Genome-wide analysis revealed the stepwise origin and functional diversification of HSDs from lower to higher plant species.

Hydroxysteroid dehydrogenase (HSDs) is an oil-body sterol protein (steroleosin) with an NADP(H) binding domain that belongs to the short-chain dehydrogenase/reductase (SDR) superfamily. There are numerous studies on the characterization of HSDs in plants. However, thus far, the evolutionary differentiation and divergence analysis of these genes remain to be explored. The current study used an integrated method to elucidate the sequential evolution of HSDs in 64 sequenced plant genomes. Analyses were conducted on their origins, distribution, duplication, evolutionary paths, domain functions, motif composition, properties, and cis-elements. Results indicate that except for algae, HSD1 was widely distributed in plant species ranging from lower to higher plants, while HSD5 was restricted to terrestrial plants, and HSD2 was identified in fewer monocots and several dicot plants. Phylogenetic analysis of HSD proteins revealed that monocotyledonous HSD1 in moss and ferns appeared closest to the outgroup, V. carteri HSD-like, M. musculus HSD1, and H. sapiens HSD1. These data support the hypothesis that HSD1 originated in bryophytes and then in non-vascular and vascular plants, followed by HSD5 only in land plants. Gene structure analysis suggests that HSDs in plant species came up with a fixed number of six exons, and the intron phase was primarily 0, 1, 0, 0, and 0. Similarly, duplication analysis revealed that segmental duplications were the main reason for HSDs in plant species. Physicochemical properties suggest that dicotyledonous HSD1s and HSD5s were mainly acidic. The monocotyledonous HSD1s and HSD2s and the dicotyledonous HSD2s, HSD3s, HSD4s, and HSD6s were mainly basic, implying that HSDs in plants may have a variety of functions. Cis-regulatory elements and expression analysis revealed that HSDs in plants might have roles in several abiotic stresses. Due to the high expression of HSD1s and HSD5s in seeds, these HSDs in plants may have roles in fatty acid accumulation and degradation.

Abscisic acid inhibits primary root growth by impairing ABI4-mediated cell cycle and auxin biosynthesis.

Cell cycle progression and the phytohormones auxin and abscisic acid (ABA) play key roles in primary root growth, but how ABA mediates the transcription of cell cycle-related genes and the mechanism of crosstalk between ABA and auxin requires further research. Here, we report that ABA inhibits primary root growth by regulating the ABA INSENSITIVE4 (ABI4)-CYCLIN-DEPENDENT KINASE B2;2 (CDKB2;2)/CYCLIN B1;1 (CYCB1;1) module-mediated cell cycle as well as auxin biosynthesis in Arabidopsis (Arabidopsis thaliana). ABA induced ABI4 transcription in the primary root tip, and the abi4 mutant showed an ABA-insensitive phenotype in primary root growth. Compared with the wild type (WT), the meristem size and cell number of the primary root in abi4 increased in response to ABA. Further, the transcription levels of several cell-cycle positive regulator genes, including CDKB2;2 and CYCB1;1, were upregulated in abi4 primary root tips. Subsequent chromatin immunoprecipitation (ChIP)-seq, ChIP-qPCR, and biochemical analysis revealed that ABI4 repressed the expression of CDKB2;2 and CYCB1;1 by physically interacting with their promoters. Genetic analysis demonstrated that overexpression of CDKB2;2 or CYCB1;1 fully rescued the shorter primary root phenotype of ABI4-overexpression lines, and consistently, abi4/cdkb2;2-cr or abi4/cycb1;1-cr double mutations largely rescued the ABA-insensitive phenotype of abi4 with regard to primary root growth. The expression levels of DR5promoter-GFP and PIN1promoter::PIN1-GFP in abi4 primary root tips were significantly higher than those in WT after ABA treatment, with these changes being consistent with changes in auxin concentration and expression patterns of auxin biosynthesis genes. Taken together, these findings indicated that ABA inhibits primary root growth through ABI4-mediated cell cycle and auxin-related regulatory pathways.

Seed Dormancy and Longevity: A Mutual Dependence or a Trade-Off?

Seed dormancy is an important agronomic trait in cereals and leguminous crops as low levels of seed dormancy during harvest season, coupled with high humidity, can cause preharvest sprouting. Seed longevity is another critical trait for commercial crop propagation and production, directly influencing seed germination and early seedling establishment. Both traits are precisely regulated by the integration of genetic and environmental cues. Despite the significance of these two traits in crop production, the relationship between them at the molecular level is still elusive, even with contradictory conclusions being reported. Some studies have proposed a positive correlation between seed dormancy and longevity in association with differences in seed coat permeability or seed reserve accumulation, whereas an increasing number of studies have highlighted a negative relationship, largely with respect to phytohormone-dependent pathways. In this review paper, we try to provide some insights into the interactions between regulatory mechanisms of genetic and environmental cues, which result in positive or negative relationships between seed dormancy and longevity. Finally, we conclude that further dissection of the molecular mechanism responsible for this apparently contradictory relationship between them is needed.

Repressors: the gatekeepers of phytohormone signaling cascades.

Coordinated phytohormone signal transduction, in which repressors are the key players, is essential to balance plant development and stress response. In the absence of phytohormones, repressors interplay to terminate the transcription of phytohormone-responsive genes. For phytohormone signal transduction, degradation or inactivation of the repressors is a prerequisite, a process in which proteasomal degradation or protein modifications, such as phosphorylation, are involved. In this review, we summarize the various repressor proteins and their methods of regulation. In addition, we also shed light on other post-transcriptional modifications, including protein sumoylation, acetylation, methylation, and S-nitrosylation, which might be involved in repressor regulation. We conclude that repressors are the gatekeepers of phytohormone signaling, allowing transcription of phytohormone-responsive genes only when required and thus serving as a universal mechanism to conserve energy in plants. Finally, we strongly recommend that plant research should be focused further on elucidating the mechanisms regulating repressor abundance or activity, to improve our understanding of phytohormone signal transduction.

Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat (Avena sativa L.).

BACKGROUND: Oat (Avena sativa L.), a hexaploid crop with unknown genome, has valuable nutritional, medicinal and pharmaceutical uses. However, no suitable RGs (reference genes) for qPCR (quantitative real-time PCR) has been documented for oat yet. Single-copy gene is often selected as RG, which is challengeable or impactable in unexplored polyploids. RESULTS: In this study, eleven candidate RGs, including four duplicated genes, were selected from oat transcriptome. The stability and the optimal combination of these candidate RGs were assessed in 18 oat samples by using four statistical algorithms including the ΔCt method, geNorm, NormFinder and BestKeeper. The most stable RGs for "all samples", "shoots and roots of seedlings", "developing seeds" and "developing endosperms" were EIF4A (Eukaryotic initiation factor 4A-3), UBC21 (Ubiquitin-Conjugating Enzyme 21), EP (Expressed protein) and EIF4A respectively. Among these RGs, UBC21 was a four-copy duplicated gene. The reliability was validated by the expression patterns of four various genes normalized to the most and the least stable RGs in different sample sets. CONCLUSIONS: Results provide a proof of concept that the duplicated RG is feasible for qPCR in polyploids. To our knowledge, this study is the first systematic research on the optimal RGs for accurate qPCR normalization of gene expression in different organs and tissues of oat.

Effect of poly-γ-glutamic acid on hydration and structure of wheat gluten.

In recent years, hydrocolloids have been used extensively as enhancers in dough products. However, studies on the effect of hydrophilic polymers on wheat gluten (WG) within the dough are scarce. In the present study, poly-γ-glutamic acid (γ-PGA), a new and healthy food additive, was added to the WG to investigate its effect on hydration, rheological properties, and structures of WG. Results showed that with the addition of γ-PGA, the water-holding capacity (WHC) of WG and the content of bound water increased, whereas the content of immobilized water decreased. In addition, γ-PGA changed the rheological properties of WG. The elastic properties of WG gradually weakened and the viscous properties gradually increased. Furthermore, scanning electron microscopy (SEM) results showed that with the addition of γ-PGA, the structure of the WG network became more uniform and the pore size was smaller. A change also occurred in the secondary structure of WG, in which the α-helix content was significantly reduced while the contents of ß-turn angles were significantly increased, thereby suggesting that γ-PGA not only functions as a filler in the WG system, but also interacts with WG. From the present study, we conclude that γ-PGA can interact with WG and water to change the WG secondary structure. γ-PGA can also restrict moisture migration and enhance the WHC of WG, thereby changing the WG microstructure and improving its functional properties. This condition provides the basis for γ-PGA to be recommended as WG enhancer for addition in WG-containing products such as bread, seitan (meat replacement), and others. PRACTICAL APPLICATION: WG performance plays a key role in the quality of flour products. Thus, many studies have been conducted to improve the WG quality to produce highly popular flour products. The results of this study showed that γ-PGA can interact with WG and water, and had a good effect on improving the WHC of WG, which means that γ-PGA has potential usefulness in improving the quality of WG and WG-containing products such as bread, seitan (meat replacement), and others.

Combined Kinetin and Spermidine Treatments Ameliorate Growth and Photosynthetic Inhibition in Vigna angularis by Up-Regulating Antioxidant and Nitrogen Metabolism under Cadmium Stress.

Pot experiments were conducted to investigate the probable beneficial role of the individual as well as combined application of kinetin (50 µM Kn) and spermidine (200 µM Spd) on Vigna angularis under cadmium (Cd) stress. Cd treatment reduced growth by declining the content of chlorophylls and carotenoids, photosynthesis, and gas exchange parameters. Exogenously, Kn and Spd application enhanced the photosynthetic parameters and up-regulated the antioxidant system by improving the activities of antioxidant enzymes and the content of non-enzymatic components. In addition, the application of Kn and Spd resulted in significant improvement in the content of sugars, proline, and glycine betaine, ameliorating the decline in relative water content. Oxidative stress parameters including hydrogen peroxide, superoxide, lipid peroxidation, lipoxygenase activity, and electrolyte leakage increased due to Cd stress; however, the application of Kn and Spd imparted a significant decline in all these parameters. Further, reduced Cd uptake was also observed due to Kn and Spd application. Total phenols and flavonoids also increased due to Kn and Spd treatments under normal as well as Cd stress conditions, which may have further helped with the elimination of reactive oxygen species. Reduction in the activity of nitrate reductase and the content of nitrogen was ameliorated due to the exogenous application of Kn and Spd. Therefore, the exogenous application of Kn and Spd benefited Vigna angularis counteracting the damaging effects of Cd stress by up-regulating the tolerance mechanisms, including antioxidant and osmolyte metabolism.

Influence of Exogenous Salicylic Acid and Nitric Oxide on Growth, Photosynthesis, and Ascorbate-Glutathione Cycle in Salt Stressed Vigna angularis.

The present study was carried out to investigate the beneficial role of exogenous application of salicylic acid (1 mM SA) and nitric oxide (100 µM NO) in preventing the oxidative damage in Vigna angularis triggered by salinity stress. Salinity (100 mM NaCl) stress reduced growth, biomass accumulation, chlorophyll synthesis, photosynthesis, gas exchange parameters, and photochemical efficiency (Fv/Fm) significantly. Exogenous application of SA and NO was affective in enhancing these growth and photosynthetic parameters. Salinity stress reduced relative water content over control. Further, the application of SA and NO enhanced the synthesis of proline, glycine betaine, and sugars as compared to the control as well as NaCl treated plants contributing to the maintenance of tissue water content. Exogenous application of SA and NO resulted in up-regulation of the antioxidant system. Activities of enzymatic antioxidants including superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), and glutathione reductase (GR), as well as the content of non-enzymatic components, were more in SA + NO treated seedlings as compared to control and salinity stressed counterparts resulting in significant alleviation of the NaCl mediated oxidative damage. Content of nitrogen, potassium, and calcium increased due to SA and NO under normal conditions and NaCl stress conditions while as Na and Cl content reduced significantly.

Genome-wide analysis reveals the evolution and structural features of WRINKLED1 in plants.

WRINKLED1 (WRI1), an AP2/ERE transcription factor, is one of the most important regulators of oil accumulation. It has been extensively studied in angiosperms, but its evolution and overview features in plants remain unknown. In this study, WRI1s, as well as WRI1-likes in non-WRI1 species, were investigated in 64 genome-sequenced plants. Their origin, distribution, duplication, evolution, functional domains, motifs, properties, and cis-elements were analyzed. Results suggest that WRI1 and WRI1-like may originate from Chlorophyta, and WRI1-likes in angiosperms resemble phylogenetically and structurally WRI1s from Chlorophyta and non-vascular plants. WRI1 or WRI1-like may be essential to vascular plants but not to non-vascular plants. Two YRG elements and two RAYD elements, as well as their phosphorylation sites and the 14-3-3 binding motif, are relatively conserved from Chlorophyta to angiosperm. The predicted DNA-binding domains are slightly shorter than the combination of one YRG element and one RAYD element. WRI1 gradually evolves from alkalinity to acidity. More motifs were developed in N-terminuses and C-terminuses in vascular plants. A short acidic amino-acid-enriched domain in the C-terminal region is predicted to be the putative transactivation domain. The VYL exon appears randomly in different WRI1 transcripts and it is not important for the function of WRI1. In addition, more cis-elements developed during WRI1 evolution may suggest its more complicated regulation and physiological functions. These results will assist future function studies of WRI1 and evolution studies of fatty acid biosynthesis regulation in plants.