SHINE transcription factors act redundantly to pattern the archetypal surface of Arabidopsis flower organs

Characterization of the Helicase activity of Pif-like Helicases from Arabidopsis thaliana and role in gene regulation and abiotic stress response

Regulation in gene expression is rendered by the dynamic structural transitions between classical B-form DNA and non-canonical DNA folds such as G-Quadruplexes (GQS). Several proteins interact with GQSes and regulate a range of biological processes including regulation of DNA replication, transcription, and translation. Several GQS helicases resolve these structures and contribute to maintaining genomic stability. Arabidopsis has 3 homologs of Pif-Like-Helicases (AtPLHs) which have been characterized in this study. Cellular localization and tissue-specific profiling of these homologs revealed nuclear localization and expression in seedling, leaves, and flower tissues suggesting they might play a role in gene regulation and plant development. Molecular characterization of recombinant AtPLH2 and AtPLH3 suggested DNA binding, ATPase, and helicase activity of these two proteins. Further, phenotyping of Atplh mutants revealed alterated seedling root and hypocotyl growth and pollen germination. Transcriptomic profiling of mutants revealed the upregulation of genes associated with processes like systemic acquired resistance, glutathione metabolic process, cellular oxidant detoxification, β-glucosidase activity, SAM-dependent methyltransferase activity, heme binding, calmodulin binding, etc, with these genes harboring WRKY and AP2/EREB TF binding sites in their promoters. These mutants showed susceptibility to different abiotic stresses like salinity and ABA stress as well as to hydroxyurea. Further, AtPLH2 and AtPLH3 mutants showed no root elongation under low pH suggesting root elongation is affected in the absence of these genes. Our study highlights the role of these GQS helicases in regulating genes involved in root development and stress tolerance.

The SAGA histone acetyltransferase complex functions in concert with RNA processing machinery to regulate wheat wax biosynthesis

Wax mixtures comprising very long-chain fatty acids and their derivatives represent the major cuticular components and protect plant tissues from environmental stresses. Uncovering the regulatory mechanisms underlying wax biosynthesis is essential for the genetic improvement of the agronomically important crop bread wheat (Triticum aestivum L.). Herein, partially redundant ECERIFERUM 3 (TaCER3) proteins were characterized as essential components of wheat wax biosynthetic machinery. Furthermore, we demonstrated that the wheat enoyl-CoA reductase promoter-binding MYB transcription factor 1 (TaEPBM1)could directly target TaCER3 genes and recruit components of the SAGA histone acetyltransferase complex to mediate histone acetylation, thereby stimulating TaCER3 transcription and potentiating wax biosynthesis. Wheat RNA processing machineries, including the RNA exosome, SUPERKILLER complex, cap-binding complex (CBC) components, TaSERRATE, and its partners, as well as elongator subunits, affected the accumulation of TaCER3 transcripts and controlled wax biosynthesis. Silencing of wheat CBC components, TaSERRATE, and elongator subunits resulted in the accumulation of TaCER3 transcripts and increased wax biosynthesis. Importantly, the activation of wheat wax biosynthesis in the absence of RNA processing factors was suppressed by silencing TaCER3 expression. These findings suggest that the SAGA histone acetyltransferase complex functions in concert with the RNA processing machinery to regulate wheat wax biosynthesis, probably via affecting TaCER3 genes.

Building beauty: Understanding how hormone signaling regulates petal patterning and morphogenesis

The corolla of flowering plants provides pivotal functions for the reproduction of angiosperms, directly impacting the fitness of individuals. Different petal shapes and patterns contribute to these functions and, thus, participate in the production of morphological diversity and the emergence of new species. During petal morphogenesis, the coordination of cell fate specification, cell division, and cell expansion is coherent and robust across the petal blade and is set according to proximo-distal, medio-lateral, and abaxial-adaxial axes. However, the mechanisms specifying petal polarity and controlling cell behavior in a position-dependent manner as petals develop remain poorly understood. In this review, we draw parallels with other evolutionarily related plant lateral organs such as leaves to argue that hormones likely play central, yet largely unexplored, roles in such coordination. By examining petal development in Arabidopsis and other angiosperms, we frame what are the knowns and the unknowns of hormones contributions to petal morphogenesis and patterning. Finally, we argue that using emerging model organisms can provide invaluable information to tackle questions that have long remained unanswered, broadening our understanding by allowing us to investigate petal morphogenesis and the tinkering of phytohormone signaling through an evolutionary lens.

Update on the structure and regulated biosynthesis of the apoplastic polymers cutin and suberin

The plant lipid polymers cutin and suberin play a critical role in many aspects of plant growth, development, and physiology. The mechanisms of cutin and suberin biosynthesis are relatively well understood thanks to just over 2 decades of work with primarily Arabidopsis (Arabidopsis thaliana) mutants. Recent advances in our understanding of cutin and suberin structure have arisen through the application of novel chemistries targeted at quantitative comprehension of intermolecular linkages, isolating intact suberins and cutins, and the application of advanced analytical techniques. The advent of high-throughput transcription factor binding assays and next-generation sequencing has facilitated the discovery of numerous cutin and suberin-regulating transcription factors and their gene promoter targets. Herein we provide an overview of aspects of cutin and suberin structure, biosynthesis, and transcriptional regulation of their synthesis highlighting recent developments in our understanding of these facets of cutin and suberin biology. We further identify outstanding questions in these respective areas and provide perspectives on how to advance the field to address these questions.

Wheat WW Domain-Containing Protein TaCFL1 Negatively Regulates Cuticular Wax Biosynthesis

Waxy cuticle covers plant aerial organs and protects plants against environmental challenges. Although improved cuticle-associated traits are aimed at the wheat breeding programs, the mechanism governing wheat cuticular wax biosynthesis remains to be elucidated. Herein, wheat WW domain-containing protein TaCFL1 is characterized as a negative regulator of wax biosynthesis. The knockdown of TaCFL1 expression results in a 15% increase in wax accumulation and decreased leaf cuticle permeability in bread wheat. Furthermore, wheat class IV homeodomain transcription factors TaHDG1.1 and TaHDG1.2 are identified as partially redundant activators of wax biosynthesis. The silencing of TaHDG1.1 or TaHDG1.2 expression leads to an 11% reduction in epidermal wax accumulation and an increase in leaf cuticle permeability wax, while the co-silencing of TaHDG1.1 and TaHDG1.2 results in a 31% reduction in epidermal wax accumulation and a further increase in wax in the leaf cuticle permeability. Moreover, wheat 3-Ketoacyl-CoA synthase TaKCS10 is isolated as an essential component of the wax biosynthetic machinery. The silencing of TaKCS10 expression results in a 22% reduction in wax accumulation and increased leaf cuticle permeability. In addition, we demonstrated that the TaKCS10 expression is activated by TaHDG1.1 and TaHDG1.2, and that TaCFL1 attenuates the TaHDG1-mediated transcriptional activation of TaKCS10. This evidence supports that the WW domain-containing protein TaCFL1 negatively regulates wax biosynthesis via attenuating the transcriptional activation of the TaKCS10 gene mediated by HD-ZIP IV transcription factor TaHDG1.

Shedding New Light on the Hull-Pericarp Adhesion Mechanisms of Barley Grains by Transcriptomics Analysis of Isogenic NUD1 and nud1 Lines

In barley having adherent hulls, an irreversible connection between the pericarp with both palea and lemma is formed during grain maturation. A mutation in the NUDUM 1 (NUD1) gene prevents this connection and leads to the formation of barley with non-adherent hulls. A genetic model of two isogenic lines was used to elucidate the genetic mechanisms of hull adhesion: a doubled haploid line having adherent hulls and its derivative with non-adherent hulls obtained by targeted mutagenesis of the NUD1 gene. Comparative transcriptomics analysis of the grain coats was performed at two stages of development: the milk stage, when the hulls can still be easily detached from the pericarp, and the dough stage when the hull adhesion process occurs. It was shown that the main differences in the transcriptomes lie in the genes related to DNA replication and chromatin assembly, cell wall organization, and cuticle formation. Meanwhile, genes involved in lipid biosynthesis mostly show minor differences in expression between stages and genotypes and represent a limited set of active genes. Among the 3-ketoacyl-CoA synthase (KCS) genes active during grain development, candidates for key enzymes responsible for very long-chain fatty acid elongation were identified.

Wheat Topoisomerase VI Positively Regulates the Biosynthesis of Cuticular Wax and Cutin

Lipophilic cuticles mainly composed of wax mixtures and cutin matrices seal the plant epidermis and control plant development and environmental adaptation. Although cuticle-associated traits have been selected in the breeding of agronomically important cereal bread wheat, the biosynthesis of wheat cuticular wax and cutin remains poorly understood. Herein, wheat topoisomerase VI was characterized as an essential activator of cuticular wax and cutin biosynthesis. Knock-down of wheat TaTOP6A, TaTOP6B, TaRHL1, or TaBIN4 gene encoding component of topoisomerase VI resulted in decreased loads of leaf cuticular wax and cutin, as well as increased leaf cuticle permeability. Moreover, TaCYP86A2 was identified as a key component of the wheat cutin biosynthetic machinery. Reduction of wheat TaCYP86A2 expression led to decreased cutin accumulation and enhanced cuticle permeability. In addition, TaTOP6A, TaTOP6B, TaRHL1, or TaBIN4 was shown to enrich at the promoter regions of the wax biosynthesis gene TaKCS1 and the cutin biosynthesis gene TaCYP86A2. Importantly, chromatin at TaKCS1 and TaCYP86A2 promoters is marked by high nucleosome occupancy and low histone acetylation in TaTOP6A-, TaTOP6B-, TaRHL1-, or TaBIN4-silenced wheat leaves. These results collectively support that wheat topoisomerase VI positively regulates the biosynthesis of cuticular wax and cutin probably via maintaining a permissive chromatin state at TaKCS1 and TaCYP86A2 genes.

Wheat Transcription Factor TaMYB60 Modulates Cuticular Wax Biosynthesis by Activating TaFATB and TaCER1 Expression

Cuticular wax mixtures cover the epidermis of land plants and shield plant tissues from abiotic and biotic stresses. Although cuticular wax-associated traits are employed to improve the production of bread wheat, regulatory mechanisms underlying wheat cuticular wax biosynthesis remain poorly understood. In this research, partially redundant transcription factors TaMYB60-1 and TaMYB60-2 were identified as positive regulators of wheat cuticular wax biosynthesis. Knock-down of wheat TaMYB60-1 and TaMYB60-2 genes by virus-induced gene silencing resulted in attenuated wax accumulation and enhanced cuticle permeability. The roles of wheat fatty acyl-ACP thioesterase genes TaFATB1 and TaFATB2 in cuticular wax biosynthesis were characterized. Silencing wheat TaFATB1 and TaFATB2 genes led to reduced wax accumulation and increased cuticle permeability, suggesting that TaFATB1 and TaFATB2 genes positively contribute to wheat cuticular wax biosynthesis. Importantly, transcription factors TaMYB60-1 and TaMYB60-2 exhibit transcriptional activation ability and could stimulate the expression of wax biosynthesis genes TaFATB1, TaFATB2, and ECERIFERUM 1 (TaCER1). These findings support that transcription factor TaMYB60 positively regulates wheat cuticular wax biosynthesis probably by activating transcription of TaFATB1, TaFATB2, and TaCER1 genes.

NtWIN1 regulates the biosynthesis of scopoletin and chlorogenic acid by targeting NtF6'H1 and NtCCoAMT genes in Nicotiana tabacum

Scopoletin and chlorogenic acid (CGA) are important polyphenols that regulate plant growth, development, and stress resistance. The ERF transcription factor WAX INDUCER1 (WIN1) promotes the biosynthesis of cutin, suberine, and wax. However, its full roles in regulating the accumulation of plant secondary metabolites still remain to be further clarified. In this study, NtWIN1 gene encoding a SHINE-type AP2/ERF transcription factor of the Va subgroup was identified from N. tabacum. NtWIN1 showed high expression levels in tobacco stems, sepals, and pistils. Overexpression (OE) and knock-out of NtWIN1 showed that it promoted the accumulation of total polyphenols and altered their composition. Compare to that of WT plants, the CGA contents significantly increased by 25%-50% in the leaves, flowers, and capsules of OE lines, while the scopoletin contents in the OE plants significantly decreased by 30%-67%. In contrast, the CGA contents in ntwin1 lines reduced by 23%-26%, and the scopoletin contents in ntwin1 increased by 38%-75% compare to that of WT plants. Chromatin immunoprecipitation and Dual-Luc transcription activation assays showed that NtWIN1 could bind to the promoters of NtF6'H1 and NtCCoAMT, thereby modulating their expression. The scopoletin content in ntwin1/ntf6'h1 double mutant was significantly lower than that in ntwin1 and WT plants, but showed no significant differences with that in ntf6'h1 mutant, further indicating that the inhibition of NtWIN1 on scopoletin accumulation depends on the activity of NtF6'H1. Our study illustrates the new roles of NtWIN1, and provides a possible target for regulating the synthesis of polyphenols in tobacco.

Identification of candidate genes associated with double flowers via integrating BSA-seq and RNA-seq in Brassica napus

As a Brassica crop, Brassica napus typically has single flowers that contain four petals. The double-flower phenotype of rapeseed has been a desirable trait in China because of its potential commercial value in ornamental tourism. However, few double-flowered germplasms have been documented in B. napus, and knowledge of the underlying genes is limited. Here, B. napus D376 was characterized as a double-flowered strain that presented an average of 10.92 ± 1.40 petals and other normal floral organs. F1, F2 and BC1 populations were constructed by crossing D376 with a single-flowered line reciprocally. Genetic analysis revealed that the double-flower trait was a recessive trait controlled by multiple genes. To identify the key genes controlling the double-flower trait, bulk segregant analysis sequencing (BSA-seq) and RNA-seq analyses were conducted on F2 individual bulks with opposite extreme phenotypes. Through BSA-seq, one candidate interval was mapped at the region of chromosome C05: 14.56-16.17 Mb. GO and KEGG enrichment analyses revealed that the DEGs were significantly enriched in carbohydrate metabolic processes, notably starch and sucrose metabolism. Interestingly, five and thirty-six DEGs associated with floral development were significantly up- and down-regulated, respectively, in the double-flowered plants. A combined analysis of BSA-seq and RNA-seq data revealed that five genes were candidates associated with the double flower trait, and BnaC05.ERS2 was the most promising gene. These findings provide novel insights into the breeding of double-flowered varieties and lay a theoretical foundation for unveiling the molecular mechanisms of floral development in B. napus.

Variation in a Poaceae-conserved fatty acid metabolic gene cluster controls rice yield by regulating male fertility

A wide variety of metabolic gene clusters exist in eukaryotic genomes, but fatty acid metabolic gene clusters have not been discovered. Here, combining with metabolic and phenotypic genome-wide association studies, we identify a major locus containing a six-gene fatty acid metabolic gene cluster on chromosome 3 (FGC3) that controls the cutin monomer hydroxymonoacylglycerols (HMGs) contents and rice yield, possibly through variation in the transcription of FGC3 members. We show that HMGs are sequentially synthesized in the endoplasmic reticulum by OsFAR2, OsKCS11, OsGPAT6, OsCYP704B2 and subsequently transported to the apoplast by OsABCG22 and OsLTPL82. Mutation of FGC3 members reduces HMGs, leading to defective male reproductive development and a significant decrease in yield. OsMADS6 and OsMADS17 directly regulate FGC3 and thus influence male reproduction and yield. FGC3 is conserved in Poaceae and likely formed prior to the divergence of Pharus latifolius. The eukaryotic fatty acid and plant primary metabolic gene cluster we identified show a significant impact on the origin and evolution of Poaceae and has potential for application in hybrid crop breeding.

An ethylene response factor AcERF116 identified from A. catechu is involved in fruitlet abscission

Procedural abscission of outer reproductive organs during flower and fruit development occurs in most plant lineages. Undesired abscission, such as fruitlet shedding causes considerable yield loss in many fruit-producing species. Ethylene is one of the key factors regulating organ abscission. However, the participants involved in the ethylene-mediated abscission pathway remains largely unidentified. In this study, we focused on the ethylene response transcription factors (ERFs) regulating fruitlet abscission in an industrial tree species, A. catechu. A total of 165 ERF genes have been found in the A. catechu genome and eight of these showed distinct expression between the "about-to-abscise" and "non-abscised" samples. An AcERF116 gene with high expression level in the fruit abscission zone (FAZ) was selected for further study. Overexpression of the AcERF116 gene accelerated cell separation in the abscission zone (AZ) and promoted pedicel abscission in transgenic tomato lines. The PG (ploygalacturonase) activity was enhanced in the FAZs of A. catechu fruitlets during ethylene-induced fruitlet abscission, while the PME (pectin methylesterase) activity was suppressed. In addition, cytosolic alkalization was observed in the AZs during abscission in both tomato and A. catechu. Our results suggest that AcERF116 plays a critical role in the crosstalk of ethylene and fruitlet abscission in A. catechu.

Wheat MIXTA-like Transcriptional Activators Positively Regulate Cuticular Wax Accumulation

MIXTA-like transcription factors AtMYB16 and AtMYB106 play important roles in the regulation of cuticular wax accumulation in dicot model plant Arabidopsis thaliana, but there are very few studies on the MIXTA-like transcription factors in monocot plants. Herein, wheat MIXTA-like transcription factors TaMIXTA1 and TaMIXTA2 were characterized as positive regulators of cuticular wax accumulation. The virus-induced gene silencing experiments showed that knock-down of wheat TaMIXTA1 and TaMIXTA2 expressions resulted in the decreased accumulation of leaf cuticular wax, increased leaf water loss rate, and potentiated chlorophyll leaching. Furthermore, three wheat orthologous genes of ECERIFERUM 5 (TaCER5-1A, 1B, and 1D) and their function in cuticular wax deposition were reported. The silencing of TaCER5 by BSMV-VIGS led to reduced loads of leaf cuticular wax and enhanced rates of leaf water loss and chlorophyll leaching, indicating the essential role of the TaCER5 gene in the deposition of wheat cuticular wax. In addition, we demonstrated that TaMIXTA1 and TaMIXTA2 function as transcriptional activators and could directly stimulate the transcription of wax biosynthesis gene TaKCS1 and wax deposition gene TaCER5. The above results strongly support that wheat MIXTA-Like transcriptional activators TaMIXTA1 and TaMIXTA2 positively regulate cuticular wax accumulation via activating TaKCS1 and TaCER5 gene transcription.

AtMYB41 acts as a dual-function transcription factor that regulates the formation of lipids in an organ- and development-dependent manner

The plant cuticle controls non-stomatal water loss and can serve as a barrier against biotic agents, whereas the heteropolymer suberin and its associated waxes are deposited constitutively at specific cell wall locations. While several transcription factors controlling cuticle formation have been identified, those involved in the transcriptional regulation of suberin biosynthesis remain poorly characterized. The major goal of this study was to further analyse the function of the R2R3-Myeloblastosis (MYB) transcription factor AtMYB41 in formation of the cuticle, suberin, and suberin-associated waxes throughout plant development. For functional analysis, the organ-specific expression pattern of AtMYB41 was analysed and Atmyb41ge alleles were generated using the CRISPR/Cas9 system. These were investigated for root growth and water permeability upon stress. In addition, the fatty acid, wax, cutin, and suberin monomer composition of different organs was evaluated by gas chromatography. The characterization of Atmyb41ge mutants revealed that AtMYB41 negatively regulates the production of cuticular lipids and fatty acid biosynthesis in leaves and seeds, respectively. Remarkably, biochemical analyses indicate that AtMYB41 also positively regulates the formation of cuticular waxes in stems of Arabidopsis thaliana. Overall, these results suggest that the AtMYB41 acts as a negative regulator of cuticle and fatty acid biosynthesis in leaves and seeds, respectively, but also as a positive regulator of wax production in A. thaliana stems.

The cuticular wax composition and crystal coverage of leaves and petals differ in a consistent manner between plant species

Both leaves and petals are covered in a cuticle, which itself contains and is covered by cuticular waxes. The waxes perform various roles in plants' lives, and the cuticular composition of leaves has received much attention. To date, the cuticular composition of petals has been largely ignored. Being the outermost boundary between the plant and the environment, the cuticle is the first point of contact between a flower and a pollinator, yet we know little about how plant-pollinator interactions shape its chemical composition. Here, we investigate the general structure and composition of floral cuticular waxes by analysing the cuticular composition of leaves and petals of 49 plant species, representing 19 orders and 27 families. We show that the flowers of plants from across the phylogenetic range are nearly devoid of wax crystals and that the total wax load of leaves in 90% of the species is higher than that of petals. The proportion of alkanes is higher, and the chain lengths of the aliphatic compounds are shorter in petals than in leaves. We argue these differences are a result of adaptation to the different roles leaves and petals play in plant biology.

Germination and Growth Characteristics of nud Knockout and win1 Knockout Barley Lines under Salt Stress

Hordeum vulgare genes NUD (HvNUD) and WIN1 (HvWIN1) play a regulatory role in cuticle organization. Because the cuticle is a key evolutionary acquisition of plants for protection against environmental factors, a knockout (KO) of each gene may alter their ability to adapt to unfavorable conditions. A potential pleiotropic effect of HvNUD or HvWIN1 gene mutations can be assessed under salt stress. Initial developmental stages are the most sensitive in living organisms; therefore, we evaluated salt tolerance of nud KO and win1 KO barley lines at the seedling stage. Air-dried barley grains of the KO lines and of a wild-type (WT) line were germinated in NaCl solutions (50, 100, or 150 mM). Over 30 physiological and morphological parameters of seedlings were assessed. Potential pleiotropic effects of the HvNUD gene KO under salt stress included the stimulation of root growth (which was lower under control conditions) and root necrosis. The pleiotropic effects of the HvWIN1 gene KO under the stressful conditions manifested themselves as maintenance of longer root length as compared to the other lines; stable variation of most of morphological parameters; lack of correlation between root lengths before and after exposure to NaCl solutions, as well as between shoot lengths; and the appearance of twins. Salt tolerance of the analyzed barley lines could be ranked as follows: nud KO > win1 KO ≈ WT, where nud KO lines were the most salt-tolerant. A comparison of effects of salinity and ionizing radiation on nud KO and win1 KO barley lines indicated differences in tolerance of the lines to these stressors.

Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

BACKGROUND

Agropyron cristatum (L.) is a valuable genetic resource for expanding the genetic diversity of common wheat. Pubing3228, a novel wheat-A. cristatum hybrid germplasm, exhibits several desirable agricultural traits, including high grain number per spike (GNS). Understanding the genetic architecture of GNS in Pubing3228 is crucial for enhancing wheat yield. This study aims to analyze the specific genetic regions and alleles associated with high GNS in Pubing3228.

METHODS

The study employed a recombination inbred line (RIL) population derived from a cross between Pubing3228 and Jing4839 to investigate the genetic regions and alleles linked to high GNS. Quantitative Trait Loci (QTL) analysis and candidate gene investigation were utilized to explore these traits.

RESULTS

A total of 40 QTLs associated with GNS were identified across 16 chromosomes, accounting for 4.25-17.17% of the total phenotypic variation. Five QTLs (QGns.wa-1D, QGns.wa-5 A, QGns.wa-7Da.1, QGns.wa-7Da.2 and QGns.wa-7Da.3) accounter for over 10% of the phenotypic variation in at least two environments. Furthermore, 94.67% of the GNS QTL with positive effects originated from Pubing3228. Candidate gene analysis of stable QTLs identified 11 candidate genes for GNS, including a senescence-associated protein gene (TraesCS7D01G148000) linked to the most significant SNP (AX-108,748,734) on chromosome 7D, potentially involved in reallocating nutrients from senescing tissues to developing seeds.

CONCLUSION

This study provides new insights into the genetic mechanisms underlying high GNS in Pubing3228, offering valuable resources for marker-assisted selection in wheat breeding to enhance yield.

Time-Course Transcriptomic Analysis Reveals Molecular Insights into the Inflorescence and Flower Development of Cardiocrinum giganteum

Cardiocrinum giganteum is an endemic species of east Asia which is famous for its showy inflorescence and medicinal bulbs. Its inflorescence is a determinate raceme and the flowers bloom synchronously. Morphological observation and time-course transcriptomic analysis were combined to study the process of inflorescence and flower development of C. giganteum. The results show that the autonomic pathway, GA pathway, and the vernalization pathway are involved in the flower formation pathway of C. giganteum. A varied ABCDE flowering model was deduced from the main development process. Moreover, it was found that the flowers in different parts of the raceme in C. giganteum gradually synchronized during development, which is highly important for both evolution and ecology. The results obtained in this work improve our understanding of the process and mechanism of inflorescence and flower development and could be useful for the flowering period regulation and breeding of C. giganteum.

Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis

BACKGROUND

GDSL esterase/lipases (GELPs) play important roles in plant growth, development, and response to biotic and abiotic stresses. Presently, an extensive and in-depth analysis of GELP family genes in cotton is still not clear enough, which greatly limits the further understanding of cotton GELP function and regulatory mechanism.

RESULTS

A total of 389 GELP family genes were identified in three cotton species of Gossypium hirsutum (193), G. arboreum (97), and G. raimondii (99). These GELPs could be classified into three groups and eight subgroups, with the GELPs in same group to have similar gene structures and conserved motifs. Evolutionary event analysis showed that the GELP family genes tend to be diversified at the spatial dimension and certain conservative at the time dimension, with a trend of potential continuous expansion in the future. The orthologous or paralogous GELPs among different genomes/subgenomes indicated the inheritance from genome-wide duplication during polyploidization, and the paralogous GELPs were derived from chromosomal segment duplication or tandem replication. GELP genes in the A/D subgenome underwent at least three large-scale replication events in the evolutionary process during the period of 0.6-3.2 MYA, with two large-scale evolutionary events between 0.6-1.8 MYA that were associated with tetraploidization, and the large-scale duplication between 2.6-9.1 MYA that occurred during diploidization. The cotton GELPs indicated diverse expression patterns in tissue development, ovule and fiber growth, and in response to biotic and abiotic stresses, combining the existing cis-elements in the promoter regions, suggesting the GELPs involvements of functions to be diversification and of the mechanisms to be a hormone-mediated manner.

CONCLUSIONS

Our results provide a systematic and comprehensive understanding the function and regulatory mechanism of cotton GELP family, and offer an effective reference for in-depth genetic improvement utilization of cotton GELPs.

LcERF10 functions as a positive regulator of litchi fruitlet abscission

Phytohormone ethylene is well-known in positive modulation of plant organ abscission. However, the molecular mechanism underlying ethylene-induced abscission remains largely unknown. Here, we identified an ethylene-responsive factor, LcERF10, as a key regulatory gene in litchi fruitlet abscission. LcERF10 was strongly induced in the fruitlet abscission zone (FAZ) during the ethylene-activated abscission. Silencing of LcERF10 in litchi weakened the cytosolic alkalization of the FAZ and reduced fruitlet abscission. Moreover, LcERF10 directly bound the promoter and repressed the expression of LcNHX7, a Na+/H+ exchanger that was down-regulated in FAZ following the ethylene-activated abscission and up-regulated after LcERF10 silencing. Additionally, ectopic expression of LcERF10 in Arabidopsis promoted the cytosolic alkalization of the floral organ AZ and accelerated the floral organ abscission. Collectively, our results suggest that the transcription factor LcERF10 plays a positive role in litchi fruitlet abscission.

Time course of changes in the transcriptome during russet induction in apple fruit

BACKGROUND

Russeting is a major problem in many fruit crops. Russeting is caused by environmental factors such as wounding or moisture exposure of the fruit surface. Despite extensive research, the molecular sequence that triggers russet initiation remains unclear. Here, we present high-resolution transcriptomic data by controlled russet induction at very early stages of fruit development. During Phase I, a patch of the fruit surface is exposed to surface moisture. For Phase II, moisture exposure is terminated, and the formerly exposed surface remains dry. We targeted differentially expressed transcripts as soon as 24 h after russet induction.

RESULTS

During moisture exposure (Phase I) of 'Pinova' apple, transcripts associated with the cell cycle, cell wall, and cuticle synthesis (SHN3) decrease, while those related to abiotic stress increase. NAC35 and MYB17 were the earliest induced genes during Phase I. They are therefore linked to the initial processes of cuticle microcracking. After moisture removal (Phase II), the expression of genes related to meristematic activity increased (WOX4 within 24 h, MYB84 within 48 h). Genes related to lignin synthesis (MYB52) and suberin synthesis (MYB93, WRKY56) were upregulated within 3 d after moisture removal. WOX4 and AP2B3 are the earliest differentially expressed genes induced in Phase II. They are therefore linked to early events in periderm formation. The expression profiles were consistent between two different seasons and mirrored differences in russet susceptibility in a comparison of cultivars. Furthermore, expression profiles during Phase II of moisture induction were largely identical to those following wounding.

CONCLUSIONS

The combination of a unique controlled russet induction technique with high-resolution transcriptomic data allowed for the very first time to analyse the formation of cuticular microcracks and periderm in apple fruit immediately after the onset of triggering factors. This data provides valuable insights into the spatial-temporal dynamics of russeting, including the synthesis of cuticles, dedifferentiation of cells, and impregnation of cell walls with suberin and lignin.

Regulation of capsule spine formation in castor

Castor (Ricinus communis L.) is a dicotyledonous oilseed crop that can have either spineless or spiny capsules. Spines are protuberant structures that differ from thorns or prickles. The developmental regulatory mechanisms governing spine formation in castor or other plants have remained largely unknown. Herein, using map-based cloning in 2 independent F2 populations, F2-LYY5/DL01 and F2-LYY9/DL01, we identified the RcMYB106 (myb domain protein 106) transcription factor as a key regulator of capsule spine development in castor. Haplotype analyses demonstrated that either a 4,353-bp deletion in the promoter or a single nucleotide polymorphism leading to a premature stop codon in the RcMYB106 gene could cause the spineless capsule phenotype in castor. Results of our experiments indicated that RcMYB106 might target the downstream gene RcWIN1 (WAX INDUCER1), which encodes an ethylene response factor known to be involved in trichome formation in Arabidopsis (Arabidopsis thaliana) to control capsule spine development in castor. This hypothesis, however, remains to be further tested. Nevertheless, our study reveals a potential molecular regulatory mechanism underlying the spine capsule trait in a nonmodel plant species.

Cutinized and suberized barriers in leaves and roots: Similarities and differences

Anatomical, histochemical, chemical, and biosynthetic similarities and differences of cutinized and suberized plant cell walls are presented and reviewed in brief. Based on this, the functional properties of cutinized and suberized plant cell walls acting as transport barriers are compared and discussed in more detail. This is of general importance because fundamental misconceptions about relationships in plant-environment water relations are commonly encountered in the scientific literature. It will be shown here, that cuticles represent highly efficient apoplastic transport barriers significantly reducing the diffusion of water and dissolved compounds. The transport barrier of cuticles is mainly established by the deposition of cuticular waxes. Upon wax extraction, with the cutin polymer remaining, cuticular permeability for water and dissolved non-ionized and lipophilic solutes are increasing by 2-3 orders of magnitude, whereas polar and charged substances (e.g., nutrient ions) are only weakly affected (2- to 3-fold increases in permeability). Suberized apoplastic barriers without the deposition of wax are at least as permeable as the cutin polymer matrix without waxes and hardly offer any resistance to the free movement of water. Only upon the deposition of significant amounts of wax, as it is the case with suberized periderms exposed to the atmosphere, an efficient transport barrier for water can be established by suberized cell walls. Comparing the driving forces (gradients between water potentials inside leaves and roots and the surrounding environment) for water loss acting on leaves and roots, it is shown that leaves must have a genetically pre-defined highly efficient transpiration barrier fairly independent from rapidly changing environmental influences. Roots, in most conditions facing a soil environment with relative humidities very close to 100%, are orders of magnitude more permeable to water than leaf cuticles. Upon desiccation, the permanent wilting point of plants is defined as -1.5 MPa, which still corresponds to nearly 99% relative humidity in soil. Thus, the main reason for plant water stress leading to dehydration is the inability of root tissues to decrease their internal water potential to values more negative than -1.5 MPa and not the lack of a transport barrier for water in roots and leaves. Taken together, the commonly mentioned concepts that a drought-induced increase of cuticular wax or root suberin considerably strengthens the apoplastic leaf or root transport barriers and thus aids in water conservation appears highly questionable.

Annotation of the Turnera subulata (Passifloraceae) Draft Genome Reveals the S-Locus Evolved after the Divergence of Turneroideae from Passifloroideae in a Stepwise Manner

A majority of Turnera species (Passifloraceae) exhibit distyly, a reproductive system involving both self-incompatibility and reciprocal herkogamy. This system differs from self-incompatibility in Passiflora species. The genetic basis of distyly in Turnera is a supergene, restricted to the S-morph, and containing three S-genes. How supergenes and distyly evolved in Turnera, and the other Angiosperm families exhibiting distyly remain largely unknown. Unraveling the evolutionary origins in Turnera requires the generation of genomic resources and extensive phylogenetic analyses. Here, we present the annotated draft genome of the S-morph of distylous Turnera subulata. Our annotation allowed for phylogenetic analyses of the three S-genes' families across 56 plant species ranging from non-seed plants to eudicots. In addition to the phylogenetic analysis, we identified the three S-genes' closest paralogs in two species of Passiflora. Our analyses suggest that the S-locus evolved after the divergence of Passiflora and Turnera. Finally, to provide insights into the neofunctionalization of the S-genes, we compared expression patterns of the S-genes with close paralogs in Arabidopsis and Populus trichocarpa. The annotation of the T. subulata genome will provide a useful resource for future comparative work. Additionally, this work has provided insights into the convergent nature of distyly and the origin of supergenes.

Functional conservation of an AP2/ERF transcription factor in cuticle formation suggests an important role in the terrestrialization of early land plants

The formation of a hydrophobic cuticle layer on aerial plant parts was a critical innovation for protection from the terrestrial environment during the evolution of land plants. However, little is known about the molecular mechanisms underlying cuticle biogenesis in early terrestrial plants. Here, we report an APETALA2/Ethylene Response Factor (AP2/ERF) transcriptional activator, PpWIN1, involved in cutin and cuticular wax biosynthesis in Physcomitrium patens and Arabidopsis. The transcript levels of PpWIN1 were 2.5-fold higher in gametophores than in the protonema, and increased by approximately 3- to 4.7-fold in the protonema and gametophores under salt and osmotic stresses. PpWIN1 harbouring transcriptional activation activity is localized in the nucleus of tobacco leaf epidermal cells. Δppwin1 knockout mutants displayed a permeable cuticle, increased water loss, and cutin- and wax-deficient phenotypes. In contrast, increased total cutin and wax loads, and decreased water loss rates were observed in PpWIN1-overexpressing Arabidopsis plants. The transcript levels of genes involved in cutin or wax biosynthesis were significantly up-regulated in PpWIN1-overexpressing Arabidopsis lines, indicating that PpWIN1 acts as a transcriptional activator in cuticle biosynthesis. This study suggests that Arabidopsis WIN1/SHN1 orthologs may be functionally conserved from early to vascular land plants.

Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration

In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A genome-wide association study was performed for each phenotype independently using six different single-locus models implemented in the GAPIT3 R package. Moreover, we applied a multivariate linear mixed model implemented in the GEMMA package to account for trait correlations and potential pleiotropic effects of polymorphisms. The analyses revealed a number of genomic variants associated with different fiber traits, implying the complex and polygenic control. All stable variants demonstrate a statistically significant allelic effect across all 3 years of the experiment. We tested the validity of the predicted variants using gene expression data available for the flax fiber studies. The results shed new light on the processes and pathways associated with the complex fiber traits, while the pinpointed candidate genes may be further used for marker-assisted selection.

The AP2 Transcription Factor BrSHINE3 Regulates Wax Accumulation in Nonheading Chinese Cabbage

Wax is an acellular structural substance attached to the surface of plant tissues. It forms a protective barrier on the epidermis of plants and plays an important role in resisting abiotic and biotic stresses. In this paper, nonheading Chinese cabbage varieties with and without wax powder were observed using scanning electron microscopy, and the surface of waxy plants was covered with a layer of densely arranged waxy crystals, thus differentiating them from the surface of waxless plants. A genetic analysis showed that wax powder formation in nonheading Chinese cabbage was controlled by a pair of dominant genes. A preliminary bulked segregant analysis sequencing (BSA-seq) assay showed that one gene was located at the end of chromosome A09. Within this interval, we identified BraA09000626, encoding an AP2 transcription factor homologous to Arabidopsis AtSHINE3, and we named it BrSHINE3. By comparing the CDS of the gene in the two parental plants, a 35 bp deletion in the BrSHINE3 gene of waxless plants resulted in a frameshift mutation. Tissue analysis showed that BrSHINE3 was expressed at significantly higher levels in waxy plant rosette stage petioles and bolting stage stems than in the tissues of waxless plants. We speculate that this deletion in BrSHINE3 bases in the waxless material may inhibit wax synthesis. The overexpression of BrSHINE3 in Arabidopsis induced the accumulation of wax on the stem surface, indicating that BrSHINE3 is a key gene that regulates the formation of wax powder in nonheading Chinese cabbage. The analysis of the subcellular localization showed that BrSHINE3 is mainly located in the nucleus and chloroplast of tobacco leaves, suggesting that the gene may function as a transcription factor. Subsequent transcriptome analysis of the homology of BrSHINE3 downstream genes in nonheading Chinese cabbage showed that these genes were downregulated in waxless materials. These findings provide a basis for a better understanding of the nonheading Chinese cabbage epidermal wax synthesis pathway and provide important information for the molecular-assisted breeding of nonheading Chinese cabbage.

Solving the regulation puzzle of periderm development using advances in fruit skin

Periderm protects enlarged organs of most dicots and gymnosperms as a barrier to water loss and disease invasion during their secondary growth. Its development undergoes a complex process with genetically controlled and environmental stress-induced characters. Different development of periderm makes the full and partial russet of fruit skin, which diverges in inheritance with qualitative and quantitative characters, respectively, in pear pome. In addition to its specific genetics, fruit periderm has similar development and structure as that of stem and other organs, making it an appropriate material for periderm research. Recently, progress in histochemical as well as transcriptome and proteome analyses, and quantitative trait locus (QTL) mapping have revealed the regulatory molecular mechanism in the periderm based on the identification of switch genes. In this review, we concentrate on the periderm development, propose the conservation of periderm regulation between fruit and other plant organs based on their morphological and molecular characteristics, and summarize a regulatory network with the elicitors and repressors for the tissue development. Spontaneous programmed-cell death (PCD) or environmental stress produces the original signal that triggers the development of periderm. Spatio-temporal specific PCD produced by PyPPCD1 gene and its homologs can play a key role in the coordinated regulation of cell death related tissue development.

Identification and characterization of putative targets of VEGETATIVE1/FULc, a key regulator of development of the compound inflorescence in pea and related legumes

Inflorescence architecture contributes to essential plant traits. It determines plant shape, contributing to morphological diversity, and also determines the position and number of flowers and fruits produced by the plant, thus influencing seed yield. Most legumes have compound inflorescences, where flowers are produced in secondary inflorescences (I2), formed at the flanks of the main primary inflorescence (I1), in contrast to simple inflorescences of plants like Arabidopsis, in which flowers are directly formed on the I1. The pea VEGETATIVE1/FULc (VEG1) gene, and its homologs in other legumes, specify the formation of the I2 meristem, a function apparently restricted to legumes. To understand the control of I2 development, it is important to identify the genes working downstream of VEG1. In this study, we adopted a novel strategy to identify genes expressed in the I2 meristem, as potential regulatory targets of VEG1. To identify pea I2-meristem genes, we compared the transcriptomes of inflorescence apices from wild-type and mutants affected in I2 development, such as proliferating inflorescence meristems (pim, with more I2 meristems), and veg1 and vegetative2 (both without I2 meristems). Analysis of the differentially expressed genes using Arabidopsis genome databases combined with RT-qPCR expression analysis in pea allowed the selection of genes expressed in the pea inflorescence apex. In situ hybridization of four of these genes showed that all four genes are expressed in the I2 meristem, proving our approach to identify I2-meristem genes was successful. Finally, analysis by VIGS (virus-induced gene silencing) in pea identified one gene, PsDAO1, whose silencing leads to small plants, and another gene, PsHUP54, whose silencing leads to plants with very large stubs, meaning that this gene controls the activity of the I2 meristem. PsHUP54-VIGS plants are also large and, more importantly, produce large pods with almost double the seeds as the control. Our study shows a new useful strategy to isolate I2-meristem genes and identifies a novel gene, PsHUP54, which seems to be a promising tool to improve yield in pea and in other legumes.

AtMYB31 is a wax regulator associated with reproductive development in Arabidopsis

AtMYB31, a R2R3-MYB transcription factor that modulates wax biosynthesis in reproductive tissues, is involved in seed development in Arabidopsis. R2R3-MYB transcription factors play important roles in plant development; yet, the exact role of each of them remains to be resolved. Here we report that the Arabidopsis AtMYB31 is required for wax biosynthesis in epidermis of reproductive tissues, and is involved in seed development. AtMYB31 was ubiquitously expressed in both vegetative and reproductive tissues with higher expression levels in siliques and seeds, while AtMYB31 was localized to the nucleus and cytoplasm. Loss of function of AtMYB31 reduced wax accumulation in the epidermis of silique and flower tissues, disrupted seed coat epidermal wall development and mucilage production, altered seed proanthocyanidin and polyester content. AtMYB31 could direct activate expressions of several wax biosynthetic target genes. Altogether, AtMYB31, a R2R3-MYB transcription factor, regulates seed development in Arabidopsis.

BnKAT2 Positively Regulates the Main Inflorescence Length and Silique Number in Brassica napus by Regulating the Auxin and Cytokinin Signaling Pathways

Brassica napus is the dominant oil crop cultivated in China for its high quality and high yield. The length of the main inflorescence and the number of siliques produced are important traits contributing to rapeseed yield. Therefore, studying genes related to main inflorescence and silique number is beneficial to increase rapeseed yield. Herein, we focused on the effects of BnKAT2 on the main inflorescence length and silique number in B. napus. We explored the mechanism of BnKAT2 increasing the effective length of main inflorescence and the number of siliques through bioinformatics analysis, transgenic technology, and transcriptome sequencing analysis. The full BnKAT2(BnaA01g09060D) sequence is 3674 bp, while its open reading frame is 2055 bp, and the encoded protein comprises 684 amino acids. BnKAT2 is predicted to possess two structural domains, namely KHA and _CNMP-binding domains. The overexpression of BnKAT2 effectively increased the length of the main inflorescence and the number of siliques in B. napus, as well as in transgenic Arabidopsis thaliana. The type-A Arabidopsis response regulator (A-ARR), negative regulators of the cytokinin, are downregulated in the BnKAT2-overexpressing lines. The Aux/IAA, key genes in auxin signaling pathways, are downregulated in the BnKAT2-overexpressing lines. These results indicate that BnKAT2 might regulate the effective length of the main inflorescence and the number of siliques through the auxin and cytokinin signaling pathways. Our study provides a new potential function gene responsible for improvement of main inflorescence length and silique number, as well as a candidate gene for developing markers used in MAS (marker-assisted selection) breeding to improve rapeseed yield.

Groovy and Gnarly: Surface Wrinkles as a Multifunctional Motif for Terrestrial and Marine Environments

From large ventral pleats of humpback whales to nanoscale ridges on flower petals, wrinkled structures are omnipresent, multifunctional, and found at hugely diverse scales. Depending on the particulars of the biological system-its environment, morphology, and mechanical properties-wrinkles may control adhesion, friction, wetting, or drag; promote interfacial exchange; act as flow channels; or contribute to stretching, mechanical integrity, or structural color. Undulations on natural surfaces primarily arise from stress-induced instabilities of surface layers (e.g., buckling) during growth or aging. Variation in the material properties of surface layers and in the magnitude and orientation of intrinsic stresses during growth lead to a variety of wrinkling morphologies and patterns which, in turn, reflect the wide range of biophysical challenges wrinkled surfaces can solve. Therefore, investigating how surface wrinkles vary and are implemented across biological systems is key to understanding their structure-function relationships. In this work, we synthesize the literature in a metadata analysis of surface wrinkling in various terrestrial and marine organisms to review important morphological parameters and classify functional aspects of surface wrinkles in relation to the size and ecology of organisms. Building on our previous and current experimental studies, we explore case studies on nano/micro-scale wrinkles in biofilms, plant surfaces, and basking shark filter structures to compare developmental and structure-vs-function aspects of wrinkles with vastly different size scales and environmental demands. In doing this and by contrasting wrinkle development in soft and hard biological systems, we provide a template of structure-function relationships of biological surface wrinkles and an outlook for functionalized wrinkled biomimetic surfaces.

The SlSHN2 transcription factor contributes to cuticle formation and epidermal patterning in tomato fruit

Tomato (Solanum lycopersicum) is an established model for studying plant cuticle because of its thick cuticle covering and embedding the epidermal cells of the fruit. In this study, we screened an EMS mutant collection of the miniature tomato cultivar Micro-Tom for fruit cracking mutants and found a mutant displaying a glossy fruit phenotype. By using an established mapping-by-sequencing strategy, we identified the causal mutation in the SlSHN2 transcription factor that is specifically expressed in outer epidermis of growing fruit. The point mutation in the shn2 mutant introduces a K to N amino acid change in the highly conserved 'mm' domain of SHN proteins. The cuticle from shn2 fruit showed a ~ fivefold reduction in cutin while abundance and composition of waxes were barely affected. In addition to alterations in cuticle thickness and properties, epidermal patterning and polysaccharide composition of the cuticle were changed. RNAseq analysis further highlighted the altered expression of hundreds of genes in the fruit exocarp of shn2, including genes associated with cuticle and cell wall formation, hormone signaling and response, and transcriptional regulation. In conclusion, we showed that a point mutation in the transcriptional regulator SlSHN2 causes major changes in fruit cuticle formation and its coordination with epidermal patterning.

Functional copy number variation of CsSHINE1 is associated with fruit skin netting intensity in cucumber, Cucumis sativus

Fruit skin netting in cucumber (Cucumis sativus) is associated with important fruit quality attributes. Two simply inherited genes H (Heavy netting) and Rs (Russet skin) control skin netting, but their molecular basis is unknown. Here, we reported map-based cloning and functional characterization of the candidate gene for the Rs locus that encodes CsSHINE1 (CsSHN1), an AP2 domain containing ethylene-responsive transcription factor protein. Comparative phenotypic analysis in near-isogenic lines revealed that fruit with netted skin had different epidermal structures from that with smooth skin including thicker cuticles, smaller, palisade-shaped epidermal and sub-epidermal cells with heavily suberized and lignified cell walls, higher peroxidase activities, which suggests multiple functions of CsSHN1 in regulating fruit skin netting and epidermal cell patterning. Among three representative cucumber inbred lines, three haplotypes at three polymorphic sites were identified inside CsSHN1: a functional copy in Gy14 (wild type) with light fruit skin netting, a copy number variant with two tandemly arrayed functional copies in WI7120 with heavy skin netting, and a loss-of-function copy in 9930 with smooth skin. The expression level of CsSHN1 in fruit exocarp of three lines was positively correlated with the skin netting intensity. Comparative analysis between cucumber and melon revealed conserved and divergent genetic mechanisms underlying fruit skin netting/reticulation that may reflect the different selection histories in the two crops. A discussion was made on genetic basis of fruit skin netting in the context of natural and artificial selections of fruit quality-related epidermal features during cucumber breeding.

CmNF-YB8 affects drought resistance in chrysanthemum by altering stomatal status and leaf cuticle thickness

Drought is a major abiotic stress that limits plant growth and development. Adaptive mechanisms have evolved to mitigate drought stress, including the capacity to adjust water loss rate and to modify the morphology and structure of the epidermis. Here, we show that the expression of CmNF-YB8, encoding a nuclear factor Y (NF-Y) B-type subunit, is lower under drought conditions in chrysanthemum (Chrysanthemum morifolium). Transgenic chrysanthemum lines in which transcript levels of CmNF-YB8 were reduced by RNA interference (CmNF-YB8-RNAi) exhibited enhanced drought resistance relative to control lines, whereas lines overexpressing CmNF-YB8 (CmNF-YB8-OX) were less tolerant to drought. Compared to wild type (WT), CmNF-YB8-RNAi plants showed reduced stomatal opening and a thicker epidermal cuticle that correlated with their water loss rate. We also identified genes involved in stomatal adjustment (CBL-interacting protein kinase 6, CmCIPK6) and cuticle biosynthesis (CmSHN3) that are more highly expressed in CmNF-YB8-RNAi lines than in WT, CmCIPK6 being a direct downstream target of CmNF-YB8. Virus-induced gene silencing of CmCIPK6 or CmSHN3 in the CmNF-YB8-RNAi background abolished the effects of CmNF-YB8-RNAi on stomatal closure and cuticle deposition, respectively. CmNF-YB8 thus regulates CmCIPK6 and CmSHN3 expression to alter stomatal movement and cuticle thickness in the leaf epidermis, thereby affecting drought resistance.

Plant GDSL Esterases/Lipases: Evolutionary, Physiological and Molecular Functions in Plant Development

GDSL esterases/lipases (GELPs), present throughout all living organisms, have been a very attractive research subject in plant science due mainly to constantly emerging properties and functions in plant growth and development under both normal and stressful conditions. This review summarizes the advances in research on plant GELPs in several model plants and crops, including Arabidopsis, rice, maize and tomato, while focusing on the roles of GELPs in regulating plant development and plant-environment interactions. In addition, the possible regulatory network and mechanisms of GELPs have been discussed.

R2R3-MYB genes coordinate conical cell development and cuticular wax biosynthesis in Phalaenopsis aphrodite

Petals of the monocot Phalaenopsis aphrodite (Orchidaceae) possess conical epidermal cells on their adaxial surfaces, and a large amount of cuticular wax is deposited on them to serve as a primary barrier against biotic and abiotic stresses. It has been widely reported that subgroup 9A members of the R2R3-MYB gene family, MIXTA and MIXTA-like in eudicots, act to regulate the differentiation of conical epidermal cells. However, the molecular pathways underlying conical epidermal cell development and cuticular wax biosynthesis in monocot petals remain unclear. Here, we characterized two subgroup 9A R2R3-MYB genes, PaMYB9A1 and PaMYB9A2 (PaMYB9A1/2), from P. aphrodite through the transient overexpression of their coding sequences and corresponding chimeric repressors in developing petals. We showed that PaMYB9A1/2 function to coordinate conical epidermal cell development and cuticular wax biosynthesis. In addition, we identified putative targets of PaMYB9A1/2 through comparative transcriptome analyses, revealing that PaMYB9A1/2 acts to regulate the expression of cell wall-associated and wax biosynthetic genes. Furthermore, a chemical composition analysis of cuticular wax showed that even-chain n-alkanes and odd-chain primary alcohols are the main chemical constituents of cuticular wax deposited on petals, which is inconsistent with the well-known biosynthetic pathways of cuticular wax, implying a distinct biosynthetic pathway occurring in P. aphrodite flowers. These results reveal that the function of subgroup 9A R2R3-MYB family genes in regulating the differentiation of epidermal cells is largely conserved in monocots and dicots. Furthermore, both PaMYB9A1/2 have evolved additional functions controlling the biosynthesis of cuticular wax.

Misregulation of MYB16 expression causes stomatal cluster formation by disrupting polarity during asymmetric cell divisions

Stomatal pores and the leaf cuticle regulate evaporation from the plant body and balance the tradeoff between photosynthesis and water loss. MYB16, encoding a transcription factor involved in cutin biosynthesis, is expressed in stomatal lineage ground cells, suggesting a link between cutin biosynthesis and stomatal development. Here, we show that the downregulation of MYB16 in meristemoids is directly mediated by the stomatal master transcription factor SPEECHLESS (SPCH) in Arabidopsis thaliana. The suppression of MYB16 before an asymmetric division is crucial for stomatal patterning, as its overexpression or ectopic expression in meristemoids increased stomatal density and resulted in the formation of stomatal clusters, as well as affecting the outer cell wall structure. Expressing a cutinase gene in plants ectopically expressing MYB16 reduced stomatal clustering, suggesting that cutin affects stomatal signaling or the polarity setup in asymmetrically dividing cells. The clustered stomatal phenotype was rescued by overexpressing EPIDERMAL PATTERNING FACTOR2, suggesting that stomatal signaling was still functional in these plants. Growing seedlings ectopically expressing MYB16 on high-percentage agar plates to modulate tensile strength rescued the polarity and stomatal cluster defects of these seedlings. Therefore, the inhibition of MYB16 expression by SPCH in the early stomatal lineage is required to correctly place the polarity protein needed for stomatal patterning during leaf morphogenesis.

Cuticular lipids and associated gene expression analysis under NaCl stress in Thellungiella salsuginea

Cuticular lipids, including wax and cutin, protect plants against external environmental stress. The relationship between the cuticle properties and salt tolerance is not clear. In this article, photosynthetic and physiological characteristics related to water use and cuticle permeability were assessed in the leaves of Thellungiella salsuginea under NaCl stress. The chemical composition of wax and cutin monomers, and the expression of cuticle-associated genes were also analyzed. The results showed that the net photosynthetic rate and stomatal conductance in the leaves of T. salsuginea decreased, and the water use efficiency increased with increasing NaCl concentration. Salt stress caused a significant increase in total wax, but total cutin monomers only increased under high salt. Transcriptome sequencing and lipid metabolism pathway analysis were performed on rosette leaves of T. salsuginea after 24 h of NaCl treatment. We analyzed the expression of 42 genes involved in cuticle lipid metabolism, and found that most of them exhibited higher expression levels at 0.15 mol L^-1 NaCl, but lower expression levels at 0.3 mol L^-1 NaCl. The expression of 12 of these genes was further detected by qRT-PCR after 1 week of NaCl treatment: most of them were upregulated both under low and high NaCl stress. Hence, we speculate that the cuticle acts as an adaptive trait in T. salsuginea in salty environments.

Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses

BACKGROUND

AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis.

RESULTS

A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger.

CONCLUSION

A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and qRT-PCR showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.

Arabidopsis thaliana TCP15 interacts with the MIXTA-like transcription factor MYB106/NOECK

MYB106 and MYB16 are MIXTA-like transcription factors that control trichome maturation and cuticle formation in Arabidopsis. In a recent study, we found that the TEOSINTE BRANCHED 1, CYCLOIDEA and PROLIFERATING CELL FACTORS (TCP) transcription factor TCP15 also acts as an important regulator of aerial epidermis specialization in Arabidopsis through the control of trichome development and cuticle formation. TCP15 and MYB106 regulate the expression of common groups of genes, including genes coding for transcription factors and enzymes of the cuticle biosynthesis pathway. In this study, we report that TCP15 physically interacts with MYB106 when both proteins are expressed in yeast cells or Nicotiana bentamiana leaves. Furthermore, we also observed interaction in leaves of Arabidopsis thaliana. Altogether, our findings raise the possibility that TCP15 and MYB106 bind together to the promoters of target genes to exert their action. Our data provide a base to investigate the role of TCP-MIXTA complexes in the context of cuticle development in Arabidopsis thaliana.

Cutin:xyloglucan transacylase (CXT) activity covalently links cutin to a plant cell-wall polysaccharide

The shoot epidermal cell wall in land-plants is associated with a polyester, cutin, which controls water loss and possibly organ expansion. Covalent bonds between cutin and its neighbouring cell-wall polysaccharides have long been proposed. However, the lack of biochemical evidence makes cutin-polysaccharide linkages largely conjectural. Here we optimised a portfolio of radiochemical assays to look for cutin-polysaccharide ester bonds in the epidermis of pea epicotyls, ice-plant leaves and tomato fruits, based on the hypothesis that a transacylase remodels cutin in a similar fashion to cutin synthase and cutin:cutin transacylase activities. Through in-situ enzyme assays and chemical degradations coupled with chromatographic analysis of the 3H-labelled products, we observed that among several wall-related oligosaccharides tested, only a xyloglucan oligosaccharide ([3H]XXXGol) could acquire ester-bonds from endogenous cutin, suggesting a cutin:xyloglucan transacylase (CXT). CXT activity was heat-labile, time-dependent, and maximal at near-neutral pH values. In-situ CXT activity peaked in nearly fully expanded tomato fruits and ice-plant leaves. CXT activity positively correlated with organ growth rate, suggesting that it contributes to epidermal integrity during rapid expansion. This study uncovers hitherto unappreciated re-structuring processes in the plant epidermis and provides a step towards the identification of CXT and its engineering for biotechnological applications.

Plant Transcription Factors Involved in Drought and Associated Stresses

Transcription factors (TFs) play a significant role in signal transduction networks spanning the perception of a stress signal and the expression of corresponding stress-responsive genes. TFs are multi-functional proteins that may simultaneously control numerous pathways during stresses in plants-this makes them powerful tools for the manipulation of regulatory and stress-responsive pathways. In recent years, the structure-function relationships of numerous plant TFs involved in drought and associated stresses have been defined, which prompted devising practical strategies for engineering plants with enhanced stress tolerance. Vast data have emerged on purposely basic leucine zipper (bZIP), WRKY, homeodomain-leucine zipper (HD-Zip), myeloblastoma (MYB), drought-response elements binding proteins/C-repeat binding factor (DREB/CBF), shine (SHN), and wax production-like (WXPL) TFs that reflect the understanding of their 3D structure and how the structure relates to function. Consequently, this information is useful in the tailored design of variant TFs that enhances our understanding of their functional states, such as oligomerization, post-translational modification patterns, protein-protein interactions, and their abilities to recognize downstream target DNA sequences. Here, we report on the progress of TFs based on their interaction pathway participation in stress-responsive networks, and pinpoint strategies and applications for crops and the impact of these strategies for improving plant stress tolerance.

ABCG transporters export cutin precursors for the formation of the plant cuticle

The plant cuticle is deposited on the surface of primary plant organs, such as leaves, fruits, and floral organs, forming a diffusion barrier and protecting the plant against various abiotic and biotic stresses. Cutin, the structural polyester of the plant cuticle, is synthesized in the apoplast. Plasma-membrane-localized ATP-binding cassette (ABC) transporters of the G family have been hypothesized to export cutin precursors. Here, we characterize SlABCG42 of tomato representing an ortholog of AtABCG32 in Arabidopsis. SlABCG42 expression in Arabidopsis complements the cuticular deficiencies of the Arabidopsis pec1/abcg32 mutant. RNAi-dependent downregulation of both tomato genes encoding proteins highly homologous to AtABCG32 (SlABCG36 and SlABCG42) leads to reduced cutin deposition and formation of a thinner cuticle in tomato fruits. By using a tobacco (Nicotiana benthamiana) protoplast system, we show that AtABCG32 and SlABCG42 have an export activity for 10,16-dihydroxy hexadecanoyl-2-glycerol, a cutin precursor in vivo. Interestingly, also free ω-hydroxy hexadecanoic acid as well as hexadecanedioic acid were exported, furthering the research on the identification of cutin precursors in vivo and the respective mechanisms of their integration into the cutin polymer.

Structure, Assembly and Function of Cuticle from Mechanical Perspective with Special Focus on Perianth

This review is devoted to the structure, assembly and function of cuticle. The topics are discussed from the mechanical perspective and whenever the data are available a special attention is paid to the cuticle of perianth organs, i.e., sepals, petals or tepals. The cuticle covering these organs is special in both its structure and function and some of these peculiarities are related to the cuticle mechanics. In particular, strengthening of the perianth surface is often provided by a folded cuticle that functionally resembles profiled plates, while on the surface of the petal epidermis of some plants, the cuticle is the only integral continuous layer. The perianth cuticle is distinguished also by those aspects of its mechanics and development that need further studies. In particular, more investigations are needed to explain the formation and maintenance of cuticle folding, which is typical for the perianth epidermis, and also to elucidate the mechanical properties and behavior of the perianth cuticle in situ. Gaps in our knowledge are partly due to technical problems caused by very small thicknesses of the perianth cuticle but modern tools may help to overcome these obstacles.

Variation in Petal and Leaf Wax Deposition Affects Cuticular Transpiration in Cut Lily Flowers

The vase life of cut flowers is largely affected by post-harvest water loss. Cuticular wax is the primary barrier to uncontrolled water loss for aerial plant organs. Studies on leaf cuticular transpiration have been widely conducted; however, little is known about cuticular transpiration in flowers. Here, the cuticular transpiration rate and wax composition of three lily cultivars were determined. The minimum water conductance of tepal cuticles was higher at the green bud than open flower stage. Lily cuticular transpiration exhibited cultivar- and organ-specific differences, where transpiration from the tepals was higher than leaves and was higher in the 'Huang Tianba' than 'Tiber' cultivar. The overall wax coverage of the tepals was higher compared to that of the leaves. Very-long-chain aliphatics were the main wax constituents and were dominated by n-alkanes with carbon (C) chain lengths of C₂₇ and C₂₉, and C₂₉ and C₃₁ in the tepal and leaf waxes, respectively. Primary alcohols and fatty acids as well as small amounts of alkyl esters, ketones, and branched or unsaturated n-alkanes were also detected in both tepal and leaf waxes, depending on the cultivar and organ. In addition, the chain-length distributions were similar between compound classes within cultivars, whereas the predominant C-chain lengths were substantially different between organs. This suggests that the less effective transpiration barrier provided by the tepal waxes may result from the shorter C-chain aliphatics in the tepal cuticle, compared to those in the leaf cuticle. These findings provide further insights to support the exploration of potential techniques for extending the shelf life of cut flowers based on cuticular transpiration barrier properties.

Arabidopsis sepals: A model system for the emergent process of morphogenesis

During development, Arabidopsis thaliana sepal primordium cells grow, divide and interact with their neighbours, giving rise to a sepal with the correct size, shape and form. Arabidopsis sepals have proven to be a good system for elucidating the emergent processes driving morphogenesis due to their simplicity, their accessibility for imaging and manipulation, and their reproducible development. Sepals undergo a basipetal gradient of growth, with cessation of cell division, slow growth and maturation starting at the tip of the sepal and progressing to the base. In this review, I discuss five recent examples of processes during sepal morphogenesis that yield emergent properties: robust size, tapered tip shape, laminar shape, scattered giant cells and complex gene expression patterns. In each case, experiments examining the dynamics of sepal development led to the hypotheses of local rules. In each example, a computational model was used to demonstrate that these local rules are sufficient to give rise to the emergent properties of morphogenesis.

The Complex Architecture of Plant Cuticles and Its Relation to Multiple Biological Functions

Terrestrialization of vascular plants, i.e., Angiosperm, is associated with the development of cuticular barriers that prevent biotic and abiotic stresses and support plant growth and development. To fulfill these multiple functions, cuticles have developed a unique supramolecular and dynamic assembly of molecules and macromolecules. Plant cuticles are not only an assembly of lipid compounds, i.e., waxes and cutin polyester, as generally presented in the literature, but also of polysaccharides and phenolic compounds, each fulfilling a role dependent on the presence of the others. This mini-review is focused on recent developments and hypotheses on cuticle architecture-function relationships through the prism of non-lipid components, i.e., cuticle-embedded polysaccharides and polyester-bound phenolics.