A MYB Triad Controls Primary and Phenylpropanoid Metabolites for Pollen Coat Patterning

MYB transcription factors in Peucedanum Praeruptorum Dunn: the diverse roles of the R2R3-MYB subfamily in mediating coumarin biosynthesis

BACKGROUND

The MYB superfamily (v-myb avian myeloblastosis viral oncogene homolog) plays a role in plant growth and development, environmental stress defense, and synthesis of secondary metabolites. Little is known about the regulatory function of MYB genes in Peucedanum praeruptorum Dunn, although many MYB family members, especially R2R3-MYB genes, have been extensively studied in model plants.

RESULTS

A total of 157 R2R3-MYB transcription factors from P. praeruptorum were identified using bioinformatics analysis. Comprehensive analyses including chromosome location, microsynteny, gene structure, conserved motif, phylogenetic tree, and conserved domain were further performed. The length of the 157 transcription factors ranged from 120 to 1,688 amino acids (molecular weight between 14.21 and 182.69 kDa). All proteins were hydrophilic. Subcellular localization predictions showed that 155 PpMYB proteins were localized in the nucleus, with PpMYB12 and PpMYB157 localized in the chloroplasts and mitochondria, respectively. Ten conserved motifs were identified in the PpMYBs, all of which contained typical MYB domains. Transcriptome analysis identified 47,902 unigenes. Kyoto Encyclopedia of Genes and Genomes analysis revealed 136 pathways, of which 524 genes were associated with the phenylpropanoid pathway. Differential expressed genes (DEGs) before and after bolting showed that 11 genes were enriched in the phenylpropanoid pathway. Moreover, the expression patterns of transcription genes were further verified by qRT-PCR. With high-performance liquid chromatography (HPLC), 8 coumarins were quantified from the root, stem, and leaf tissue samples of P. praeruptorum at different stages. Praeruptorin A was found in both roots and leaves before bolting, whereas praeruptorin B was mainly concentrated in the roots, and the content of both decreased in the roots and stems after bolting. Praeruptorin E content was highest in the leaves and increased with plant growth. The correlation analysis between transcription factors and coumarin content showed that the expression patterns of PpMYB3 and PpMYB103 in roots align with the accumulation trends of praeruptorin A, praeruptorin B, praeruptorin E, scopoletin, and isoscopoletin, which declined in content after bolting, suggesting that these genes may positively regulate the biosynthesis of coumarins. Eleven distinct metabolites and 48 DEGs were identified. Correlation analysis revealed that the expression of all DEGs were significantly related to the accumulation of coumarin metabolites, indicating that these genes are involved in the regulation of coumarin biosynthesis.

CONCLUSIONS

R2R3-MYB transcription factors may be involved in the synthesis of coumarin. Our findings provide basic data and a rationale for future an in-depth studies on the role of R2R3-MYB transcription factors in the growth and regulation of coumarin synthesis.

Genome-Wide Analysis of CSL Family Genes Involved in Petiole Elongation, Floral Petalization, and Response to Salinity Stress in Nelumbo nucifera

Lotus (Nelumbo nucifera), a perennial aquatic plant, endures various environmental stresses. Its diverse ornamental traits make it an ideal model for studying multigene family functional differentiation and abiotic stress responses. The cellulose synthase-like (CSL) gene family includes multiple subfamilies and holds potentially pivotal roles in plant growth, development, and stress responses. Thus, understanding this family is essential for uncovering the attributes of ancient dicotyledonous lotus species and offering new genetic resources for targeted genetic improvement. Herein, we conducted a genome-wide NnCSL gene identification study, integrating tissue-specific expression analysis, RNA-seq, and qRT-PCR validation. We identified candidate NnCSL genes linked to petiole elongation, floral petalization, salinity stress responses, and potential co-expressed TFs. 22 NnCSL genes were categorized into six subfamilies: NnCSLA, NnCSLB, NnCSLC, NnCSLD, NnCSLE, and NnCSLG. Promoter regions contain numerous cis-acting elements related to growth, development, stress responses, and hormone regulation. Nineteen NnCSL genes showed specific differential expression in LPA (large plant architecture) versus SPA (small plant architecture): petioles, petalized carpels (CP) and normal carpels (C), and petalized stamens (SP) and normal stamens (S). Notably, most NnCSLC, NnCSLA, and NnCSLB subfamily genes play diverse roles in various aspects of lotus growth and development, while NnCSLE and NnCSLG are specifically involved in carpel petalization and petiole elongation, respectively. Additionally, 11 candidate NnCSL genes responsive to salinity stress were identified, generally exhibiting antagonistic effects on growth and developmental processes. These findings provide an important theoretical foundation and novel insights for the functional study of NnCSL genes in growth, development, and stress resistance in lotus.

Characterization and functions of Myeloblastosis (MYB) transcription factors in cucurbit crops

Myeloblastosis (MYB) is one of the largest family of transcription factors (TFs) in plants. It plays a key role in plant life activities, such as metabolic regulation, stress resistant, as well as helpful for plant growth and development. In China, cucurbit is an important and nutrients rich vegetable crop, which have high medicinal and socio-economic values. In this review, we discussed the structure and characterization of MYB TFs and how do regulate flower development, fruit maturity, fruit quality, and flavonoid biosynthesis. Furthermore, we highlight the effect and contribution of MYB TFs in the regulation of biotic and abiotic stress resistance. This comprehensive review will provide a new reference for the more effective application of MYB TF in quality control, stress resistance research and molecular breeding of cucurbit crops.

Transcriptome Remodeling in Arabidopsis: A Response to Heterologous Poplar MSL-lncRNAs Overexpression

Stamens are vital reproductive organs in angiosperms, essential for plant growth, reproduction, and development. The genetic regulation and molecular mechanisms underlying stamen development are, however, complex and varied among different plant species. MSL-lncRNAs, a gene specific to the Y chromosome of Populus deltoides, is predominantly expressed in male flower buds. Heterologous expression of MSL-lncRNAs in Arabidopsis thaliana resulted in an increase in both stamen and anther count, without affecting pistil development or seed set. To reveal the molecular regulatory network influenced by MSL-lncRNAs on stamen development, we conducted transcriptome sequencing of flowers from both wild-type and MSL-lncRNAs-overexpressing Arabidopsis. A total of 678 differentially expressed genes were identified between wild-type and transgenic Arabidopsis. Among these, 20 were classified as transcription factors, suggesting a role for these regulatory proteins in stamen development. GO enrichment analysis revealed that the differentially expressed genes were significantly associated with processes such as pollen formation, polysaccharide catabolic processes, and secondary metabolism. KEGG pathway analysis indicated that MSL-lncRNAs might promote stamen development by upregulating genes involved in the phenylpropanoid biosynthesis pathway. The top three upregulated genes, all featuring the DUF295 domain, were found to harbor an F-box motif at their N-termini, which is implicated in stamen development. Additionally, in transgenic Arabidopsis flowers, genes implicated in tapetum formation and anther development were also observed to be upregulated, implying a potential role for MSL-lncRNAs in modulating pollen development through the positive regulation of these genes. The findings from this study establish a theoretical framework for elucidating the genetic control exerted by MSL-lncRNAs over stamen and pollen development.

Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR

BACKGROUND

Flavonoids, an important class of specialized metabolites, are synthesized from phenylalanine and present in almost all plant species. Different branches of flavonoid biosynthesis lead to products like flavones, flavonols, anthocyanins, and proanthocyanidins. Dihydroflavonols form the branching point towards the production of non-colored flavonols via flavonol synthase (FLS) and colored anthocyanins via dihydroflavonol 4-reductase (DFR). Despite the wealth of publicly accessible data, there remains a gap in understanding the mechanisms that mitigate competition between FLS and DFR for the shared substrate, dihydroflavonols.

RESULTS

An angiosperm-wide comparison of FLS and DFR sequences revealed the amino acids at positions associated with the substrate specificity in both enzymes. A global analysis of the phylogenetic distribution of these amino acid residues revealed that monocots generally possess FLS with Y132 (FLSY) and DFR with N133 (DFRN). In contrast, dicots generally possess FLSH and DFRN, DFRD, and DFRA. DFRA, which restricts substrate preference to dihydrokaempferol, previously believed to be unique to strawberry species, is found to be more widespread in angiosperms and has evolved independently multiple times. Generally, angiosperm FLS appears to prefer dihydrokaempferol, whereas DFR appears to favor dihydroquercetin or dihydromyricetin. Moreover, in the FLS-DFR competition, the dominance of one over the other is observed, with typically only one gene being expressed at any given time.

CONCLUSION

This study illustrates how almost mutually exclusive gene expression and substrate-preference determining residues could mitigate competition between FLS and DFR, delineates the evolution of these enzymes, and provides insights into mechanisms directing the metabolic flux of the flavonoid biosynthesis, with potential implications for ornamental plants and molecular breeding strategies.

Chromosome-level genome assembly and population genomics reveals crucial selection for subgynoecy development in chieh-qua

Chieh-qua is an important cucurbit crop and very popular in South China and Southeast Asia. Despite its significance, its genetic basis and domestication history are unclear. In this study, we have successfully generated a chromosome-level reference genome assembly for the chieh-qua 'A36' using a hybrid assembly strategy that combines PacBio long reads and Illumina short reads. The assembled genome of chieh-qua is approximately 953.3 Mb in size and is organized into 12 chromosomes, with contig N50 of 6.9 Mb and scaffold N50 of 68.2 Mb. Notably, the chieh-qua genome is comparable in size to the wax gourd genome. Through gene prediction analysis, we have identified a total of 24 593 protein-coding genes in the A36 genome. Additionally, approximately 56.6% (539.3 Mb) of the chieh-qua genome consists of repetitive sequences. Comparative genome analysis revealed that chieh-qua and wax gourd are closely related, indicating a close evolutionary relationship between the two species. Population genomic analysis, employing 129 chieh-qua accessions and 146 wax gourd accessions, demonstrated that chieh-qua exhibits greater genetic diversity compared to wax gourd. We also employed the GWAS method to identify related QTLs associated with subgynoecy, an interested and important trait in chieh-qua. The MYB59 (BhiCQ0880026447) exhibited relatively high expression levels in the shoot apex of four subgynoecious varieties compared with monoecious varieties. Overall, this research provides insights into the domestication history of chieh-qua and offers valuable genomic resources for further molecular research.

Transcription Factors and Their Regulatory Roles in the Male Gametophyte Development of Flowering Plants

Male gametophyte development in plants relies on the functions of numerous genes, whose expression is regulated by transcription factors (TFs), non-coding RNAs, hormones, and diverse environmental stresses. Several excellent reviews are available that address the genes and enzymes associated with male gametophyte development, especially pollen wall formation. Growing evidence from genetic studies, transcriptome analysis, and gene-by-gene studies suggests that TFs coordinate with epigenetic machinery to regulate the expression of these genes and enzymes for the sequential male gametophyte development. However, very little summarization has been performed to comprehensively review their intricate regulatory roles and discuss their downstream targets and upstream regulators in this unique process. In the present review, we highlight the research progress on the regulatory roles of TF families in the male gametophyte development of flowering plants. The transcriptional regulation, epigenetic control, and other regulators of TFs involved in male gametophyte development are also addressed.

MYB transcription factors and their roles in the male reproductive development of flowering plants

As one of the largest transcription factor families with complex functional differentiation in plants, the MYB transcription factors (MYB TFs) play important roles in the physiological and biochemical processes of plant growth and development. Male reproductive development, an essential part of sexual reproduction in flowering plants, is undoubtedly regulated by MYB TFs. In this review, we summarize the roles of the MYB TFs involved in the three stages of male reproductive development: pollen grains formation and maturation, filament elongation and anther dehiscence, and fertilization. Also, the potential downstream target genes and upstream regulators of these MYB TFs are discussed. Furthermore, we propose the underlying regulatory mechanisms of these MYB TFs: (1) A complex network of MYB TFs regulates various aspects of male reproductive development; (2) MYB homologous genes in different species may be functionally conserved or differentiated; (3) MYB TFs often form regulatory complexes with bHLH TFs.

Overexpression of a Grape MYB Transcription Factor Gene VhMYB2 Increases Salinity and Drought Tolerance in Arabidopsis thaliana

In viticulture, the highly resistant rootstock 'Beta' is widely used in Chinese grape production to avoid the effects of soil salinization and drought on grape growth. However, the mechanism of high resistance to abiotic stress in the 'Beta' rootstock is not clear. In this study, we demonstrated that VhMYB2 as a transcription factor made a significant contribution to salinity and drought stress, which was isolated from the 'Beta' rootstock. The coding sequence of the VhMYB2 gene was 858 bp, encoding 285 amino acids. The subcellular localization of VhMYB2 was located in the nucleus of tobacco epidermal cells. Moreover, RT-qPCR found that VhMYB2 was predominantly expressed in the mature leaf and root of the grape. Under salinity and drought stress, overexpressing VhMYB2 showed a higher resistant phenotype and survival rates in A. thaliana while the transgenic lines had a survival advantage by measuring the contents of proline, chlorophyll, and MDA, and activities of POD, SOD, and CAT, and expression levels of related stress response genes. The results reveal that VhMYB2 may be an important transcription factor regulating 'Beta' resistance in response to abiotic stress.

Industrial chicory genome gives insights into the molecular timetable of anther development and male sterility

Industrial chicory (Cichorium intybus var. sativum) is a biannual crop mostly cultivated for extraction of inulin, a fructose polymer used as a dietary fiber. F1 hybrid breeding is a promising breeding strategy in chicory but relies on stable male sterile lines to prevent self-pollination. Here, we report the assembly and annotation of a new industrial chicory reference genome. Additionally, we performed RNA-Seq on subsequent stages of flower bud development of a fertile line and two cytoplasmic male sterile (CMS) clones. Comparison of fertile and CMS flower bud transcriptomes combined with morphological microscopic analysis of anthers, provided a molecular understanding of anther development and identified key genes in a range of underlying processes, including tapetum development, sink establishment, pollen wall development and anther dehiscence. We also described the role of phytohormones in the regulation of these processes under normal fertile flower bud development. In parallel, we evaluated which processes are disturbed in CMS clones and could contribute to the male sterile phenotype. Taken together, this study provides a state-of-the-art industrial chicory reference genome, an annotated and curated candidate gene set related to anther development and male sterility as well as a detailed molecular timetable of flower bud development in fertile and CMS lines.

Unique and overlapping functions for the transcriptional regulators KANADI1 and ULTRAPETALA1 in Arabidopsis gynoecium and stamen gene regulation

Plants generate their reproductive organs, the stamens and the carpels, de novo within the flowers that form when the plant reaches maturity. The carpels comprise the female reproductive organ, the gynoecium, a complex organ that develops along several axes of polarity and is crucial for plant reproduction, fruit formation, and seed dispersal. The epigenetic trithorax group (trxG) protein ULTRAPETALA1 (ULT1) and the GARP domain transcription factor KANADI1 (KAN1) act cooperatively to regulate Arabidopsis thaliana gynoecium patterning along the apical-basal polarity axis; however, the molecular pathways through which this patterning activity is achieved remain to be explored. In this study, we used transcriptomics to identify genome-wide ULT1 and KAN1 target genes during reproductive development. We discovered 278 genes in developing flowers that are regulated by ULT1, KAN1, or both factors together. Genes involved in developmental and reproductive processes are overrepresented among ULT1 and/or KAN1 target genes, along with genes involved in biotic or abiotic stress responses. Consistent with their function in regulating gynoecium patterning, a number of the downstream target genes are expressed in the developing gynoecium, including a unique subset restricted to the stigmatic tissue. Further, we also uncovered a number of KAN1- and ULT1-induced genes that are transcribed predominantly or exclusively in developing stamens. These findings reveal a potential cooperative role for ULT1 and KAN1 in male as well as female reproductive development that can be investigated with future genetic and molecular experiments.

Rice anther tapetum: a vital reproductive cell layer for sporopollenin biosynthesis and pollen exine patterning

The tapetum is the innermost layer of the four layers of the rice anther that provides protection and essential nutrients to pollen grain development and delivers precursors for pollen exine formation. The tapetum has a key role in the normal development of pollen grains and tapetal programmed cell death (PCD) that is linked with sporopollenin biosynthesis and transport. Recently, many genes have been identified that are involved in tapetum formation in rice and Arabidopsis. Genetic mutation in PCD-associated genes could affect normal tapetal PCD, which finally leads to aborted pollen grains and male sterility in rice. In this review, we discuss the most recent research on rice tapetum development, including genomic, transcriptomic and proteomic studies. Furthermore, tapetal PCD, sporopollenin biosynthesis, ROS activity for tapetum function and its role in male reproductive development are discussed in detail. This will improve our understanding of the role of the tapetum in male fertility using rice as a model system, and provide information that can be applied in rice hybridization and that of other major crops.

CsMYC2 is involved in the regulation of phenylpropanoid biosynthesis induced by trypsin in cucumber (Cucumis sativus) during storage

Trypsin has a new activity of scavenging superoxide anion and generating hydrogen peroxide. Trypsin can significantly improve the storage quality of C. sativus. To illustrate the mechanism of trypsin-induced resistance in fruits and vegetables, an integrated analysis of widely targeted metabolomics and transcriptomics was carried out. Transcriptomic results showed that 1068 genes highly related to phenylpropanoid biosynthesis gathered in the brown module were obtained by WGCNA. In KEGG analysis, differentially expressed genes (DEGs) were also highly enriched in EIP (Environmental Information Processing) pathways "Plant hormone signal transduction (map04075)" and "MAPK signaling pathway-plant (map04016)". Next, 87 genes were identified as the leading edge by GSEA analysis. So far, CsMYC2 was highlighted as a key transcription factor that regulates phenylpropanoid biosynthesis identified by GSEA and WGCNA. Furthermore, the major route of biosynthesis of phenylpropanoid compounds including coumarins, lignins, chlorogenic acid, flavonoids, and derivatives regulated by trypsin was also illustrated by both transcriptomic and metabolomic data. Results of O2PLS showed that CsMYC2 was positively correlated with Rosmarinic acid-3-O-glucoside, Epigallocatechin, Quercetin-3-O-sophoroside (Baimaside), and so on. Correlation between CsMYC2, phenylpropanoid related genes, and metabolites in C. sativus was illustrated by co-expression networks. Roles of CsMYC2 were further checked in C. sativus by VIGS. The results of this study might give new insight into the exploration of the postharvest resistance mechanism of C. sativus induced by trypsin and provide useful information for the subsequent mining of resistance genes in C. sativus.

OsCCRL1 is Essential for Phenylpropanoid Metabolism in Rice Anthers

Phenylpropanoid metabolism and timely tapetal degradation are essential for anther and pollen development, but the underlying mechanisms are unclear. In the current study, to investigate this, we identified and analyzed the male-sterile mutant, osccrl1 (cinnamoyl coA reductase-like 1), which exhibited delayed tapetal programmed cell death (PCD) and defective mature pollen. Map-based cloning, genetic complementation, and gene knockout revealed that OsCCRL1 corresponds to the gene LOC_Os09g32020.2, a member of SDR (short-chain dehydrogenase/reductase) family enzyme. OsCCRL1 was preferentially expressed in the tapetal cells and microspores, and localized to the nucleus and cytoplasm in both rice protoplasts and Nicotiana benthamiana leaves. The osccrl1 mutant exhibited reduced CCRs enzyme activity, less lignin accumulation, delayed tapetum degradation, and disrupted phenylpropanoid metabolism. Furthermore, an R2R3 MYB transcription factor OsMYB103/OsMYB80/OsMS188/BM1, involved in tapetum and pollen development, regulates the expression of OsCCRL1. Finally, the osmyb103 osccrl1 double mutants, exhibited the same phenotype as the osmyb103 single mutant, further indicating that OsMYB103/OsMYB80/OsMS188/BM1 functions upstream of OsCCRL1. These findings help to clarify the role of phenylpropanoid metabolism in male sterility and the regulatory network underlying the tapetum degradation.

The full-length Auxin Response Factor 8 isoform ARF8.1 controls pollen cell wall formation and directly regulates TDF1, AMS and MS188 expression

Auxin Response Factor 8 plays a key role in late stamen development: its splice variants ARF8.4 and ARF8.2 control stamen elongation and anther dehiscence. Here, we characterized the role of ARF8 isoforms in pollen fertility. By phenotypic and ultrastructural analysis of arf8-7 mutant stamens, we found defects in pollen germination and viability caused by alterations in exine structure and pollen coat deposition. Furthermore, tapetum degeneration, a prerequisite for proper pollen wall formation, is delayed in arf8-7 anthers. In agreement, the genes encoding the transcription factors TDF1, AMS, MS188 and MS1, required for exine and pollen coat formation, and tapetum development, are downregulated in arf8-7 stamens. Consistently, the sporopollenin content is decreased, and the expression of sporopollenin synthesis/transport and pollen coat protein biosynthetic genes, regulated by AMS and MS188, is reduced. Inducible expression of the full-length isoform ARF8.1 in arf8-7 inflorescences complements the pollen (and tapetum) phenotype and restores the expression of the above transcription factors. Chromatin immunoprecipitation-quantitative polymerase chain reaction assay revealed that ARF8.1 directly targets the promoters of TDF1, AMS and MS188. In conclusion, the ARF8.1 isoform controls pollen and tapetum development acting directly on the expression of TDF1, AMS and MS188, which belong to the pollen/tapetum genetic pathway.

Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci

The anther-enriched phased, small interfering RNAs (phasiRNAs) play vital roles in sustaining male fertility in grass species. Their long non-coding precursors are synthesized by RNA polymerase II and are likely regulated by transcription factors (TFs). A few putative transcriptional regulators of the 21- or 24-nucleotide phasiRNA loci (referred to as 21- or 24-PHAS loci) have been identified in maize (Zea mays), but whether any of the individual TFs or TF combinations suffice to activate any PHAS locus is unclear. Here, we identified the temporal gene coexpression networks (modules) associated with maize anther development, including two modules highly enriched for the 21- or 24-PHAS loci. Comparisons of these coexpression modules and gene sets dysregulated in several reported male sterile TF mutants provided insights into TF timing with regard to phasiRNA biogenesis, including antagonistic roles for OUTER CELL LAYER4 and MALE STERILE23. Trans-activation assays in maize protoplasts of individual TFs using bulk-protoplast RNA-sequencing showed that two of the TFs coexpressed with 21-PHAS loci could activate several 21-nucleotide phasiRNA pathway genes but not transcription of 21-PHAS loci. Screens for combinatorial activities of these TFs and, separately, the recently reported putative transcriptional regulators of 24-PHAS loci using single-cell (protoplast) RNA-sequencing, did not detect reproducible activation of either 21-PHAS or 24-PHAS loci. Collectively, our results suggest that the endogenous transcriptional machineries and/or chromatin states in the anthers are necessary to activate reproductive PHAS loci.

MYB transcription factors-master regulators of phenylpropanoid biosynthesis and diverse developmental and stress responses

Phenylpropanoids, the largest class of natural products including flavonoids, anthocyanins, monolignols and tannins perform multiple functions ranging from photosynthesis, nutrient uptake, regulating growth, cell division, maintenance of redox homeostasis and biotic and abiotic stress responses. Being sedentary life forms, plants possess several regulatory modules that increase their performance in varying environments by facilitating activation of several signaling cascades upon perception of developmental and stress signals. Of the various regulatory modules, those involving MYB transcription factors are one of the extensive groups involved in regulating the phenylpropanoid metabolic enzymes in addition to other genes. R2R3 MYB transcription factors are a class of plant-specific transcription factors that regulate the expression of structural genes involved in anthocyanin, flavonoid and monolignol biosynthesis which are indispensable to several developmental pathways and stress responses. The aim of this review is to present the regulation of the phenylpropanoid pathway by MYB transcription factors via Phospholipase D/phosphatidic acid signaling, downstream activation of the structural genes, leading to developmental and/or stress responses. Specific MYB transcription factors inducing or repressing specific structural genes of anthocyanin, flavonoid and lignin biosynthetic pathways are discussed. Further the roles of MYB in activating biotic and abiotic stress responses are delineated. While several articles have reported the role of MYB's in stress responses, they are restricted to two or three specific MYB factors. This review is a consolidation of the diverse roles of different MYB transcription factors involved both in induction and repression of anthocyanin, flavonoid, and lignin biosynthesis.

Global transcriptome analysis reveals potential genes associated with genic male sterility of rapeseed (Brassica napus L.)

Rapeseed is the third leading source of edible oil in the world. Genic male sterility (GMS) lines provide crucial material for harnessing heterosis for rapeseed. GMS lines have been widely used successfully for rapeseed hybrid production. The physiological and molecular mechanism of pollen development in GMS lines of rapeseed (Brassica napus L.) need to be determined for the creation of hybrids and cultivation of new varieties. However, limited studies have focused on systematically mining genes that regulate the pollen development of GMS lines in B. napus. In the present study, to determine the stage at which pollen development begins to show abnormality in the GMS lines, we performed semi-thin section analysis of the anthers with five pollen development stages. The results indicated that the abnormal pollen development in DGMS lines might start at the meiotic stage, and abnormal pollen development in RGMS lines probably occurred before the tetrad stage. To investigate the critical genes and pathways involved in pollen development in GMS lines, we constructed and sequenced 24 transcriptome libraries for the flower buds from the fertile and sterile lines of two recessive GMS (RGMS) lines (6251AB and 6284AB) and two dominant GMS (DGMS) lines (4001AB and 4006AB). A total of 23,554 redundant DEGs with over two-fold change between sterile and fertile lines were obtained. A total of 346 DEGs were specifically related to DGMS, while 1,553 DEGs were specifically related to RGMS. A total of 1,545 DEGs were shared between DGMS and RGMS. And 253 transcription factors were found to be differentially expressed between the sterile and fertile lines of GMS. In addition, 6,099 DEGs possibly related to anther, pollen, and microspore development processes were identified. Many of these genes have been reported to be involved in anther and microspore developmental processes. Several DEGs were speculated to be key genes involved in the regulation of fertility. Three differentially expressed genes were randomly selected and their expression levels were verified by quantitative PCR (qRT-PCR). The results of qRT-PCR largely agreed with the transcriptome sequencing results. Our findings provide a global view of genes that are potentially involved in GMS occurrence. The expression profiles and function analysis of these DEGs were provided to expand our understanding of the complex molecular mechanism in pollen and sterility development in B. napus.

The methyl-CpG-binding domain family member PEM1 is essential for Ubisch body formation and pollen exine development in rice

Pollen exine is composed of finely-organized nexine, bacula and tectum, and is crucial for pollen viability and function. Pollen exine development involves a complicated molecular network that coordinates the interaction between pollen and tapetal cells, as well as the biosynthesis, transport and assembly of sporopollenin precursors; however, our understanding of this network is very limited. Here, we report the roles of PEM1, a member of methyl-CpG-binding domain family, in rice pollen development. PEM1 expressed constitutively and, in anthers, its expression was detectable in tapetal cells and pollen. This predicted PEM1 protein of 240 kDa had multiple epigenetic-related domains. pem1 mutants exhibited abnormal Ubisch bodies, delayed exine occurrence and, finally, defective exine, including invisible bacula, amorphous and thickened nexine and tectum layer structures, and also had the phenotype of increased anther cuticle. The mutation in PEM1 did not affect the timely degradation of tapetum. Lipidomics revealed much higher wax and cutin contents in mutant anthers than in wild-type. Accordingly, this mutation up-regulated the expression of a set of genes implicated in transcriptional repression, signaling and diverse metabolic pathways. These results indicate that PEM1 mediates Ubisch body formation and pollen exine development mainly by negatively modulating the expression of genes. Thus, the PEM1-mediated molecular network represents a route for insights into mechanisms underlying pollen development. PEM1 may be a master regulator of pollen exine development.

Potato virus X-delivered CRISPR activation programs lead to strong endogenous gene induction and transient metabolic reprogramming in Nicotiana benthamiana

Programmable transcriptional regulators based on CRISPR architecture are promising tools for the induction of plant gene expression. In plants, CRISPR gene activation is effective with respect to modulating development processes, such as the flowering time or customizing biochemical composition. The most widely used method for delivering CRISPR components into the plant is Agrobacterium tumefaciens-mediated genetic transformation, either transient or stable. However, as a result of their versatility and their ability to move, virus-derived systems have emerged as an interesting alternative for supplying the CRISPR components to the plant, in particular guide RNA (gRNA), which represents the variable component in CRISPR strategies. In the present study, we describe a Potato virus X-derived vector that, upon agroinfection in Nicotiana benthamiana, serves as a vehicle for delivery of gRNAs, producing highly specific virus-induced gene activation. The system works in combination with a N. benthamiana transgenic line carrying the remaining complementary CRISPR gene activation components, specifically the dCasEV2.1 cassette, which has been shown previously to mediate strong programmable transcriptional activation in plants. Using an easily scalable, non-invasive spraying method, we show that gRNA-mediated activation programs move locally and systemically, generating a strong activation response in different target genes. Furthermore, by activating three different endogenous MYB transcription factors, we demonstrate that this Potato virus X-based virus-induced gene reprogramming strategy results in program-specific metabolic fingerprints in N. benthamiana leaves characterized by distinctive phenylpropanoid-enriched metabolite profiles.

A whiff of the future: functions of phenylalanine-derived aroma compounds and advances in their industrial production

Plants produce myriad aroma compounds-odorous molecules that are key factors in countless aspects of the plant's life cycle, including pollinator attraction and communication within and between plants. For humans, aroma compounds convey accurate information on food type, and are vital for assessing the environment. The phenylpropanoid pathway is the origin of notable aroma compounds, such as raspberry ketone and vanillin. In the last decade, great strides have been made in elucidating this pathway with the identification of numerous aroma-related biosynthetic enzymes and factors regulating metabolic shunts. These scientific achievements, together with public acknowledgment of aroma compounds' medicinal benefits and growing consumer demand for natural products, are driving the development of novel biological sources for wide-scale, eco-friendly, and inexpensive production. Microbes and plants that are readily amenable to metabolic engineering are garnering attention as suitable platforms for achieving this goal. In this review, we discuss the importance of aroma compounds from the perspectives of humans, pollinators and plant-plant interactions. Focusing on vanillin and raspberry ketone, which are of high interest to the industry, we present key knowledge on the biosynthesis and regulation of phenylalanine-derived aroma compounds, describe advances in the adoption of microbes and plants as platforms for their production, and propose routes for improvement.

Analysis of flavonol regulator evolution in the Brassicaceae reveals MYB12, MYB111 and MYB21 duplications and MYB11 and MYB24 gene loss

BACKGROUND

Flavonols are the largest subgroup of flavonoids, possessing multiple functions in plants including protection against ultraviolet radiation, antimicrobial activities, and flower pigmentation together with anthocyanins. They are of agronomical and economical importance because the major off-taste component in rapeseed protein isolates is a flavonol derivative, which limits rapeseed protein use for human consumption. Flavonol production in Arabidopsis thaliana is mainly regulated by the subgroup 7 (SG7) R2R3-MYB transcription factors MYB11, MYB12, and MYB111. Recently, the SG19 MYBs MYB21, MYB24, and MYB57 were shown to regulate flavonol accumulation in pollen and stamens. The members of each subgroup are closely related, showing gene redundancy and tissue-specific expression in A. thaliana. However, the evolution of these flavonol regulators inside the Brassicaceae, especially inside the Brassiceae, which include the rapeseed crop species, is not fully understood.

RESULTS

We studied the SG7 and SG19 MYBs in 44 species, including 31 species of the Brassicaceae, by phylogenetic analyses followed by synteny and gene expression analyses. Thereby we identified a deep MYB12 and MYB111 duplication inside the Brassicaceae, which likely occurred before the divergence of Brassiceae and Thelypodieae. These duplications of SG7 members were followed by the loss of MYB11 after the divergence of Eruca vesicaria from the remaining Brassiceae species. Similarly, MYB21 experienced duplication before the emergence of the Brassiceae tribe, where the gene loss of MYB24 is also proposed to have happened. The members of each subgroup revealed frequent overlapping spatio-temporal expression patterns in the Brassiceae member B. napus, which are assumed to compensate for the loss of MYB11 and MYB24 in the analysed tissues.

CONCLUSIONS

We identified a duplication of MYB12, MYB111, and MYB21 inside the Brassicaceae and MYB11 and MYB24 gene loss inside the tribe Brassiceae. We propose that polyploidization events have shaped the evolution of the flavonol regulators in the Brassicaceae, especially in the Brassiceae.

TDTHub, a web server tool for the analysis of transcription factor binding sites in plants

Transcriptional regulation underlies most developmental programs and physiological responses to environmental changes in plants. Transcription factors (TFs) play a key role in the regulation of gene expression by binding specifically to short DNA sequences in the regulatory regions of genes: the TF binding sites (TFBSs). In recent years, several bioinformatic tools have been developed to detect TFBSs in candidate genes, either by de novo prediction or by directly mapping experimentally known TFBSs. However, most of these tools contain information for only a few species or require multi-step procedures, and are not always intuitive for non-experienced researchers. Here we present TFBS-Discovery Tool Hub (TDTHub), a web server for quick and intuitive studies of transcriptional regulation in plants. TDTHub uses pre-computed TFBSs in 40 plant species and allows the choice of two mapping algorithms, providing a higher versatility. Besides the main TFBS enrichment tool, TDTHub includes additional tools to assist in the analysis and visualization of data. In order to demonstrate the effectiveness of TDTHub, we analyzed the transcriptional regulation of the anthocyanin biosynthesis pathway. We also analyzed the transcriptional cascades in response to jasmonate and wounding in Arabidopsis and tomato (Solanum lycopersicum), respectively. In these studies, TDTHub helped to verify the most relevant TF nodes and to propose new ones with a prominent role in these pathways. TDTHub is available at http://acrab.cnb.csic.es/TDTHub/, and it will be periodically upgraded and expanded for new species and gene annotations.

Quantitative Proteomics Analysis Reveals Proteins Associated with High Melatonin Content in Barley Seeds under NaCl-Induced Salt Stress

Soil salinization limits hull-less barley cultivation in the Qinghai-Tibet Plateau of China. However, some wild hull-less barley seeds accumulate high melatonin (MEL) during germination with improved salt tolerance; but the mechanism of melatonin-mediated salt tolerance in hull-less barley is not well understood at the protein level. This study investigated proteome changes resulting in high melatonin content in germinating hull-less barley seeds under high saline conditions. The proteome profiles of seed treatment with 240 mM-NaCl (N), water (H), and control (C) taken 7 days after germination were compared using the TMT-based quantitative proteomics. Our results indicate that salt stress-induced global changes in the proteomes of germinating hull-less barley seeds, altering the expression and abundance of proteins related to cell cycle and control, carbohydrate and energy metabolism, and amino acid transport and metabolism including proteins related to melatonin production. Furthermore, proteins associated with cellular redox homeostasis, osmotic stress response, and secondary metabolites derived primarily from amino acid metabolism, purine degradation, and shikimate pathways increased significantly in abundance and may contribute to the high melatonin content in seeds under salt stress. Consequently, triggering the robust response to oxidative stress occasioned by the NaCl-induced salt stress, improved seed germination and strong adaptation to salt stress.

The Role of Hydroxycinnamic Acid Amide Pathway in Plant Immunity

The compounds involved in the hydroxycinnamic acid amide (HCAA) pathway are an important class of metabolites in plants. Extensive studies have reported that a variety of plant hydroxycinnamamides exhibit pivotal roles in plant-pathogen interactions, such as p-coumaroylagmatine and ferulic acid. The aim of this review is to discuss the emerging findings on the functions of hydroxycinnamic acid amides (HCAAs) accumulation associated with plant defenses against plant pathologies, antimicrobial activity of HCAAs, and the mechanism of HCAAs involved in plant immune responses (such as reactive oxygen species (ROS), cell wall response, plant defense hormones, and stomatal immunity). However, these advances have also revealed the complexity of HCAAs participation in plant defense reactions, and many mysteries remain to be revealed. This review provides an overview of the mechanistic and conceptual insights obtained so far and highlights areas for future exploration of phytochemical defense metabolites.

The R2R3-MYB transcription factor FaMYB63 participates in regulation of eugenol production in strawberry

The biosynthetic pathway of volatile phenylpropanoids, including 4-allyl-2-methoxyphenol (eugenol), has been investigated in petunia (Petunia hybrida). However, the regulatory network for eugenol accumulation in strawberry (Fragaria × ananassa Duch.) fruit remains unclear. Here, an R2R3-type MYB transcription factor (TF; FaMYB63) was isolated from strawberry by yeast one-hybrid (Y1H) screening using the promoter of the FaEGS1 (eugenol synthase 1 [EGS 1]) gene, which encodes the enzyme responsible for the last step in eugenol biosynthesis. FaMYB63 is phylogenetically distinct from other R2R3-MYB TFs, including FaEOBІІ (EMISSION OF BENZENOID II [EOBII]), which also participates in regulating eugenol biosynthesis in strawberry receptacles. Reverse transcription quantitative PCR (RT-qPCR) assays showed that the expression of FaMYB63 was tissue-specific and consistent with eugenol content through strawberry fruit development, was repressed by abscisic acid, and was activated by auxins (indole-3-acetic acid). Overexpression and RNA interference-mediated silencing of FaMYB63 resulted in marked changes in the transcript levels of the biosynthetic genes FaEGS1, FaEGS2, and FaCAD1 (cinnamyl alcohol dehydrogenase 1 [CAD1]) and, thereby, the accumulation of eugenol. Electrophoretic mobility shift, Y1H, GUS activity, and dual-luciferase activity assays demonstrated that the transcript levels of FaEOBІІ and FaMYB10 were regulated by FaMYB63, but not the other way around. Together, these results demonstrate that FaMYB63 directly activates FaEGS1, FaEGS2, FaCAD1, FaEOBІІ, and FaMYB10 to induce eugenol biosynthesis during strawberry fruit development. These findings deepen the understanding of the regulatory network that influences eugenol metabolism in an edible fruit crop.

MYB2 Is Important for Tapetal PCD and Pollen Development by Directly Activating Protease Expression in Arabidopsis

Tapetal programmed cell death (PCD) is a complex biological process that plays an important role in pollen formation and reproduction. Here, we identified the MYB2 transcription factor expressed in the tapetum from stage 5 to stage 11 that was essential for tapetal PCD and pollen development in Arabidopsis thaliana. Downregulation of MYB2 retarded tapetal degeneration, produced defective pollen, and decreased pollen vitality. EMSA and transcriptional activation analysis revealed that MYB2 acted as an upstream activator and directly regulated expression of the proteases CEP1 and βVPE. The expression of these proteases was lower in the buds of the myb2 mutant. Overexpression of either/both CEP1 or/and βVPE proteases partially recover pollen vitality in the myb2 background. Taken together, our results revealed that MYB2 regulates tapetal PCD and pollen development by directly activating expression of the proteases CEP1 and βVPE. Thus, a transcription factor/proteases regulatory and activated cascade was established for tapetal PCD during another development in Arabidopsis thaliana. Highlight: MYB2 is involved in tapetal PCD and pollen development by directly regulating expression of the protease CEP1 and βVPE and establishes a transcription factor/proteases regulatory and activated cascade.

ODORANT1 targets multiple metabolic networks in petunia flowers

Scent bouquets produced by the flowers of Petunia spp. (petunia) are composed of a complex mixture of floral volatile benzenoid and phenylpropanoid compounds (FVBPs), which are specialized metabolites derived from phenylalanine (Phe) through an interconnected network of enzymes. The biosynthesis and emission of high levels of these volatiles requires coordinated transcriptional activation of both primary and specialized metabolic networks. The petunia R2R3-MYB transcription factor ODORANT 1 (ODO1) was identified as a master regulator of FVBP production and emission; however, our knowledge of the direct regulatory targets of ODO1 has remained limited. Using chromatin immunoprecipitation followed by sequencing (ChIP-seq) in petunia flowers, we identify genome-wide ODO1-bound genes that are enriched not only in genes involved in the biosynthesis of the Phe precursor, as previously reported, but also genes associated with the specialized metabolic pathways involved in generating phenylpropanoid intermediates for FVBPs. ODO1-bound genes are also involved in methionine and S-adenosylmethionine metabolism, which could modulate methyl group supplies for certain FVBPs. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and RNA-seq analysis in an ODO1 RNAi knockdown line revealed that ODO1-bound targets are expressed at lower levels when ODO1 is suppressed. A cis-regulatory motif, CACCAACCCC, was identified as a potential binding site for ODO1 in the promoters of genes that are both bound and activated by ODO1, which was validated by in planta promoter reporter assays with wild-type and mutated promoters. Overall, our work presents a mechanistic model for ODO1 controlling an extensive gene regulatory network that contributes to FVBP production to give rise to floral scent.

Functions of Redox Signaling in Pollen Development and Stress Response

Cellular redox homeostasis is crucial for normal plant growth and development. Each developmental stage of plants has a specific redox mode and is maintained by various environmental cues, oxidants, and antioxidants. Reactive oxygen species (ROS) and reactive nitrogen species are the chief oxidants in plant cells and participate in cell signal transduction and redox balance. The production and removal of oxidants are in a dynamic balance, which is necessary for plant growth. Especially during reproductive development, pollen development depends on ROS-mediated tapetal programmed cell death to provide nutrients and other essential substances. The deviation of the redox state in any period will lead to microspore abortion and pollen sterility. Meanwhile, pollens are highly sensitive to environmental stress, in particular to cell oxidative burst due to its peculiar structure and function. In this regard, plants have evolved a series of complex mechanisms to deal with redox imbalance and oxidative stress damage. This review summarizes the functions of the main redox components in different stages of pollen development, and highlights various redox protection mechanisms of pollen in response to environmental stimuli. In continuation, we also discuss the potential applications of plant growth regulators and antioxidants for improving pollen vigor and fertility in sustaining better agriculture practices.

Characterization of the Brassica napus Flavonol Synthase Gene Family Reveals Bifunctional Flavonol Synthases

Flavonol synthase (FLS) is a key enzyme for the formation of flavonols, which are a subclass of the flavonoids. FLS catalyzes the conversion of dihydroflavonols to flavonols. The enzyme belongs to the 2-oxoglutarate-dependent dioxygenases (2-ODD) superfamily. We characterized the FLS gene family of Brassica napus that covers 13 genes, based on the genome sequence of the B. napus cultivar Express 617. The goal was to unravel which BnaFLS genes are relevant for seed flavonol accumulation in the amphidiploid species B. napus. Two BnaFLS1 homeologs were identified and shown to encode bifunctional enzymes. Both exhibit FLS activity as well as flavanone 3-hydroxylase (F3H) activity, which was demonstrated in vivo and in planta. BnaFLS1-1 and -2 are capable of converting flavanones into dihydroflavonols and further into flavonols. Analysis of spatio-temporal transcription patterns revealed similar expression profiles of BnaFLS1 genes. Both are mainly expressed in reproductive organs and co-expressed with the genes encoding early steps of flavonoid biosynthesis. Our results provide novel insights into flavonol biosynthesis in B. napus and contribute information for breeding targets with the aim to modify the flavonol content in rapeseed.

Transcriptome-Based WGCNA Analysis Reveals Regulated Metabolite Fluxes between Floral Color and Scent in Narcissus tazetta Flower

A link between the scent and color of Narcissus tazetta flowers can be anticipated due to their biochemical origin, as well as their similar biological role. Despite the obvious aesthetic and ecological significance of these colorful and fragrant components of the flowers and the molecular profiles of their pigments, fragrant formation has addressed in some cases. However, the regulatory mechanism of the correlation of fragrant components and color patterns is less clear. We simultaneously used one way to address how floral color and fragrant formation in different tissues are generated during the development of an individual plant by transcriptome-based weighted gene co-expression network analysis (WGCNA). A spatiotemporal pattern variation of flavonols/carotenoids/chlorophyll pigmentation and benzenoid/phenylpropanoid/ monoterpene fragrant components between the tepal and corona in the flower tissues of Narcissus tazetta, was exhibited. Several candidate transcription factors: MYB12, MYB1, AP2-ERF, bZIP, NAC, MYB, C2C2, C2H2 and GRAS are shown to be associated with metabolite flux, the phenylpropanoid pathway to the production of flavonols/anthocyanin, as well as related to one branch of the phenylpropanoid pathway to the benzenoid/phenylpropanoid component in the tepal and the metabolite flux between the monoterpene and carotenoids biosynthesis pathway in coronas. It indicates that potential competition exists between floral pigment and floral fragrance during Narcissus tazetta individual plant development and evolutionary development.

Involvement of the R2R3-MYB transcription factor MYB21 and its homologs in regulating flavonol accumulation in Arabidopsis stamen

Commonly found flavonols in plants are synthesized from dihydroflavonols by flavonol synthase (FLS). The genome of Arabidopsis thaliana contains six FLS genes, among which FLS1 encodes a functional enzyme. Previous work has demonstrated that the R2R3-MYB subgroup 7 transcription factors MYB11, MYB12, and MYB111 redundantly regulate flavonol biosynthesis. However, flavonol accumulation in pollen grains was unaffected in the myb11myb12myb111 triple mutant. Here we show that MYB21 and its homologs MYB24 and MYB57, which belong to subgroup 19, promote flavonol biosynthesis through regulation of FLS1 gene expression. We used a combination of genetic and metabolite analysis to identify the role of MYB21 in regulating flavonol biosynthesis through direct binding to the GARE cis-element in the FLS1 promoter. Treatment with kaempferol or overexpression of FLS1 rescued stamen defects in the myb21 mutant. We also observed that excess reactive oxygen species (ROS) accumulated in the myb21 stamen, and that treatment with the ROS inhibitor diphenyleneiodonium chloride partly rescued the reduced fertility of the myb21 mutant. Furthermore, drought increased ROS abundance and impaired fertility in myb21, myb21myb24myb57, and chs, but not in the wild type or myb11myb12myb111, suggesting that pollen-specific flavonol accumulation contributes to drought-induced male fertility by ROS scavenging in Arabidopsis.

Genome-Wide Identification, Classification and Expression Analysis of the MYB Transcription Factor Family in Petunia

A lot of researches have been focused on the evolution and function of MYB transcription factors (TFs). For revealing the formation of petunia flower color diversity, MYB gene family in petunia was identified and analyzed. In this study, a total of 155 MYB genes, including 40 1R-MYBs, 106 R2R3-MYBs, 7 R1R2R3-MYBs and 2 4R-MYBs, have been identified in the Petunia axillaris genome. Most R2R3 genes contain three exons and two introns, whereas the number of PaMYB introns varies from 0 to 12. The R2R3-MYB members could be divided into 28 subgroups. Analysis of gene structure and protein motifs revealed that members within the same subgroup presented similar exon/intron and motif organization, further supporting the results of phylogenetic analysis. Genes in subgroup 10, 11 and 21 were mainly expressed in petal, not in vegetative tissues. Genes in subgroup 9, 19, 25 and 27 expressed in all tissues, but the expression patterns of each gene were different. According to the promoter analysis, five R2R3-MYB and two MYB-related genes contained MBSI cis-element, which was involved in flavonoid biosynthetic regulation. PaMYB100/DPL has been reported to positively regulate to pigmentation. However, although PaMYB82, PaMYB68 and Pa1RMYB36 contained MBSI cis-element, their function in flavonoid biosynthesis has not been revealed. Consistent with existing knowledge, PaMYBs in subgroup 11 had similar function to AtMYBs in subgroup 6, genes in which played an important role in anthocyanin biosynthesis. In addition, PaMYB1 and PaMYB40 belonged to P9 (S7) and were potentially involved in regulation of flavonoid synthesis in petunia vegetative organs. This work provides a comprehensive understanding of the MYB gene family in petunia and lays a significant foundation for future studies on the function and evolution of MYB genes in petunia.

Formation pattern and regulatory mechanisms of pollen wall in Arabidopsis

In angiosperms, mature pollen is wrapped by a pollen wall, which is important for maintaining pollen structure and function. Pollen walls provide protection from various environmental stresses and preserve pollen germination and pollen tube growth. The pollen wall structure has been described since pollen ultrastructure investigations began in the 1960s. Pollen walls, which are the most intricate cell walls in plants, are composed of two layers: the exine layer and intine layer. Pollen wall formation is a complex process that occurs via a series of biological events that involve a large number of genes. In recent years, many reports have described the molecular mechanisms of pollen exine development. The formation process includes the development of the callose wall, the wavy morphology of primexine, the biosynthesis and transport of sporopollenin in the tapetum, and the deposition of the pollen coat. The formation mechanism of the intine layer is different from that of the exine layer. However, few studies have focused on the regulatory mechanisms of intine development. The primary component of the intine layer is pectin, which plays an essential role in the polar growth of pollen tubes. Demethylesterified pectin is mainly distributed in the shank region of the pollen tube, which can maintain the hardness of the pollen tube wall. Methylesterified pectin is mainly located in the top region, which is beneficial for improving the plasticity of the pollen tube top. In this review, we summarize the developmental process of the anther, pollen and pollen wall in Arabidopsis; furthermore, we describe the research progress on the pollen wall formation pattern and its molecular mechanisms in detail.

Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores

Plants experience different abiotic/biotic stresses, which trigger their molecular machinery to cope with them. Besides general mechanisms prompted by many stresses, specific mechanisms have been introduced to optimize the response to individual threats. However, these key mechanisms are difficult to identify. Here, we introduce an in-depth species-specific transcriptomic analysis and conduct an extensive meta-analysis of the responses to related species to gain more knowledge about plant responses. The spider mite Tetranychus urticae was used as the individual species, several arthropod herbivores as the related species for meta-analysis, and Arabidopsis thaliana plants as the common host. The analysis of the transcriptomic data showed typical common responses to herbivory, such as jasmonate signaling or glucosinolate biosynthesis. Also, a specific set of genes likely involved in the particularities of the Arabidopsis-spider mite interaction was discovered. The new findings have determined a prominent role in this interaction of the jasmonate-induced pathways leading to the biosynthesis of anthocyanins and tocopherols. Therefore, tandem individual/general transcriptomic profiling has been revealed as an effective method to identify novel relevant processes and specificities in the plant response to environmental stresses.

Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions

Phenylpropanoid metabolism is one of the most important metabolisms in plants, yielding more than 8,000 metabolites contributing to plant development and plant-environment interplay. Phenylpropanoid metabolism materialized during the evolution of early freshwater algae that were initiating terrestrialization and land plants have evolved multiple branches of this pathway, which give rise to metabolites including lignin, flavonoids, lignans, phenylpropanoid esters, hydroxycinnamic acid amides, and sporopollenin. Recent studies have revealed that many factors participate in the regulation of phenylpropanoid metabolism, and modulate phenylpropanoid homeostasis when plants undergo successive developmental processes and are subjected to stressful environments. In this review, we summarize recent progress on elucidating the contribution of phenylpropanoid metabolism to the coordination of plant development and plant-environment interaction, and metabolic flux redirection among diverse metabolic routes. In addition, our review focuses on the regulation of phenylpropanoid metabolism at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and in response to phytohormones and biotic and abiotic stresses.

The Arabidopsis Protein Disulfide Isomerase Subfamily M Isoform, PDI9, Localizes to the Endoplasmic Reticulum and Influences Pollen Viability and Proper Formation of the Pollen Exine During Heat Stress

Plants adapt to heat via thermotolerance pathways in which the activation of protein folding chaperones is essential. In eukaryotes, protein disulfide isomerases (PDIs) facilitate the folding of nascent and misfolded proteins in the secretory pathway by catalyzing the formation and isomerization of disulfide bonds and serving as molecular chaperones. In Arabidopsis, several members of the PDI family are upregulated in response to chemical inducers of the unfolded protein response (UPR), including both members of the non-classical PDI-M subfamily, PDI9 and PDI10. Unlike classical PDIs, which have two catalytic thioredoxin (TRX) domains separated by two non-catalytic TRX-fold domains, PDI-M isoforms are orthologs of mammalian P5/PDIA6 and possess two tandem catalytic domains. Here, PDI9 accumulation was found to be upregulated in pollen in response to heat stress. Histochemical staining of plants harboring the PDI9 and PDI10 promoters fused to the gusA gene indicated they were actively expressed in the anthers of flowers, specifically in the pollen and tapetum. Immunoelectron microscopy revealed that PDI9 localized to the endoplasmic reticulum in root and pollen cells. transfer DNA (T-DNA) insertional mutations in the PDI9 gene disrupted pollen viability and development in plants exposed to heat stress. In particular, the pollen grains of pdi9 mutants exhibited disruptions in the reticulated pattern of the exine and an increased adhesion of pollen grains. Pollen in the pdi10 single mutant did not display similar heat-associated defects, but pdi9 pdi10 double mutants (DMs) completely lost exine reticulation. Interestingly, overexpression of PDI9 partially led to heat-associated defects in the exine. We conclude that PDI9 plays an important role in pollen thermotolerance and exine biogenesis. Its role fits the mechanistic theory of proteostasis in which an ideal balance of PDI isoforms is required in the endoplasmic reticulum (ER) for normal exine formation in plants subjected to heat stress.

The spatio-temporal biosynthesis of floral flavonols is controlled by differential phylogenetic MYB regulators in Freesia hybrida

Floral flavonols play specific pivotal roles in pollinator attraction, pollen germination and fertility, in addition to other functions in vegetative organs. For many plants, the process of flavonol biosynthesis in late flower development stages and in mature flower tissues is poorly understood, in contrast to early flower development stages. It is thought that this process may be regulated independently of subgroup 7 R2R3 MYB (SG7 MYB) transcription factors. In this study, two FLS genes were shown to be expressed synchronously with the flower development-specific and tissue-specific biosynthesis of flavonols in Freesia hybrida. FhFLS1 contributed to flavonol biosynthesis in early flower buds, toruses and calyxes, and was regulated by four well-known SG7 MYB proteins, designated as FhMYBFs, with at least partial regulatory redundancy. FhFLS2 accounted for flavonols in late developed flowers and in the petals, stamens and pistils, and was targeted directly by non SG7 MYB protein FhMYB21L2. In parallel, AtMYB21 and AtMYB24 also activated AtFLS1, a gene highly expressed in Arabidopsis anthers and pollen, indicating the conserved regulatory roles of MYB21 against FLS genes in these two evolutionarily divergent angiosperm plants. Our results reveal a novel regulatory and synthetic mechanism underlying flavonol biosynthesis in floral organs and tissues which may be exploited to investigate supplementary roles of flavonols in flowers.

Dual-Localized WHIRLY1 Affects Salicylic Acid Biosynthesis via Coordination of ISOCHORISMATE SYNTHASE1, PHENYLALANINE AMMONIA LYASE1, and S-ADENOSYL-L-METHIONINE-DEPENDENT METHYLTRANSFERASE1

Salicylic acid (SA) influences developmental senescence and is spatiotemporally controlled by various mechanisms, including biosynthesis, transport, and conjugate formation. Altered localization of Arabidopsis WHIRLY1 (WHY1), a repressor of leaf natural senescence, in the nucleus or chloroplast causes a perturbation in SA homeostasis, resulting in adverse plant senescence phenotypes. WHY1 loss-of-function mutation resulted in SA peaking 5 d earlier compared to wild-type plants, which accumulated SA at 42 d after germination. SA accumulation coincided with an early leaf-senescence phenotype, which could be prevented by ectopic expression of the nuclear WHY1 isoform (nWHY1). However, expressing the plastid WHY1 isoform (pWHY1) greatly enhanced cellular SA levels. Transcriptome analysis in the WHY1 loss-of-function mutant background following expression of either pWHY1 or nWHY1 indicated that hormone metabolism-related genes were most significantly altered. The pWHY1 isoform predominantly affected stress-related gene expression, whereas nWHY1 primarily controlled developmental gene expression. Chromatin immunoprecipitation-quantitative PCR assays indicated that nWHY1 directly binds to the promoter region of isochorismate synthase1 (ICS1), thus activating its expression at later developmental stages, but that it indirectly activates S-adenosyl- l -Met-dependent methyltransferase1 (BSMT1) expression via ethylene response factor 109 (ERF109). Moreover, nWHY1 repressed expression of Phe ammonia lyase-encoding gene (PAL1) via R2R3-MYB member 15 (MYB15) during the early stages of development. Interestingly, rising SA levels exerted a feedback effect by inducing nWHY1 modification and pWHY1 accumulation. Thus, the alteration of WHY1 organelle isoforms and the feedback of SA are involved in a circularly integrated regulatory network during developmental or stress-induced senescence in Arabidopsis.

Identification of transcription factors controlling floral morphology in wild Petunia species with contrasting pollination syndromes

Adaptation to different pollinators is an important driver of speciation in the angiosperms. Genetic approaches such as QTL mapping have been successfully used to identify the underlying speciation genes. However, these methods are often limited by widespread suppression of recombination due to divergence between species. While the mutations that caused the interspecific differences in floral color and scent have been elucidated in a variety of plant genera, the genes that are responsible for morphological differences remain mostly unknown. Differences in floral organ length determine the pollination efficiency of hawkmoths and hummingbirds, and therefore the genes that control these differences are potential speciation genes. Identifying such genes is challenging, especially in non-model species and when studying complex traits for which little prior genetic and biochemical knowledge is available. Here we combine transcriptomics with detailed growth analysis to identify candidate transcription factors underlying interspecific variation in the styles of Petunia flowers. Starting from a set of 2284 genes, stepwise filtering for expression in styles, differential expression between species, correlation with growth-related traits, allele-specific expression in interspecific hybrids, and/or high-impact polymorphisms resulted in a set of 43 candidate speciation genes. Validation by virus-induced gene silencing identified two MYB transcription factors, EOBI and EOBII, that were previously shown to regulate floral scent emission, a trait associated with pollination by hawkmoths.

MYB43 in Oilseed Rape (Brassica napus) Positively Regulates Vascular Lignification, Plant Morphology and Yield Potential but Negatively Affects Resistance to Sclerotinia sclerotiorum

Arabidopsis thaliana MYB43 (AtMYB43) is suggested to be involved in cell wall lignification. PtrMYB152, the Populus orthologue of AtMYB43, is a transcriptional activator of lignin biosynthesis and vessel wall deposition. In this research, MYB43 genes from Brassica napus (rapeseed) and its parental species B. rapa and B. oleracea were molecularly characterized, which were dominantly expressed in stem and other vascular organs and showed responsiveness to Sclerotinia sclerotiorum infection. The BnMYB43 family was silenced by RNAi, and the transgenic rapeseed lines showed retardation in growth and development with smaller organs, reduced lodging resistance, fewer silique number and lower yield potential. The thickness of the xylem layer decreased by 28%; the numbers of sclerenchymatous cells, vessels, interfascicular fibers, sieve tubes and pith cells in the whole cross section of the stem decreased by 28%, 59%, 48%, 34% and 21% in these lines, respectively. The contents of cellulose and lignin decreased by 17.49% and 16.21% respectively, while the pectin content increased by 71.92% in stems of RNAi lines. When inoculated with S. sclerotiorum, the lesion length was drastically decreased by 52.10% in the stems of transgenic plants compared with WT, implying great increase in disease resistance. Correspondingly, changes in the gene expression patterns of lignin biosynthesis, cellulose biosynthesis, pectin biosynthesis, cell cycle, SA- and JA-signals, and defensive pathways were in accordance with above phenotypic modifications. These results show that BnMYB43, being a growth-defense trade-off participant, positively regulates vascular lignification, plant morphology and yield potential, but negatively affects resistance to S. sclerotiorum. Moreover, this lignification activator influences cell biogenesis of both lignified and non-lignified tissues of the whole vascular organ.

The Tapetal Major Facilitator NPF2.8 Is Required for Accumulation of Flavonol Glycosides on the Pollen Surface in Arabidopsis thaliana

The exine of angiosperm pollen grains is usually covered by a complex mix of metabolites including pollen-specific hydroxycinnamic acid amides (HCAAs) and flavonoid glycosides. Although the biosynthetic pathways resulting in the formation of HCAAs and flavonol glycosides have been characterized, it is unclear how these compounds are transported to the pollen surface. In this report we provide several lines of evidence that a member of the nitrate/peptide transporter family is required for the accumulation and transport of pollen-specific flavonol 3-o-sophorosides, characterized by a glycosidic β-1,2-linkage, to the pollen surface of Arabidopsis (Arabidopsis thaliana). Ectopic, transient expression in Nicotiana benthamiana epidermal leaf cells demonstrated localization of this flavonol sophoroside transporter (FST1) at the plasmalemma when fused to green fluorescent protein (GFP). We also confirmed the tapetum-specific expression of FST1 by GFP reporter lines driven by the FST1 promoter. In vitro characterization of FST1 activity was achieved by microbial uptake assays based on ¹⁴C-labeled flavonol glycosides. Finally, rescue of an fst1 insertion mutant by complementation with an FST1 genomic fragment restored the accumulation of flavonol glycosides in pollen grains to wild-type levels, corroborating the requirement of FST1 for transport of flavonol-3-o-sophorosides from the tapetum to the pollen surface.

Fertilization in flowering plants: an odyssey of sperm cell delivery

In light of the available discoveries in the field, this review manuscript discusses on plant reproduction mechanism and molecular players involved in the process. Sperm cells in angiosperms are immotile and are physically distant to the female gametophytes (FG). To secure the production of the next generation, plants have devised a clever approach by which the two sperm cells in each pollen are safely delivered to the female gametophyte where two fertilization events occur (by each sperm cell fertilizing an egg cell and central cell) to give rise to embryo and endosperm. Each of the successfully fertilized ovules later develops into a seed. Sets of macromolecules play roles in pollen tube (PT) guidance, from the stigma, through the transmitting tract and funiculus to the micropylar end of the ovule. Other sets of genetic players are involved in PT reception and in its rupture after it enters the ovule, and yet other sets of genes function in gametic fusion. Angiosperms have come long way from primitive reproductive structure development to today's sophisticated, diverse, and in most cases flamboyant organ. In this review, we will be discussing on the intricate yet complex molecular mechanism of double fertilization and how it might have been shaped by the evolutionary forces focusing particularly on the model plant Arabidopsis.

Combined Analysis of the Metabolome and Transcriptome Identified Candidate Genes Involved in Phenolic Acid Biosynthesis in the Leaves of Cyclocarya paliurus

To assess changes of metabolite content and regulation mechanism of the phenolic acid biosynthesis pathway at different developmental stages of leaves, this study performed a combined metabolome and transcriptome analysis of Cyclocarya paliurus leaves at different developmental stages. Metabolite and transcript profiling were conducted by ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometer and high-throughput RNA sequencing, respectively. Transcriptome identification showed that 58 genes were involved in the biosynthesis of phenolic acid. Among them, 10 differentially expressed genes were detected between every two developmental stages. Identification and quantification of metabolites indicated that 14 metabolites were located in the phenolic acid biosynthetic pathway. Among them, eight differentially accumulated metabolites were detected between every two developmental stages. Association analysis between metabolome and transcriptome showed that six differentially expressed structural genes were significantly positively correlated with metabolite accumulation and showed similar expression trends. A total of 128 transcription factors were identified that may be involved in the regulation of phenolic acid biosynthesis; these include 12 MYBs and 10 basic helix–loop–helix (bHLH) transcription factors. A regulatory network of the phenolic acid biosynthesis was established to visualize differentially expressed candidate genes that are involved in the accumulation of metabolites with significant differences. The results of this study contribute to the further understanding of phenolic acid biosynthesis during the development of leaves of C. paliurus.

NtMYB3, an R2R3-MYB from Narcissus, Regulates Flavonoid Biosynthesis

R2R3-MYB transcription factors play important roles in the regulation of plant flavonoid metabolites. In the current study, NtMYB3, a novel R2R3-MYB transcriptional factor isolated from Chinese narcissus (Narcissus tazetta L. var. chinensis), was functionally characterized. Phylogenetic analysis indicated that NtMYB3 belongs to the AtMYB4-like clade, which includes repressor MYBs involved in the regulation of flavonoid biosynthesis. Transient assays showed that NtMYB3 significantly reduced red pigmentation induced by the potato anthocyanin activator StMYB-AN1 in agro-infiltrated leaves of tobacco. Over-expression of NtMYB3 decreased the red color of transgenic tobacco flowers, with qRT-PCR analysis showing that NtMYB3 repressed the expression levels of genes involved in anthocyanin and flavonol biosynthesis. However, the proanthocyanin content in flowers of transgenic tobacco increased as compared to wild type. NtMYB3 showed expression in all examined narcissus tissues; the expression level in basal plates of the bulb was highest. A 968 bp promoter fragment of narcissus FLS (NtFLS) was cloned, and transient expression and dual luciferase assays showed NtMYB3 repressed the promoter activity. These results reveal that NtMYB3 is involved in the regulation of flavonoid biosynthesis in narcissus by repressing the biosynthesis of flavonols, and this leads to proanthocyanin accumulation in the basal plate of narcissus.

Jasmonate-Inducible R2R3-MYB Transcription Factor Regulates Capsaicinoid Biosynthesis and Stamen Development in Capsicum

Jasmonates (JAs) play an important role in plant developmental processes and regulate the biosynthesis of various specialized metabolites, and transcription factors are crucial in mediating JA signaling to regulate these processes. Capsaicinoids (Caps) are intriguing specialized metabolites produced uniquely by Capsicum species that give their fruits a pungent flavor to defend against herbivory and pathogens. In this study, we identify a R2R3-MYB transcription factor CaMYB108 and demonstrate its roles in regulating the biosynthesis of Caps and stamen development. Transcriptional analysis indicated that CaMYB108 was preferentially expressed in the flower and fruit, while the subcellular localization of CaMYB108 was shown to be the nucleus. Virus-induced gene silencing of CaMYB108 led to the expression of capsaicinoid biosynthetic genes (CBGs), and the contents of Caps dramatically reduce. Moreover, the CaMYB108-silenced plants showed delayed anther dehiscence and reduced pollen viability. Transient overexpression of CaMYB108 caused the expression of CBGs to be upregulated, and the Caps content significantly increased. The results of dual-luciferase reporter assays showed that CaMYB108 targeted CBG promoters. In addition, the expression of CaMYB108 and CBGs was inducible by methyl jasmonate and was consistent with the increased content of Caps. Overall, our results indicate that CaMYB108 is involved in the regulation of Caps biosynthesis and stamen development.

Overexpression of a stamen-specific R2R3-MYB gene BcMF28 causes aberrant stamen development in transgenic Arabidopsis

In flowering plants, stamen development is a complex multistage process, which is highly regulated by a series of transcription factors. In this study, BcMF28, which encodes a R2R3-MYB transcription factor, was isolated from Brassica campestris. BcMF28 is localized in the nucleus and cytoplasm, and acts as a transcriptional activator. Quantitative real-time PCR and promoter activity analysis revealed that BcMF28 was predominately expressed in inflorescences. The expression of BcMF28 was specifically detected in tapetum, developing microspores, anther endothecium, and filaments during late stamen development. The overexpression of BcMF28 in Arabidopsis resulted in aberrant stamen development, including filament shortening, anther indehiscence, and pollen abortion. Detailed analysis of anther development in transgenic plants revealed that the degeneration of septum and stomium did not occur, and endothecium lignification was affected. Furthermore, the expression levels of genes involved in the phenylpropanoid metabolism pathway were altered in BcMF28-overexpressing transgenic plants. Our results suggest that BcMF28 plays an important regulatory role during late stamen development.

The MYB transcription factor Emission of Methyl Anthranilate 1 stimulates emission of methyl anthranilate from Medicago truncatula hairy roots

Plants respond to herbivore or pathogen attacks by activating specific defense programs that include the production of bioactive specialized metabolites to eliminate or deter the attackers. Volatiles play an important role in the interaction of a plant with its environment. Through transcript profiling of jasmonate-elicited Medicago truncatula cells, we identified Emission of Methyl Anthranilate (EMA) 1, a MYB transcription factor that is involved in the emission of the volatile compound methyl anthranilate when expressed in M. truncatula hairy roots, giving them a fruity scent. RNA sequencing (RNA-Seq) analysis of the fragrant roots revealed the upregulation of a methyltransferase that was subsequently characterized to catalyze the O-methylation of anthranilic acid and was hence named M. truncatula anthranilic acid methyl transferase (MtAAMT) 1. Given that direct activation of the MtAAMT1 promoter by EMA1 could not be unambiguously demonstrated, we further probed the RNA-Seq data and identified the repressor protein M. truncatula plant AT-rich sequence and zinc-binding (MtPLATZ) 1. Emission of Methyl Anthranilate 1 binds a tandem repeat of the ACCTAAC motif in the MtPLATZ1 promoter to transactivate gene expression. Overexpression of MtPLATZ1 in transgenic M. truncatula hairy roots led to transcriptional silencing of EMA1, indicating that MtPLATZ1 may be part of a negative feedback loop to control the expression of EMA1. Finally, application of exogenous methyl anthranilate boosted EMA1 and MtAAMT1 expression dramatically, thus also revealing a positive amplification loop. Such positive and negative feedback loops seem to be the norm rather than the exception in the regulation of plant specialized metabolism.