AtMYB50 regulates root cell elongation by upregulating PECTIN METHYLESTERASE INHIBITOR 8 in Arabidopsis thaliana.

Plant root development involves multiple signal transduction pathways. Notably, phytohormones like auxin and cytokinin are well characterized for their molecular mechanisms of action. Reactive oxygen species (ROS) serve as crucial signaling molecules in controlling root development. The transcription factor, UPBEAT1 (UPB1) is responsible for maintaining ROS homeostasis at the root tip, influencing the transition from cell proliferation to differentiation. While UPB1 directly regulates peroxidase expression to control ROS homeostasis, it targets genes other than peroxidases, suggesting its involvement in root growth through non-ROS signals. Our investigation focused on the transcription factor MYB50, a direct target of UPB1, in Arabidopsis thaliana. By analyzing multiple fluorescent proteins and conducting RNA-seq and ChIP-seq, we unraveled a step in the MYB50 regulatory gene network. This analysis, in conjunction with the UPB1 regulatory network, demonstrated that MYB50 directly regulates the expression of PECTIN METHYLESTERASE INHIBITOR 8 (PMEI8). Overexpressing PMEI8, similar to the MYB50, resulted in reduced mature cell length. These findings establish MYB50 as a regulator of root growth within the UPB1 gene regulatory network. Our study presents a model involving transcriptional regulation by MYB50 in the UPB1 regulated root growth system and sheds light on cell elongation via pectin modification.

A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis.

Lateral roots (LRs) are critical to root system architecture development in plants. Although the molecular mechanisms by which auxin regulates LR development have been extensively studied, several additional regulatory systems are hypothesized to be involved. Recently, the regulatory role of very long chain fatty acids (VLCFAs) has been shown in LR development. Our analysis showed that LTPG1 and LTPG2, transporters of VLCFAs, are specifically expressed in the developing LR primordium (LRP), while the number of LRs is reduced in the ltpg1/ltpg2 double mutant. Moreover, late LRP development was hindered when the VLCFA levels were reduced by the VLCFA synthesis enzyme mutant, kcs1-5. However, the details of the regulatory mechanisms of LR development controlled by VLCFAs remain unknown. In this study, we propose a novel method to analyze the LRP development stages with high temporal resolution using a deep neural network and identify a VLCFA-responsive transcription factor, MYB93, via transcriptome analysis of kcs1-5. MYB93 showed a carbon chain length-specific expression response following treatment of VLCFAs. Furthermore, myb93 transcriptome analysis suggested that MYB93 regulated the expression of cell wall organization genes. In addition, we also found that LTPG1 and LTPG2 are involved in LR development through the formation of root cap cuticle, which is different from transcriptional regulation by VLCFAs. Our results suggest that VLCFA is a regulator of LRP development through transcription factor-mediated regulation of gene expression and the transportation of VLCFAs is also involved in LR development through root cap cuticle formation.

Root system architecture analysis in Mesembryanthemum crystallinum (ice plant) seedlings reveals characteristic root halotropic response.

One of the major environmental stress factors that affect root growth is salinity. Arabidopsis thaliana, a glycophyte, shows halotropism, whereby it alters the direction of root growth in a non-gravitropic pattern to evade high soil salinity. Asymmetric auxin distribution regulated by the relocation of auxin-efflux carrier proteins is a key cellular event in the halotropic response. However, there are no reports of halotropism in halophytes. Here, we investigated root growth traits in Mesembryanthemum crystallinum (ice plant), under high salinity conditions. We hypothesized that ice plant roots would show halotropic responses different from those of Arabidopsis Notably, similar to halotropism observed in Arabidopsis, ice plant roots showed continuous root bending under salinity stress. However, the root elongation rate did not change in ice plants. Expression analyses of several genes revealed that auxin transport might be partially involved in ice plant halotropism. This study enhances our understanding of halophyte root adaptation to high salinity stress.

Rapid and easy method for in vitro determination of transcription factor binding core motifs.

We introduce a rapid method for easily elucidating transcription factor (TF) cis-elements by adopting a highly efficient in vitro protein synthesis method and identifying protein-DNA interactions using PCR. We determined two cis-elements for plant TFs using this method, and the results confirmed our method as an easy and time-saving alternative for elucidating TF cis-elements using common laboratory procedures.

ANAC032 regulates root growth through the MYB30 gene regulatory network.

Reactive oxygen species (ROS) play important roles as root growth regulators. We previously reported a comprehensive transcriptomic atlas, which we named ROS-map, that revealed ROS-responsible genes in Arabidopsis root tips. By using ROS-map, we have characterised an early ROS response key transcription factor, MYB30, as a regulator of root cell elongation under ROS signals. However, there are other ROS-responsible transcription factors which have the potential to regulate root growth. In the present study, we characterised the function of another early ROS-responsible transcription factor, ANAC032, that was selected from ROS-map. Overexpression of ANAC032 fused with the transcriptional activation domain, VP16, inhibited root growth, especially decreasing cell elongation. By transcriptome analysis, we revealed that ANAC032 regulated many stress-responsible genes in the roots. Intriguingly, ANAC032 upregulated MYB30 and its target genes. The upregulation of MYB30 target genes was completely abolished in the ANAC032-VP16x2 OX and ANAC032 estradiol-inducible line in myb30-2 mutants. Moreover, root growth inhibition was alleviated in ANAC032-OX in myb30-2 mutants. Overall, we characterised an upstream transcription factor, ANAC032, of the MYB30 transcriptional cascade which is a key regulator for root cell elongation under ROS signalling.

MYB30 regulates root cell elongation under abscisic acid signaling.

Reactive oxygen species (ROS) and plant hormones play important roles in regulating plant growth and stress responses as signaling molecules. Abscisic acid (ABA) is known as the key regulator of both abiotic and biotic stress responses. During stress responses, ABA is known to regulate ROS production, indicating that important crosstalk occurs between ROS and ABA signaling. We recently reported that MYB30, an MYB-type transcription factor, regulates root cell elongation under ROS signaling. In this study, we analyzed the molecular interaction between ROS and ABA signal during for root development, which is mediated through MYB30 transcriptional regulation. We showed that MYB30-regulated root cell elongation was mediated by ROS production under ABA signaling. Our findings will provide one piece of evidence of the complex cross talk between ROS and hormone signaling that regulates root development.

MYB30 links ROS signaling, root cell elongation, and plant immune responses.

Reactive oxygen species (ROS) are known to be important signal molecules that are involved in biotic and abiotic stress responses as well as in growth regulation. However, the molecular mechanisms by which ROS act as a growth regulator, as well as how ROS-dependent growth regulation relates to its roles in stress responses, are not well understood. We performed a time-course microarray analysis of Arabidopsis root tips upon treatment with hydrogen peroxide, which we named "ROS-map." Using the ROS-map, we identified an MYB transcription factor, MYB30, which showed a strong response to ROS treatment and is the key regulator of a gene network that leads to the hydrogen peroxide-dependent inhibition of root cell elongation. Intriguingly, this network contained multiple genes involved in very-long-chain fatty acid (VLCFA) transport. Finally, we showed that MYB30 is necessary for root growth regulation during defense responses, thus providing a molecular link between these two ROS-associated processes.

Ectopic expression of Mesembryanthemum crystallinum sodium transporter McHKT2 provides salt stress tolerance in Arabidopsis thaliana.

Most plants do not tolerate highly saline environments; the development of salt stress tolerance is crucial for improving crop yield. An efficient way of finding genes involved in salt tolerance is to study and use data from halophytes. In this study, we used the Mesembryanthemum crystallinum (ice plant) expression data-set and selected for further study the gene McHKT2, which encodes for the Arabidopsis sodium transporter ortholog AtHKT1. In comparison with the HKT1 amino acid sequences from other plants, McHKT2 has several unique features. It seems to be localized to the plasma membrane, and its overexpression confers strong salt tolerance in Arabidopsis thaliana. Our results indicate that McHKT2 is a suitable candidate protein that can induce salt tolerance in non-halophytes. Like McHKT2, using transcriptome data-sets from halophytes such as ice plant give us an efficiency way to obtain new gene resources that might involve in plant salt tolerance.

A link among DNA replication, recombination, and gene expression revealed by genetic and genomic analysis of TEBICHI gene of Arabidopsis thaliana.

Spatio-temporal regulation of gene expression during development depends on many factors. Mutations in Arabidopsis thaliana TEBICHI (TEB) gene encoding putative helicase and DNA polymerase domains-containing protein result in defects in meristem maintenance and correct organ formation, as well as constitutive DNA damage response and a defect in cell cycle progression; but the molecular link between these phenotypes of teb mutants is unknown. Here, we show that mutations in the DNA replication checkpoint pathway gene, ATR, but not in ATM gene, enhance developmental phenotypes of teb mutants, although atr suppresses cell cycle defect of teb mutants. Developmental phenotypes of teb mutants are also enhanced by mutations in RAD51D and XRCC2 gene, which are involved in homologous recombination. teb and teb atr double mutants exhibit defects in adaxial-abaxial polarity of leaves, which is caused in part by the upregulation of ETTIN (ETT)/AUXIN RESPONSIVE FACTOR 3 (ARF3) and ARF4 genes. The Helitron transposon in the upstream of ETT/ARF3 gene is likely to be involved in the upregulation of ETT/ARF3 in teb. Microarray analysis indicated that teb and teb atr causes preferential upregulation of genes nearby the Helitron transposons. Furthermore, interestingly, duplicated genes, especially tandemly arrayed homologous genes, are highly upregulated in teb or teb atr. We conclude that TEB is required for normal progression of DNA replication and for correct expression of genes during development. Interplay between these two functions and possible mechanism leading to altered expression of specific genes will be discussed.

Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings.

During development of plant seeds, embryos import nutrients and store massive amounts of reserves. Seed reserves are rapidly degraded and mobilized to support seedling development after germination. HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE 2 (HSI2) of Arabidopsis thaliana is a B3 DNA-binding domain protein that represses the transcription of sugar-inducible reporter gene. Although disruption of HSI2 or HSI2-Like 1 (HSL1) did not affect growth, seeds with disruption of both HSI2 and HSL1 (KK mutant) developed abortive seedlings that stopped growing 7-9 days after imbibition. KK seedlings developed swollen hypocotyls that accumulated seed storage proteins and oil on medium containing sucrose or other metabolizable sugars, and calluses developed from KK seedlings also accumulated seed storage reserves. The expression of seed maturation genes, which include LEAFY COTYLEDON-type master regulators, in KK seedlings depended on the concentration of sucrose, suggesting that sugar controls the expression of seed maturation genes. Our results suggest that HSI2 and HSL1 repress the sugar-inducible expression of the seed maturation program in seedlings and play an essential role in regulating the transition from seed maturation to seedling growth.

Arabidopsis TEBICHI, with helicase and DNA polymerase domains, is required for regulated cell division and differentiation in meristems.

In plant meristems, each cell divides and differentiates in a spatially and temporally regulated manner, and continuous organogenesis occurs using cells derived from the meristem. We report the identification of the Arabidopsis thaliana TEBICHI (TEB) gene, which is required for regulated cell division and differentiation in meristems. The teb mutants show morphological defects, such as short roots, serrated leaves, and fasciation, as well as defective patterns of cell division and differentiation in the meristem. The TEB gene encodes a homolog of Drosophila MUS308 and mammalian DNA polymerase theta, which prevent spontaneous or DNA damage-induced production of DNA double strand breaks. As expected from the function of animal homologs, teb mutants show constitutively activated DNA damage responses. Unlike other fasciation mutants with activated DNA damage responses, however, teb mutants do not activate transcriptionally silenced genes. teb shows an accumulation of cells expressing cyclinB1;1:GUS in meristems, suggesting that constitutively activated DNA damage responses in teb lead to a defect in G2/M cell cycle progression. Furthermore, other fasciation mutants, such as fasciata2 and tonsoku/mgoun3/brushy1, also show an accumulation of cells expressing cyclinB1;1:GUS in meristems. These results suggest that cell cycle progression at G2/M is important for the regulation of the pattern of cell division and of differentiation during plant development.

Activation tagging of a gene for a protein with novel class of CCT-domain activates expression of a subset of sugar-inducible genes in Arabidopsis thaliana.

In the current studies, we examined sugar-inducible gene expression using the Arabidopsis thaliana line sGsL, which carries luciferase (LUC) and beta-glucuronidase (GUS) reporter genes under the control of a 210-bp promoter derived from the sweet potato sporamin gene (Spo(min)). We isolated an enhancer activation-tagged mutant of this line that showed high-level expression of LUC and GUS under non-inducing low-sugar conditions. The Activator ofSpo(min)::LUC2 (ASML2) gene located close to the enhancer encodes a protein belonging to a previously uncharacterized class of CCT (CONSTANS, CONSTANS-like, TOC1) domain proteins. Overexpression of ASML2 cDNA in the sGsL line resulted in enhanced expression of not only LUC and GUS reporters but also several endogenous sugar-inducible genes, including Atbeta-Amy, ApL3, and VSP2. Transient co-expression of 35S::ASML2 with the Spo(min)::LUC or Atbeta-Amy::LUC reporter in protoplasts resulted in an approximately 2.4 or 5.6-fold transactivation of LUC expression, respectively. Expression of ASML2 was high in reproductive organs, and expression in seedlings was slightly enhanced by sugars, but not by abscisic acid. These results suggest that ASML2 functions as a transcriptional activator and regulates the expression of at least a subset of sugar-inducible genes.

An Arabidopsis protein with a novel calcium-binding repeat sequence interacts with TONSOKU/MGOUN3/BRUSHY1 involved in meristem maintenance.

TONSOKU(TSK)/MGOUN3/BRUSHY1 from Arabidopsis thaliana, which plays an important role in the maintenance of meristem organization, contains an LGN repeat motif similar to that found in animal proteins involved in asymmetric cell division. One protein that interacts with the LGN motif of TSK in a yeast two-hybrid screen, TSK-associating protein 1 (TSA1), contains a 10-fold repeat of a unique 41 amino acid sequence. The repeat sequence, with a glutamic acid-phenylalanine-glutamic acid (EFE) conserved core sequence, is enriched with acidic amino acids. TSA1 also contains an N-terminal putative signal peptide and it interacts with the LGN motif of TSK through a C-terminal region separated from the EFE repeats by a putative membrane-spanning region. The recombinant protein consisting of EFE repeats was rich in alpha-helical structure and possessed Ca2+-binding activity. Unlike nuclear localization of TSK, the TSA1 fused with green fluorescent protein (GFP) expressed in tobacco BY-2 cells was localized in small cytoplasmic vesicles during interphase. However, cellular localization of both TSA1-GFP and GFP-TSK changed dynamically during mitosis. In particular, both GFP-TSK and TSA1-GFP were concentrated in limited areas that are close to the ends of spindle microtubules ahead of separating chromatids. These results are discussed in terms of the possible involvement of TSK and TSA1 in mitosis.

Analysis of a sugar response mutant of Arabidopsis identified a novel B3 domain protein that functions as an active transcriptional repressor.

A recessive mutation hsi2 of Arabidopsis (Arabidopsis thaliana) expressing luciferase (LUC) under control of a short promoter derived from a sweet potato (Ipomoea batatas) sporamin gene (Spo(min)LUC) caused enhanced LUC expression under both low- and high-sugar conditions, which was not due to increased level of abscisic acid. The hsi2 mutant contained a nonsense mutation in a gene encoding a protein with B3 DNA-binding domain. HSI2 and two other Arabidopsis proteins appear to constitute a novel subfamily of B3 domain proteins distinct from ABI3, FUS3, and LEC2, which are transcription activators involved in seed development. The C-terminal part of HSI2 subfamily proteins contained a sequence similar to the ERF-associated amphiphilic repression (EAR) motif. Deletion of the C-terminal portion of HSI2 lost in the hsi2 mutant caused reduced nuclear targeting of HSI2. Null allele of HSI2 showed even higher Spo(min)LUC expression than the hsi2 mutant, whereas overexpression of HSI2 reduced the LUC expression. Transient coexpression of 35SHSI2 with Spo(min)LUC in protoplasts repressed the expression of LUC activity, and deletion or mutation of the EAR motif significantly reduced the repression activity of HSI2. These results indicate that HSI2 and related proteins are B3 domain-EAR motif active transcription repressors.

ACTIVATOR of Spomin::LUC1/WRINKLED1 of Arabidopsis thaliana transactivates sugar-inducible promoters.

We isolated an enhancer activation-tagged mutant of Arabidopsis thaliana line sGsL carrying the luciferase (LUC) gene under control of a short sugar-inducible promoter derived from a sweet potato sporamin gene (Spomin) that showed high level expression of LUC under non-inducing conditions. The activator of Spomin::LUC1 (ASML1) gene located downstream of the enhancer encoded an APETALA2 (AP2)-type AP2 domain protein, and this gene was shown recently to be responsible for the wrinkled1 mutation which causes defective accumulation of seed storage oil. Overexpression of ASML1 cDNA in sGsL plants resulted in enhanced expression of not only the LUC reporter but also endogenous sugar-inducible genes including Atbeta-Amy encoding beta-amylase. Transient co-expression of 35S::ASML1 with Spomin::LUC or Atbeta-Amy::LUC reporters in protoplasts resulted in an approximately 10-fold transactivation of LUC expression. This transactivation was lost when the C-terminal acidic region of ASML1 was deleted. Expression of ASML1 was high in reproductive organs, and ASML1 mRNA showed transient accumulation in leaves after treatment with 6% sucrose, whereas it did not respond to abscisic acid. These results suggest that ASML1/WRI1 is a transcriptional activator involved in the activation of a subset of sugar-responsive genes and the control of carbon flow from sucrose import to oil accumulation in developing seeds.

TONSOKU is expressed in S phase of the cell cycle and its defect delays cell cycle progression in Arabidopsis.

TONSOKU(TSK)/MGOUN3/BRUSHY1 of Arabidopsis thaliana encodes a nuclear leucine-glycine-aspargine (LGN) domain protein implicated to be involved in genome maintenance, and mutants with defects in TSK show a fasciated stem with disorganized meristem structures. We identified a homolog of TSK from tobacco BY-2 cells (NtTSK), which showed high sequence conservation both in the LGN domain and in leucine-rich repeats with AtTSK. The NtTSK gene was expressed during S phase of the cell cycle in tobacco BY-2 cells highly synchronized for cell division. The tsk mutants of Arabidopsis contained an increased proportion of cells with 4C nuclei and cells expressing cyclin B1 compared with the wild type. These results suggest that TSK is required during the cell cycle and defects of TSK cause the arrest of cell cycle progression at G2/M phase.

Two cis-acting regulatory elements are involved in the sucrose-inducible expression of the sporamin gene promoter from sweet potato in transgenic tobacco.

In this study, we generated transgenic tobacco plants that express the beta-glucuronidase (GUS) gene under the control of the 305-bp 5'-upstream region of a gene coding for sporamin A of sweet potato. Expression of GUS in excised tobacco leaves was induced by sucrose, mimicking the sugar-inducible expression of the endogenous sporamin genes in sweet potato. Deletion of the sequences extending from position -305 (relative to the transcription start site) to -283 and from -146 to -87 resulted in an approximately 40-fold enhancement in GUS reporter expression. Furthermore, the sequence from -282 to -165 conferred sucrose-inducibility on the -89 core promoter of the Cauliflower Mosaic Virus 35S RNA gene. Analysis of internal deletions, linker scanning and the introduction of base substitutions in the sequence between positions -282 and -165 indicated that sucrose-responsiveness conferred by this region was dependent on the presence of two cis-acting elements, termed CMSREs (carbohydrate metabolite signal responsive elements) 1 and 2, which are separated by a spacer. A sequence similar or identical to the core of CMSRE-1 (TGGACGG) is also present in the promoters of several other sugar-inducible genes, and sequences encopassing the TGGACGG-related motifs from two of these could functionally replace the CMSRE-1 in the truncated sporamin A promoter. These results suggest that the TGGACGG element plays an important role in the sucrose-inducible expression of a group of plant genes.

A novel Arabidopsis gene TONSOKU is required for proper cell arrangement in root and shoot apical meristems.

Root apical meristem (RAM) and shoot apical meristem (SAM) are vital for the correct development of the plant. The direction, frequency, and timing of cell division must be tightly controlled in meristems. Here, we isolated new Arabidopsis mutants with shorter roots and fasciated stems. In the tonsoku (tsk) mutant, disorganized RAM and SAM formation resulted from the frequent loss of proper alignment of the cell division plane. Irregular cell division also occurred in the tsk embryo, and the size of cells in meristems and embryo in tsk mutant was larger than in the wild type. In the enlarged SAM of the tsk mutant, multiple centers of cells expressing WUSCHEL (WUS) were observed. In addition, expression of SCARECROW (SCR) in the quiescent center (QC) disappeared in the disorganized RAM of tsk mutant. These results suggest that disorganized cell arrangements in the tsk mutants result in disturbed positional information required for the determination of cell identity. The TSK gene was found to encode a protein with 1311 amino acids that possesses two types of protein-protein interaction motif, leucine-glycine-asparagine (LGN) repeats and leucine-rich repeats (LRRs). LGN repeats are present in animal proteins involved in asymmetric cell division, suggesting the possible involvement of TSK in cytokinesis. On the other hand, the localization of the TSK-GFP (green fluorescent protein) fusion protein in nuclei of tobacco BY-2 cells and phenotypic similarity of tsk mutants to other fasciated mutants suggest that the tsk mutation may cause disorganized cell arrangements through defects in genome maintenance.

The SCARECROW gene's role in asymmetric cell divisions in rice plants.

Asymmetric cell division is one of the most important mechanisms in the diversification of cell function and fate. In Arabidopsis, SCARECROW (SCR) is essential for the asymmetric division of the cortex/endodermis progenitor cell in the root. To learn more about how SCR is involved in asymmetric division, we analyzed the rice SCR (OsSCR) expression. In the root tip, OsSCR expression was observed in the endodermal cell layer and downregulated in the daughter cortex cell after asymmetric division, just as with Arabidopsis SCR. In leaf primordia, expression of OsSCR was observed in stomatal and ligule formation. In stomatal development, OsSCR was specifically expressed in the stomatal cell files before formation of guard mother cells (GMCs), and then, its expression was localized in GMCs, when the first asymmetric division occurred to generate the GMCs. Before the second asymmetric division of subsidiary mother cells (SMCs), localized OsSCR expression was observed in SMCs in the area close to the GMCs. Before these asymmetric divisions, the localization of OsSCR mRNA in GMC-forming cells and SMCs was observed in the area of the daughter GMC and subsidiary cells. OsSCR expression was also observed in the initiation area of ligule formation, and its downregulation occurred in the inner L2 cells generated by asymmetric division. Based on these observations, we proposed that OsSCR is involved not only in the asymmetric division of the cortex/endodermis progenitor cell but also during stomata and ligule formation by establishing the polarization of cytoplasm.

Isolation and characterization of a rice WUSCHEL-type homeobox gene that is specifically expressed in the central cells of a quiescent center in the root apical meristem.

The Arabidopsis WUSCHEL (WUS) protein, which plays an important role in the specification of the stem cells in the shoot apical meristem (SAM), contains an 'atypical' homeodomain (HD) with extra residues in its loop and turn regions. We speculated that a WUS-type atypical HD protein might also be involved in the specification and maintenance of the root apical meristem (RAM) stem cells of rice. To investigate this possibility, we isolated and characterized a rice WUS-type homeobox gene designated quiescent-center-specific homeobox (QHB) gene. Using transformants carrying the QHB promoter-GUS and in situ hybridization, we found that QHB was specifically expressed in the central cells of a quiescent center (QC) of the root. During embryogenesis and crown root formation, QHB expression was observed prior to the morphological differentiation of the root. However, we detected different QHB expression patterns in the process of the RAM development, specifically between radicle and crown root formation, suggesting that the cell-fate determination of the QC may be controlled by different mechanisms. We also produced transformants that overexpress QHB or Arabidopsis WUS. These transformants did not form crown roots, but developed multiple shoots from ectopic SAMs with malformed leaves. On the basis of these observations, we propose that the WUS-type homeobox gene is involved in the specification and maintenance of the stem cells (QC cells) in the RAM, by a mechanism similar to that for WUS in the SAM.