Activation tagging in Arabidopsis

UV-B Radiation Disrupts Membrane Lipid Organization and Suppresses Protein Mobility of GmNARK in Arabidopsis

While it is well known that plants interpret UV-B as an environmental cue and a potential stressor influencing their growth and development, the specific effects of UV-B-induced oxidative stress on the dynamics of membrane lipids and proteins remain underexplored. Here, we demonstrate that UV-B exposure notably increases the formation of ordered lipid domains on the plasma membrane (PM) and significantly alters the behavior of the Glycine max nodule autoregulation receptor kinase (GmNARK) protein in Arabidopsis leaves. The GmNARK protein was located on the PM and accumulated as small particles in the cytoplasm. We found that UV-B irradiation interrupted the lateral diffusion of GmNARK proteins on the PM. Furthermore, UV-B light decreases the efficiency of surface molecule internalization by clathrin-mediated endocytosis (CME). In brief, UV-B irradiation increased the proportion of the ordered lipid phase and disrupted clathrin-dependent endocytosis; thus, the endocytic trafficking and lateral mobility of GmNARK protein on the plasma membrane are crucial for nodule formation tuning. Our results revealed a novel role of low-intensity UV-B stress in altering the organization of the plasma membrane and the dynamics of membrane-associated proteins.

ATP Hydrolases Superfamily Protein 1 (ASP1) Maintains Root Stem Cell Niche Identity through Regulating Reactive Oxygen Species Signaling in Arabidopsis

The maintenance of the root stem cell niche identity in Arabidopsis relies on the delicate balance of reactive oxygen species (ROS) levels in root tips; however, the intricate molecular mechanisms governing ROS homeostasis within the root stem cell niche remain unclear. In this study, we unveil the role of ATP hydrolase superfamily protein 1 (ASP1) in orchestrating root stem cell niche maintenance through its interaction with the redox regulator cystathionine β-synthase domain-containing protein 3 (CBSX3). ASP1 is exclusively expressed in the quiescent center (QC) cells and governs the integrity of the root stem cell niche. Loss of ASP1 function leads to enhanced QC cell division and distal stem cell differentiation, attributable to reduced ROS levels and diminished expression of SCARECROW and SHORT ROOT in root tips. Our findings illuminate the pivotal role of ASP1 in regulating ROS signaling to maintain root stem cell niche homeostasis, achieved through direct interaction with CBSX3.

Rhamnogalacturonan lyase 1 (RGL1), as a suppressor of E3 ubiquitin ligase Arabidopsis thaliana ring zinc finger 1 (AtRZF1), is involved in dehydration response to mediate proline synthesis and pectin rhamnogalacturonan-I composition

Proline metabolism plays a crucial role in both environmental stress responses and plant growth. However, the specific mechanism by which proline contributes to abiotic stress processes remains to be elucidated. In this study, we utilized atrzf1 (Arabidopsis thaliana ring zinc finger 1) as a parental line for T-DNA tagging mutagenesis and identified a suppressor mutant of atrzf1, designated proline content alterative 31 (pca31). The pca31 mutant suppressed the insensitivity of atrzf1 to dehydration stress during early seedling growth. Using Thermal Asymmetric Interlaced-PCR, we found that the T-DNA of pca31 was inserted into the promoter region of the At2g22620 gene, which encodes the cell wall enzyme rhamnogalacturonan lyase 1 (RGL1). Enzymatic assays indicated that RGL1 exhibited rhamnogalacturonan lyase activity, influencing cell wall pectin composition. The decrease in RGL1 gene expression suppressed the transcriptomic perturbation of the atrzf1 mutant. Silencing of the RGL1 gene in atrzf1 resulted in a sensitive phenotype similar to pca31 under osmotic stress conditions. Treatment with mannitol, salt, hydrogen peroxide, and abscisic acid induced RGL1 expression. Furthermore, we uncovered that RGL1 plays a role in modulating root growth and vascular tissue development. Molecular, physiological, and genetic experiments revealed that the positive modulation of RGL1 during abiotic stress was linked to the AtRZF1 pathway. Taken together, these findings establish that pca31 acts as a suppressor of atrzf1 in abiotic stress responses through proline and cell wall metabolisms.

Plant genome information facilitates plant functional genomics

MAIN CONCLUSION

In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.

Plant Functional Genomics Based on High-Throughput CRISPR Library Knockout Screening: A Perspective

Plant biology studies in the post-genome era have been focused on annotating genome sequences' functions. The established plant mutant collections have greatly accelerated functional genomics research in the past few decades. However, most plant genome sequences' roles and the underlying regulatory networks remain substantially unknown. Clustered, regularly interspaced short palindromic repeat (CRISPR)-associated systems are robust, versatile tools for manipulating plant genomes with various targeted DNA perturbations, providing an excellent opportunity for high-throughput interrogation of DNA elements' roles. This study compares methods frequently used for plant functional genomics and then discusses different DNA multi-targeted strategies to overcome gene redundancy using the CRISPR-Cas9 system. Next, this work summarizes recent reports using CRISPR libraries for high-throughput gene knockout and function discoveries in plants. Finally, this work envisions the future perspective of optimizing and leveraging CRISPR library screening in plant genomes' other uncharacterized DNA sequences.

A genetic screen for dominant chloroplast reactive oxygen species signaling mutants reveals life stage-specific singlet oxygen signaling networks

Introduction

Plants employ intricate molecular mechanisms to respond to abiotic stresses, which often lead to the accumulation of reactive oxygen species (ROS) within organelles such as chloroplasts. Such ROS can produce stress signals that regulate cellular response mechanisms. One ROS, singlet oxygen (1O2), is predominantly produced in the chloroplast during photosynthesis and can trigger chloroplast degradation, programmed cell death (PCD), and retrograde (organelle-to-nucleus) signaling. However, little is known about the molecular mechanisms involved in these signaling pathways or how many different signaling 1O2 pathways may exist.

Methods

The Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant conditionally accumulates chloroplast 1O2, making fc2 a valuable genetic system for studying chloroplast 1O2-initiated signaling. Here, we have used activation tagging in a new forward genetic screen to identify eight dominant fc2 activation-tagged (fas) mutations that suppress chloroplast 1O2-initiated PCD.

Results

While 1O2-triggered PCD is blocked in all fc2 fas mutants in the adult stage, such cellular degradation in the seedling stage is blocked in only two mutants. This differential blocking of PCD suggests that life-stage-specific 1O2-response pathways exist. In addition to PCD, fas mutations generally reduce 1O2-induced retrograde signals. Furthermore, fas mutants have enhanced tolerance to excess light, a natural mechanism to produce chloroplast 1O2. However, general abiotic stress tolerance was only observed in one fc2 fas mutant (fc2 fas2). Together, this suggests that plants can employ general stress tolerance mechanisms to overcome 1O2 production but that this screen was mostly specific to 1O2 signaling. We also observed that salicylic acid (SA) and jasmonate (JA) stress hormone response marker genes were induced in 1O2-stressed fc2 and generally reduced by fas mutations, suggesting that SA and JA signaling is correlated with active 1O2 signaling and PCD.

Discussion

Together, this work highlights the complexity of 1O2 signaling by demonstrating that multiple pathways may exist and introduces a suite of new 1O2 signaling mutants to investigate the mechanisms controlling chloroplast-initiated degradation, PCD, and retrograde signaling.

How flower development genes were identified using forward genetic screens in Arabidopsis thaliana

In the later part of the 1980s, the time was ripe for identifying genes controlling flower development. In that pregenomic era, the easiest way to do this was to induce random mutations in seeds by chemical mutagens (or irradiation) and to screen thousands of plants for those with phenotypes specifically defective in floral morphogenesis. Here, we discuss the results of premolecular screens for flower development mutants in Arabidopsis thaliana, carried out at Caltech and Monash University, emphasizing the usefulness of saturation mutagenesis, multiple alleles to identify full loss-of-function, conclusions based on multiple mutant analyses, and from screens for enhancer and suppressor modifiers of original mutant phenotypes. One outcome was a series of mutants that led to the ABC floral organ identity model (AP1, AP2, AP3, PI, and AG). In addition, genes controlling flower meristem identity (AP1, CAL, and LFY), floral meristem size (CLV1 and CLV3), development of individual floral organ types (CRC, SPT, and PTL), and inflorescence meristem properties (TFL1, PIN1, and PID) were defined. These occurrences formed targets for cloning that eventually helped lead to an understanding of transcriptional control of the identity of floral organs and flower meristems, signaling within meristems, and the role of auxin in initiating floral organogenesis. These findings in Arabidopsis are now being applied to investigate how orthologous and paralogous genes act in other flowering plants, allowing us to wander in the fertile fields of evo-devo.

Arabidopsis AtMSRB5 functions as a salt-stress protector for both Arabidopsis and rice

Salinity, drought and low temperature are major environmental factors that adversely affect crop productivity worldwide. In this study we adopted an activation tagging approach to identify salt tolerant mutants of Arabidopsis. Thousands of tagged Arabidopsis lines were screened to obtain several potential mutant lines resistant to 150 mM NaCl. Transcript analysis of a salt-stress tolerance 1 (sst1) mutant line indicated activation of AtMSRB5 and AtMSRB6 which encode methionine sulfoxide reductases. Overexpression of AtMSRB5 in Arabidopsis (B5OX) showed a similar salt tolerant phenotype. Furthermore, biochemical analysis indicated stability of the membrane protein, H+-ATPase 2 (AHA2) through regulation of Na+/K+ homeostasis which may be involved in a stress tolerance mechanism. Similarly, overexpression of AtMSRB5 in transgenic rice demonstrated a salt tolerant phenotype via the modulation of Na+/K+ homeostasis without a yield drag under salt and oxidative stress conditions.

The thylakoid membrane protein NTA1 is an assembly factor of the cytochrome b6f complex essential for chloroplast development in Arabidopsis

The cytochrome b_6f (Cyt b_6f) complex is a multisubunit protein complex in chloroplast thylakoid membranes required for photosynthetic electron transport. Here we report the isolation and characterization of the new tiny albino 1 (nta1) mutant in Arabidopsis, which has severe defects in Cyt b_6f accumulation and chloroplast development. Gene cloning revealed that the nta1 phenotype was caused by disruption of a single nuclear gene, NTA1, which encodes an integral thylakoid membrane protein conserved across green algae and plants. Overexpression of NTA1 completely rescued the nta1 phenotype, and knockout of NTA1 in wild-type plants recapitulated the mutant phenotype. Loss of NTA1 function severely impaired the accumulation of multiprotein complexes related to photosynthesis in thylakoid membranes, particularly the components of Cyt b_6f. NTA1 was shown to directly interact with four subunits (Cyt b₆/PetB, PetD, PetG, and PetN) of Cyt b_6f through the DUF1279 domain and C-terminal sequence to mediate their assembly. Taken together, our results identify NTA1 as a new and key regulator of chloroplast development that plays essential roles in assembly of the Cyt b_6f complex by interacting with multiple Cyt b_6f subunits.

Genetic Screens for Floral Mutants in Arabidopsis thaliana: Enhancers and Suppressors

The flower is a hallmark feature that has contributed to the evolutionary success of land plants. Diverse mutagenic agents have been employed as a tool to genetically perturb flower development and identify genes involved in floral patterning and morphogenesis. Since the initial studies to identify genes governing processes such as floral organ specification, mutagenesis in sensitized backgrounds has been used to isolate enhancers and suppressors to further probe the molecular basis of floral development. Here, we first describe two commonly employed methods for mutagenesis (using ethyl methanesulfonate (EMS) or T-DNAs as mutagens), and then describe three methods for identifying a mutation that leads to phenotypic alterations: traditional map-based cloning, modified high-efficiency thermal asymmetric interlaced PCR (mhiTAIL-PCR), and deep sequencing in the plant model Arabidopsis thaliana.

Misexpression Approaches for the Manipulation of Flower Development

The generation of dominant gain-of-function mutants through activation tagging is a forward genetic approach that can be applied to study the mechanisms of flower development, complementing the screening of loss-of-function mutants. In addition, the functions of genes of interest can be further analyzed through reverse genetics. A commonly used method is gene overexpression, where ectopic expression can result in an opposite phenotype to that caused by a loss-of-function mutation. When overexpression is detrimental, the misexpression of a gene using tissue-specific promoters can be useful to study spatial-specific function. As flower development is a multistep process, it can be advantageous to control gene expression, or its protein product activity, in a temporal and/or spatial manner. This has been made possible through several inducible promoter systems as well as inducible proteins by constructing chimeric fusions between the ligand-binding domain of the glucocorticoid receptor (GR) and the protein of interest. The recently introduced CRISPR-Cas9-based platform provides a new way of bioengineering transcriptional regulators in plants. By fusing a catalytically inactive dCas9 with functional activation or repression domains, the CRISPR-Cas9 module can achieve transcriptional activation or repression of endogenous genes. All these methods allow us to genetically manipulate gene expression during flower development. In this chapter, we describe methods to produce the expression constructs, method of screening, and more general applications of the techniques.

Multifaceted roles of the ERECTA family in plant organ morphogenesis

Receptor-like kinases (RLKs) can participate in multiple signalling pathways and are considered one of the most critical components of the early events of intercellular signalling. As an RLK, the ERECTA family (ERf), which comprises ERECTA (ER), ERECTA-Like1 (ERL1), and ERECTA-Like2 (ERL2) in Arabidopsis, regulates multiple signalling pathways in plant growth and development. Despite its indispensability, detailed information on ERf-manipulated signalling pathways remains elusive. In this review, we attempt to summarize the essential roles of the ERf in plant organ morphogenesis, including shoot apical meristem, stem, and reproductive organ development.

CRY2 interacts with CIS1 to regulate thermosensory flowering via FLM alternative splicing

Cryptochromes (CRYs) are evolutionarily conserved photolyase-like photoreceptors found in almost all species, including mammals. CRYs regulate transcription by modulating the activity of several transcription factors, but whether and how they affect pre-mRNA processing are unknown. Photoperiod and temperature are closely associated seasonal cues that influence reproductive timing in plants. CRYs mediate photoperiod-responsive floral initiation, but it is largely unknown whether and how they are also involved in thermosensory flowering. We establish here that blue light and CRY2 play critical roles in thermosensory flowering in Arabidopsis thaliana by regulating RNA alternative splicing (AS) to affect protein expression and development. CRY2 INTERACTING SPLICING FACTOR 1 (CIS1) interacts with CRY2 in a blue light-dependent manner and promotes CRY2-mediated thermosensory flowering. Blue light, CRYs, and CISs affect transcriptome-wide AS profiles, including those of FLOWERING LOCUS M (FLM), which is critical for temperature modulation of flowering. Moreover, CIS1 binds to the FLM pre-mRNA to regulate its AS, while CRY2 regulates the RNA-binding activity of CIS1. Thus, blue light regulates thermosensory flowering via a CRY2-CIS1-FLM signaling pathway that links flowering responses to both light and ambient temperature.

The RNA helicase UAP56 and the E3 ubiquitin ligase COP1 coordinately regulate alternative splicing to repress photomorphogenesis in Arabidopsis

Light is a key environmental signal that regulates plant growth and development. While posttranscriptional regulatory mechanisms of gene expression include alternative splicing (AS) of pre-messenger RNA (mRNA) in both plants and animals, how light signaling affects AS in plants is largely unknown. Here, we identify DExD/H RNA helicase U2AF65-associated protein (UAP56) as a negative regulator of photomorphogenesis in Arabidopsis thaliana. UAP56 is encoded by the homologs UAP56a and UAP56b. Knockdown of UAP56 led to enhanced photomorphogenic responses and diverse developmental defects during vegetative and reproductive growth. UAP56 physically interacts with the central light signaling repressor constitutive photomorphogenic 1 (COP1) and U2AF65. Global transcriptome analysis revealed that UAP56 and COP1 co-regulate the transcription of a subset of genes. Furthermore, deep RNA-sequencing analysis showed that UAP56 and COP1 control pre-mRNA AS in both overlapping and distinct manners. Ribonucleic acid immunoprecipitation assays showed that UAP56 and COP1 bind to common small nuclear RNAs and mRNAs of downstream targets. Our study reveals that both UAP56 and COP1 function as splicing factors that coordinately regulate AS during light-regulated plant growth and development.

DEFECTIVELY ORGANIZED TRIBUTARIES 5 is not required for leaf venation patterning in Arabidopsis thaliana

The search for genetic regulators of leaf venation patterning started over 30 years ago, primarily focused on mutant screens in the eudicotyledon Arabidopsis thaliana. Developmental perturbations in either cotyledons or true leaves led to the identification of transcription factors required to elaborate the characteristic reticulated vein network. An ortholog of one of these, the C2H2 zinc finger protein DEFECTIVELY ORGANIZED TRIBUTARIES 5 (AtDOT5), was recently identified through transcriptomics as a candidate regulator of parallel venation in maize (Zea mays) leaves. To elucidate how AtDOT5 regulates vein patterning, we generated three independent loss-of-function mutations by gene editing in Arabidopsis. Surprisingly, none of them exhibited any obvious phenotypic perturbations. To reconcile our findings with earlier reports, we re-evaluated the original Atdot5-1 and Atdot5-2 alleles. By genome sequencing, we show that reported mutations at the Atdot5-1 locus are actually polymorphisms between Landsberg erecta and Columbia ecotypes, and that other mutations present in the background most likely cause the pleiotropic mutant phenotype observed. We further show that a T-DNA insertion in the Atdot5-2 locus has no impact on leaf venation patterns when segregated from other T-DNA insertions present in the original line. We thus conclude that AtDOT5 plays no role in leaf venation patterning in Arabidopsis.

Pivotal role of STIP in ovule pattern formation and female germline development in Arabidopsis thaliana

In spermatophytes the sporophytic (diploid) and the gametophytic (haploid) generations co-exist in ovules, and the coordination of their developmental programs is of pivotal importance for plant reproduction. To achieve efficient fertilization, the haploid female gametophyte and the diploid ovule structures must coordinate their development to form a functional and correctly shaped ovule. WUSCHEL-RELATED HOMEOBOX (WOX) genes encode a family of transcription factors that share important roles in a wide range of processes throughout plant development. Here, we show that STIP is required for the correct patterning and curvature of the ovule in Arabidopsis thaliana. The knockout mutant stip-2 is characterized by a radialized ovule phenotype due to severe defects in outer integument development. In addition, alteration of STIP expression affects the correct differentiation and progression of the female germline. Finally, our results reveal that STIP is required to tightly regulate the key ovule factors INNER NO OUTER, PHABULOSA and WUSCHEL, and they define a novel genetic interplay in the regulatory networks determining ovule development.

SUPPRESSOR OF PHYTOCHROME B-4 #3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days

SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3) is a member of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family of transcription factors that are involved in light-mediated growth in Arabidopsis thaliana, affecting processes such as hypocotyl elongation. The majority of the research on the AHLs has been conducted in continuous light. However, there are unique molecular events that promote growth in short days (SD) compared to constant light conditions. Therefore, we investigated how AHLs affect hypocotyl elongation in SD. Firstly, we observed that AHLs inhibit hypocotyl growth in SD, similar to their effect in constant light. Next, we identified AHL-regulated genes in SD-grown seedlings by performing RNA-seq in two sob3 mutants at different time points. Our transcriptomic data indicate that PHYTOCHROME INTERACTING FACTORS (PIFs) 4, 5, 7, and 8 along with PIF-target genes are repressed by SOB3 and/or other AHLs. We also identified PIF target genes that are repressed and have not been previously described as AHL-regulated, including PRE1, PIL1, HFR1, CDF5, and XTR7. Interestingly, our RNA-seq data also suggest that AHLs activate the expression of growth repressors to control hypocotyl elongation, such as HY5 and IAA17. Notably, many growth-regulating and other genes identified from the RNA-seq experiment were differentially regulated between these two sob3 mutants at the time points tested. Surprisingly, our ChIP-seq data suggest that SOB3 mostly binds to similar genes throughout the day. Collectively, these data suggest that AHLs affect gene expression in a time point-specific manner irrespective of changes in binding to DNA throughout SD.

The New Variation in the Promoter Region of FLOWERING LOCUS T Is Involved in Flowering in Brassica rapa

Flowering time is an important agronomic trait in Brassica rapa and has a wide range of variation. The change from vegetative to reproductive development is a major transition period, especially in flowering vegetable crops. In this study, two non-heading Chinese cabbage varieties with significantly different flowering times, Pak-choi (B. rapa var. communis Tesn et Lee) and Caitai (B. rapa var. tsaitai Hort.), were used to construct segregated F₂ populations. The bulk-segregant approach coupled with whole genome re-sequencing was used for QTL sequencing (QTL-seq) analysis to map flowering time traits. The candidate genes controlling flowering time in B. rapa were predicted by homologous gene alignment and function annotation. The major-effect QTL ft7.1 was detected on chromosome A07 of B. rapa, and the FT family gene BrFT was predicted as the candidate gene. Moreover, a new promoter regional difference of 1577 bp was revealed by analyzing the sequence of the BrFT gene. The promoter region activity analysis and divergent gene expression levels indicated that the difference in the promoter region may contribute to different flowering times. These findings provide insights into the mechanisms underlying the flowering time in Brassica and the candidate genes regulating flowering in production.

AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) proteins of ancient origin radiate new functions

AHL (AT-HOOK MOTIF NUCLEAR LOCALIZED) protein is an important transcription factor in plants that regulates a wide range of biological process. It is considered to have evolved from an independent PPC domain in prokaryotes to a complete protein in modern plants. AT-hook motif and PPC conserved domains are the main functional domains of AHL. Since the discovery of AHL, their evolution and function have been continuously studied. The AHL gene family has been identified in multiple species and the functions of several members of the gene family have been studied. Here, we summarize the evolution and structural characteristics of AHL genes, and emphasize their biological functions. This review will provide a basis for further functional study and crop breeding.

A BTB-TAZ protein is required for gene activation by Cauliflower mosaic virus 35S multimerized enhancers

The Arabidopsis (Arabidopsis thaliana) BTB-TAZ DOMAIN PROTEIN 2 (BT2) contains an N-terminal BTB domain, a central TAZ zinc-finger protein-protein interaction domain, and a C-terminal calmodulin-binding domain. We previously demonstrated that BT2 regulates telomerase activity and mediates multiple responses to nutrients, hormones, and abiotic stresses in Arabidopsis. Here, we describe the essential role of BT2 in activation of genes by multimerized Cauliflower mosaic virus 35S (35S) enhancers. Loss of BT2 function in several well-characterized 35S enhancer activation-tagged lines resulted in suppression of the activation phenotypes. Suppression of the phenotypes was associated with decreased transcript abundance of the tagged genes. Nuclear run-on assays, mRNA decay studies, and bisulfite sequencing revealed that BT2 is required to maintain the transcriptionally active state of the multimerized 35S enhancers, and lack of BT2 leads to hypermethylation of the 35S enhancers. The TAZ domain and the Ca++/calmodulin-binding domain of BT2 are critical for its function and 35S enhancer activity. We further demonstrate that BT2 requires CULLIN3 and two bromodomain-containing Global Transcription factor group E proteins (GTE9 and GTE11), to regulate 35S enhancer activity. We propose that the BT2-CULLIN3 ubiquitin ligase, through interactions with GTE9 and GTE11, regulates 35S enhancer activity in Arabidopsis.

Identification and Characterization of Transcription Factors Regulating Terpenoid Indole Alkaloid Biosynthesis in Catharanthus roseus

Biosynthesis of the therapeutically valuable terpenoid indole alkaloids (TIAs), in the medicinal plant Catharanthus roseus, is one of the most elaborate and complex metabolic processes. Although genomic and transcriptomic resources have significantly accelerated gene discovery in the TIA pathway, relatively few genes of transcription factors (TFs) have been identified and characterized thus far. Systematic identification of TFs and elucidation of their functions are crucial for understanding TIA pathway regulation. The successful discovery of TFs in the TIA pathway has relied mostly on three different approaches, (1) identification of cis-regulatory motifs (CRMs) present in the pathway gene promoters as they often provide clues on potential TFs that bind to the promoters, (2) co-expression analysis, based on the assumption that TFs regulating a metabolic or developmental pathway exhibit similar spatiotemporal expression as the pathway genes, and (3) isolation of homologs of TFs known to regulate structurally similar or diverse specialized metabolites in different plant species. TFs regulating TIA pathway have been isolated using either an individual or a combination of the three approaches. Here we describe transcriptome-based coexpression analysis and cis-element determination to identify TFs in C. roseus. In addition, we describe the protocols for generation of transgenic hairy roots, Agrobacterium infiltration of flowers, and electrophoretic mobility shift assay (EMSA). The methods described here are useful for the identification and characterization of potential TFs involved in the regulation of special metabolism in other medicinal plants.

Using Machine Learning Approaches to Predict Target Gene Expression in Rice T-DNA Insertional Mutants

To change the expression of the flanking genes by inserting T-DNA into the genome is commonly used in rice functional gene research. However, whether the expression of a gene of interest is enhanced must be validated experimentally. Consequently, to improve the efficiency of screening activated genes, we established a model to predict gene expression in T-DNA mutants through machine learning methods. We gathered experimental datasets consisting of gene expression data in T-DNA mutants and captured the PROMOTER and MIDDLE sequences for encoding. In first-layer models, support vector machine (SVM) models were constructed with nine features consisting of information about biological function and local and global sequences. Feature encoding based on the PROMOTER sequence was weighted by logistic regression. The second-layer models integrated 16 first-layer models with minimum redundancy maximum relevance (mRMR) feature selection and the LADTree algorithm, which were selected from nine feature selection methods and 65 classified methods, respectively. The accuracy of the final two-layer machine learning model, referred to as TIMgo, was 99.3% based on fivefold cross-validation, and 85.6% based on independent testing. We discovered that the information within the local sequence had a greater contribution than the global sequence with respect to classification. TIMgo had a good predictive ability for target genes within 20 kb from the 35S enhancer. Based on the analysis of significant sequences, the G-box regulatory sequence may also play an important role in the activation mechanism of the 35S enhancer.

SET DOMAIN GROUP 721 protein functions in saline-alkaline stress tolerance in the model rice variety Kitaake

To isolate the genetic locus responsible for saline-alkaline stress tolerance, we developed a high-throughput activation tagging-based T-DNA insertion mutagenesis method using the model rice (Oryza sativa L.) variety Kitaake. One of the activation-tagged insertion lines, activation tagging 7 (AC7), showed increased tolerance to saline-alkaline stress. This phenotype resulted from the overexpression of a gene that encodes a SET DOMAIN GROUP 721 protein with H3K4 methyltransferase activity. Transgenic plants overexpressing OsSDG721 showed saline-alkaline stress-tolerant phenotypes, along with increased leaf angle, advanced heading and ripening dates. By contrast, ossdg721 loss-of-function mutants showed increased sensitivity to saline-alkaline stress characterized by decreased survival rates and reduction in plant height, grain size, grain weight and leaf angle. RNA sequencing (RNA-seq) analysis of wild-type Kitaake and ossdg721 mutants indicated that OsSDG721 positively regulates the expression level of HIGH-AFFINITY POTASSIUM (K⁺ ) TRANSPORTER1;5 (OsHKT1;5), which encodes a Na⁺ -selective transporter that maintains K⁺ /Na⁺ homeostasis under salt stress. Furthermore, we showed that OsSDG721 binds to and deposits the H3K4me3 mark in the promoter and coding region of OsHKT1;5, thereby upregulating OsHKT1;5 expression under saline-alkaline stress. Overall, by generating Kitaake activation-tagging pools, we established that the H3K4 methyltransferase OsSDG721 enhances saline-alkaline stress tolerance in rice.

Activation of CDC48 and acetyltransferase encoding genes contributes to enhanced abiotic stress tolerance and improved productivity traits in rice

World-wide crop productivity is highly impacted by various extreme environmental conditions. In the present investigation, activation tagged (AT) line A10-Ds-RFP6 of rice endowed with improved agronomic attributes was tested for its tolerance ability against drought and salinity stress conditions as well as identification of genes associated with these traits. Under both drought and salinity stress conditions, A10-Ds-RFP6 line exhibited increased seed germination rates and improved plant growth characteristics at seedling, vegetative and reproductive stages as compared to wild-type (WT) plants. Moreover, A10-Ds-RFP6 revealed effective antioxidant systems resulting in decreased accumulation of reactive oxygen species and delayed stress symptoms compared to WT plants. Reduced accumulation of malondialdehyde with concomitant increase in proline and soluble sugars in A10-Ds-RFP6 line further endorse its improved stress tolerance levels. Furthermore, A10-Ds-RFP6 disclosed enhanced plant water content, photosynthetic efficiency, stomatal conductance, water use efficiency and maximum quantum yield compared to WT plants. TAIL and qRT-PCR analyses of AT rice line revealed the integration site of Ds element in the genome and increased expression levels of CDC48 and acetyltransferase genes involved in various aspects of plant development and stress tolerance. As such, the promising AT line plausibly serve as a rare genetic resource for fortifying stress tolerance and productivity traits of elite rice cultivars.

Molecular characterization and expression of cyclic nucleotide gated ion channels 19 and 20 in Arabidopsis thaliana for their potential role in salt stress

Cyclic nucleotide gated ion channels (CNGCs) in plants have very important role in signaling and development. The study reports role of CNGC19 and CNGC20 in salt stress in A. thaliana. In-silico, genome wide analysis showed that CNGC19 and CNGC20 are related to salt stress with maximum expression after 6 h in A. thaliana. The position of inserted T-DNA was determined (in-vivo) through TAIL-PCR for activation tagged mutants of CNGC19 and CNGC20 under salt stress. The expression of AtCNGC19 and AtCNGC20 after cloning under 35S promoter of expression vectors pBCH1 and pEarleyGate100 was determined in A. thaliana by real-time PCR analysis. Genome wide analysis showed that AtCNGC11 had lowest and AtCNGC20 highest molecular weight as well as number of amino acid residues. In-vivo expression of AtCNGC19 and AtCNGC20 was enhanced through T-DNA insertion and 35S promoter in over-expressed plants under high salt concentration. AtCNGC19 was activated twice in control and about five times under 150 mM NaCl stress level, and expression value was also higher than AtCNGC20. Phenotypically, over-expressed plants and calli were healthier while knock-out plants and calli showed retarded growth under salinity stress. The study provides new insight for the role of AtCNGC19 and AtCNGC20 under salt stress regulation in A. thaliana and will be helpful for improvement of crop plants for salt stress to combat food shortage and security.

Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development

Gene silencing is a negative feedback mechanism that regulates gene expression to define cell fate and also regulates metabolism and gene expression throughout the life of an organism. In plants, gene silencing occurs via transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). TGS obscures transcription via the methylation of 5' untranslated region (5'UTR), whereas PTGS causes the methylation of a coding region to result in transcript degradation. In this review, we summarized the history and molecular mechanisms of gene silencing and underlined its specific role in plant growth and crop production.

Spatial and temporal localization of SPIRRIG and WAVE/SCAR reveal roles for these proteins in actin-mediated root hair development

Root hairs are single-cell protrusions that enable roots to optimize nutrient and water acquisition. These structures attain their tubular shapes by confining growth to the cell apex, a process called tip growth. The actin cytoskeleton and endomembrane systems are essential for tip growth; however, little is known about how these cellular components coordinate their activities during this process. Here, we show that SPIRRIG (SPI), a beige and Chediak Higashi domain-containing protein involved in membrane trafficking, and BRK1 and SCAR2, subunits of the WAVE/SCAR (W/SC) actin nucleating promoting complex, display polarized localizations in Arabidopsis thaliana root hairs during distinct developmental stages. SPI accumulates at the root hair apex via post-Golgi compartments and positively regulates tip growth by maintaining tip-focused vesicle secretion and filamentous-actin integrity. BRK1 and SCAR2 on the other hand, mark the root hair initiation domain to specify the position of root hair emergence. Consistent with the localization data, tip growth was reduced in spi and the position of root hair emergence was disrupted in brk1 and scar1234. BRK1 depletion coincided with SPI accumulation as root hairs transitioned from initiation to tip growth. Taken together, our work uncovers a role for SPI in facilitating actin-dependent root hair development in Arabidopsis through pathways that might intersect with W/SC.

VipariNama: RNA viral vectors to rapidly elucidate the relationship between gene expression and phenotype

Synthetic transcription factors have great promise as tools to help elucidate relationships between gene expression and phenotype by allowing tunable alterations of gene expression without genomic alterations of the loci being studied. However, the years-long timescales, high cost, and technical skill associated with plant transformation have limited their use. In this work, we developed a technology called VipariNama (ViN) in which vectors based on the tobacco rattle virus are used to rapidly deploy Cas9-based synthetic transcription factors and reprogram gene expression in planta. We demonstrate that ViN vectors can implement activation or repression of multiple genes systemically and persistently over several weeks in Nicotiana benthamiana, Arabidopsis (Arabidopsis thaliana), and tomato (Solanum lycopersicum). By exploring strategies including RNA scaffolding, viral vector ensembles, and viral engineering, we describe how the flexibility and efficacy of regulation can be improved. We also show how this transcriptional reprogramming can create predictable changes to metabolic phenotypes, such as gibberellin biosynthesis in N. benthamiana and anthocyanin accumulation in Arabidopsis, as well as developmental phenotypes, such as plant size in N. benthamiana, Arabidopsis, and tomato. These results demonstrate how ViN vector-based reprogramming of different aspects of gibberellin signaling can be used to engineer plant size in a range of plant species in a matter of weeks. In summary, ViN accelerates the timeline for generating phenotypes from over a year to just a few weeks, providing an attractive alternative to transgenesis for synthetic transcription factor-enabled hypothesis testing and crop engineering.

Gain-of-function mutagenesis through activation tagging identifies XPB2 and SEN1 helicase genes as potential targets for drought stress tolerance in rice

XPB2 and SEN1 helicases were identified through activation tagging as potential candidate genes in rice for inducing high water-use efficiency (WUE) and maintaining sustainable yield under drought stress. As a follow-up on the high-water-use-efficiency screening and physiological analyses of the activation-tagged gain-of-function mutant lines that were developed in an indica rice variety, BPT-5204 (Moin et al. in Plant Cell Environ 39:2440-2459, 2016a, https://doi.org/10.1111/pce.12796 ), we have identified two gain-of-function mutant lines (XM3 and SM4), which evidenced the activation of two helicases, ATP-dependent DNA helicase (XPB2) and RNA helicase (SEN1), respectively. We performed the transcript profiling of XPB2 and SEN1 upon exposure to various stress conditions and found their significant upregulation, particularly in ABA and PEG treatments. Extensive morpho-physiological and biochemical analyses based on 24 metrics were performed under dehydration stress (PEG) and phytohormone (ABA) treatments for the wild-type and the two mutant lines. Principal component analysis (PCA) performed on the dataset captured 72.73% of the cumulative variance using the parameters influencing the first two principal components. The tagged mutants exhibited reduced leaf wilting, improved revival efficiency, constant amylose:amylopectin ratio, high chlorophyll and proline contents, profuse tillering, high quantum efficiency and yield-related traits with respect to their controls. These observations were further validated under greenhouse conditions by the periodic withdrawal of water at the pot level. Germination of the seeds of these mutant lines indicated their insensitivity to high ABA concentration. The associated upregulation of stress-specific genes further suggests that their drought tolerance might be because of the coordinated expression of several stress-responsive genes in these two mutants. Altogether, our results provided a firm basis for SEN1 and XPB2 as potential candidates for manipulation of drought tolerance and improving rice performance and yield under limited water conditions.

An Efficient Virus-Induced Gene Silencing System for Functional Genomics Research in Walnut (Juglans regia L.) Fruits

The Persian walnut (Juglans regia L.) is a leading source of woody oil in warm temperate regions and has high nutritional and medicinal values. It also provides both tree nuts and woody products. Nevertheless, incomplete characterization of the walnut genetic system limits the walnut gene function analysis. This study used the tobacco rattle virus (TRV) vector to construct an infectious pTRV-JrPDS recombinant clone. A co-culture inoculation method utilizing Agrobacterium was screened out from four inoculation methods and optimized to set up an efficient virus-induced gene silencing (VIGS) system for J. regia fruit. The optimized VIGS-TRV system induced complete photobleaching phenotype on the walnut fruits of four cultivars, and the JrPDS transcript levels decreased by up to 88% at 8 days post-inoculation (dpi). While those of browning-related J. regia polyphenol oxidase (PPO) genes JrPPO1 and JrPPO2 decreased by 67 and 80% at 8 dpi, respectively, accompanied by a significant reduction in fruit browning phenotype. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis screening and Western Blot showed that the PPO protein levels were significantly reduced. Moreover, a model of TRV-mediated VIGS system for inoculating J. regia fruit with efficient silence efficiency via co-culture was developed. These results indicate that the VIGS-TRV system is an efficient tool for rapid gene function analysis in J. regia fruits.

Two sides of the same story in grapevine-pathogen interactions

Proteases are an integral part of plant defence systems, and their role in plant-pathogen interactions is unequivocal. Emerging evidence suggests that different protease families contribute to the establishment not only of hypersensitive response, priming, and signalling, but also of recognition events through complex proteolytic cascades. Moreover, they play a crucial role in pathogen/microbe-associated molecular pattern (PAMP/MAMP)-triggered immunity as well as in effector-triggered immunity. However, despite important advances in our understanding of the role of proteases in plant defence, the contribution of proteases to pathogen defence in grapevine remains poorly understood. In this review, we summarize current knowledge of the main grapevine pathosystems and explore the role of serine, cysteine, and aspartic proteases from both the host and pathogen point of views.

Analysis of sticky generative cell mutants reveals that suppression of callose deposition in the generative cell is necessary for generative cell internalization and differentiation in Arabidopsis

In flowering plants, double fertilization between male and female gametophytes, which are separated by distance, largely depends on the unique pattern of the male gametophyte (pollen): two non-motile sperm cells suspended within a tube-producing vegetative cell. A morphological screen to elucidate the genetic control governing the strategic patterning of pollen has led to the isolation of a sticky generative cell (sgc) mutant that dehisces abnormal pollen with the generative cell immobilized at the pollen wall. Analyses revealed that the sgc mutation is specifically detrimental to pollen development, causing ectopic callose deposition that impedes the timely internalization and differentiation of the generative cell. We found that the SGC gene encodes the highly conserved domain of unknown function 707 (DUF707) gene that is broadly expressed but is germline specific during pollen development. Additionally, transgenic plants co-expressing fluorescently fused SGC protein and known organelle markers showed that SGC localizes in the endoplasmic reticulum, Golgi apparatus and vacuoles in pollen. A yeast two-hybrid screen with an SGC bait identified a thaumatin-like protein that we named GCTLP1, some homologs of which bind and/or digest β-1,3-glucans, the main constituent of callose. GCTLP1 is expressed in a germline-specific manner and colocalizes with SGC during pollen development, indicating that GCTLP1 is a putative SGC interactor. Collectively, our results show that SGC suppresses callose deposition in the nascent generative cell, thereby allowing the generative cell to fully internalize into the vegetative cell and correctly differentiate as the germline progenitor, with the potential involvement of the GCTLP1 protein, during pollen development in Arabidopsis.

Function of histone H2B monoubiquitination in transcriptional regulation of auxin biosynthesis in Arabidopsis

The auxin IAA is a vital plant hormone in controlling growth and development, but our knowledge about its complicated biosynthetic pathways and molecular regulation are still limited and fragmentary. cytokinin induced root waving 2 (ckrw2) was isolated as one of the auxin-deficient mutants in a large-scale forward genetic screen aiming to find more genes functioning in auxin homeostasis and/or its regulation. Here we show that CKRW2 is identical to Histone Monoubiquitination 1 (HUB1), a gene encoding an E3 ligase required for histone H2B monoubiquitination (H2Bub1) in Arabidopsis. In addition to pleiotropic defects in growth and development, loss of CKRW2/HUB1 function also led to typical auxin-deficient phenotypes in roots, which was associated with significantly lower expression levels of several functional auxin synthetic genes, namely TRP2/TSB1, WEI7/ASB1, YUC7 and AMI1. Corresponding defects in H2Bub1 were detected in the coding regions of these genes by chromatin immunoprecipitation (ChIP) analysis, indicating the involvement of H2Bub1 in regulating auxin biosynthesis. Importantly, application of exogenous cytokinin (CK) could stimulate CKRW2/HUB1 expression, providing an epigenetic avenue for CK to regulate the auxin homeostasis. Our results reveal a previously unknown mechanism for regulating auxin biosynthesis via HUB1/2-mediated H2Bub1 at the chromatin level.

Arabidopsis Carboxylesterase 20 Binds Strigolactone and Increases Branches and Tillers When Ectopically Expressed in Arabidopsis and Maize

Severe drought stress can delay maize silk emergence relative to the pollen shedding period, resulting in poor fertilization and reduced grain yield. Methods to minimize the delay in silking could thus improve yield stability. An Arabidopsis enhancer-tagged carboxylesterase 20 (AtCXE20) line was identified in a drought tolerance screen. Ectopic expression of AtCXE20 in Arabidopsis and maize resulted in phenotypes characteristic of strigolactone (SL)-deficient mutants, including increased branching and tillering, decreased plant height, delayed senescence, hyposensitivity to ethylene, and reduced flavonols. Maize silk growth was increased by AtCXE20 overexpression, and this phenotype was partially complemented by exogenous SL treatments. In drought conditions, the transgenic maize plants silked earlier than controls and had decreased anthesis-silking intervals. The purified recombinant AtCXE20 protein bound SL in vitro, as indicated by SL inhibiting AtCXE20 esterase activity and altering AtCXE20 intrinsic fluorescence. Homology modeling of the AtCXE20 three-dimensional (3D) protein structure revealed a large hydrophobic binding pocket capable of accommodating, but not hydrolyzing SLs. The AtCXE20 protein concentration in transgenic maize tissues was determined by mass spectrometry to be in the micromolar range, well-above known endogenous SL concentrations. These results best support a mechanism where ectopic expression of AtCXE20 with a strong promoter effectively lowers the concentration of free SL by sequestration. This study revealed an agriculturally important role for SL in maize silk growth and provided a new approach for altering SL levels in plants.

Development of mPing-based activation tags for crop insertional mutagenesis

Modern plant breeding increasingly relies on genomic information to guide crop improvement. Although some genes are characterized, additional tools are needed to effectively identify and characterize genes associated with crop traits. To address this need, the mPing element from rice was modified to serve as an activation tag to induce expression of nearby genes. Embedding promoter sequences in mPing resulted in a decrease in overall transposition rate; however, this effect was negated by using a hyperactive version of mPing called mmPing20. Transgenic soybean events carrying mPing-based activation tags and the appropriate transposase expression cassettes showed evidence of transposition. Expression analysis of a line that contained a heritable insertion of the mmPing20F activation tag indicated that the activation tag induced overexpression of the nearby soybean genes. This represents a significant advance in gene discovery technology as activation tags have the potential to induce more phenotypes than the original mPing element, improving the overall effectiveness of the mutagenesis system.

A Composite Analysis of Flowering Time Regulation in Lettuce

Plants undergo profound physiological changes when transitioning from vegetative to reproductive growth. These changes affect crop production, as in the case of leafy vegetables. Lettuce is one of the most valuable leafy vegetable crops in the world. Past genetic studies have identified multiple quantitative trait loci (QTLs) that affect the timing of the floral transition in lettuce. Extensive functional molecular studies in the model organism Arabidopsis provide the opportunity to transfer knowledge to lettuce to explore the mechanisms through which genetic variations translate into changes in flowering time. In this review, we integrated results from past genetic and molecular studies for flowering time in lettuce with orthology and functional inference from Arabidopsis. This summarizes the basis for all known genetic variation underlying the phenotypic diversity of flowering time in lettuce and how the genetics of flowering time in lettuce projects onto the established pathways controlling flowering time in plants. This comprehensive overview reveals patterns across experiments as well as areas in need of further study. Our review also represents a resource for developing cultivars with delayed flowering time.

Activation of ACS7 in Arabidopsis affects vascular development and demonstrates a link between ethylene synthesis and cambial activity

Ethylene is a gaseous hormone that affects many processes of plant growth and development. During vascular development, ethylene positively regulates cambial cell division in parallel with tracheary element differentiation inhibitory factor (TDIF) peptide signaling. In this study, we identified an ethylene overproducing mutant, acs7-d, exhibiting enhanced cambial activity and reduced wall development in fiber cells. Using genetic analysis, we found that ethylene signaling is necessary for the phenotypes of enhanced cambial cell division as well as defects in stem elongation and fiber cell wall development. Further, the cambial cell proliferation phenotype of acs7-d depends on WOX4, indicating that the two parallel pathways, ethylene and TDIF signaling, converge at WOX4 in regulating cambium activity. Gene expression analysis showed that ethylene impedes fiber cell wall biosynthesis through a conserved hierarchical transcriptional regulation. These results advance our understanding of the molecular mechanisms of ethylene in regulating vascular meristem activity.

Activation tagging identifies Arabidopsis transcription factor AtMYB68 for heat and drought tolerance at yield determining reproductive stages

Heat stress occurring at reproductive stages can result in significant and permanent damage to crop yields. However, previous genetic studies in understanding heat stress response and signaling were performed mostly on seedling and plants at early vegetative stages. Here we identify, using a developmentally defined, gain-of-function genetic screen with approximately 18 000 Arabidopsis thaliana activation-tagged lines, a mutant that maintained productive seed set post-severe heat stress during flowering. Genome walking indicated this phenotype was caused by the insertion of 35S enhancers adjacent to a nuclear localized transcription factor AtMYB68. Subsequent overexpression analysis confirmed that AtMYB68 was responsible for the reproductive heat tolerance of the mutant. Furthermore, these transgenic Arabidopsis plants exhibited enhanced abscisic acid sensitivity at and post-germination, reduced transpirational water loss during a drought treatment, and enhanced seed yield under combined heat and drought stress during flowering. Ectopic expression of AtMYB68 in Brassica napus driven either by 35S or by heat-inducible promoter recapitulated the enhanced reproductive heat stress and drought tolerance phenotypes observed in the transgenic Arabidopsis. The improvement to heat stress is likely due to enhanced pollen viability observed in the transgenic plants. More importantly, the transgenic canola showed significant yield advantages over the non-transgenic controls in multiple locations, multiple season field trials under various drought and heat stress conditions. Together these results suggest that AtMYB68 regulate plant stress tolerance at the most important yield determining stage of plant development, and is an effective target for crop yield protection under current global climate volatility.

The piperazine compound ASP activates an auxin response in Arabidopsis thaliana

Background

Auxins play key roles in the phytohormone network. Early auxin response genes in the AUX/IAA, SAUR, and GH3 families show functional redundancy, which makes it very difficult to study the functions of individual genes based on gene knockout analysis or transgenic technology. As an alternative, chemical genetics provides a powerful approach that can be used to address questions relating to plant hormones.

Results

By screening a small-molecule chemical library of compounds that can induce abnormal seedling and vein development, we identified and characterized a piperazine compound 1-[(4-bromophenoxy) acetyl]-4-[(4-fluorophenyl) sulfonyl] piperazine (ASP). The Arabidopsis DR5::GFP line was used to assess if the effects mentioned were correlated with the auxin response, and we accordingly verified that ASP altered the auxin-related pathway. Subsequently, we examined the regulatory roles of ASP in hypocotyl and root development, auxin distribution, and changes in gene expression. Following ASP treatment, we detected hypocotyl elongation concomitant with enhanced cell elongation. Furthermore, seedlings showed retarded primary root growth, reduced gravitropism and increased root hair development. These phenotypes were associated with an increased induction of DR5::GUS expression in the root/stem transition zone and root tips. Auxin-related mutants including tir1–1, aux1–7 and axr2–1 showed phenotypes with different root-development pattern from that of the wild type (Col-0), and were insensitive to ASP. Confocal images of propidium iodide (PI)-stained root tip cells showed no detectable damage by ASP. Furthermore, RT-qPCR analyses of two other genes, namely, Ethylene Response Factor (ERF115) and Mediator 18 (MED18), which are related to cell regeneration and damage, indicated that the ASP inhibitory effect on root growth was not attributable to toxicity. RT-qPCR analysis provided further evidence that ASP induced the expression of early auxin-response-related genes.

Conclusions

ASP altered the auxin response pathway and regulated Arabidopsis growth and development. These results provide a basis for dissecting specific molecular components involved in auxin-regulated developmental processes and offer new opportunities to discover novel molecular players involved in the auxin response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07203-8.

State-of-the-Art Technologies for Understanding Brassinosteroid Signaling Networks

Brassinosteroids, the steroid hormones of plants, control physiological and developmental processes through its signaling pathway. The major brassinosteroid signaling network components, from the receptor to transcription factors, have been identified in the past two decades. The development of biotechnologies has driven the identification of novel brassinosteroid signaling components, even revealing several crosstalks between brassinosteroid and other plant signaling pathways. Herein, we would like to summarize the identification and improvement of several representative brassinosteroid signaling components through the development of new technologies, including brassinosteroid-insensitive 1 (BRI1), BRI1-associated kinase 1 (BAK1), BR-insensitive 2 (BIN2), BRI1 kinase inhibitor 1 (BKI1), BRI1-suppressor 1 (BSU1), BR signaling kinases (BSKs), BRI1 ethyl methanesulfonate suppressor 1 (BES1), and brassinazole resistant 1 (BZR1). Furthermore, improvement of BR signaling knowledge, such as the function of BKI1, BES1 and its homologous through clustered regularly interspaced short palindromic repeats (CRISPR), the regulation of BIN2 through single-molecule methods, and the new in vivo interactors of BIN2 identified by proximity labeling are described. Among these technologies, recent advanced methods proximity labeling and single-molecule methods will be reviewed in detail to provide insights to brassinosteroid and other phytohormone signaling pathway studies.

Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)

Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R² between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.

Improving nitrogen use efficiency by manipulating nitrate remobilization in plants

Increasing nitrogen use efficiency (NUE) is critical to improve crop yield, reduce N fertilizer demand and alleviate environmental pollution. N remobilization is a key component of NUE. The nitrate transporter NRT1.7 is responsible for loading excess nitrate stored in source leaves into phloem and facilitates nitrate allocation to sink leaves. Under N starvation, the nrt1.7 mutant exhibits growth retardation, indicating that NRT1.7-mediated source-to-sink remobilization of stored nitrate is important for sustaining growth in plants. To energize NRT1.7-mediated nitrate recycling, we introduced a hyperactive chimeric nitrate transporter NC4N driven by the NRT1.7 promoter into the nrt1.7 mutant. NRT1.7p::NC4N::3' transgenic plants accumulated more nitrate in younger leaves, and ¹⁵NO₃^- tracing analysis revealed that more ¹⁵N was remobilized into sink tissues. Consistently, transgenic Arabidopsis, tobacco and rice plants showed improved growth or yield. Our study suggests that enhancing source-to-sink nitrate remobilization represents a new strategy for enhancing NUE and crop production.

Genome-Wide Investigation of 2,4-Diacetylphloroglucinol Protection Genes in Arabidopsis thaliana

The compound 2,4-diacetylphloroglucinol (DAPG) is a well-known secondary metabolite produced by Pseudomonas spp. that are used as biocontrol agents. DAPG displays a remarkably broad spectrum of toxic activity against pathogens of plants. Yet high concentrations of DAPG may also have negative effect on plants, but the phytotoxicity of DAPG is not clearly understood. Here, we used genome-wide activation, tagging Arabidopsis plants as the model plant to investigate the plant response to DAPG. A total of 15 lines were selected as DAPG-tolerant plants from among 62,000 lines investigated. The DAPG-responsible genes were then identified via thermal asymmetric interlaced PCR and quantitative reverse transcription PCR, and the gene ontology analysis showed the distribution of these genes having different biological processes, cellular regulations, and molecular functional properties. Collectively, these findings suggest that plants may rely on several pathways to prevent DAPG phytotoxicity.

Production location of the gelling agent Phytagel has a significant impact on Arabidopsis thaliana seedling phenotypic analysis

BACKGROUND

Recently, it was found that 1% Phytagel plates used to conduct Arabidopsis thaliana seedling phenotypic analysis no longer reproduced previously published results. This Phytagel, which is produced in China (Phytagel C), has replace American-made Phytagel (Phytagel), which is no longer commercially available. In this study, we present the impact of Phytagel produced in the United States vs. China on seedling phenotypic analysis. As a part of this study, an alternative gelling agent has been identified that is capable of reproducing previously published seedling morphometrics.

RESULTS

Phytagel and Phytagel C were investigated based on their ability to reproduce the subtle phenotype of the sob3-4 esc-8 double mutant. Fluence-rate-response analysis of seedlings grown on 1% Phytagel C plates failed to replicate the sob3-4 esc-8 subtle phenotype seen on 1% Phytagel. Furthermore, root penetrance analysis showed a significant difference between sob3-4 esc-8 seedlings grown on 1% Phytagel and 1% Phytagel C. It was also found that 1% Phytagel C was significantly harder than 1% Phytagel. As a replacement for Phytagel C, Gellan was tested. 1% Gellan was able to reproduce the subtle phenotype of sob3-4 esc-8. Furthermore, there was no significant difference in root penetration of the wild type or sob3-4 esc-8 seedlings between 1% Phytagel and 1% Gellan. This may be due to the significant reduction in hardness in 1% Gellan plates compared to 1% Phytagel plates. Finally, we tested additional concentrations of Gellan and found that seedlings on 0.6% Gellan looked more uniform while also being able to reproduce previously published results.

CONCLUSIONS

Phytagel has been the standard gelling agent for several studies involving the characterization of subtle seedling phenotypes. After production was moved to China, Phytagel C was no longer capable of reproducing these previously published results. An alternative gelling agent, Gellan, was able to reproduce previously published seedling phenotypes at both 1% and 0.6% concentrations. The information provided in this manuscript is beneficial to the scientific community as whole, specifically phenomics labs, as it details key problematic differences between gelling agents that should be performing identically (Phytagel and Phytagel C).

Genetic interactions among Pto-miR319 family members and their targets influence growth and wood properties in Populus tomentosa

MicroRNAs (miRNAs) play crucial roles in all aspects of plant growth and development, but the genetic interactions of miRNAs and their target genes in woody plants are largely unknown. Here, we integrated association genetics and expression profiling to decipher the allelic variations and interactions of the Pto-MIR319 family of miRNAs and 12 putative Pto-miR319 target genes related to wood formation in 435 unrelated individuals of Populus tomentosa Carrière (Chinese white poplar). Expression pattern analysis showed that among all pairings between expressions of pre-miRNA of Pto-MIR319 members and targets, 70.0% showed negative correlation of expression levels (r = - 0.944 to 0.674, P < 0.01) in eight tissues and organs of poplar, suggesting that Pto-miR319 may participate in the regulatory network of wood formation. Single SNP-based association studies identified 137 significant associations (P < 0.01, Q < 0.1), representing 126 unique SNPs from Pto-MIR319 members and their targets, with 10 tree growth traits, revealing that these genetic factors have common roles related to wood formation. Epistasis analysis uncovered 105 significant SNP-SNP associations (P < 0.01) influencing the 10 traits, demonstrating the close genetic interactions between Pto-MIR319 family members and the 12 Pto-miR319 target genes. Notably, one common SNP, in the precursor region of Pto-MIR319e, affected the stability of Pto-MIR319e's secondary structure by altering the stem-loop structure and minimum free energy, contributing to variations in the expression of Pto-MIR319e and Pto-miR319e target genes. This study enriches the understanding of the functions of miR319 family miRNAs in poplar and exemplifies a feasible approach to exploring the genetic effects underlying miRNA-mRNA interactions related to complex traits in trees.

Coordinated Transcriptional Regulation by the UV-B Photoreceptor and Multiple Transcription Factors for Plant UV-B Responses

Non-damaging ultraviolet B (UV-B) light promotes photomorphogenic development and stress acclimation through UV-B-specific signal transduction in Arabidopsis. UV-B irradiation induces monomerization and nuclear translocation of the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8). However, it is not clear how the nuclear localization of UVR8 leads to changes in global gene expression. Here, we reveal that nuclear UVR8 governs UV-B-responsive transcriptional networks in concert with several previously known transcription factors, including ELONGATED HYPOCOTYL 5 (HY5) and PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Based on the transcriptomic analysis, we identify MYB13 as a novel positive regulator in UV-B-induced cotyledon expansion and stress acclimation. MYB13 is UV-B inducible and is predominantly expressed in the cotyledons. Our results demonstrate that MYB13 protein functions as a transcription factor to regulate the expression of genes involved in auxin response and flavonoid biosynthesis through direct binding with their promoters. In addition, photoactivated UVR8 interacts with MYB13 in a UV-B-dependent manner and differentially modulates the affinity of MYB13 with its targets. Taken together, our results elucidate the cooperative function of the UV-B photoreceptor UVR8 with various transcription factors in the nucleus to orchestrate the expression of specific sets of downstream genes and, ultimately, mediate plant responses to UV-B light.

A membrane-associated NAC domain transcription factor XVP interacts with TDIF co-receptor and regulates vascular meristem activity

Vascular stem cell maintenance is regulated by a peptide signaling involving Tracheary Element Differentiation Inhibitory Factor (TDIF) and Receptor TDR/PXY (Phloem intercalated with Xylem) and co-receptor BAK1 (BRI1-associated receptor kinase1). The regulatory mechanism of this signaling pathway is largely unknown despite its importance in stem cell maintenance in the vascular meristem. We report that activation of a NAC domain transcription factor XVP leads to precocious Xylem differentiation, disruption of Vascular Patterning, and reduced cell numbers in vascular bundles. We combined molecular and genetic studies to elucidate the biological functions of XVP. XVP is expressed in the cambium, localized on the plasma membrane and forms a complex with TDIF co-receptors PXY-BAK1. Simultaneous mutation of XVP and its close homologous NAC048 enhances TDIF signaling. In addition, genetics analysis indicated that XVP promotes xylem differentiation through a known master regulator VASCULAR-RELATED NAC-DOMAIN6 (VND6). Expression analyses indicate that XVP activates CLAVATA3/ESR (CLE)-related protein 44 (CLE44), the coding gene of TDIF, whereas TDIF represses XVP expression, suggesting a feedback mechanism. Therefore, XVP functions as a negative regulator of the TDIF-PXY module and fine-tunes TDIF signaling in vascular development. These results shed new light on the mechanism of vascular stem cell maintenance.

A simple, non-toxic method for separating seeds based on density, and its application in isolating Arabidopsis thaliana seed oil mutants

PREMISE

Seed oil is an economically important trait in Brassica oilseed crops. A novel method was developed to isolate Arabidopsis thaliana seeds with altered oil content.

METHODS AND RESULTS

In A. thaliana, seed oil content is correlated with seed density, with high-oil seeds being less dense than wild type and tending to float in solution, and low-oil seeds being denser and tending to sink. In contrast to previous methods, which used toxic chemicals and density gradient centrifugation, different concentrations of calcium chloride (CaCl2) were employed to separate seeds without the need for centrifugation. The method was validated using known seed oil mutants, and 120,822 T-DNA mutagenized A. thaliana lines were then screened for novel seed density phenotypes.

CONCLUSIONS

A number of candidate mutants, as well as new alleles of two genes known to influence seed oil biosynthesis, were successfully isolated.

Inhibition of Arabidopsis thaliana CIN-like TCP transcription factors by Agrobacterium T-DNA-encoded 6B proteins

Agrobacterium T-DNA-encoded 6B proteins cause remarkable growth effects in plants. Nicotiana otophora carries two cellular T-DNAs with three slightly divergent 6b genes (TE-1-6b-L, TE-1-6b-R and TE-2-6b) originating from a natural transformation event. In Arabidopsis thaliana, expression of 2×35S:TE-2-6b, but not 2×35S:TE-1-6b-L or 2×35S:TE-1-6b-R, led to plants with crinkly leaves, which strongly resembled mutants of the miR319a/TCP module. This module is composed of MIR319A and five CIN-like TCP (TEOSINTHE BRANCHED1, CYCLOIDEA and PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTOR) genes (TCP2, TCP3, TCP4, TCP10 and TCP24) targeted by miR319a. The CIN-like TCP genes encode transcription factors and are required for cell division arrest at leaf margins during development. MIR319A overexpression causes excessive growth and crinkly leaves. TE-2-6b plants did not show increased miR319a levels, but the mRNA levels of the TCP4 target gene LOX2 were decreased, as in jaw-D plants. Co-expression of green fluorescent protein (GFP)-tagged TCPs with native or red fluorescent protein (RFP)-tagged TE-6B proteins led to an increase in TCP protein levels and formation of numerous cytoplasmic dots containing 6B and TCP proteins. Yeast double-hybrid experiments confirmed 6B/TCP binding and showed that TE-1-6B-L and TE-1-6B-R bind a smaller set of TCP proteins than TE-2-6B. A single nucleotide mutation in TE-1-6B-R enlarged its TCP-binding repertoire to that of TE-2-6B and caused a crinkly phenotype in Arabidopsis. Deletion analysis showed that TE-2-6B targets the TCP4 DNA-binding domain and directly interferes with transcriptional activation. Taken together, these results provide detailed insights into the mechanism of action of the N. otophora TE-encoded 6b genes.

MYB81, a microspore-specific GAMYB transcription factor, promotes pollen mitosis I and cell lineage formation in Arabidopsis

Sexual reproduction in flowering plants relies on the production of haploid gametophytes that consist of germline and supporting cells. During male gametophyte development, the asymmetric mitotic division of an undetermined unicellular microspore segregates these two cell lineages. To explore genetic regulation underlying this process, we screened for pollen cell patterning mutants and isolated the heterozygous myb81-1 mutant that sheds ~50% abnormal pollen. Typically, myb81-1 microspores fail to undergo pollen mitosis I (PMI) and arrest at polarized stage with a single central vacuole. Although most myb81-1 microspores degenerate without division, a small fraction divides at later stages and fails to acquire correct cell fates. The myb81-1 allele is transmitted normally through the female, but rarely through pollen. We show that myb81-1 phenotypes result from impaired function of the GAMYB transcription factor MYB81. The MYB81 promoter shows microspore-specific activity and a MYB81-RFP fusion protein is only expressed in a narrow window prior to PMI. Ectopic expression of MYB81 driven by various promoters can severely impair vegetative or reproductive development, reflecting the strict microspore-specific control of MYB81. Our data demonstrate that MYB81 has a key role in the developmental progression of microspores, enabling formation of the two male cell lineages that are essential for sexual reproduction in Arabidopsis.