Arabidopsis WRKY57 functions as a node of convergence for jasmonic acid- and auxin-mediated signaling in jasmonic acid-induced leaf senescence

RhMYB108, an R2R3-MYB transcription factor, is involved in ethylene- and JA-induced petal senescence in rose plants

Rose (Rosa hybrida) plants are major ornamental species worldwide, and their commercial value greatly depends on their open flowers, as both the quality of fully open petals and long vase life are important. Petal senescence can be started and accelerated by various hormone signals, and ethylene is considered an accelerator of petal senescence in rose. To date, however, the underlying mechanism of signaling crosstalk between ethylene and other hormones such as JA in petal senescence remains largely unknown. Here, we isolated RhMYB108, an R2R3-MYB transcription factor, which is highly expressed in senescing petals as well as in petals treated with exogenous ethylene and JA. Applications of exogenous ethylene and JA markedly accelerated petal senescence, while the process was delayed in response to applications of 1-MCP, an ethylene action inhibitor. In addition, silencing of RhMYB108 alter the expression of SAGs such as RhNAC029, RhNAC053, RhNAC092, RhSAG12, and RhSAG113, and finally block ethylene- and JA-induced petal senescence. Furthermore, RhMYB108 was identified to target the promoters of RhNAC053, RhNAC092, and RhSAG113. Our results reveal a model in which RhMYB108 functions as a receptor of ethylene and JA signals to modulate the onset of petal senescence by targeting and enhancing senescence-associated gene expression.

Transcriptome profiling of postharvest shoots identifies PheNAP2- and PheNAP3-promoted shoot senescence

The juvenile shoots of Phyllostachys edulis have been used as a food source for thousands of years, and it is recognized as a potential source of nutraceuticals. However, its rapid senescence restricts bamboo production and consumption, and the underlying molecular mechanisms of rapid shoot senescence remain largely unclear. In the present study, transcriptome profiling was employed to investigate the molecular regulation of postharvest senescence in shoots, along with physiological assays and anatomical dissections. Results revealed a distinct shift in expression postharvest, specifically transitions from cellular division and differentiation to the relocation of nutrients and programmed cell death. A number of regulatory and signaling factors were induced during postharvest senescence. Moreover, transcription factors, including NAM, ATAF and CUC (NAC) transcription factors, basic helix-loop-helix transcription factors, basic region/leucine zipper transcription factors, MYB transcription factors and WRKY transcription factors, were critical for shoot postharvest senescence, of which NACs were the most abundant. PheNAP2 and PheNAP3 were induced in postharvest shoots and found to promote leaf senescence in Arabidopsis by inducing the expression of AtSAG12 and AtSAG113. PheNAP2 and PheNAP3 could both restore the stay-green Arabidopsis nap to the wild-type phenotype either under normal growth condition or under abscisic acid treatment. Collectively, these results suggest that PheNAPs may promote shoot senescence. These findings provide a systematic view of shoot senescence and will inform future studies on the underlying molecular mechanisms responsible for shoot degradation during storage.

Genome-Wide Characterization, Expression Profile Analysis of WRKY Family Genes in Santalum album and Functional Identification of Their Role in Abiotic Stress

WRKY proteins are a large superfamily of transcription factors that are involved in diverse biological processes including development, as well as biotic and abiotic stress responses in plants. WRKY family proteins have been extensively characterized and analyzed in many plant species, including Arabidopsis, rice, and poplar. However, knowledge on WRKY transcription factors in Santalum album is scarce. Based on S. album genome and transcriptome data, 64 SaWRKY genes were identified in this study. A phylogenetic analysis based on the structures of WRKY protein sequences divided these genes into three major groups (I, II, III) together with WRKY protein sequences from Arabidopsis. Tissue-specific expression patterns showed that 37 SaWRKY genes were expressed in at least one of five tissues (leaves, roots, heartwood, sapwood, or the transition zone), while the remaining four genes weakly expressed in all of these tissues. Analysis of the expression profiles of the 42 SaWRKY genes after callus was initiated by salicylic acid (SA) and methyl jasmonate (MeJA) revealed that 25 and 24 SaWRKY genes, respectively, were significantly induced. The function of SaWRKY1, which was significantly up-regulated by SA and MeJA, was analyzed. SaWRKY1 was localized in the nucleus and its overexpression improved salt tolerance in transgenic Arabidopsis. Our study provides important information to further identify the functions of SaWRKY genes and to understand the roles of SaWRKY family genes involved in the development and in SA- and MeJA-mediated stress responses.

Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation

A precise understanding of the molecular mechanism involved in stress conditions has great importance for crop improvement. Biomolecules, such as WRKY proteins, which are the largest transcription factor family that is widely distributed in higher plants, plays a significant role in plant defense response against various biotic and abiotic stressors. In the present study, an extensive homology-based three-dimensional model construction and subsequent interaction study of WRKY DNA-binding domain (DBD) in CcWRKY1 (Type I), CcWRKY51 (Type II), and CcWRKY70 (Type III) belonging to pigeonpea, a highly tolerant crop species, was performed. Evaluation of the generated protein models was done to check their reliability and accuracy based on the quantitative and qualitative parameters. The final model was subjected to investigate the comparative binding analysis of different types of WRKY–DBD with DNA-W-box (a cis-acting element) by protein–DNA docking and molecular dynamics (MD) simulation. The DNA binding specificity with WRKY variants was scrutinized through protein–DNA interaction using the HADDOCK server. The stability, as well as conformational changes of protein–DNA complex, was investigated through molecular dynamics (MD) simulations for 100 ns using GROMACS. Additionally, the comparative stability and dynamic behavior of each residue of the WRKY–DBD type were analyzed in terms of root mean square deviation (RMSD), root mean square fluctuation (RMSF)values of the backbone atoms for each frame taking the minimized structure as a reference. The details of DNA binding activity of three different types of WRKY–DBD provided here will be helpful to better understand the regulation of WRKY gene family members in plants.

Characterization and Mapping of a Novel Premature Leaf Senescence Mutant in Common Tobacco (Nicotiana tabacum L.)

As the last stage of plant development, leaf senescence has a great impact on plant’s life cycle. Genetic manipulation of leaf senescence has been used as an efficient approach in improving the yield and quality of crop plants. Here we describe an ethyl methane sulfonate (EMS) mutagenesis induced premature leaf senescence mutant yellow leaf 1 (yl1) in common tobacco (Nicotiana tabacum L.). The yl1 plants displayed early leaf yellowing. Physiological parameters and marker genes expression indicated that the yl1 phenotype was caused by premature leaf senescence. Genetic analyses indicated that the yl1 phenotype was controlled by a single recessive gene that was subsequently mapped to a specific interval of tobacco linkage group 11 using simple sequence repeat (SSR) markers. Exogenous plant hormone treatments of leaves showed that the yl1 mutant was more sensitive to ethylene and jasmonic acid than the wild type. No similar tobacco premature leaf senescence mutants have been reported. This study laid a foundation for finding the gene controlling the mutation phenotype and revealing the molecular regulation mechanism of tobacco leaf senescence in the next stage.

Negative Regulation of Age-Related Developmental Leaf Senescence by the IAOx Pathway, PEN1, and PEN3

Early age-related developmental senescence was observed in Arabidopsis cyp79B2/cyp79B3 double mutants that cannot produce indole-3-acetaldoxime (IAOx), the precursor to indole glucosinolates (IGs), camalexin and auxin. The early senescence phenotype was not observed when senescence was induced by darkness. The cyp79B2/cyp79B3 mutants had lower auxin levels, but did not display auxin-deficient phenotypes. Camalexin biosynthesis mutants senesced normally; however, IG transport and exosome-related pen1/pen3 double mutants displayed early senescence. The early senescence in pen1/pen3 mutants depended on salicylic acid and was not observed in pen1 or pen3 single mutants. Quantitation of IGs showed reduced levels in cyp79B2/cyp79B3 mutants, but unchanged levels in pen1/pen3, even though both of these double mutants display early senescence. We discuss how these genetic data provide evidence that IAOx metabolites are playing a protective role in leaf senescence that is dependent on proper trafficking by PEN1 and PEN3, perhaps via the formation of exosomes.

Comprehensive Analysis of TIFY Transcription Factors and Their Expression Profiles under Jasmonic Acid and Abiotic Stresses in Watermelon

The TIFY gene family is plant-specific and encodes proteins involved in the regulation of multiple biological processes. Here, we identified 15 TIFY genes in the watermelon genome, which were divided into four subfamilies (eight JAZs, four ZMLs, two TIFYs, and one PPD) in the phylogenetic tree. The ClTIFY genes were unevenly located on eight chromosomes, and three segmental duplication events and one tandem duplication event were identified, suggesting that gene duplication plays a vital role in the expansion of the TIFY gene family in watermelon. Further analysis of the protein architectures, conserved domains, and gene structures provided additional clues for understanding the putative functions of the TIFY family members. Analysis of qRT-PCR and RNA-seq data revealed that the detected ClTIFY genes had preferential expression in specific tissues. qRT-PCR analysis revealed that nine selected TIFY genes were responsive to jasmonic acid (JA) and abiotic stresses including salt and drought. JA activated eight genes and suppressed one gene, among which ClJAZ1 and ClJAZ7 were the most significantly induced. Salt and drought stress activated nearly all the detected genes to different degrees. These results lay a foundation for further functional characterization of TIFY family genes in Citrullus lanatus.

MdWRKY40 promotes wounding-induced anthocyanin biosynthesis in association with MdMYB1 and undergoes MdBT2-mediated degradation

Wounding stress leads to anthocyanin accumulation. However, the underlying molecular mechanism remains elusive. In this study, MdWRKY40 was found to promote wounding-induced anthocyanin biosynthesis in association with MdMYB1 and undergo MdBT2-mediated degradation in apple. We found that MdMYB1, a positive regulator of anthocyanin biosynthesis, was essential for the wounding-induced anthocyanin biosynthesis in apple. MdWRKY40 was identified as an MdMYB1-interacting protein, and enhanced the binding of MdMYB1 to its target genes in response to wounding. We found that MdBT2 interacted physically with MdWRKY40 and was involved in its degradation through the 26S proteasome pathway. Our results demonstrate that MdWRKY40 is a key modulator in the wounding-induced anthocyanin biosynthesis, which provides new insights into the regulation of wounding-induced anthocyanin biosynthesis at both the transcriptional and post-translational levels in apple.

Arabidopsis Class II TCP Transcription Factors Integrate with the FT-FD Module to Control Flowering

The appropriate timing of flowering is critical for plant reproductive success. Although the FLOWERING LOCUS T (FT)-FD module plays crucial roles in the photoperiodic flowering pathway, the underlying mechanisms and signaling pathways involved still remain elusive. Here, we demonstrate that class II TCP transcription factors (TFs) integrate into the FT-FD complex to control floral initiation in Arabidopsis (Arabidopsis thaliana). Class II CINCINNATA (CIN) TCP TFs function as transcriptional activators by directly binding to the promoters of downstream floral meristem identity genes, such as APETALA1 (AP1). In addition, these TCPs directly interact with FD, a basic Leu zipper TF that plays a critical role in photoperiodic flowering, which further activates AP1 expression. Genetic analyses indicated that class II CIN TCP TFs function synergistically with FT and FD, to positively regulate flowering in an AP1-dependent manner. Thus, our results provide compelling evidence that class II CIN TCP TFs act directly at the AP1 promoter to enhance its transcription, thus further elucidating the molecular mechanisms underlying the regulation of photoperiodic flowering in Arabidopsis.

Overexpression of the maize transcription factor ZmVQ52 accelerates leaf senescence in Arabidopsis

Leaf senescence plays an important role in the improvement of maize kernel yields. However, the underlying regulatory mechanisms of leaf senescence in maize are largely unknown. We isolated ZmVQ52 and studied the function of ZmVQ52 which encoded, a VQ family transcription factor. ZmVQ52 is constitutively expressed in maize tissues, and mainly expressed in the leaf; it is located in the nucleus of maize protoplasts. Four WRKY family proteins-ZmWRKY20, ZmWRKY36, ZmWRKY50, and ZmWRKY71-were identified as interacting with ZmVQ52. The overexpression of ZmVQ52 in Arabidopsis accelerated premature leaf senescence. The leaf of the ZmVQ52-overexpression line showed a lower chlorophyll content and higher senescence rate than the WT. A number of leaf senescence regulating genes were up-regulated in the ZmVQ52-overexpression line. Additionally, hormone treatments revealed that the leaf of the ZmVQ52-overexpressed line was more sensitive to salicylic acid (SA) and jasmonic acid (JA), and had an enhanced tolerance to abscisic acid (ABA). Moreover, a transcriptome analysis of the ZmVQ52-overexpression line revealed that ZmVQ52 is mainly involved in the circadian pathway and photosynthetic pathways.

BrTCP7 Transcription Factor Is Associated with MeJA-Promoted Leaf Senescence by Activating the Expression of BrOPR3 and BrRCCR

The plant hormone jasmonic acid (JA) has been recognized as an important promoter of leaf senescence in plants. However, upstream transcription factors (TFs) that control JA biosynthesis during JA-promoted leaf senescence remain unknown. In this study, we report the possible involvement of a TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) TF BrTCP7 in methyl jasmonate (MeJA)-promoted leaf senescence in Chinese flowering cabbage. Exogenous MeJA treatment reduced maximum quantum yield (Fv/Fm) and total chlorophyll content, accompanied by the increased expression of senescence marker and chlorophyll catabolic genes, and accelerated leaf senescence. To further understand the transcriptional regulation of MeJA-promoted leaf senescence, a class I member of TCP TFs BrTCP7 was examined. BrTCP7 is a nuclear protein and possesses trans-activation ability through subcellular localization and transcriptional activity assays. A higher level of BrTCP7 transcript was detected in senescing leaves, and its expression was up-regulated by MeJA. The electrophoretic mobility shift assay and transient expression assay showed that BrTCP7 binds to the promoter regions of a JA biosynthetic gene BrOPR3 encoding OPDA reductase3 (OPR3) and a chlorophyll catabolic gene BrRCCR encoding red chlorophyll catabolite reductase (RCCR), activating their transcriptions. Taken together, these findings reveal that BrTCP7 is associated with MeJA-promoted leaf senescence at least partly by activating JA biosynthesis and chlorophyll catabolism, thus expanding our knowledge of the transcriptional mechanism of JA-mediated leaf senescence.

Reaumuria trigyna transcription factor RtWRKY23 enhances salt stress tolerance and delays flowering in plants

Reaumuria trigyna (Reaumuria Linn genus, family Tamaricaceae), an endangered dicotyledonous shrub with the features of a recretohalophyte, is endemic to the Eastern Alxa-Western Ordos area of China. Based on R. trigyna transcriptome data and expression pattern analysis of RtWRKYs, RtWRKY23, a Group II WRKY transcription factor, was isolated from R. trigyna cDNA. RtWRKY23 was mainly expressed in the stem and was induced by salt, drought, cold, ultraviolet radiation, and ABA treatments, but suppressed by heat treatment. Overexpression of RtWRKY23 in Arabidopsis increased chlorophyll content, root length, and fresh weight of the transgenic lines under salt stress. Real-time quantitative PCR (qPCR) analysis and yeast one-hybrid analysis demonstrated that RtWRKY23 protein directly or indirectly modulated the expression levels of downstream genes, including stress-related genes AtPOD, AtPOD22, AtPOD23, AtP5CS1, AtP5CS2, and AtPRODH2, and reproductive development-related genes AtMAF5, AtHAT1, and AtANT. RtWRKY23 transgenic Arabidopsis had higher proline content, peroxidase activity, and superoxide anion clearance rate, and lower H₂O₂ and malondialdehyde content than WT plants under salt stress conditions. Moreover, RtWRKY23 transgenic Arabidopsis exhibited later flowering and shorter pods, but little change in seed yield, compared with WT plants under salt stress. Our study demonstrated that RtWRKY23 not only enhanced salt stress tolerance through maintaining the ROS and osmotic balances in plants, but also participated in the regulation of flowering under salt stress.

Association of transcription factor WRKY56 gene from Populus simonii × P. nigra with salt tolerance in Arabidopsis thaliana

The WRKY transcription factor family is one of the largest groups of transcription factor in plants, playing important roles in growth, development, and biotic and abiotic stress responses. Many WRKY genes have been cloned from a variety of plant species and their functions have been analyzed. However, the studies on WRKY transcription factors in tree species under abiotic stress are still not well characterized. To understand the effects of the WRKY gene in response to abiotic stress, mRNA abundances of 102 WRKY genes in Populus simonii × P. nigra were identified by RNA sequencing under normal and salt stress conditions. The expression of 23 WRKY genes varied remarkably, in a tissue-specific manner, under salt stress. Since the WRKY56 was one of the genes significantly induced by NaCl treatment, its cDNA fragment containing an open reading frame from P. simonii × P. nigra was then cloned and transferred into Arabidopsis using the floral dip method. Under salt stress, the transgenic Arabidopsis over-expressed the WRKY56 gene, showing an increase in fresh weight, germination rate, proline content, and peroxidase and superoxide dismutase activity, when compared with the wild type. In contrast, transgenic Arabidopsis displayed a decrease in malondialdehyde content under salt stress. Overall, these results indicated that the WRKY56 gene played an important role in regulating salt tolerance in transgenic Arabidopsis.

Genome-Wide Identification and Expression Analysis of the Metacaspase Gene Family in Gossypium Species

Metacaspases (MCs) are cysteine proteases that are important for programmed cell death (PCD) in plants. In this study, we identified 89 MC genes in the genomes of four Gossypium species (Gossypium raimondii, Gossypium barbadense, Gossypium hirsutum, and Gossypium arboreum), and classified them as type-I or type-II genes. All of the type-I and type-II MC genes contain a sequence encoding the peptidase C14 domain. During developmentally regulated PCD, type-II MC genes may play an important role related to fiber elongation, while type-I genes may affect the thickening of the secondary wall. Additionally, 13 genes were observed to be differentially expressed between two cotton lines with differing fiber strengths, and four genes (GhMC02, GhMC04, GhMC07, and GhMC08) were predominantly expressed in cotton fibers at 5–30 days post-anthesis (DPA). During environmentally induced PCD, the expression levels of four genes were affected in the root, stem, and leaf tissues within 6 h of an abiotic stress treatment. In general, the MC gene family affects the development of cotton fibers, including fiber elongation and fiber thickening while four prominent fiber- expressed genes were identified. The effects of the abiotic stress and hormone treatments imply that the cotton MC gene family may be important for fiber development. The data presented herein may form the foundation for future investigations of the MC gene family in Gossypium species.

The Transcription Factor INDUCER OF CBF EXPRESSION1 Interacts with ABSCISIC ACID INSENSITIVE5 and DELLA Proteins to Fine-Tune Abscisic Acid Signaling during Seed Germination in Arabidopsis

ABSCISIC ACID INSENSITIVE5 (ABI5) is a crucial regulator of abscisic acid (ABA) signaling pathways involved in repressing seed germination and postgerminative growth in Arabidopsis (Arabidopsis thaliana). ABI5 is precisely modulated at the posttranslational level; however, the transcriptional regulatory mechanisms underlying ABI5 and its interacting transcription factors remain largely unknown. Here, we found that INDUCER OF CBF EXPRESSION1 (ICE1) physically associates with ABI5. ICE1 negatively regulates ABA responses during seed germination and directly suppresses ABA-responsive LATE EMBRYOGENESIS ABUNDANT6 (EM6) and EM1 expression. Genetic analysis demonstrated that the ABA-hypersensitive phenotype of the ice1 mutant requires ABI5. ICE1 interferes with the transcriptional activity of ABI5 to mediate downstream regulons. Importantly, ICE1 also interacts with DELLA proteins, which stimulate ABI5 during ABA signaling. Disruption of ICE1 partially restored the ABA-hyposensitive phenotype of the della mutant, gai-t6 rga-t2 rgl1-1 rgl2-1, indicating that ICE1 functions antagonistically with DELLA in ABA signaling. Consistently, DELLA proteins repress ICE1's transcriptional function and the antagonistic effect of ICE1 on ABI5. Collectively, our study demonstrates that ICE1 antagonizes ABI5 and DELLA activity to maintain the appropriate level of ABA signaling during seed germination, providing a mechanistic understanding of how ABA signaling is fine-tuned by a transcriptional complex involving ABI5 and its interacting partners.

JAZ proteins modulate seed germination through interaction with ABI5 in bread wheat and Arabidopsis

Appropriate regulation of crop seed germination is of significance for agriculture production. In this study, we show that TaJAZ1, most closely related to Arabidopsis JAZ3, negatively modulates abscisic acid (ABA)-inhibited seed germination and ABA-responsive gene expression in bread wheat. Biochemical interaction assays demonstrate that the C-terminal part containing the Jas domain of TaJAZ1 physically interacts with TaABI5. Similarly, Arabidopsis jasmonate-ZIM domain (JAZ) proteins also negatively modulate ABA responses. Further we find that a subset of JAZ proteins could interact with ABI5 using the luciferase complementation imaging assays. Choosing JAZ3 as a representative, we demonstrate that JAZ3 interacts with ABI5 in vivo and represses the transcriptional activation activity of ABI5. ABA application could abolish the enrichment of JAZ proteins in the ABA-responsive gene promoter. Furthermore, we find that ABA application could induce the expression of jasmonate (JA) biosynthetic genes and then increase the JA concentrations partially dependent on the function of ABI5, consequently leading to the degradation of JAZ proteins. This study sheds new light on the crosstalk between JA and ABA in modulating seed germination in bread wheat and Arabidopsis.

Deep Sequencing Reveals Early Reprogramming of Arabidopsis Root Transcriptomes Upon Ralstonia solanacearum Infection

Bacterial wilt caused by the bacterial pathogen Ralstonia solanacearum is one of the most devastating crop diseases worldwide. The molecular mechanisms controlling the early stage of R. solanacearum colonization in the root remain unknown. Aiming to better understand the mechanism of the establishment of R. solanacearum infection in root, we established four stages in the early interaction of the pathogen with Arabidopsis roots and determined the transcriptional profiles of these stages of infection. A total 2,698 genes were identified as differentially expressed genes during the initial 96 h after infection, with the majority of changes in gene expression occurring after pathogen-triggered root-hair development observed. Further analysis of differentially expressed genes indicated sequential activation of multiple hormone signaling cascades, including abscisic acid (ABA), auxin, jasmonic acid, and ethylene. Simultaneous impairment of ABA receptor genes promoted plant wilting symptoms after R. solanacearum infection but did not affect primary root growth inhibition or root-hair and lateral root formation caused by R. solanacearum. This indicated that ABA signaling positively regulates root defense to R. solanacearum. Moreover, transcriptional changes of genes involved in primary root, lateral root, and root-hair formation exhibited high temporal dynamics upon infection. Taken together, our results suggest that successful infection of R. solanacearum on roots is a highly programmed process involving in hormone crosstalk.

Isolation and Characterization of CsWRKY7, a Subgroup IId WRKY Transcription Factor from Camellia sinensis, Linked to Development in Arabidopsis

WRKY transcription factors (TFs) containing one or two WRKY domains are a class of plant TFs that respond to diverse abiotic stresses and are associated with developmental processes. However, little has been known about the function of WRKY gene in tea plant. In this study, a subgroup IId WRKY gene CsWRKY7 was isolated from Camellia sinensis, which displayed amino acid sequence homology with Arabidopsis AtWRKY7 and AtWRKY15. Subcellular localization prediction indicated that CsWRKY7 localized to nucleus. Cis-acting elements detected in the promotor region of CsWRKY7 are mainly involved in plant response to environmental stress and growth. Consistently, expression analysis showed that CsWRKY7 transcripts responded to NaCl, mannitol, PEG, and diverse hormones treatments. Additionally, CsWRKY7 exhibited a higher accumulation both in old leaves and roots compared to bud. Seed germination and root growth assay indicated that overexpressed CsWRKY7 in transgenic Arabidopsis was not sensitive to NaCl, mannitol, PEG, and low concentration of ABA treatments. CsWRKY7 overexpressing Arabidopsis showed a late-flowering phenotype under normal conditions compared to wild type. Furthermore, gene expression analysis showed that the transcription levels of the flowering time integrator gene FLOWERING LOCUS T (FT) and the floral meristem identity genes APETALA1 (AP1) and LEAFY (LFY) were lower in WRKY7-OE than in the WT. Taken together, these findings indicate that CsWRKY7 TF may participate in plant growth. This study provides a potential strategy to breed late-blooming tea cultivar.

Uncovering anthocyanin biosynthesis related microRNAs and their target genes by small RNA and degradome sequencing in tuberous roots of sweetpotato

BACKGROUND

Compared with white-fleshed sweetpotato (WFSP), purple-fleshed sweetpotato (PFSP) is a desirable resource for functional food development because of the abundant anthocyanin accumulation in its tuberous roots. Some studies have shown that the expression regulation mediated by miRNA plays an important role in anthocyanin biosynthesis in plants. However, few miRNAs and their corresponding functions related to anthocyanin biosynthesis in tuberous roots of sweetpotato have been known.

RESULTS

In this study, small RNA (sRNA) and degradome libraries from the tuberous roots of WFSP (Xushu-18) and PFSP (Xuzishu-3) were constructed, respectively. Totally, 191 known and 33 novel miRNAs were identified by sRNA sequencing, and 180 target genes cleaved by 115 known ib-miRNAs and 5 novel ib-miRNAs were identified by degradome sequencing. Of these, 121 miRNAs were differently expressed between Xushu-18 and Xuzishu-3. Integrated analysis of sRNA, degradome sequencing, GO, KEGG and qRT-PCR revealed that 26 differentially expressed miRNAs and 36 corresponding targets were potentially involved in the anthocyanin biosynthesis. Of which, an inverse correlation between the expression of ib-miR156 and its target ibSPL in WFSP and PFSP was revealed by both qRT-PCR and sRNA sequencing. Subsequently, ib-miR156 was over-expressed in Arabidopsis. Interestingly, the ib-miR156 over-expressing plants showed suppressed abundance of SPL and a purplish phenotype. Concomitantly, upregulated expression of four anthocyanin pathway genes was detected in transgenic Arabidopsis plants. Finally, a putative ib-miRNA-target model involved in anthocyanin biosynthesis in sweetpotato was proposed.

CONCLUSIONS

The results represented a comprehensive expression profiling of miRNAs related to anthocyanin accumulation in sweetpotato and provided important clues for understanding the regulatory network of anthocyanin biosynthesis mediated by miRNA in tuberous crops.

Transcriptome analysis reveals the different compatibility between LAAA × AA and LAAA × LL in Lilium

To unveil the mechanism of the compatibility of odd-allotetraploid lily (LAAA) as female with diploid male lily, the differences of expressed unigenes in the ovaries and leaves between LAAA × AA and LAAA × LL were investigated using transcriptome analysis. The results showed the fruits of LAAA × AA well developed, while those of LAAA × LL aborted. The number of differentially expressed genes was less in the ovaries of LAAA × AA than those of LAAA × LL, but it showed opposite trend in those of leaves. The unigenes related with auxins, cytokinins, gibberellins, antioxidants, expansins, chlorophylls, carbohydrates, transport proteins were usually up-expressed in the ovaries and leaves of LAAA × AA but not in LAAA × LL; while those of abscisic acid, ethylene, jasmonic acid, and salicylic acid were increased in the ovaries or leaves of LAAA × LL but not in LAAA × AA. The up-expressed unigenes in the ovaries and leaves of LAAA × AA played positive roles in its fruit development because the products of the genes, like phytohormones and antioxidants, had functions protecting leaves from senescence or scavenging ROS, and thus LAAA was compatible with AA, while those of LAAA × LL played negative roles and caused its fruits aborted, and hence LAAA was incompatible with LL.

Jasmonic Acid Signaling Pathway in Plants

Jasmonic acid (JA) and its precursors and dervatives, referred as jasmonates (JAs) are important molecules in the regulation of many physiological processes in plant growth and development, and especially the mediation of plant responses to biotic and abiotic stresses. JAs biosynthesis, perception, transport, signal transduction and action have been extensively investigated. In this review, we will discuss the initiation of JA signaling with a focus on environmental signal perception and transduction, JA biosynthesis and metabolism, transport of signaling molecules (local transmission, vascular bundle transmission, and airborne transportation), and biological function (JA signal receptors, regulated transcription factors, and biological processes involved).

Characterization of phytohormone and transcriptome reprogramming profiles during maize early kernel development

BACKGROUND

During maize early kernel development, the dramatic transcriptional reprogramming determines the rate of developmental progression, and phytohormone plays critical role in these important processes. To investigate the phytohormone levels and transcriptome reprogramming profiles during maize early kernel development, two maize inbreds with similar genetic background but different mature kernel sizes (ILa and ILb) were used.

RESULTS

The levels of indole-3-acetic acid (IAA) were increased continuously in maize kernels from 5 days after pollination (DAP) to 10 DAP. ILa had smaller mature kernels than ILb, and ILa kernels had significantly lower IAA levels and significantly higher SA levels than ILb at 10 DAP. The different phytohormone profiles correlated with different transcriptional reprogramming in the two kernels. The global transcriptomes in ILa and ILb kernels were strikingly different at 5 DAP, and their differences peaked at 8 DAP. Functional analysis showed that the biggest transcriptome difference between the two kernels is those response to biotic and abiotic stresses. Further analyses indicated that the start of dramatic transcriptional reprogramming and the onset of significantly enriched functional categories, especially the "plant hormone signal transduction" and "starch and sucrose metabolism", was earlier in ILa than in ILb, whereas more significant enrichment of those functional categories occurred at later stage of kernel development in ILb.

CONCLUSIONS

These results indicate that later onset of the significantly enriched functional categories, coincide with their stronger activities at a later developmental stage and higher IAA level, are necessary for young kernels to undergo longer mitotic activity and finally develop a larger kernel size. The different onset times and complex interactions of the important functional categories, especially phytohormone signal, and carbohydrate metabolism, form the most important molecular regulators mediating maize early kernel development.

Characterization of S40-like proteins and their roles in response to environmental cues and leaf senescence in rice

BACKGROUND

Senescence affects the quality and yield of plants by regulating different traits of plants. A few members of S40 gene family, the barley HvS40 and the Arabidopsis AtS40-3, have been shown to play a role in leaf senescence in Barley and Arabidopsis. Although we previously reported that S40 family exist in most of plants, up to now, no more function of S40 members in plant has been demonstrated. The aim of this study was to provide the senescence related information of S40 gene family in rice as rice is a major crop that feeds about half of the human population in the world.

RESULTS

A total of 16 OsS40 genes were identified from the genome database of Oryza sativa L. japonica by bioinformatics analysis. Phylogenetic analysis reveals that the 16 OsS40 proteins are classified into five groups, and 4 of the 16 members belong to group I to which also the HvS40 and AtS40-3 is assigned. S40 genes of rice show high structural similarities, as 13 out of the 16 genes have no intron and the other 3 genes have only 1 or 2 introns. The expression patterns of OsS40 genes were analyzed during natural as well as stress-induced leaf senescence in correspondence with senescence marker genes. We found that 6 of them displayed differential but clearly up-regulated transcript profiles under diverse situations of senescence, including darkness, nitrogen deficiency, hormone treatments as well as pathogen infection. Furthermore, three OsS40 proteins were identified as nuclear located proteins by transient protoplast transformation assay.

CONCLUSIONS

Taking all findings together, we concluded that OsS40-1, OsS40-2, OsS40-12 and OsS40-14 genes have potential regulatory function of crosstalk among abiotic, biotic and developmental senescence in rice. Our results provide valuable baseline for functional validation studies of the rice S40 genes in rice leaf senescence.

The R2R3-MYB Transcription Factor MYB49 Regulates Cadmium Accumulation

Abscisic acid (ABA) reduces accumulation of potentially toxic cadmium (Cd) in plants. How the ABA signal is transmitted to modulate Cd uptake remains largely unclear. Here, we report that the basic region/Leu zipper transcription factor ABSCISIC ACID-INSENSITIVE5 (ABI5), a central ABA signaling molecule, is involved in ABA-repressed Cd accumulation in plants by physically interacting with a previously uncharacterized R2R3-type MYB transcription factor, MYB49. Overexpression of the Cd-induced MYB49 gene in Arabidopsis (Arabidopsis thaliana) resulted in a significant increase in Cd accumulation, whereas myb49 knockout plants and plants expressing chimeric repressors of MYB49:ERF-associated amphiphilic repression motif repression domain (SRDX49) exhibited reduced accumulation of Cd. Further investigations revealed that MYB49 positively regulates the expression of the basic helix-loop-helix transcription factors bHLH38 and bHLH101 by directly binding to their promoters, leading to activation of IRON-REGULATED TRANSPORTER1, which encodes a metal transporter involved in Cd uptake. MYB49 also binds to the promoter regions of the heavy metal-associated isoprenylated plant proteins (HIPP22) and HIPP44, resulting in up-regulation of their expression and subsequent Cd accumulation. On the other hand, as a feedback mechanism to control Cd uptake and accumulation in plant cells, Cd-induced ABA up-regulates the expression of ABI5, whose protein product interacts with MYB49 and prevents its binding to the promoters of downstream genes, thereby reducing Cd accumulation. Our results provide new insights into the molecular feedback mechanisms underlying ABA signaling-controlled Cd uptake and accumulation in plants.

Leaf Senescence: Systems and Dynamics Aspects

Leaf senescence is an important developmental process involving orderly disassembly of macromolecules for relocating nutrients from leaves to other organs and is critical for plants' fitness. Leaf senescence is the response of an intricate integration of various environmental signals and leaf age information and involves a complex and highly regulated process with the coordinated actions of multiple pathways. Impressive progress has been made in understanding how senescence signals are perceived and processed, how the orderly degeneration process is regulated, how the senescence program interacts with environmental signals, and how senescence regulatory genes contribute to plant productivity and fitness. Employment of systems approaches using omics-based technologies and characterization of key regulators have been fruitful in providing newly emerging regulatory mechanisms. This review mainly discusses recent advances in systems understanding of leaf senescence from a molecular network dynamics perspective. Genetic strategies for improving the productivity and quality of crops are also described.

The Role and Regulation of Autophagy and the Proteasome During Aging and Senescence in Plants

Aging and senescence in plants has a major impact on agriculture, such as in crop yield, the value of ornamental crops, and the shelf life of vegetables and fruits. Senescence represents the final developmental phase of the leaf and inevitably results in the death of the organ. Still, the process is completely under the control of the plant. Plants use their protein degradation systems to maintain proteostasis and transport or salvage nutrients from senescing organs to develop reproductive parts. Herein, we present an overview of current knowledge about the main protein degradation pathways in plants during senescence: The proteasome and autophagy. Although both pathways degrade proteins, autophagy appears to prevent aging, while the proteasome functions as a positive regulator of senescence.

Trehalose phosphate synthase 5-dependent trehalose metabolism modulates basal defense responses in Arabidopsis thaliana

Despite the recent discovery that trehalose synthesis is important for plant development and abiotic stress tolerance, the effects of trehalose on biotic stress responses remain relatively unknown. In this study, we demonstrate that TREHALOSE PHOSPHATE SYNTHASE 5 (TPS5)-dependent trehalose metabolism regulates Arabidopsis thaliana defenses against pathogens (necrotrophic Botrytis cinerea and biotrophic Pseudomonas syringae). Pathogen infection increased trehalose levels and upregulated TPS5 expression. Application of exogenous trehalose significantly improved plant defenses against B. cinerea, but increased the susceptibility of plants to P. syringae. We demonstrate that elevated trehalose biosynthesis, in transgenic plants over-expressing TPS5, also increased the susceptibility to P. syringae, but decreased the disease symptoms caused by B. cinerea. The knockout of TPS5 prevented the accumulation of trehalose and enhanced defense responses against P. syringae. Additionally, we observed that a TPS5-interacting protein (multiprotein bridging factor 1c) was required for induced expression of TPS5 during pathogen infections. Furthermore, we show that trehalose promotes P. syringae growth and disease development, via a mechanism involving suppression of the plant defense gene, Pathogenesis-Related Protein 1. These findings provide insight into the function of TPS5-dependent trehalose metabolism in plant basal defense responses.

MdbHLH93, an apple activator regulating leaf senescence, is regulated by ABA and MdBT2 in antagonistic ways

The molecular mechanism of leaf senescence in apple (Malus domestica) is still not fully understood. We used gene expression analysis and protein-protein interactions to decipher the relationships of abscisic acid (ABA) and two proteins, MdbHLH93 and MdBT2, in the senescence process. We found that MdbHLH93 promoted leaf senescence and the expression of senescence-related genes, which exhibited similar effects to ABA on leaf senescence. MdbHLH93 activated directly the transcription of MdSAG18. We also found that an ABA-responsive protein, MdBT2, interacted directly with MdbHLH93, and induced the ubiquitination and degradation of the MdbHLH93 protein, and thus delayed leaf senescence. Our findings provide new insights into the regulatory network of leaf senescence through the functional interactions among ABA, MdbHLH93 and MdBT2.

The WRKY transcription factor GhWRKY27 coordinates the senescence regulatory pathway in upland cotton (Gossypium hirsutum L.)

BACKGROUND

Premature senescence can reduce the yield and quality of crops. WRKY transcription factors (TFs) play important roles during leaf senescence, but little is known about their ageing mechanisms in cotton.

RESULTS

In this study, a group III WRKY TF, GhWRKY27, was isolated and characterized. The expression of GhWRKY27 was induced by leaf senescence and was higher in an early-ageing cotton variety than in a non-early-ageing cotton variety. Overexpression of GhWRKY27 in Arabidopsis promoted leaf senescence, as determined by reduced chlorophyll content and elevated expression of senescence-associated genes (SAGs). Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that GhWRKY27 interacted with an MYB TF, GhTT2. Putative target genes of GhWRKY27 were identified via chromatin immunoprecipitation followed by sequencing (ChIP-seq). Yeast one-hybrid (Y1H) assay and electrophoretic mobility shift assay (EMSA) revealed that GhWRKY27 binds directly to the promoters of cytochrome P450 94C1 (GhCYP94C1) and ripening-related protein 2 (GhRipen2-2). In addition, the expression patterns of GhTT2, GhCYP94C1 and GhRipen2-2 were identified during leaf senescence. Transient dual-luciferase reporter assay indicated that GhWRKY27 could activate the expression of GhCYP94C1 and GhRipen2-2.

CONCLUSIONS

Our work lays the foundation for further study of the functional roles of WRKY genes during leaf senescence in cotton. In addition, our data provide new insights into the senescence-associated mechanisms of WRKY genes in cotton.

Roles of potential plant hormones and transcription factors in controlling leaf senescence and drought tolerance

Plant leaves offer an exclusive windowpane to uncover the changes in organs, tissues, and cells as they advance towards the process of senescence and death. Drought-induced leaf senescence is an intricate process with remarkably coordinated phases of onset, progression, and completion implicated in an extensive reprogramming of gene expression. Advancing leaf senescence remobilizes nutrients to younger leaves thereby contributing to plant fitness. However, numerous mysteries remain unraveled concerning leaf senescence. We are not still able to correlate leaf senescence and drought stress to endogenous and exogenous environments. Furthermore, we need to decipher how molecular mechanisms of the leaf senescence and levels of drought tolerance are advanced and how is the involvement of SAGs in drought tolerance and plant fitness. This review provides the perspicacity indispensable for facilitating our coordinated point of view pertaining to leaf senescence together with inferences on progression of whole plant aging. The main segments discussed in the review include coordination between hormonal signaling, leaf senescence, drought tolerance, and crosstalk between hormones in leaf senescence regulation.

The WRKY transcription factor, WRKY13, activates PDR8 expression to positively regulate cadmium tolerance in Arabidopsis

Cadmium (Cd) extrusion is an important mechanism conferring Cd tolerance by decreasing its accumulation in plants. Previous studies have identified an Arabidopsis ABC transporter, PDR8, as a Cd extrusion pump conferring Cd tolerance. However, the regulation of PDR8 in response to Cd stress is still largely unknown. In this study, we identified an Arabidopsis cadmium-tolerant dominant mutant, designated xcd3-D, from the XVE-tagging T-DNA insertion lines by a gain-of-function genetic screen. The corresponding gene was cloned and shown to encode a nuclear WRKY transcription factor WRKY13. Expression of WRKY13 was induced by Cd stress. Overexpression of WRKY13 resulted in decreased Cd accumulation and enhanced Cd tolerance, whereas loss-of-function of WRKY13 led to increased Cd accumulation and sensitivity. Further analysis showed that WRKY13 activates the transcription of PDR8 by directly binding to its promoter. Genetic analysis indicated that WRKY13 acts upstream of PDR8 to positively regulate Cd tolerance. Our results provide evidence that WRKY13 directly targets PDR8 to positively regulate Cd tolerance in Arabidopsis.

The Cotton GhWRKY91 Transcription Factor Mediates Leaf Senescence and Responses to Drought Stress in Transgenic Arabidopsis thaliana

WRKY transcription factors (TFs) play essential roles in the plant response to leaf senescence and abiotic stress. However, the WRKY TFs involved in leaf senescence and stress tolerance in cotton (Gossypium hirsutum L.) are still largely unknown. In this study, a WRKY gene, GhWRKY91, was isolated and thoroughly characterized. Transcriptional activity assays showed that GhWRKY91 could activate transcription in yeast. The expression pattern of GhWRKY91 during leaf senescence, and in response to abscisic acid (ABA) and drought stress was evaluated. β-Glucuronidase (GUS) activity driven by the GhWRKY91 promoter in transgenic Arabidopsis was reduced upon exposure to ABA and drought treatments. Constitutive expression of GhWRKY91 in Arabidopsis delayed natural leaf senescence. GhWRKY91 transgenic plants exhibited increased drought tolerance and presented delayed drought-induced leaf senescence, as accompanied by reinforced expression of stress-related genes and attenuated expression of senescence-associated genes (SAGs). Yeast one-hybrid (Y1H) assays and electrophoretic mobility shift assays (EMSAs) revealed that GhWRKY91 directly targets GhWRKY17, a gene associated with ABA signals and reactive oxygen species (ROS) production. A transient dual-luciferase reporter assay demonstrated that GhWRKY91 activated the expression of GhWRKY17. Our results suggest that GhWRKY91 might negatively regulate natural and stress-induced leaf senescence and provide a foundation for further functional studies on leaf senescence and the stress response in cotton.

WRKY12 represses GSH1 expression to negatively regulate cadmium tolerance in Arabidopsis

The WRKY transcription factor WRKY12 negatively regulates Cd tolerance in Arabidopsis via the glutathione-dependent phytochelatin synthesis pathway by directly targeting GSH1 and indirectly repressing phytochelatin synthesis-related gene expression. Cadmium (Cd) is a widespread pollutant toxic to plants. The glutathione (GSH)-dependent phytochelatin (PC) synthesis pathway plays key roles in Cd detoxification. However, its regulatory mechanism remains largely unknown. Here, we showed a previously unknown function of the WRKY transcription factor WRKY12 in the regulation of Cd tolerance by repressing the expression of PC synthesis-related genes. The expression of WRKY12 was inhibited by Cd stress. Enhanced Cd tolerance was observed in the WRKY12 loss-of-function mutants, whereas increased Cd sensitivity was found in the WRKY12-overexpressing plants. Overexpression and loss-of-function of WRKY12 were associated respectively with increased and decreased Cd accumulation by repressing or releasing the expression of the genes involved in the PC synthesis pathway. Transient expression assay showed that WRKY12 repressed the expression of GSH1, GSH2, PCS1, and PCS2. Further analysis indicated that WRKY12 could directly bind to the W-box of the promoter in GSH1 but not in GSH2, PCS1, and PCS2 in vivo. Together, our results suggest that WRKY12 directly targets GSH1 and indirectly represses PC synthesis-related gene expression to negatively regulate Cd accumulation and tolerance in Arabidopsis.

Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development

Background

Leaf development is a complex biological process that is accompanied by wide transcriptional changes. Many protein-coding genes have been characterized in plant leaves, but little attention has been given to noncoding RNAs (ncRNAs). Moreover, increasing evidence indicates that an intricate interplay among RNA species, including protein-coding RNAs and ncRNAs, exists in eukaryotic transcriptomes, however, it remains elusive in plant leaves.

Results

We detected novel ncRNAs, such as circular RNAs (circRNAs) and long noncoding RNAs (lncRNAs), and further constructed and analyzed their associated competitive endogenous RNA (ceRNA) networks in Arabidopsis leaves. Transcriptome profiling showed extensive changes during leaf development. In addition, comprehensive detection of circRNAs in other plant leaves suggested that circRNAs are widespread in plant leaves. To investigate the complex post-transcriptional interactions in Arabidopsis leaves, we constructed a global circRNA/lncRNA-associated ceRNA network. Functional analysis revealed that ceRNAs were highly correlated with leaf development. These ceRNAs could be divided into six clusters, which were enriched for different functional classes. Stage-specific ceRNA networks were further constructed and comparative analysis revealed different roles of stage common and specific hub ceRNAs.

Conclusions

Our results demonstrate that understanding the ceRNA interactions will lead insights into gene regulations implicated in leaf development.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4993-2) contains supplementary material, which is available to authorized users.

Arabidopsis VQ18 and VQ26 proteins interact with ABI5 transcription factor to negatively modulate ABA response during seed germination

Seed germination and early seedling establishment, critical developmental stages in the life cycle of seed plants, are modulated by diverse endogenous hormones and the surrounding environment. Arabidopsis ABSCISIC ACID-INSENSITIVE5 (ABI5) is a central transcription factor of abscisic acid (ABA) signaling that represses those processes. ABI5 is precisely modulated at post-translational level; however, whether it interacts with other crucial transcriptional regulators remains to be investigated. In this study, VQ18 and VQ26, two members of the recently-identified VQ family, were found to interact with ABI5 in vitro and in vivo. Phenotypic analysis showed that VQ18 and VQ26 are responsive to ABA and negatively mediate ABA signaling redundantly during seed germination. Simultaneously decreasing VQ18 and VQ26 expression levels enhanced ABA signaling to suppress seed germination, whereas overexpressing these two VQ genes resulted in the germinated seeds being less ABA-sensitive. Consistently, the expression levels of several ABI5 targets were modulated by VQ18 and VQ26. The increased ABA signaling of plants in which VQ18 and VQ26 were simultaneously suppressed required ABI5. Additionally, VQ18 and VQ26 acted as negative interactors of the ABI5 transcription factor. Our study reveals a previously unidentified regulatory role of VQ proteins, which act antagonistically with ABI5 to maintain the appropriate ABA signaling level to fine-tune seed germination and early seedling establishment.

Characterization of wheat (Triticum aestivum) TIFY family and role of Triticum Durum TdTIFY11a in salt stress tolerance

The TIFY proteins constitute a plant-specific super-family and they are involved in regulating many plant processes, such as development, defences and stress responses. The Jasmonate-ZIM-Domain (JAZ) proteins, the best-characterized sub-group of the TIFY family are key regulator of the jasmonic acid (JA) signalling pathway. Jasmonates regulate several aspects of plant development, and play a primary role in defence mechanisms as well as in plant responses to abiotic stresses. The TIFY family is well studied in dicots but poorly investigated in monocots. The present study reports an extensive genomic identification of TIFY proteins from Triticum aestivum. We identified 49 TIFY genes, which were annotated according to three sub-genomes (AABBDD) of T. aestivum. Following their clustering with Oryza sativa and Brachypodium distachyon, the 49 genes were grouped in 18 different TIFY homeologous subsets. Expression analyses of 6 representative TIFY genes on Tunisian durum wheat seedlings revealed their differential regulation by various stress treatment, including JA, ABA and salt stress. TIFY11a was specifically induced after salt treatment. Transgenic lines over-expressing TdTIFY11a showed higher germination and growth rates under high salinity conditions, compared to wild type plants. In summary, our results outline a relevant role of wheat TIFY proteins in promoting germination under salt stress.

Synchronisation of Arabidopsis flowering time and whole-plant senescence in seasonal environments

Synchronisation of flowering phenology has often been observed between individuals within plant species. We expected that a critical role of flowering-time control under natural conditions is a phenological synchronisation. However, no studies have quantified the level of synchronisation of reproductive timing relative to germination timing under natural conditions. In a sequential seeding experiment (SSE) in which we manipulated the germination timing of Arabidopsis thaliana accessions, we developed a quantification index to evaluate reproductive synchrony in annual plants. In the SSE, we identified a novel phenomenon of reproductive synchrony: senescence synchrony. The role of vernalisation in realising flowering synchrony between plants of different ages under natural conditions was demonstrated by synchronisation and de-synchronisation of flowering initiation in vernalisation-sensitive and less-vernalisation-sensitive accessions, respectively. We also observed up-regulation of senescence-related genes at corresponding times. The approach we developed in this study provides a set of concepts and procedures that can be used to study reproductive synchrony experimentally under natural conditions.

Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress

Background

WRKY proteins comprise a large family of transcription factors that play important roles in many aspects of physiological processes and adaption to environment. However, little information was available about the WRKY genes in pineapple (Ananas comosus), an important tropical fruits. The recent release of the whole-genome sequence of pineapple allowed us to perform a genome-wide investigation into the organization and expression profiling of pineapple WRKY genes.

Results

In the present study, 54 pineapple WRKY (AcWRKY) genes were identified and renamed on the basis of their respective chromosome distribution. According to their structural and phylogenetic features, the 54 AcWRKYs were further classified into three main groups with several subgroups. The segmental duplication events played a major role in the expansion of pineapple WRKY gene family. Synteny analysis and phylogenetic comparison of group III WRKY genes provided deep insight into the evolutionary characteristics of pineapple WRKY genes. Expression profiles derived from transcriptome data and real-time quantitative PCR analysis exhibited distinct expression patterns of AcWRKY genes in various tissues and in response to different abiotic stress and hormonal treatments.

Conclusions

Fifty four WRKY genes were identified in pineapple and the structure of their encoded proteins, their evolutionary characteristics and expression patterns were examined in this study. This systematic analysis provided a foundation for further functional characterization of WRKY genes with an aim of pineapple crop improvement.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4880-x) contains supplementary material, which is available to authorized users.

An oilseed rape WRKY-type transcription factor regulates ROS accumulation and leaf senescence in Nicotiana benthamiana and Arabidopsis through modulating transcription of RbohD and RbohF

MAIN CONCLUSION

Overexpression of BnaWGR1 causes ROS accumulation and promotes leaf senescence. BnaWGR1 binds to promoters of RbohD and RbohF and regulates their expression. Manipulation of leaf senescence process affects agricultural traits of crop plants, including biomass, seed yield and stress resistance. Since delayed leaf senescence usually enhances tolerance to multiple stresses, we analyzed the function of specific MAPK-WRKY cascades in abiotic and biotic stress tolerance as well as leaf senescence in oilseed rape (Brassica napus L.), one of the important oil crops. In the present study, we showed that expression of one WRKY gene from oilseed rape, BnaWGR1, induced an accumulation of reactive oxygen species (ROS), cell death and precocious leaf senescence both in Nicotiana benthamiana and transgenic Arabidopsis (Arabidopsis thaliana). BnaWGR1 regulates the transcription of two genes encoding key enzymes implicated in production of ROS, that is, respiratory burst oxidase homolog (Rboh) D and RbohF. A dual-luciferase reporter assay confirmed the transcriptional regulation of RbohD and RbohF by BnaWGR1. In vitro electrophoresis mobility shift assay (EMSA) showed that BnaWGR1 could bind to W-box cis-elements within promoters of RbohD and RbohF. Moreover, RbohD and RbohF were significantly upregulated in transgenic Arabidopsis overexpressing BnaWGR1. In summary, these results suggest that BnaWGR1 could positively regulate leaf senescence through regulating the expression of RbohD and RbohF genes.

Modularity in Jasmonate Signaling for Multistress Resilience

The plant hormone jasmonate coordinates immune and growth responses to increase plant survival in unpredictable environments. The core jasmonate signaling pathway comprises several functional modules, including a repertoire of COI1-JAZ (CORONATINE INSENSITIVE1-JASMONATE-ZIM DOMAIN) coreceptors that couple jasmonoyl-l-isoleucine perception to the degradation of JAZ repressors, JAZ-interacting transcription factors that execute physiological responses, and multiple negative feedback loops to ensure timely termination of these responses. Here, we review the jasmonate signaling pathway with an emphasis on understanding how transcriptional responses are specific, tunable, and evolvable. We explore emerging evidence that JAZ proteins integrate multiple informational cues and mediate crosstalk by propagating changes in protein-protein interaction networks. We also discuss recent insights into the evolution of jasmonate signaling and highlight how plant-associated organisms manipulate the pathway to subvert host immunity. Finally, we consider how this mechanistic foundation can accelerate the rational design of jasmonate signaling for improving crop resilience and harnessing the wellspring of specialized plant metabolites.

WRKY2/34-VQ20 Modules in Arabidopsis thaliana Negatively Regulate Expression of a Trio of Related MYB Transcription Factors During Pollen Development

Male gametogenesis in plants is tightly controlled and involves the complex and precise regulation of transcriptional reprogramming. Interactions between WRKY proteins and VQ motif-containing proteins are required to control these complicated transcriptional networks. However, our understanding of the mechanisms by which these complexes affect downstream gene expression is quite limited. In this study, we found that WRKY2 and WKRY34 repress MYB97, MYB101, and MYB120 expression during male gametogenesis. MYB expression was up-regulated in the wrky2-1 wrky34-1 vq20-1 triple mutant during male gametogenesis. The expression levels of six potential targets of the three MYBs increased the most in the wrky2-1 wrky34-1 vq20-1 triple mutant, followed by the wrky2-1 wrky34-1 double mutant, compared with in wild-type. Yeast one-hybrid and dual luciferase reporter assays indicated that WRKY2 and WRKY34 recognized the MYB97 promoter by binding to its W-boxes. MYB97 overexpression caused defects in pollen germination and pollen tube length, which impacted male fertility. Thus, WRKY2/34-VQ20 complexes appear to negatively regulate the expression of certain MYBs during plant male gametogenesis.

Characterization of a Transcriptional Regulator, BrWRKY6, Associated with Gibberellin-Suppressed Leaf Senescence of Chinese Flowering Cabbage

Phytohormone gibberellin (GA) and plant-specific WRKY transcription factors (TFs) are reported to play important roles in leaf senescence. The association of WRKY TFs with GA-mediated leaf senescence of economically important leafy vegetables like Chinese flowering cabbage, however, remains largely unknown. In this study, we showed that exogenous application of GA₃ suppressed Chinese flowering cabbage leaf senescence, with GA₃-treated cabbages maintaining a higher level of maximum quantum yield (Fv/Fm) and total chlorophyll content. GA₃ treatment also led to lower electrolyte leakage and expression level of a series of senescence-associated genes (SAGs) including BrSAG12 and BrSAG19, and chlorophyll catabolic genes (CCGs) BrPPH1, BrNYC1, and BrSGRs. In addition, higher transcription levels of GA biosynthetic genes BrKAO2 and BrGA20ox2 were found after GA₃ treatment. More importantly, a GA-repressible, nuclear-localized WRKY TF, BrWRKY6, a homologue of the Arabidopsis AtWRKY6, was identified and characterized. BrWRKY6 was GA-repressible and localized in the nucleus. Further experiments revealed that BrWRKY6 repressed the expression of BrKAO2 and BrGA20ox2, while it activated BrSAG12, BrNYC1, and BrSGR1, through binding to their promoters via the W-box cis-element. Together, the novel GA-WRKY link reported in our study provides new insight into the transcriptional regulation of GA-suppressed leaf senescence in Chinese flowering cabbage.

Genetic redundancy of senescence-associated transcription factors in Arabidopsis

Leaf senescence is a genetically programmed process that constitutes the last stage of leaf development, and involves massive changes in gene expression. As a result of the intensive efforts that have been made to elucidate the molecular genetic mechanisms underlying leaf senescence, 184 genes that alter leaf senescence phenotypes when mutated or overexpressed have been identified in Arabidopsis thaliana over the past two decades. Concurrently, experimental evidence on functional redundancy within senescence-associated genes (SAGs) has increased. In this review, we focus on transcription factors that play regulatory roles in Arabidopsis leaf senescence, and describe the relationships among gene duplication, gene expression level, and senescence phenotypes. Previous findings and our re-analysis demonstrate the widespread existence of duplicate SAG pairs and a correlation between gene expression levels in duplicate genes and senescence-related phenotypic severity of the corresponding mutants. We also highlight effective and powerful tools that are available for functional analyses of redundant SAGs. We propose that the study of duplicate SAG pairs offers a unique opportunity to understand the regulation of leaf senescence and can guide the investigation of the functions of redundant SAGs via reverse genetic approaches.

New insights into the regulation of leaf senescence in Arabidopsis

Plants undergo developmental changes throughout their life history. Senescence, the final stage in the life history of a leaf, is an important and unique developmental process whereby plants relocate nutrients from leaves to other developing organs, such as seeds, stems, or roots. Recent attempts to answer fundamental questions about leaf senescence have employed a combination of new ideas and advanced technologies. As senescence is an integral part of a plant's life history that is linked to earlier developmental stages, age-associated leaf senescence may be analysed from a life history perspective. The successful utilization of multi-omics approaches has resolved the complicated process of leaf senescence, replacing a component-based view with a network-based molecular mechanism that acts in a spatial-temporal manner. Senescence and death are critical for fitness and are thus evolved characters. Recent efforts have begun to focus on understanding the evolutionary basis of the developmental process that incorporates age information and environmental signals into a plant's survival strategy. This review describes recent insights into the regulatory mechanisms of leaf senescence in terms of systems-level spatiotemporal changes, presenting them from the perspectives of life history strategy and evolution.

The biochemistry and molecular biology of chlorophyll breakdown

Chlorophyll breakdown is one of the most obvious signs of leaf senescence and fruit ripening. The resulting yellowing of leaves can be observed every autumn, and the color change of fruits indicates their ripening state. During these processes, chlorophyll is broken down in a multistep pathway, now termed the 'PAO/phyllobilin' pathway, acknowledging the core enzymatic breakdown step catalysed by pheophorbide a oxygenase, which determines the basic linear tetrapyrrole structure of the products of breakdown that are now called 'phyllobilins'. This review provides an update on the PAO/phyllobilin pathway, and focuses on recent biochemical and molecular progress in understanding phyllobilin-modifying reactions as the basis for phyllobilin diversity, on the evolutionary diversity of the pathway, and on the transcriptional regulation of the pathway genes.

Aux/IAA Gene Family in Plants: Molecular Structure, Regulation, and Function

Auxin plays a crucial role in the diverse cellular and developmental responses of plants across their lifespan. Plants can quickly sense and respond to changes in auxin levels, and these responses involve several major classes of auxin-responsive genes, including the Auxin/Indole-3-Acetic Acid (Aux/IAA) family, the auxin response factor (ARF) family, small auxin upregulated RNA (SAUR), and the auxin-responsive Gretchen Hagen3 (GH3) family. Aux/IAA proteins are short-lived nuclear proteins comprising several highly conserved domains that are encoded by the auxin early response gene family. These proteins have specific domains that interact with ARFs and inhibit the transcription of genes activated by ARFs. Molecular studies have revealed that Aux/IAA family members can form diverse dimers with ARFs to regulate genes in various ways. Functional analyses of Aux/IAA family members have indicated that they have various roles in plant development, such as root development, shoot growth, and fruit ripening. In this review, recently discovered details regarding the molecular characteristics, regulation, and protein-protein interactions of the Aux/IAA proteins are discussed. These details provide new insights into the molecular basis of the Aux/IAA protein functions in plant developmental processes.

WHIRLY1 Occupancy Affects Histone Lysine Modification and WRKY53 Transcription in Arabidopsis Developmental Manner

Single-stranded DNA-binding proteins (SSBs) are assumed to involve in DNA replication, DNA repairmen, and gene transcription. Here, we provide the direct evidence on the functionality of an Arabidopsis SSB, WHIRLY1, by using loss- or gain-of-function lines. We show that WHIRLY1 binding to the promoter of WRKY53 represses the enrichment of H3K4me3, but enhances the enrichment of H3K9ac at the region contained WHIRLY1-binding sequences and TATA box or the translation start region of WRKY53, coincided with a recruitment of RNAPII. In vitro ChIP assays confirm that WHIRLY1 inhibits H3K4me3 enrichment at the preinitiation complex formation stage, while promotes H3K9ac enrichment and RNAPII recruitment at the elongation stage, consequently affecting the transcription of WRKY53. These results further explore the molecular actions underlying SSB-mediated gene transcription through epigenetic regulation in plant senescence.

Association of BrERF72 with methyl jasmonate-induced leaf senescence of Chinese flowering cabbage through activating JA biosynthesis-related genes

The ethylene response factor (ERF) and phytohormone jasmonate (JA) are reported to function in leaf senescence. The involvement of ERF in JA-mediated leaf senescence, however, needs to be elucidated. In the present work, we demonstrate a Chinese flowering cabbage ERF transcription factor (TF), BrERF72, that is associated with JA-promoted leaf senescence. Exogenous application of methyl jasmonate (MeJA)-accelerated leaf senescence of Chinese flowering cabbage, evidenced by the data that MeJA treatment led to the stronger reduction in the maximum quantum yield (Fv/Fm), photosynthetic electron transport rate (ETR), and total chlorophyll content, while significant induction in the expression of several senescence-associated genes (SAGs) including BrSAG12, BrSAG19, and chlorophyll catabolic genes (CCGs) BrPAO1, BrNYC1, BrPPH1, and BrSGR1. Increases in levels of endogenous JA and transcripts of JA biosynthetic genes BrLOX4, BrAOC3, and BrOPR3 were also found after MeJA treatment. BrERF72 was a MeJA-inducible, nucleus-localized protein, and possessed trans-activation ability. Transient overexpression of BrERF72 in tobacco leaves also promoted leaf senescence. More importantly, further experiments revealed that BrERF72 directly activated expression of BrLOX4, BrAOC3, and BrOPR3 through binding to their promoters via the GCC or DRE/CRT cis-element. Together, the novel JA-ERF association reported in our study uncovers a new insight into the transcriptional regulation of JA production mediated by ERF during JA-promoted leaf senescence in Chinese flowering cabbage.

Initiation, Progression, and Genetic Manipulation of Leaf Senescence

As a representative form of plant senescence, leaf senescence has received the most attention during the last two decades. In this chapter we summarize the initiation of leaf senescence by various internal and external signals, the progression of senescence including switches in gene expression, as well as changes at the biochemical and cellular levels during leaf senescence. Impacts of leaf senescence in agriculture and genetic approaches that have been used in manipulating leaf senescence of crop plants are discussed.

Transcription Factor WRKY75 Interacts with DELLA Proteins to Affect Flowering

Flowering time is tightly controlled by both endogenous and exogenous signals. Although several lines of evidence have suggested the involvement of WRKY transcription factors in floral initiation, the underlying mechanisms and signaling pathways involved remain elusive. Here, we newly identified Arabidopsis (Arabidopsis thaliana) WRKY DNA binding protein75 (WRKY75) as a positive regulator of flowering initiation. Mutation of WRKY75 resulted in a delay in flowering, whereas overexpression of WRKY75 significantly accelerated flowering in Arabidopsis. Gene expression analysis showed that the transcript abundance of the flowering time integrator gene FLOWERING LOCUS T (FT) was lower in wrky75 mutants than in the wild type, but greater in WRKY75-overexpressing plants. Chromatin immunoprecipitation assays revealed that WRKY75 directly binds to the promoter of FT Both in vivo and in vitro biochemical analyses demonstrated that WRKY75 interacts with DELLA proteins. We found that both REPRESSOR OF ga1-3 (RGA) RGA-LIKE1 (RGL1) and GA INSENSITIVE (GAI) can repress the activation ability of WRKY75, thereby attenuating expression of its regulon. Genetic analyses indicated that WRKY75 positively regulates flowering in a FT-dependent manner and overexpression of RGL1 or gain-of-function of GAI could partially rescue the early flowering phenotype of WRKY75-overexpressing plants. Taken together, our results demonstrate that WRKY75 may function as a new component of the GA-mediated signaling pathway to positively regulate flowering in Arabidopsis.