Genome Identification and Expression Analysis of GRAS Family Related to Development, Hormone and Pathogen Stress in Brachypodium distachyon

GRAS transcription factors are widely present in the plant kingdom and play important roles in regulating multiple plant physiological processes. Brachypodium distachyon is a model for grasses for researching plant-pathogen interactions. However, little is known about the BdGRAS family genes involved in plant response to biotic stress. In this study, we identified 63 genes of the GRAS family in B. distachyon. The phylogenetic analysis showed that BdGRAS genes were divided into ten subfamilies and unevenly distributed on five chromosomes. qRT-PCR results showed that the BdGRAS family genes were involved in the growth and development of B. distachyon. Moreover, the expression of the HAM subfamily genes of BdGRAS changed during the interaction between B. distachyon and Magnaporthe oryzae. Interestingly, BdGRAS31 in the HAM subfamily was regulated by miR171 after inoculation with M. oryzae. These results provide insight into the potential functions of the BdGRAS family in disease resistance.

PpGRAS12 acts as a positive regulator of meristem formation in Physcomitrium patens

Key message This study focused on the key regulatory function of Physcomitrium patens GRAS12 gene underlying an increasing plant complexity, an important step in plant terrestrialization and the evolutionary history of life. Abstract The miR171‐GRAS module has been identified as a key player in meristem maintenance in angiosperms. PpGRAS12 is a member of the GRAS family and a validated target for miR171 in Physcomitrium (Physcomitrella) patens. Here we show a regulatory function of miR171 at the gametophytic vegetative growth stage and targeted deletion of the PpGRAS12 gene adversely affects sporophyte production since fewer sporophytes were produced in ΔPpGRAS12 knockout lines compared to wild type moss. Furthermore, highly specific and distinct growth arrests were observed in inducible PpGRAS12 overexpression lines at the protonema stage. Prominent phenotypic aberrations including the formation of multiple apical meristems at the gametophytic vegetative stage in response to elevated PpGRAS12 transcript levels were discovered via scanning electron microscopy. The production of multiple buds in the PpGRAS12 overexpression lines similar to ΔPpCLV1a/1b disruption mutants is accompanied by an upregulation of PpCLE and downregulation of PpCLV1, PpAPB, PpNOG1, PpDEK1, PpRPK2 suggesting that PpGRAS12 acts upstream of these genes and negatively regulates the proposed pathway to specify simplex meristem formation. As CLV signaling pathway components are not present in the chlorophytic or charophytic algae and arose with the earliest land plants, we identified a key regulatory function of PpGRAS12 underlying an increasing plant complexity, an important step in plant terrestrialization and the evolutionary history of life.

Gene Regulation via the Combination of Transcription Factors in the INDETERMINATE DOMAIN and GRAS Families

INDETERMINATE DOMAIN (IDD) family proteins are plant-specific transcription factors. Some Arabidopsis IDD (AtIDD) proteins regulate the expression of SCARECROW (SCR) by interacting with GRAS family transcription factors SHORT-ROOT (SHR) and SCR, which are involved in root tissue formation. Some AtIDD proteins regulate genes involved in the synthesis (GA3ox1) or signaling (SCL3) of gibberellic acid (GA) by interacting with DELLA proteins, a subfamily of the GRAS family. We analyzed the DNA binding properties and protein–protein interactions of select AtIDD proteins. We also investigated the transcriptional activity of the combination of AtIDD and GRAS proteins (AtIDD proteins combined with SHR and SCR or with REPRESSOR of ga1-3 (RGA)) on the promoters of SCR, SCL3, and GA3ox1 by conducting a transient assay using Arabidopsis culture cells. Our results showed that the SCR promoter could be activated by the IDD and RGA complexes and that the SCL3 and GA3ox1 promoters could be activated by the IDD, SHR, and SCR complexes, indicating the possibility that these complexes regulate and consequently coordinate the expression of genes involved in GA synthesis (GA3ox1), GA signaling (SCL3), and root formation (SCR).

Genome-Wide Characterization of GRAS Family and Their Potential Roles in Cold Tolerance of Cucumber (Cucumis sativus L.)

Cucumber (Cucumis sativus L.) is one of the most important cucurbit vegetables but is often subjected to stress during cultivation. GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) genes encode a family of transcriptional factors that regulate plant growth and development. In the model plant Arabidopsis thaliana, GRAS family genes function in formation of axillary meristem and root radial structure, phytohormone (gibberellin) signal transduction, light signal transduction and abiotic/biological stress. In this study, a gene family was comprehensively analyzed from the aspects of evolutionary tree, gene structure, chromosome location, evolutionary and expression pattern by means of bioinformatics; 37 GRAS gene family members have been screened from cucumber. We reconstructed an evolutionary tree based on multiple sequence alignment of the typical GRAS domain and conserved motif sequences with those of other species (A. thaliana and Solanum lycopersicum). Cucumber GRAS family was divided into 10 groups according to the classification of Arabidopsis and tomato genes. We conclude that tandem and segmental duplication have played important roles in the expansion and evolution of the cucumber GRAS (CsaGRAS) family. Expression patterns of CsaGRAS genes in different tissues and under cold treatment, combined with gene ontology annotation and interaction network analysis, revealed potentially different functions for CsaGRAS genes in response to cold tolerance, with members of the SHR, SCR and DELLA subfamilies likely playing important roles. In conclusion, this study provides valuable information and candidate genes for improving cucumber tolerance to cold stress.

CHARACTERISTICS OF miRNA INTERACTION WITH mRNA GENES OF T. AESTIVUM C2H2, ERF, GRAS TRANSCRIPTION FACTORS FAMILIES

The molecular mechanisms for increasing plant productivity remain poorly understood. Genes of C2H2, GRAS, ERF transcription factors (TFs) families play a key role in the physiological processes of plants, including wheat. In recent years, the important role of miRNAs in the regulation of the expression of many genes involved in the formation of productivity has been established. Wheat miRNA (mRNA-inhibiting RNA) target genes are involved in the regulation of the development of flowers, seeds, root, shoots, and responses to abiotic and biotic stresses. The miRNAs binding sites in mRNAs of C2H2, ERF, GRAS TFs families were performed using the MirTarget program, which calculates the free energy of miRNA binding with mRNA, the schemes and positions of nucleotide interactions with binding sites. Wheat genes were used as the object of the study, since wheat is one of the main grain crops in Kazakhstan and in many other countries. The presence of miRNA binding sites with high nucleotide complementarity in mRNA of C2H2, ERF, GRAS TF genes of wheat was shown. All binding sites of these miRNAs were located in the CDS of mRNA target genes. Of the 125 miRNAs of T. aestivum, miR319-3p efficiently bound with mRNA of C2H2 family genes with the value of ΔG/ΔGm equal 91 %. miR7757-5p interacted with mRNA of ERF and GRAS family genes with the value of ΔG/ΔGm equal to 92 % and 90 % respectively. miR9778-5p bound with mRNA of C2H2, ERF, GRAS family genes to varying degrees. Each of the miR408-3p, miR9780-3p, and miR9778-5p had four target genes with the value of ΔG/ΔGm equal to 87 % and 89 %. These data indicate the dependency of C2H2, GRAS, ERF TFs families expression on miRNA. The obtained results expand the fundamental ideas about the regulatory mechanisms of miRNA in the process of plant growth and development.

Temporal expression of polysaccharide biosynthesis genes in the leaves of Cyclocarya paliurus at different developmental stages

Background: Cyclocarya paliurus (Batal.) Iljinskaja is a common endemic tree species. The leaves of C. paliurus are used as a Chinese medicine and the main active components are polysaccharides. However, the temporal pattern of polysaccharide synthesis at different leaf developmental stages has not been reported to date. Results: With the development of leaves, the content of polysaccharides increased first and the highest content was found at the F3 stage (the third larger full expanded leaf). A total of 499710194 clean reads were obtained using C. paliurus genomic data and were assembled into 296593 unigenes. Among 4708 identified DEGs, 429 DEGs were up-regulated and 451 DEGs were down-regulated from F1 stage (the smallest full expanded leaf) to F2 stage (the second larger full expanded leaf), 630 DEGs were up-regulated and 60 DEGs were down-regulated from F2 stage to F3 stage, and 1833 up-regulated and 1816 down-regulated DEGs from F3 stage to F4 stage. Forty DEGs associated with GT belong to 13 GT families. Among them, only one gene was down-regulated from F1 stage to F2 stage, two genes were down-regulated from F2 to F3 stages, and 23 genes were down-regulated and 15 genes were up-regulated from F3 stage to F4 stage, respectively. A significant correlation exists between the five unigenes and the polysaccharide content. UDP-glucose 4-epimerase gene was significantly positively correlated with the polysaccharide content. A pathway map for the biosynthesis of C. paliurus polysaccharide was proposed. Among 150 transcription factors identified from DEGs, the majority was members of the AP2/ERF family (21, 14%), followed by the C2H2 family (14, 9.33%), the MYB family (12, 8%), the C2C2-GATA family (10, 6.67%), the GRAS family (9, 6%), and the zf-HD family (7, 4.67%). Conclusions: These results identified genes involved in the biosynthesis of Cyclocarya paliurus polysaccharides during different leaf developmental stages and provided evidence for the change of polysaccharide content during the development of C. paliurus leaves. Possible synthetic pathways and related transcription factors were suggested. This study provides information for the screening of polysaccharide biosynthesis related genes and elucidates the mechanism underlying polysaccharide biosynthesis in C. paliurus.

Overexpression of SlGRAS7 Affects Multiple Behaviors Leading to Confer Abiotic Stresses Tolerance and Impacts Gibberellin and Auxin Signaling in Tomato

Abiotic stresses remain the key environmental issues that reduce plant development and therefore affect crop production. Transcription factors, such as the GRAS family, are involved in various functions of abiotic stresses and plant growth. The GRAS family of tomato (Solanum lycopersicum), SlGRAS7, is described in this study. We produced overexpressing SlGARS7 plants to learn more about the GRAS transcription factors. Plants overexpressing SlGARS7 (SlGRAS7-OE) showed multiple phenotypes related to many behaviors, including plant height, root and shoot length, and flowering time. We observed that many genes in the SlGRAS7-OE seedlings that are associated with auxin and gibberellin (GA) are downregulated and have altered sensitivity to GA3/IAA. SlGRAS7 was upregulated during abiotic stresses following treatment with sodium chloride (NaCl) and D-mannitol in the wild-type (WT) tomato. Tomato plants overexpressing SlGRAS7 showed more resistance to drought and salt stress comparison with WT. Our study of SlGRAS7 in tomato demonstrates how GRAS showed an integrative role, improving resistance to abiotic stresses and enhancing gibberellin/auxin signaling through reproductive as well as vegetative processes.