Genome-Wide Identification and Expression Analysis of the Stearoyl-Acyl Carrier Protein Δ9 Desaturase Gene Family under Abiotic Stress in Barley.

Stearoyl-acyl carrier protein (ACP) Δ9 desaturase (SAD) is a critical fatty acid dehydrogenase in plants, playing a prominent role in regulating the synthesis of unsaturated fatty acids (UFAs) and having a significant impact on plant growth and development. In this study, we conducted a comprehensive genomic analysis of the SAD family in barley (Hordeum vulgare L.), identifying 14 HvSADs with the FA_desaturase_2 domain, which were divided into four subgroups based on sequence composition and phylogenetic analysis, with members of the same subgroup possessing similar genes and motif structures. Gene replication analysis suggested that tandem and segmental duplication may be the major reasons for the expansion of the SAD family in barley. The promoters of HvSADs contained various cis-regulatory elements (CREs) related to light, abscisic acid (ABA), and methyl jasmonate (MeJA). In addition, expression analysis indicated that HvSADs exhibit multiple tissue expression patterns in barley as well as different response characteristics under three abiotic stresses: salt, drought, and cold. Briefly, this evolutionary and expression analysis of HvSADs provides insight into the biological functions of barley, supporting a comprehensive analysis of the regulatory mechanisms of oil biosynthesis and metabolism in plants under abiotic stress.

Identification and expression pattern analysis of the OsSnRK2 gene family in rice.

Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a class of plant-specific serine/threonine (Ser/Thr) protein kinase that plays an important role in rice stress tolerance, growth and development. However, systematic bioinformatics and expression pattern analysis have not been reported. In the current study, ten OsSnRK2 genes were identified in the rice genome and located on 7 chromosomes, which can be classified into three subfamilies (I, II, and III). Many cis-regulatory elements were identified in the promoter region of OsSnRK2 genes, including hormone response elements, defense and stress responsive elements, indicating that the OsSnRK2 family may play a crucial role in response to hormonal and abiotic stress. Quantitative tissue analysis showed that OsSnRK2 genes expressed in all tissues of rice, but the expression abundance varied from different tissues and showed varietal variability. In addition, expression pattern of OsSnRK2 were analyzed under abiotic stress (salt, drought, salt and drought) and showed obvious difference in diverse abiotic stress. In general, these results provide useful information for understanding the OsSnRK2 gene family and analyzing its functions in rice in response to ABA, salt and drought stress, especially salt-drought combined stress.

Ethylene Insensitive 3-Like 2 is a Brassicaceae-specific transcriptional regulator involved in fine-tuning ethylene responses in Arabidopsis thaliana.

Ethylene signaling directs a pleiotropy of developmental processes in plants. In Arabidopsis, ethylene signaling converges at the master transcription factor Ethylene Insensitive 3 (EIN3), which has five homologs, EIN3-like 1-5 (EIL1-EIL5). EIL1 is most fully characterized and operates similarly to EIN3, while EIL3-5 are not involved in ethylene signaling. EIL2 remains less investigated. Our phylogenetic analysis revealed that EIL2 homologs have only been retrieved in the Brassicaceae family, suggesting that EIL2 diverged to have specific functions in the mustard family. By characterizing eil2 mutants, we found that EIL2 is involved in regulating ethylene-specific developmental processes in Arabidopsis thaliana, albeit in a more subtle way compared with EIN3/EIL1. EIL2 steers ethylene-triggered hypocotyl elongation in light-grown seedlings and is involved in lateral root formation. Furthermore, EIL2 takes part in regulating flowering time as eil2 mutants flower on average 1 d earlier and have fewer leaves. A pEIL2:EIL2:GFP translational reporter line revealed that EIL2 protein abundance is restricted to the stele of young developing roots. EIL2 expression, and not EIL2 protein stability, is regulated by ethylene in an EIN3/EIL1-dependent way. Despite EIL2 taking part in several developmental processes, the precise upstream and downstream regulation of this ethylene- and Brassicaceae-specific transcription factor remains to be elucidated.

Something old, something new: Conservation of the ethylene precursor 1-amino-cyclopropane-1-carboxylic acid as a signaling molecule.

In seed plants, 1-amino-cyclopropane-1-carboxylic acid (ACC) is the well-known precursor of the plant hormone ethylene. In nonseed plants, the current view is that ACC is produced but is inefficiently converted to ethylene. Distinct responses to ACC that are uncoupled from ethylene biosynthesis have been discovered in diverse aspects of growth and development in liverworts and angiosperms, indicating that ACC itself can function as a signal. Evolutionarily, ACC may have served as a signal before acquiring its role as the ethylene precursor in seed plants. These findings pave the way for unraveling a potentially conserved ACC signaling pathway in plants and have ramifications for the use of ACC as a substitute for ethylene treatment in seed plants.

Ethylene-independent signaling by the ethylene precursor ACC in Arabidopsis ovular pollen tube attraction.

The phytohormone ethylene has numerous effects on plant growth and development. Its immediate precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), is a non-proteinogenic amino acid produced by ACC SYNTHASE (ACS). ACC is often used to induce ethylene responses. Here, we demonstrate that ACC exhibits ethylene-independent signaling in Arabidopsis thaliana reproduction. By analyzing an acs octuple mutant with reduced seed set, we find that ACC signaling in ovular sporophytic tissue is involved in pollen tube attraction, and promotes secretion of the pollen tube chemoattractant LURE1.2. ACC activates Ca2+-containing ion currents via GLUTAMATE RECEPTOR-LIKE (GLR) channels in root protoplasts. In COS-7 cells expressing moss PpGLR1, ACC induces the highest cytosolic Ca2+ elevation compared to all twenty proteinogenic amino acids. In ovules, ACC stimulates transient Ca2+ elevation, and Ca2+ influx in octuple mutant ovules rescues LURE1.2 secretion. These findings uncover a novel ACC function and provide insights for unraveling new physiological implications of ACC in plants.

Integrated analysis of high-throughput sequencing data shows abscisic acid-responsive genes and miRNAs in strawberry receptacle fruit ripening.

The perception and signal transduction of the plant hormone abscisic acid (ABA) are crucial for strawberry fruit ripening, but the underlying mechanism of how ABA regulates ripening-related genes has not been well understood. By employing high-throughput sequencing technology, we comprehensively analyzed transcriptomic and miRNA expression profiles simultaneously in ABA- and nordihydroguaiaretic acid (NDGA, an ABA biosynthesis blocker)-treated strawberry fruits with temporal resolution. The results revealed that ABA regulated many genes in different pathways, including hormone signal transduction and the biosynthesis of secondary metabolites. Transcription factor genes belonging to WRKY and heat shock factor (HSF) families might play key roles in regulating the expression of ABA inducible genes, whereas the KNOTTED1-like homeobox protein and Squamosa Promoter-Binding-like protein 18 might be responsible for ABA-downregulated genes. Additionally, 20 known and six novel differentially expressed miRNAs might be important regulators that assist ABA in regulating target genes that are involved in versatile physiological processes, such as hormone balance regulation, pigments formation and cell wall degradation. Furthermore, degradome analysis showed that one novel miRNA, Fa_novel6, could degrade its target gene HERCULES1, which likely contributed to fruit size determination during strawberry ripening. These results expanded our understanding of how ABA drives the strawberry fruit ripening process as well as the role of miRNAs in this process.

SlAREB1 transcriptional activation of NOR is involved in abscisic acid-modulated ethylene biosynthesis during tomato fruit ripening.

Many studies have shown that abscisic acid (ABA) regulates climacteric fruits ripening by inducing ethylene production. Nevertheless, the key components involved in the crosstalk between these two phytohormones in controlling fruit ripening remain unknown. SlAREB1, a downstream transcription factor in ABA signaling pathway, has been reported to mediate ABA signaling that regulates tomato ripening through induction of ethylene biosynthetic genes. NOR, a member of NAC domain family, was proved to act upstream of ethylene and essential for ripening- and ethylene-associated genes expression. Here, we found that the expression of SlAREB1 and NOR are both ABA-inducible, and SlAREB1 transcription reaches the peak level prior to NOR during the ripening process. Yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA) and dual luciferase assay indicated NOR as a novel direct target of SlAREB1. Transient over-expression of SlAREB1 in tomato fruits results in elevated expression of NOR as well as a number of downstream ethylene biosynthetic genes including SlACS2, SlACS4 and SlACO1, suggesting that SlAREB1 can mediate ABA signal to activate NOR transcription and ultimately promote ethylene synthesis. Based on these data, we present a model suggesting that the SlAREB1-NOR regulation is a crucial node modulating ABA-regulated ethylene biosynthesis during tomato fruit ripening.

Suppression of Cell Wall Degrading Enzymes and their Encoding Genes in Button Mushrooms (Agaricus bisporus) by CaCl2 and Citric Acid.

Fresh button mushrooms (Agaricus bisporus) were harvested and treated with a solution of 1.5% CaCl2 + 0.5% citric acid and stored for 16 days at 12 °C. The effects of this treatment on firmness, weight, color, cell wall compositions (cellulose and chitin) and cell wall degrading enzymes (cel1ulase, beta-1, 3 glucanase, chitinase and phenylalanine ammonialyase) were investigated during post-harvest storage. The expressions of major genes (Cel1, Glu1, Chi1 and PAL1) involved in cell wall degradation during post-harvest storage were also monitored. The results revealed that the post-harvest chemical treatment maintained better firmness, weight, color and inhibited cellulase, beta-1, 3 glucanase, chitinase and phenylalanine ammonialyase activities. These findings showed that the down-regulation of cell wall degrading enzymes is a possible mechanism that delays the softening of button mushrooms by the application of combined chemical treatment.

Developmental and stress regulation on expression of a novel miRNA, Fan-miR73, and its target ABI5 in strawberry.

Abscisic acid (ABA) is a critical plant hormone for fruit ripening and adaptive stress responses in strawberry. Previous high-throughput sequencing results indicated that ABA-insensitive (ABI)5, an important transcription factor in the ABA signaling pathway, was a target for a novel microRNA (miRNA), Fan-miR73. In the present study, exogenous ABA treatment was found to accelerate fruit ripening through differentially regulating the transcripts of ABA metabolism and signal transduction related genes, including NCED1, PYR1, ABI1, and SnRK2.2. Expression of Fan-miR73 was down-regulated in response to exogenous ABA treatment in a dosage-dependent manner, which resulted in an accumulation of ABI5 transcripts in the ripening-accelerated fruits. In addition, both UV-B radiation and salinity stress reduced the transcript levels of Fan-miR73, whereas promoted ABI5 expression. Furthermore, high negative correlations between the transcriptional abundance of Fan-miR73 and ABI5 were observed during ripening and in response to stress stimuli. These results enriched the possible regulatory role of miRNA involved in the post-transcriptional modification of ABI5 during strawberry ripening, as well as responses to environmental stresses.

Comprehensive Analysis of ABA Effects on Ethylene Biosynthesis and Signaling during Tomato Fruit Ripening.

ABA has been widely acknowledged to regulate ethylene biosynthesis and signaling during fruit ripening, but the molecular mechanism underlying the interaction between these two hormones are largely unexplored. In the present study, exogenous ABA treatment obviously promoted fruit ripening as well as ethylene emission, whereas NDGA (Nordihydroguaiaretic acid, an inhibitor of ABA biosynthesis) application showed the opposite biological effects. Combined RNA-seq with time-course RT-PCR analysis, our study not only helped to illustrate how ABA regulated itself at the transcription level, but also revealed that ABA can facilitate ethylene production and response probably by regulating some crucial genes such as LeACS4, LeACO1, GR and LeETR6. In addition, investigation on the fruits treated with 1-MCP immediately after ABA exposure revealed that ethylene might be essential for the induction of ABA biosynthesis and signaling at the onset of fruit ripening. Furthermore, some specific transcription factors (TFs) known as regulators of ethylene synthesis and sensibility (e.g. MADS-RIN, TAGL1, CNR and NOR) were also observed to be ABA responsive, which implied that ABA influenced ethylene action possibly through the regulation of these TFs expression. Our comprehensive physiological and molecular-level analysis shed light on the mechanism of cross-talk between ABA and ethylene during the process of tomato fruit ripening.

Comparative Transcriptome Analysis Reveals the Influence of Abscisic Acid on the Metabolism of Pigments, Ascorbic Acid and Folic Acid during Strawberry Fruit Ripening.

A comprehensive investigation of abscisic acid (ABA) biosynthesis and its influence on other important phytochemicals is critical for understanding the versatile roles that ABA plays during strawberry fruit ripening. Using RNA-seq technology, we sampled strawberry fruit in response to ABA or nordihydroguaiaretic acid (NDGA; an ABA biosynthesis blocker) treatment during ripening and assessed the expression changes of genes involved in the metabolism of pigments, ascorbic acid (AsA) and folic acid in the receptacles. The transcriptome analysis identified a lot of genes differentially expressed in response to ABA or NDGA treatment. In particular, genes in the anthocyanin biosynthesis pathway were actively regulated by ABA, with the exception of the gene encoding cinnamate 4-hydroxylase. Chlorophyll degradation was accelerated by ABA mainly owing to the higher expression of gene encoding pheide a oxygenase. The decrease of ß-carotene content was accelerated by ABA treatment and delayed by NDGA. A high negative correlation rate was found between ABA and ß-carotene content, indicating the importance of the requirement for ABA synthesis during fruit ripening. In addition, evaluation on the folate biosynthetic pathway indicate that ABA might have minor function in this nutrient's biosynthesis process, however, it might be involved in its homeostasis. Surprisingly, though AsA content accumulated during fruit ripening, expressions of genes involved in its biosynthesis in the receptacles were significantly lower in ABA-treated fruits. This transcriptome analysis expands our understanding of ABA's role in phytochemical metabolism during strawberry fruit ripening and the regulatory mechanisms of ABA on these pathways were discussed. Our study provides a wealth of genetic information in the metabolism pathways and may be helpful for molecular manipulation in the future.

Transcriptomic Analysis Reveals Possible Influences of ABA on Secondary Metabolism of Pigments, Flavonoids and Antioxidants in Tomato Fruit during Ripening.

Abscisic acid (ABA) has been proven to be involved in the regulation of climacteric fruit ripening, but a comprehensive investigation of its influence on ripening related processes is still lacking. By applying the next generation sequencing technology, we conducted a comparative analysis of the effects of exogenous ABA and NDGA (Nordihydroguaiaretic acid, an inhibitor of ABA biosynthesis) on tomato fruit ripening. The high throughput sequencing results showed that out of the 25728 genes expressed across all three samples, 10388 were identified as significantly differently expressed genes. Exogenous ABA was found to enhance the transcription of genes involved in pigments metabolism, including carotenoids biosynthesis and chlorophyll degradation, whereas NDGA treatment inhibited these processes. The results also revealed the crucial role of ABA in flavonoids synthesis and regulation of antioxidant system. Intriguingly, we also found that an inhibition of endogenous ABA significantly enhanced the transcriptional abundance of genes involved in photosynthesis. Our results highlighted the significance of ABA in regulating tomato ripening, which provided insight into the regulatory mechanism of fruit maturation and senescence process.