Proteomics study of COI1-regulated proteins in Arabidopsis flower

The adaptor protein ECAP, the corepressor LEUNIG, and the transcription factor BEH3 interact and regulate microsporocyte generation in Arabidopsis

Histospecification and morphogenesis of anthers during development in Arabidopsis (Arabidopsis thaliana) are well understood. However, the regulatory mechanism of microsporocyte generation at the pre-meiotic stage remains unclear, especially how archesporial cells are specified and differentiate into 2 cell lineages with distinct developmental fates. SPOROCYTELESS (SPL) is a key reproductive gene that is activated during early anther development and remains active. In this study, we demonstrated that the EAR motif-containing adaptor protein (ECAP) interacts with the Gro/Tup1 family corepressor LEUNIG (LUG) and the BES1/BZR1 HOMOLOG3 (BEH3) transcription factor to form a transcription activator complex, epigenetically regulating SPL transcription. SPL participates in microsporocyte generation by modulating the specification of archesporial cells and the archesporial cell-derived differentiation of somatic and reproductive cell layers. This study illustrates the regulation of SPL expression by the ECAP-LUG-BEH3 complex, which is essential for the generation of microsporocytes. Moreover, our findings identified ECAP as a key transcription regulator that can combine with different partners to regulate gene expression in distinct ways, thereby facilitating diverse processes in various aspects of plant development.

Transcriptomics analyses reveal the key genes involved in stamen petaloid formation in Alcea rosea L

Alcea rosea L. is a traditional flower with a long cultivation history. It is extensively cultivated in China and is widely planted in green belt parks or used as cut flowers and potted ornamental because of its rich colors and flower shapes. Double-petal A. rosea flowers have a higher aesthetic value compared to single-petal flowers, a phenomenon determined by stamen petaloid. However, the underlying molecular mechanism of this phenomenon is still very unclear. In this study, an RNA-based comparative transcriptomic analysis was performed between the normal petal and stamen petaloid petal of A. rosea. A total of 3,212 differential expressed genes (DEGs), including 2,620 up-regulated DEGs and 592 down-regulated DEGs, were identified from 206,188 unigenes. Numerous DEGs associated with stamen petaloid were identified through GO and KEGG enrichment analysis. Notably, there were 63 DEGs involved in the plant hormone synthesis and signal transduction, including auxin, cytokinin, gibberellin, abscisic acid, ethylene, brassinosteroid, jasmonic acid, and salicylic acid signaling pathway and 56 key transcription factors (TFs), such as MADS-box, bHLH, GRAS, and HSF. The identification of these DEGs provides an important clue for studying the regulation pathway and mechanism of stamen petaloid formation in A. rosea and provides valuable information for molecular plant breeding.

Cotton proteomics: Dissecting the stress response mechanisms in cotton

The natural environment of plants comprises a complex set of biotic and abiotic stresses, and plant responses to these stresses are complex as well. Plant proteomics approaches have significantly revealed dynamic changes in plant proteome responses to stress and developmental processes. Thus, we reviewed the recent advances in cotton proteomics research under changing environmental conditions, considering the progress and challenging factors. Finally, we highlight how single-cell proteomics is revolutionizing plant research at the proteomics level. We envision that future cotton proteomics research at the single-cell level will provide a more complete understanding of cotton's response to stresses.

Exogenous melatonin improves the resistance to cucumber bacterial angular leaf spot caused by Pseudomonas syringae pv. Lachrymans

Pseudomonas syringae pv. Lachrymans (Psl) is a bacterial pathogen that causes cucumber bacterial angular leaf spot (BALS). It is known that melatonin (MT), as a pleiotropic signal molecule, can improve plant stress tolerance, but less information is available about the function of MT on plant resistance to bacteria disease. Here, we investigated the effect of MT on cucumber BALS. Our results show that MT inhibited the bacteria Psl growth significantly in vitro and attenuated cucumber BALS remarkably in vivo. The concentration of bacteria in leaves treated with 0.1 mM MT was approximately 10,000 times reduced at 5 days-post-inoculation (dpi), compared to the control without MT. Transcriptomic analysis showed that 225 differentially expressed genes (DEGs) were induced in leaves after just MT treatment for 3 h. The functions of these DEGs were mainly associated with hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling pathway, and photosynthesis, suggesting that MT could regulate plant growth and induce plant immunity. Moreover, 665 DEGs were induced when leaves were treated with exogenous MT in combination with the bacteria inoculation for 12 h. The functions of these DEGs were much related to plant-pathogen interaction, hormone signal transduction, and amino acids biosynthesis pathways. Many MT-induced DEGs were involved in some distinct signal transduction pathways, such as calmodulin (CaM), polyamines (PAs), nitric oxide (NO), and salicylic acid (SA). The physiological analysis shows that exogenous MT spray reduced the stomatal aperture and enhanced the activities of antioxidant and defense enzymes, which were in consistent with the results of the transcriptome analysis. In addition, MT may function in regulating the metabolic balance between plant growth and defense. In conclusion, our results demonstrate that MT could alleviate the cucumber BALS via inhibiting propagation and invasion of Psl, activating plant signaling, enhancing antioxidative and defense systems, inducing stress-related genes expression, and regulating the plant growth-defense balance.

A cotton (Gossypium hirsutum) WRKY transcription factor (GhWRKY22) participates in regulating anther/pollen development

Anther/pollen development is a highly programmed process in flowering plants. However, the molecular mechanism of regulating anther/pollen development is still largely unclear so far. Here, we report a cotton WRKY transcription factor (GhWRKY22) that functions in anther/pollen development. Quantitative RT-PCR and GUS activity analyses revealed that GhWRKY22 is predominantly expressed in the late developing anther/pollen of cotton. The transgenic Arabidopsis plants expressing GhWRKY22 displayed the male fertility defect with the fewer viable pollen grains. Expression of the genes involved in jasmonate (JA) biosynthesis was up-regulated, whereas expression of the JA-repressors (JAZ1 and JAZ8) was down-regulated in the transgenic Arabidopsis plants expressing GhWRKY22, compared with those in wild type. Yeast one-hybrid and ChIP-qPCR assays demonstrated that GhWRKY22 modulated the expression of JAZ genes by directly binding to their promoters for regulating anther/pollen development. Yeast two-hybrid assay indicated that GhMYB24 could interact with GhJAZ8-A and GhJAZ13-A. Furthermore, expression of AtMYB24, AtPAL2 and AtANS2 was enhanced in the transgenic Arabidopsis plants, owing to GhWRKY22 overexpression. Taking the data together, our results suggest that GhWRKY22 acts as a transcriptional repressor to regulate anther/pollen development possibly by modulating the expression of the JAZ genes.

Genome-Wide Identification and Characterization of JAZ Protein Family in Two Petunia Progenitors

Jasmonate ZIM-domain (JAZ) family proteins are the key repressors in the jasmonate signaling pathway and play crucial roles in plant development, defenses, and responses to stresses. However, our knowledge about the JAZ protein family in petunia is limited. This research respectively identified 12 and 16 JAZ proteins in two Petunia progenitors, Petunia axillaris and Petunia inflata. Phylogenetic analysis showed that the 28 proteins could be divided into four groups (Groups A–D) and further classified into six subgroups (A1, A2, B1, B3, C, and D1); members in the same subgroup shared some similarities in motif composition and sequence structure. The Ka/Ks ratios of seven paralogous pairs were less than one, suggesting the petunia JAZ family might have principally undergone purifying selection. Quantitative real-time PCR (qRT-PCR) analysis revealed that PaJAZ genes presented differential expression patterns during the development of flower bud and anther in petunia, and the expression of PaJAZ5, 9, 12 genes was generally up-regulated after MeJA treatment. Subcellular localization assays demonstrated that proteins PaJAZ5, 9, 12 were localized in nucleus. Yeast two hybrid (Y2H) elucidated most PaJAZ proteins (PaJAZ1-7, 9, 12) might interact with transcription factor MYC2. This study provides insights for further investigation of functional analysis in petunia JAZ family proteins.

The R2R3-MYB transcription factor MdMYB24-like is involved in methyl jasmonate-induced anthocyanin biosynthesis in apple

Anthocyanins in apple species are important secondary metabolites that are beneficial for human health. Previous studies revealed that methyl jasmonate (MeJA) promotes anthocyanin accumulation by up-regulating the transcription of related genes. In this study, we isolated a jasmonate (JA)-induced apple MYB gene, MdMYB24-like (MdMYB24L). The encoded nuclear protein contains a conserved R2R3 domain and is homologous to Arabidopsis thaliana AtMYB24. Additionally, MdMYB24L was observed to interact with JA signaling factors (MdJAZ8, MdJAZ11, and MdMYC2) in yeast and in planta. The MdMYC2 protein was also targeted by MdJAZ8 and MdJAZ11, which are rapidly degraded under MeJA treatment. The overexpression of MdMYB24L resulted in higher anthocyanin contents in the transgenic apple 'Orin' calli than in the wild-type control calli. Moreover, the expression levels of the anthocyanin biosynthesis structural genes MdUFGT and MdDFR were up-regulated in the transgenic calli. Furthermore, MdMYB24L positively regulated the transcription of MdDFR and MdUFGT by binding to the MYB-binding site motifs in their promoters. Interestingly, the interaction between MdMYC2 and MdMYB24L further enhanced the transcription of MdUFGT, whereas MdJAZ8 and MdJAZ11 attenuated this effect. We herein provide new details regarding the molecular mechanism by which MYB transcription factors help regulate anthocyanin biosynthesis via JA signaling pathways.

Heterologous Expression of the Grapevine JAZ7 Gene in Arabidopsis Confers Enhanced Resistance to Powdery Mildew but Not to Botrytis cinerea

Jasmonate ZIM-domain (JAZ) family proteins comprise a class of transcriptional repressors that silence jasmonate-inducible genes. Although a considerable amount of research has been carried out on this gene family, there is still very little information available on the role of specific JAZ gene members in multiple pathogen resistance, especially in non-model species. In this study, we investigated the potential resistance function of the VqJAZ7 gene from a disease-resistant wild grapevine, Vitis quinquangularis cv. “Shang-24”, through heterologous expression in Arabidopsis thaliana. VqJAZ7-expressing transgenic Arabidopsis were challenged with three pathogens: the biotrophic fungus Golovinomyces cichoracearum, necrotrophic fungus Botrytis cinerea, and semi-biotrophic bacteria Pseudomonas syringae pv. tomato DC3000. We found that plants expressing VqJAZ7 showed greatly reduced disease symptoms for G. cichoracearum, but not for B. cinerea or P. syringae. In response to G cichoracearum infection, VqJAZ7-expressing transgenic lines exhibited markedly higher levels of cell death, superoxide anions (O₂¯, and H₂O₂ accumulation, relative to nontransgenic control plants. Moreover, we also tested the relative expression of defense-related genes to comprehend the possible induced pathways. Taken together, our results suggest that VqJAZ7 in grapevine participates in molecular pathways of resistance to G. cichoracearum, but not to B. cinerea or P. syringae.

THF1 mutations lead to increased basal and wound-induced levels of oxylipins that stimulate anthocyanin biosynthesis via COI1 signaling in Arabidopsis

Mutants defective in chloroplast development or photosynthesis are liable to accumulate higher levels of anthocyanin in photo-oxidative stress. However, regulatory mechanisms of anthocyanin biosynthesis in the mutants remain unclear. Here, we investigated the mechanism by which the deletion of thylakoid formation1 (THF1) leads to an increased level of anthocyanin in Arabidopsis thaliana L. Physiological and genetic evidence showed that the increased level of anthocyanin in thf1 is dependent on coronatine-insensitive1 (COI1) signaling. Our data showed that thf1 had higher levels of basal α-linolenic acid (α-LeA), and methyl jasmonate (JA)-induced α-LeA and 12-oxophytodienoic acid (OPDA) than the wild type (WT). Consistently, expression levels of phospholipase genes including pPLAIIα and PLA-Iγ1 were elevated in thf1. Furthermore, inhibition of lipase activity by bromoenol lactone, a specific inhibitor of plant pPLA, led to producing identical levels of anthocyanins in WT and thf1 plants. Interestingly, OPDA biosynthesis was triggered by light illumination in isolated chloroplasts, indicating that new protein import into chloroplasts is not required for OPDA biosynthesis. Thus, we conclude that the elevated anthocyanin accumulation in thf1 is attributed to an increase in JA levels. This JA-mediated signaling to coordinate plant metabolism and growth in stress may be conserved in other photosensitive mutants.

Regulation of stamen development by coordinated actions of jasmonate, auxin, and gibberellin in Arabidopsis

Proper stamen development is essential for plants to achieve their life cycles. Defects in stamen development will cause male sterility. A vast array of research efforts have been made to understand stamen developmental processes and regulatory mechanisms over the past decades. It is so far reported that phytohormones, including jasmonate, auxin, gibberellin, brassinosteroid, and cytokinin, play essential roles in regulation of stamen development. This review will briefly summarize the molecular basis for coordinated regulation of stamen development by jasmonate, auxin, and gibberellin in Arabidopsis.

Transcriptome analysis of Gerbera hybrida ray florets: putative genes associated with gibberellin metabolism and signal transduction

In this study, the transcriptome of the Gerbera hybrida ray floret was constructed using a high-throughput Illumina sequencing platform. All 47,104 UniGenes with an average length of 845 nt and an N50 equaling 1321 nt were generated from 72,688,546 total primary reads after filtering and assembly. A total of 36,693 transcripts were annotated by comparison with non-redundant National Center for Biotechnology Information (NCBI) protein (Nr), non-redundant NCBI nucleotide (Nt), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases after removing exogenous contaminated sequences. The majority of the genes that are associated with gibberellin metabolism and signal transduction were identified. The targets for signal transduction of other plant hormones were also enumerated. Our study provides a systematic overview of the hormone signal transduction genes that are involved in ray floral development in Asteraceae and should facilitate further understanding of the crucial roles of phytohormones in plant growth.

60 years of development of the journal of integrative plant biology

In celebration of JIPB's 60(th) anniversary, this paper summarizes and reviews the development process of the journal. To start, we offer our heartfelt thanks to JIPB's pioneer Editors-in-Chief who helped get the journal off the ground and make it successful. Academic achievement is the soul of academic journals, and this paper summarizes JIPB's course of academic development by analyzing it in four stages: the first two stages are mostly qualitative analyses, and the latter two stages are dedicated to quantitative analyses. Most-cited papers were statistically analyzed. Improvements in editing, publication, distribution and online accessibility--which are detailed in this paper--contribute to JIPB's sustainable development. In addition, JIPB's evaluation index and awards are provided with accompanying pictures. At the end of the paper, JIPB's milestones are listed chronologically. We believe that JIPB's development, from a national journal to an international one, parallels the development of the Chinese plant sciences.

Proteomic identification of differentially expressed proteins in Gossypium thurberi inoculated with cotton Verticillium dahliae

Thurber's cotton (Gossypium thurberi) is the wild relative of cultivated cotton. It is highly resistant to cotton Verticillium wilt, a disease that significantly affects cotton yield and quality. To reveal the mechanism of disease resistance in G. thurberi and to clone resistance-related genes, we used two-dimensional electrophoresis (2-DE) and tandem time-of-flight mass spectrometry (MALDI-TOF-MS) to identify differentially expressed proteins in Thurber's cotton after inoculation with Verticillium dahliae. A total of 57 different protein spots were upregulated, including 52 known proteins representing 11% of the total protein spots. These proteins are involved in resistance to stress and disease, transcriptional regulation, signal transduction, protein processing and degradation, photosynthesis, production capacity, basic metabolism, and other processes. In addition, five disease resistance proteins showed intense upregulation, indicating that resistance genes (R genes) may play a critical role in resistance to Verticillium wilt in Thurber's cotton. Our results suggest that disease and stress resistance are the combined effects of multiple co-expressed genes. This provides a basis for further, detailed investigation into the mechanisms underlying Verticillium wilt resistance of G. thurberi and for cloning essential genes into cotton cultivars to produce Verticillium wilt resistant plants.

Global analysis of non-coding small RNAs in Arabidopsis in response to jasmonate treatment by deep sequencing technology

In plants, non-coding small RNAs play a vital role in plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate (JA) pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. Thirty new miRNAs and 27 new miRNA candidates were identified through bioinformatics approach. Forty-nine known miRNAs (belonging to 24 families), 15 new miRNAs and new miRNA candidates (belonging to 11 families) and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs (belonging to 9 families) were repressed by JA.

The Arabidopsis extracellular UNUSUAL SERINE PROTEASE INHIBITOR functions in resistance to necrotrophic fungi and insect herbivory

Protease inhibitors (PIs) function in the precise regulation of proteases, and are thus involved in diverse biological processes in many organisms. Here, we studied the functions of the Arabidopsis UNUSUAL SERINE PROTEASE INHIBITOR (UPI) gene, which encodes an 8.8 kDa protein of atypical sequence relative to other PIs. Plants harboring a loss-of-function UPI allele displayed enhanced susceptibility to the necrotrophic fungi Botrytis cinerea and Alternaria brassicicola as well as the generalist herbivore Trichoplusia ni. Further, ectopic expression conferred increased resistance to B. cinerea and T. ni. In contrast, the mutant has wild-type responses to virulent, avirulent and non-pathogenic strains of Pseudomonas syringae, thus limiting the defense function of UPI to necrotrophic fungal infection and insect herbivory. Expression of UPI is significantly induced by jasmonate, salicylic acid and abscisic acid, but is repressed by ethylene, indicating complex phytohormone regulation of UPI expression. The upi mutant also shows significantly delayed flowering, associated with decreased SOC1 expression and elevated levels of MAF1, two regulators of floral transition. Recombinant UPI strongly inhibits the serine protease chymotrypsin but also weakly blocks the cysteine protease papain. Interestingly, jasmonate induces intra- and extracellular UPI accumulation, suggesting a possible role in intercellular or extracellular functions. Overall, our results show that UPI is a dual-specificity PI that functions in plant growth and defense, probably through the regulation of endogenous proteases and/or those of biotic invaders.

The Jasmonate-ZIM domain proteins interact with the R2R3-MYB transcription factors MYB21 and MYB24 to affect Jasmonate-regulated stamen development in Arabidopsis

The Arabidopsis thaliana F-box protein CORONATINE INSENSITIVE1 (COI1) perceives jasmonate (JA) signals and subsequently targets the Jasmonate-ZIM domain proteins (JAZs) for degradation by the SCF(COI1)-26S proteasome pathway to mediate various jasmonate-regulated processes, including fertility, root growth, anthocyanin accumulation, senescence, and defense. In this study, we screened JAZ-interacting proteins from an Arabidopsis cDNA library in the yeast two-hybrid system. MYB21 and MYB24, two R2R3-MYB transcription factors, were found to interact with JAZ1, JAZ8, and JAZ11 in yeast and in planta. Genetic and physiological experiments showed that the myb21 myb24 double mutant exhibited defects specifically in pollen maturation, anther dehiscence, and filament elongation leading to male sterility. Transgenic expression of MYB21 in the coi1-1 mutant was able to rescue male fertility partially but unable to recover JA-regulated root growth inhibition, anthocyanin accumulation, and plant defense. These results demonstrate that the R2R3-MYB transcription factors MYB21 and MYB24 function as direct targets of JAZs to regulate male fertility specifically. We speculate that JAZs interact with MYB21 and MYB24 to attenuate their transcriptional function; upon perception of JA signal, COI1 recruits JAZs to the SCF(COI1) complex for ubiquitination and degradation through the 26S proteasome; MYB21 and MYB24 are then released to activate expression of various genes essential for JA-regulated anther development and filament elongation.

Proteomic study identifies proteins involved in brassinosteroid regulation of rice growth

Brassinosteroids (BRs) are essential hormones for growth and development of plant. In rice, BRs regulate multiple developmental processes and affect many important traits such as height, leaf angle, fertility and seed filling. We identified brassinosteroid-regulated proteins in rice using proteomic approaches and performed functional analysis of some BR-regulated proteins by overexpression experiments. Using two-dimensional difference gel electrophoresis (2-D DIGE) followed by protein identification by mass spectrometry, we compared proteomic differences in the shoots and roots of the BR-insensitive mutant d61-4 and BR-deficient mutant brd1-3. We identified a large number of proteins differentially expressed in the mutants compared with wild type control. These include a glycine-rich RNA-binding protein (OsGRP1) and a DREPP2 protein, which showed reduced levels in the BR mutants. Overexpression of these two proteins partially suppressed the dwarf phenotype of the Arabidopsis BR-insensitive mutant bri1-5. In contrast to the reduced protein level, the RNA level of OsGRP1 was not significantly affected in the BR mutants or by BR treatment, suggesting BR regulation of OsGRP1 at the posttranslational level. This study identifies many BR-regulated proteins and demonstrates that OsGRP1 functions downstream in the BR signal transduction pathway to promote cell expansion.

Using proteomics to study sexual reproduction in angiosperms

While a relative latecomer to the postgenomics era of functional biology, the application of mass spectrometry-based proteomic analysis has increased exponentially over the past 10 years. Some of this increase is the result of transition of chemists, physicists, and mathematicians to the study of biology, and some is due to improved methods, increased instrument sensitivity, and better techniques of bioinformatics-based data analysis. Proteomic Biological processes are typically studied in isolation, and seldom are efforts made to coordinate results obtained using structural, biochemical, and molecular-genetic strategies. Mass spectrometry-based proteomic analysis can serve as a platform to bridge these disparate results and to additionally incorporate both temporal and anatomical considerations. Recently, proteomic analyses have transcended their initial purely descriptive applications and are being employed extensively in studies of posttranslational protein modifications, protein interactions, and control of metabolic networks. Herein, we provide a brief introduction to sample preparation, comparison of gel-based versus gel-free methods, and explanation of data analysis emphasizing plant reproductive applications. We critically review the results from the relatively small number of extant proteomics-based analyses of angiosperm reproduction, from flowers to seedlings, and speculate on the utility of this strategy for future developments and directions.