencing to ultimately obtain 659 cotton ESTs. GO and KEGG analyses mapped most of the cotton ESTs to plant biological process, cellular component, and molecular function categories. Next, 156 potential stress-responsive cotton genes were identified from the cotton-FOX-Arabidopsis library under drought, salt, ABA, and other stress conditions. Four stress-related genes identified from the library, designated as GhCAS, GhAPX, GhSDH, and GhPOD, were cloned from cotton complementary DNA, and their expression patterns under stress were analyzed. Phenotypic experiments indicated that overexpression of these cotton genes in Arabidopsis affected the response to abiotic stress. The method developed in this study lays a foundation for high-throughput cloning and rapid identification of cotton functional genes.

Integrated transcriptomics and metabolomics analysis of catechins, caffeine and theanine biosynthesis in tea plant (Camellia sinensis) over the course of seasons

BACKGROUND

Catechins, caffeine, and theanine as three important metabolites in the tea leaves play essential roles in the formation of specific taste and shows potential health benefits to humans. However, the knowledge on the dynamic changes of these metabolites content over seasons, as well as the candidate regulatory factors, remains largely undetermined.

RESULTS

An integrated transcriptomic and metabolomic approach was used to analyze the dynamic changes of three mainly metabolites including catechins, caffeine, and theanine, and to explore the potential influencing factors associated with these dynamic changes over the course of seasons. We found that the catechins abundance was higher in Summer than that in Spring and Autumn, and the theanine abundance was significantly higher in Spring than that in Summer and Autumn, whereas caffeine exhibited no significant changes over three seasons. Transcriptomics analysis suggested that genes in photosynthesis pathway were significantly down-regulated which might in linkage to the formation of different phenotypes and metabolites content in the tea leaves of varied seasons. Fifty-six copies of nine genes in catechins biosynthesis, 30 copies of 10 genes in caffeine biosynthesis, and 12 copies of six genes in theanine biosynthesis were detected. The correlative analysis further presented that eight genes can be regulated by transcription factors, and highly correlated with the changes of metabolites abundance in tea-leaves.

CONCLUSION

Sunshine intensity as a key factor can affect photosynthesis of tea plants, further affect the expression of major Transcription factors (TFs) and structural genes in, and finally resulted in the various amounts of catechins, caffeine and theaine in tea-leaves over three seasons. These findings provide new insights into abundance and influencing factors of metabolites of tea in different seasons, and further our understanding in the formation of flavor, nutrition and medicinal function.

ABC1K10a, an atypical kinase, functions in plant salt stress tolerance

BACKGROUND

ABC1K (Activity of BC1 complex Kinase) is an evolutionarily primitive atypical kinase family widely distributed among prokaryotes and eukaryotes. The ABC1K protein kinases in Arabidopsis are predicted to localize either to the mitochondria or chloroplasts, in which plastid-located ABC1K proteins are involved in the response against photo-oxidative stress and cadmium-induced oxidative stress.

RESULTS

Here, we report that the mitochondria-localized ABC1K10a functions in plant salt stress tolerance by regulating reactive oxygen species (ROS). Our results show that the ABC1K10a expression is induced by salt stress, and the mutations in this gene result in overaccumulation of ROS and hypersensitivity to salt stress. Exogenous application of the ROS-scavenger GSH significantly represses ROS accumulation and rescues the salt hypersensitive phenotype of abc1k10a. ROS overaccumulation in abc1k10a mutants under salt stress is likely due to the defect in mitochondria electron transport chain. Furthermore, defects of several other mitochondria-localized ABC1K genes also result in salt hypersensitivity.

CONCLUSIONS

Taken together, our results reveal that the mitochondria-located ABC1K10a regulates mitochondrial ROS production and is a positive regulator of salt tolerance in Arabidopsis.

Comparative Transcriptome Analysis of Two Aegilops tauschii with Contrasting Drought Tolerance by RNA-Seq

As the diploid progenitor of common wheat, Aegilops tauschii is considered to be a valuable resistance source to various biotic and abiotic stresses. However, little has been reported concerning the molecular mechanism of drought tolerance in Ae. tauschii. In this work, the drought tolerance of 155 Ae. tauschii accessions was firstly screened on the basis of their coleoptile lengths under simulated drought stress. Subsequently, two accessions (XJ002 and XJ098) with contrasting coleoptile lengths were selected and intensively analyzed on rate of water loss (RWL) as well as physiological characters, confirming the difference in drought tolerance at the seedling stage. Further, RNA-seq was utilized for global transcriptome profiling of the two accessions seedling leaves under drought stress conditions. A total of 6969 differentially expressed genes (DEGs) associated with drought tolerance were identified, and their functional annotations demonstrated that the stress response was mediated by pathways involving alpha-linolenic acid metabolism, starch and sucrose metabolism, peroxisome, mitogen-activated protein kinase (MAPK) signaling, carbon fixation in photosynthetic organisms, and glycerophospholipid metabolism. In addition, DEGs with obvious differences between the two accessions were intensively analyzed, indicating that the expression level of DEGs was basically in alignment with the physiological changes of Ae. tauschii under drought stress. The results not only shed fundamental light on the regulatory process of drought tolerance in Ae. tauschii, but also provide a new gene resource for improving the drought tolerance of common wheat.

Transcriptome Analysis Reveals Key Pathways and Hormone Activities Involved in Early Microtuber Formation of Dioscorea opposita

Chinese yam (Dioscorea opposita) is an important tuberous crop used for both food and medicine. Despite a long history of cultivation, the understanding of D. opposita genetics and molecular biology remains scant, which has limited its genetic improvement. This work presents a de novo transcriptome sequencing analysis of microtuber formation in D. opposita. We assembled cDNA libraries from different stages during the process of microtuber formation, designated as initial explants (EXP), axillary bud proliferation after three weeks (BUD), and microtuber visible after four weeks (MTV). More differentially expressed genes (DEGs) and pathways were identified between BUD vs. EXP than in MTV vs. BUD, indicating that proliferation of the axillary bud is the key stage of microtuber induction. Gene classification and pathway enrichment analysis showed that microtuber formation is tightly coordinated with primary metabolism, such as amino acid biosynthesis, ribosomal component biosynthesis, and starch and sucrose metabolism. The formation of the microtuber is regulated by a variety of plant hormones, including ABA. Combined with analysis of physiological data, we suggest that ABA positively regulates tuberization in D. opposita. This study will serve as an empirical foundation for future molecular studies and for the propagation of D. opposita germplasm in field crops.

Genomic Organization and Comparative Phylogenic Analysis of NBS-LRR Resistance Gene Family in Solanum pimpinellifolium and Arabidopsis thaliana

NBS-LRR (nucleotide-binding site and leucine-rich repeat) is one of the largest resistance gene families in plants. The completion of the genome sequencing of wild tomato Solanum pimpinellifolium provided an opportunity to conduct a comprehensive analysis of the NBS-LRR gene superfamily at the genome-wide level. In this study, gene identification, chromosome mapping, and phylogenetic analysis of the NBS-LRR gene family were analyzed using the bioinformatics methods. The results revealed 245 NBS-LRRs in total, similar to that in the cultivated tomato. These genes are unevenly distributed on 12 chromosomes, and ~59.6% of them form gene clusters, most of which are tandem duplications. Phylogenetic analysis divided the NBS-LRRs into 2 subfamilies (CNL-coiled-coil NBS-LRR and TNL-TIR NBS-LRR), and the expansion of the CNL subfamily was more extensive than the TNL subfamily. Novel conserved structures were identified through conserved motif analysis between the CNL and TNL subfamilies. Compared with the NBS-LRR sequences from the model plant Arabidopsis thaliana, wide genetic variation occurred after the divergence of S. pimpinellifolium and A thaliana. Species-specific expansion was also found in the CNL subfamily in S. pimpinellifolium. The results of this study provide the basis for the deeper analysis of NBS-LRR resistance genes and contribute to mapping and isolation of candidate resistance genes in S. pimpinellifolium.

New Insights into Evolution of Plant Heat Shock Factors (Hsfs) and Expression Analysis of Tea Genes in Response to Abiotic Stresses

Heat shock transcription factor (Hsf) is one of key regulators in plant abotic stress response. Although the Hsf gene family has been identified from several plant species, original and evolution relationship have been fragmented. In addition, tea, an important crop, genome sequences have been completed and function of the Hsf family genes in response to abiotic stresses was not illuminated. In this study, a total of 4208 Hsf proteins were identified within 163 plant species from green algae (Gonium pectorale) to angiosperm (monocots and dicots), which were distributed unevenly into each of plant species tested. The result indicated that Hsf originated during the early evolutionary history of chlorophytae algae and genome-wide genetic varies had occurred during the course of evolution in plant species. Phylogenetic classification of Hsf genes from the representative nine plant species into ten subfamilies, each of which contained members from different plant species, imply that gene duplication had occurred during the course of evolution. In addition, based on RNA-seq data, the member of the Hsfs showed different expression levels in the different organs and at the different developmental stages in tea. Expression patterns also showed clear differences among Camellia species, indicating that regulation of Hsf genes expression varied between organs in a species-specific manner. Furthermore, expression of most Hsfs in response to drought, cold and salt stresses, imply a possible positive regulatory role under abiotic stresses. Expression profiles of nineteen Hsf genes in response to heat stress were also analyzed by quantitative real-time RT-PCR. Several stress-responsive Hsf genes were highly regulated by heat stress treatment. In conclusion, these results lay a solid foundation for us to elucidate the evolutionary origin of plant Hsfs and Hsf functions in tea response to abiotic stresses in the future.

Dual regulation of xylem formation by an auxin-mediated PaC3H17-PaMYB199 module in Populus

Wood (secondary xylem) formation in tree species is dependent on auxin-mediated vascular cambium activity in stems. However, the complex regulatory networks underlying xylem formation remain elusive. Xylem development in Populus was characterized based on microscopic observations of stem sections in transgenic plants. Transcriptomic, quantitative real-time PCR, chromatin immunoprecipitation PCR, and electrophoretic mobility shift assay analyses were conducted to identify target genes involved in xylem development. Yeast two-hybrid, pull-down, bimolecular fluorescence complementation, and co-immunoprecipitation assays were used to validate protein-protein interactions. PaC3H17 and its target PaMYB199 were found to be predominantly expressed in the vascular cambium and developing secondary xylem in Populus stems and play opposite roles in controlling cambial cell proliferation and secondary cell wall thickening through an overlapping pathway. Further, PaC3H17 interacts with PaMYB199 to form a complex, attenuating PaMYB199-driven suppression of its xylem targets. Exogenous auxin application enhances the dual control of the PaC3H17-PaMYB199 module during cambium division, thereby promoting secondary cell wall deposition. Dual regulation of xylem formation by an auxin-mediated PaC3H17-PaMYB199 module represents a novel regulatory mechanism in Populus, increasing our understanding of the regulatory networks involved in wood formation.

Transcriptome analysis of the molecular mechanism of Chrysanthemum flower color change under short-day photoperiods

Chrysanthemum [Dendranthema morifolium Tzvel.] is an ornamental plant grown under long-term artificial cultivation conditions. In production, early Chrysanthemum blossoms are often promoted by artificial short-day treatment. However, we found that the flower colour of Chrysanthemum blossoms induced by artificial short-day treatment was lighter than those induced by the natural photoperiod. To explore the intrinsic mechanism of colour fading in flowers, we performed full-length transcriptome sequencing of Chrysanthemum morifolium cv. 'Jinbeidahong' using single-molecule real-time sequencing and RNA-sequencing under natural daylight (ND) and short daylight (SD) conditions. The clustered transcriptome sequences were assigned to various databases, such as NCBI, Swiss-Prot, Gene Ontology and so on. The comparative results of digital gene expression analysis revealed that there were differentially expressed transcripts (DETs) in the four stages under ND and SD conditions. In addition, the expression patterns of anthocyanin biosynthesis structural genes were verified by quantitative real-time PCR. The major regulators of the light signalling ELONGATED HYPOCOTYL5 genes were markedly upregulated under ND conditions. The patterns of anthocyanin accumulation were consistent with the expression patterns of CHI1 and 3GT1. The results showed that the anthocyanin synthesis is tightly regulated by the photoperiod, which will be useful for molecular breeding of Chrysanthemum.

The Soybean GmNAC019 Transcription Factor Mediates Drought Tolerance in Arabidopsis in an Abscisic Acid-Dependent Manner

Being master regulators of gene expression, transcription factors (TFs) play important roles in determining plant growth, development and reproduction. To date, many TFs have been shown to positively mediate plant responses to environmental stresses. In the current study, the biological functions of a stress-responsive NAC [NAM (No Apical Meristem), ATAF1/2 (Arabidopsis Transcription Activation Factor1/2), CUC2 (Cup-shaped Cotyledon2)]-TF encoding gene isolated from soybean (GmNAC019) in relation to plant drought tolerance and abscisic acid (ABA) responses were investigated. By using a heterologous transgenic system, we revealed that transgenic Arabidopsis plants constitutively expressing the GmNAC019 gene exhibited higher survival rates in a soil-drying assay, which was associated with lower water loss rate in detached leaves, lower cellular hydrogen peroxide content and stronger antioxidant defense under water-stressed conditions. Additionally, the exogenous treatment of transgenic plants with ABA showed their hypersensitivity to this phytohormone, exhibiting lower rates of seed germination and green cotyledons. Taken together, these findings demonstrated that GmNAC019 functions as a positive regulator of ABA-mediated plant response to drought, and thus, it has potential utility for improving plant tolerance through molecular biotechnology.

Molecular cloning and functional analysis of lotus salt-induced NnDREB2C, NnPIP1-2 and NnPIP2-1 in Arabidopsis thaliana

Dehydration-responsive element bindings transcription factor (DREBs) and plasma membrane intrinsic proteins (PIPs) have been characterized multi-functions in plant growth and metabolism, as well as in the adaptation to various stresses. In this study, we cloned the full-length cDNA of NnDREB2C from a salt-tolerated lotus species with RT-PCR methods. Analysis of qRT-PCR demonstrated that NnDREB2C mRNA in the leaf dramatically increased after the treatments of NaCl, abscisic acid, low temperature and mannitol. Next, NnDREB2C was cloned into constitutive expression vector pSN1301, which in turn transformed into Arabidopsis thaliana to investigate its function in plants. NnDREB2C overexpression significantly elevated Arabidopsis tolerance against salt and drought stresses, showing higher survival rates, lower conductivity and more chlorophyll content than those of wild-type plants. Moreover, higher germination rates were observed in the NnDREB2C overproducing plants when subjected into the stresses of NaCl and mannitol. Furthermore, we investigate the potential down-stream genes regulated by NnDREB2C and observed a significant increase in expressions of several genes belonging to PIPs family, including PIP1-1, PIP1-2, PIP1-3, PIP1-4 and PIP1-5. Consistently, overexpressed NnPIP1-2 and NnPIP2-1 conferred Arabidopsis the tolerance to stresses. Taken together, we concluded that overexpression of NnDREB2C enhanced the tolerance of salt and drought stresses in plants, which might probably be derived from the increased expression of the genes belonging to PIPs family.

Genome-Wide Analysis of the YABBY Gene Family in Grapevine and Functional Characterization of VvYABBY4

Genes of the plant-specific YABBY transcription factor family have various roles, including lateral organ development, establishment of dorsoventral polarity, and response to abiotic stress. In this study, we carried out a genomic census of YABBY genes in grapevine (Vitis vinifera) and characterized their expression pattern during ovule development. We identified seven YABBY genes and classified them into five subfamilies, based on peptide sequence, similarity of exon-intron structure and composition of peptide sequence motifs. Analysis of YABBY gene expression in various grapevine structures and organs suggested that these genes function in diverse aspects of development and physiology. Analysis of expression during ovule development in four cultivars showed that one gene, VvYABBY4, was preferentially expressed during the period of ovule abortion in seedless cultivars. Transgenic expression of VvYABBY4 in tomato conferred reduced plant stature, dark green leaves, elongated pistil, and reduced size of fruit and seeds. Reduced seed size was associated with smaller endosperm cells. Expression of VvYABBY4 also affected expression of numerous tomato genes with presumed roles in seed development. These data suggest the potential for VvYABBY4 to influence seed development in grapevine, which may impact seedless grape breeding.

BZU2/ZmMUTE controls symmetrical division of guard mother cell and specifies neighbor cell fate in maize

Intercellular communication in adjacent cell layers determines cell fate and polarity, thus orchestrating tissue specification and differentiation. Here we use the maize stomatal apparatus as a model to investigate cell fate determination. Mutations in ZmBZU2 (bizui2, bzu2) confer a complete absence of subsidiary cells (SCs) and normal guard cells (GCs), leading to failure of formation of mature stomatal complexes. Nuclear polarization and actin accumulation at the interface between subsidiary mother cells (SMCs) and guard mother cells (GMCs), an essential pre-requisite for asymmetric cell division, did not occur in Zmbzu2 mutants. ZmBZU2 encodes a basic helix-loop-helix (bHLH) transcription factor, which is an ortholog of AtMUTE in Arabidopsis (BZU2/ZmMUTE). We found that a number of genes implicated in stomatal development are transcriptionally regulated by BZU2/ZmMUTE. In particular, BZU2/ZmMUTE directly binds to the promoters of PAN1 and PAN2, two early regulators of protodermal cell fate and SMC polarization, consistent with the low levels of transcription of these genes observed in bzu2-1 mutants. BZU2/ZmMUTE has the cell-to-cell mobility characteristic similar to that of BdMUTE in Brachypodium distachyon. Unexpectedly, BZU2/ZmMUTE is expressed in GMC from the asymmetric division stage to the GMC division stage, and especially in the SMC establishment stage. Taken together, these data imply that BZU2/ZmMUTE is required for early events in SMC polarization and differentiation as well as for the last symmetrical division of GMCs to produce the two GCs, and is a master determinant of the cell fate of its neighbors through cell-to-cell communication.

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Transcription Factor in Chenopodium quinoa

The NAC (NAM, ATAF, and CUC) family is one of the largest families of plant-specific transcription factors. It is involved in many plant growth and development processes, as well as abiotic/biotic stress responses. So far, little is known about the NAC family in Chenopodium quinoa. In the present study, a total of 90 NACs were identified in quinoa (named as CqNAC1-CqNAC90) and phylogenetically divided into 14 distinct subfamilies. Different subfamilies showed diversities in gene proportions, exon-intron structures, and motif compositions. In addition, 28 CqNAC duplication events were investigated, and a strong subfamily preference was found during the NAC expansion in quinoa, indicating that the duplication event was not random across NAC subfamilies during quinoa evolution. Moreover, the analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios suggested that the duplicated CqNACs might have mainly experienced purifying selection pressure with limited functional divergence. Additionally, 11 selected CqNACs showed significant tissue-specific expression patterns, and all the CqNACs were positively regulated in response to salt stress. The result provided evidence for selecting candidate genes for further characterization in tissue/organ specificity and their functional involvement in quinoa's strong salinity tolerance.

Biosynthesis of DHGA12 and its roles in Arabidopsis seedling establishment

Seed germination and photoautotrophic establishment are controlled by the antagonistic activity of the phytohormones gibberellins (GAs) and abscisic acid (ABA). Here we show that Arabidopsis thaliana GAS2 (Gain of Function in ABA-modulated Seed Germination 2), a protein belonging to the Fe-dependent 2-oxoglutarate dioxygenase superfamily, catalyzes the stereospecific hydration of GA₁₂ to produce GA₁₂ 16, 17-dihydro-16α-ol (DHGA₁₂). We show that DHGA₁₂, a C₂₀-GA has an atypical structure compared to known active GAs but can bind to the GA receptor (GID1c). DHGA₁₂ can promote seed germination, hypocotyl elongation and cotyledon greening. Silencing and over-expression of GAS2 alters the ABA/GA ratio and sensitivity to ABA during seed germination and photoautotrophic establishment. Hence, we propose that GAS2 acts to modulate hormonal balance during early seedling development.

Gibberellins are a major class of phytohormones that regulate plant growth and development. Here the authors show that the Arabidopsis GAS2 protein catalyses production of DHGA₁₂, an atypical bioactive GA, and show that GAS2 regulates ABA sensitivity during seed germination and early development.

The Constitutive Expression of a Chrysanthemum ERF Transcription Factor Influences Flowering Time in Arabidopsis thaliana

AP2/ERF transcription factors (TFs) represent valuable targets for the genetic manipulation of crop plants, as they participate in the control of metabolism, growth and development, as well as in the plants' response to environmental stimuli. Here, an ERF TF encoded by the chrysanthemum (Chrysanthemum morifolium) genome, designated CmERF110, was cloned and functionally characterized. The predicted CmERF110 polypeptide included a conserved DNA-binding AP2/ERF domain. A transient expression experiment revealed that the protein was deposited in the nucleus, and a transactivation experiment in yeast suggested that it had no transcriptional activity. The gene was transcribed in the chrysanthemum root, stem and leaf, with its transcript level following a circadian rhythm under both long and short days. The effect of constitutively expressing the gene in Arabidopsis thaliana was to accelerate flowering. Transcriptional profiling implied that its effect on floral initiation operated through the photoperiod pathway.

Analysis of the chromatin binding affinity of retrotransposases reveals novel roles in diploid and tetraploid cotton

LTR-retrotransposable elements are major components of diploid (Gossypium arboreum) and tetraploid (Gossypium hirsutum) cotton genomes that have undergone dramatic increases in copy number during the course of evolution. However, little is known about the biological functions of LTR-retrotransposable elements in cotton. Here, we show that a copia-like LTR-retrotransposable element has maintained considerable activity in both G. arboreum and G. hirsutum. We identified two functional domains of the retrotransposon and analyzed their expression levels in various cotton tissues, including leaves, ovules, and germinating seeds. ChIP-qPCR (chromatin immunoprecipitation followed by quantitative PCR), using a copia-specific antibody, established that copia-like proteins primarily bind to the first exons of several protein-coding genes in cotton cells. This finding suggests that retrotransposons play a novel, important role in regulating the transcriptional activities of protein-coding genes with various biological activities.

HY5 Contributes to Light-Regulated Root System Architecture Under a Root-Covered Culture System

Light is essential for plant organogenesis and development. Light-regulated shoot morphogenesis has been extensively studied; however, the mechanisms by which plant roots perceive and respond to aboveground light are largely unknown, particularly because the roots of most terrestrial plants are usually located underground in darkness. To mimic natural root growth conditions, we developed a root-covered system (RCS) in which the shoots were illuminated and the plant roots could be either exposed to light or cultivated in darkness. Using the RCS, we observed that root growth of wild-type plants was significantly promoted when the roots were in darkness, whereas it was inhibited by direct light exposure. This growth change seems to be regulated by ELONGATED HYPOCOTYL 5 (HY5), a master regulator of photomorphogenesis. Light was found to regulate HY5 expression in the roots, while a HY5 deficiency partially abolished the inhibition of growth in roots directly exposed to light, suggesting that HY5 expression is induced by direct light exposure and inhibits root growth. However, no differences in HY5 expression were observed between illuminated and dark-grown cop1 roots, indicating that HY5 may be regulated by COP1-mediated proteasome degradation. We confirmed the crucial role of HY5 in regulating root development in response to light under soil-grown conditions. A transcriptomic analysis revealed that light controls the expression of numerous genes involved in phytohormone signaling, stress adaptation, and metabolic processes in a HY5-dependent manner. In combination with the results of the flavonol quantification and exogenous quercetin application, these findings suggested that HY5 regulates the root response to light through a complex network that integrates flavonol biosynthesis and reactive oxygen species signaling. Collectively, our results indicate that HY5 is a master regulator of root photomorphogenesis.

A C2H2 zinc-finger protein OsZFP213 interacts with OsMAPK3 to enhance salt tolerance in rice

Improvement of salt tolerance is one of the major targets in rice breeding. Here, we report that the zinc-finger protein (ZFP) OsZFP213 functions in enhancing salt tolerance in rice. OsZFP213 is localized in the nucleus and has transactivation activity. Transgenic rice overexpressing OsZFP213 showed enhanced salt tolerance compared with wild type and OsZFP213 RNAi plants. Furthermore, OsZFP213 overexpression plants showed higher transcription levels of antioxidant system genes and higher catalytic activity of scavenging enzymes of reactive oxygen, such as superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT), and glutathione reductase (GR), and a lower level of ROS accumulation than that in wild type and OsZFP213 RNAi plants under salt treatment. Yeast two-hybrid, pull-down, and BiFC analysis showed that OsMAPK3 is a direct partner of OsZFP213, and this interaction enhanced the transactivation activity of OsZFP213. Taken together, these results suggest that OsZFP213 cooperates with OsMAPK3 in the regulation of rice salt stress tolerance by enhancing the ability of scavenging reactive oxygen.