BRS1 Function in Facilitating Lateral Root Emergence in Arabidopsis

Brassinosteroid biosynthesis and signaling: Conserved and diversified functions of core genes across multiple plant species

Brassinosteroids (BRs) are important regulators that control myriad aspects of plant growth and development, including biotic and abiotic stress responses, such that modulating BR homeostasis and signaling presents abundant opportunities for plant breeding and crop improvement. Enzymes and other proteins involved in the biosynthesis and signaling of BRs are well understood from molecular genetics and phenotypic analysis in Arabidopsis thaliana; however, knowledge of the molecular functions of these genes in other plant species, especially cereal crop plants, is minimal. In this manuscript, we comprehensively review functional studies of BR genes in Arabidopsis, maize, rice, Setaria, Brachypodium, and soybean to identify conserved and diversified functions across plant species and to highlight cases for which additional research is in order. We performed phylogenetic analysis of gene families involved in the biosynthesis and signaling of BRs and re-analyzed publicly available transcriptomic data. Gene trees coupled with expression data provide a valuable guide to supplement future research on BRs in these important crop species, enabling researchers to identify gene-editing targets for BR-related functional studies.

24-epibrassinolide improves cadmium tolerance and lateral root growth associated with regulating endogenous auxin and ethylene in Kentucky bluegrass

The application of phytohormones is a viable technique to increase the efficiency of phytoremediation in heavy metal-contaminated soils. The objective of this study was to determine how the application of 24-epibrassinolide (EBR), a brassinosteroid analog, could regulate root growth and tolerance to cadmium (Cd) stress in Kentucky bluegrass. As a result, the number of lateral root primordia and total root length in the Cd-treated seedlings decreased by 33.1 % and 56.5 %, respectively. After the application of EBR, Cd accumulation in roots and leaves, and the negative effect of Cd on root growth were reduced under Cd stress. Additionally, the expression of the brassinosteroid signaling gene PpBRI1 was significantly upregulated by exogenous EBR. Moreover, exogenous EBR upregulated the expression of genes encoding antioxidant enzymes and improved the activity of antioxidant enzymes, thereby reduced oxidative stress in roots. Finally, targeted hormonomics analysis highlighted the utility of the application of EBR to alleviate the effect of Cd on the reduction in auxin (IAA) content and the increase in ethylene (ACC) content. These were known to be associated with the upregulation in the expression of auxin biosynthesis gene PpYUCCA1 and downregulation in the expression of ethylene biosynthesis gene PpACO1 in the roots treated with Cd stress. Overall, the application of EBR alleviated Cd-induced oxidative stress in addition to improving root elongation and lateral root growth crosstalk with auxin and ethylene in Kentucky bluegrass subjected to Cd stress. This study further highlights the potential role of brassinosteroids in improving the efficiency of phytoremediation for Cd-contaminated soils.

The Arabidopsis TETRATRICOPEPTIDE-REPEAT THIOREDOXIN-LIKE (TTL) family members are involved in root system formation via their interaction with cytoskeleton and cell wall remodeling

Lateral roots (LR) are essential components of the plant edaphic interface; contributing to water and nutrient uptake, biotic and abiotic interactions, stress survival, and plant anchorage. We have identified the TETRATRICOPEPTIDE-REPEAT THIOREDOXIN-LIKE 3 (TTL3) gene as being related to LR emergence and later development. Loss of function of TTL3 leads to a reduced number of emerged LR due to delayed development of lateral root primordia (LRP). This trait is further enhanced in the triple mutant ttl1ttl3ttl4. TTL3 interacts with microtubules and endomembranes, and is known to participate in the brassinosteroid (BR) signaling pathway. Both ttl3 and ttl1ttl3ttl4 mutants are less sensitive to BR treatment in terms of LR formation and primary root growth. The ability of TTL3 to modulate biophysical properties of the cell wall was established under restrictive conditions of hyperosmotic stress and loss of root growth recovery, which was enhanced in ttl1ttl3ttl4. Timing and spatial distribution of TTL3 expression is consistent with its role in development of LRP before their emergence and subsequent growth of LR. TTL3 emerged as a component of the root system morphogenesis regulatory network.

The Effects of NAA on the Tuberous Root Yield and Quality of Rehmannia glutinosa and Its Regulatory Mechanism by Transcriptome and Metabolome Profiling

Naphthylacetic acid (NAA) was used to increase the tuberous root yield of Rehmannia glutinosa, but the differences between its NAA-treated and control tuberous roots (NT and CG) and the regulatory mechanism of NAA effect remain unclear. In order to investigate them, NTs and CGs were used as materials, and both yield-related indices were measured; the metabolomics and transcriptomics were used to capture differentially accumulated metabolites (DAM) and to validate them via mining differentially expressed genes (DEGs), respectively. The effects of NAA treatment: increased NT mass per plant by 21.14%, through increasing the number of roots and increasing the mean root diameter; increased catalpol content by 1.2234% (p < 0.05); up-regulated 11DAMs and 596DEGs; and down-regulated 18 DAMs and 517DEGs. In particular, we discovered that NAA regulated its DAMs and biomass via 10 common metabolic pathways, and that the number of NAA-down-regulated DAMs was more than that of NAA-up-regulated DAMs in its tuberous root. Furthermore, HPLC validated the changes of several DAMs and 15 DEGs (4CL, ARF, CCoAOMT, ARGOS, etc.) associated with the yield increase and DAMs were verified by RT-qPCR. This study provided some valuable resources, such as tuberous root indices, key genes, and DAMs of Rehmannia glutinosa in response to NAA for distinguishing the CGs from NTs, and novel insights into the regulatory mechanism of NAA effects on both at the transcriptomic and metabolomic levels, so it will lay a theoretical foundation for NAA-regulated plant yield and quality, and provide references for prohibiting the uses of NAA as a swelling agent in medicinal tuber plants in China.

BRS1 mediates plant redox regulation and cold responses

BACKGROUND

Brassinosteroid-insensitive 1 suppressor 1 (BRS1) is a serine carboxypeptidase that mediates brassinosteroid signaling and participates in multiple developmental processes in Arabidopsis. However, little is known about the precise role of BRS1 in this context.

RESULTS

In this study, we analyzed transcriptional and proteomic profiles of Arabidopsis seedlings overexpressing BRS1 and found that this gene was involved in both cold stress responses and redox regulation. Further proteomic evidence showed that BRS1 regulated cell redox by indirectly interacting with cytosolic NADP + -dependent isocitrate dehydrogenase (cICDH). One novel alternative splice form of BRS1 was identified in over-expression mutants brs1-1D, which may confer a new role in plant development and stress responses.

CONCLUSIONS

This study highlights the role of BRS1 in plant redox regulation and stress responses, which extends our understanding of extracellular serine carboxypeptidases.

Graphene oxide and indole-3-acetic acid cotreatment regulates the root growth of Brassica napus L. via multiple phytohormone pathways

BACKGROUND

Studies have indicated that graphene oxide (GO) could regulated Brassica napus L. root growth via abscisic acid (ABA) and indole-3-acetic acid (IAA). To study the mechanism and interaction between GO and IAA further, B. napus L (Zhongshuang No. 9) seedlings were treated with GO and IAA accordance with a two factor completely randomized design.

RESULTS

GO and IAA cotreatment significantly regulated the root length, number of adventitious roots, and contents of IAA, cytokinin (CTK) and ABA. Treatment with 25 mg/L GO alone or IAA (> 0.5 mg/L) inhibited root development. IAA cotreatment enhanced the inhibitory role of GO, and the inhibition was strengthened with increased in IAA concentration. GO treatments caused oxidative stress in the plants. The ABA and CTK contents decreased; however, the IAA and gibberellin (GA) contents first increased but then decreased with increasing IAA concentration when IAA was combined with GO compared with GO alone. The 9-cis-epoxycarotenoid dioxygenase (NCED) transcript level strongly increased when the plants were treated with GO. However, the NCED transcript level and ABA concentration gradually decreased with increasing IAA concentration under GO and IAA cotreatment. GO treatments decreased the transcript abundance of steroid 5-alpha-reductase (DET2) and isochorismate synthase 1 (ICS), which are associated with brassinolide (BR) and salicylic acid (SA) biosynthesis, but increased the transcript abundance of brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1), cam-binding protein 60-like G (CBP60) and calmodulin binding protein-like protein 1, which are associated with BR and SA biosynthesis. Last, GO treatment increased the transcript abundance of 1-aminocyclopropane-1-carboxylic acid synthase 2 (ACS2), which is associated with the ethylene (ETH) pathway.

CONCLUSIONS

Treatment with 25 mg/L GO or IAA (> 0.5 mg/L) inhibited root development. However, IAA and GO cotreatment enhanced the inhibitory role of GO, and this inhibition was strengthened with increased IAA concentration. IAA is a key factor in the response of B. napus L to GO and the responses of B. napus to GO and IAA cotreatment involved in multiple pathways, including those involving ABA, IAA, GA, CTK, BR, SA. Specifically, GO and IAA cotreatment affected the GA content in the modulation of B. napus root growth.

StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis

Background

Recently, a number of studies have been conducted to investigate how plants respond to stress at the cellular molecular level by measuring gene expression profiles over time. As a result, a set of time-series gene expression data for the stress response are available in databases. With the data, an integrated analysis of multiple stresses is possible, which identifies stress-responsive genes with higher specificity because considering multiple stress can capture the effect of interference between stresses. To analyze such data, a machine learning model needs to be built.

Results

In this study, we developed StressGenePred, a neural network-based machine learning method, to integrate time-series transcriptome data of multiple stress types. StressGenePred is designed to detect single stress-specific biomarker genes by using a simple feature embedding method, a twin neural network model, and Confident Multiple Choice Learning (CMCL) loss. The twin neural network model consists of a biomarker gene discovery and a stress type prediction model that share the same logical layer to reduce training complexity. The CMCL loss is used to make the twin model select biomarker genes that respond specifically to a single stress. In experiments using Arabidopsis gene expression data for four major environmental stresses, such as heat, cold, salt, and drought, StressGenePred classified the types of stress more accurately than the limma feature embedding method and the support vector machine and random forest classification methods. In addition, StressGenePred discovered known stress-related genes with higher specificity than the Fisher method.

Conclusions

StressGenePred is a machine learning method for identifying stress-related genes and predicting stress types for an integrated analysis of multiple stress time-series transcriptome data. This method can be used to other phenotype-gene associated studies.

Integration of QTL Mapping and Gene Fishing Techniques to Dissect the Multi-Main Stem Trait in Rapeseed (Brassica napus L.)

Rapeseed is one of the most important oilseed crops in the world. Improving the production of rapeseed is beneficial to relieve the shortage of edible vegetable oil. As the organ of support and transport, the main stem of rapeseed controls the plant architecture, transports the water and nutrients, and determines the number of inflorescence. Increasing the number of main stems would be helpful for the yield improvement in Brassica napus (B. napus). This attractive multi-main stem (MMS) trait was observed in the KN DH population. We investigated not only the frequency of MMS traits but also dissected the genetic basis with QTL mapping analysis and Gene-Fishing technique. A total of 43 QTLs were identified for MMS based on high-density linkage map, which explained 2.95-14.9% of the phenotypic variation, among which two environmental stable QTLs (cqMMS.A3-2 and cqMMS.C3-5) were identified in winter and semi-winter environments. Epistatic interaction analysis indicated cqMMS.C3-5 was an important loci for MMS. According to the functional annotation, 159 candidate genes within QTL confidence intervals, corresponding to 148 Arabidopsis thaliana (A. thaliana) homologous genes, were identified, which regulated lateral bud development and tiller of stem, such as shoot meristemless (STM), WUSCHEL-regulated-related genes, cytokinin response factors (CRF5), cytokinin oxidase (CKX4), gibberellin-regulated (RDK1), auxin-regulated gene (ARL, IAR4), and auxin-mediated signaling gene (STV1). Based on Gene-Fishing analysis between the natural plants and the double-main stem (DMS) plant, 31 differentially expressed genes (DEGs) were also obtained, which were related to differentiation and formation of lateral buds, biotic stimulus, defense response, drought and salt-stress responses, as well as cold-response functional genes. In addition, by combining the candidate genes in QTL regions with the DEGs that were obtained by Gene-Fishing technique, six common candidate genes (RPT2A, HLR, CRK, LRR-RLK, AGL79, and TCTP) were identified, which might probably be related to the formation of MMS phenotype. The present results not only would give a new insight into the genetic basis underlying the regulation of MMS but also would provide clues for plant architecture breeding in rapeseed.

Brassinosteroid Regulates Root Development with Highly Redundant Genes in Hexaploid Wheat

Brassinosteroid (BR) plays an important role in plant development and biotic and abiotic stress tolerance, but its specific function remains largely unknown in wheat (Triticum aestivum L.), preventing its utilization in this important crop. In this study, the function of BR and its underlying cytological role in wheat root development were comprehensively investigated. Our findings demonstrated that BR has a conserved function in regulating root length in wheat, and novel roles in regulating lateral root emergence and root diameter were uncovered. Analyses of BR homologous gene composition and evolutionary divergence demonstrated that the genetic framework of the wheat BR pathway was close to that of rice, but contained highly redundant homologous copies of genes from the subgenome A, B and D. These homologous copies showed active expression and shared a conserved BR response. The expression of wheat DWF4 and glycogen synthase kinase (GSK) genes in Arabidopsis confirmed that multiple homologous copies maintained their conserved function in regulating root development, highlighting their redundant status and indicating that a special challenge exists in wheat gene modification to deal with this high redundancy. However, our results suggested that the hypermorphic effect of T. aestivum GSK (TaGSK) genes with point mutations may be an effective approach to overcome this redundancy in the manipulation of BR signaling in wheat. Our study provides fundamental data uncovering the function of BR in wheat root development, the underlying genetic basis and a possible strategy to manipulate BR signaling in hexaploid wheat.

Characterization of bHLH/HLH genes that are involved in brassinosteroid (BR) signaling in fiber development of cotton (Gossypium hirsutum)

BACKGROUND

Basic helix-loop-helix/helix-loop-helix (bHLH/HLH) transcription factors play important roles in plant development. Many reports have suggested that bHLH/HLH proteins participate in brassinosteroid (BR) hormone signaling pathways to promote cell elongation. Cotton fibers are single-cells and derived from seed surface. To explore the roles of bHLH/HLH proteins in cotton fiber development progress by modulating BR signaling pathway, we performed a systematic analysis of the bHLH/HLH gene family in upland cotton (Gossypium hirsutum) genome.

RESULTS

In this study, we identified 437 bHLH/HLH genes in upland cotton (G. hirsutum) genome. Phylogenetic analysis revealed that GhbHLH/HLH proteins were split into twenty six clades in the tree. These GhbHLH/HLH genes are distributed unevenly in different chromosomes of cotton genome. Segmental duplication is the predominant gene duplication event and the major contributor for amplification of GhbHLH/HLH gene family. The GhbHLH/HLHs within the same group have conserved exon/intron pattern and their encoding proteins show conserved motif composition. Based on transcriptome data, we identified 77 GhbHLH/HLH candidates that are expressed at relatively high levels in cotton fibers. As adding exogenous BR (brassinolide, BL) or brassinazole (Brz, a BR biosynthesis inhibitor), expressions of these GhbHLH/HLH genes were up-regulated or down-regulated in cotton fibers. Furthermore, overexpression of GhbHLH282 (one of the BR-response genes) in Arabidopsis not only promoted the plant growth, but also changed plant response to BR signaling.

CONCLUSION

Collectively, these data suggested that these GhbHLH/HLH genes may participate in BR signaling transduction during cotton fiber development. Thus, our results may provide a valuable reference data as the basis for further studying the roles of these bHLH/HLH genes in cotton fiber development.