Cell cycle entry, maintenance, and exit during plant development

The lowdown on breakdown: Open questions in plant proteolysis

Proteolysis, including post-translational proteolytic processing as well as protein degradation and amino acid recycling, is an essential component of the growth and development of living organisms. In this article, experts in plant proteolysis pose and discuss compelling open questions in their areas of research. Topics covered include the role of proteolysis in the cell cycle, DNA damage response, mitochondrial function, the generation of N-terminal signals (degrons) that mark many proteins for degradation (N-terminal acetylation, the Arg/N-degron pathway, and the chloroplast N-degron pathway), developmental and metabolic signaling (photomorphogenesis, abscisic acid and strigolactone signaling, sugar metabolism, and postharvest regulation), plant responses to environmental signals (endoplasmic-reticulum-associated degradation, chloroplast-associated degradation, drought tolerance, and the growth-defense trade-off), and the functional diversification of peptidases. We hope these thought-provoking discussions help to stimulate further research.

Induced genetic diversity through mutagenesis in wheat gene pool and significant use of SCoT markers to underpin key agronomic traits

BACKGROUND

This research explores the efficacy of mutagenesis, specifically using sodium azide (SA) and hydrazine hydrate (HZ) treatments, to introduce genetic diversity and enhance traits in three wheat (Triticum aestivum L.) genotypes. The experiment entails subjecting the seeds to different doses of SA and HZ and cultivating them in the field for two consecutive generations: M1 (first generation) and M2 (second generation). We then employed selective breeding techniques with Start Codon Targeted (SCoT) markers to select traits within the wheat gene pool. Also, the correlation between SCoT markers and specific agronomic traits provides insights into the genetic mechanisms underlying mutagenesis-induced changes in wheat.

RESULTS

In the study, eleven genotypes were derived from parent varieties Sids1, Sids12, and Giza 168, and eight mutant genotypes were selected from the M1 generation and further cultivated to establish the M2 generation. The results revealed that various morphological and agronomical characteristics, such as plant height, spikes per plant, spike length, spikelet per spike, grains per spikelet, and 100-grain weight, showed increases in different genotypes from M1 to M2. SCoT markers were employed to assess genetic diversity among the eleven genotypes. The bioinformatics analysis identified a correlation between SCoT markers and the transcription factors ABSCISIC ACID INSENSITIVE3 (ABI3) and VIVIPAROUS1 (VP1), crucial for plant development, growth, and stress adaptation. A comprehensive examination of genetic distance and the function identification of gene-associated SCoT markers may provide valuable insights into the mechanisms by which SA and HZ act as mutagens, enhancing wheat agronomic qualities.

CONCLUSIONS

This study demonstrates the effective use of SA and HZ treatments to induce gene diversity through mutagenesis in the wheat gene pool, resulting in the enhancement of agronomic traits, as revealed by SCoT markers. The significant improvements in morphological and agronomical characteristics highlight the potential of mutagenesis techniques for crop improvement. These findings offer valuable information for breeders to develop effective breeding programs to enhance wheat quality and resilience through increased genetic diversity.

RETINOBLASTOMA RELATED 1 switches mitosis to meiosis in rice

The transition from mitosis to meiosis is a critical event in the reproductive development of all sexually reproducing species. However, the mechanisms that regulate this process in plants remain largely unknown. Here, we find that the rice (Oryza sativa L.) protein RETINOBLASTOMA RELATED 1 (RBR1) is essential to the transition from mitosis to meiosis. Loss of RBR1 function results in hyper-proliferative sporogenous-cell-like cells (SCLs) in the anther locules during early stages of reproductive development. These hyper-proliferative SCLs are unable to initiate meiosis, eventually stagnating and degrading at late developmental stages to form pollen-free anthers. These results suggest that RBR1 acts as a gatekeeper of entry into meiosis. Furthermore, cytokinin content is significantly increased in rbr1 mutants, whereas the expression of type-B response factors, particularly LEPTO1, is significantly reduced. Given the known close association of cytokinins with cell proliferation, these findings imply that hyper-proliferative germ cells in the anther locules may be attributed to elevated cytokinin concentrations and disruptions in the cytokinin pathway. Using a genetic strategy, the association between germ cell hyper-proliferation and disturbed cytokinin signaling in rbr1 has been confirmed. In summary, we reveal a unique role of RBR1 in the initiation of meiosis; our results clearly demonstrate that the RBR1 regulatory module is connected to the cytokinin signaling pathway and switches mitosis to meiosis in rice.

OsNAC103, an NAC transcription factor negatively regulates plant height in rice

MAIN CONCLUSION

OsNAC103 negatively regulates rice plant height by influencing the cell cycle and crosstalk of phytohormones. Plant height is an important characteristic of rice farming and is directly related to agricultural yield. Although there has been great progress in research on plant growth regulation, numerous genes remain to be elucidated. NAC transcription factors are widespread in plants and have a vital function in plant growth. Here, we observed that the overexpression of OsNAC103 resulted in a dwarf phenotype, whereas RNA interference (RNAi) plants and osnac103 mutants showed no significant difference. Further investigation revealed that the cell length did not change, indicating that the dwarfing of plants was caused by a decrease in cell number due to cell cycle arrest. The content of the bioactive cytokinin N6-Δ2-isopentenyladenine (iP) decreased as a result of the cytokinin synthesis gene being downregulated and the enhanced degradation of cytokinin oxidase. OsNAC103 overexpression also inhibited cell cycle progression and regulated the activity of the cell cyclin OsCYCP2;1 to arrest the cell cycle. We propose that OsNAC103 may further influence rice development and gibberellin-cytokinin crosstalk by regulating the Oryza sativa homeobox 71 (OSH71). Collectively, these results offer novel perspectives on the role of OsNAC103 in controlling plant architecture.

HECT-type ubiquitin ligase KAKTUS mediates the proteasome-dependent degradation of cyclin-dependent kinase inhibitor KRP2 during trichome morphogenesis in Arabidopsis

Trichome development is a fascinating model to elaborate the plant cell differentiation and growth processes. A wealth of information has pointed to the contributions of the components associated with cell cycle control and ubiquitin/26S proteasome system (UPS) to trichome morphogenesis, but how these two pathways are connected remains obscure. Here, we report that HECT‐type ubiquitin ligase KAKTUS (KAK) targets the cyclin‐dependent kinase (CDK) inhibitor KRP2 (for kip‐related protein 2) for proteasome‐dependent degradation during trichome branching in Arabidopsis. We show that over‐expression of KRP2 promotes trichome branching and endoreduplication which is similar to kak loss of function mutants. KAK directly interacts with KRP2 and mediates KRP2 degradation. Mutation of KAK results in the accumulation of steady‐state KRP2. Consistently, in kak pKRP2:KRP2‐GFP plants, the trichome branching is further induced compared with the single mutant. Taken together, our studies bridge the cell cycle control and UPS pathways during trichome development and underscore the importance of post‐translational control in epidermal differentiation.

Changes in Metabolite Profiling and Expression Levels of Key Genes Involved in the Terpenoid Biosynthesis Pathway in Garden Sage (Salvia officinalis) under the Effect of Hydrazine Hydrate

Mutagenesis is a highly efficient tool for establishing genetic variation and is widely used for genetic enhancement in various plants. The key benefit of mutation breeding is the prospect of enhancing one or several characteristics of a variety without altering the genetic background. In this study, we exposed the seeds of Salvia officinalis to four concentrations of hydrazine hydrate (HZ), i.e., (0%, 0.1%, 0.2%, and 0.3%) for 6 h. The contents of terpenoid compounds in the S. officinalis plantlets driven from the HZ-treated seeds were determined by GC-MS, which resulted in the identification of a total of 340 phytochemical compounds; 163 (87.48%), 145 (84.49%), 65 (97.45%), and 62 (98.32%), from the four concentrations of HZ (0%, 0.1%, 0.2%, and 0.3%), respectively. Furthermore, we used the qRT-PCR system to disclose the "transcriptional control" for twelve TPS genes related to terpenoid and terpene biosynthesis, namely, SoGPS, SoMYRS, SoNEOD, SoCINS, SoSABS, SoLINS, SoFPPS, SoHUMS, SoTPS6, SoSQUS, SoGGPS, and SoGA2. Altogether, results are likely to ensure some positive relationship between the concentrations of the chemical mutagen HZ used for treating the seeds, the type and amount of the produced terpenes, and the expression of their corresponding genes.

Transcriptome profiling reveals the genes involved in tuberous root expansion in Pueraria (Pueraria montana var. thomsonii)

BACKGROUND

Pueraria is a dry root commonly used in Traditional Chinese Medicine or as food and fodder, and tuberous root expansion is an important agronomic characteristic that influences its yield. However, no specific genes regulating tuberous root expansion in Pueraria have been identified. Therefore, we aimed to explore the expansion mechanism of Pueraria at six developmental stages (P1-P6), by profiling the tuberous roots of an annual local variety "Gange No.1" harvested at 105, 135, 165, 195, 225, and 255 days after transplanting.

RESULTS

Observations of the tuberous root phenotype and cell microstructural morphology revealed that the P3 stage was a critical boundary point in the expansion process, which was preceded by a thickening diameter and yield gain rapidly of the tuberous roots, and followed by longitudinal elongation at both ends. A total of 17,441 differentially expressed genes (DEGs) were identified by comparing the P1 stage (unexpanded) against the P2-P6 stages (expanded) using transcriptome sequencing; 386 differential genes were shared across the six developmental stages. KEGG pathway enrichment analysis showed that the DEGs shared by P1 and P2-P6 stages were mainly involved in pathways related to the "cell wall and cell cycle", "plant hormone signal transduction", "sucrose and starch metabolism", and "transcription factor (TF)". The finding is consistent with the physiological data collected on changes in sugar, starch, and hormone contents. In addition, TFs including bHLHs, AP2s, ERFs, MYBs, WRKYs, and bZIPs were involved in cell differentiation, division, and expansion, which may relate to tuberous root expansion. The combination of KEGG and trend analyses revealed six essential candidate genes involved in tuberous root expansion; of them, CDC48, ARF, and EXP genes were significantly upregulated during tuberous root expansion while INV, EXT, and XTH genes were significantly downregulated.

CONCLUSION

Our findings provide new insights into the complex mechanisms of tuberous root expansion in Pueraria and candidate target genes, which can aid in increasing Pueraria yield.

Confocal Microscopic Assays of Mitotically Active Proteins in an Agrobacterial Infiltration-Based, Cell Division-Enabled Leaf System of Tobacco (Nicotiana benthamiana)

The production of tissues and organs in plants is brought about by mitotic cell divisions, starting from the zygote. Successful mitosis and cytokinesis harness the functional input of proteins that are expressed in cell cycle-dependent manners to regulate cytoskeletal reorganization and intracellular motility. Fluorescence microscopic assays of mitotically active proteins have been dependent on time-consuming transformation experiments in a host plant or cultured cells. To facilitate the detection and observation of cell cycle-dependent localization and dynamics of plant proteins, we demonstrate, in this chapter, a transiently induced cell division system in Nicotiana benthamiana, named the cell division-enabled leaf system (CDELS). Plasmid constructs which express the D-type cyclin along with a fluorescent fusion protein(s) of interest are delivered to the leaves of N. benthamiana by agrobacterial infiltration. Ectopic expression of cyclin D induces leaf epidermal cells to re-enter mitosis and subsequently cytokinesis, allowing the dynamic localization of fluorescent fusion protein(s) to be observed throughout the course of mitotic cell division using live-cell fluorescence microscopy. This effective approach not only allows one to detect mitotic activities of novel proteins but also record their dynamics and relationship with others during mitosis and cytokinesis in a greatly shortened period of time.

Characterization of the soybean KRP gene family reveals a key role for GmKRP2a in root development

Kip-related proteins (KRPs), as inhibitory proteins of cyclin-dependent kinases, are involved in the growth and development of plants by regulating the activity of the CYC-CDK complex to control cell cycle progression. The KRP gene family has been identified in several plants, and several KRP proteins from Arabidopsis thaliana have been functionally characterized. However, there is little research on KRP genes in soybean, which is an economically important crop. In this study, we identified nine GmKRP genes in the Glycine max genome using HMM modeling and BLASTP searches. Protein subcellular localization and conserved motif analysis showed soybean KRP proteins located in the nucleus, and the C-terminal protein sequence was highly conserved. By investigating the expression patterns in various tissues, we found that all GmKRPs exhibited transcript abundance, while several showed tissue-specific expression patterns. By analyzing the promoter region, we found that light, low temperature, an anaerobic environment, and hormones-related cis-elements were abundant. In addition, we performed a co-expression analysis of the GmKRP gene family, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) set enrichment analysis. The co-expressing genes were mainly involved in RNA synthesis and modification and energy metabolism. Furthermore, the GmKRP2a gene, a member of the soybean KRP family, was cloned for further functional analysis. GmKRP2a is located in the nucleus and participates in root development by regulating cell cycle progression. RNA-seq results indicated that GmKRP2a is involved in cell cycle regulation through ribosome regulation, cell expansion, hormone response, stress response, and plant pathogen response pathways. To our knowledge, this is the first study to identify and characterize the KRP gene family in soybean.

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

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

Evaluation of morpho-physiological responses and genotoxicity in Eruca sativa (Mill.) grown in hydroponics from seeds exposed to X-rays

Due to its potential applications in cultivated plants, ionizing radiation (IR) and its effect on organisms is increasingly studied. Here we measured the effects of ionizing radiation on Eruca sativa by analyzing plants from irradiated seeds (1 and 10 Gy) grown in hydroponics. We measured several morpho-physiological traits and genotoxicity. Radiation stress induced a noticeable variability of the morpho-physiological traits highlighting decreased plant vigor. Shoot length and leaf number were significantly higher in 1 Gy-treated samples, whereas root length was significantly higher in 10 Gy treated plants. Stomata number significantly increased with IR dose, whereas both pigment and Rubisco content decreased under radiation stress. Phenol content significantly increased in 1 Gy treated samples, otherwise from total antioxidants, which were not different from control. Most results could find a feasible explanation in a hormesis-like pattern and in a decreased plant vigor under radiation stress. IR induced genotoxic damage, evaluated by ISSR markers, in 15 day old leaves; specifically, a severe decrease in the genome template stability was observed. However, a partial recovery occurred after 2 weeks, especially under the lowest dose (i.e., 1 Gy), suggesting that DNA damage detection and repair mechanisms are active. Pigment content and genotoxic damage may serve as proxies for evaluating plant responses to IR stress, since they show univocal dose-dependent trends. The use of more checkpoints for analyses and more doses over a wider range, as well as the focus on different metabolites, could help elucidate plant response in terms of morpho-physiological changes.

Development specifies, diversifies and empowers root immunity

Roots are a highly organised plant tissue consisting of different cell types with distinct developmental functions defined by cell identity networks. Roots are the target of some of the most devastating diseases and possess a highly effective immune system. The recognition of microbe- or plant-derived molecules released in response to microbial attack is highly important in the activation of complex immunity gene networks. Development and immunity are intertwined, and immunity activation can result in growth inhibition. In turn, by connecting immunity and cell identity regulators, cell types are able to launch a cell type-specific immunity based on the developmental function of each cell type. By this strategy, fundamental developmental processes of each cell type contribute their most basic functions to drive cost-effective but highly diverse and, thus, efficient immune responses. This review highlights the interdependence of root development and immunity and how the developmental age of root cells contributes to positive and negative outcomes of development-immunity cross-talk.

The role of APC/C in cell cycle dynamics, growth and development in cereal crops

Cereal crops can be considered the basis of human civilization. Thus, it is not surprising that these crops are grown in larger quantities worldwide than any other food supply and provide more energy to humankind than any other provision. Additionally, attempts to harness biomass consumption continue to increase to meet human energy needs. The high pressures for energy will determine the demand for crop plants as resources for biofuel, heat, and electricity. Thus, the search for plant traits associated with genetic increases in yield is mandatory. In multicellular organisms, including plants, growth and development are driven by cell division. These processes require a sequence of intricated events that are carried out by various protein complexes and molecules that act punctually throughout the cycle. Temporal controlled degradation of key cell division proteins ensures a correct onset of the different cell cycle phases and exit from the cell division program. Considering the cell cycle, the Anaphase-Promoting Complex/Cyclosome (APC/C) is an important conserved multi-subunit ubiquitin ligase, marking targets for degradation by the 26S proteasome. Studies on plant APC/C subunits and activators, mainly in the model plant Arabidopsis, revealed that they play a pivotal role in several developmental processes during growth. However, little is known about the role of APC/C in cereal crops. Here, we discuss the current understanding of the APC/C controlling cereal crop development.

Comparative Transcriptome Analysis Reveals Common and Developmental Stage-Specific Genes That Respond to Low Nitrogen in Maize Leaves

A growing leaf can be divided into three sections: division zone, elongation zone, and maturation zone. In previous studies, low nitrogen (LN) inhibited maize growth and development, especially leaf growth; however, the gene expression in response to LN in different regions in leaf were not clear. Here, using hydroponics and a transcriptome approach, we systematically analyzed the molecular responses of those zones and differentially expressed genes (DEG) in response to LN supply. Developmental stage-specific genes (SGs) were highly stage-specific and involved in distinct biological processes. SGs from division (SGs–DZ) and elongation zones (SGs–EZ) were more related to developmentally dependent processes, whereas SGs of the maturation zone (SGs–MZ) were more related to metabolic processes. The common genes (CGs) were overrepresented in carbon and N metabolism, suggesting that rebalancing carbon and N metabolism in maize leaves under LN condition was independent of developmental stage. Coexpression modules (CMs) were also constructed in our experiment and a total of eight CMs were detected. Most of SGs–DZ and SGs–EZ were classified into a set termed CM turquoise, which was mainly enriched in ribosome and DNA replication, whereas several genes from SGs–MZ and CGs were clustered into CM blue, which mainly focused on photosynthesis and carbon metabolism. Finally, a comprehensive coexpression network was extracted from CM blue, and several maize CONSTANS-LIKE(ZmCOL) genes seemed to participate in regulating photosynthesis in maize leaves under LN condition in a developmental stage-specific manner. With this study, we uncovered the LN-responsive CGs and SGs that are important for promoting plant growth and development under insufficient nitrogen supply.

A hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis

How cell size and number are determined during organ development remains a fundamental question in cell biology. Here, we identified a GRAS family transcription factor, called SCARECROW-LIKE28 (SCL28), with a critical role in determining cell size in Arabidopsis. SCL28 is part of a transcriptional regulatory network downstream of the central MYB3Rs that regulate G2 to M phase cell cycle transition. We show that SCL28 forms a dimer with the AP2-type transcription factor, AtSMOS1, which defines the specificity for promoter binding and directly activates transcription of a specific set of SIAMESE-RELATED (SMR) family genes, encoding plant-specific inhibitors of cyclin-dependent kinases and thus inhibiting cell cycle progression at G2 and promoting the onset of endoreplication. Through this dose-dependent regulation of SMR transcription, SCL28 quantitatively sets the balance between cell size and number without dramatically changing final organ size. We propose that this hierarchical transcriptional network constitutes a cell cycle regulatory mechanism that allows to adjust cell size and number to attain robust organ growth.

Antagonistic Effect of Sucrose Availability and Auxin on Rosa Axillary Bud Metabolism and Signaling, Based on the Transcriptomics and Metabolomics Analysis

Shoot branching is crucial for successful plant development and plant response to environmental factors. Extensive investigations have revealed the involvement of an intricate regulatory network including hormones and sugars. Recent studies have demonstrated that two major systemic regulators-auxin and sugar-antagonistically regulate plant branching. However, little is known regarding the molecular mechanisms involved in this crosstalk. We carried out two complementary untargeted approaches-RNA-seq and metabolomics-on explant stem buds fed with different concentrations of auxin and sucrose resulting in dormant and non-dormant buds. Buds responded to the combined effect of auxin and sugar by massive reprogramming of the transcriptome and metabolome. The antagonistic effect of sucrose and auxin targeted several important physiological processes, including sink strength, the amino acid metabolism, the sulfate metabolism, ribosome biogenesis, the nucleic acid metabolism, and phytohormone signaling. Further experiments revealed a role of the TOR-kinase signaling pathway in bud outgrowth through at least downregulation of Rosa hybrida BRANCHED1 (RhBRC1). These new findings represent a cornerstone to further investigate the diverse molecular mechanisms that drive the integration of endogenous factors during shoot branching.

Disruption in the DNA Mismatch Repair Gene MSH2 by CRISPR-Cas9 in Indica Rice Can Create Genetic Variability

Genetic variation is crucial for crop improvement. We adopted a gene editing approach to create variations in the rice genome by targeting the mutator locus homolog 2 (MSH2), a DNA mismatch repair gene. The hypothesis is that disruption of the MSH2 gene leads to a reduced DNA mismatch repair that creates INDELs, resulting in altered phenotypes. The Indica rice (IR-64) genotype was transformed with a guide RNA targeted to the MSH2 gene using an Agrobacterium-mediated in planta method. Many plants showed integration of Cas9 and gRNA constructs in rice plants. One of the msh2 mutants showed a superior phenotype due to editing and possible INDELs in the whole genome. The stable integration of the transgene and its flanking sequence analysis confirms no disruption of any gene, and the observed phenotype is due to the mutations in the MSH2 gene. Few transgenic plants showed disruption of genes due to T-DNA integration that led to altered phenotypes. The plants with altered phenotypes having more tiller number, early flowering, and robust growth with a high biomass were identified. These genetically reprogrammed rice plants could be a potential resource to create more segregating population or act as donor lines to stabilize the important agronomic traits that may help in a speed breeding process.

Biological pathway expression complementation contributes to biomass heterosis in Arabidopsis

The mechanisms underlying heterosis have long remained a matter of debate, despite its agricultural importance. How changes in transcriptional networks during plant development are relevant to the continuous manifestation of growth vigor in hybrids is intriguing and unexplored. Here, we present an integrated high-resolution analysis of the daily dynamic growth phenotypes and transcriptome atlases of young Arabidopsis seedlings (parental ecotypes [Col-0 and Per-1] and their F₁ hybrid). Weighted gene coexpression network analysis uncovered divergent expression patterns between parents of the network hub genes, in which genes related to the cell cycle were more highly expressed in one parent (Col-0), whereas those involved in photosynthesis were more highly expressed in the other parent (Per-1). Notably, the hybrid exhibited spatiotemporal high-parent-dominant expression complementation of network hub genes in the two pathways during seedling growth. This suggests that the integrated capacities of cell division and photosynthesis contribute to hybrid growth vigor, which could be enhanced by temporal advances in the progression of leaf development in the hybrid relative to its parents. Altogether, this study provides evidence of expression complementation between fundamental biological pathways in hybrids and highlights the contribution of expression dominance in heterosis.

Hormonal Regulation of Stem Cell Proliferation at the Arabidopsis thaliana Root Stem Cell Niche

The root stem cell niche (SCN) of Arabidopsis thaliana consists of the quiescent center (QC) cells and the surrounding initial stem cells that produce progeny to replenish all the tissues of the root. The QC cells divide rather slowly relative to the initials, yet most root tissues can be formed from these cells, depending on the requirements of the plant. Hormones are fundamental cues that link such needs with the cell proliferation and differentiation dynamics at the root SCN. Nonetheless, the crosstalk between hormone signaling and the mechanisms that regulate developmental adjustments is still not fully understood. Developmental transcriptional regulatory networks modulate hormone biosynthesis, metabolism, and signaling, and conversely, hormonal responses can affect the expression of transcription factors involved in the spatiotemporal patterning at the root SCN. Hence, a complex genetic-hormonal regulatory network underlies root patterning, growth, and plasticity in response to changing environmental conditions. In this review, we summarize the scientific literature regarding the role of hormones in the regulation of QC cell proliferation and discuss how hormonal signaling pathways may be integrated with the gene regulatory network that underlies cell fate in the root SCN. The conceptual framework we present aims to contribute to the understanding of the mechanisms by which hormonal pathways act as integrators of environmental cues to impact on SCN activity.

Large-scale Proteomic and Phosphoproteomic Analyses of Maize Seedling Leaves During De-etiolation

De-etiolation consists of a series of developmental and physiological changes that a plant undergoes in response to light. During this process light, an important environmental signal, triggers the inhibition of mesocotyl elongation and the production of photosynthetically active chloroplasts, and etiolated leaves transition from the "sink" stage to the "source" stage. De-etiolation has been extensively studied in maize (Zea mays L.). However, little is known about how this transition is regulated. In this study, we described a quantitative proteomic and phosphoproteomic atlas of the de-etiolation process in maize. We identified 16,420 proteins in proteome, among which 14,168 proteins were quantified. In addition, 8746 phosphorylation sites within 3110 proteins were identified. From the combined proteomic and phosphoproteomic data, we identified a total of 17,436 proteins. Only 7.0% (998/14,168) of proteins significantly changed in abundance during de-etiolation. In contrast, 26.6% of phosphorylated proteins exhibited significant changes in phosphorylation level; these included proteins involved in gene expression and homeostatic pathways and rate-limiting enzymes involved in photosynthetic light and carbon reactions. Based on phosphoproteomic analysis, 34.0% (1057/3110) of phosphorylated proteins identified in this study contained more than 2 phosphorylation sites, and 37 proteins contained more than 16 phosphorylation sites, indicating that multi-phosphorylation is ubiquitous during the de-etiolation process. Our results suggest that plants might preferentially regulate the level of posttranslational modifications (PTMs) rather than protein abundance for adapting to changing environments. The study of PTMs could thus better reveal the regulation of de-etiolation.

The epidermis-specific cyclin CYCP3;1 is involved in the excess brassinosteroid signaling-inhibited root meristem cell division

Cell division is precisely regulated and highly tissue-specific; studies have suggested that diverse signals in the epidermis, especially the epidermal brassinosteroids (BRs), can regulate root growth. However, the underlying molecular mechanisms that integrate hormonal cues such as BR signaling with other endogenous, tissue-specific developmental programs to regulate epidermal cell proliferation remain unclear. In this study, we used molecular and biochemical approaches, microscopic imaging and genetic analysis to investigate the function and mechanisms of a P-type cyclin in root growth regulation. We found that CYCP3;1, specifically expressed in the root meristem epidermis and lateral root cap, can regulate meristem cell division. Mitotic analyses and biochemical studies demonstrated that CYCP3;1 promotes cell division at the G2-M duration by associating and activating cyclin-dependent kinase B2-1 (CDKB2;1). Furthermore, we found that CYCP3;1 expression was inhibited by BR signaling through BRI1-EMS-SUPPRESSOR1 (BES1), a positive downstream transcription factor in the BR signaling pathway. These findings not only provide a mechanism of how root epidermal-specific regulators modulate root growth, but also reveal why the excess of BRs or enhanced BR signaling inhibits cell division in the meristem to negatively regulate root growth.

Establishment of a mitotic model system by transient expression of the D-type cyclin in differentiated leaf cells of tobacco (Nicotiana benthamiana)

Investigations of plant cell division would greatly benefit from a fast, inducible system. Therefore, we aimed to establish a mitotic model by transiently expressing D-type cyclins in tobacco leaf cells. Two different D-type cyclins, CYCD3;1 and CYCD4;2 from Arabidopsis thaliana, were expressed by agrobacterial infiltration in the cells of expanded leaves in tobacco (Nicotiana benthamiana). Leaf pavement cells were examined after cyclin expression while target and reference (histone or tubulin) proteins were marked by fluorescent protein-tagging. Ectopic expression of the D-type cyclin induced pavement cells to re-enter cell division by establishing mitotic microtubule arrays. The induced leaf cells expressed M phase-specific genes of Arabidopsis encoding the mitotic kinase AtAurora 1, the microtubule-associated proteins AtEDE1 and AtMAP65-4, and the vesicle fusion protein AtKNOLLE by recognizing their genomic elements. Their distinct localizations at spindle poles (AtAurora1), spindle microtubules (AtEDE1), phragmoplast microtubules (AtMAP65-4) and the cell plate (AtKNOLLE) were indistinguishable from those in their native Arabidopsis cells. The dividing cells also revealed two rice (Oryza sativa) microtubule-associated proteins in the phragmoplast and uncovered a novel spindle-associated microtubule motor protein. Hence, this cell division-enabled leaf system predicts hypothesized cell cycle-dependent functions of heterologous genes by reporting the dynamics of encoded proteins.

A method for studying cell division in Nicotiana benthamiana pavement cells based on Agrobacterium infiltration

This article is a Commentary on Xu et al., 226: 1213–1221.

A distinct class of plant and animal viral proteins that disrupt mitosis by directly interrupting the mitotic entry switch Wee1-Cdc25-Cdk1

Many animal viral proteins, e.g., Vpr of HIV-1, disrupt host mitosis by directly interrupting the mitotic entry switch Wee1-Cdc25-Cdk1. However, it is unknown whether plant viruses may use this mechanism in their pathogenesis. Here, we report that the 17K protein, encoded by barley yellow dwarf viruses and related poleroviruses, delays G2/M transition and disrupts mitosis in both host (barley) and nonhost (fission yeast, Arabidopsis thaliana, and tobacco) cells through interrupting the function of Wee1-Cdc25-CDKA/Cdc2 via direct protein-protein interactions and alteration of CDKA/Cdc2 phosphorylation. When ectopically expressed, 17K disrupts the mitosis of cultured human cells, and HIV-1 Vpr inhibits plant cell growth. Furthermore, 17K and Vpr share similar secondary structural feature and common amino acid residues required for interacting with plant CDKA. Thus, our work reveals a distinct class of mitosis regulators that are conserved between plant and animal viruses and play active roles in viral pathogenesis.

Plant tumors: a hundred years of study

The review provides information on the mechanisms underlying the development of spontaneous and pathogen-induced tumors in higher plants. The activation of meristem-specific regulators in plant tumors of various origins suggests the meristem-like nature of abnormal plant hyperplasia. Plant tumor formation has more than a century of research history. The study of this phenomenon has led to a number of important discoveries, including the development of the Agrobacterium-mediated transformation technique and the discovery of horizontal gene transfer from bacteria to plants. There are two main groups of plant tumors: pathogen-induced tumors (e.g., tumors induced by bacteria, viruses, fungi, insects, etc.), and spontaneous ones, which are formed in the absence of any pathogen in plants with certain genotypes (e.g., interspecific hybrids, inbred lines, and mutants). The causes of the transition of plant cells to tumor growth are different from those in animals, and they include the disturbance of phytohormonal balance and the acquisition of meristematic characteristics by differentiated cells. The aim of this review is to discuss the mechanisms underlying the development of most known examples of plant tumors.

Geometric cues forecast the switch from two- to three-dimensional growth in Physcomitrella patens

During land colonization, plants acquired a range of body plan adaptations, of which the innovation of three-dimensional (3D) tissues increased organismal complexity and reproductivity. In the moss, Physcomitrella patens, a 3D leafy gametophore originates from filamentous cells that grow in a two-dimensional (2D) plane through a series of asymmetric cell divisions. Asymmetric cell divisions that coincide with different cell division planes and growth directions enable the developmental switch from 2D to 3D, but insights into the underlying mechanisms coordinating this switch are still incomplete. Using 2D and 3D imaging and image segmentation, we characterized two geometric cues, the width of the initial cell and the angle of the transition division plane, which sufficiently distinguished a gametophore initial cell from a branch initial cell. These identified cues were further confirmed in gametophore formation mutants. The identification of a fluorescent marker allowed us to successfully predict the gametophore initial cell with > 90% accuracy before morphological changes, supporting our hypothesis that, before the transition division, parental cells of the gametophore initials possess different properties from those of the branch initials. Our results suggest that the cell fate decision of the initial cell is determined in the parental cell, before the transition division.

Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita)

BACKGROUND

Yam tuber is a storage organ, derived from the modified stem. Tuber expansion is a complex process, and depends on the expressions of genes that can be influenced by environmental and endogenous factors. However, little is known about the regulatory mechanism of tuber expansion. In order to identify the genes and miRNAs involved in tuber expansion, we examined the mRNAs and small RNAs in Dioscorea opposita (Chinese yam) cv. Guihuai 16 tuber during its initiation and expansion stages.

RESULTS

A total of 14,238 differentially expressed genes in yam tuber at its expansion stage were identified by using RNA sequencing technology. Among them, 5723 genes were up-regulated, and 8515 genes were down-regulated. Functional analysis revealed the coordination of tuber plant involved in processes of cell events, metabolism, biosynthesis, and signal transduction pathways at transcriptional level, suggesting that these differentially expressed genes are somehow involved in response to tuber expansion, including CDPK, CaM, CDL, SAUR, DELLA, SuSy, and expansin. In addition, 541 transcription factor genes showed differential expression during the expansion stage at transcriptional level. MADS, bHLH, and GRAS were involved in cell differentiation, division, and expansion, which may relate to tuber expansion. Noteworthy, data analysis revealed that 22 known tuber miRNAs belong to 10 miRNA families, and 50 novel miRNAs were identified. The integrated analysis of miRNA-mRNA showed that 4 known miRNAs and 11 genes formed 14 miRNA-target mRNA pairs were co-expressed in expansion stage. miRNA160, miRNA396, miRNA535 and miRNA5021 may be involved in complex network to regulate cell division and differentiation in yam during its expansion stage.

CONCLUSION

The mRNA and miRNA datasets presented here identified a subset of candidate genes and miRNAs that are putatively associated with tuber expansion in yam, a hypothetical model of genetic regulatory network associated with tuber expansion in yam was put forward, which may provide a foundation for molecular regulatory mechanism researching on tuber expansion in Dioscorea species.

Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita)

Background

Yam tuber is a storage organ, derived from the modified stem. Tuber expansion is a complex process, and depends on the expressions of genes that can be influenced by environmental and endogenous factors. However, little is known about the regulatory mechanism of tuber expansion. In order to identify the genes and miRNAs involved in tuber expansion, we examined the mRNAs and small RNAs in Dioscorea opposita (Chinese yam) cv. Guihuai 16 tuber during its initiation and expansion stages.

Results

A total of 14,238 differentially expressed genes in yam tuber at its expansion stage were identified by using RNA sequencing technology. Among them, 5723 genes were up-regulated, and 8515 genes were down-regulated. Functional analysis revealed the coordination of tuber plant involved in processes of cell events, metabolism, biosynthesis, and signal transduction pathways at transcriptional level, suggesting that these differentially expressed genes are somehow involved in response to tuber expansion, including CDPK, CaM, CDL, SAUR, DELLA, SuSy, and expansin. In addition, 541 transcription factor genes showed differential expression during the expansion stage at transcriptional level. MADS, bHLH, and GRAS were involved in cell differentiation, division, and expansion, which may relate to tuber expansion. Noteworthy, data analysis revealed that 22 known tuber miRNAs belong to 10 miRNA families, and 50 novel miRNAs were identified. The integrated analysis of miRNA-mRNA showed that 4 known miRNAs and 11 genes formed 14 miRNA-target mRNA pairs were co-expressed in expansion stage. miRNA160, miRNA396, miRNA535 and miRNA5021 may be involved in complex network to regulate cell division and differentiation in yam during its expansion stage.

Conclusion

The mRNA and miRNA datasets presented here identified a subset of candidate genes and miRNAs that are putatively associated with tuber expansion in yam, a hypothetical model of genetic regulatory network associated with tuber expansion in yam was put forward, which may provide a foundation for molecular regulatory mechanism researching on tuber expansion in Dioscorea species.

Cellular perspectives for improving mesophyll conductance

After entering the leaf, CO2 faces an intricate pathway to the site of photosynthetic fixation embedded within the chloroplasts. The efficiency of CO2 flux is hindered by a number of structural and biochemical barriers which, together, define the ease of flow of the gas within the leaf, termed mesophyll conductance. Previous authors have identified the key elements of this pathway, raising the prospect of engineering the system to improve CO2 flux and, thus, to increase leaf photosynthetic efficiency. In this review, we provide a perspective on the potential for improving the individual elements that contribute to this complex parameter. We lay particular emphasis on generation of the cellular architecture of the leaf which sets the initial boundaries of a number of mesophyll conductance parameters, incorporating an overview of the molecular transport processes which have been proposed as major facilitators of CO2 flux across structural boundaries along the pathway. The review highlights the research areas where future effort might be invested to increase our fundamental understanding of mesophyll conductance and leaf function and, consequently, to enable translation of these findings to improve the efficiency of crop photosynthesis.

Regulation of Aegilops tauschii Coss Tiller Bud Growth by Plant Density: Transcriptomic, Physiological and Phytohormonal Responses

Aegilops tauschii Coss is one of the most hazardous weeds that severely infests wheat fields in China. The tillering ability of Ae. tauschii strongly affects the occurrence and spread by influencing its seed output. In this study, Ae. tauschii was sown at low plant density (LPD) and high plant density (HPD) to investigate the effect of plant density on tiller bud outgrowth and its potential regulators using RNA-Seq. Additionally, the chlorophyll content and photosynthesis, soluble sugar and phytohormone levels were also determined at different plant densities. The results showed that an increased plant density significantly inhibited the elongation of tiller buds in the axil of the first leaf at 15 days after planting, with 7.69 mm at LPD and 1.69 mm at HPD. A total of seven putative tiller-related genes were selected and validated using quantitative real-time PCR. Furthermore, chlorophyll levels, photosynthetic efficiency, and soluble sugar contents were distinctly inhibited by HPD in Ae. tauschii, which may be responsible for the restriction of tiller bud growth. In addition, differentially expressed genes (DEGs) were markedly enriched in indole-3-acetic acid (IAA), abscisic acid (ABA), and gibberellin metabolism and signaling. Accordingly, the levels of ABA and gibberellin A3 in Ae. tauschii were strikingly higher at HPD compared with those at LPD, yet the reverse tendency was observed for IAA. Undoubtedly, such results will be highly beneficial for illuminating the underlying regulators of the Ae. tauschii tillering response to plant density and may provide new ideas for the control of this weed in the future.

Evaluation of arsenic induced toxicity based on arsenic accumulation, translocation and its implications on physio-chemical changes and genomic instability in indica rice (Oryza sativa L.) cultivars

Arsenic (As) accumulation in rice is a principal route of As exposure for rice based population. We have tested physiochemical and molecular parameters together to identify low As accumulating rice cultivars with normal growth and vigor. The present study examined potential toxicity caused by arsenate (AsV) among four rice cultivars tested that varied with respect to accumulation of total arsenic, arsenite (AsIII) and their differential translocation rate which had deleterious impact on growth and metabolism. Intracellular homeostasis of rice cultivars viz., TN-1, IR-64, IR-20 and Tulaipanji was hampered by 21 days long As(V) treatment due to generation of reactive oxygen species (ROS) and inadequate activity of catalase (CAT; EC 1.11.1.6). Upregulation of oxidative stress markers viz., H₂O₂, proline and MDA along with alteration in enzymatic antioxidants profile were conspicuously pronounced in cv. Tulaipanji while cv. TN-1 was least affected under As(V) challenged environment. In addition to that genomic template stability and band sharing indices were qualitatively measured by DNA profiling of all tested cultivars treated with 25 μM, 50 μM, and 75 μM As(V). In rice cv. Tulaipanji genetic polymorphism was significantly detected with the application of random amplified polymorphic DNA (RAPD) tool and characterized as susceptible cultivar of As compared to cvs. TN-1, IR-64 and IR-20 that is in correlation with data obtained from cluster analysis. Hence, identified As tolerant cultivars viz., TN-1, IR64 and IR-20 especially TN-1 could be used in As contaminated agricultural field after appropriate field trial. This study could help to gather information regarding cultivar-specific tolerance strategy to avoid pollutant induced toxicity.

Mepiquat chloride promotes cotton lateral root formation by modulating plant hormone homeostasis

BACKGROUND

Mepiquat chloride (MC), a plant growth regulator, enhances root growth by promoting lateral root formation in cotton. However, the underlying molecular mechanisms of this phenomenon is still unknown.

METHODS

In this study, we used 10 cotton (Gossypium hirsutum Linn.) cultivars to perform a seed treatment with MC to investigate lateral root formation, and selected a MC sensitive cotton cultivar for dynamic monitor of root growth and transcriptome analysis during lateral root development upon MC seed treatment.

RESULTS

The results showed that MC treated seeds promotes the lateral root formation in a dosage-depended manner and the effective promotion region is within 5 cm from the base of primary root. MC treated seeds induce endogenous auxin level by altering gene expression of both gibberellin (GA) biosynthesis and signaling and abscisic acid (ABA) signaling. Meanwhile, MC treated seeds differentially express genes involved in indole acetic acid (IAA) synthesis and transport. Furthermore, MC-induced IAA regulates the expression of genes related to cell cycle and division for lateral root development.

CONCLUSIONS

Our data suggest that MC orchestrates GA and ABA metabolism and signaling, which further regulates auxin biosynthesis, transport, and signaling to promote the cell division responsible for lateral root formation.

TCP7 functions redundantly with several Class I TCPs and regulates endoreplication in Arabidopsis

TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR) proteins, a family of plant-specific transcription factors, play important roles in many developmental processes. However, genetic and functional redundancy among class I TCP limits the analysis of their biological roles. Here, we identified a dominant-negative mutant of Arabidopsis thaliana TCP7 named leaf curling-upward (lcu), which exhibits smaller leaf cells and shorter hypocotyls than the wild type, due to defective endoreplication. A septuple loss-of-function mutant of TCP7, TCP8, TCP14, TCP15, TCP21, TCP22, and TCP23 displayed similar developmental defects to those of lcu. Genome-wide RNA-sequencing showed that lcu and the septuple mutant share many misexpressed genes. Intriguingly, TCP7 directly targets the CYCLIN D1;1 (CYCD1;1) locus and activates its transcription. We determined that the C-terminus of TCP7 accounts for its transcriptional activation activity. Furthermore, the mutant protein LCU exhibited reduced transcriptional activation activity due to the introduction of an EAR-like repressive domain at its C-terminus. Together, these observations indicate that TCP7 plays important roles during leaf and hypocotyl development, redundantly, with at least six class I TCPs, and regulates the expression of CYCD1;1 to affect endoreplication in Arabidopsis.

Chloroplast-Localized Protoporphyrinogen IX Oxidase1 Is Involved in the Mitotic Cell Cycle in Arabidopsis

Protoporphyrinogen IX oxidase1 (PPO1) catalyzes the oxidation of protoporphyrinogen IX to form protoporphyrin IX in the plastid tetrapyrrole biosynthesis pathway and is also essential for plastid RNA editing in Arabidopsis thaliana. The Arabidopsis ppo1-1 mutation was previously shown to be seedling lethal; however, in this study, we showed that the heterozygous ppo1-1/+ mutant exhibited reproductive growth defects characterized by reduced silique length and seed set, as well as aborted pollen development. In this mutant, the second mitotic division was blocked during male gametogenesis, whereas female gametogenesis was impaired at the one-nucleate stage. Before perishing at the seedling stage, the homozygous ppo1-1 mutant displayed reduced hypocotyl and root length, increased levels of reactive oxygen species accumulation and elevated cell death, especially under light conditions. Wild-type seedlings treated with acifluorfen, a PPO1 inhibitor, showed similar phenotypes to the ppo1-1 mutants, and both plants possessed a high proportion of 2C nuclei and a low proportion of 8C nuclei compared with the untreated wild type. Genome-wide RNA-seq analysis showed that a number of genes, including cell cycle-related genes, were differentially regulated by PPO1. Consistently, PPO1 was highly expressed in the pollen, anther, pistil and root apical meristem cells actively undergoing cell division. Our study reveals a role for PPO1 involved in the mitotic cell cycle during gametogenesis and seedling development.

Leaf Production and Expansion: A Generalized Response to Drought Stresses from Cells to Whole Leaf Biomass-A Case Study in the Tomato Compound Leaf

It is clearly established that there is not a unique response to soil water deficit but that there are as many responses as soil water deficit characteristics: Drought intensity, drought duration, and drought position during plant cycle. For a same soil water deficit, responses can also differ on plant genotype within a same species. In spite of this variability, at least for leaf production and expansion processes, robust tendencies can be extracted from the literature when similar watering regimes are compared. Here, we present response curves and multi-scale dynamics analyses established on tomato plants exposed to different soil water deficit treatments. Results reinforce the trends already observed for other species: Reduction in plant leaf biomass under water stress was due to reduction in individual leaf biomass and areas whereas leaf production and specific leaf area were not affected. The dynamics of leaf expansion was modified both at the leaf and cell scales. Cell division and expansion were reduced by drought treatments as well as the endoreduplication process. Combining response curves analyses together with dynamic analyses of tomato compound leaf growth at different scales not only corroborate results on simple leaf responses to drought but also increases our knowledge on the cellular mechanisms behind leaf growth plasticity.

Potential of water fern (Azolla pinnata R.Br.) in phytoremediation of integrated industrial effluent of SIIDCUL, Haridwar, India: removal of physicochemical and heavy metal pollutants

Integrated industrial effluent (IIE) released from SIIDCUL causes serious environmental problems in the vicinity of Haridwar, India. Therefore, this study investigated the potential of water fern (Azolla pinnata R.Br.) for phyto-treatment of IIE. Laboratory experiments with six IIE concentrations (0 as control with bore well water, 20, 40, 60, 80 and 100%) were performed for bio-removal of selected physicochemical, microbiological and heavy metal parameters of IIE in pot type experiments. The overall results described maximum removal of physico-chemical (pH, EC, TDS, BOD, COD, TKN, Ca, Mg, Na, K), microbiological (MPN and SPC) and heavy metals (Cd, Cu, Cr, Fe, Pb, Mn, and Zn) parameters in 60% concentration of IIE, respectively. The stimulus effect of IIE concentration on pollutant removal process was confirmed using Kruskal-Wallis post hoc test, one way ANOVA (p < 0.05), and linear regression (R² < 0.85) tools. Besides this, A. pinnata relative plant growth rate was also maximum in 60% IIE treatment. This is the first report on phytoremediation of IIE while findings of this study showed that A. pinnata was useful for the eco-friendly treatment of SIIDCUL IIE and could minimize potential wastewater management issues.

Prediction of Protein Ubiquitination Sites in Arabidopsis thaliana

Background:

As one of the most important reversible protein post-translation modification types, ubiquitination plays a significant role in the regulation of many biological processes, such as cell division, signal transduction, apoptosis and immune response. Protein ubiquitination usually occurs when ubiquitin molecule is attached to a lysine on a target protein, which is also known as “lysine ubiquitination”.

Objective:

In order to investigate the molecular mechanisms of ubiquitination-related biological processes, the crucial first step is the identification of ubiquitination sites. However, conventional experimental methods in detecting ubiquitination sites are often time-consuming and a large number of ubiquitination sites remain unidentified. In this study, a ubiquitination site prediction method for Arabidopsis thaliana was developed using a Support Vector Machine (SVM).

Methods:

We collected 3009 experimentally validated ubiquitination sites on 1607 proteins in A. thaliana to construct the training set. Three feature encoding schemes were used to characterize the sequence patterns around ubiquitination sites, including AAC, Binary and CKSAAP. The maximum Relevance and Minimum Redundancy (mRMR) feature selection method was employed to reduce the dimensionality of input features. Five-fold cross-validation and independent tests were used to evaluate the performance of the established models.

Results:

As a result, the combination of AAC and CKSAAP encoding schemes yielded the best performance with the accuracy and AUC of 81.35% and 0.868 in the independent test. We also generated an online predictor termed as AraUbiSite, which is freely accessible at: http://systbio.cau.edu.cn/araubisite.

Conclusion:

We developed a well-performed prediction tool for large-scale ubiquitination site identification in A. thaliana. It is hoped that the current work will speed up the process of identification of ubiquitination sites in A. thaliana and help to further elucidate the molecular mechanisms of ubiquitination in plants.

Cell wall integrity maintenance during plant development and interaction with the environment

Cell walls are highly dynamic structures that provide mechanical support for plant cells during growth, development and adaptation to a changing environment. Thus, it is important for plants to monitor the state of their cell walls and ensure their functional integrity at all times. This monitoring involves perception of physical forces at the cell wall-plasma membrane interphase. These forces are altered during cell division and morphogenesis, as well as in response to various abiotic and biotic stresses. Mechanisms responsible for the perception of physical stimuli involved in these processes have been difficult to separate from other regulatory mechanisms perceiving chemical signals such as hormones, peptides or cell wall fragments. However, recently developed technologies in combination with more established genetic and biochemical approaches are beginning to open up this exciting field of study. Here, we will review our current knowledge of plant cell wall integrity signalling using selected recent findings and highlight how the cell wall-plasma membrane interphase can act as a venue for sensing changes in the physical forces affecting plant development and stress responses. More importantly, we discuss how these signals may be integrated with chemical signals derived from established signalling cascades to control specific adaptive responses during exposure to biotic and abiotic stresses.

The architecture of the GhD7 promoter reveals the roles of GhD7 in growth, development and the abiotic stress response in rice

Grain number, plant height and heading date 7 (GhD7) is considered to be one of the key yield-related genes in the production of high-yielding and climate-ready super rice varieties. GhD7 delays the plant's flowering under long-day conditions, which ultimately results in increased yield. Recent findings indicate that GhD7 also plays a major role in the abiotic stress response; however, the fine regulatory mechanisms controlling Ghd7 expression have yet to be uncovered. This study was carried out to explore the transcription factor binding site (TFBS) architecture of the GhD7 promoter to identify the regulatory dynamics of GhD7 transcription. The promoter sequence (-2000 to +200 base pairs from the transcription start site) was retrieved from the PlantPAN 2.0 database. Ab initio promoter analysis, DNase I hypersensitive site (DHS) analysis, and methylation analysis were carried out to identify TFBSs. The TFBS diversity among rice varieties was also assessed. In addition to the previously identified 8 cis-elements, 448 novel cis-elements were identified in the GhD7 promoter that provide binding sites for 25 transcription factor families. Furthermore, a DNase I hypersensitive site and a CpG island were also identified. The identified transcription factor families include key transcription factors involved in both development and abiotic stress responses, revealing the regulatory dynamics of GhD7. Comparative analysis of multiple GhD7 promoters identified 31 single-nucleotide polymorphisms that result in TFBS variations among rice accessions. These variations are mostly found in relation to flowering and abiotic stress responsive TFBSs on the promoter. This study supports the model that GhD7 acts as a central regulator of rice growth, development, and the abiotic stress response.

Developmental analysis of the early steps in strigolactone-mediated axillary bud dormancy in rice

By contrast with rapid progress in understanding the mechanisms of biosynthesis and signaling of strigolactone (SL), mechanisms by which SL inhibits axillary bud outgrowth are less well understood. We established a rice (Oryza sativa L.) hydroponic culture system to observe axillary buds at the critical point when the buds enter the dormant state. In situ hybridization analysis indicated that cell division stops in the leaf primordia of the buds entering dormancy. We compared transcriptomes in the axillary buds isolated by laser capture microdissection before and after entering the dormant state and identified genes that are specifically upregulated or downregulated in dormant buds respectively, in SL-mediated axillary bud dormancy. Typically, cell cycle genes and ribosomal genes are included among the active genes while abscisic acid (ABA)-inducible genes are among the dormant genes. Application of ABA to the hydroponic culture suppressed the growth of axillary buds of SL mutants to the same level as wild-type (WT) buds. Tiller number was decreased in the transgenic lines overexpressing OsNCED1, the gene that encodes ABA biosynthesis enzyme. These results indicated that the main site of SL function is the leaf primordia in the axillary bud and that ABA is involved in SL-mediated axillary bud dormancy.

Role of pyrimidine salvage pathway in the maintenance of organellar and nuclear genome integrity

Nucleotide biosynthesis proceeds through a de novo pathway and a salvage route. In the salvage route, free bases and/or nucleosides are recycled to generate the corresponding nucleotides. Thymidine kinase (TK) is the first enzyme in the salvage pathway to recycle thymidine nucleosides as it phosphorylates thymidine to yield thymidine monophosphate. The Arabidopsis genome contains two TK genes -TK1a and TK1b- that show similar expression patterns during development. In this work, we studied the respective roles of the two genes during early development and in response to genotoxic agents targeting the organellar or the nuclear genome. We found that the pyrimidine salvage pathway is crucial for chloroplast development and genome replication, as well as for the maintenance of its integrity, and is thus likely to play a crucial role during the transition from heterotrophy to autotrophy after germination. Interestingly, defects in TK activity could be partially compensated by supplementation of the medium with sugar, and this effect resulted from both the availability of a carbon source and the activation of the nucleotide de novo synthesis pathway, providing evidence for a compensation mechanism between two routes of nucleotide biosynthesis that depend on nutrient availability. Finally, we found differential roles of the TK1a and TK1b genes during the plant response to genotoxic stress, suggesting that different pools of nucleotides exist within the cells and are required to respond to different types of DNA damage. Altogether, our results highlight the importance of the pyrimidine salvage pathway, both during plant development and in response to genotoxic stress.

Arabidopsis E2Fc is required for the DNA damage response under UV-B radiation epistatically over the microRNA396 and independently of E2Fe

UV-B radiation inhibits plant growth, and this inhibition is, to a certain extent, regulated by miR396-mediated repression of Growth Regulating Transcription factors (GRFs). Moreover, E2Fe transcription factor also modulates Arabidopsis leaf growth. Here, we provide evidence that, at UV-B intensities that induce DNA damage, E2Fc participates in the inhibition of cell proliferation. We demonstrate that E2Fc-deficient plants show a lower inhibition of leaf size under UV-B conditions that damage DNA, decreased cell death after exposure and altered SOG1 and ATR expression. Interestingly, the previously reported participation of E2Fe in UV-B responses, which is a transcriptional target of E2Fc, is independent and different from that described for E2Fc. Conversely, we here demonstrate that E2Fc has an epistatic role over the miR396 pathway under UV-B conditions. Finally, we show that inhibition of cell proliferation by UV-B is independent of the regulation of class II TCP transcription factors. Together, our results demonstrate that E2Fc is required for miR396 activity on cell proliferation under UV-B, and that its role is independent of E2Fe, probably modulating DNA damage responses through the regulation of SOG1 and ATR transcript levels.

Early mannitol-triggered changes in the Arabidopsis leaf (phospho)proteome reveal growth regulators

Leaf growth is a complex, quantitative trait, controlled by a plethora of regulatory mechanisms. Diverse environmental stimuli inhibit leaf growth to cope with the perceived stress. In plant research, mannitol is often used to impose osmotic stress and study the underlying growth-repressing mechanisms. In growing leaf tissue of plants briefly exposed to mannitol-induced stress, a highly interconnected gene regulatory network is induced. However, early signalling and associated protein phosphorylation events that probably precede part of these transcriptional changes and that potentially act at the onset of mannitol-induced leaf size reduction are largely unknown. Here, we performed a proteome and phosphoproteome analysis on growing leaf tissue of Arabidopsis thaliana plants exposed to mild mannitol-induced stress and captured the fast (within the first half hour) events associated with this stress. Based on this in-depth data analysis, 167 and 172 differentially regulated proteins and phosphorylated sites were found. We provide these data sets as a community resource and we flag differentially phosphorylated proteins with described growth-regulatory functions, but we also illustrate potential novel regulators of shoot growth.

A Pelota-like gene regulates root development and defence responses in rice

BACKGROUND AND AIMS

Pelota (Pelo) are evolutionarily conserved genes reported to be involved in ribosome rescue, cell cycle control and meiotic cell division. However, there is little known about their function in plants. The aim of this study was to elucidate the function of an ethylmethane sulphonate (EMS)-derived mutation of a Pelo-like gene in rice (named Ospelo).

METHODS

A dysfunctional mutant was used to characterize the function of OsPelo. Analyses of its expression and sub-cellular localization were performed. The whole-genome transcriptomic change in leaves of Ospelo was also investigated by RNA sequencing.

KEY RESULTS

The Ospelo mutant showed defects in root system development and spotted leaves at early seedling stages. Map-based cloning revealed that the mutation occurred in the putative Pelo gene. OsPelo was found to be expressed in various tissues throughout the plant, and the protein was located in mitochondria. Defence responses were induced in the Ospelo mutant, as shown by enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae, coupled with upregulation of three pathogenesis-related marker genes. In addition, whole-genome transcriptome analysis showed that OsPelo was significantly associated with a number of biological processes, including translation, metabolism and biotic stress response. Detailed analysis showed that activation of a number of innate immunity-related genes might be responsible for the enhanced disease resistance in the Ospelo mutant.

CONCLUSIONS

These results demonstrate that OsPelo positively regulates root development while its loss of function enhances pathogen resistance by pre-activation of defence responses in rice.

Regulation of Division and Differentiation of Plant Stem Cells

A major challenge in developmental biology is unraveling the precise regulation of plant stem cell maintenance and the transition to a fully differentiated cell. In this review, we highlight major themes coordinating the acquisition of cell identity and subsequent differentiation in plants. Plant cells are immobile and establish position-dependent cell lineages that rely heavily on external cues. Central players are the hormones auxin and cytokinin, which balance cell division and differentiation during organogenesis. Transcription factors and miRNAs, many of which are mobile in plants, establish gene regulatory networks that communicate cell position and fate. Small peptide signaling also provides positional cues as new cell types emerge from stem cell division and progress through differentiation. These pathways recruit similar players for patterning different organs, emphasizing the modular nature of gene regulatory networks. Finally, we speculate on the outstanding questions in the field and discuss how they may be addressed by emerging technologies.

Evolutionary and functional potential of ploidy increase within individual plants: somatic ploidy mapping of the complex labellum of sexually deceptive bee orchids

Background and Aims

Recent tissue-level observations made indirectly via flow cytometry suggest that endoreplication (duplication of the nuclear genome within the nuclear envelope in the absence of subsequent cell division) is widespread within the plant kingdom. Here, we also directly observe ploidy variation among cells within individual petals, relating size of nucleus to cell micromorphology and (more speculatively) to function.

Methods

We compared the labella (specialized pollinator-attracting petals) of two European orchid genera: Dactylorhiza has a known predisposition to organismal polyploidy, whereas Ophrys exhibits exceptionally complex epidermal patterning that aids pseudocopulatory pollination. Confocal microscopy using multiple staining techniques allowed us to observe directly both the sizes and the internal structures of individual nuclei across each labellum, while flow cytometry was used to test for progressively partial endoreplication.

Key Results

In Dactylorhiza, endoreplication was comparatively infrequent, reached only low levels, and appeared randomly located across the labellum, whereas in Ophrys endoreplication was commonplace, being most frequent in large peripheral trichomes. Endoreplicated nuclei reflected both endomitosis and endocycling, the latter reaching the third round of genome doubling (16C) to generate polytene nuclei. All Ophrys individuals studied exhibited progressively partial endoreplication.

Conclusions

Comparison of the two genera failed to demonstrate the hypothesized pattern of frequent polyploid speciation in genera showing extensive endoreplication. Endoreplication in Ophrys appears more strongly positively correlated with cell size/complexity than with cell location or secretory role. Epigenetic control of gene overexpression by localized induction of endoreplication within individual plant organs may represent a significant component of a plant's developmental programme, contributing substantially to organ plasticity.

A Tale of Two Cycles

Two of the fundamental rhythms of eukaryotic life are the circadian clock and the cell division cycle. In this issue of Developmental Cell, Fung-Uceda and colleagues (2018) have elucidated a molecular mechanism linking the circadian clock to the cell cycle in the plant Arabidopsis thaliana.

The Pivotal Role of Ethylene in Plant Growth

Being continuously exposed to variable environmental conditions, plants produce phytohormones to react quickly and specifically to these changes. The phytohormone ethylene is produced in response to multiple stresses. While the role of ethylene in defense responses to pathogens is widely recognized, recent studies in arabidopsis and crop species highlight an emerging key role for ethylene in the regulation of organ growth and yield under abiotic stress. Molecular connections between ethylene and growth-regulatory pathways have been uncovered, and altering the expression of ethylene response factors (ERFs) provides a new strategy for targeted ethylene-response engineering. Crops with optimized ethylene responses show improved growth in the field, opening new windows for future crop improvement. This review focuses on how ethylene regulates shoot growth, with an emphasis on leaves.

Arabidopsis MLO2 is a negative regulator of sensitivity to extracellular reactive oxygen species

The atmospheric pollutant ozone (O₃ ) is a strong oxidant that causes extracellular reactive oxygen species (ROS) formation, has significant ecological relevance, and is used here as a non-invasive ROS inducer to study plant signalling. Previous genetic screens identified several mutants exhibiting enhanced O₃ sensitivity, but few with enhanced tolerance. We found that loss-of-function mutants in Arabidopsis MLO2, a gene implicated in susceptibility to powdery mildew disease, exhibit enhanced dose-dependent tolerance to O₃ and extracellular ROS, but a normal response to intracellular ROS. This phenotype is increased in a mlo2 mlo6 mlo12 triple mutant, reminiscent of the genetic redundancy of MLO genes in powdery mildew resistance. Stomatal assays revealed that enhanced O₃ tolerance in mlo2 mutants is not caused by altered stomatal conductance. We explored modulation of the mlo2-associated O₃ tolerance, powdery mildew resistance, and early senescence phenotypes by genetic epistasis analysis, involving mutants with known effects on ROS sensitivity or antifungal defence. Mining of publicly accessible microarray data suggests that these MLO proteins regulate accumulation of abiotic stress response transcripts, and transcript accumulation of MLO2 itself is O₃ responsive. In summary, our data reveal MLO2 as a novel negative regulator in plant ROS responses, which links biotic and abiotic stress response pathways.